A novel one-class SVM based negative data sampling method for reconstructing proteome-wide HTLV-human protein interaction networks.

PubMed

Mei, Suyu; Zhu, Hao

2015-01-26

Protein-protein interaction (PPI) prediction is generally treated as a problem of binary classification wherein negative data sampling is still an open problem to be addressed. The commonly used random sampling is prone to yield less representative negative data with considerable false negatives. Meanwhile rational constraints are seldom exerted on model selection to reduce the risk of false positive predictions for most of the existing computational methods. In this work, we propose a novel negative data sampling method based on one-class SVM (support vector machine, SVM) to predict proteome-wide protein interactions between HTLV retrovirus and Homo sapiens, wherein one-class SVM is used to choose reliable and representative negative data, and two-class SVM is used to yield proteome-wide outcomes as predictive feedback for rational model selection. Computational results suggest that one-class SVM is more suited to be used as negative data sampling method than two-class PPI predictor, and the predictive feedback constrained model selection helps to yield a rational predictive model that reduces the risk of false positive predictions. Some predictions have been validated by the recent literature. Lastly, gene ontology based clustering of the predicted PPI networks is conducted to provide valuable cues for the pathogenesis of HTLV retrovirus.

Diagnostic accuracy, incremental yield and prognostic value of Determine TB-LAM for routine diagnostic testing for tuberculosis in HIV-infected patients requiring acute hospital admission in South Africa: a prospective cohort.

PubMed

Lawn, Stephen D; Kerkhoff, Andrew D; Burton, Rosie; Schutz, Charlotte; Boulle, Andrew; Vogt, Monica; Gupta-Wright, Ankur; Nicol, Mark P; Meintjes, Graeme

2017-03-21

We previously reported that one-third of HIV-positive adults requiring medical admission to a South African district hospital had laboratory-confirmed tuberculosis (TB) and that almost two-thirds of cases could be rapidly diagnosed using Xpert MTB/RIF-testing of concentrated urine samples obtained on the first day of admission. Implementation of urine-based, routine, point-of-care TB screening is an attractive intervention that might be facilitated by use of a simple, low-cost diagnostic tool, such as the Determine TB-LAM lateral-flow rapid test for HIV-associated TB. Sputum, urine and blood samples were systematically obtained from unselected HIV-positive adults within 24 hours of admission to a South African township hospital. Additional clinical samples were obtained during hospitalization as clinically indicated. TB was defined by the detection of Mycobacterium tuberculosis in any sample using Xpert MTB/RIF or liquid culture. The diagnostic yield, accuracy and prognostic value of urine-lipoarabinomannan (LAM) testing were determined, but urine-LAM results did not inform treatment decisions. Consecutive HIV-positive adult acute medical admissions not already receiving TB treatment (n = 427) were enrolled regardless of clinical presentation or symptoms. TB was diagnosed in 139 patients (TB prevalence 32.6%; median CD4 count 80 cells/μL). In the first 24 hours of admission, sputum (spot and/or induced) samples were obtained from 37.0% of patients and urine samples from 99.5% of patients (P < 0.001). The diagnostic yields from these specimens were 19.4% (n = 27/139) for sputum-microscopy, 26.6% (n = 37/139) for sputum-Xpert, 38.1% (n = 53/139) for urine-LAM and 52.5% (n = 73/139) for sputum-Xpert/urine-LAM combined (P < 0.01). Corresponding yields among patients with CD4 counts <100 cells/μL were 18.9%, 24.3%, 55.4% and 63.5%, respectively (P < 0.01). The diagnostic yield of urine-LAM was unrelated to respiratory symptoms, and LAM assay specificity (using a grade-2 cut-off) was 98.9% (274/277; 95% confidence interval [CI] 96.9-99.8). Among TB cases, positive urine-LAM status was strongly associated with mortality at 90 days (adjusted hazard ratio 4.20; 95% CI 1.50-11.75). Routine testing for TB in newly admitted HIV-positive adults using Determine TB-LAM to test urine provides major incremental diagnostic yield with very high specificity when used in combination with sputum testing and has important utility among those without respiratory TB symptoms and/or unable to produce sputum. The assay also rapidly identifies individuals with a poor prognosis.

Prevalence, Distribution, and Diversity of Salmonella enterica in a Major Produce Region of California▿†

PubMed Central

Gorski, Lisa; Parker, Craig T.; Liang, Anita; Cooley, Michael B.; Jay-Russell, Michele T.; Gordus, Andrew G.; Atwill, E. Robert; Mandrell, Robert E.

2011-01-01

A survey was initiated to determine the prevalence of Salmonella enterica in the environment in and around Monterey County, CA, a major agriculture region of the United States. Trypticase soy broth enrichment cultures of samples of soil/sediment (n = 617), water (n = 252), wildlife (n = 476), cattle feces (n = 795), and preharvest lettuce and spinach (n = 261) tested originally for the presence of pathogenic Escherichia coli were kept in frozen storage and later used to test for the presence of S. enterica. A multipathogen oligonucleotide microarray was employed to identify a subset of samples that might contain Salmonella in order to test various culture methods to survey a larger number of samples. Fifty-five of 2,401 (2.3%) samples yielded Salmonella, representing samples obtained from 20 different locations in Monterey and San Benito Counties. Water had the highest percentage of positives (7.1%) among sample types. Wildlife yielded 20 positive samples, the highest number among sample types, with positive samples from birds (n = 105), coyotes (n = 40), deer (n = 104), elk (n = 39), wild pig (n = 41), and skunk (n = 13). Only 16 (2.6%) of the soil/sediment samples tested positive, and none of the produce samples had detectable Salmonella. Sixteen different serotypes were identified among the isolates, including S. enterica serotypes Give, Typhimurium, Montevideo, and Infantis. Fifty-four strains were sensitive to 12 tested antibiotics; one S. Montevideo strain was resistant to streptomycin and gentamicin. Pulsed-field gel electrophoresis (PFGE) analysis of the isolates revealed over 40 different pulsotypes. Several strains were isolated from water, wildlife, or soil over a period of several months, suggesting that they were persistent in this environment. PMID:21378057

Prevalence, distribution, and diversity of Salmonella enterica in a major produce region of California.

PubMed

Gorski, Lisa; Parker, Craig T; Liang, Anita; Cooley, Michael B; Jay-Russell, Michele T; Gordus, Andrew G; Atwill, E Robert; Mandrell, Robert E

2011-04-01

A survey was initiated to determine the prevalence of Salmonella enterica in the environment in and around Monterey County, CA, a major agriculture region of the United States. Trypticase soy broth enrichment cultures of samples of soil/sediment (n = 617), water (n = 252), wildlife (n = 476), cattle feces (n = 795), and preharvest lettuce and spinach (n = 261) tested originally for the presence of pathogenic Escherichia coli were kept in frozen storage and later used to test for the presence of S. enterica. A multipathogen oligonucleotide microarray was employed to identify a subset of samples that might contain Salmonella in order to test various culture methods to survey a larger number of samples. Fifty-five of 2,401 (2.3%) samples yielded Salmonella, representing samples obtained from 20 different locations in Monterey and San Benito Counties. Water had the highest percentage of positives (7.1%) among sample types. Wildlife yielded 20 positive samples, the highest number among sample types, with positive samples from birds (n = 105), coyotes (n = 40), deer (n = 104), elk (n = 39), wild pig (n = 41), and skunk (n = 13). Only 16 (2.6%) of the soil/sediment samples tested positive, and none of the produce samples had detectable Salmonella. Sixteen different serotypes were identified among the isolates, including S. enterica serotypes Give, Typhimurium, Montevideo, and Infantis. Fifty-four strains were sensitive to 12 tested antibiotics; one S. Montevideo strain was resistant to streptomycin and gentamicin. Pulsed-field gel electrophoresis (PFGE) analysis of the isolates revealed over 40 different pulsotypes. Several strains were isolated from water, wildlife, or soil over a period of several months, suggesting that they were persistent in this environment.

DNA extraction methods for detecting genetically modified foods: A comparative study.

PubMed

Elsanhoty, Rafaat M; Ramadan, Mohamed Fawzy; Jany, Klaus Dieter

2011-06-15

The work presented in this manuscript was achieved to compare six different methods for extracting DNA from raw maize and its derived products. The methods that gave higher yield and quality of DNA were chosen to detect the genetic modification in the samples collected from the Egyptian market. The different methods used were evaluated for extracting DNA from maize kernels (without treatment), maize flour (mechanical treatment), canned maize (sweet corn), frozen maize (sweet corn), maize starch, extruded maize, popcorn, corn flacks, maize snacks, and bread made from corn flour (mechanical and thermal treatments). The quality and quantity of the DNA extracted from the standards, containing known percentages of GMO material and from the different food products were evaluated. For qualitative detection of the GMO varieties in foods, the GMOScreen 35S/NOS test kit was used, to screen the genetic modification in the samples. The positive samples for the 35S promoter and/or the NOS terminator were identified by the standard methods adopted by EU. All of the used methods extracted yielded good DNA quality. However, we noted that the purest DNA extract were obtained using the DNA extraction kit (Roche) and this generally was the best method for extracting DNA from most of the maize-derived foods. We have noted that the yield of DNA extracted from maize-derived foods was generally lower in the processed products. The results indicated that 17 samples were positive for the presence of 35S promoter, while 34% from the samples were positive for the genetically modified maize line Bt-176. Copyright © 2010 Elsevier Ltd. All rights reserved.

Sandwich-dot enzyme-linked immunosorbent assay for the detection of canine distemper virus

PubMed Central

Li, Zhi; Zhang, Yanlong; Wang, Huiguo; Jin, Jinhua; Li, Wenzhe

2013-01-01

A sandwich-dot enzyme-linked immunosorbent assay (dot ELISA) was developed for the detection of canine distemper virus (CDV). In 56 dogs suspected to have CD the rates of detection of CDV antigen in samples of blood lymphocytes and palpebral conjunctiva by dot ELISA and ELISA were, respectively, 91% (49/54) and 81% (44/54) for the lymphocyte samples and 88% (28/32) and 75% (24/32) for the conjunctival samples. The CDV detection limits were 10 ng/50 μL for dot ELISA and 40 ng/50 μL for ELISA. The reliability of dot ELISA relative to electron microscopy was 96% with 22 samples: all 21 samples in which CDV particles were observed by electron microscopy yielded positive results with dot ELISA; the single sample in which particles were not observed yielded false-positive results with dot ELISA. The results indicate that the dot ELISA developed can serve as a reliable rapid diagnostic test in suspected cases of CD and also be useful for epidemiologic surveillance of the disease. PMID:24124274

One-day fluorescent-antibody procedure for detecting salmonellae in frozen and dried foods.

PubMed

Goepfert, J M; Mann, M E; Hicks, R

1970-12-01

The indirect fluorescent-antibody technique was used to examine 422 food samples for the presence of salmonellae. A cultural phase involving a 16-hr preenrichment in buffered nutrient broth-milk medium followed by a 4- to 5-hr subculture into fresh medium of the same composition was evaluated. This procedure yielded a sufficient population of salmonellae so that no false-negative results were obtained. Of the 31 false-positives obtained, 12 samples yielded positive cultural results upon extensive subculture of the original enrichment broths. Yeast cells and both vegetative and spore forms of bacilli were observed to fluoresce when stained with anti-Salmonella serum. Efforts to ascertain the cause of these cross-reactions and several alternate explanations are discussed.

Performance of Copan WASP for Routine Urine Microbiology

PubMed Central

Quiblier, Chantal; Jetter, Marion; Rominski, Mark; Mouttet, Forouhar; Böttger, Erik C.; Keller, Peter M.

2015-01-01

This study compared a manual workup of urine clinical samples with fully automated WASPLab processing. As a first step, two different inocula (1 and 10 μl) and different streaking patterns were compared using WASP and InoqulA BT instrumentation. Significantly more single colonies were produced with the10-μl inoculum than with the 1-μl inoculum, and automated streaking yielded significantly more single colonies than manual streaking on whole plates (P < 0.001). In a second step, 379 clinical urine samples were evaluated using WASP and the manual workup. Average numbers of detected morphologies, recovered species, and CFUs per milliliter of all 379 urine samples showed excellent agreement between WASPLab and the manual workup. The percentage of urine samples clinically categorized as positive or negative did not differ between the automated and manual workflow, but within the positive samples, automated processing by WASPLab resulted in the detection of more potential pathogens. In summary, the present study demonstrates that (i) the streaking pattern, i.e., primarily the number of zigzags/length of streaking lines, is critical for optimizing the number of single colonies yielded from primary cultures of urine samples; (ii) automated streaking by the WASP instrument is superior to manual streaking regarding the number of single colonies yielded (for 32.2% of the samples); and (iii) automated streaking leads to higher numbers of detected morphologies (for 47.5% of the samples), species (for 17.4% of the samples), and pathogens (for 3.4% of the samples). The results of this study point to an improved quality of microbiological analyses and laboratory reports when using automated sample processing by WASP and WASPLab. PMID:26677255

Sugar composition and concentrations in sugarcane juice as affected by sampling date and internode position

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp. hybrids) harvest season lasts about six months from late-October through mid-April in Florida. Cane juice sugar concentration and composition are important for sucrose yield and profits, however research is lacking on the influence of harvesting time and intermodal position...

Use of a tissue sectioner to expose internal structures of biological samples for scanning electron microscopy.

PubMed

Brown, M F; Brotzman, H G; Kinden, D A

1976-09-01

A procedure yielding sections of unembedded biological samples for observation by scanning electron microscopy is described. Sections of samples, fixed and hardened in OsO4, were obtained in quantity with a tissue sectioner. Subsequent treatments to osmium-coat cut surfaces were employed prior to critical point drying. The procedure yields cleanly cut surfaces through cells and cytoplasmic organelles which are retained in their normal position. Sections of apple leaf and mouse kidney are illustrated. Sections can be readily cut in a desired plane with less structural damage than is typically encountered by other sectioning or dissection techniques.

Comparison between Bactec Peds Plus F Broth and Conventional Medium for Vitreous Culture.

PubMed

Tabatabaei, Seyed Ali; Tabatabaei, Seyed Mehdi; Soleimani, Mohammad; Hejrati, Bahman; Mirshahi, Ahmad; Khadabandeh, Alireza; Ahmadraji, Aliasghar; Valipour, Niloofar

2018-05-10

To evaluate the yield of Bactec Peds Plus F broth for vitreous sample culture in cases with infectious endophthalmitis in comparison to conventional medium. Consecutive cases of clinically suspected endophthalmitis were prospectively enrolled in this study. Cultures of the vitreous sample were performed in both Bactec Peds Plus F broth and conventional mediums. Forty eyes of 40 patients who were clinically suspected of infectious endophthalmitis with different etiologies were enrolled in this study. The positive culture yield was 50% and 35% in Bactec Peds Plus F broth and conventional mediums, respectively (p = 0.07). The result of Bactec group was not significantly different among patients who had a history of intravitreal antibiotic injection (p > 0.05) (Table 2). However, results of the conventional method were significantly negative in the previous intravitreal antibiotic injection group (p = 0.02). There was no correlation between the methods of vitreous sampling in both culture methods. Although the difference between two culture methods was not statistically significant in this study, Bactec Peds Plus F broth showed higher positive culture yield in patients with a history of intravitreal antibiotic injection.

Immunomagnetic separation and conventional culture procedure for detection of naturally occurring Salmonella in raw pork sausages and chicken meat.

PubMed

Ripabelli, G; Sammarco, M L; Ruberto, A; Iannitto, G; Grasso, G M

1997-06-01

The aim of the study was to compare immunomagnetic separation (IMS) and conventional selective enrichment procedures using selenite cystine broth (SC) and Rappaport-Vassiliadis broth (RV) in 137 naturally contaminated food samples (69 raw pork sausages and 68 chicken meat). The utilization of SC or IMS appeared to be the most appropriate enrichment procedure: 15 out of 18 Salmonella-positive samples (83.3%) were detected by SC and 12 (66.7%) by IMS; RV yielded only seven positive isolations (38.9%). However, RV yielded the highest count of Salmonella colonies per plate and the lowest interference by competing organisms. IMS could become a reliable alternative to standard enrichment procedures and a combined IMS and selective enrichment broth could increase the chance of Salmonella recovery.

Volume dependency for culture of fungi from respiratory secretions and increased sensitivity of Aspergillus quantitative PCR.

PubMed

Fraczek, Marcin G; Kirwan, Marie B; Moore, Caroline B; Morris, Julie; Denning, David W; Richardson, Malcolm D

2014-02-01

Diagnosis of aspergillosis is often difficult. We compared fungal yields from respiratory specimens using the Health Protection Agency standard culture method (BSOP57), a higher volume undiluted culture method Mycology Reference Centre Manchester (MRCM) and Aspergillus quantitative real time polymerase chain reaction (qPCR). Sputum, bronchial aspirate and bronchoalveolar lavage (BAL) samples (total 23) were collected from aspergillosis patients. One fraction of all samples was cultured using the MRCM method, one BSOP57 and one was used for qPCR. The recovery rate for fungi was significantly higher by MRCM (87%) than by BSOP57 (8.7%) from all 23 specimens. Sputum samples were 44% positive by MRCM compared to no fungi isolated (0%) by BSOP57. Bronchial aspirates were 75% positive by MRCM and 0% by BSOP57. BAL samples were positive in 20% by MRCM and 10% by BSOP57. qPCR was always more sensitive than culture (95.6%) from all samples. In general, over 100 mould colonies (81 Aspergillus fumigatus) were grown using the MRCM method compared with only one colony from BSOP57. This study provides a reference point for standardisation of respiratory sample processing in diagnostic laboratories. Culture from higher volume undiluted respiratory specimens has a much higher yield for Aspergillus than BSOP57. qPCR is much more sensitive than culture and the current UK method requires revision. © 2013 Blackwell Verlag GmbH.

Polymerase chain reaction-based detection of B-cell monoclonality in cytologic specimens.

PubMed

Chen, Y T; Mercer, G O; Chen, Y

1993-11-01

Thirty-seven cytologic cell blocks were evaluated for B-cell monoclonality by polymerase chain reaction (PCR), 16 of them cytologically positive for lymphoma, and 21 suspicious for lymphoma but morphologically nondiagnostic. Of 37 specimens, 13 (35%) showed B-cell monoclonality, including six of 16 cytologically positive samples and seven of 21 cytologically suspicious ones. Of these 13 positive samples, seven were positive using crude lysates as substrates, and six additional positive samples were identified only when DNAs were purified and concentrated. Analysis of the DNAs further revealed poor polymerase chain reaction amplifiability and low DNA yield in many samples, indicating that cell block materials are suboptimal for this assay. We concluded that B-cell monoclonality can be detected in ethanol-fixed cytologic samples, and usage of unembedded material will likely improve the sensitivity. In specimens cytologically suspicious for lymphoma, polymerase chain reaction-based identification of monoclonal B-cell population supports the diagnosis of B-cell lymphoma and is a potentially useful test in solving this diagnostic dilemma.

Prevalence of Campylobacter spp., Escherichia coli, and Salmonella serovars in retail chicken, turkey, pork, and beef from the Greater Washington, D.C., area.

PubMed

Zhao, C; Ge, B; De Villena, J; Sudler, R; Yeh, E; Zhao, S; White, D G; Wagner, D; Meng, J

2001-12-01

A total of 825 samples of retail raw meats (chicken, turkey, pork, and beef) were examined for the presence of Escherichia coli and Salmonella serovars, and 719 of these samples were also tested for Campylobacter spp. The samples were randomly obtained from 59 stores of four supermarket chains during 107 sampling visits in the Greater Washington, D.C., area from June 1999 to July 2000. The majority (70.7%) of chicken samples (n = 184) were contaminated with Campylobacter, and a large percentage of the stores visited (91%) had Campylobacter-contaminated chickens. Approximately 14% of the 172 turkey samples yielded Campylobacter, whereas fewer pork (1.7%) and beef (0.5%) samples were positive for this pathogen. A total of 722 Campylobacter isolates were obtained from 159 meat samples; 53.6% of these isolates were Campylobacter jejuni, 41.3% were Campylobacter coli, and 5.1% were other species. Of the 212 chicken samples, 82 (38.7%) yielded E. coli, while 19.0% of the beef samples, 16.3% of the pork samples, and 11.9% of the turkey samples were positive for E. coli. However, only 25 (3.0%) of the retail meat samples tested were positive for Salmonella. Significant differences in the bacterial contamination rates were observed for the four supermarket chains. This study revealed that retail raw meats are often contaminated with food-borne pathogens; however, there are marked differences in the prevalence of such pathogens in different meats. Raw retail meats are potential vehicles for transmitting food-borne diseases, and our findings stress the need for increased implementation of hazard analysis of critical control point (HACCP) and consumer food safety education efforts.

Prevalence of Campylobacter spp., Escherichia coli, and Salmonella Serovars in Retail Chicken, Turkey, Pork, and Beef from the Greater Washington, D.C., Area

PubMed Central

Zhao, Cuiwei; Ge, Beilei; De Villena, Juan; Sudler, Robert; Yeh, Emily; Zhao, Shaohua; White, David G.; Wagner, David; Meng, Jianghong

2001-01-01

A total of 825 samples of retail raw meats (chicken, turkey, pork, and beef) were examined for the presence of Escherichia coli and Salmonella serovars, and 719 of these samples were also tested for Campylobacter spp. The samples were randomly obtained from 59 stores of four supermarket chains during 107 sampling visits in the Greater Washington, D.C., area from June 1999 to July 2000. The majority (70.7%) of chicken samples (n = 184) were contaminated with Campylobacter, and a large percentage of the stores visited (91%) had Campylobacter-contaminated chickens. Approximately 14% of the 172 turkey samples yielded Campylobacter, whereas fewer pork (1.7%) and beef (0.5%) samples were positive for this pathogen. A total of 722 Campylobacter isolates were obtained from 159 meat samples; 53.6% of these isolates were Campylobacter jejuni, 41.3% were Campylobacter coli, and 5.1% were other species. Of the 212 chicken samples, 82 (38.7%) yielded E. coli, while 19.0% of the beef samples, 16.3% of the pork samples, and 11.9% of the turkey samples were positive for E. coli. However, only 25 (3.0%) of the retail meat samples tested were positive for Salmonella. Significant differences in the bacterial contamination rates were observed for the four supermarket chains. This study revealed that retail raw meats are often contaminated with food-borne pathogens; however, there are marked differences in the prevalence of such pathogens in different meats. Raw retail meats are potential vehicles for transmitting food-borne diseases, and our findings stress the need for increased implementation of hazard analysis of critical control point (HACCP) and consumer food safety education efforts. PMID:11722889

Patterns of lymph node sampling and the impact of lymph node density in favorable histology Wilms tumor: An analysis of the national cancer database.

PubMed

Saltzman, A F; Carrasco, A; Amini, A; Aldrink, J H; Dasgupta, R; Gow, K W; Glick, R D; Ehrlich, P F; Cost, N G

2018-04-01

There is controversy about the role of lymph node (LN) sampling or dissection in the management of favorable histology (FH) Wilms tumor (WT), specifically how it performed and how it may impact survival. The objective of this study was to analyze factors affecting LN sampling patterns and the impact of LN yield and density (number of positive LNs/LNs examined) on overall survival (OS) in patients with advanced-stage favorable histology Wilms tumor (FHWT). The National Cancer Database (NCDB) was queried for patients with FHWT during 2004-2013. Demographic, clinical and OS data were abstracted for those who underwent surgical resection. Poisson regression was performed to analyze how factors influenced LN yield. Patients with positive LNs had LN density calculated and were further analyzed. A total of 2340 patients met criteria, with a median age at diagnosis of 3 years (range 0-78 years). The median number of LNs examined was three (range 0-87). Lymph node yield was affected by age, race, insurance, tumor size, laterality, advanced stage, LN positivity, and institutional volume. A total of 390 (16.6%) patients had LN-positive disease. Median LN density for these LN-positive patients was 0.38 (range 0.02-1) (Summary Figure). Estimated 5-year OS was significantly improved for those with LN density ≤0.38 vs. >0.38 (94% vs. 84.6%, P = 0.012). In this population, on multivariate analysis, age and LN density were significant predictors of OS. It is difficult to compile large numbers of cases in rare diseases like WT, and fortunately a large administrative database such as the NCDB can serve as a great resource. However, administrative data come with inherent limitations such as missing data and inability to account for a variety of factors that may influence LN yield and/or OS (specimen designation, pathologist experience, surgeon experience/volume, institutional Children's Oncology Group (COG) association, etc.). In this specific disease, the American Joint Committee on Cancer staging (captured by the NCDB) is different than the COG WT staging system that is used clinically, and the NCDB does not capture oncologic outcomes beyond OS. In a review of the NCDB, various factors associated with LN yield and observed LN density were identified to be significantly associated with OS in patients with LN-positive FHWT. This reinforces the need for adequate LN sampling at the time of WT surgery, to maximize surgical disease control. It was proposed that LN density as a metric may allow for improved risk-stratification, and possibly allow for therapeutic reduction in a sub-set of patients with low LN density. Copyright © 2017 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.

[Comparison of two different real-time PCR systems in postmortem diagnosis of tuberculosis in paraffin-embedded tissues].

PubMed

Yağmur, Gülhan; Albayrak, Nurhan; Daş, Taner; Yıldırım, Muzaffer; Ozgün, Ayşe; Büyük, Yalçın

2014-10-01

Tuberculosis (TB) is one of those infections with high morbidity and mortality in all around the world. Hundreds of people died from this disease without diagnosed or due to resistant strains in Turkey. Therefore, it is important to identify postmortem cases who have died from tuberculosis. Molecular methods have been widely used as well as conventional methods in the diagnosis of tuberculosis. The aim of this study was to compare the two different real-time polymerase chain reaction (Rt-PCR) system in the postmortem diagnosis of Mycobacterium tuberculosis infections in paraffin-embedded tissues. A total of 40 paraffin-embedded tissue samples [lung (n= 35), brain (n= 2), heart (n= 2), lymph node (n= 1)] in which histopathologic findings consistent with TB (necrotizing granulomatous inflammation, gelatinous caseous pneumonia, necrotic fibrous nodul) obtained from 37 autopsy cases (31 male, 6 female; age range: 25-85 yrs) were included in the study. Paraffin-embedded tissues were deparafinized with xylene and ethyl alcohol and then DNA isolation was done with QIAsymphony DSP Virus/Pathogen Midi kit in the QIAsymphony device. DNA amplification process was performed by Rt-PCR using the kit Artus® M. tuberculosis RG-PCR in the Rotor-Gene® Q device (Qiagen, Germany). Likewise, after deparafinization process, samples placed in the cartridge and isolation and Rt-PCR was performed by Xpert® MTB/RIF (Cepheid, USA) system, simultaneosly. Seventeen and 20 out of the 40 paraffin-embedded tissues yielded positive results with Qiagen and Xpert system, respectively. M.tuberculosis DNA was found positive in 13 (32.5%) and negative in 16 (40%) of the samples by both of the systems, exhibiting 72.5% (29/40) of concordance. On the other hand, seven (17.5%) samples that were positive with Xpert system yielded negative result with the Qiagen, while four (10%) samples that were positive with Qiagen yielded negative result with the Xpert system. Of the 20 positive cases detected with Xpert MTB/RIF system, 15 were found rifampicin-susceptible, and three were rifampicin-resistant. In two samples in which M. tuberculosis DNA was low positive, rifampicin resistance could not be detected. The identification of M.tuberculosis infections in postmortem cases will contribute epidemiological data in Turkey. In these cases, effective sampling and diagnosing of M.tuberculosis infections by acid-fast stain and culture methods are crucial. However, in cases without microbiological sampling the detection of M.tuberculosis DNA in paraffin-embedded tissues with PCR, although there are differences between PCR systems has diagnostic value. In conclusion, our data indicated that Xpert MTB/RIF system is more favourable to detect M.tuberculosis DNA in paraffin-embedded tissues, with the advantages of determination of rifampicin resistance, and detection of more positive results within a shorter time.

Evaluation of meat, fruit and vegetables from retail stores in five United Kingdom regions as sources of extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant Escherichia coli.

PubMed

Randall, L P; Lodge, M P; Elviss, N C; Lemma, F L; Hopkins, K L; Teale, C J; Woodford, N

2017-01-16

We determined the prevalence and types of extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant Escherichia coli in raw retail beef, chicken, pork, fruit and vegetables in five UK regions in 2013-14. Raw meat (n=397), and fruit and vegetable samples (n=400) were purchased from retail stores in London, East Anglia, North West England, Scotland and Wales. Samples were tested for the presence of ESBL-producing E. coli by plating enriched samples on CHROMagar CTX and CHROMagar ESBL, for AmpC-type E. coli by plating on "CHROMagar FOX" (CHROMagar ECC+16mg/L cefoxitin), and for carbapenem-resistant E. coli by plating on CHROMagar KPC. Additionally, pre-enrichment counts were performed on the above agars, and on CHROMagar ECC. Isolates of interest were characterised by MALDI-ToF to confirm identification, by PCR for bla CIT, bla CTX-M, bla OXA , bla SHV and bla TEM genes; ESBL or bla CIT genes were sequenced. Only 1.9% and 2.5% of beef and pork samples, respectively were positive for ESBL-producing E. coli after enrichment compared with 65.4% of chicken samples. 85.6% positive samples from chicken meat carried bla CTX-M-1 ; bla CTX-M-15 was not detected. None of the fruits or vegetables yielded ESBL-producing E. coli and none of the meat, fruit or vegetable samples yielded carbapenem-resistant E. coli. Retail chicken was more frequently a source of ESBL-producing E. coli than were beef, pork, fruit or vegetables. None of the foodstuffs yielded E. coli with CTX-M-15 ESBL, which dominates in human clinical isolates in the UK, and none yielded carbapenem-resistant E. coli. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Cross-sectional study of serum antibodies against Sarcocystis neurona in cats tested for antibodies against Toxoplasma gondii.

PubMed

Rossano, Mary G; Murphy, Alice J; Vrable, Ruth A; Vanzo, Nicole E; Lewis, Stacy K; Sheline, Katherine D; Kaneene, John B; Mansfield, Linda S

2002-08-15

To determine apparent seroprevalence of antibodies against Sarcocystis neurona in a population of domestic cats previously tested for antibodies against Toxoplasma gondii. Cross-sectional study. Serum from 196 domestic cats. Banked serum samples submitted to the Michigan State University Animal Health Diagnostic Laboratory for T. gondii diagnostic testing were tested for antibodies against S. neurona by use of an indirect fluorescent antibody (IFA) test and a western blot test. Submission records were analyzed to determine descriptive statistics and test for associations between positive results of a test for S. neurona and other variables in the data set. 10 of 196 (5%) samples yielded positive results for antibodies against S. neurona by use of western blot analysis, whereas 27 samples yielded positive results by use of the IFA. No association was found between S. neurona western blot test results and T. gondii test results, age, sex, or the reason for T. gondii testing. The S. neurona IFA titer was positively and significantly associated with positive results of western blot analysis. Domestic cats are not likely to play a substantial role as intermediate hosts in the natural life cycle of S. neurona. Results indicate that natural infection of domestic cats may occur, and small animal practitioners should be aware of this fact when evaluating cats with neurologic disease. The S. neurona IFA test had lower specificity than western blot analysis.

The environmental deposition of influenza virus from patients infected with influenza A(H1N1)pdm09: Implications for infection prevention and control.

PubMed

Killingley, Benjamin; Greatorex, Jane; Digard, Paul; Wise, Helen; Garcia, Fayna; Varsani, Harsha; Cauchemez, Simon; Enstone, Joanne E; Hayward, Andrew; Curran, Martin D; Read, Robert C; Lim, Wei S; Nicholson, Karl G; Nguyen-Van-Tam, Jonathan S

2016-01-01

In a multi-center, prospective, observational study over two influenza seasons, we sought to quantify and correlate the amount of virus recovered from the nares of infected subjects with that recovered from their immediate environment in community and hospital settings. We recorded the symptoms of adults and children with A(H1N1)pdm09 infection, took nasal swabs, and sampled touched surfaces and room air. Forty-two infected subjects were followed up. The mean duration of virus shedding was 6.2 days by PCR (Polymerase Chain Reaction) and 4.2 days by culture. Surface swabs were collected from 39 settings; 16 (41%) subject locations were contaminated with virus. Overall, 33 of the 671 (4.9%) surface swabs were PCR positive for influenza, of which two (0.3%) yielded viable virus. On illness Day 3, subjects yielding positive surface samples had significantly higher nasal viral loads (geometric mean ratio 25.7; 95% CI 1.75, 376.0, p=0.021) and a positive correlation (r=0.47, p=0.006) was observed between subject nasal viral loads and viral loads recovered from the surfaces around them. Room air was sampled in the vicinity of 12 subjects, and PCR positive samples were obtained for five (42%) samples. Influenza virus shed by infected subjects did not detectably contaminate the vast majority of surfaces sampled. We question the relative importance of the indirect contact transmission of influenza via surfaces, though our data support the existence of super-spreaders via this route. The air sampling results add to the accumulating evidence that supports the potential for droplet nuclei (aerosol) transmission of influenza. Copyright © 2015 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Ltd. All rights reserved.

Bone Marrow Biopsy: RNA Isolation with Expression Profiling in Men with Metastatic Castration-resistant Prostate Cancer—Factors Affecting Diagnostic Success

PubMed Central

Afonso, P. Diana; Vinson, Emily N.; Turnbull, James D.; Morris, Karla K.; Foye, Adam; Madden, John F.; Roy Choudhury, Kingshuk; Febbo, Phillip G.; George, Daniel J.

2013-01-01

Purpose To determine the rate at which computed tomographically guided pelvic percutaneous bone biopsy in men with metastatic castration-resistant prostate cancer (mCRPC) yields adequate tissue for genomic profiling and to identify issues likely to affect diagnostic yields. Materials and Methods This study was institutional review board approved, and written informed consent was obtained. In a phase II trial assessing response to everolimus, 31 men with mCRPC underwent 54 biopsy procedures (eight men before and 23 men both before and during treatment). Variables assessed were lesion location (iliac wing adjacent to sacroiliac joint, iliac wing anterior and/or superior to sacroiliac joint, sacrum, and remainder of pelvis), mean lesion attenuation, subjective lesion attenuation (purely sclerotic vs mixed), central versus peripheral lesion sampling, lesion size, core number, and use of zoledronic acid for more than 1 year. Results Of 54 biopsy procedures, 21 (39%) yielded adequate tissue for RNA isolation and genomic profiling. Three of four sacral biopsies were adequate. Biopsies of the ilium adjacent to the sacroiliac joints were more likely adequate than those from elsewhere in the ilium (48% vs 28%, respectively). All five biopsies performed in other pelvic locations yielded inadequate tissue for RNA isolation. Mean attenuation of lesions with inadequate tissue was 172 HU greater than those with adequate tissue (621.1 HU ± 166 vs 449 HU ± 221, respectively; P = .002). Use of zoledronic acid, peripheral sampling, core number, and lesion size affected yields, but the differences were not statistically significant. Histologic examination with hematoxylin-eosin staining showed that results of 36 (67%) biopsies were positive for cancer; only mean attenuation differences were significant (707 HU ± 144 vs 473 HU ± 191, negative vs positive, respectively; P < .001). Conclusion In men with mCRPC, percutaneous sampling of osseous metastases for genomic profiling is possible, but use of zoledronic acid for more than 1 year may reduce the yield of adequate tissue for RNA isolation. Sampling large low-attenuating lesions at their periphery maximizes yield. © RSNA, 2013 PMID:23925271

Relative fission product yield determination in the USGS TRIGA Mark I reactor

NASA Astrophysics Data System (ADS)

Koehl, Michael A.

Fission product yield data sets are one of the most important and fundamental compilations of basic information in the nuclear industry. This data has a wide range of applications which include nuclear fuel burnup and nonproliferation safeguards. Relative fission yields constitute a major fraction of the reported yield data and reduce the number of required absolute measurements. Radiochemical separations of fission products reduce interferences, facilitate the measurement of low level radionuclides, and are instrumental in the analysis of low-yielding symmetrical fission products. It is especially useful in the measurement of the valley nuclides and those on the extreme wings of the mass yield curve, including lanthanides, where absolute yields have high errors. This overall project was conducted in three stages: characterization of the neutron flux in irradiation positions within the U.S. Geological Survey TRIGA Mark I Reactor (GSTR), determining the mass attenuation coefficients of precipitates used in radiochemical separations, and measuring the relative fission products in the GSTR. Using the Westcott convention, the Westcott flux, modified spectral index, neutron temperature, and gold-based cadmium ratios were determined for various sampling positions in the USGS TRIGA Mark I reactor. The differential neutron energy spectrum measurement was obtained using the computer iterative code SAND-II-SNL. The mass attenuation coefficients for molecular precipitates were determined through experiment and compared to results using the EGS5 Monte Carlo computer code. Difficulties associated with sufficient production of fission product isotopes in research reactors limits the ability to complete a direct, experimental assessment of mass attenuation coefficients for these isotopes. Experimental attenuation coefficients of radioisotopes produced through neutron activation agree well with the EGS5 calculated results. This suggests mass attenuation coefficients of molecular precipitates can be approximated using EGS5, especially in the instance of radioisotopes produced predominantly through uranium fission. Relative fission product yields were determined for three sampling positions in the USGS TRIGA Mark I reactor through radiochemical analysis. The relative mass yield distribution for valley nuclides decreases with epithermal neutrons compared to thermal neutrons. Additionally, a proportionality constant which related the measured beta activity of a fission product to the number of fissions that occur in a sample of irradiated uranium was determined for the detector used in this study and used to determine the thermal and epithermal flux. These values agree well with a previous study which used activation foils to determine the flux. The results of this project clearly demonstrate that R-values can be measured in the GSTR.

Evaluation of Microscopic Observation Drug Susceptibility (MODS) and the string test for rapid diagnosis of pulmonary tuberculosis in HIV/AIDS patients in Bolivia.

PubMed

Lora, Meredith H; Reimer-McAtee, Melissa J; Gilman, Robert H; Lozano, Daniel; Saravia, Ruth; Pajuelo, Monica; Bern, Caryn; Castro, Rosario; Espinoza, Magaly; Vallejo, Maya; Solano, Marco; Challapa, Roxana; Torrico, Faustino

2015-06-06

Tuberculosis (TB) is the most common opportunistic infection and the leading cause of death in HIV-positive people worldwide. Diagnosing TB is difficult, and is more challenging in resource-scarce settings where culture-based diagnostic methods rely on poorly sensitive smear microscopy by Ziehl-Neelsen stain (ZN). We performed a cross-sectional study examining the diagnostic utility of Microscopic Observation Drug Susceptibility liquid culture (MODS) versus traditional Ziehl-Neelsen staining (ZN) and Lowenstein Jensen culture (LJ) of pulmonary tuberculosis (TB) and multidrug-resistant tuberculosis (MDRTB) in HIV-infected patients in Bolivia. For sputum scarce individuals we assessed the value of the string test and induced sputum for TB diagnosis. The presence of Mycobacterium tuberculosis (Mtb) in the sputum of 107 HIV-positive patients was evaluated by ZN, LJ, and MODS. Gastric secretion samples obtained by the string test were evaluated by MODS in 102 patients. The TB-HIV co-infection rate of HIV patients with respiratory symptoms by sputum sample was 45 % (48/107); 46/48 (96 %) were positive by MODS, 38/48 (79 %) by LJ, and 30/48 (63 %) by ZN. The rate of MDRTB was 9 % (4/48). Median time to positive culture was 10 days by MODS versus 34 days by LJ (p < 0.0001). In smear-negative patients, MODS detected TB in 17/18 patients, compared to 11/18 by LJ (94.4 % vs 61.0 %, p = 0.03 %). In patients unable to produce a sputum sample without induction, the string test cultured by MODS yielded Mtb in of 9/11 (82 %) TB positive patients compared to 11/11 (100 %) with induced sputum. Of the 10 patients unable to produce a sputum sample, 4 were TB-positive by string test. MODS was faster and had a higher Mtb detection yield compared to LJ, with a greater difference in yield between the two in smear-negative patients. The string test is a valuable diagnostic technique for HIV sputum-scarce or sputum-absent patients, and should be considered as an alternative test to induced sputum to obtain sample for Mtb in resource-limited settings. Nine percent of our TB+ patients had MDRTB, which reinforces the need for rapid detection with direct drug susceptibility testing in HIV patients in Bolivia.

Specific detection of viable Listeria monocytogenes in Spanish wastewater treatment plants by Fluorescent In Situ Hybridization and PCR.

PubMed

Moreno, Yolanda; Ballesteros, Lorena; García-Hernández, Jorge; Santiago, Paula; González, Ana; Ferrús, M Antonia

2011-10-01

Listeria monocytogenes detection in wastewater can be difficult because of the large amount of background microbiota and the presence of viable but non-culturable forms in this environment. The aim of this study was to evaluate a Fluorescent In Situ Hybridization (FISH) assay combined with Direct Viable Count (DVC) method for detecting viable L. monocytogenes in wastewater samples, as an alternative to conventional culture methods. 16S rRNA sequence data were used to design a specific oligonucleotide probe. In order to assess the suitability of the method, the assays were performed on naturally (n=87) and artificially (n=14) contaminated samples and results were compared to those obtained with the isolation of cells on selective media and with a PCR method. The detection limit of FISH and PCR assays was 10(4) cells/mL without enrichment and 10 cells/mL after enrichment. A total of 47 samples, including 3 samples from effluent sites, yielded FISH positive results for L. monocytogenes. Using DVC-FISH technique, the presence of viable L. monocytogenes cells was detected in 23 out of these 47 FISH positive wastewater samples. PCR and culture methods yielded 27 and 23 positive results, respectively. According to these results, FISH technique has the potential to be used as a sensitive method for the detection and enumeration of L. monocytogenes in environmental wastewater samples. Copyright © 2011 Elsevier Ltd. All rights reserved.

Progress in ethanol production from corn kernel by applying cooking pre-treatment.

PubMed

Voca, Neven; Varga, Boris; Kricka, Tajana; Curic, Duska; Jurisic, Vanja; Matin, Ana

2009-05-01

In order to improve technological properties of corn kernel for ethanol production, samples were treated with a hydrothermal pre-treatment of cooking (steaming), prior to drying. Two types of cooking process parameters were applied; steam pressure of 0.5 bars during a 10 min period, and steam pressure of 1.5 bars during a 30 min period. Afterwards, samples were dried at four different temperatures, 70, 90, 110 and 130 degrees C. Control sample was also submitted to the aforementioned drying parameters. Since the results showed that starch utilization, due to the gelatinization process, was considerably higher in the samples pre-treated before the ethanol production process, it was found that the cooking treatment had a positive effect on ethanol yield from corn kernel. Therefore, the highest ethanol yield was found in the corn kernel samples cooked for 30 min at steam pressure 1.5 bars and dried at 130 degrees C. Due to the similarity of processes used for starch fermentation, introduction of cooking pre-treatment will not significantly increase the overall ethanol production costs, whereas it will result in significantly higher ethanol yield.

Experiment 13: The Study of Dopant Segregation Behavior During the Growth of GaAs in Microgravity on USML-2

NASA Technical Reports Server (NTRS)

Matthiesen, David H.; Kaforey, Monica L.; Bly, J. M.; Chait, Arnon; Kafalas, James; Carlson, Douglas

1998-01-01

An investigation into the segregation behavior of selenium doped gallium arsenide (Se/GaAs) during directional solidification in the microgravity environment was conducted using the Crystal Growth Furnace (CGF) aboard the second United States Microgravity Laboratory (USML-2). Two crystals were successfully processed on USML-2, which lasted from October 20 to November 7, 1995. The first sample was processed for 67 hours, 45 minutes (MET 5/04:53:45-8/00:23:50) and included 19 hours of growth at 0.5 microns/sec which yielded 3.42 cm of sample length, and 5 hours of growth at 1.5 microns/sec which yielded 2.7 cm of sample. During the second experiment, the furnace temperature was adjusted to move the melt-solid interface position towards the hot end of the furnace. The second sample was processed for 50 hours, 10 minutes (MET 8/18:48:49-10/21:58:54) and included 11 hours of growth at 0.5 microns/sec which yielded 1.98 cm of sample, and 1 hour, 25 minutes of growth at 5.0 microns/sec which yielded 2.6 cm of sample. This sample provides an order of magnitude change in growth rate and reproduces one of the growth rates used during USML-1. In contrast to the results from USML-1, no voids were present in either crystal grown on USML-2. The absence of voids in either sample indicates that growth rate changes alone were not responsible for the formation of voids found in the crystals grown on USML-1. Sections of the ground-based and flight crystals grown on USML-2 were cut and polished. All of the interface demarcation lines expected from the current pulse interface demarcation (CPID) system have been identified. These measurements have been analyzed for interface positions, interface shapes, and growth rates. Using a newly developed technique, based on experimental and numerical results, the seeding interface reproducibility from run to run was <= 2.5 mm. The seeding interface position could be controllably moved, with respect to the furnace zones, by adjusting the control set points of the heating zones. The interface shapes flattened slightly as the interface position moved closer to the hot zone but was always an unfavorable concave into the solid shape. The growth rate was found to equal the furnace translation rate, after a 2 -hour transient, for growth rates <= 1.0 microns/sec. Segregation measurements for the ground-based crystals are indicative of complete mixing behavior, as expected. Segregation measurements of the flight crystals are still in progress.

Determining bovine viral diarrhea and infectious bovine rhinotracheitis infections in dairy cattle using precolostral blood.

PubMed

Baillargeon, Paul; Arango-Sabogal, Juan C; Wellemans, Vincent; Fecteau, Gilles

2017-04-01

The objective of this study was to determine if precolostral blood samples are useful to detect apparent fetal infections with bovine viral diarrhea (BVD) and infectious bovine rhinotracheitis (IBR) viruses. A convenience sample of 317 sera from 50 Canadian herds was used in the study. Antibody level was measured using 2 commercial IBR and BVD ELISA kits. Precolostral status of sera was confirmed on 304 samples using serum gamma-glutamyl transferase activity. Postcolostral serum samples yielded a higher proportion of positive results to IBR (OR = 86; 95% CI: 17.8 to 415.7) and BVD (OR = 199.3; 95% CI: 41.7 to 952.3) than did precolostral samples. All positive precolostral serum samples ( n = 7 of 304) originated from calves born to vaccinated cows. Postcolostral positive serum samples ( n = 11 of 13) originated mostly (60%) from calves born to non-vaccinated cows. Precolostral serum sampling can detect apparent fetal infections in a herd.

Missed diagnostic opportunities within South Africa's early infant diagnosis program, 2010-2015.

PubMed

Haeri Mazanderani, Ahmad; Moyo, Faith; Sherman, Gayle G

2017-01-01

Samples submitted for HIV PCR testing that fail to yield a positive or negative result represent missed diagnostic opportunities. We describe HIV PCR test rejections and indeterminate results, and the associated delay in diagnosis, within South Africa's early infant diagnosis (EID) program from 2010 to 2015. HIV PCR test data from January 2010 to December 2015 were extracted from the National Health Laboratory Service Corporate Data Warehouse, a central data repository of all registered test-sets within the public health sector in South Africa, by laboratory number, result, date, facility, and testing laboratory. Samples that failed to yield either a positive or negative result were categorized according to the rejection code on the laboratory information system, and descriptive analysis performed using Microsoft Excel. Delay in diagnosis was calculated for patients who had a missed diagnostic opportunity registered between January 2013 and December 2015 by means of a patient linking-algorithm employing demographic details. Between 2010 and 2015, 2 178 582 samples were registered for HIV PCR testing of which 6.2% (n = 134 339) failed to yield either a positive or negative result, decreasing proportionally from 7.0% (n = 20 556) in 2010 to 4.4% (n = 21 388) in 2015 (p<0.001). Amongst 76 972 coded missed diagnostic opportunities, 49 585 (64.4%) were a result of pre-analytical error and 27 387 (35.6%) analytical error. Amongst 49 694 patients searched for follow-up results, 16 895 (34.0%) had at least one subsequent HIV PCR test registered after a median of 29 days (IQR: 13-57), of which 8.4% tested positive compared with 3.6% of all samples submitted for the same period. Routine laboratory data provides the opportunity for near real-time surveillance and quality improvement within the EID program. Delay in diagnosis and wastage of resources associated with missed diagnostic opportunities must be addressed and infants actively followed-up as South Africa works towards elimination of mother-to-child transmission.

A false sense of security? Can tiered approach be trusted to accurately classify immunogenicity samples?

PubMed

Jaki, Thomas; Allacher, Peter; Horling, Frank

2016-09-05

Detecting and characterizing of anti-drug antibodies (ADA) against a protein therapeutic are crucially important to monitor the unwanted immune response. Usually a multi-tiered approach that initially rapidly screens for positive samples that are subsequently confirmed in a separate assay is employed for testing of patient samples for ADA activity. In this manuscript we evaluate the ability of different methods used to classify subject with screening and competition based confirmatory assays. We find that for the overall performance of the multi-stage process the method used for confirmation is most important where a t-test is best when differences are moderate to large. Moreover we find that, when differences between positive and negative samples are not sufficiently large, using a competition based confirmation step does yield poor classification of positive samples. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

How Many Cultures Are Necessary to Identify Pathogens in the Management of Total Hip and Knee Arthroplasty Infections?

PubMed

Gandhi, Rikesh; Silverman, Edward; Courtney, Paul M; Lee, Gwo-Chin

2017-09-01

Identification of the infecting organism is critical to the successful management of deep prosthetic joint infections about the hip and the knee. However, the number of culture specimens and which culture specimens are best to identify these organisms is unknown. We evaluated 113 consecutive patients with infected total hip and total knee arthroplasties and correlated the type of culture specimen and number of specimens taken during surgery to the likelihood of a positive culture result. From these data, we subsequently developed a model to maximize culture yield at the time of surgical intervention. After exclusions, 74 patients meeting the Musculoskeletal Infection Society criteria were left for final analysis. From this cohort, 63 of 74 patients had a positive culture result (85%). The odds of a fluid culture result being positive was 35 of 47 (0.75), whereas the likelihood of tissue cultures yielding a positive result was 164 of 245 (0.67; P = .313). The sample designated "best culture" specimen was the only culture with a positive result in 1 of 48 cases in which a best culture was identified. The optimal number of cultures needed to yield a positive test result was 4 (specificity = 0.61 and sensitivity = 0.63). Increasing the number of samples increases sensitivity but reduces specificity. A minimum of 4 tissue cultures from representative areas is necessary to maximize the chance of identifying the infecting organism during management of the infected total hip and total knee arthroplasties. The designation of the best culture specimen for additional testing is arbitrary and may not be clinically efficacious. Copyright © 2017 Elsevier Inc. All rights reserved.

Character strengths and well-being across the life span: data from a representative sample of German-speaking adults living in Switzerland

PubMed Central

Martínez-Martí, María L.; Ruch, Willibald

2014-01-01

Character strengths are positive, morally valued traits of personality. This study aims at assessing the relationship between character strengths and subjective well-being (i.e., life satisfaction, positive and negative affect) in a representative sample of German-speaking adults living in Switzerland (N = 945). We further test whether this relationship is consistent at different stages in life. Results showed that hope, zest, love, social intelligence and perseverance yielded the highest positive correlations with life satisfaction. Hope, zest, humor, gratitude and love presented the highest positive correlations with positive affect. Hope, humor, zest, honesty, and open-mindedness had the highest negative correlations with negative affect. When examining the relationship between strengths and well-being across age groups, in general, hope, zest and humor consistently yielded the highest correlations with well-being. Additionally, in the 27–36 years group, strengths that promote commitment and affiliation (i.e., kindness and honesty) were among the first five positions in the ranking of the relationship between strengths and well-being. In the 37–46 years group, in addition to hope, zest and humor, strengths that promote the maintenance of areas such as family and work (i.e., love, leadership) were among the first five positions in the ranking. Finally, in the 47–57 years group, in addition to hope, zest and humor, strengths that facilitate integration and a vital involvement with the environment (i.e., gratitude, love of learning) were among the first five positions in the ranking. This study partially supports previous findings with less representative samples on the association between character strengths and well-being, and sheds light on the relative importance of some strengths over others for well-being across the life span. PMID:25408678

Combustion of solid carbon rods in zero and normal gravity. Ph.D. Thesis - Toledo Univ., Ohio

NASA Technical Reports Server (NTRS)

Spuckler, C. M.

1981-01-01

In order to investigate the mechanism of carbon combustion and to assess the importance of gravitational induced convection on the process, zero and normal gravity experiments were conducted in which spectroscopic carbon rods were resistance ignitied and burned in dry oxygen environments. In the zero-gravity drop tower tests, a blue flame surrounded the rod, showing that a gas phase reaction in which carbon monoxide was oxidized to carbon dioxide was taking place. The ratio of flame diameter to rod diameter was obtained as a function of time. It was found that this ratio was inversely proportional to both the oxygen pressure and the rod diameter. In the normal gravity tests, direct mass spectrometric sampling was used to measure gas phase concentrations. The gas sampling probe was positioned near the circumference of a horizontally mounted 0.615 cm diameter carbon rod, either at the top or at angles of 45 deg to 90 deg from the top, and yielded concentration profiles of CO2, CO, and O2 as a function of distance from the surface. The mechanism controlling the combustion process was found to change from chemical process control at the 90 deg and 45 deg probe positions to mass transfer control at the 0 deg probe position at the top of the rod. Under the experimental conditions used, carbon combustion was characterized by two surface reactions, 2C + O2 yields 2CO and CO2 + C yields 2CO, and a gas phase reaction, 2CO + O2 yields 2CO2.

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

PubMed

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

2000-09-01

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

RECOIL LABELING OF ORGANIC COMPOUNDS (in Japanese)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oae, S.; Hamada, M.; Otsuji, Y.

1963-01-01

The results of C/sup 14/-labeling under neutron irradiation of two groups of compounds are reported: (1) naphthalene, phenanthrene, and anthracene in an attempt to determine whether or not high energy C/sup 14/ fragments formed by nuclear recoil would favor or discriminate against any particular position in product formations; (2) pseudoephedrine, 2-amino-pyrimidine, and 3,6- dihydroxypyridazine as complex nitrogen-containing compounds. These samples were irradiated with thermal neutrons obtained from a pile. To determine the radiochemical yields and the relative ratios of the C/sup 14/ distributions in the respective compounds, the samples were purified radlochemically and were degraded chemically. The results deduced frommore » the experimental data are the following: (1) higher distribution of C/sup 14/ was found in the positions where the localizations of electrons are known to be higher; (2) the re-entry of C/sup 14/ into angular positions was very small; (3) the difference of phase affected the yield but not the distribution of C/sup 14/ in the products; (4) the relatively complex compounds could be labeled directly by this method. (A.G.W.)« less

Comparison of three DNA extraction kits to establish maximum yield and quality of coral-associated microbial DNA

USGS Publications Warehouse

Baker, Erin J.; Kellogg, Christina A.

2014-01-01

Coral microbiology is an expanding field, yet there is no standard DNA extraction protocol. Although many researchers depend on commercial extraction kits, no specific kit has been optimized for use with coral samples. Both soil and plant DNA extraction kits from MO BIO Laboratories, Inc., have been used by many research groups for this purpose. MO BIO recently replaced their PowerPlant® kit with an improved PowerPlantPro kit, but it was unclear how these changes would affect the kit’s use with coral samples. In order to determine which kit produced the best results, we conducted a comparison between the original PowerPlant kit, the new PowerPlantPro kit, and an alternative kit, PowerSoil, using samples from several different coral genera. The PowerPlantPro kit had the highest DNA yields, but the lack of 16S rRNA gene amplification in many samples suggests that much of the yield may be coral DNA rather than microbial DNA. The most consistent positive amplifications came from the PowerSoil kit.

MALDI-MS/MS with Traveling Wave Ion Mobility for the Structural Analysis of N-Linked Glycans

NASA Astrophysics Data System (ADS)

Harvey, David J.; Scarff, Charlotte A.; Crispin, Max; Scanlan, Christopher N.; Bonomelli, Camille; Scrivens, James H.

2012-11-01

The preference for singly charged ion formation by MALDI makes it a better choice than electrospray ionization for profiling mixtures of N-glycans. For structural analysis, fragmentation of negative ions often yields more informative spectra than fragmentation of positive ones but such ions are more difficult to produce from neutral glycans under MALDI conditions. This work investigates conditions for the formation of both positive and negative ions by MALDI from N-linked glycans released from glycoproteins and their subsequent MS/MS and ion mobility behaviour. 2,4,6-Trihydroxyacetophenone (THAP) doped with ammonium nitrate was found to give optimal ion yields in negative ion mode. Ammonium chloride or phosphate also yielded prominent adducts but anionic carbohydrates such as sulfated N-glycans tended to ionize preferentially. Carbohydrates adducted with all three adducts (phosphate, chloride, and nitrate) produced good negative ion CID spectra but those adducted with iodide and sulfate did not yield fragment ions although they gave stronger signals. Fragmentation paralleled that seen following electrospray ionization providing superior spectra than could be obtained by PSD on MALDI-TOF instruments or with ion traps. In addition, ion mobility drift times of the adducted glycans and the ability of this technique to separate isomers also mirrored those obtained following ESI sample introduction. Ion mobility also allowed profiles to be obtained from samples whose MALDI spectra showed no evidence of such ions allowing the technique to be used in conditions where sample amounts were limiting. The method was applied to N-glycans released from the recombinant human immunodeficiency virus glycoprotein, gp120.

Effect of enzymatic mash treatment and storage on phenolic composition, antioxidant activity, and turbidity of cloudy apple juice.

PubMed

Oszmiański, Jan; Wojdylo, Aneta; Kolniak, Joanna

2009-08-12

The effects of different commercial enzymatic mash treatments on yield, turbidity, color, and polyphenolic and sediment of procyanidins content of cloudy apple juice were studied. Addition of pectolytic enzymes to mash treatment had positive effect on the production of cloud apple juices by improving polyphenolic contents, especially procyanidins and juice yields (68.3% in control samples to 77% after Pectinex Yield Mash). As summary of the effect of enzymatic mash treatment, polyphenol contents in cloudy apple juices significantly increased after Pectinex Yield Mash, Pectinex Smash XXL, and Pectinex XXL maceration were applied but no effect was observed after Pectinex Ultra-SPL I Panzym XXL use, compared to the control samples. The content of polymeric procyanidins represented 50-70% of total polyphenols, but in the present study, polymeric procyanidins were significantly lower in juices than in fruits and also affected by enzymatic treatment (Pectinex AFP L-4 and Panzym Yield Mash) compared to the control samples. The enzymatic treatment decreased procyanidin content in most sediment with the exception of Pectinex Smash XXL and Pectinex AFP L-4. Generally in samples that were treated by pectinase, radical scavenging activity of cloudy apple juices was increased compared to the untreated reference samples. The highest radical scavenging activity was associated with Pectinex Yield Mash, Pectinex Smash XXL, and Pectinex XXL enzyme and the lowest activity with Pectinex Ultra SP-L and Pectinex APFL-4. However, in the case of enzymatic mash treatment cloudy apple juices showed instability of turbidity and low viscosity. These results must be ascribed to the much higher hydrolysis of pectin by enzymatic preparation which is responsible for viscosity. During 6 months of storage at 4 degrees C small changes in analyzed parameters of apple juices were observed.

Ciguatoxin-like substances in edible fish on the eastern Mediterranean.

PubMed

Bentur, Yedidia; Spanier, Ehud

2007-09-01

The consumption of edible fish (e.g., Siganus spp) was assumed to have caused ciguatera poisoning at an atypical site, the eastern Mediterranean. This pilot study assesses the presence of ciguatoxin-like substances in edible fish on the eastern Mediterranean coast of Israel. Samples of Siganus rivulatus from polluted seawater (Haifa Bay), Siganus rivulatus from relatively clean seawater (Dor), and fish from the freshwater Sea of Galilee not inhabited by toxic algae were analyzed during summertime. Ciguatoxin-like substances were tested by a membrane immunobead assay that yields a color reaction (positive, weakly positive, negative). Significantly more large and small fish from Haifa Bay yielded positive color reactions compared to fish from Dor. Sea of Galilee fish gave no positive color reactions. Our results suggest the presence of ciguatoxin-like substances in edible fish of the eastern Mediterranean. Additional analyses are needed to determine whether these substances are ciguatoxins or related polyethers.

Raman spectroscopy-based screening of hepatitis C and associated molecular changes

NASA Astrophysics Data System (ADS)

Bilal, Maria; Bilal, M.; Saleem, M.; Khan, Saranjam; Ullah, Rahat; Fatima, Kiran; Ahmed, M.; Hayat, Abbas; Shahzada, Shaista; Ullah Khan, Ehsan

2017-09-01

This study presents the optical screening of hepatitis C and its associated molecular changes in human blood sera using a partial least-squares regression model based on their Raman spectra. In total, 152 samples were tested through enzyme-linked immunosorbent assay for confirmation. This model utilizes minor spectral variations in the Raman spectra of the positive and control groups. Regression coefficients of this model were analyzed with reference to the variations in concentration of associated molecules in these two groups. It was found that trehalose, chitin, ammonia, and cytokines are positively correlated while lipids, beta structures of proteins, and carbohydrate-binding proteins are negatively correlated with hepatitis C. The regression vector yielded by this model is utilized to predict hepatitis C in unknown samples. This model has been evaluated by a cross-validation method, which yielded a correlation coefficient of 0.91. Moreover, 30 unknown samples were screened for hepatitis C infection using this model to test its performance. Sensitivity, specificity, accuracy, and area under the receiver operating characteristic curve from these predictions were found to be 93.3%, 100%, 96.7%, and 1, respectively.

SIMPLE MEASURES ARE AS EFFECTIVE AS INVASIVE TECHNIQUES IN THE DIAGNOSIS OF PULMONARY TUBERCULOSIS IN MALAWI

PubMed Central

Bell, David J; Dacombe, Russell; Graham, Stephen M; Hicks, Alexander; Cohen, Danielle; Chikaonda, Tarsizio; French, Neil; Molyneux, Malcolm E; Zijlstra, Ed E; Squire, S Bertel; Gordon, Stephen B

2010-01-01

Setting Detection of smear-positive pulmonary tuberculosis (PTB) cases is vital for tuberculosis control. Methods to augment sputum collection are available but their additional benefit is uncertain in resource-limited settings. Objective To compare the diagnostic yields using five methods to obtain sputum from adults diagnosed with smear-negative PTB in Malawi. Design Self-expectorated sputum was collected under supervision for microscopy and mycobacterial culture in the study laboratory. Confirmed smear-negative patients, provided physiotherapy-assisted sputum and induced sputum followed, the next morning, by gastric washing and bronchoalveolar-lavage samples. Results 150 patients, diagnosed with smear-negative PTB by the hospital service, were screened. 39 (26%) were smear-positive from supervised self-expectorated sputum examined in the study laboratory. The remaining 111 confirmed smear-negative patients were enrolled; 89% were HIV positive. Seven additional smear-positive cases were diagnosed using the augmented sputum collection techniques. No differences were observed in the numbers of cases detected using the different methods. 44 (95.6%) of the 46 smear-positive cases could be detected from self-expectorated and physiotherapy-assisted samples Conclusions For countries like Malawi, the best use of limited resources to detect smear-positive PTB cases would be to improve the quality of self-expectorated sputum collection and microscopy. The additional diagnostic yield using bronchoalveolar-lavage after induced sputum is limited. PMID:19105886

Determination of the Presence of Three Antimicrobials in Surface Water Collected from Urban and Rural Areas

PubMed Central

Iglesias, Alejandra; Nebot, Carolina; Miranda, Jose M.; Vázquez, Beatriz I.; Abuín, Carlos M. Franco; Cepeda, Alberto

2013-01-01

Due to the continuous release of antimicrobials into the environment, the aim of this study was to compare the frequency of detection of sulfamethazine, sulfamethoxypyridazine and trimethoprim in surface water collected from urban and rural areas in Northwestern Spain. A monitoring study was conducted with 314 river water samples analyzed by high-performance liquid chromatography coupled to tandem mass spectrometry. The results indicated that 37% of the samples contained residues of at least one of the investigated antimicrobials, and every sampling site yielded positive samples. At sites located near the discharge points of wastewater treatment plants and near the collection point of a drinking-water treatment plant, more than 6% of the samples were positive for the presence of antimicrobial residues. PMID:27029291

Comparative Effectiveness of Frame-based, Frameless and Intraoperative MRI Guided Brain Biopsy Techniques

PubMed Central

Lu, Yi; Yeung, Cecil; Radmanesh, Alireza; Wiemann, Robert; Black, Peter M.; Golby, Alexandra J.

2015-01-01

Objective Intraoperative MRI (IoMRI) guided brain biopsy provides a real time visual feedback of the lesion that is sampled during surgery. The objective of the study is to compare the diagnostic yield and safety profiles of ioMRI needle brain biopsy with two traditional brain biopsy methods: frame-based and frameless stereotactic brain biopsies. Methods A retrospective analysis from 288 consecutive needle brain biopsies in 277 patients undergoing stereotactic brain biopsy with any of the three biopsy methods at Brigham and Women's Hospital from 2000 to 2008 was performed. Variables such as age, sex, history of radiation and previous surgery, pathology results, complications and postoperative stays were analyzed. Results Over the course of eight years, 288 brain biopsies were performed. 253 (87.8%) biopsies yielded positive diagnostic tissue. Young age (<40 years), history of brain radiation or surgery were significant negative predictors for a positive biopsy diagnostic yield. Excluding patients with prior radiation or surgeries, no significant difference in diagnostic yield was detected among the three groups, with frame-based, frameless and ioMRI guided needle biopsies yield 96.9%, 91.8% and 89.9% positive diagnostic yield, respectively. 19 biopsies (6.6%) were complicated by serious adverse events. The ioMRI-guided brain biopsy was associated with less serious adverse events and the shortest postoperative hospital stay. Conclusions Frame-based, frameless stereotactic and ioMRI guided brain needle biopsy have comparable diagnostic yield for patients with no prior treatments (either radiation or surgery). IoMRI guided brain biopsy is associated with fewer serious adverse events and shorter hospital stay. PMID:25088233

Monitoring baseline suspended sediment in forested basins: the effects of sampling on suspended sediment rating curves

Treesearch

Robert B. Thomas

1988-01-01

Abstract - Rating curves are widely used for directly assessing changes in the suspended sediment delivery process and indirectly for estimating total yields. Four sampling methods were simulated-over a 31-day record of suspended sediment from the North Fork of the Mad River near Korbel, California. The position and size of the four groups of plotted slope/intercept...

Guidelines for the use and interpretation of nucleic acid detection tests for Neisseria gonorrhoeae in Australia: a position paper on behalf of the Public Health Laboratory Network.

PubMed

Smith, David W; Tapsall, John W; Lum, Gary

2005-01-01

The Public Health Laboratory Network (PHLN) convened a workshop of Australian experts in Melbourne on 23 March 2005 to identify laboratory issues of relevance and suggest guidelines for use of nucleic acid detection tests (NADT) for diagnosis of gonorrhoea in Australia. The proceedings of that meeting were endorsed by the members of the PHLN and the Communicable Diseases Network of Australia. Given the present state of knowledge and experience of conditions currently existing in Australia, the following recommendations were made: Recommendation 1: Assays using detection of the cppB gene should not be used for either screening or supplemental assays. Recommendation 2: All in-house screening assays that are positive should also be positive on a reliable supplemental assay before a positive result is reported. Recommendation 3: All commercial screening assays that are positive should also be positive on a reliable supplemental assay before a positive result is reported. Recommendation 4: If a sample is positive in a screening assay but a suitable supplemental assay is negative, then the result should be reported as negative. Recommendation 5: Laboratories should ensure that the test combination they use would yield a positive predictive value of at least 90 per cent in a population with a prevalence of 1 per cent. Recommendation 6: For the purposes of test evaluation, as distinct from diagnostic testing, true positives be defined by meeting one or more of the following criteria: 1) culture positive using contemporary isolation and identification techniques; 2) positive result on NADTs directed to targets on three separate genes that are known to have discriminatory capacity; 3) sequencing of a gene known to separate gonococcal from non-gonococcal species. Recommendation 7: Inhibitor controls should be routinely included in all NADT. Recommendation 8: Cultures are the preferred test for samples from non-genital sites. If however it is necessary to perform a NADT, then more stringent criteria should be applied, and positive samples should meet the 'test evaluation' criteria for a 'true positive'. Recommendation 9: In order to properly assess the routine diagnostic system in Australia, the following quality assurance samples should be distributed in addition to the routine samples currently used: 1. cppB negative N. gonorrhoeae; 2. Non-gonococcal species known to cause false positive reactions: these should be dispatched both as a single species, as well as mixture with N. gonorrhoeae. In the latter circumstance, the non-gonococcal species should be present in 10-fold excess; 3. Urine samples: preferably a single patient sample, otherwise a spiked sample. 4. Validation panels should be made that include samples that are culture positive but PCR negative. True positive samples should also be made available. In addition, a process should be established for full phenotypic and genotypic characterisation of unidentified species that yield false positive results in NADT for gonococci. Recommendation 10: Strategies should be put in place to ensure that sufficient numbers of gonococcal isolates are obtained to allow reliable monitoring of antimicrobial resistance. Recommendation 11: Public health practitioners need to define the relevant populations that need to be targeted and identify any that require enhanced surveillance.

Direct microscopy versus sputum cytology analysis and bleach sedimentation for diagnosis of tuberculosis: a prospective diagnostic study

PubMed Central

2010-01-01

Background Diagnostic options for pulmonary tuberculosis in resource-poor settings are commonly limited to smear microscopy. We investigated whether bleach concentration by sedimentation and sputum cytology analysis (SCA) increased the positivity rate of smear microscopy for smear-positive tuberculosis. Methods We did a prospective diagnostic study in a Médecins Sans Frontières-supported hospital in Mindouli, Republic of Congo. Three sputum samples were obtained from 280 consecutive pulmonary tuberculosis suspects, and were processed according to WHO guidelines for direct smear microscopy. The remainder of each sputum sample was homogenised with 2.6% bleach, sedimented overnight, smeared, and examined blinded to the direct smear result for acid-fast bacilli (AFB). All direct smears were assessed for quality by SCA. If a patient produced fewer than three good-quality sputum samples, further samples were requested. Sediment smear examination was performed independently of SCA result on the corresponding direct smear. Positivity rates were compared using McNemar's test. Results Excluding SCA, 43.2% of all patients were diagnosed as positive on direct microscopy of up to three samples. 47.9% were diagnosed on sediment microscopy, with 48.2% being diagnosed on direct microscopy, sediment microscopy, or both. The positivity rate increased from 43.2% to 47.9% with a case definition of one positive smear (≥1 AFB/100 high power fields) of three, and from 42.1% to 43.9% with two positive smears. SCA resulted in 87.9% of patients producing at least two good-quality sputum samples, with 75.7% producing three or more. Using a case definition of one positive smear, the incremental yield of bleach sedimentation was 14/121, or 11.6% (95% CI 6.5-18.6, p = 0.001) and in combination with SCA was 15/121, or 12.4% (95% CI 7.1-19.6, p = 0.002). Incremental yields with two positive smears were 5/118, or 4.2% (95% CI 1.4-9.6, p = 0.062) and 7/118, or 5.9% (95% CI 2.4-11.8, p = 0.016), respectively. Conclusions The combination of bleach sedimentation and SCA resulted in significantly increased microscopy positivity rates with a case definition of either one or two positive smears. Implementation of bleach sedimentation led to a significant increase in the diagnosis of smear-positive patients. Implementation of SCA did not result in significantly increased diagnosis of tuberculosis, but did result in improved sample quality. Requesting extra sputum samples based on SCA results, combined with bleach sedimentation, could significantly increase the detection of smear-positive patients if routinely implemented in resource-limited settings where gold standard techniques are not available. We recommend that a pilot phase is undertaken before routine implementation to determine the impact in a particular context. PMID:20858253

Study of the Wavelength Dependence in Laser Ablation of Advanced Ceramics and Glass-Ceramic Materials in the Nanosecond Range

PubMed Central

Sola, Daniel; Peña, Jose I.

2013-01-01

In this work, geometrical dimensions and ablation yields as a function of the machining method and reference position were studied when advanced ceramics and glass-ceramic materials were machined with pulsed lasers in the nanosecond range. Two laser systems, emitting at 1064 and 532 nm, were used. It was shown that the features obtained depend on whether the substrate is processed by means of pulse bursts or by grooves. In particular, when the samples were processed by grooves, machined depth, removed volume and ablation yields reached their maximum, placing the sample out of focus. It was shown that these characteristics do not depend on the processing conditions, the wavelength or the optical configuration, and that this is intrinsic behavior of the processing method. Furthermore, the existence of a close relation between material hardness and ablation yields was demonstrated. PMID:28788391

Structure in the 3D Galaxy Distribution. III. Fourier Transforming the Universe: Phase and Power Spectra

NASA Technical Reports Server (NTRS)

Scargle, Jeffrey D.; Way, M. J.; Gazis, P. G.

2017-01-01

We demonstrate the effectiveness of a relatively straightforward analysis of the complex 3D Fourier transform of galaxy coordinates derived from redshift surveys. Numerical demonstrations of this approach are carried out on a volume-limited sample of the Sloan Digital Sky Survey redshift survey. The direct unbinned transform yields a complex 3D data cube quite similar to that from the Fast Fourier Transform of finely binned galaxy positions. In both cases, deconvolution of the sampling window function yields estimates of the true transform. Simple power spectrum estimates from these transforms are roughly consistent with those using more elaborate methods. The complex Fourier transform characterizes spatial distributional properties beyond the power spectrum in a manner different from (and we argue is more easily interpreted than) the conventional multipoint hierarchy. We identify some threads of modern large-scale inference methodology that will presumably yield detections in new wider and deeper surveys.

A comparison between minerals-modified glutamate medium and lauryl tryptose lactose broth for the enumeration of Escherichia coli and coliform organisms in water by the multiple tube method.

PubMed Central

1980-01-01

In a multi-laboratory trial, minerals-modified glutamate medium (MMGM) was compared with lauryl tryptose lactose broth (LTLB) in the multiple tube method for the enumeration of coliform organisms, including Escherichia coli, in water. Samples of raw and chlorinated waters yielded a total of 2313 positive tube-reactions with MMGM and 2174 with LTLB. These were interpreted either as E. coli; other coliform organisms; or as false positive reactions. The results at first reading (18 or 24 h) and at 48 h have been analysed statistically in terms of (i) most probable numbers of coliform organisms; (ii) positive reactions and their interpretation; and (iii) whether or not the sample yielded any E. coli or other coliform organisms. All three analyses indicated the same trends. For the detection of E. coli in raw waters LTLB was better than MMGM at 18-24 h, but MMGM was better at 48 h with waters containing small numbers of coliform organisms; for raw waters with greater numbers of organisms, both media performed equally well. Analysis of a subset of samples read at both 18 and 24 h indicated that the superiority of LTLB over MMGM with raw waters disappeared by 24 h. For chlorinated waters, LTLB yielded more positive gas reactions at 18-24 h, but fewer of these were E. coli than with MMGM; at 48 h MMGM was clearly better than LTLB for total coliform organisms including E. coli--especially if the numbers were small. MMGM therefore remains the medium of choice for the detection of E. coli as an indicator of faecal contamination of chlorinated drinking water supplies. It is also better for the detection of small numbers of E. coli in other waters. PMID:6762395

Decontamination methods for samples preserved in cetylpyridinium chloride and cultured on thin-layer agar.

PubMed

Ardizzoni, E; Mulders, W; Sanchez-Padilla, E; Varaine, F; de Jong, B C; Rigouts, L

2014-08-01

Long transportation times of samples to culture laboratories can lead to higher contamination rates and significant loss of viability, resulting in lower culture positivity rates. Thin-layer agar (TLA) is a sensitive culture method for the isolation of Mycobacterium tuberculosis that has been optimised with N-acetyl-L-cysteine-sodium hydroxide (NALC-NaOH) decontaminated samples. The combination of the TLA culture method and other decontamination procedures has not been extensively validated. Among 390 smear-positive samples, we compared the culture positivity of samples decontaminated using the Petroff method vs. NALC-NaOH neutralised with phosphate buffer (PBS), applied to samples preserved with cetylpyridinium chloride (CPC) or CPC-free, and then of CPC-preserved samples decontaminated with NALC-NaOH neutralised using Difco neutralising buffer. The sediments were inoculated on TLA, and then on MGIT 960 or Löwenstein-Jensen (LJ) as gold standards. Decontamination with NALC-NaOH yielded higher culture positivity in TLA than in the Petroff method, which was further enhanced by neutralising CPC with the Difco buffer. Surprisingly, culture positivity on LJ also increased after using Difco buffer, suggesting that CPC may not be completely neutralised in egg-based medium. After transportation in CPC, decontamination using NALC-NaOH followed by neutralisation using Difco buffer resulted in the best recovery rates for samples inoculated on TLA and on LJ.

Fast Atom Bombardment Mass Spectrometry.

ERIC Educational Resources Information Center

Rinehart, Kenneth L., Jr.

1982-01-01

Discusses reactions and characteristics of fast atom bombardment (FAB) mass spectroscopy in which samples are ionized in a condensed state by bombardment with xenon or argon atoms, yielding positive/negative secondary ions. Includes applications of FAB to structural problems and considers future developments using the technique. (Author/JN)

Comparative evaluation of paired blood culture (aerobic/aerobic) and single blood culture, along with clinical importance in catheter versus peripheral line at a tertiary care hospital.

PubMed

Tarai, B; Das, P; Kumar, D; Budhiraja, S

2012-01-01

Paired blood culture (PBC) is uncommon practice in hospitals in India, leading to delayed and inadequate diagnosis. Also contamination remains a critical determinant in hampering the definitive diagnosis. To establish the need of PBC over single blood culture (SBC) along with the degree of contamination, this comparative retrospective study was initiated. We processed 2553 PBC and 4350 SBC in BacT/ALERT 3D (bioMerieux) between October 2010 and June 2011. The positive cultures were identified in VITEK 2 Compact (bioMerieux). True positivity and contaminants were also analyzed in 486 samples received from catheter and peripheral line. Out of 2553 PBC samples, positivity was seen in 350 (13.70%). In 4350 SBC samples, positivity was seen in 200 samples (4.59%). In PBC true pathogens were 267 (10.45%) and contaminants were 83 (3.25%), whereas in SBC 153 (3.51%) were true positives and contaminants were 47 (1.08%). Most of the blood cultures (99.27 %) grew within 72 h and 95.8% were isolated within 48 h. In 486 PBCs received from catheter/periphery (one each), catheter positivity was found in 85 (true positives were 48, false positives 37). In peripheral samples true positives were 50 and false positives were 8. Significantly higher positive rates were seen in PBCs compared with SBCs. Automated blood culture and identification methods significantly reduced the time required for processing of samples and also facilitated yield of diverse/rare organisms. Blood culture from catheter line had higher false positives than peripheral blood culture. Thus every positive result from a catheter must be correlated with clinical findings and requires further confirmation.

Prevalence and distribution of Arcobacter spp. in raw milk and retail raw beef.

PubMed

Shah, A H; Saleha, A A; Murugaiyah, M; Zunita, Z; Memon, A A

2012-08-01

A total of 106 beef samples which consisted of local (n = 59) and imported (n = 47) beef and 180 milk samples from cows (n = 86) and goats (n = 94) were collected from Selangor, Malaysia. Overall, 30.2% (32 of 106) of beef samples were found positive for Arcobacter species. Imported beef was significantly more contaminated (46.80%) than local beef (16.9%). Arcobacter butzleri was the species isolated most frequently from imported (81.8%) and local (60%) beef, followed by Arcobacter cryaerophilus in local (33.3%) and imported (18.2%) beef samples. Only one local beef sample (10%) yielded Arcobacter skirrowii. Arcobacter species were detected from cow's milk (5.8%), with A. butzleri as the dominant species (60%), followed by A. cryaerophilus (40%), whereas none of the goat's milk samples were found positive for Arcobacter. This is the first report of the detection of Arcobacter in milk and beef in Malaysia.

Useful ion yields for Cameca IMS 3f and 6f SIMS: Limits on quantitative analysis

USGS Publications Warehouse

Hervig, R.L.; Mazdab, F.K.; Williams, Pat; Guan, Y.; Huss, G.R.; Leshin, L.A.

2006-01-01

The useful yields (ions detected/atom sputtered) of major and trace elements in NIST 610 glass were measured by secondary ion mass spectrometry (SIMS) using Cameca IMS 3f and 6f instruments. Useful yields of positive ions at maximum transmission range from 10-4 to 0.2 and are negatively correlated with ionization potential. We quantified the decrease in useful yields when applying energy filtering or high mass resolution techniques to remove molecular interferences. The useful yields of selected negative ions (O, S, Au) in magnetite and pyrite were also determined. These data allow the analyst to determine if a particular analysis (trace element contents or isotopic ratio) can be achieved, given the amount of sample available and the conditions of the analysis. ?? 2005 Elsevier B.V. All rights reserved.

Extensive cultivation of soil and water samples yields various pathogens in patients with cystic fibrosis but not Burkholderia multivorans.

PubMed

Peeters, Charlotte; Depoorter, Eliza; Praet, Jessy; Vandamme, Peter

2016-11-01

While the epidemiology of Burkholderia cepacia complex (Bcc) bacteria in cystic fibrosis (CF) patients suggests that Burkholderia multivorans is acquired from environmental sources, this species has rarely been isolated from soil and water samples. Multiple isolation strategies were applied to water and soil samples that were previously shown to be B. multivorans PCR positive. These included direct plating and liquid enrichment procedures and the use of selective media, acclimatizing recovery and co-cultivation with CF sputum. MALDI-TOF mass spectrometry and sequence analysis of 16S rRNA and housekeeping genes were used to identify all isolates. None of the approaches yielded B. multivorans isolates. Other Burkholderia species, several Gram-negative non-fermenting bacteria (including Cupriavidus, Inquilinus, Pandoraea, Pseudomonas and Stenotrophomonas) and rapidly growing mycobacteria (including Mycobacterium chelonae) were all isolated from water and soil samples. The use of Bcc isolation media yielded a surprisingly wide array of rare but often clinically relevant CF pathogens, confirming that soil and water are reservoirs of these infectious agents. Copyright © 2016 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Half a decade of mini-pool nucleic acid testing: Cost-effective way for improving blood safety in India

PubMed Central

Chandrashekar, Shivaram

2014-01-01

Background and Objectives: It is well established that Nucleic acid testing (NAT) reduces window phase of transfusion transmissible infections (TTI) and helps improve blood safety. NAT testing can be done individually or in pools. The objectives of this study were to determine the utility, feasibility and cost effectiveness of an in-house minipool-NAT(MP-NAT). Materials and Methods: Blood donors were screened by history, tested by ELISA and sero-negative samples were subjected to an in-house NAT by using reverse transcriptase-polymerase chain reaction (RT-PCR). Testing was done in mini-pools of size eight (8). Positive pools were repeated with individual samples. Results: During the study period of Oct 2005-Sept 2010 (5 years) all blood donors (n=53729) were screened by ELISA. Of which 469 (0.87%) were positive for HIV-1, HBV or HCV. Sero-negative samples (n=53260) were screened by in-house MP-NAT. HIV-NAT yield was 1/53260 (n=1) and HBV NAT yield (n=2) was 1/26630. Conclusion: NAT yield was lower than other India studies possibly due to the lower sero-reactivity amongst our donors. Nevertheless it intercepted 9 lives including the components prepared. The in-house assay met our objective of improving blood safety at nominal cost and showed that it is feasible to set up small molecular biology units in medium-large sized blood banks and deliver blood within 24-48 hours. The utility of NAT (NAT yield) will vary based on the donor population, the type of serological test used, the nature of kit employed and the sensitivity of NAT test used. The limitations of our in-house MP-NAT consisted of stringent sample preparation requirements, with labor and time involved. The benefits of our MP-NAT were that it acted as a second level of check for ELISA tests, was relatively inexpensive compared to ID-NAT and did not need sophisticated equipment. PMID:24678172

Fertilizer nitrogen, soil chemical properties, and their determinacy on rice yield: Evidence from 92 paddy fields of a large-scale farm in the Kanto Region of Japan

NASA Astrophysics Data System (ADS)

Li, D.; Nanseki, T.; Chomei, Y.; Yokota, S.

2017-07-01

Rice, a staple crop in Japan, is at risk of decreasing production and its yield highly depends on soil fertility. This study aimed to investigate determinants of rice yield, from the perspectives of fertilizer nitrogen and soil chemical properties. The data were sampled in 2014 and 2015 from 92 peat soil paddy fields on a large-scale farm located in the Kanto Region of Japan. The rice variety used was the most widely planted Koshihikari in Japan. Regression analysis indicated that fertilizer nitrogen significantly affected the yield, with a significant sustained effect to the subsequent year. Twelve soil chemical properties, including pH, cation exchange capacity, content of pyridine base elements, phosphoric acid, and silicic acid, were estimated. In addition to silicic acid, magnesia, in forms of its exchangeable content, saturation, and ratios to potassium and lime, positively affected the yield, while phosphoric acid negatively affected the yield. We assessed the soil chemical properties by soil quality index and principal component analysis. Positive effects were identified for both approaches, with the former performing better in explaining the rice yield. For soil quality index, the individual standardized soil properties and margins for improvement were indicated for each paddy field. Finally, multivariate regression on the principal components identified the most significant properties.

Correlation between viral loads of cytomegalovirus in blood and bronchoalveolar lavage specimens from lung transplant recipients determined by histology and immunohistochemistry.

PubMed

Chemaly, Roy F; Yen-Lieberman, Belinda; Castilla, Elias A; Reilly, Amy; Arrigain, Susana; Farver, Carol; Avery, Robin K; Gordon, Steven M; Procop, Gary W

2004-05-01

Cytomegalovirus (CMV) is an important pathogen in lung transplant recipients. Early detection of CMV end-organ disease should help with treatment management. We determined the CMV viral load by hybrid capture in bronchoalveolar lavage (BAL) fluid samples from patients who had undergone lung transplantation. For 39 of these samples (from 25 patients), corresponding transbronchial biopsy samples were available for CMV immunohistochemistry (IHC). The CMV IHC results were interpreted and categorized as positive or negative, and the positive results were subcategorized as typical if cells with both significant nuclear enlargement or Cowdry A-type inclusions and positive staining were present or as atypical if definitive nuclear staining was seen but significant nuclear enlargement was not. Diagnostic CMV viral inclusions were reported in the anatomic diagnosis, based on hematoxylin-eosin staining alone, for three (8%) of the biopsy samples. CMV was detected by IHC in 13 (33%) samples (5 typical, 8 atypical). The median CMV viral load in BAL samples was 0 copies/ml for BAL samples from patients with IHC-negative biopsy samples; 47,678 copies/ml for BAL samples from patients with biopsy samples with positive, atypical staining; and 1,548,827 copies/ml for BAL samples from patients with biopsy samples with positive, typical staining (P < 0.001). Compared to routine pathology of biopsy samples, the use of IHC increased the diagnostic yield of CMV. Also, the CMV viral load in BAL fluid samples increased along with immunoreactivity from negative to positive, atypical staining to positive, typical staining. The CMV viral load determined with the end-organ sample, the BAL fluid sample, was higher than the corresponding viral load determined with blood. Both IHC and determination of the CMV viral load in BAL samples may be useful for the detection of individuals at risk for the development of fulminant invasive CMV disease.

Introducing English and German versions of the Adolescent Time Attitude Scale.

PubMed

Worrell, Frank C; Mello, Zena R; Buhl, Monika

2013-08-01

In this study, the authors report on the development of English and German versions of the Adolescent Time Attitude Scale (ATAS). The ATAS consists of six subscales assessing Past Positive, Past Negative, Present Positive, Present Negative, Future Positive, and Future Negative time attitudes. The authors describe the development of the scales and present data on the reliability and structural validity of ATAS scores in samples of American (N = 300) and German (N = 316) adolescents. Internal consistency estimates for scores on the English and German versions of the ATAS were in the .70 to .80 range. Confirmatory factor analyses indicated that a six-factor structure yielded the best fit for scores and that the scores were invariant across samples.

Ethnic Variation in Depressive Symptoms in a Community Sample in Hawai‘i

PubMed Central

Kanazawa, Asako; White, Patricia M.; Hampson, Sarah E.

2008-01-01

A modified CES-D was administered to a community sample of 176 European Americans (EA), 209 Native Hawaiians (NH), and 357 Japanese Americans (JA), yielding measures of depression, positive affect, depressed affect, somatic disturbance and disturbed interpersonal relations. Positive affect was lower in JA relative to EA, consistent with findings among Native Japanese, a pattern attributed to cultural variation in emotion regulation. NH reported lower positive affect than EA, accompanied by elevated negative affect and somatic disturbance, suggesting generally higher levels of depressive symptoms. The three ethnic groups varied in mental healthcare usage with differing associations between depressive symptoms and experiences of stressful life events. Taken together, these results suggest ethnic variation in depressive symptoms may arise from differing cultural beliefs. PMID:17227175

Calibration of the JET neutron activation system for DT operation

NASA Astrophysics Data System (ADS)

Bertalot, L.; Roquemore, A. L.; Loughlin, M.; Esposito, B.

1999-01-01

The neutron activation system at JET is a pneumatic transfer system capable of positioning activation samples close to the plasma. Its primary purpose is to provide a calibration for the time-dependent neutron yield monitors (fission chambers and solid state detectors). Various activation reactions with different high energy thresholds were used including 56Fe(n,p) 56Mn, 27Al(n,α) 24Na, 93Nb(n,2n) 92mNb, and 28Si(n,p) 28Al reactions. The silicon reaction, with its short half life (2.25 min), provides a prompt determination of the 14 MeV DT yield. The neutron induced γ-ray activity of the Si samples was measured using three sodium iodide scintillators, while two high purity germanium detectors were used for other foils. It was necessary to use a range of sample masses and different counting geometries in order to cover the wide range of neutron yields (1015-1019 neutrons) while avoiding excessive count rates in the detectors. The absolute full energy peak efficiency calibration of the detectors was measured taking into account the source-detector geometry, the self-attenuation of the samples and cross-talk effects. An error analysis of the neutron yield measurement was performed including uncertainties in efficiency calibration, neutron transport calculations, cross sections, and counting statistics. Cross calibrations between the different irradiation ends were carried out in DD and DT (with 1% and 10% tritium content) discharges. The effect of the plasma vertical displacement was also experimentally studied. An agreement within 10% was found between the 14 MeV neutron yields measured from Si, Fe, Al, Nb samples in DT discharges.

Direct Detection and Identification of Prosthetic Joint Infection Pathogens in Synovial Fluid by Metagenomic Shotgun Sequencing.

PubMed

Ivy, Morgan I; Thoendel, Matthew J; Jeraldo, Patricio R; Greenwood-Quaintance, Kerryl E; Hanssen, Arlen D; Abdel, Matthew P; Chia, Nicholas; Yao, Janet Z; Tande, Aaron J; Mandrekar, Jayawant N; Patel, Robin

2018-05-30

Background: Metagenomic shotgun sequencing has the potential to transform how serious infections are diagnosed by offering universal, culture-free pathogen detection. This may be especially advantageous for microbial diagnosis of prosthetic joint infection (PJI) by synovial fluid analysis, since synovial fluid cultures are not universally positive, and synovial fluid is easily obtained pre-operatively. We applied a metagenomics-based approach to synovial fluid in an attempt to detect microorganisms in 168 failed total knee arthroplasties. Results: Genus- and species-level analysis of metagenomic sequencing yielded the known pathogen in 74 (90%) and 68 (83%) of the 82 culture-positive PJIs analyzed, respectively, with testing of two (2%) and three (4%) samples, respectively, yielding additional pathogens not detected by culture. For the 25 culture-negative PJIs tested, genus- and species-level analysis yielded 19 (76%) and 21 (84%) samples with insignificant findings, respectively, and 6 (24%) and 4 (16%) with potential pathogens detected, respectively. Genus- and species-level analysis of the 60 culture-negative aseptic failure cases yielded 53 (88.3%) and 56 (93.3%) cases with insignificant findings, and 7 (11.7%) and 4 (6.7%) with potential clinically-significant organisms detected, respectively. There was one case of aseptic failure with synovial fluid culture growth; metagenomic analysis showed insignificant findings, suggesting possible synovial fluid culture contamination. Conclusion: Metagenomic shotgun sequencing can detect pathogens involved in PJI when applied to synovial fluid and may be particularly useful for culture-negative cases. Copyright © 2018 American Society for Microbiology.

[Investigation of the presence of Cryptosporidium spp. in different water sources in Mersin province, Turkey].

PubMed

Aslan, Gönül; Bayram, Gül; Otağ, Feza; Direkel, Sahin; Taylan Özkan, Ayşegül; Ceber, Kemal; Emekdaş, Gürol

2012-01-01

Cryptosporidium is an intracellular protozoon that causes enteritis in human and animals. Contaminated water and food are the major sources for the transmission of oocysts via oral-fecal route. It is reported that the prevalence of cryptosporidiosis is higher in developing countries than developed countries because of inefficient sanitation and disinfection facilities for drinking water. The most frequently detected species is Cryptosporidium parvum leading to high morbidity in healthy subjects and also fatal infections in immunocompromised patients. The acid-fast staining method is widely used in the diagnosis of cryptosporidiosis. Nowadays, Cryptosporidium could easily be detected in water supplies and asymptomatic carriers by molecular techniques to obtain epidemiological data. In this study it was aimed to detect and identify Cryptosporidium oocysts in different water sources in Mersin province, Turkey. A total of 135 water samples (70 taps, 50 wells and 15 sewage) collected from city center (n= 25) and from Tarsus (n= 32), Mezitli (n= 33) and Karaduvar (n= 45) counties between March 2007 and May 2009 were included in the study. Water samples in 10 liter volumes, were filtered by 0.45 µm pore-sized membrane filter vacuum/ pressure pumping technique. Cryptosporidium oocysts in filtrates were detected by modified cold Kinyoun acid-fast stain (MCK) technique and also identified and typed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. MCK yielded three and PCR yielded seven positive results. All the strains were identified as C.parvum by PCR-RFLP method. All of the three MCK-positive samples were also found positive with PCR, however four PCR positive samples were MCK-negative. Thus, the prevalence of C.parvum was estimated as 5.2% (7/135) in our region. Of seven positive samples, one was a sewage water sample collected from the city center, while the remaining (two tap water, two well water and two sewage water samples) belonged to the samples collected from Karaduvar county, interestingly. It was thought that deficient infrastructure and use of well water as drinking water supply in Karaduvar region might be the cause of high rate of Cryptosporidium (6/45; 13.3%). Further studies which will determine the genotypes and investigate the phylogenetic relationship between these Cryptosporidium spp., might aid to the epidemiology of cryptosporidiosis in our region.

Comparing the Yield of Nasopharyngeal Swabs, Nasal Aspirates, and Induced Sputum for Detection of Bordetella pertussis in Hospitalized Infants.

PubMed

Nunes, Marta C; Soofie, Nasiha; Downs, Sarah; Tebeila, Naume; Mudau, Azwi; de Gouveia, Linda; Madhi, Shabir A

2016-12-01

 Advances in molecular laboratory techniques are changing the landscape of Bordetella pertussis illness diagnosis. Polymerase chain reaction (PCR) assays have greatly improved the sensitivity detection and the turnaround time to diagnosis compared to culture. Moreover, different respiratory specimens, such as flocked nasopharyngeal swabs (NPSs), nasopharyngeal aspirates (NPAs), and induced sputum, have been used for B. pertussis detection, although there is limited head-to-head comparison to evaluating the PCR yield from the 3 sampling methods.  Hospitalized infants <6 months of age who fulfilled a broad syndromic criteria of respiratory illness were tested for B. pertussis infection by PCR on paired NPSs and NPAs; or paired NPSs and induced sputum. An exploratory analysis of B. pertussis culture was performed on induced sputum specimens and in a subset of NPSs.  From November 2014 to May 2015, 484 infants with paired NPSs and NPAs were tested; 15 (3.1%) PCR-confirmed pertussis cases were identified, 13 of which were PCR positive on both samples, while 1 each were positive only on NPS or NPA. From March to October 2015, 320 infants had NPSs and induced sputum collected, and 11 (3.4%) pertussis cases were identified by PCR, including 8 (72.7%) positive on both samples, 1 (9.1%) only positive on NPS, and 2 (18.2%) only positive on induced sputum. The 3 types of specimens had similar negative predictive value >99% and sensitivity >83%. Compared to PCR, culture sensitivity was 60% in induced sputum and 40% in NPSs.  Flocked nasopharyngeal swabs, nasopharyngeal aspirates, and induced sputum performed similarly for the detection of B. pertussis infection in young infants by PCR. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America.

Comparing the Yield of Nasopharyngeal Swabs, Nasal Aspirates, and Induced Sputum for Detection of Bordetella pertussis in Hospitalized Infants

PubMed Central

Nunes, Marta C.; Soofie, Nasiha; Downs, Sarah; Tebeila, Naume; Mudau, Azwi; de Gouveia, Linda; Madhi, Shabir A.

2016-01-01

Background. Advances in molecular laboratory techniques are changing the landscape of Bordetella pertussis illness diagnosis. Polymerase chain reaction (PCR) assays have greatly improved the sensitivity detection and the turnaround time to diagnosis compared to culture. Moreover, different respiratory specimens, such as flocked nasopharyngeal swabs (NPSs), nasopharyngeal aspirates (NPAs), and induced sputum, have been used for B. pertussis detection, although there is limited head-to-head comparison to evaluating the PCR yield from the 3 sampling methods. Methods. Hospitalized infants <6 months of age who fulfilled a broad syndromic criteria of respiratory illness were tested for B. pertussis infection by PCR on paired NPSs and NPAs; or paired NPSs and induced sputum. An exploratory analysis of B. pertussis culture was performed on induced sputum specimens and in a subset of NPSs. Results. From November 2014 to May 2015, 484 infants with paired NPSs and NPAs were tested; 15 (3.1%) PCR-confirmed pertussis cases were identified, 13 of which were PCR positive on both samples, while 1 each were positive only on NPS or NPA. From March to October 2015, 320 infants had NPSs and induced sputum collected, and 11 (3.4%) pertussis cases were identified by PCR, including 8 (72.7%) positive on both samples, 1 (9.1%) only positive on NPS, and 2 (18.2%) only positive on induced sputum. The 3 types of specimens had similar negative predictive value >99% and sensitivity >83%. Compared to PCR, culture sensitivity was 60% in induced sputum and 40% in NPSs. Conclusions. Flocked nasopharyngeal swabs, nasopharyngeal aspirates, and induced sputum performed similarly for the detection of B. pertussis infection in young infants by PCR. PMID:27838671

The Effect of Fermentation and Drying on Clicanthus Nutans Lindai Extract Chemical Constituents and Bioactivity

NASA Astrophysics Data System (ADS)

Lee, Y. Y.; Teh, P. S.; Kumaresan, S.; Tiong, C. H.

2017-06-01

In this study, two processes (fermentation and drying) were conducted on Clicanthus Nutans Lindau, which is well-known for its antioxidant activities. The aim of this research is to investigate the effects of these processes towards the Total Phenolic Content (TPC), antioxidant activity and the crude yield of the leaves. For the fermentation process, the fermentation time is varied for 6, 12, 24, 48 and 72 hours. For drying, oven drying (40, 45 and 50°C, freeze-drying and shade drying are investigated. Blanching was also conducted for oven dried samples (90°C for 1 minute). It was found that 12 hours fermentation produced the highest yield corresponding to Total Phenolic Content at 0.33 while 6 hours fermentation produced the highest Antioxidant Activity and yield at 2.218 x 10-10 mg/mL and 0.64 . On the other hand, 48 hours fermentation produced the highest overall extract yield at 0.64 . Analysis for antioxidant activity was carried out using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and Folin-Ciocalteau method for Total Phenolic Content. Thermal inactivation kinetics (blanching) has been investigated for oven drying samples. Results showed that 40°C oven drying and 50°C oven drying with blanching has better retention of bioactive constituents. Blanching has no significant effect on phenolic content but has increased the crude extract for higher temperature oven drying. It has no positive effect on antioxidant activity. Drying is also a better processing method compared to fermentation as drying has slightly favorable results in all three aspects. Through comparison with extraction time of 60 minutes for 40°C oven drying and 6 hour fermented samples, yield of total phenolic content and overall yield of oven dried sample is higher than fermented sample by 4.14 and 0.39 respectively as well as showing better antioxidant activity.

Audit of the practice of sputum smear examination for patients with suspected pulmonary tuberculosis in Fiji.

PubMed

Gounder, Shakti; Tayler-Smith, Katherine; Khogali, Mohammed; Raikabula, Maopa; Harries, Anthony D

2013-07-01

In Fiji, patients with suspected pulmonary tuberculosis (PTB) currently submit three sputum specimens for smear microscopy for acid-fast bacilli, but there is little information about how well this practice is carried out. A cross-sectional retrospective review was carried out in all four TB diagnostic laboratories in Fiji to determine among new patients presenting with suspected PTB in 2011: the quality of submitted sputum; the number of sputum samples submitted; the relationship between quality and number of submitted samples to smear-positivity; and positive yield from first, second and third samples. Of 1940 patients with suspected PTB, 3522 sputum samples were submitted: 997 (51.4%) patients submitted one sample, 304 (15.7%) patients submitted two samples and 639 (32.9%) submitted three samples. Sputum quality was recorded in 2528 (71.8%) of samples, of which 1046 (41.4%) were of poor quality. Poor quality sputum was more frequent in females, inpatients and children (0-14 years). Good quality sputum and a higher number of submitted samples positively correlated with smear-positivity for acid-fast bacilli. There were 122 (6.3%) patients with suspected PTB who were sputum smear positive. Of those, 89 had submitted three sputum samples: 79 (89%) were diagnosed based on the first sputum sample, 6 (7%) on the second sample and 4 (4%) on the third sample. This study shows that there are deficiencies in the practice of sputum smear examination in Fiji with respect to sputum quality and recommended number of submitted samples, although the results support the continued use of three sputum samples for TB diagnosis. Ways to improve sputum quality and adherence to recommended guidelines are needed.

Agreement between pre-operative and intra-operative bacteriological samples in 85 chronic peri-prosthetic infections.

PubMed

Matter-Parrat, V; Ronde-Oustau, C; Boéri, C; Gaudias, J; Jenny, J-Y

2017-04-01

Whether pre-operative microbiological sampling contributes to the management of chronic peri-prosthetic infection remains controversial. We assessed agreement between the results of pre-operative and intra-operative samples in patients undergoing single-stage prosthesis exchange to treat chronic peri-prosthetic infection. Agreement between pre-operative and intra-operative samples exceeds 75% in patients undergoing single-stage exchange of a hip or knee prosthesis to treat chronic peri-prosthetic infection. This single-centre retrospective study included 85 single-stage prosthesis exchange procedures in 82 patients with chronic peri-prosthetic infection at the hip or knee. Agreement between pre-operative and intra-operative sample results was evaluated. Changes to the initial antibiotic regimen made based on the intra-operative sample results were recorded. Of 149 pre-operative samples, 109 yielded positive cultures, in 75/85 cases. Of 452 intra-operative samples, 354 yielded positive cultures, in 85/85 cases. Agreement was complete in 54 (63%) cases and partial in 9 (11%) cases; there was no agreement in the remaining 22 (26%) cases. The complete agreement rate was significantly lower than 75% (P=0.01). The initial antibiotic regimen was inadequate in a single case. Pre-operative sampling may contribute to the diagnosis of peri-prosthetic infection but is neither necessary nor sufficient to confirm the diagnosis and identify the causative agent. The spectrum of the initial antibiotic regimen cannot be safely narrowed based on the pre-operative sample results. We suggest the routine prescription of a probabilistic broad-spectrum antibiotic regimen immediately after the prosthesis exchange, even when a pathogen was identified before surgery. IV, retrospective study. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Diagnostic exome sequencing provides a molecular diagnosis for a significant proportion of patients with epilepsy.

PubMed

Helbig, Katherine L; Farwell Hagman, Kelly D; Shinde, Deepali N; Mroske, Cameron; Powis, Zöe; Li, Shuwei; Tang, Sha; Helbig, Ingo

2016-09-01

To assess the yield of diagnostic exome sequencing (DES) and to characterize the molecular findings in characterized and novel disease genes in patients with epilepsy. In an unselected sample of 1,131 patients referred for DES, overall results were compared between patients with and without epilepsy. DES results were examined based on age of onset and epilepsy diagnosis. Positive/likely positive results were identified in 112/293 (38.2%) epilepsy patients compared with 210/732 (28.7%) patients without epilepsy (P = 0.004). The diagnostic yield in characterized disease genes among patients with epilepsy was 33.4% (105/314). KCNQ2, MECP2, FOXG1, IQSEC2, KMT2A, and STXBP1 were most commonly affected by de novo alterations. Patients with epileptic encephalopathies had the highest rate of positive findings (43.4%). A likely positive novel genetic etiology was proposed in 14/200 (7%) patients with epilepsy; this frequency was highest in patients with epileptic encephalopathies (17%). Three genes (COQ4, DNM1, and PURA) were initially reported as likely positive novel disease genes and were subsequently corroborated in independent peer-reviewed publications. DES with analysis and interpretation of both characterized and novel genetic etiologies is a useful diagnostic tool in epilepsy, particularly in severe early-onset epilepsy. The reporting on novel genetic etiologies may further increase the diagnostic yield.Genet Med 18 9, 898-905.

Yellow Fever Outbreak, Imatong, Southern Sudan

PubMed Central

Ofula, Victor O.; Sang, Rosemary C.; Konongoi, Samson L.; Sow, Abdourahmane; De Cock, Kevin M.; Tukei, Peter M.; Okoth, Fredrick A.; Swanepoel, Robert; Burt, Felicity J.; Waters, Norman C.; Coldren, Rodney L.

2004-01-01

In May 2003, the World Health Organization received reports about a possible outbreak of a hemorrhagic disease of unknown cause in the Imatong Mountains of southern Sudan. Laboratory investigations were conducted on 28 serum samples collected from patients in the Imatong region. Serum samples from 13 patients were positive for immunoglobulin M antibody to flavivirus, and serum samples from 5 patients were positive by reverse transcription–polymerase chain reaction with both the genus Flavivirus–reactive primers and yellow fever virus–specific primers. Nucleotide sequencing of the amplicons obtained with the genus Flavivirus oligonucleotide primers confirmed yellow fever virus as the etiologic agent. Isolation attempts in newborn mice and Vero cells from the samples yielded virus isolates from five patients. Rapid and accurate laboratory diagnosis enabled an interagency emergency task force to initiate a targeted vaccination campaign to control the outbreak. PMID:15207058

Duration of Dengue Viremia in Blood Donors and Relationships Between Donor Viremia, Infection Incidence and Clinical Case Reports During a Large Epidemic

PubMed Central

Busch, Michael P.; Sabino, Ester C.; Brambilla, Donald; Lopes, Maria Esther; Capuani, Ligia; Chowdhury, Dhuly; McClure, Christopher; Linnen, Jeffrey M.; Prince, Harry; Simmons, Graham; Lee, Tzong-Hae; Kleinman, Steven; Custer, Brian

2016-01-01

Background. Dengue viruses (DENV-1–4) pose a transfusion-transmission risk. This study estimated the dengue RNA detection period in asymptomatic blood donors and relationships between donor viremia and dengue incidence during a large epidemic. Methods. Donor samples from the 2012 dengue transmission season in Rio de Janeiro, Brazil, were tested for DENV RNA by a transcription-mediated amplification (TMA) assay, with DENV types and viral loads determined by polymerase chain reaction. Samples collected during the first and last weeks of enrollment were tested for DENV immunoglobulin (Ig) G and IgM to estimate incidence during the study period, which was analyzed relative to nucleic acid amplification technology (NAT) yield to estimate the duration of NAT-detectable viremia and compared with reported clinical dengue cases in Rio. Results. Samples from 16 241 donations were tested; 87 (0.54%) were confirmed as DENV-4 RNA positive. Dengue IgM-positive/IgG-positive reactivity increased from 2.8% to 8.8%, indicating a 6.2% incidence (95% confidence interval [CI], 3.2%–9.1%) during the study period. Based on these data, we estimated a 9.1-day period (95% CI, 4.4–13.9 days) of RNA detectable with TMA. With 100 475 reported cases of clinical dengue, 1 RNA-positive donation was identified per 800 DENV cases. Conclusions. These parameters allow projections of dengue incidence from donor NAT yield data and vice versa, and suggest that viremic donations will be rare relative to clinical disease cases. PMID:27302934

Quantitative trait locus for reading disability on chromosome 6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardon, L.R.; Smith, S.D.; Kimberling, W.J.

1994-10-14

Interval mapping of data from two independent samples of sib pairs, at least one member of whom was reading disabled, revealed evidence for a quantitative trait locus (QTL) on chromosome 6. Results obtained from analyses of reading performance from 114 sib pairs genotyped for DNA markers localized the QTL to 6p21.3. Analyses of corresponding data from an independent sample of 50 dizygotic twin pairs provided evidence for linkage to the same region. In combination, the replicate samples yielded a x{sup 2} value of 16.73 (P = 0.0002). Examination of twin and kindred siblings with more extreme deficits in reading performancemore » yielded even stronger evidence for a QTL (x{sup 2} = 27.35, P < 0.00001). The position of the QTL was narrowly defined with a 100:1 confidence interval to a 2-centimorgan region within the human leukocyte antigen complex. 23 refs., 4 figs.« less

[On the importance of the steam trap to the efficient sterilization of solutions in stored blood bottles by saturated steam under pressure (author's transl)].

PubMed

Schreiber, M; Göbel, M

1979-01-01

Biological tests with soil samples were performed to fix the sterilization time for a new steam sterilizer. These tests yielded repeatedly positive spore findings despite modifications of the conditions of sterilization. Having excluded a series of possible sources of trouble, the authors stated that the quality of the steam was the assignable cause. After restoration of the functionality of the steam traps, the biological tests yielded negative results also under normal conditions of sterilization.

[Diagnostic yield of paediatric respiratory samples in the Balearic Islands Sentinel Influenza Surveillance Network].

PubMed

Reina, J; Nicolau, A; Galmes, A; Arbona, B

2009-05-01

Influenza disease is subjected to surveillance by national networks (RC) that predict the epidemic behaviour by reporting clinical and virological data. To evaluate the effectiveness of the paediatric respiratory samples in the Balearic Islands RC in the last five epidemic seasons. A breath sample was taken from paediatric patients in the RC who had flu symptoms. The samples were inoculated in the MDCK cell line. We reviewed the epidemiological data of patients with a culture positive to influenza A and B. A total of 338 pharyngeal swabs from the RC were analysed during the study period. Of these, 65 (19.3%) belonged to <14 years old patients, and 44.6% of the samples were positive as opposed to 39.1% of adult respiratory samples. The influenza A virus was isolated in 24 paediatric samples (82.7%) and the influenza B virus in 5 (17.3%). The mean age of the paediatric patients of the RC who were positive was 8.5 years. Only 3 patients in the 0-4 year old group were positive (10.3%) and 26 patients (89.7%) in the 5-14 years old group. In spite that paediatricians represented only 22% of the RC doctors and obtain the 19.3% of all respiratory samples, the percentage and effectiveness of these is higher that that obtained in the adult population.

Comparison of Mycobacterium tuberculosis culture using liquid culture medium and Lowenstein Jensen medium in abdominal tuberculosis.

PubMed

Shah, Sudeep R; Shenai, Shubhada; Desai, Devendra C; Joshi, Anand; Abraham, Philip; Rodrigues, Camilla

2010-11-01

Traditionally, the Lowenstein Jensen (LJ) medium has been used for culturing Mycobacterium tuberculosis. In abdominal tuberculosis (TB), the reported yield from tissue culture is between 20% and 60%. Liquid cultures are reported to give a higher yield but there is little data available in abdominal TB. To compare the yield of TB culture with BACTEC 460TB liquid medium and LJ medium for patients with suspected abdominal TB and determine cost effectiveness. This prospective study was done in consecutive cases with clinical, radiological, endoscopic/surgical, and histological suspicion of abdominal TB. Tissue biopsies obtained at colonoscopy or surgery were processed and plated on LJ medium as well as the BACTEC 460TB system. NAP (ρ-nitro-α-acetylamino-β-hydroxy-propiophenone) differentiation was carried out to determine species. The cost of each method and cost per yield were calculated. Of the 29 cases, 22 cases (76%) were positive on BACTEC 460TB culture while 14 (48%) were positive on LJ medium giving a 64% increment in yield. However, the culture of one patient grew on LJ medium, where the BACTEC 460TB was negative. The additional cost of BACTEC 460TB is Rs. 460 and LJ is Rs. 40. Samples from patients with abdominal TB should be processed on both liquid and LJ medium. For high yield, the use of a liquid culture medium system is essential.

A Rapid Dot Immunoassay for the Detection of Serum Antibodies to Eastern Equine Encephalomyelitis and Saint Louis Encephalitis Viruses in Sentinel Chickens

DTIC Science & Technology

1988-01-01

tion inhibition (HI) tests .6 uses a novel membrane, polyvinylydine difluor- EEE and SLE viruses are significant public ide (PVDF), and yields a...only 3 aged values between the two tests (Fig. 3). Vari- of 6 SLE virus-inoculated birds developed an- ability in EIA titer was observed with samples... SLE samples negative by EIA were location. Four serum samples from each of 3 also negative by DotIA. EEE-positive chickens were tested by EIA and A

Impact of erosion and tillage on the productivity and quality of selected semiarid soils of Iran

NASA Astrophysics Data System (ADS)

Mehdizade, B.; Asadi, H.; Shabanpour, M.; Ghadiri, H.

2013-09-01

This greenhouse research was carried out to study the effects of water and tillage erosion on agricultural productivity and soil quality in soil samples from a semiarid region of Iran. A factorial experiment of complete randomized block design was used to compare the effects of soil erosion (eroded and non-eroded soils), slope position, water stress and fertilizer (N-P-K) on yield and yield components of wheat as soil productivity index. The results showed that erosion ie water and tillage erosion has a significant effect (p<0.01) in decreasing soil productivity due to its negative impact on soil organic matter, nutrients (N and K) and hydraulic conductivity. Complete N-P-K fertilization and water stress had significant effects on increasing and decreasing of wheat yield, respectively. The effect of water stress in particular was so high that it could eclipse the erosion impact on yield reduction. Wheat dry matter and grain mass on foot and mid slopes were significantly higher than that on upslope positions where total N and available K were the lowest and equivalent calcium carbonate the highest. Saturated hydraulic conductivity and total nitrogen were found to be the most important soil properties as far as their correlations to wheat yield are concerned.

Systematic studies of small scintillators for new sampling calorimeter

NASA Astrophysics Data System (ADS)

Jacosalem, E. P.; Iba, S.; Nakajima, N.; Ono, H.; Sanchez, A. L. C.; Bacala, A. M.; Miyata, H.

2007-12-01

A new sampling calorimeter using very thin scintillators and the multi-pixel photon counter (MPPC) has been proposed to produce better position resolution for the international linear collider (ILC) experiment. As part of this R&D study, small plastic scintillators of different sizes, thickness and wrapping reflectors are systematically studied. The scintillation light due to beta rays from a collimated ^{90}Sr source are collected from the scintillator by wavelength-shifting (WLS) fiber and converted into electrical signals at the PMT. The wrapped scintillator that gives the best light yield is determined by comparing the measured pulse height of each 10 × 40 × 2 mm strip scintillator covered with 3M reflective mirror film, teflon, white paint, black tape, gold, aluminum and white paint+teflon. The pulse height dependence on position, length and thickness of the 3M reflective mirror film and teflon wrapped scintillators are measured. Results show that the 3M radiant mirror film-wrapped scintillator has the greatest light yield with an average of 9.2 photoelectrons. It is observed that light yield slightly increases with scintillator length, but increases to about 100% when WLS fiber diameter is increased from 1.0 mm to 1.6 mm. The position dependence measurement along the strip scintillator showed the uniformity of light transmission from the sensor to the PMT. A dip across the strip is observed which is 40% of the maximum pulse height. The block type scintillator pulse height, on the other hand, is found to be almost proportional to scintillator thickness.

STRUCTURE IN THE 3D GALAXY DISTRIBUTION: III. FOURIER TRANSFORMING THE UNIVERSE: PHASE AND POWER SPECTRA.

PubMed

Scargle, Jeffrey D; Way, M J; Gazis, P R

2017-04-10

We demonstrate the effectiveness of a relatively straightforward analysis of the complex 3D Fourier transform of galaxy coordinates derived from redshift surveys. Numerical demonstrations of this approach are carried out on a volume-limited sample of the Sloan Digital Sky Survey redshift survey. The direct unbinned transform yields a complex 3D data cube quite similar to that from the Fast Fourier Transform (FFT) of finely binned galaxy positions. In both cases deconvolution of the sampling window function yields estimates of the true transform. Simple power spectrum estimates from these transforms are roughly consistent with those using more elaborate methods. The complex Fourier transform characterizes spatial distributional properties beyond the power spectrum in a manner different from (and we argue is more easily interpreted than) the conventional multi-point hierarchy. We identify some threads of modern large scale inference methodology that will presumably yield detections in new wider and deeper surveys.

STRUCTURE IN THE 3D GALAXY DISTRIBUTION: III. FOURIER TRANSFORMING THE UNIVERSE: PHASE AND POWER SPECTRA

PubMed Central

Scargle, Jeffrey D.; Way, M. J.; Gazis, P. R.

2017-01-01

We demonstrate the effectiveness of a relatively straightforward analysis of the complex 3D Fourier transform of galaxy coordinates derived from redshift surveys. Numerical demonstrations of this approach are carried out on a volume-limited sample of the Sloan Digital Sky Survey redshift survey. The direct unbinned transform yields a complex 3D data cube quite similar to that from the Fast Fourier Transform (FFT) of finely binned galaxy positions. In both cases deconvolution of the sampling window function yields estimates of the true transform. Simple power spectrum estimates from these transforms are roughly consistent with those using more elaborate methods. The complex Fourier transform characterizes spatial distributional properties beyond the power spectrum in a manner different from (and we argue is more easily interpreted than) the conventional multi-point hierarchy. We identify some threads of modern large scale inference methodology that will presumably yield detections in new wider and deeper surveys. PMID:29628519

Structure in the 3D Galaxy Distribution. III. Fourier Transforming the Universe: Phase and Power Spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scargle, Jeffrey D.; Way, M. J.; Gazis, P. R., E-mail: Jeffrey.D.Scargle@nasa.gov, E-mail: Michael.J.Way@nasa.gov, E-mail: PGazis@sbcglobal.net

We demonstrate the effectiveness of a relatively straightforward analysis of the complex 3D Fourier transform of galaxy coordinates derived from redshift surveys. Numerical demonstrations of this approach are carried out on a volume-limited sample of the Sloan Digital Sky Survey redshift survey. The direct unbinned transform yields a complex 3D data cube quite similar to that from the Fast Fourier Transform of finely binned galaxy positions. In both cases, deconvolution of the sampling window function yields estimates of the true transform. Simple power spectrum estimates from these transforms are roughly consistent with those using more elaborate methods. The complex Fouriermore » transform characterizes spatial distributional properties beyond the power spectrum in a manner different from (and we argue is more easily interpreted than) the conventional multipoint hierarchy. We identify some threads of modern large-scale inference methodology that will presumably yield detections in new wider and deeper surveys.« less

Structure in the 3D Galaxy Distribution: III. Fourier Transforming the Universe: Phase and Power Spectra

NASA Technical Reports Server (NTRS)

Scargle, Jeffrey D.; Way, M. J.; Gazis, P. R.

2017-01-01

We demonstrate the effectiveness of a relatively straightforward analysis of the complex 3D Fourier transform of galaxy coordinates derived from redshift surveys. Numerical demonstrations of this approach are carried out on a volume-limited sample of the Sloan Digital Sky Survey redshift survey. The direct unbinned transform yields a complex 3D data cube quite similar to that from the Fast Fourier Transform (FFT) of finely binned galaxy positions. In both cases deconvolution of the sampling window function yields estimates of the true transform. Simple power spectrum estimates from these transforms are roughly consistent with those using more elaborate methods. The complex Fourier transform characterizes spatial distributional properties beyond the power spectrum in a manner different from (and we argue is more easily interpreted than) the conventional multi-point hierarchy. We identify some threads of modern large scale inference methodology that will presumably yield detections in new wider and deeper surveys.

[Comparison of the performance of the ECLusys anti-HCV reagent with the Lumipulse f and HISCL 2000-i HCVAb assays].

PubMed

Sugiura, Aya; Iwahara, Kunihiro; Suga, Yasuyuki; Uchiyama, Sachinori; Maekawa, Masato

2012-09-01

We compared the ECLusys Anti-HCV (ECL) reagent to the Lumipulse f (LPf) and HISCL (HIS) HCV assays. In a correlation test using 210 routine clinical specimens measured using the Lumipulse method (96 positive and 114 negative), most of the results were consistent for all specimens. In a dilution sensitivity test using three different routine positive specimens, the ECL assay enabled detection at higher levels of sensitivity than either the LPf or the HIS assay. Moreover, when the distribution of the cut-off index (C.O.I.) values of the routine LPf negative specimens were compared to those on the ECL and HIS assays, it was found that on the ECL assay, most of the specimens had cut-off index values < 0.1, indicating a more clear-cut distribution. In a specificity test using high RF positive specimens(n = 33), pregnancy specimens (n = 35), cytomegalovirus (CMV) antibody positive specimens (n = 36), and high M protein positive specimens (n = 21), the ECL assay yielded positive results for a CMV antibody positive specimen and three high M protein positive specimens. Further testing using samples from the same patients collected on different days than these four samples resulted in a second positive result for the CMV positive specimen, and single antigen measurement yielded a Core/NS3 positive result, as well, suggesting past infection. However, since negative results were obtained for the three M protein positive specimens, the possibility of this being a ECLusys non-specific reaction could not be ruled out. The above results confirmed that the ECL assay provides superior fundamental performance, and possesses test performance nearly identical to that of the existing measurement methods that are widely used at a large number of facilities, and would therefore be a suitable assay for use in routine HCV antibody screening.

Detection and characterization of atypical capripoxviruses among small ruminants in India.

PubMed

Santhamani, Ramasamy; Venkatesan, Gnanavel; Minhas, Sanjeevna Kumari; Shivachandra, Sathish Bhadravati; Muthuchelvan, Dhanavelu; Pandey, Awadh Bihari; Ramakrishnan, Muthannan Andavar

2015-08-01

Recent developments in molecular biology shed light on cross-species transmission of SPPV and GTPV. The present study was planned to characterize the capripoxviruses which were circulating in the field condition among sheep and goats using RPO30 gene-based viral lineage (SPPV/GTPV) differentiating PCR and sequencing of RPO30 and GPCR genes from clinical samples. Out of 58 scabs (35 sheep and 23 goats) screened, 27 sheep and 18 goat scabs were found positive for capripox virus infections. With the exception of one sheep and one goat scabs, all the positive samples yielded amplicon size according to host origin, i.e. SPPV in sheep and GTPV in goats. In the above two exceptional cases, goat scab and sheep scab yielded amplicon size as that of SPPV and GTPV, respectively. Further, sequencing and phylogenetic analyses of complete ORFs of RPO30 and GPCR genes from six sheep and three goat scabs revealed that with the exception of above two samples, all had host-specific signatures and clustered according to their host origin. In case of cross-species infecting samples, sheep scab possessed GTPV-like signatures and goat scab possessed SPPV-like signatures. Our study identifies the circulation of cross-infecting SPPV and GTPV in the field and warrants the development of single-strain vaccine which can protect the animals from both sheeppox and goatpox diseases.

Development and Validation of a Real-Time PCR Assay for Rapid Detection of Candida auris from Surveillance Samples

PubMed Central

Leach, L.; Zhu, Y.

2017-01-01

ABSTRACT 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 (ITS2) 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. PMID:29187562

Development and Validation of a Real-Time PCR Assay for Rapid Detection of Candida auris from Surveillance Samples.

PubMed

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.

Strength gradient enhances fatigue resistance of steels

NASA Astrophysics Data System (ADS)

Ma, Zhiwei; Liu, Jiabin; Wang, Gang; Wang, Hongtao; Wei, Yujie; Gao, Huajian

2016-02-01

Steels are heavily used in infrastructure and the transportation industry, and enhancing their fatigue resistance is a major challenge in materials engineering. In this study, by introducing a gradient microstructure into 304 austenitic steel, which is one of the most widely used types of stainless steel, we show that a strength gradient substantially enhances the fatigue life of the material. Pre-notched samples with negative strength gradients in front of the notch’s tip endure many more fatigue cycles than do samples with positive strength gradients during the crack initiation stage, and samples with either type of gradient perform better than do gradient-free samples with the same average yield strength. However, as a crack grows, samples with positive strength gradients exhibit better resistance to fatigue crack propagation than do samples with negative gradients or no gradient. This study demonstrates a simple and promising strategy for using gradient structures to enhance the fatigue resistance of materials and complements related studies of strength and ductility.

Strength gradient enhances fatigue resistance of steels

PubMed Central

Ma, Zhiwei; Liu, Jiabin; Wang, Gang; Wang, Hongtao; Wei, Yujie; Gao, Huajian

2016-01-01

Steels are heavily used in infrastructure and the transportation industry, and enhancing their fatigue resistance is a major challenge in materials engineering. In this study, by introducing a gradient microstructure into 304 austenitic steel, which is one of the most widely used types of stainless steel, we show that a strength gradient substantially enhances the fatigue life of the material. Pre-notched samples with negative strength gradients in front of the notch’s tip endure many more fatigue cycles than do samples with positive strength gradients during the crack initiation stage, and samples with either type of gradient perform better than do gradient-free samples with the same average yield strength. However, as a crack grows, samples with positive strength gradients exhibit better resistance to fatigue crack propagation than do samples with negative gradients or no gradient. This study demonstrates a simple and promising strategy for using gradient structures to enhance the fatigue resistance of materials and complements related studies of strength and ductility. PMID:26907708

Effective removal of co-purified inhibitors from extracted DNA samples using synchronous coefficient of drag alteration (SCODA) technology.

PubMed

Schmedes, Sarah; Marshall, Pamela; King, Jonathan L; Budowle, Bruce

2013-07-01

Various types of biological samples present challenges for extraction of DNA suitable for subsequent molecular analyses. Commonly used extraction methods, such as silica membrane columns and phenol-chloroform, while highly successful may still fail to provide a sufficiently pure DNA extract with some samples. Synchronous coefficient of drag alteration (SCODA), implemented in Boreal Genomics' Aurora Nucleic Acid Extraction System (Boreal Genomics, Vancouver, BC), is a new technology that offers the potential to remove inhibitors effectively while simultaneously concentrating DNA. In this initial study, SCODA was tested for its ability to remove various concentrations of forensically and medically relevant polymerase chain reaction (PCR) inhibitors naturally found in tissue, hair, blood, plant, and soil samples. SCODA was used to purify and concentrate DNA from intentionally contaminated DNA samples containing known concentrations of hematin, humic acid, melanin, and tannic acid. The internal positive control (IPC) provided in the Quantifiler™ Human DNA Quantification Kit (Life Technologies, Foster City, CA) and short tandem repeat (STR) profiling (AmpFℓSTR® Identifiler® Plus PCR Amplification Kit; Life Technologies, Foster City, CA) were used to measure inhibition effects and hence purification. SCODA methodology yielded overall higher efficiency of purification of highly contaminated samples compared with the QIAquick® PCR Purification Kit (Qiagen, Valencia, CA). SCODA-purified DNA yielded no cycle shift of the IPC for each sample and yielded greater allele percentage recovery and relative fluorescence unit values compared with the QIAquick® purification method. The Aurora provided an automated, minimal-step approach to successfully remove inhibitors and concentrate DNA from challenged samples.

Comparison of individual and pooled sampling methods for detecting bacterial pathogens of fish

USGS Publications Warehouse

Mumford, Sonia; Patterson, Chris; Evered, J.; Brunson, Ray; Levine, J.; Winton, J.

2005-01-01

Examination of finfish populations for viral and bacterial pathogens is an important component of fish disease control programs worldwide. Two methods are commonly used for collecting tissue samples for bacteriological culture, the currently accepted standards for detection of bacterial fish pathogens. The method specified in the Office International des Epizooties Manual of Diagnostic Tests for Aquatic Animals permits combining renal and splenic tissues from as many as 5 fish into pooled samples. The American Fisheries Society (AFS) Blue Book/US Fish and Wildlife Service (USFWS) Inspection Manual specifies the use of a bacteriological loop for collecting samples from the kidney of individual fish. An alternative would be to more fully utilize the pooled samples taken for virology. If implemented, this approach would provide substantial savings in labor and materials. To compare the relative performance of the AFS/USFWS method and this alternative approach, cultures of Yersinia ruckeri were used to establish low-level infections in groups of rainbow trout (Oncorhynchus mykiss) that were sampled by both methods. Yersinia ruckeri was cultured from 22 of 37 groups by at least 1 method. The loop method yielded 18 positive groups, with 1 group positive in the loop samples but negative in the pooled samples. The pooled samples produced 21 positive groups, with 4 groups positive in the pooled samples but negative in the loop samples. There was statistically significant agreement (Spearman coefficient 0.80, P < 0.001) in the relative ability of the 2 sampling methods to permit detection of low-level bacterial infections of rainbow trout.

Optimizing anti-coking abilities of zeolites by ethylene diamine tetraacetie acid modification on catalytic fast pyrolysis of corn stalk

NASA Astrophysics Data System (ADS)

Zhang, Bo; Zhong, Zhaoping; Song, Zuwei; Ding, Kuan; Chen, Paul; Ruan, Roger

2015-12-01

In order to minimize coke yield during biomass catalytic fast pyrolysis (CFP) process, ethylene diamine tetraacetie acid (EDTA) chemical modification method is carried out to selectively remove the external framework aluminum of HZSM-5 catalyst. X-ray diffraction (XRD), nitrogen (N2)-adsorption and ammonia-temperature programmed desorption (NH3-TPD) techniques are employed to investigate the porosity and acidity characteristics of original and modified HZSM-5 samples. Py-GC/MS and thermo-gravimetric analyzer (TGA) experiments are further conducted to explore the catalytic effect of modified HZSM-5 samples on biomass CFP and to verify the positive effect on coke reduction. Results show that EDTA treatment does not damage the crystal structure of HZSM-5 zeolites, but leads to a slight increase of pore volume and pore size. Meanwhile, the elimination of the strong acid peak indicates the dealumination of outer surface of HZSM-5 zeolites. Treatment time of 2 h (labeled EDTA-2H) is optimal for acid removal and hydrocarbon formation. Among all modified catalysts, EDTA-2H performs the best for deacidification and can obviously increase the yields of positive chemical compositions in pyrolysis products. Besides, EDTA modification can improve the anti-coking properties of HZSM-5 zeolites, and EDTA-2H gives rise to the lowest coke yield.

New criteria for isotropic and textured metals

NASA Astrophysics Data System (ADS)

Cazacu, Oana

2018-05-01

In this paper a isotropic criterion expressed in terms of both invariants of the stress deviator, J2 and J3 is proposed. This criterion involves a unique parameter, α, which depends only on the ratio between the yield stresses in uniaxial tension and pure shear. If this parameter is zero, the von Mises yield criterion is recovered; if a is positive the yield surface is interior to the von Mises yield surface whereas when a is negative, the new yield surface is exterior to it. Comparison with polycrystalline calculations using Taylor-Bishop-Hill model [1] for randomly oriented face-centered (FCC) polycrystalline metallic materials show that this new criterion captures well the numerical yield points. Furthermore, the criterion reproduces well yielding under combined tension-shear loadings for a variety of isotropic materials. An extension of this isotropic yield criterion such as to account for orthotropy in yielding is developed using the generalized invariants approach of Cazacu and Barlat [2]. This new orthotropic criterion is general and applicable to three-dimensional stress states. The procedure for the identification of the material parameters is outlined. Illustration of the predictive capabilities of the new orthotropic is demonstrated through comparison between the model predictions and data on aluminum sheet samples.

Evaluation of Xpert® MTB/RIF Assay in Induced Sputum and Gastric Lavage Samples from Young Children with Suspected Tuberculosis from the MVA85A TB Vaccine Trial.

PubMed

Bunyasi, Erick Wekesa; Tameris, Michele; Geldenhuys, Hennie; Schmidt, Bey-Marrie; Luabeya, Angelique Kany Kany; Mulenga, Humphrey; Scriba, Thomas J; Hanekom, Willem A; Mahomed, Hassan; McShane, Helen; Hatherill, Mark

2015-01-01

Diagnosis of childhood tuberculosis is limited by the paucibacillary respiratory samples obtained from young children with pulmonary disease. We aimed to compare accuracy of the Xpert® MTB/RIF assay, an automated nucleic acid amplification test, between induced sputum and gastric lavage samples from young children in a tuberculosis endemic setting. We analyzed standardized diagnostic data from HIV negative children younger than four years of age who were investigated for tuberculosis disease near Cape Town, South Africa [2009-2012]. Two paired, consecutive induced sputa and early morning gastric lavage samples were obtained from children with suspected tuberculosis. Samples underwent Mycobacterial Growth Indicator Tube [MGIT] culture and Xpert MTB/RIF assay. We compared diagnostic yield across samples using the two-sample test of proportions and McNemar's χ2 test; and Wilson's score method to calculate sensitivity and specificity. 1,020 children were evaluated for tuberculosis during 1,214 admission episodes. Not all children had 4 samples collected. 57 of 4,463[1.3%] and 26 of 4,606[0.6%] samples tested positive for Mycobacterium tuberculosis on MGIT culture and Xpert MTB/RIF assay respectively. 27 of 2,198[1.2%] and 40 of 2,183[1.8%] samples tested positive [on either Xpert MTB/RIF assay or MGIT culture] on induced sputum and gastric lavage samples, respectively. 19/1,028[1.8%] and 33/1,017[3.2%] admission episodes yielded a positive MGIT culture or Xpert MTB/RIF assay from induced sputum and gastric lavage, respectively. Sensitivity of Xpert MTB/RIF assay was 8/30[26.7%; 95% CI: 14.2-44.4] for two induced sputum samples and 7/31[22.6%; 11.4-39.8] [p = 0.711] for two gastric lavage samples. Corresponding specificity was 893/893[100%;99.6-100] and 885/890[99.4%;98.7-99.8] respectively [p = 0.025]. Sensitivity of Xpert MTB/RIF assay was low, compared to MGIT culture, but diagnostic performance of Xpert MTB/RIF did not differ sufficiently between induced sputum and gastric lavage to justify selection of one sampling method over the other, in young children with suspected pulmonary TB. ClinicalTrials.gov NCT00953927.

Enrichment isolation of adipose-derived stem/stromal cells from the liquid portion of liposuction aspirates with the use of an adherent column.

PubMed

Doi, Kentaro; Kuno, Shinichiro; Kobayashi, Akira; Hamabuchi, Takahisa; Kato, Harunosuke; Kinoshita, Kahori; Eto, Hitomi; Aoi, Noriyuki; Yoshimura, Kotaro

2014-03-01

Adipose-derived stem/progenitor cells (ASCs) are typically obtained from the lipoaspirates; however, a smaller number of ASCs can be isolated without enzymatic digestion from the infranatant liposuction aspirate fluid (LAF). We evaluated the effectiveness of an adherent column, currently used to isolate mesenchymal stromal cells from bone marrow, to isolate LAF cells. We applied peripheral blood (PB), PB mixed with cultured ASCs (PB-ASC), and LAF solution to the column and divided it into two fractions, the adherent (positive) and the non-adherent (negative) fractions. We compared this method with hypotonic hemolysis (lysis) for the red blood cell count, nucleated cells count and cell compositions as well as functional properties of isolated mesenchymal cells. The column effectively removed red blood cells, though the removal efficiency was slightly inferior to hemolysis. After column processing of PB-ASC, 60.5% of ASCs (53.2% by lysis) were selectively collected in the positive fraction, and the negative fraction contained almost no ASCs. After processing of LAF solution, nucleated cell yields were comparable between the column and hemolysis; however, subsequent adherent culture indicated that a higher average ASC yield was obtained from the column-positive samples than from the lysis samples, suggesting that the column method may be superior to hemolysis for obtaining viable ASCs. Mesenchymal differentiation and network formation assays showed no statistical differences in ASC functions between the lysis and column-positive samples. Our results suggest that a column with non-woven rayon and polyethylene fabrics is useful for isolating stromal vascular fraction cells from LAF solutions for clinical applications. Copyright © 2014 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

Evaluation of the Ortho-Clinical Diagnostics Vitros ECi Anti-HCV test: comparison with three other methods.

PubMed

Watterson, Jeannette M; Stallcup, Paulina; Escamilla, David; Chernay, Patrick; Reyes, Alfred; Trevino, Sylvia C

2007-01-01

After observing a high incidence of low positive hepatitis C virus (HCV) antibody screens by the Ortho-Clinical Vitros ECi test (Orthoclinical Diagnostics, Raritan, NJ), we compared results against those obtained using another chemiluminescent analyzer, as well as two U.S. Food and Drug Administration (FDA)-approved confirmatory methodologies. To ascertain the true anti-HCV status of samples deemed low-positive by the Ortho-Clinical Vitros ECi test, we tested samples using the ADVIA Centaur HCV screen test (Siemens Medical Solutions Diagnostics), the Chiron recombinant immunoblot assay (RIBA) test (Chiron Corp., Emeryville, CA), and the Roche COBAS Amplicor HCV qualitative test (Roche Diagnostics, Indianapolis, IN) in a series of studies. Of 94 specimens positive by Vitros ECi, 19% were observed to be negative by Centaur. A separate study of 91 samples with signal-to-cutoff (s/co) values less than 8.0 showed that all but one was negative for HCV ribonucleic acid (RNA). In comparison with RIBA, 100% (77) samples positive by the Vitros ECi test with s/co values less than 12.0 were negative or indeterminate by RIBA. A final study comparing all four methods side-by-side showed 63% disagreement by Centaur for Vitros ECi low-positive samples, 75% disagreement by RIBA, and 97% disagreement by polymerase chain reaction (PCR). In conclusion, the Ortho-Clinical Vitros ECi Anti-HCV test yields a high rate of false-positive results in the low s/co range in our patient population. (c) 2007 Wiley-Liss, Inc.

Coagulase-negative Staphylococcus species in bulk milk: Prevalence, distribution, and associated subgroup- and species-specific risk factors.

PubMed

De Visscher, A; Piepers, S; Haesebrouck, F; Supré, K; De Vliegher, S

2017-01-01

Coagulase-negative staphylococci (CNS) have become the main pathogens causing bovine mastitis in recent years. A huge variation in species distribution among herds has been observed in several studies, emphasizing the need to identify subgroup- and species-specific herd-level factors to improve our understanding of the differences in ecological and epidemiological nature between species. The use of bulk milk samples enables the inclusion of a large(r) number of herds needed to identify herd-level risk factors and increases the likelihood of recovering enough isolates per species needed for conducting subgroup- and, eventually, species-specific analyses at the same time. This study aimed to describe the prevalence and distribution of CNS species in bulk milk samples and to identify associated subgroup- and species-specific herd-level factors. Ninety percent of all bulk milk samples yielded CNS. Staphylococcus equorum was the predominant species, followed by Staphylococcus haemolyticus and Staphylococcus epidermidis. A seasonal effect was observed for several CNS species. Bulk milk samples from herds with a loose-pack or a tiestall housing system were more likely to yield CNS species compared with herds with a freestall barn, except for S. epidermidis, Staphylococcus simulans, and Staphylococcus cohnii. In September, herds in which udders were clipped had lower odds of yielding Staphylococcus chromogenes, S. simulans, and Staphylococcus xylosus, the CNS species assumed to be most relevant for udder health, in their bulk milk than herds in which udder clipping was not practiced. Bulk milk of herds participating in a monthly veterinary udder health-monitoring program was more likely to yield these 3 CNS species. Herds always receiving their milk quality premium or predisinfecting teats before attachment of the milking cluster had lower odds of having S. equorum in their bulk milk. Herds not using a single dry cotton or paper towel for each cow during premilking udder preparation were more likely to have S. cohnii-positive bulk milk. Herds in which flushing with hot water or steam of the milking cluster after having milked a cow with a (sub)clinical mastitis was applied, were less likely to yield S. simulans, S. haemolyticus, and S. cohnii in their bulk milk. Always wearing gloves during milking decreased the odds of having Staphylococcus devriesei-positive bulk milk. Tap water from the public drinking system used as drinking water increased the odds of yielding S. simulans in the bulk milk. In conclusion, CNS are highly prevalent in bulk milk and might originate from the environment for some species (we hypothesize this is true for S. equorum or S. cohnii), or from within the udder (e.g., for S. simulans). Studies collecting bulk milk and quarter milk samples at the same time along with environmental samples are needed to determine the exact origin of the different (subgroups of) CNS species present in bulk milk using strain-typing techniques. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Comparison of ambient solvent extraction methods for the analysis of fatty acids in non-starch lipids of flour and starch

PubMed Central

Bahrami, Niloufar; Yonekura, Lina; Linforth, Robert; Carvalho da Silva, Margarida; Hill, Sandra; Penson, Simon; Chope, Gemma; Fisk, Ian Denis

2014-01-01

BACKGROUND Lipids are minor components of flours, but are major determinants of baking properties and end-product quality. To the best of our knowledge, there is no single solvent system currently known that efficiently extracts all non-starch lipids from all flours without the risk of chemical, mechanical or thermal damage. This paper compares nine ambient solvent systems (monophasic and biphasic) with varying polarities: Bligh and Dyer (BD); modified Bligh and Dyer using HCl (BDHCL); modified BD using NaCl (BDNaCl); methanol–chloroform–hexane (3:2:1, v/v); Hara and Radin (hexane–isopropanol, 3:2, v/v); water-saturated n-butanol; chloroform; methanol and hexane for their ability to extract total non-starch lipids (separated by lipid classes) from wheat flour (Triticum aestivum L.). Seven ambient extraction protocols were further compared for their ability to extract total non-starch lipids from three alternative samples: barley flour (Hordeum vulgare L.), maize starch (Zea mays L.) and tapioca starch (Manihot esculenta Crantz). RESULTS For wheat flour the original BD method and those containing HCl or NaCl tended to extract the maximum lipid and a significant correlation between lipid extraction yield (especially the glycolipids and phospholipids) and the polarity of the solvent was observed. For the wider range of samples BD and BD HCl repeatedly offered the maximum extraction yield and using pooled standardized (by sample) data from all flours, total non-starch lipid extraction yield was positively correlated with solvent polarity (r = 0.5682, P < 0.05) and water ratio in the solvent mixture (r = 0.5299, P < 0.05). CONCLUSION In general, BD-based methods showed better extraction yields compared to methods without the addition of water and, most interestingly, there was much greater method dependence of lipid yields in the starches when compared to the flour samples, which is due to the differences in lipid profiles between the two sample types (flours and starches). PMID:24132804

Methods to enhance seismic faults and construct fault surfaces

NASA Astrophysics Data System (ADS)

Wu, Xinming; Zhu, Zhihui

2017-10-01

Faults are often apparent as reflector discontinuities in a seismic volume. Numerous types of fault attributes have been proposed to highlight fault positions from a seismic volume by measuring reflection discontinuities. These attribute volumes, however, can be sensitive to noise and stratigraphic features that are also apparent as discontinuities in a seismic volume. We propose a matched filtering method to enhance a precomputed fault attribute volume, and simultaneously estimate fault strikes and dips. In this method, a set of efficient 2D exponential filters, oriented by all possible combinations of strike and dip angles, are applied to the input attribute volume to find the maximum filtering responses at all samples in the volume. These maximum filtering responses are recorded to obtain the enhanced fault attribute volume while the corresponding strike and dip angles, that yield the maximum filtering responses, are recoded to obtain volumes of fault strikes and dips. By doing this, we assume that a fault surface is locally planar, and a 2D smoothing filter will yield a maximum response if the smoothing plane coincides with a local fault plane. With the enhanced fault attribute volume and the estimated fault strike and dip volumes, we then compute oriented fault samples on the ridges of the enhanced fault attribute volume, and each sample is oriented by the estimated fault strike and dip. Fault surfaces can be constructed by directly linking the oriented fault samples with consistent fault strikes and dips. For complicated cases with missing fault samples and noisy samples, we further propose to use a perceptual grouping method to infer fault surfaces that reasonably fit the positions and orientations of the fault samples. We apply these methods to 3D synthetic and real examples and successfully extract multiple intersecting fault surfaces and complete fault surfaces without holes.

[Incidence of Campylobacter spp. and Salmonella spp. in raw and roasted chicken in Guadalajara, Mexico].

PubMed

Castillo-Ayala, A; Salas-Ubiarco, M G; Márquez-Padilla, M L; Osorio-Hernández, M D

1993-01-01

The presence of Campylobacter spp. and Salmonella was studied in 70 samples of fresh retail chicken pieces and in 40 samples of roast chicken. Total plate count was performed in every sample as well. Most of the samples of fresh chicken yielded total plate counts > 10(8)/piece (thigh), while in roast chicken these counts ranged from 10(3) to 10(5)/piece (leg and thigh). Campylobacter was isolated from 33% of fresh chicken and from no sample of roast chicken. Salmonella was isolated from 69% of fresh chicken and 2.5% of roast chicken. There was no relationship between total plate counts in fresh chicken and isolation of either Campylobacter or Salmonella. Sixty percent of the Salmonella isolates belonged to serotype S. anatum, and about 50% of the isolates of Campylobacter were identified as being C. coli. The only Salmonella-positive sample of roast chicken yielded three serotypes: S. give, S. muenster, and S. manhattan. Presence of Campylobacter and Salmonella in chicken is of concern, due to the risk of spreading from the raw food to other cooked foods. The isolation of pathogens from roast chicken indicates mishandling during processing and/or storage of the product.

Detection of EBV-DNA in serum samples of an immunosuppressed child during a three years follow-up: association of clinical and PCR data with active infection.

PubMed

Okay, Thelma Suely; Del Negro, Gilda Maria Barbaro; Yamamoto, Lídia; Raiz Júnior, Roberto

2005-01-01

Twenty-four whole blood and serum samples were drawn from an eight year-old heart transplant child during a 36 months follow-up. EBV serology was positive for VCA-IgM and IgG, and negative for EBNA-IgG at the age of five years old when the child presented with signs and symptoms suggestive of acute infectious mononucleosis. After 14 months, serological parameters were: positive VCA-IgG, EBNA-IgG and negative VCA-IgM. This serological pattern has been maintained since then even during episodes suggestive of EBV reactivation. PCR amplified a specific DNA fragment from the EBV gp220 (detection limit of 100 viral copies). All twenty-four whole blood samples yielded positive results by PCR, while 12 out of 24 serum samples were positive. We aimed at analyzing whether detection of EBV-DNA in serum samples by PCR was associated with overt disease as stated by the need of antiviral treatment and hospitalization. Statistical analysis showed agreement between the two parameters evidenced by the Kappa test (value 0.750; p < 0.001). We concluded that detection of EBV-DNA in serum samples of immunosuppressed patients might be used as a laboratory marker of active EBV disease when a Real-Time PCR or another quantitative method is not available.

Self-referencing remote optical probe

DOEpatents

O'Rourke, Patrick E.; Prather, William S.; Livingston, Ronald R.

1991-01-01

A probe for remote spectrometric measurements of fluid samples having a hollow probe body with a sliding reflective plug therein and a lens at one end, ports for admitting and expelling the fluid sample and a means for moving the reflector so that reference measurement can be made with the reflector in a first position near the lens and a sample measurement can be made with the reflector away from the lens and the fluid sample between the reflector and the lens. Comparison of the two measurements will yield the composition of the fluid sample. The probe is preferably used for remote measurements and light is carried to and from the probe via fiber optic cables.

Self-referencing remote optical probe

DOEpatents

O'Rourke, P.E.; Prather, W.S.; Livingston, R.R.

1991-08-13

A probe is described for remote spectrometric measurements of fluid samples having a hollow probe body with a sliding reflective plug therein and a lens at one end, ports for admitting and expelling the fluid sample and a means for moving the reflector so that reference measurement can be made with the reflector in a first position near the lens and a sample measurement can be made with the reflector away from the lens and the fluid sample between the reflector and the lens. Comparison of the two measurements will yield the composition of the fluid sample. The probe is preferably used for remote measurements and light is carried to and from the probe via fiber optic cables. 3 figures.

Antibody levels correlate with detection of Trypanosoma cruzi DNA by sensitive PCR assays in seropositive blood donors and possible resolution of infection over time

PubMed Central

Sabino, E.C.; Lee, T.H.; Montalvo, L.; Nguyen, M.L.; Leiby, D.A.; Carrick, D.M.; Otani, M.M.; Vinelli, E.; Wright, D.; Stramer, S.L.; Busch, M.

2013-01-01

Background The clinical significance of anti-T. cruzi low-level reactive samples is incompletely understood. PCR-positive rates and antibody levels among seropositive blood donors in three countries are described. Methods Follow-up whole blood and plasma samples were collected from T. cruzi-seropositive donors from 2008-2010 in the US (n=195) and Honduras (n=58). Also 143 samples from Brazil in 1996-2002, originally positive by three serological assays, were available and paired with contemporary follow-up samples from these donors. All samples were retested with the FDA-approved Ortho ELISA. PCR assays were performed on coded sample panels by two laboratories (BSRI and ARC) that amplified kinetoplast minicircle DNA sequences of T. cruzi. Results PCR testing at BSRI yielded slightly higher overall sensitivity and specificity (33% and 98%) compared with the ARC lab (28% and 94%). Among seropositive donors, PCR-positive rates varied by country (p<0.0001) for the BSRI laboratory: Brazil (57%), Honduras (32%) and the US (14%). ELISA signal/cutoff (S/CO) ratios were significantly higher for PCR-positive compared to PCR-negative donors (p<0.05 for all comparisons). Additionally, PCR-negative Brazilian donors exhibited greater frequencies of antibody decline over time versus PCR-positive donors (p=0.003). Conclusion For all three countries, persistent DNA positivity correlated with higher ELISA S/CO values, suggesting that high-level seroreactivity reflects chronic parasitemia. The higher rate of PCR positivity for Brazilian donors was likely attributable to required reactivity on three assays available a decade ago. Significant S/CO declines in 10% of the PCR-negative Brazilian donors may indicate seroreversion following parasite clearance in the absence of treatment. PMID:23002996

Relationship between soybean yield/quality and soil quality in a major soybean-producing area based on a 2D-QSAR model

NASA Astrophysics Data System (ADS)

Gao, Ming; Li, Shiwei

2017-05-01

Based on experimental data of the soybean yield and quality from 30 sampling points, a quantitative structure-activity relationship model (2D-QSAR) was established using the soil quality (elements, pH, organic matter content and cation exchange capacity) as independent variables and soybean yield or quality as the dependent variable, with SPSS software. During the modeling, the full data set (30 and 14 compounds) was divided into a training set (24 and 11 compounds) for model generation and a test set (6 and 3 compounds) for model validation. The R2 values of the resulting models and data were 0.826 and 0.808 for soybean yield and quality, respectively, and all regression coefficients were significant (P < 0.05). The correlation coefficient R2pred of observed values and predicted values of the soybean yield and soybean quality in the test set were 0.961 and 0.956, respectively, indicating that the models had a good predictive ability. Moreover, the Mo, Se, K, N and organic matter contents and the cation exchange capacity of soil had a positive effect on soybean production, and the B, Mo, Se, K and N contents and cation exchange coefficient had a positive effect on soybean quality. The results are instructive for enhancing soils to improve the yield and quality of soybean, and this method can also be used to study other crops or regions, providing a theoretical basis to improving the yield and quality of crops.

Radiocarbon measurements of small gaseous samples at CologneAMS

NASA Astrophysics Data System (ADS)

Stolz, A.; Dewald, A.; Altenkirch, R.; Herb, S.; Heinze, S.; Schiffer, M.; Feuerstein, C.; Müller-Gatermann, C.; Wotte, A.; Rethemeyer, J.; Dunai, T.

2017-09-01

A second SO-110 B (Arnold et al., 2010) ion source was installed at the 6 MV CologneAMS for the measurement of gaseous samples. For the gas supply a dedicated device from Ionplus AG was connected to the ion source. Special effort was devoted to determine optimized operation parameters for the ion source, which give a high carbon current output and a high 14C- yield. The latter is essential in cases when only small samples are available. Additionally a modified immersion lens and modified target pieces were tested and the target position was optimized.

Optimizing methods and dodging pitfalls in microbiome research.

PubMed

Kim, Dorothy; Hofstaedter, Casey E; Zhao, Chunyu; Mattei, Lisa; Tanes, Ceylan; Clarke, Erik; Lauder, Abigail; Sherrill-Mix, Scott; Chehoud, Christel; Kelsen, Judith; Conrad, Máire; Collman, Ronald G; Baldassano, Robert; Bushman, Frederic D; Bittinger, Kyle

2017-05-05

Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies. Typically, samples will need to be stored, so we provide data on best practices for several sample types. We then discuss design and analysis of positive and negative controls, which should always be run with experimental samples. We introduce a convenient set of non-biological DNA sequences that can be useful as positive controls for high-volume analysis. Careful analysis of negative and positive controls is particularly important in studies of samples with low microbial biomass, where contamination can comprise most or all of a sample. Lastly, we summarize approaches to enhancing experimental robustness by careful control of multiple comparisons and to comparing discovery and validation cohorts. We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors.

Transition of carbon nanostructures in heptane diffusion flames

NASA Astrophysics Data System (ADS)

Hu, Wei-Chieh; Hou, Shuhn-Shyurng; Lin, Ta-Hui

2017-02-01

The flame synthesis has high potential in industrial production of carbon nanostructure (CNS). Unfortunately, the complexity of combustion chemistry leads to less controlling of synthesized products. In order to improve the understanding of the relation between flames and CNSs synthesized within, experiments were conducted through heptane flames in a stagnation-point liquid-pool system. The operating parameters for the synthesis include oxygen supply, sampling position, and sampling time. Two kinds of nanostructures were observed, carbon nanotube (CNT) and carbon nano-onion (CNO). CNTs were synthesized in a weaker flame near extinction. CNOs were synthesized in a more sooty flame. The average diameter of CNTs formed at oxygen concentration of 15% was in the range of 20-30 nm. For oxygen concentration of 17%, the average diameter of CNTs ranged from 24 to 27 nm, while that of CNOs was around 28 nm. For oxygen concentration of 19%, the average diameter of CNOs produced at the sampling position 0.5 mm below the flame front was about 57 nm, while the average diameters of CNOs formed at the sampling positions 1-2.5 mm below the flame front were in the range of 20-25 nm. A transition from CNT to CNO was observed by variation of sampling position in a flame. We found that the morphology of CNS is directly affected by the presence of soot layer due to the carbonaceous environment and the growth mechanisms of CNT and CNO. The sampling time can alter the yield of CNSs depending on the temperature of sampling position, but the morphology of products is not affected.

The relative utility of the autologous control and the antiglobulin test phase of the crossmatch.

PubMed

Perkins, J T; Arruza, M; Fong, K; Sosler, S D; Saporito, C

1990-01-01

A retrospective study of pretransfusion testing records compared the utility of the antiglobulin test (AGT) phase of the crossmatch and the autologous control (autocontrol) for detecting clinically significant alloimmunization to red cells (RBCs). Of 110,780 consecutive crossmatches, 141 were positive after a negative antibody screening test; only 4 of these were due to alloantibodies of potential clinical significance, for a predictive value of a positive AGT crossmatch, after a negative antibody screen, of 2.8 percent (4/141). The frequency of potentially shortened RBC survival was 1 in 27,685 units crossmatched. During a similar period, 56,090 autocontrols were performed with the antibody screen. The autocontrol was positive on 902 samples in which the antibody screen was negative. Antibody identification performed in 684 cases generally yielded only cold or warm autoagglutinins. In 96 cases, some form of alloantibody was detected, but only 25 had potential clinical significance by our criteria. Eight of these alloantibodies had concurrently caused in vivo sensitization of RBCs and were classified as delayed hemolytic transfusion reactions. The predictive value of the autocontrol, calculated as the number of significant alloantibodies detected in autocontrol-positive, antibody-screen-negative samples, was 3.6 percent (25/684). Inspection of these cases revealed 11 in which shortened RBC survival might have resulted if the serologic abnormality had not been detected. Thus, the autocontrol had a slightly greater yield of clinically significant findings than the AGT crossmatch.(ABSTRACT TRUNCATED AT 250 WORDS)

Efficiency of the Lung Flute for sputum induction in patients with presumed pulmonary tuberculosis.

PubMed

Sakashita, Kentaro; Fujita, Akira; Takamori, Mikio; Nagai, Takayuki; Matsumoto, Tomoshige; Saito, Takefumi; Nakagawa, Taku; Ogawa, Kenji; Shigeto, Eriko; Nakatsumi, Yasuto; Goto, Hajime; Mitarai, Satoshi

2018-04-01

High quality sputum helps increase the sensitivity of the diagnosis of pulmonary tuberculosis. To evaluate the efficiency of the acoustic device (Lung Flute; LF) in sputum induction compared with the conventional method, hypertonic saline inhalation (HSI). In this crossover study, patients with presumed pulmonary tuberculosis submitted 3 consecutive sputa: the first sputum without induction and the second and third ones using LF and HSI. We compared the efficiency of the 2 induction methods. Sixty-four participants were eligible. Thirty-five (54.6%) patients had negative smears on the first sputum without induction. Among those patients, 25.7% and 22.9% patients were smear-positive after using LF and HSI, respectively (P = .001). The positive conversion rate was not significantly different between the methods. The first samples without induction yielded 65.7% positive cultures, whereas 71.4% and 77.1% of the samples from LF and HSI were positive, respectively (P = .284). Similar results were observed in the nucleic acid amplification test [no induction (60.0%), LF (72.0%) and HSI (60.0%); P = .341]. In 29 smear-positive patients on the first sputum without induction, we observed no significant increase in smear grade, culture yield and nucleic acid amplification test positivity with either method. LF tended to induce fewer adverse events; desaturation (3.1% vs 11.1%; P = .082) and throat pain (1.5% vs 9.5%; P = .057). LF showed significantly fewer total adverse events (15.8% vs 34.9%; P = .023). Our study showed LF had similar sputum induction efficiency to HSI with relatively fewer complications. © 2017 The Authors. The Clinical Respiratory Journal Published by John Wiley & Sons Ltd.

Systematic screening for mutations in the promoter and the coding region of the 5-HT{sub 1A} gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erdmann, J.; Shimron-Abarbanell, D.; Cichon, S.

1995-10-09

In the present study we sought to identify genetic variation in the 5-HT{sub 1A} receptor gene which through alteration of protein function or level of expression might contribute to the genetic predisposition to neuropsychiatric diseases. Genomic DNA samples from 159 unrelated subjects (including 45 schizophrenic, 46 bipolar affective, and 43 patients with Tourette`s syndrome, as well as 25 healthy controls) were investigated by single-strand conformation analysis. Overlapping PCR (polymerase chain reaction) fragments covered the whole coding sequence as well as the 5{prime} untranslated region of the 5-HT{sub 1A} gene. The region upstream to the coding sequence we investigated contains amore » functional promoter. We found two rare nucleotide sequence variants. Both mutations are located in the coding region of the gene: a coding mutation (A{yields}G) in nucleotide position 82 which leads to an amino acid exchange (Ile{yields}Val) in position 28 of the receptor protein and a silent mutation (C{yields}T) in nucleotide position 549. The occurrence of the Ile-28-Val substitution was studied in an extended sample of patients (n = 352) and controls (n = 210) but was found in similar frequencies in all groups. Thus, this mutation is unlikely to play a significant role in the genetic predisposition to the diseases investigated. In conclusion, our study does not provide evidence that the 5-HT{sub 1A} gene plays either a major or a minor role in the genetic predisposition to schizophrenia, bipolar affective disorder, or Tourette`s syndrome. 29 refs., 4 figs., 1 tab.« less

Value of different bronchoscopic sampling techniques in diagnosis of sarcoidosis: a prospective study of 151 patients.

PubMed

Goyal, Abhishek; Gupta, Dheeraj; Agarwal, Ritesh; Bal, Amanjit; Nijhawan, Raje; Aggarwal, Ashutosh N

2014-07-01

The exact position of routine bronchoscopic sampling techniques in diagnostic workup of sarcoidosis is often debated. Herein, we ascertain the role of transbronchial needle aspiration (TBNA), endobronchial ultrasound-guided TBNA (EBUS-TBNA), transbronchial lung biopsy (TBLB), and endobronchial biopsy (EBB) in diagnosis of sarcoidosis. Consecutive patients with suspected sarcoidosis who underwent fiberoptic bronchoscopy were studied. TBLB, EBB, TBNA, or EBUS-TBNA was performed as indicated in a standardized manner. A diagnosis of sarcoidosis was established based on the finding of non-necrotizing granulomas or on clinical grounds at 6-month follow-up. Individual and cumulative yield of various procedures and their correlation with clinicoradiologic parameters was analyzed. Of the 164 patients studied, 151 were finally diagnosed as sarcoidosis. Granulomas were demonstrated in 127 (84.2%) patients. Diagnostic yield of TBLB, EBB, TBNA, and EBUS-TBNA was 68.7%, 49.6%, 22.43%, and 57.1%, respectively. Cumulative yields of various procedures were: EBB+TBLB 81.4%; TBLB+TBNA 73.7%; TBNA+EBB 62.9%; TBLB+EBB+TBNA 86.9%; and TBLB+EBB+EBUS-TBNA 86.4%. In those with visible mucosal abnormalities, TBLB+EBB conferred the highest diagnostic yield (92.8%). Clinical findings or radiologic stage had no impact on diagnostic yield. TBLB is an important tool in bronchoscopic diagnosis of sarcoidosis. If endobronchial abnormalities are seen during bronchoscopy, TBLB with EBB gives the best results otherwise TBLB combined with conventional TBNA and EBB or EBUS-TBNA are required to maximize the diagnostic yield.

Multi-source irradiation facility with improved space configuration for neutron activation analysis: Design optimization.

PubMed

Kotb, N A; Solieman, Ahmed H M; El-Zakla, T; Amer, T Z; Elmeniawi, S; Comsan, M N H

2018-05-01

A neutron irradiation facility consisting of six 241 Am-Be neutron sources of 30 Ci total activity and 6.6 × 10 7 n/s total neutron yield is designed. The sources are embedded in a cubic paraffin wax, which plays a dual role as both moderator and reflector. The sample passage and irradiation channel are represented by a cylindrical path of 5 cm diameter passing through the facility core. The proposed design yields a high degree of space symmetry and thermal neutron homogeneity within 98% of flux distribution throughout the irradiated spherical sample of 5 cm diameter. The obtained thermal neutron flux is 8.0 × 10 4 n/cm 2 .s over the sample volume, with thermal-to-fast and thermal-to-epithermal ratios of 1.20 and 3.35, respectively. The design is optimized for maximizing the thermal neutron flux at sample position using the MCNP-5 code. The irradiation facility is supposed to be employed principally for neutron activation analysis. Copyright © 2018 Elsevier Ltd. All rights reserved.

[The use of 16S rDNA sequencing in species diversity analysis for sputum of patients with ventilator-associated pneumonia].

PubMed

Yang, Xiaojun; Wang, Xiaohong; Liang, Zhijuan; Zhang, Xiaoya; Wang, Yanbo; Wang, Zhenhai

2014-05-01

To study the species and amount of bacteria in sputum of patients with ventilator-associated pneumonia (VAP) by using 16S rDNA sequencing analysis, and to explore the new method for etiologic diagnosis of VAP. Bronchoalveolar lavage sputum samples were collected from 31 patients with VAP. Bacterial DNA of the samples were extracted and identified by polymerase chain reaction (PCR). At the same time, sputum specimens were processed for routine bacterial culture. The high flux sequencing experiment was conducted on PCR positive samples with 16S rDNA macro genome sequencing technology, and sequencing results were analyzed using bioinformatics, then the results between the sequencing and bacteria culture were compared. (1) 550 bp of specific DNA sequences were amplified in sputum specimens from 27 cases of the 31 patients with VAP, and they were used for sequencing analysis. 103 856 sequences were obtained from those sputum specimens using 16S rDNA sequencing, yielding approximately 39 Mb of raw data. Tag sequencing was able to inform genus level in all 27 samples. (2) Alpha-diversity analysis showed that sputum samples of patients with VAP had significantly higher variability and richness in bacterial species (Shannon index values 1.20, Simpson index values 0.48). Rarefaction curve analysis showed that there were more species that were not detected by sequencing from some VAP sputum samples. (3) Analysis of 27 sputum samples with VAP by using 16S rDNA sequences yielded four phyla: namely Acitinobacteria, Bacteroidetes, Firmicutes, Proteobacteria. With genus as a classification, it was found that the dominant species included Streptococcus 88.9% (24/27), Limnohabitans 77.8% (21/27), Acinetobacter 70.4% (19/27), Sphingomonas 63.0% (17/27), Prevotella 63.0% (17/27), Klebsiella 55.6% (15/27), Pseudomonas 55.6% (15/27), Aquabacterium 55.6% (15/27), and Corynebacterium 55.6% (15/27). (4) Pyrophosphate sequencing discovered that Prevotella, Limnohabitans, Aquabacterium, Sphingomonas might not be detected by routine bacteria culture. Among seven species which were identified by both methods, pyrophosphate sequencing yielded higher positive rate than that of ordinary bacteria culture [Streptococcus: 88.9% (24/27) vs. 18.5% (5/27), Klebsiella: 55.6% (15/27) vs. 18.5% (5/27), Acinetobacter: 70.4% (19/27) vs. 37.0% (10/27), Corynebacterium: 55.6% (15/27) vs. 7.4% (2/27), P<0.05 or P<0.01]. Sequencing positive rate was found to increase positive rate for culture of Pseudomonas [55.6% (15/27) vs. 25.9% (7/27), P=0.050]. No significant differences were observed between sequencing and ordinary bacteria culture for detection Staphylococcus [7.4% (2/27) vs. 11.1% (3/27)] and Neisseria bacteria genera [18.5% (5/27) vs. 3.7% (1/27), both P>0.05]. 16S rDNA sequencing analysis confirmed that pathogenic bacteria in sputum of VAP were complicated with multiple drug resistant strains. Compared with routine bacterial culture, pyrophosphate sequencing had higher positive rate in detecting pathogens. 16S rDNA gene sequencing technology may become a new method for etiological diagnosis of VAP.

Gastrointestinal anthrax after an animal-hide drumming event - New Hampshire and Massachusetts, 2009.

PubMed

2010-07-23

On December 24, 2009, a woman aged 24 years from New Hampshire was confirmed to have gastrointestinal anthrax on the basis of clinical findings and a Bacillus anthracis blood culture isolate. Her symptoms began on December 5. One day before symptom onset, she had participated in a drumming event at a community organization's building where animal-hide drums of multiple ages and origins were played. This report describes the case and subsequent investigation, which identified 84 persons potentially exposed to anthrax, including those persons at the drumming event and those who lived or worked at the event site. Review of New Hampshire disease surveillance data and clinical microbiology records for periods before and after the event identified no additional anthrax cases. Initial qualitative environmental testing of the event site yielded three positive samples (two from drum heads and one composite sample of three electrical outlets in the main drumming room). Wider, targeted, semi-quantitative environmental testing of the site and additional drums yielded six positive samples (two from one drum and four from environmental locations in the building). These results suggested that aerosolization of spores from drumheads had occurred. All isolates obtained from environmental and drum samples matched the patient's isolate by multiple-locus variable-number tandem repeat analysis using eight loci (MLVA-8). Public health agencies and persons with exposure to animal-hide drums should be aware of the potential, although remote, risk for anthrax exposure associated with these drums.

Mesenchymal Stem Cell Levels of Human Spinal Tissues.

PubMed

Harris, Liam; Vangsness, C Thomas

2018-05-01

Systematic review. The aim of this study was to investigate, quantify, compare, and compile the various mesenchymal stem cell (MSC) tissue sources within human spinal tissues to act as a compendium for clinical and research application. Recent years have seen a dramatic increase in academic and clinical understanding of human MSCs. Previously limited to cells isolated from bone marrow, the past decade has illicited the characterization and isolation of human MSCs from adipose, bone marrow, synovium, muscle, periosteum, peripheral blood, umbilical cord, placenta, and numerous other tissues. As researchers explore practical applications of cells in these tissues, the absolute levels of MSCs in specific spinal tissue will be critical to guide future research. The PubMED, MEDLINE, EMBASE, and Cochrane databases were searched for articles relating to the harvest, characterization, isolation, and quantification of human MSCs from spinal tissues. Selected articles were examined for relevant data, categorized according to type of spinal tissue, and when possible, standardized to facilitate comparisons between sites. Human MSC levels varied widely between spinal tissues. Yields for intervertebral disc demonstrated roughly 5% of viable cells to be positive for MSC surface markers. Cartilage endplate cells yielded 18,500 to 61,875 cells/0.8 mm thick sample of cartilage end plate. Ligamentum flavum yielded 250,000 to 500,000 cells/g of tissue. Annulus fibrosus fluorescence activated cell sorting treatment found 29% of cells positive for MSC marker Stro-1. Nucleus pulposus yielded mean tissue samples of 40,584 to 234,137 MSCs per gram of tissue. Numerous tissues within and surrounding the spine represent a consistent and reliable source for the harvest and isolation of human MSCs. Among the tissues of the spine, the annulus fibrosus and ligamentum flavum each offer considerable levels of MSCs, and may prove comparable to that of bone marrow. 5.

Spot sputum samples are at least as good as early morning samples for identifying Mycobacterium tuberculosis.

PubMed

Murphy, Michael E; Phillips, Patrick P J; Mendel, Carl M; Bongard, Emily; Bateson, Anna L C; Hunt, Robert; Murthy, Saraswathi; Singh, Kasha P; Brown, Michael; Crook, Angela M; Nunn, Andrew J; Meredith, Sarah K; Lipman, Marc; McHugh, Timothy D; Gillespie, Stephen H

2017-10-27

The use of early morning sputum samples (EMS) to diagnose tuberculosis (TB) can result in treatment delay given the need for the patient to return to the clinic with the EMS, increasing the chance of patients being lost during their diagnostic workup. However, there is little evidence to support the superiority of EMS over spot sputum samples. In this new analysis of the REMoxTB study, we compare the diagnostic accuracy of EMS with spot samples for identifying Mycobacterium tuberculosis pre- and post-treatment. Patients who were smear positive at screening were enrolled into the study. Paired sputum samples (one EMS and one spot) were collected at each trial visit pre- and post-treatment. Microscopy and culture on solid LJ and liquid MGIT media were performed on all samples; those missing corresponding paired results were excluded from the analyses. Data from 1115 pre- and 2995 post-treatment paired samples from 1931 patients enrolled in the REMoxTB study were analysed. Patients were recruited from South Africa (47%), East Africa (21%), India (20%), Asia (11%), and North America (1%); 70% were male, median age 31 years (IQR 24-41), 139 (7%) co-infected with HIV with a median CD4 cell count of 399 cells/μL (IQR 318-535). Pre-treatment spot samples had a higher yield of positive Ziehl-Neelsen smears (98% vs. 97%, P = 0.02) and LJ cultures (87% vs. 82%, P = 0.006) than EMS, but there was no difference for positivity by MGIT (93% vs. 95%, P = 0.18). Contaminated and false-positive MGIT were found more often with EMS rather than spot samples. Surprisingly, pre-treatment EMS had a higher smear grading and shorter time-to-positivity, by 1 day, than spot samples in MGIT culture (4.5 vs. 5.5 days, P < 0.001). There were no differences in time to positivity in pre-treatment LJ culture, or in post-treatment MGIT or LJ cultures. Comparing EMS and spot samples in those with unfavourable outcomes, there were no differences in smear or culture results, and positive results were not detected earlier in Kaplan-Meier analyses in either EMS or spot samples. Our data do not support the hypothesis that EMS samples are superior to spot sputum samples in a clinical trial of patients with smear positive pulmonary TB. Observed small differences in mycobacterial burden are of uncertain significance and EMS samples do not detect post-treatment positives any sooner than spot samples.

A multisystemic Acanthamoeba infection in a dog in Tenerife, Canary Islands, Spain.

PubMed

Valladares, María; Reyes-Batlle, María; Mora-Peces, Inmaculada; Martín-Navarro, Carmen M; López-Arencibia, Atteneri; Dorta-Gorrín, Alexis; Comyn-Afonso, Estefanía; Martínez-Carretero, Enrique; Maciver, Sutherland K; Piñero, José E; Valladares, Basilio; Lorenzo-Morales, Jacob

2014-10-15

A 22-month-old male Spanish water dog was hospitalized after its physical examination revealed fever and movement difficulty. After 24h, the dog was found to have a high fever (39.5 °C) and was treated empirically with doxycycline/ciprofloxacin. At 48 h, after submission the fever rose to 41 °C and the animal presented with a stiff neck and dehydration. Peripheral blood and cerebrospinal fluid (CSF) were sampled and trophozoites with an Acanthamoeba-like morphology were observed in the CSF. PCR specific for Acanthamoeba, Naegleria fowleri and Balamuthia mandrillaris were performed and the CSF sample found positive for Acanthamoeba. Lungs, kidney, liver and spleen samples were collected post mortem. All collected organ samples were positive for Acanthamoeba by PCR, thus confirming a multisystemic infection. Water samples taken at a suspected site of infection yielded an almost identical PCR fragment to those of the clinical samples, indicating that this was probably where the infection originated. This is the first report of a fatal case of Acanthamoeba disseminated infection in a dog in Spain. Copyright © 2014 Elsevier B.V. All rights reserved.

Detection of Toxoplasma gondii DNA in Brazilian oysters (Crassostrea rhizophorae).

PubMed

Ribeiro, L A; Santos, L K N S S; Brito, P A; Maciel, B M; Da Silva, A V; Albuquerque, G R

2015-05-04

The aim of this study was to detect evidence of Toxoplasma gondii using polymerase chain reaction (PCR)-based techniques in oysters (Crassostrea rhizophorae) obtained from the southern coastal region of Bahia, Brazil. A total of 624 oysters were collected, and the gills and digestive glands were dissected. Each tissue sample was separated into pools containing tissues (of the same type) from three animals, leading to a total of 416 experimental samples for analysis (208 samples each from the gills and digestive glands). Molecular analysis using PCR-based detection of the T. gondii AF 146527 repetitive fragment yielded negative results for all samples. However, when nested-PCR was used for detection of the T. gondii SAG-1 gene, 17 samples were positive, with the gills being the tissue with maximal detection of the parasite. These positive results were confirmed by sample sequencing. It is therefore suggested that C. rhizophorae oysters are capable of filtering and retaining T. gondii oocysts in their tissue. This represents a risk to public health because they are traditionally ingested in natura.

Gram-positive bacteria of marine origin: a numerical taxonomic study on Mediterranean isolates.

PubMed

Ortigosa, M; Garay, E; Pujalte, M J

1997-12-01

A numerical taxonomic study was performed on 65 Gram-positive wild strains of heterotrophic, aerobic, marine bacteria, and 9 reference strains. The isolates were obtained from oysters and seawater sampled monthly over one year, by direct plating on Marine Agar. The strains were characterized by 96 morphological, biochemical, physiological and nutritional tests. Clustering yielded 13 phena at 0.62 similarity level (Sl coefficient). Only one of the seven phena containing wild isolates could be identified (Bacillus marinus). A pronounced salt requirement was found in most isolates.

Posttraumatic Stress Disorder Symptom Clusters and the Interpersonal Theory of Suicide in a Large Military Sample.

PubMed

Pennings, Stephanie M; Finn, Joseph; Houtsma, Claire; Green, Bradley A; Anestis, Michael D

2017-10-01

Prior studies examining posttraumatic stress disorder (PTSD) symptom clusters and the components of the interpersonal theory of suicide (ITS) have yielded mixed results, likely stemming in part from the use of divergent samples and measurement techniques. This study aimed to expand on these findings by utilizing a large military sample, gold standard ITS measures, and multiple PTSD factor structures. Utilizing a sample of 935 military personnel, hierarchical multiple regression analyses were used to test the association between PTSD symptom clusters and the ITS variables. Additionally, we tested for indirect effects of PTSD symptom clusters on suicidal ideation through thwarted belongingness, conditional on levels of perceived burdensomeness. Results indicated that numbing symptoms are positively associated with both perceived burdensomeness and thwarted belongingness and hyperarousal symptoms (dysphoric arousal in the 5-factor model) are positively associated with thwarted belongingness. Results also indicated that hyperarousal symptoms (anxious arousal in the 5-factor model) were positively associated with fearlessness about death. The positive association between PTSD symptom clusters and suicidal ideation was inconsistent and modest, with mixed support for the ITS model. Overall, these results provide further clarity regarding the association between specific PTSD symptom clusters and suicide risk factors. © 2016 The American Association of Suicidology.

Hunting the most distant stars in the Milky Way: methods and initial results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bochanski, John J.; Willman, Beth; West, Andrew A.

2014-04-01

We present a new catalog of 404 M giant candidates found in the UKIRT Infrared Deep Sky Survey (UKIDSS). The 2400 deg{sup 2} available in the UKIDSS Large Area Survey Data Release 8 resolve M giants through a volume four times larger than that of the entire Two Micron All Sky Survey. Combining near-infrared photometry with optical photometry and proper motions from the Sloan Digital Sky Survey yields an M giant candidate catalog with less M dwarf and quasar contamination than previous searches for similarly distant M giants. Extensive follow-up spectroscopy of this sample will yield the first map ofmore » our Galaxy's outermost reaches over a large area of sky. Our initial spectroscopic follow-up of ∼30 bright candidates yielded the positive identification of five M giants at distances ∼20-90 kpc. Each of these confirmed M giants have positions and velocities consistent with the Sagittarius stream. The fainter M giant candidates in our sample have estimated photometric distances ∼200 kpc (assuming [Fe/H] = 0.0), but require further spectroscopic verification. The photometric distance estimates extend beyond the Milky Way's virial radius, and increase by ∼50% for each 0.5 dex decrease in assumed [Fe/H]. Given the number of M giant candidates, initial selection efficiency, and volume surveyed, we loosely estimate that at least one additional Sagittarius-like accretion event could have contributed to the hierarchical build-up of the Milky Way's outer halo.« less

[Superficial infections caused by Microsporum canis in humans and animals].

PubMed

Segundo, Carolina; Martínez, Alejandrina; Arenas, Roberto; Fernández, Ramón; Cervantes, Roberto A

2004-03-01

Dermatophytic infections caused by M. canis in humans and animals have a world wide distribution and they are zoonotic. The objective in this work was to know the frequency of M. canis infections in humans and pets. We studied our cases from January 1994 to December 2002. The human samples were obtained from a Dermatological Department in a General Hospital and we registered the next data: age, sex, job, and affected area. The animal samples were obtained from a mycological veterinary laboratory, and we registered the presence or absence of clinical lesions. A total of 46 clinical cases of M. canis infections were recorded, 26 female and 20 males: tinea capitis 21, tinea corporis 17, tinea pedis five, onychomycosis two, and only one case with tinea faciei. The 46 cases with positive culture yield 42 positive samples in KOH. The age range varied from 2 to 60 years. Among the animals, we studied 461 dogs and found six KOH positive (1%) samples and cultured 23 isolates (4.98%): 21 M. canis, one M. gypseum and one Trichophyton spp. From the 68 samples of cats, eight (11.76%) were positive to KOH, being 26 (38.23%) M. canis isolates. In M. canis infections in humans, the age rage was wide with predominance in women. In animals, M. canis isolates represented the most dermatophytic infection.

Procedural justice and layoff survivors' commitment: a quantitative review.

PubMed

Grubb, W Lee

2006-10-01

Layoffs are common in today's organizations. Most studies that have examined the correlation between procedural justice and the organizational commitment of layoff survivors have yielded positive correlations, but the magnitude of the correlations varies widely. This study is the first to estimate the population correlation and to identify the primary sources that cause variation in the correlation across studies. The results indicated that justice and commitment correlations can always be expected to be positive. Based on a total sample size of 9080 individuals, the estimated mean population correlation was .34. Variation was primarily explained by attributes of the justice measure where multiple items scales and scales composed of both interactional and procedural justice items yielded higher correlations than single item measures. Therefore, it is important that employers recognize the substantial assuaging affect that procedural and interactional justice can have on survivors' organizational commitment.

New records of sylvatic plague in Kansas

USGS Publications Warehouse

Cully, J.F.; Carter, L.G.; Gage, K.L.

2000-01-01

Sylvatic plague, or plague of wild rodents is caused by Yersinia pestis and entered California (USA) from Asia about 1899. Extensive sampling during the 1930's and 1940's documented the spread of plague to approximately its current distribution in North America. Records from the Centers for Disease Control and Prevention document plague in Kansas (USA) between 1945 and 1950, but since then there has been no documentation of plague in the state. Following a die-off of a black-tailed prairie dog (Cynomys ludovicianus) colony on the Cimarron National Grassland, in the southwestern corner of Kansas (37??10???N, 101??45???W), we sampled fleas from burrows in June 1997, and tested them for Yersinia pestis. Twelve of 13 pools of Oropsyla hirsuta and one of two Pulex sp. were positive. A similar sample of fleas, from another colony where black-tailed prairie dogs were active at the time, yielded no positive fleas.

Tensile properties of the human glenoid labrum

PubMed Central

Smith, C D; Masouros, S D; Hill, A M; Wallace, A L; Amis, A A; Bull, A M J

2008-01-01

Human fresh-frozen cadaveric glenoid labrae from 16 donors were harvested and ten of these had no gross degeneration. These ten were divided into eight equal circumferential sections. Each section was cut to produce test-samples from the core layer with a cross-section of 1 × 1 mm. Tensile testing was performed within a controlled environment unit at 37 ± 1 °C and 100% relative humidity. Each test-sample was precycled to a quasi-static state to alleviate the effects of deep-freezing, prior to final testing. The tangent modulus was calculated for each test-sample before and after a 5-min period of stress relaxation and at yield. The mean elastic modulus and yield stress of the glenoid labrum were 22.8 ± 11.4 and 2.5 ± 2.1 MPa, respectively. The anterosuperior portion had a lower elastic modulus and lower yield stress than the inferior portion (both P < 0.02). The pre-stress relaxation tangent modulus was significantly lower than the post-stress relaxation tangent modulus for all portions of the labrum. The glenoid labrum has similar tensile material properties to articular cartilage. Its elastic modulus varies around its circumference. This suggests that the labrum may encounter different forces at different positions. PMID:18031481

[Serological examinations for swine vesicular disease (SVD) in a closed pig breeding herd using ELISA].

PubMed

Pannwitz, Gunter; Haas, Bernd; Hoffmann, Bernd; Fischer, Sebastian

2009-01-01

In a closed pig establishment housing about 18,000 pigs, 2895 gilts were tested pre-export for SVD (swine vesicular disease) antibodies using Ceditest/PrioCHECK SVDV-AB ELISA. 130 gilts (4.5%) tested positive. In addition, 561 animals of this farm were sampled per random for SVD serology. One in 241 weaners (0.4%), eight in 150 gilts (5.3%) and 18 in 170 (10.6%) pregnant sows tested ELISA SVD-antibody positive. Of the ELISA positive samples, 23 tested positive in VNT (virus neutralization test). Of these, 20 VNT-positive animals were re-sampled two weeks later and re-tested via ELISA and VNT in different laboratories, displaying falling titres with one to two animals remaining VNT-positive. Epidemiological investigations and clinical examinations on site did not yield any evidence for SVD. 745 faecal samples taken from individual pigs and collected from pens tested negative in SVDV-RNA-PCR. 40 of these samples tested negative in virus isolation on cell culture. Pathological examinations on fallen pigs did not reveal any evidence for SVD either. After comparing our ELISA results with data recorded in the ELISA validation by Chenard et al. (1998), we propose that the published test performance is perhaps not currently applicable for the commercial test. Provided that SVD-antibody negative pigs were tested, a specificity of 99.6% in weaners, 95.5% in gilts and 89.4% in pregnant sows would appear to be more appropriate for the Ceditest/PrioCHECK SVDV-AB ELISA. Details are provided for all examined pigs regarding husbandry, breed, age, weeks pregnant and previous vaccinations. The results of other serological tests on the same sera are given. Possible clusterings of false-positive SVD-ELISA results are discussed.

Oscillational instabilities in single-mode acoustic levitators

NASA Technical Reports Server (NTRS)

Rudnick, Joseph; Barmatz, M.

1990-01-01

An extension of standard results for the acoustic force on an object in a single-mode resonant chamber yields predictions for the onset of oscillational instabilities when objects are levitated or positioned in these chambers. The results are consistent with experimental investigations. The present approach accounts for the effect of time delays on the response of a cavity to the motion of an object inside it. Quantitative features of the instabilities are investigated. The experimental conditions required for sample stability, saturation of sample oscillations, hysteretic effects, and the loss of the ability to levitate are discussed.

Comparison of oral fluid collection methods for the molecular detection of hepatitis B virus.

PubMed

Portilho, M M; Mendonça, Acf; Marques, V A; Nabuco, L C; Villela-Nogueira, C A; Ivantes, Cap; Lewis-Ximenez, L L; Lampe, E; Villar, L M

2017-11-01

This study aims to compare the efficiency of four oral fluid collection methods (Salivette, FTA Card, spitting and DNA-Sal) to detect HBV DNA by qualitative PCR. Seventy-four individuals (32 HBV reactive and 42 with no HBV markers) donated serum and oral fluid. In-house qualitative PCR to detect HBV was used for both samples and commercial quantitative PCR for serum. HBV DNA was detected in all serum samples from HBV-infected individuals, and it was not detected in control group. HBV DNA from HBV group was detected in 17 samples collected with Salivette device, 16 samples collected by FTA Card device, 16 samples collected from spitting and 13 samples collected by DNA-Sal device. Samples that corresponded to a higher viral load in their paired serum sample could be detected using all oral fluid collection methods, but Salivette collection device yielded the largest numbers of positive samples and had a wide range of viral load that was detected. It was possible to detect HBV DNA using all devices tested, but higher number of positive samples was observed when samples were collected using Salivette device, which shows high concordance to viral load observed in the paired serum samples. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd. All rights reserved.

Immunochemical assessment of mycotoxins in 1989 grain foods: evidence for deoxynivalenol (vomitoxin) contamination.

PubMed Central

Abouzied, M M; Azcona, J I; Braselton, W E; Pestka, J J

1991-01-01

To assess the potential for mycotoxin contamination of the human food supply following the 1988 U.S. drought, 92 grain food samples were purchased from retail outlets in the summer of 1989 and surveyed for aflatoxin B1, zearalenone, and deoxynivalenol (DON [vomitoxin]) by monoclonal antibody-based competitive enzyme-linked immunosorbent assay (ELISA). Only one sample (buckwheat flour) was found to contain aflatoxin B1 (12 ng/g), whereas zearalenone was found in 26% of the samples at a mean concentration of 19 ng/g. In contrast, the DON ELISA was positive in 50% of the samples at a detection level of 1.0 micrograms/g. Between 63 and 88% of corn cereals, wheat flour/muffin mixes, rice cereals, and corn meal/muffin mixes yielded positive results for DON, whereas 25 to 50% of oat cereals, wheat- and oat-based cookies/crackers, corn chips, popcorn, and mixed-grain cereals were positive for DON. The mean DON content of the positive samples was 4.0 micrograms/g, and the minimum and maximum levels were 1.2 and 19 micrograms/g, respectively. When positive ELISA samples were also analyzed by high-performance liquid chromatography, a strong correlation between the two methods was found. The presence of DON in the two highest samples, corn meal and mixed-grain cereal, which contained 19 and 16 micrograms/g, respectively, was quantitatively confirmed by gas chromatography-mass spectrometry. The results indicated that DON was present in 1989 retail food products at concentrations that exceeded those found in previous market surveys and that have been experimentally associated with impaired animal health. Images PMID:1828138

MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling.

PubMed

Song, Yifan; Mao, Junjun; Gunner, M R

2009-11-15

Multiconformation continuum electrostatics (MCCE) explores different conformational degrees of freedom in Monte Carlo calculations of protein residue and ligand pK(a)s. Explicit changes in side chain conformations throughout a titration create a position dependent, heterogeneous dielectric response giving a more accurate picture of coupled ionization and position changes. The MCCE2 methods for choosing a group of input heavy atom and proton positions are described. The pK(a)s calculated with different isosteric conformers, heavy atom rotamers and proton positions, with different degrees of optimization are tested against a curated group of 305 experimental pK(a)s in 33 proteins. QUICK calculations, with rotation around Asn and Gln termini, sampling His tautomers and torsion minimum hydroxyls yield an RMSD of 1.34 with 84% of the errors being <1.5 pH units. FULL calculations adding heavy atom rotamers and side chain optimization yield an RMSD of 0.90 with 90% of the errors <1.5 pH unit. Good results are also found for pK(a)s in the membrane protein bacteriorhodopsin. The inclusion of extra side chain positions distorts the dielectric boundary and also biases the calculated pK(a)s by creating more neutral than ionized conformers. Methods for correcting these errors are introduced. Calculations are compared with multiple X-ray and NMR derived structures in 36 soluble proteins. Calculations with X-ray structures give significantly better pK(a)s. Results with the default protein dielectric constant of 4 are as good as those using a value of 8. The MCCE2 program can be downloaded from http://www.sci.ccny.cuny.edu/~mcce. 2009 Wiley Periodicals, Inc.

Women with symptoms of a urinary tract infection but a negative urine culture: PCR-based quantification of Escherichia coli suggests infection in most cases.

PubMed

Heytens, S; De Sutter, A; Coorevits, L; Cools, P; Boelens, J; Van Simaey, L; Christiaens, T; Vaneechoutte, M; Claeys, G

2017-09-01

Our objective was to examine whether or not women with symptoms of a urinary tract infection but with a negative culture (20%-30%) do have an infection. We performed quantitative PCR (qPCR) for Escherichia coli and Staphylococcus saprophyticus, on top of a standard culture, in urine samples from 220 women with dysuria and/or frequency and/or urgency and from 86 women without symptoms. For symptomatic women, qPCR was also carried out for four sexually transmitted agents. In the symptomatic group, 80.9% (178/220) of the urine cultures were positive for any uropathogen and 95.9% (211/220) were E. coli qPCR-positive. For the control group, cultures for E. coli and E. coli qPCR were positive in, respectively, 10.5% (9/86) and 11.6% (10/86). In the symptomatic group, qPCR yielded 19 positive samples for S. saprophyticus qPCR, one positive sample for Mycoplasma genitalium and one for Trichomonas vaginalis. These findings suggest that almost all women with typical urinary complaints and a negative culture still have an infection with E. coli. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Sputum colour and bacteria in chronic bronchitis exacerbations: a pooled analysis.

PubMed

Miravitlles, Marc; Kruesmann, Frank; Haverstock, Daniel; Perroncel, Renee; Choudhri, Shurjeel H; Arvis, Pierre

2012-06-01

We examined the correlation between sputum colour and the presence of potentially pathogenic bacteria in acute exacerbations of chronic bronchitis (AECBs). Data were pooled from six multicentre studies comparing moxifloxacin with other antimicrobials in patients with an AECB. Sputum was collected before antimicrobial therapy, and bacteria were identified by culture and Gram staining. Association between sputum colour and bacteria was determined using logistic regression. Of 4,089 sputum samples, a colour was reported in 4,003; 1,898 (46.4%) were culture-positive. Green or yellow sputum samples were most likely to yield bacteria (58.9% and 45.5% of samples, respectively), compared with 18% of clear and 39% of rust-coloured samples positive for potentially pathogenic microorganisms. Factors predicting a positive culture were sputum colour (the strongest predictor), sputum purulence, increased dyspnoea, male sex and absence of fever. Green or yellow versus white sputum colour was associated with a sensitivity of 94.7% and a specificity of 15% for the presence of bacteria. Sputum colour, particularly green and yellow, was a stronger predictor of potentially pathogenic bacteria than sputum purulence and increased dyspnoea in AECB patients. However, it does not necessarily predict the need for antibiotic treatment in all patients with AECB.

Spatial Sampling of Weather Data for Regional Crop Yield Simulations

NASA Technical Reports Server (NTRS)

Van Bussel, Lenny G. J.; Ewert, Frank; Zhao, Gang; Hoffmann, Holger; Enders, Andreas; Wallach, Daniel; Asseng, Senthold; Baigorria, Guillermo A.; Basso, Bruno; Biernath, Christian;

Satellite-based assessment of yield variation and its determinants in smallholder African systems

PubMed Central

Lobell, David B.

2017-01-01

The emergence of satellite sensors that can routinely observe millions of individual smallholder farms raises possibilities for monitoring and understanding agricultural productivity in many regions of the world. Here we demonstrate the potential to track smallholder maize yield variation in western Kenya, using a combination of 1-m Terra Bella imagery and intensive field sampling on thousands of fields over 2 y. We find that agreement between satellite-based and traditional field survey-based yield estimates depends significantly on the quality of the field-based measures, with agreement highest (R2 up to 0.4) when using precise field measures of plot area and when using larger fields for which rounding errors are smaller. We further show that satellite-based measures are able to detect positive yield responses to fertilizer and hybrid seed inputs and that the inferred responses are statistically indistinguishable from estimates based on survey-based yields. These results suggest that high-resolution satellite imagery can be used to make predictions of smallholder agricultural productivity that are roughly as accurate as the survey-based measures traditionally used in research and policy applications, and they indicate a substantial near-term potential to quickly generate useful datasets on productivity in smallholder systems, even with minimal or no field training data. Such datasets could rapidly accelerate learning about which interventions in smallholder systems have the most positive impact, thus enabling more rapid transformation of rural livelihoods. PMID:28202728

Satellite-based assessment of yield variation and its determinants in smallholder African systems.

PubMed

Burke, Marshall; Lobell, David B

2017-02-28

The emergence of satellite sensors that can routinely observe millions of individual smallholder farms raises possibilities for monitoring and understanding agricultural productivity in many regions of the world. Here we demonstrate the potential to track smallholder maize yield variation in western Kenya, using a combination of 1-m Terra Bella imagery and intensive field sampling on thousands of fields over 2 y. We find that agreement between satellite-based and traditional field survey-based yield estimates depends significantly on the quality of the field-based measures, with agreement highest ([Formula: see text] up to 0.4) when using precise field measures of plot area and when using larger fields for which rounding errors are smaller. We further show that satellite-based measures are able to detect positive yield responses to fertilizer and hybrid seed inputs and that the inferred responses are statistically indistinguishable from estimates based on survey-based yields. These results suggest that high-resolution satellite imagery can be used to make predictions of smallholder agricultural productivity that are roughly as accurate as the survey-based measures traditionally used in research and policy applications, and they indicate a substantial near-term potential to quickly generate useful datasets on productivity in smallholder systems, even with minimal or no field training data. Such datasets could rapidly accelerate learning about which interventions in smallholder systems have the most positive impact, thus enabling more rapid transformation of rural livelihoods.

Type-specific detection of high-risk human papillomavirus (HPV) in self-sampled cervicovaginal cells applied to FTA elute cartridge.

PubMed

Gustavsson, Inger; Sanner, Karin; Lindell, Monica; Strand, Anders; Olovsson, Matts; Wikström, Ingrid; Wilander, Erik; Gyllensten, Ulf

2011-08-01

Most procedures for self-sampling of cervical cells are based on liquid-based media for transportation and storage. An alternative is to use a solid support, such as dry filter paper media. To evaluate if self-sampling of cervicovaginal fluid using a cytobrush (Viba-brush; Rovers Medical Devices B.V., Oss, The Netherlands) and a solid support such as the Whatman Indicating FTA Elute cartridge (GE Healthcare, United Kingdom) can be used for reliable typing of human papillomavirus (HPV), as compared to cervical samples obtained by a physician using a cytobrush and the indicating FTA Elute Micro card and biopsy analysis. A total of 50 women with a previous high-risk (HR) HPV positive test were invited to perform self-sampling using the Viba-brush and the FTA cartridge and thereafter a physician obtained a cervical sample using the cytobrush and a FTA card, together with a cervical biopsy for histology and HPV typing. Detection of HR-HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58 and 59 was performed using three multiplex real-time polymerase chain reaction (PCR) assays. All samples contained sufficient amounts of genomic DNA and the self-samples yielded on average 3.5 times more DNA than those obtained by the physician. All women that were positive for HR-HPV in the biopsy sample also typed positive both by self-sampling and physician-obtained sampling. For women with a histological diagnosis of cervical intraepithelial neoplasia grades 2-3 (CIN 2-3) all three HPV samples showed 100% concordance. A higher number of women were HPV positive by self-sampling than by physician-obtained sampling or by biopsy analysis. The Viba-brush and the FTA cartridge are suitable for self-sampling of vaginal cells and subsequent HR-HPV typing. Copyright © 2011 Elsevier B.V. All rights reserved.

Rapid Screening of Carboxylic Acids from Waste and Surface Waters by ESI-MS/MS Using Barium Ion Chemistry and On-Line Membrane Sampling.

PubMed

Duncan, Kyle D; Volmer, Dietrich A; Gill, Chris G; Krogh, Erik T

2016-03-01

Negative ion tandem mass spectrometric analysis of aliphatic carboxylic acids often yields only non-diagnostic ([M - H](-)) ions with limited selective fragmentation. However, carboxylates cationized with Ba(2+) have demonstrated efficient dissociation in positive ion mode, providing structurally diagnostic product ions. We report the application of barium adducts followed by collision induced dissociation (CID), to improve selectivity for rapid screening of carboxylic acids in complex aqueous samples. The quantitative MS/MS method presented utilizes common product ions of [M - H + Ba](+) precursor ions. The mechanism of product ion formation is investigated using isotopically labeled standards and a series of structurally related carboxylic acids. The results suggest that hydrogen atoms in the β and γ positions yield common product ions ([BaH](+) and [BaOH](+)). Furthermore, the diagnostic product ion at m/z 196 serves as a qualifying ion for carboxylate species. This methodology has been successfully used in conjunction with condensed phase membrane introduction mass spectrometry (CP-MIMS), with barium acetate added directly to the methanol acceptor phase. The combination enables rapid screening of carboxylic acids directly from acidified water samples (wastewater effluent, spiked natural waters) using a capillary hollow fiber PDMS membrane immersion probe. We have applied this technique for the direct analysis of complex naphthenic acid mixtures spiked into natural surface waters using CP-MIMS. Selectivity at the ionization and tandem mass spectrometry level eliminate isobaric interferences from hydroxylated species present within the samples, which have been observed in negative electrospray ionization.

Homogenisation of cystic fibrosis sputum by sonication--an essential step for Aspergillus PCR.

PubMed

Baxter, Caroline G; Jones, Andrew M; Webb, Kevin; Denning, David W

2011-04-01

The importance of Aspergillus as a lung pathogen in cystic fibrosis (CF) is becoming increasingly recognised. However, fungal culture of CF sputum is unreliable and there is no consensus for identifying phenotypes beyond ABPA that may benefit from antifungal therapy. There are no published studies using real-time PCR to detect Aspergillus in CF sputum. The major barrier to sensitive detection of Aspergillus using PCR is sputum homogenisation. This study aimed to optimise sputum homogenisation utilising sonication to improve Aspergillus DNA extraction. Sonication amplitude and duration that enabled sputum homogenisation but ensured preservation of DNA integrity were first determined. 160 sputum samples were collected from CF patients. 49 of the sputum samples were split, one half was used for standard culture and the other half was homogenised with NALC-NaOH before undergoing DNA extraction. The subsequent 111 samples were homogenised with dithiothreitol plus sonication prior to culture and DNA extraction. Real-time PCR targeting a portion of the 18S rDNA of Aspergillus was performed on all DNA extractions. In the 49 samples with no sonication 8 (16%) were culture positive but only 4 of these were PCR positive. However, PCR was positive in 11 culture negative samples. PCR after sonication showed a significant improvement in sensitivity: 33 (30%) were culture and PCR positive, 48 (43%) were culture negative, but PCR positive (p<0.0001) and 30 (27%) were culture and PCR negative. The combination of dithiothreitol and sonication to homogenise sputum increases PCR yield, with PCR being substantially more sensitive than culture. Copyright © 2011 Elsevier B.V. All rights reserved.

Development and Evaluation of a Rapid and Sensitive EBOV-RPA Test for Rapid Diagnosis of Ebola Virus Disease.

PubMed

Yang, Mingjuan; Ke, Yuehua; Wang, Xuesong; Ren, Hang; Liu, Wei; Lu, Huijun; Zhang, Wenyi; Liu, Shiwei; Chang, Guohui; Tian, Shuguang; Wang, Lihua; Huang, Liuyu; Liu, Chao; Yang, Ruifu; Chen, Zeliang

2016-06-01

Confirming Ebola virus disease (EVD), a deadly infectious disease, requires real-time RT-PCR, which takes up to a few hours to yield results. Therefore, a rapid diagnostic assay is imperative for EVD diagnosis. A rapid nucleic acid test based on recombinase polymerase amplification (EBOV-RPA) was developed to specifically detect the 2014 outbreak strains. The EBOV-RPA assay was evaluated by testing samples from suspected EVD patients in parallel with RT-PCR. An EBOV-RPA, which could be completed in 20 min, was successfully developed. Of 271 patients who tested positive for Ebola virus by RT-PCR, 264 (sensitivity: 97%, 95% CI: 95.5-99.3%) were positive by EBOV-RPA; 101 of 104 patients (specificity: 97%, 95% CI: 93.9-100%) who tested negative by RT-PCR were also negative by EBOV-RPA. The sensitivity values for samples with a Ct value of <34, which accounted for 95.59% of the samples, was 100%. Discordant samples positive by RT-PCR but negative by EBOV-RPA had significantly high Ct values. Results of external quality assessment samples with EBOV-RPA were 100%, consistent with those of RT-PCR. The EBOV-RPA assay showed 97% sensitivity and 97% specificity for all EVD samples tested, making it a rapid and sensitive test for EVD diagnosis.

Global Crop Yields, Climatic Trends and Technology Enhancement

NASA Astrophysics Data System (ADS)

Najafi, E.; Devineni, N.; Khanbilvardi, R.; Kogan, F.

2016-12-01

During the last decades the global agricultural production has soared up and technology enhancement is still making positive contribution to yield growth. However, continuing population, water crisis, deforestation and climate change threaten the global food security. Attempts to predict food availability in the future around the world can be partly understood from the impact of changes to date. A new multilevel model for yield prediction at the country scale using climate covariates and technology trend is presented in this paper. The structural relationships between average yield and climate attributes as well as trends are estimated simultaneously. All countries are modeled in a single multilevel model with partial pooling and/or clustering to automatically group and reduce estimation uncertainties. El Niño Southern Oscillation (ENSO), Palmer Drought Severity Index (PDSI), Geopotential height (GPH), historical CO2 level and time-trend as a relatively reliable approximation of technology measurement are used as predictors to estimate annual agricultural crop yields for each country from 1961 to 2007. Results show that these indicators can explain the variability in historical crop yields for most of the countries and the model performs well under out-of-sample verifications.

Pathways between primary production and fisheries yields of large marine ecosystems.

PubMed

Friedland, Kevin D; Stock, Charles; Drinkwater, Kenneth F; Link, Jason S; Leaf, Robert T; Shank, Burton V; Rose, Julie M; Pilskaln, Cynthia H; Fogarty, Michael J

2012-01-01

The shift in marine resource management from a compartmentalized approach of dealing with resources on a species basis to an approach based on management of spatially defined ecosystems requires an accurate accounting of energy flow. The flow of energy from primary production through the food web will ultimately limit upper trophic-level fishery yields. In this work, we examine the relationship between yield and several metrics including net primary production, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production. We also evaluate the relationship between yield and two additional rate measures that describe the export of energy from the pelagic food web, particle export flux and mesozooplankton productivity. We found primary production is a poor predictor of global fishery yields for a sample of 52 large marine ecosystems. However, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production were positively associated with yields. The latter two measures provide greater mechanistic insight into factors controlling fishery production than chlorophyll concentration alone. Particle export flux and mesozooplankton productivity were also significantly related to yield on a global basis. Collectively, our analyses suggest that factors related to the export of energy from pelagic food webs are critical to defining patterns of fishery yields. Such trophic patterns are associated with temperature and latitude and hence greater yields are associated with colder, high latitude ecosystems.

Pathways between Primary Production and Fisheries Yields of Large Marine Ecosystems

PubMed Central

Friedland, Kevin D.; Stock, Charles; Drinkwater, Kenneth F.; Link, Jason S.; Leaf, Robert T.; Shank, Burton V.; Rose, Julie M.; Pilskaln, Cynthia H.; Fogarty, Michael J.

2012-01-01

The shift in marine resource management from a compartmentalized approach of dealing with resources on a species basis to an approach based on management of spatially defined ecosystems requires an accurate accounting of energy flow. The flow of energy from primary production through the food web will ultimately limit upper trophic-level fishery yields. In this work, we examine the relationship between yield and several metrics including net primary production, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production. We also evaluate the relationship between yield and two additional rate measures that describe the export of energy from the pelagic food web, particle export flux and mesozooplankton productivity. We found primary production is a poor predictor of global fishery yields for a sample of 52 large marine ecosystems. However, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production were positively associated with yields. The latter two measures provide greater mechanistic insight into factors controlling fishery production than chlorophyll concentration alone. Particle export flux and mesozooplankton productivity were also significantly related to yield on a global basis. Collectively, our analyses suggest that factors related to the export of energy from pelagic food webs are critical to defining patterns of fishery yields. Such trophic patterns are associated with temperature and latitude and hence greater yields are associated with colder, high latitude ecosystems. PMID:22276100

Toxoplasma gondii in stranded marine mammals from the North Sea and Eastern Atlantic Ocean: Findings and diagnostic difficulties.

PubMed

van de Velde, Norbert; Devleesschauwer, Brecht; Leopold, Mardik; Begeman, Lineke; IJsseldijk, Lonneke; Hiemstra, Sjoukje; IJzer, Jooske; Brownlow, Andrew; Davison, Nicholas; Haelters, Jan; Jauniaux, Thierry; Siebert, Ursula; Dorny, Pierre; De Craeye, Stéphane

2016-10-30

The occurrence of the zoonotic protozoan parasite Toxoplasma gondii in marine mammals remains a poorly understood phenomenon. In this study, samples from 589 marine mammal species and 34 European otters (Lutra lutra), stranded on the coasts of Scotland, Belgium, France, The Netherlands and Germany, were tested for the presence of T. gondii. Brain samples were analysed by polymerase chain reaction (PCR) for detection of parasite DNA. Blood and muscle fluid samples were tested for specific antibodies using a modified agglutination test (MAT), a commercial multi-species enzyme-linked immunosorbent assay (ELISA) and an immunofluorescence assay (IFA). Out of 193 animals tested by PCR, only two harbour porpoise (Phocoena phocoena) cerebrum samples, obtained from animals stranded on the Dutch coast, tested positive. The serological results showed a wide variation depending on the test used. Using a cut-off value of 1/40 dilution in MAT, 141 out of 292 animals (41%) were positive. Using IFA, 30 out of 244 tested samples (12%) were positive at a 1/50 dilution. The commercial ELISA yielded 7% positives with a cut-off of the sample-to-positive (S/P) ratio≥50; and 12% when the cut-off was set at S/P ratio≥20. The high number of positives in MAT may be an overestimation due to the high degree of haemolysis of the samples and/or the presence of lipids. The ELISA results could be an underestimation due to the use of a multispecies conjugate. Our results confirm the presence of T. gondii in marine mammals in The Netherlands and show exposure to the parasite in both the North Sea and the Eastern Atlantic Ocean. We also highlight the limitations of the tests used to diagnose T. gondii in stranded marine mammals. Copyright © 2016 Elsevier B.V. All rights reserved.

Genotypic character relationship and phenotypic path coefficient analysis in chili pepper genotypes grown under tropical condition.

PubMed

Usman, Magaji G; Rafii, Mohd Y; Martini, Mohammad Y; Oladosu, Yusuff; Kashiani, Pedram

2017-03-01

Studies on genotypic and phenotypic correlations among characters of crop plants are useful in planning, evaluating and setting selection criteria for the desired characters in a breeding program. The present study aimed to estimate the phenotypic correlation coefficients among yield and yield attributed characters and to work out the direct and indirect effects of yield-related characters on yield per plant using path coefficient analysis. Twenty-six genotypes of chili pepper were laid out in a randomized complete block design with three replications. Yield per plant showed positive and highly significant (P ≤ 0.01) correlations with most of the characters studied at both the phenotypic and genotypic levels. By contrast, disease incidence and days to flowering showed a significant negative association with yield. Fruit weight and number of fruits exerted positive direct effect on yield and also had a positive and significant (P ≤ 0.01) correlation with yield per plant. However, fruit length showed a low negative direct effect with a strong and positive indirect effect through fruit weight on yield and had a positive and significant association with yield. Longer fruits, heavy fruits and a high number of fruits are variables that are related to higher yields of chili pepper under tropical conditions and hence could be used as a reliable indicator in indirect selection for yield. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Feasibility of track-based multiple scattering tomography

NASA Astrophysics Data System (ADS)

Jansen, H.; Schütze, P.

2018-04-01

We present a tomographic technique making use of a gigaelectronvolt electron beam for the determination of the material budget distribution of centimeter-sized objects by means of simulations and measurements. In both cases, the trajectory of electrons traversing a sample under test is reconstructed using a pixel beam-telescope. The width of the deflection angle distribution of electrons undergoing multiple Coulomb scattering at the sample is estimated. Basing the sinogram on position-resolved estimators enables the reconstruction of the original sample using an inverse radon transform. We exemplify the feasibility of this tomographic technique via simulations of two structured cubes—made of aluminium and lead—and via an in-beam measured coaxial adapter. The simulations yield images with FWHM edge resolutions of (177 ± 13) μm and a contrast-to-noise ratio of 5.6 ± 0.2 (7.8 ± 0.3) for aluminium (lead) compared to air. The tomographic reconstruction of a coaxial adapter serves as experimental evidence of the technique and yields a contrast-to-noise ratio of 15.3 ± 1.0 and a FWHM edge resolution of (117 ± 4) μm.

Pathogens as Predictors of Honey Bee Colony Strength in England and Wales.

PubMed

Budge, Giles E; Pietravalle, Stéphane; Brown, Mike; Laurenson, Lynn; Jones, Ben; Tomkies, Victoria; Delaplane, Keith S

2015-01-01

Inspectors with the UK National Bee Unit were asked for 2007-2008 to target problem apiaries in England and Wales for pathogen screening and colony strength measures. Healthy colonies were included in the sampling to provide a continuum of health conditions. A total of 406 adult bee samples was screened and yielded 7 viral, 1 bacterial, and 2 microsporidial pathogens and 1 ectoparasite (Acarapis woodi). In addition, 108 samples of brood were screened and yielded 4 honey bee viruses. Virus prevalence varied from common (deformed wing virus, black queen cell virus) to complete absence (Israeli acute paralysis virus). When colonies were forced into one of two classes, strong or weak, the weak colonies contained more pathogens in adult bees. Among observed pathogens, only deformed wing virus was able to predict colony strength. The effect was negative such that colonies testing positive for deformed wing virus were likely to have fewer combs of bees or brood. This study constitutes the first record for Nosema ceranae in Great Britain. These results contribute to the growing body of evidence linking pathogens to poor honey bee health.

Evaluation of TECRA broth, Bolton broth, and direct plating for recovery of Campylobacter spp, from broiler carcass rinsates from commercial processing plants.

PubMed

Richardson, L J; Cox, N A; Bailey, J S; Berrang, M E; Cox, J M; Buhr, R J; Fedorka-Cray, P J; Harrison, M A

2009-05-01

The purpose of this study was to compare a conventional culture broth method (Bolton enrichment), a newly developed proprietary broth method (TECRA Campylobacter enrichment), and direct plating for recovery of Campylobacter spp. from chicken carcass rinsates. Whole carcass rinses were taken from 140 carcasses at rehang (immediately after defeathering but before evisceration) and from 140 carcasses at postchill from eight different processing plants in the United States. The rinsate samples were packed in ice and shipped overnight to the laboratory. Aliquots of the rinsate were transferred into Bolton and TECRA enrichment broths and were direct plated. Standard laboratory procedures with Campy-cefex plates were followed for recovery of Campylobacter spp. For rehang carcasses, 94% were positive for Campylobacter spp. with the TECRA enrichment broth and 74% were positive with the Bolton enrichment broth. For postchill carcasses, 74% were positive for Campylobacter spp. with the TECRA enrichment broth and 71% were positive with the Bolton enrichment broth. Compared with the Bolton enrichment broth, TECRA enrichment broth significantly suppressed non-Campylobacter microflora (P < 0.05). Overall, TECRA enrichment broth yielded an 11% higher total number of Campylobacter-positive samples compared with the Bolton enrichment broth. Campylobacter spp. detection in postchill samples was significantly greater (P < 0.05) by enrichment (84%) than by direct plating (19%). The high number of Campylobacter-positive samples obtained with all procedures indicated that 99% of the carcass rinsates obtained at rehang and 84% obtained at postchill contained Campylobacter spp.

Comparison of four β-glucuronidase and β-galactosidase-based commercial culture methods used to detect Escherichia coli and total coliforms in water.

PubMed

Maheux, Andrée F; Dion-Dupont, Vanessa; Bouchard, Sébastien; Bisson, Marc-Antoine; Bergeron, Michel G; Rodriguez, Manuel J

2015-06-01

The MI agar, Colilert(®), Chromocult coliform(®) agar, and DC with BCIG agar chromogenic culture-based methods used to assess microbiological quality of drinking water were compared in terms of their ubiquity, sensitivity, ease of use, growth of atypical colonies and affordability. For ubiquity, 129 total coliform (representing 76 species) and 19 Escherichia coli strains were tested. Then, 635 1-L well water samples were divided into 100 mL subsamples for testing by all four methods. Test results showed that 70.5, 52.7, 36.4, and 23.3% of the non-E. coli total coliform strains and 94.7, 94.7, 89.5, and 89.5% of the 19 E. coli strains yielded a positive signal with the four methods, respectively. They also yielded a total coliform positive signal for 66.5, 51.7, 64.9, and 55.0% and an E. coli positive signal for 16.1, 14.8, 17.3, and 13.4% of the 635 well water samples tested, respectively. Results showed that Colilert(®) is the most expensive method tested in terms of reactants, yet it is the easiest to use. Large numbers of atypical colonies were also often observed on Chromocult coliform(®) and DC with BCIG, thereby challenging the target microorganism count. Thus, the MI agar method seems to be the best option for the assessment of drinking water quality.

False-Positive Gen-Probe Direct Mycobacterium tuberculosis Amplification Test Results for Patients with Pulmonary M. kansasii and M. avium Infections

PubMed Central

Jorgensen, James H.; Salinas, Jesse R.; Paxson, Rosemary; Magnon, Karen; Patterson, Jan E.; Patterson, Thomas F.

1999-01-01

The Gen-Probe Amplified Mycobacterium Tuberculosis Direct (MTD) test has been approved for use in the United States for the rapid diagnosis of pulmonary tuberculosis in patients with acid-fast smear-positive sputum samples since 1996. Four patients infected with human immunodeficiency virus and one chronic pulmonary-disease patient seen in our institutions with abnormal chest radiographs and fluorochrome stain-positive sputa were evaluated for tuberculosis, including performance of the MTD test on expectorated sputum samples. Three of these five patients’ sputa were highly smear-positive (i.e., more than 100 bacilli per high-power field), while two patient’s sputa contained 1 to 10 bacilli per field. MTD results on sputum specimens from these patients ranged from 43,498 to 193,858 relative light units (RLU). Gen-Probe has defined values of at least 30,000 RLU as indicative of a positive test, i.e., the presence of Mycobacterium tuberculosis RNA. Four of the patients’ sputum cultures yielded growth of M. kansasii within 6 to 12 days, and the fifth produced growth of M. avium only. One patient’s culture contained both M. kansasii and M. avium, but none of the initial or follow-up cultures from these five patients revealed M. tuberculosis. However, subsequent cultures from three of the patients again revealed M. kansasii. During the period of this study, in which MTD tests were performed on smear-positive sputum specimens from 82 patients, four of seven patients with culture-proven M. kansasii pulmonary infections yielded one or more false-positive MTD tests. The MTD sensitivity observed in this study was 93.8%, and the specificity was 85.3%. Five cultures of M. kansasii (including three of these patients’ isolates and M. kansasii ATCC 12478), and cultures of several other species were examined at densities of 105 to 107 viable CFU/ml by the MTD test. All five isolates of M. kansasii and three of three isolates of M. simiae yielded false-positive test results, with readings of 75,191 to 335,591 RLU. These findings indicate that low-level false-positive MTD results can occur due to the presence of M. kansasii, M. avium, and possibly other Mycobacterium species other than M. tuberculosis in sputum. Low-level positive MTD results of 30,000 to 500,000 RLU should be interpreted in light of these findings. It remains to be determined if the enhanced MTD test (MTD 2) recently released by Gen-Probe will provide greater specificity than that observed in this report with its first-generation test. PMID:9854086

The zoonotic potential of Giardia intestinalis assemblage E in rural settings.

PubMed

Abdel-Moein, Khaled A; Saeed, Hossam

2016-08-01

Giardiasis is a globally re-emerging protozoan disease with veterinary and public health implications. The current study was carried out to investigate the zoonotic potential of livestock-specific assemblage E in rural settings. For this purpose, a total of 40 microscopically positive Giardia stool samples from children with gastrointestinal complaints with or without diarrhea were enrolled in the study as well as fecal samples from 46 diarrheic cattle (18 dairy cows and 28 calves). Animal samples were examined by sedimentation method to identify Giardia spp., and then, all Giardia positive samples from human and animals were processed for molecular detection of livestock-specific assemblage E through amplification of assemblage-specific triosephosphate isomerase (tpi) gene using nested polymerase chain reaction (PCR). The results of the study revealed high unexpected occurrence of assemblage E among human samples (62.5 %), whereas the distribution among patients with diarrhea and those without was 42.1 and 81 %, respectively. On the other hand, the prevalence of Giardia spp. among diarrheic dairy cattle was (8.7 %), while only calves yielded positive results (14.3 %) and all bovine Giardia spp. were genetically classified as Giardia intestinalis assemblage E. Moreover, DNA sequencing of randomly selected one positive human sample and another bovine one revealed 100 and 99 % identity with assemblage E tpi gene sequences available at GenBank after BLAST analysis. In conclusion, the current study highlights the wide dissemination of livestock-specific assemblage E among humans in rural areas, and thus, zoonotic transmission cycle should not be discounted during the control of giardiasis in such settings.

Environmental DNA Marker Development with Sparse Biological Information: A Case Study on Opossum Shrimp (Mysis diluviana).

PubMed

Carim, Kellie J; Christianson, Kyle R; McKelvey, Kevin M; Pate, William M; Silver, Douglas B; Johnson, Brett M; Galloway, Benjamin T; Young, Michael K; Schwartz, Michael K

2016-01-01

The spread of Mysis diluviana, a small glacial relict crustacean, outside its native range has led to unintended shifts in the composition of native fish communities throughout western North America. As a result, biologists seek accurate methods of determining the presence of M. diluviana, especially at low densities or during the initial stages of an invasion. Environmental DNA (eDNA) provides one solution for detecting M. diluviana, but building eDNA markers that are both sensitive and species-specific is challenging when the distribution and taxonomy of closely related non-target taxa are poorly understood, published genetic data are sparse, and tissue samples are difficult to obtain. To address these issues, we developed a pair of independent eDNA markers to increase the likelihood of a positive detection of M. diluviana when present and reduce the probability of false positive detections from closely related non-target species. Because tissue samples of closely-related and possibly sympatric, non-target taxa could not be obtained, we used synthetic DNA sequences of closely related non-target species to test the specificity of eDNA markers. Both eDNA markers yielded positive detections from five waterbodies where M. diluviana was known to be present, and no detections in five others where this species was thought to be absent. Daytime samples from varying depths in one waterbody occupied by M. diluviana demonstrated that samples near the lake bottom produced 5 to more than 300 times as many eDNA copies as samples taken at other depths, but all samples tested positive regardless of depth.

Post-therapy lesions in patients with non-Hodgkin's lymphoma characterized by 18F-FDG PET/CT-guided biopsy using automated robotic biopsy arm.

PubMed

Radhakrishnan, Renjith K; Mittal, Bhagwant R; Basher, Rajender K; Prakash, Gaurav; Malhotra, Pankaj; Kalra, Naveen; Das, Ashim

2018-01-01

The aim of this study was to analyse the positive predictive value (PPV) of post-therapy fluorine-18-fluorodeoxyglucose (F-FDG) PET/CT performed for response or recurrence evaluation in patients with non-Hodgkin's lymphoma (NHL) and to appraise the diagnostic utility of F-FDG PET/CT-guided biopsy in this setting. A total of 17 patients with NHL showing F-FDG avid lesions in F-FDG PET/CT performed for response or recurrence assessment underwent F-FDG PET/CT-guided biopsy using automated robotic biopsy arm needle navigation technique. The objectives were analysed in reference to histopathology. In all, 15 of the 17 (88.5%) procedures yielded adequate representative tissue samples. Nine out of 15 lesions were positive for residual disease and the remaining revealed benign findings on histopathology. One patient with inconclusive biopsy underwent surgical resection and histopathology confirmed the presence of residual disease. PPV of theF-FDG PET/CT was observed to be 62.5% (10/16). F-FDG PET/CT for response evaluation in NHL possesses a low PPV and hence warrants histopathological correlation when F-FDG PET/CT findings influence management decision. Diagnostic yield of F-FDG PET/CT-guided biopsy is high and has the potential to reduce sampling errors.

A new graphite preparation line for AMS 14C dating in the Zagreb Radiocarbon Laboratory

NASA Astrophysics Data System (ADS)

Krajcar Bronić, I.; Horvatinčić, N.; Sironić, A.; Obelić, B.; Barešić, J.; Felja, I.

2010-04-01

The new line for preparation of graphite samples for 14C dating by AMS has been constructed in the Zagreb Radiocarbon Laboratory. The performance of the rig and sample preparation procedure has been validated by preparing graphites from various reference materials of known 14C activity. The yield of the graphitization was good and the measured fraction of modern carbon ( Fm) values have not significantly deviated from the expected ones. Detailed analysis of measured Fm values indicates a slight bias to more positive values and should be carefully investigated.

Oscillational instabilities in single mode acoustics levitators

NASA Technical Reports Server (NTRS)

Rudnick, J.; Barmatz, Martin

1990-01-01

An extention of standard results for the acoustic force on an object in a single-mode resonant chamber yields predictions for the onset of oscillational instabilities when objects are levitated or positioned in these chambers. The authors' results are consistent with those of experimental investigators. The present approach accounts for the effects of time delays in the response of a cavity to the motion of an object inside of it. Quantitative features of the instabilities are investigated. The experimental conditions required for sample stability, saturation of sample oscillations, hysteretic effects, and the loss of ability to levitate are discussed.

Therapeutic effects of antimicrobial treatment during lactation of recently acquired bovine subclinical mastitis: two linked randomized field trials.

PubMed

van den Borne, B H P; van Schaik, G; Lam, T J G M; Nielen, M

2010-01-01

Two linked randomized field trials were performed on 39 herds in the Netherlands to 1) determine therapeutic effects of antimicrobial treatment of recently acquired subclinical mastitis (RASCM) during lactation, 2) evaluate the effect of duration of subclinical mastitis on therapeutic outcome, and 3) identify factors related to the therapeutic success of RASCM. Cows with a first elevated composite somatic cell count (CSCC) after 2 consecutive low CSCC measurements were eligible for enrollment in trial 1 (treatment at the first elevated CSCC). Quarter milk samples were collected to determine bacteriological status for major pathogens and coagulase-negative staphylococci. Cows with one or more culture-positive quarters with a quarter somatic cell count (QSCC) >or=100,000 cells/mL were defined to have RASCM and were randomly assigned treatment or control (no treatment). Untreated cows from trial 1 that had a second elevated CSCC at the next milk recording were eligible for enrollment in trial 2 (treatment at the second elevated CSCC). In trial 2, staphylococci-positive cows (Staphylococcus aureus and coagulase-negative staphylococci) were randomly assigned to treatment or control. Farmers used their own treatment protocols to treat quarters in both trials. Bacteriological cure was defined as absence of the pathogen identified pre-intervention in 2 samples post-intervention; QSCC, CSCC, and milk yield were also analyzed. Hierarchical logistic and linear models were used to determine therapeutic effects and to identify factors related to therapy outcome. Treated quarters had a higher bacteriological cure rate than control quarters for all pathogens in both trials. Treatment resulted in lower QSCC and CSCC, whereas milk yield was not affected by treatment. Bacteriological cure of RASCM was better in quarters with a low QSCC pre-intervention and in coagulase-negative staphylococci-positive quarters. Control quarters with a single culture-positive sample pre-intervention also had a higher bacteriological cure than control quarters with >or=2 culture-positive samples. Time of antimicrobial treatment affected bacteriological cure for penicillin-sensitive Staph. aureus. Bacteriological cure tended to be higher for Staph. aureus after treatment at the first elevated CSCC compared with treatment at the second elevated CSCC. Thus, early treatment of Staph. aureus might be more effective than later treatment. Copyright 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Detection of Chlamydophila psittaci from feral pigeons in environmental samples: problems with currently available techniques.

PubMed

Geigenfeind, Ila; Haag-Wackernagel, Daniel

2010-03-01

Chlamydophila psittaci (Lillie, 1930) Everett et al., 1999, the pathogenic agent of human ornithosis, is widespread in feral pigeon populations and many cases of transmission from feral pigeons to humans have been reported. The aim of the present study was to detect C. psittaci in environmental samples to find out more about possible transmission routes and, therefore, to assess the zoonotic risk for humans. Fecal samples were collected from nest boxes in a feral pigeon loft. Additionally, samples were taken from the feather dust film covering the water surface of public fountains where pigeons regularly bathe. The samples were tested for the presence of chlamydial antigen using an antigen enzyme-linked immunosorbent assay to prove shedding of C. psittaci by feral pigeons. This test detects a genus specific lipopolysaccharide in the outer membrane of the chlamydial bacteria. Samples were tested using the IDEIA PCE Chlamydia Test kit (DakoCytomation) and positive results were verified with IDEIA Chlamydia Blocking Reagents (DakoCytomation). The IDEIA PCE Chlamydia Test yields a high proportion of positive results. However, when IDEIA Chlamydia Blocking was performed, most of the positive results turned out to be negative or could not be interpreted. We conclude that antigen-enzyme-linked immunosorbent assay tests are not suitable for detecting C. psittaci in environmental samples. Previous publications where no blocking test was used should be reconsidered critically. © 2010 ISZS, Blackwell Publishing and IOZ/CAS.

Importance of sample preparation for molecular diagnosis of lyme borreliosis from urine.

PubMed

Bergmann, A R; Schmidt, B L; Derler, A-M; Aberer, E

2002-12-01

Urine PCR has been used for the diagnosis of Borrelia burgdorferi infection in recent years but has been abandoned because of its low sensitivity and the irreproducibility of the results. Our study aimed to analyze technical details related to sample preparation and detection methods. Crucial for a successful urine PCR were (i) avoidance of the first morning urine sample; (ii) centrifugation at 36,000 x g; and (iii) the extraction method, with only DNAzol of the seven different extraction methods used yielding positive results with patient urine specimens. Furthermore, storage of frozen urine samples at -80 degrees C reduced the sensitivity of a positive urine PCR result obtained with samples from 72 untreated erythema migrans (EM) patients from 85% in the first 3 months to <30% after more than 3 months. Bands were detected at 276 bp on ethidium bromide-stained agarose gels after amplification by a nested PCR. The specificity of bands for 32 of 33 samples was proven by hybridization with a GEN-ETI-K-DEIA kit and for a 10 further positive amplicons by sequencing. By using all of these steps to optimize the urine PCR technique, B. burgdorferi infection could be diagnosed by using urine samples from EM patients with a sensitivity (85%) substantially better than that of serological methods (50%). This improved method could be of future importance as an additional laboratory technique for the diagnosis of unclear, unrecognized borrelia infections and diseases possibly related to Lyme borreliosis.

Antibody detection against Borrelia burgdorferi in horses located in the suburban areas of Monterrey, Nuevo León.

PubMed

Salinas-Mélendez, J A; Galván de la Garza, S; Riojas-Valdés, V M; Wong González, A; Avalos-Ramírez, R

2001-01-01

The aim of the present study was to determine the presence of Borrelia burgdorferi antibodies in horses from the metropolitan area of Monterrey, Nuevo León, México. Blood serum was obtained from a total of 100 horses residing at different counties in the area. From each animal data was obtained on age, sex, county of residence, presence of ectoparasites and clinical signs. All sera samples were analyzed by indirect immunofluoresence and the sera that resulted positive to this test was analyzed by Western blot. The serological test yielded 34 positive sera at 1:64 dilution, and from them 6 were positive at 1:128 dilution, 3 at 1:256, and only one at 1:512. Confirmation of the infection by Western blot was obtained only in the sample positive at the 1:512 dilution. These results shown a low frequency of seropositivity to B. burgdorferi of the horses in the area, confirming previous studies indicating that in northeast Mexico Lyme disease is present in different animal species.

Experimental Investigations on Subsequent Yield Surface of Pure Copper by Single-Sample and Multi-Sample Methods under Various Pre-Deformation.

PubMed

Liu, Gui-Long; Huang, Shi-Hong; Shi, Che-Si; Zeng, Bin; Zhang, Ke-Shi; Zhong, Xian-Ci

2018-02-10

Using copper thin-walled tubular specimens, the subsequent yield surfaces under pre-tension, pre-torsion and pre-combined tension-torsion are measured, where the single-sample and multi-sample methods are applied respectively to determine the yield stresses at specified offset strain. The rule and characteristics of the evolution of the subsequent yield surface are investigated. Under the conditions of different pre-strains, the influence of test point number, test sequence and specified offset strain on the measurement of subsequent yield surface and the concave phenomenon for measured yield surface are studied. Moreover, the feasibility and validity of the two methods are compared. The main conclusions are drawn as follows: (1) For the single or multi-sample method, the measured subsequent yield surfaces are remarkably different from cylindrical yield surfaces proposed by the classical plasticity theory; (2) there are apparent differences between the test results from the two kinds of methods: the multi-sample method is not influenced by the number of test points, test order and the cumulative effect of residual plastic strain resulting from the other test point, while those are very influential in the single-sample method; and (3) the measured subsequent yield surface may appear concave, which can be transformed to convex for single-sample method by changing the test sequence. However, for the multiple-sample method, the concave phenomenon will disappear when a larger offset strain is specified.

Viscosity and medium effects on the fluorescence and photochemical behaviour of some aryl chalcones

NASA Astrophysics Data System (ADS)

Ebeid, El-Zeiny M.; Abdel-Kader, Mahmood H.; Issa, Raafat M.; El-Daly, Samy A.

1988-05-01

The emission, excitation and absorption spectra toghether with the fluorescence and photochemical quantum yields of some chalcone derivatives have been studied in organic solvents and micellar and microemulsion media. Both 4-[2-(2-pyridyl)ethenyl] ( I) and 4-[2-(4-pyridyl)ethenyl ( II) chalcones show large positive solvatochromic effects. The fluorescence quantum yields increase substantially as the medium viscosity increases with a subsequent decrease in the photochemical quatum yield. Compounds I and II undergo excited-state molecular aggregation in concentrated solutions giving excimer-like emission that coincides with emission from crystalline samples. The enthalpies of photoassociation have been estimated. The chalcone derivative I acts as an efficient quencher of the fluorescence of the laser dye 1,4-bis (β-pyridyl-2-vinyl)benzene via a long-range mechanism. The excited-state lifetimes of both I and II are short and at 20°C their τ values are less than 800 ps.

Development and testing of monoclonal antibody-based rapid immunodiagnostic test kits for direct detection of Vibrio cholerae O139 synonym Bengal.

PubMed

Hasan, J A; Huq, A; Nair, G B; Garg, S; Mukhopadhyay, A K; Loomis, L; Bernstein, D; Colwell, R R

1995-11-01

We report on the development and testing of two monoclonal antibody-based rapid immunodiagnostic test kits, BengalScreen, a coagglutination test, and Bengal DFA, a direct fluorescent-antibody test, for direct detection of Vibrio cholerae O139 synonym Bengal in clinical and environmental specimens. The BengalScreen test requires less than 5 min to complete and can be used in the field. Bengal DFA, being more sensitive than BengalScreen, requires only one reagent and less than 20 min for detection and enumeration of V. cholerae O139 synonym Bengal. In tests for specificity, all 40 strains of V. cholerae O139 reacted with both test kits, whereas 157 strains of heterologous species examined did not, yielding 100% specificity in this study. A field trial was conducted in with both BengalScreen and Bengal DFA, and the results were compared with those obtained by conventional culture methods. BengalScreen demonstrated a sensitivity of 95%, a specificity of 100%, a positive predictive value of 100%, and a negative predictive value of 94%. Results obtained by Bengal DFA, on the other hand, were 100% sensitive and 100% specific and yielded 100% positive and negative predictive values compared with culture methods. In a second evaluation, 93 stool specimens from Mexico that were negative for V. cholerae O139 by culture were also tested with both the BengalScreen and Bengal DFA kits. None of the 93 specimens were positive for V. cholerae O139 by both tests. A concentration method was optimized for screening of environmental water samples for V. cholerae O139 synonym Bengal with rapid test kits. BengalScreen results were unequivocally positive when water samples contained at least 2.0 x 10(3) CFU/ml, whereas Bengal DFA demonstrated an unequivocally positive reaction when the water sample contained at least 1.5 x 10(2) CFU/ml. When Bengal DFA was compared with conventional culture methods for enumeration of V. cholerae O139 synonym Bengal organisms, no difference was observed.

Isolation of leptospira Serovars Canicola and Copenhageni from cattle urine in the state of ParanÁ, Brazil

PubMed Central

Zacarias, Francielle Gibson da Silva; Vasconcellos, Silvio Arruda; Anzai, Eleine Kuroki; Giraldi, Nilson; de Freitas, Julio Cesar; Hartskeerl, Rudy

2008-01-01

In 2001, 698 urine samples were randomly collected from cattle at a slaughterhouse in the State of Paraná, Brazil. Direct examination using dark field microscopy was carried out immediately after collection. Five putative positive samples were cultured in modified EMJH medium, yielding two positive cultures (LO-14 and LO-10). Typing with monoclonal antibodies revealed that the two isolates were similar to Canicola (LO-14) and Copenhageni (LO-10). Microscopic agglutination test results show that Hardjo is the most common serovar in cattle in Brazil. Rats and dogs are the common maintenance hosts of serovars Copenhageni and Canicola. The excretion of highly pathogenic serovars such as Copenhageni and Canicola by cattle can represent an increasing risk for severe leptospirosis is large populations, mainly living in rural areas. PMID:24031301

Occurrence and characterization of Campylobacter in the Brazilian production and processing of broilers.

PubMed

Kuana, S L; Santos, L R; Rodrigues, L B; Borsoi, A; Moraes, H L S; Salle, C T P; Nascimento, V P

2008-12-01

Twenty-two commercial broiler flocks and their carcasses, totaling 546 samples (450 collected from a poultry farm and 96 from a slaughterhouse), were surveyed for the presence of Campylobacter. The positive results for Campylobacter among the analyzed samples were homogeneous, yielding 81.8% for cecal droppings, 80.9% for feces, and 80.4% for cloacal swabs. Pre-enrichment and direct plating showed that 77.85% and 81.8% of cloacal swabs, respectively, were positive for Campylobacter compared to 99.0% and 97.9% of carcasses testing positive with the pre-enrichment and direct plating methods. The Campylobacter count averaged 7.0 log10 colony-forming units (CFU)/g in cecal droppings, 5.15 log10 CFU/carcass after defeathering, and 4.24 log10 CFU/carcass after chilling. The samples were identified by the API Campy system as Campylobacter jejuni subsp. jejuni (68.8%), Campylobacter coli (8.3%), Campylobacter jejuni subsp. doylei (6.3%), Campylobacter upsaliensis (4.2%), and Campylobacter fetus subsp. fetus (2.1%). The analyzed broiler flocks were positive for Campylobacter in 81.8% of the cases, thus characterizing the occurrence of this pathogen in a broiler-producing region in southern Brazil. These results highlight the importance of programs targeted at the reduction of Campylobacter in poultry products, in order to minimize the risks for consumers.

The unexpected discovery of Brucella abortus Buck 19 vaccine in goats from Ecuador underlines the importance of biosecurity measures.

PubMed

Ron-Román, Jorge; Berkvens, Dirk; Barzallo-Rivadeneira, Daniela; Angulo-Cruz, Alexandra; González-Andrade, Pablo; Minda-Aluisa, Elizabeth; Benítez-Ortíz, Washington; Brandt, Jef; Rodríguez-Hidalgo, Richar; Saegerman, Claude

2017-03-01

Very few, mostly old, and only preliminary serological studies of brucellosis in goats exist in Ecuador. In order to assess the current epidemiological situation, we performed a cross-sectional serological study in the goat populations of Carchi (n = 160 animals), Pichincha (n = 224 animals), and Loja provinces (n = 2024 animals). Only two positive serological results (RB negative and SAT-EDTA ≥400 IU/ml) were obtained in lactating goats from the same farm in Quito (Pichincha province). Additionally, milk was sampled from 220 animals in Pichincha province. The present study indicates a low apparent prevalence in Pichincha province and absence in Carchi and Loja provinces. A total of 25 positive milk ring tests (MRT) were obtained in Pichincha province yielding a prevalence of MRT of 11.16%. Subsequent culture was performed on the positive MRT samples. All results were negative, apart from a single sample, obtained from a serologically positive goat in Quito, that was positive for Brucella abortus strain 19 (B19). Several hypotheses are forwarded concerning this unexpected result. The most likely hypothesis is the possible accidental use of a needle, previously used for vaccination of cattle with the said vaccine, for the administration of drug treatment to the goat. This hypothesis underlines the necessity of biosecurity measures to prevent this type of accidents.

Evaluation of the performance of Human Papillomavirus testing in paired urine and clinician-collected cervical samples among women aged over 30 years in Bhutan.

PubMed

Tshomo, Ugyen; Franceschi, Silvia; Tshokey, Tshokey; Tobgay, Tashi; Baussano, Iacopo; Tenet, Vanessa; Snijders, Peter J F; Gheit, Tarik; Tommasino, Massimo; Vorsters, Alex; Clifford, Gary M

2017-04-08

Urine sampling may offer a less invasive solution than cervical sampling to test for human papillomavirus (HPV) for HPV vaccine impact monitoring. Paired samples of urine and exfoliated cervical cells were obtained for 89 women with history of high-risk (HR) HPV-positive normal cytology in Bhutan. Urine sampling protocol included self-collection of first-void urine immediately into a conservation medium and procedures to optimize DNA yield. Colposcopical abnormalities were biopsied. Two HPV assays were used: a multiplex type-specific PCR (E7-MPG) and a less analytically sensitive GP5+/6+ PCR followed by reverse line blot. HPV positivity for 21 types common to both assays was similar in urine and cells by E7-MPG (62.9% and 57.3%, respectively, p = 0.32) but lower in urine by GP5+/6+ (30.3% and 40.4%, p = 0.05). HPV6/11/16/18 positivity did not significantly differ between urine and cells by either assay. Sensitivity of urine (using cells as gold standard) to detect 21 HPV types was 80% and 58% for E7-MPG and GP5+/6+, respectively, with specificity 61% and 89%. HPV type distribution in urine and cells was similar, regardless of assay. The 5 detected CIN3+ were HR-HPV positive in cells by both assays, compared to 4 and 3 by E7-MPG and GP5+/6+, respectively, in urine samples. For the monitoring of vaccine impact, we demonstrate validity of a urine sampling protocol to obtain HPV prevalence data that are broadly comparable to that from cervical cells. However, detection of HPV in urine varies according to assay sensitivity, presumably because low level infections are frequent.

Brief Report: High Sensitivity and Specificity of the Cepheid Xpert HIV-1 Qualitative Point-of-Care Test Among Newborns in Botswana.

PubMed

Ibrahim, Maryanne; Moyo, Sikhulile; Mohammed, Terence; Mupfumi, Lucy; Gaseitsiwe, Simani; Maswabi, Kenneth; Ajibola, Gbolahan; Gelman, Rebecca; Batlang, Oganne; Sakoi, Maureen; Auletta-Young, Chloe; Makhema, Joseph; Lockman, Shahin; Shapiro, Roger L

2017-08-15

HIV point-of-care (POC) testing allows for early infant HIV diagnosis and treatment, but POC accuracy at birth and in the setting of antiretroviral prophylaxis for the prevention of mother-to-child HIV transmission is unknown. We evaluated the Cepheid Xpert HIV-1 Qual POC test against the Roche Taqman HIV-1 DNA polymerase chain reaction (PCR) platform using dried blood spots from 15 HIV-infected and 75 HIV-exposed uninfected newborns. These infants were screened for HIV at <96 hours of life at 5 hospital maternity wards in Botswana; all infants received postexposure antiretroviral prophylaxis with single-dose nevirapine and zidovudine, and most mothers received 3-drug antiretroviral therapy in pregnancy and at delivery. Fourteen of the 15 PCR positive samples tested positive by Cepheid POC, yielding a sensitivity of 93.3% (95% confidence interval: 68.1 to 99.8). Baseline viral load among positive infants ranged from <40 to >10,000,000 copies/mL, with a median of 2403 copies/mL. The HIV RNA for the infant with false-negative POC testing was 1661 copies/mL. Of note, 2 infants with low HIV RNA (<40 and 272 copies/mL) were correctly identified as HIV positive by Cepheid POC. All the 75 PCR-negative samples tested negative by Cepheid POC, yielding a specificity of 100% (95% confidence interval: 96.1 to 100). Our study demonstrates high sensitivity and specificity for the Cepheid POC assay in the first week of life despite early infection and antiretroviral prophylaxis. This platform may be a useful approach for adding early infant HIV diagnosis to current testing programs.

The Effect of Alcohol-Based Hand Sanitizer Vapors on Evidential Breath Alcohol Test Results.

PubMed

Strawsine, Ellen; Lutmer, Brian

2017-11-16

This study was undertaken to determine if the application of alcohol-based hand sanitizers (ABHSs) to the hands of a breath test operator will affect the results obtained on evidential breath alcohol instruments (EBTs). This study obtained breath samples on three different EBTs immediately after application of either gel or foam ABHS to the operator's hands. A small, but significant, number of initial analyses (13 of 130, 10%) resulted in positive breath alcohol concentrations, while 41 samples (31.5%) resulted in a status code. These status codes were caused by ethanol vapors either in the room air or their inhalation by the subject, thereby causing a mouth alcohol effect. Replicate subject samples did not yield any consecutive positive numeric results. As ABHS application can cause a transitory mouth alcohol effect via inhalation of ABHS vapors, EBT operators should forego the use of ABHS in the 15 min preceding subject testing. © 2017 American Academy of Forensic Sciences.

Utility of galactomannan antigen detection in bronchoalveolar lavage fluid in immunocompromised patients.

PubMed

Brownback, Kyle R; Pitts, Lucas R; Simpson, Steven Q

2013-09-01

Diagnosis of invasive pulmonary aspergillosis (IPA) is a challenging process in immunocompromised patients. Galactomannan (GM) antigen detection in bronchoalveolar lavage (BAL) fluid is a method to detect IPA with improved sensitivity over conventional studies. We sought to determine the diagnostic yield of BAL GM assay in a diverse population of immunocompromised patients. A retrospective review of 150 fiberoptic bronchoscopy (FOB) with BAL for newly diagnosed pulmonary infiltrate in immunocompromised patients was performed. Patient information, procedural details and laboratory studies were collected. BAL and serum samples were evaluated for GM using enzyme-linked immunoassay. Of 150 separate FOB with BAL, BAL GM was obtained in 143 samples. There were 31 positive BAL GM assays. In those 31 positive tests, 13 were confirmed as IPA, giving a positive predictive value of 41.9%. There was one false negative BAL GM. Of the 18 false positive BAL GM, 4 were receiving piperacillin-tazobactam and 11 were receiving an alternative beta-lactam antibiotic. BAL GM assay shows excellent sensitivity for diagnosing IPA. There was a significant number of false positive BAL GM assays and several of those patients were receiving beta-lactam antibiotics at the time of bronchoscopy. © 2013 Blackwell Verlag GmbH.

Comparative impacts of stormwater runoff on water quality of an urban, a suburban, and a rural stream.

PubMed

Mallin, Michael A; Johnson, Virginia L; Ensign, Scott H

2009-12-01

Water quality data at 12 sites within an urban, a suburban, and a rural stream were collected contemporaneously during four wet and eight dry periods. The urban stream yielded the highest biochemical oxygen demand (BOD), orthophosphate, total suspended sediment (TSS), and surfactant concentrations, while the most rural stream yielded the highest total organic carbon concentrations. Percent watershed development and percent impervious surface coverage were strongly correlated with BOD (biochemical oxygen demand), orthophosphate, and surfactant concentrations but negatively with total organic carbon. Excessive fecal coliform abundance most frequently occurred in the most urbanized catchments. Fecal coliform bacteria, TSS, turbidity, orthophosphate, total phosphorus, and BOD were significantly higher during rain events compared to nonrain periods. Total rainfall preceding sampling was positively correlated with turbidity, TSS, BOD, total phosphorus, and fecal coliform bacteria concentrations. Turbidity and TSS were positively correlated with phosphorus, fecal coliform bacteria, BOD, and chlorophyll a, which argues for better sedimentation controls under all landscape types.

Identification of cancer stem cell markers in human malignant mesothelioma cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghani, Farhana Ishrat; Yamazaki, Hiroto; Iwata, Satoshi

2011-01-14

Research highlights: {yields} We performed serial transplantation of surgical samples and established new cell lines of malignant mesothelioma. {yields} SP cell and expressions of CD9/CD24/CD26 were often observed in mesothelioma cell lines. {yields} SP and CD24{sup +} cells proliferated by asymmetric cell division-like manner. CD9{sup +} and CD24{sup +} cells have higher potential to generate spheroid colony. {yields} The marker-positive cells have clear tendency to generate larger tumors in mice. -- Abstract: Malignant mesothelioma (MM) is an aggressive and therapy-resistant neoplasm arising from the pleural mesothelial cells and usually associated with long-term asbestos exposure. Recent studies suggest that tumors containmore » cancer stem cells (CSCs) and their stem cell characteristics are thought to confer therapy-resistance. However, whether MM cell has any stem cell characteristics is not known. To understand the molecular basis of MM, we first performed serial transplantation of surgical samples into NOD/SCID mice and established new cell lines. Next, we performed marker analysis of the MM cell lines and found that many of them contain SP cells and expressed several putative CSC markers such as CD9, CD24, and CD26. Interestingly, expression of CD26 closely correlated with that of CD24 in some cases. Sorting and culture assay revealed that SP and CD24{sup +} cells proliferated by asymmetric cell division-like manner. In addition, CD9{sup +} and CD24{sup +} cells have higher potential to generate spheroid colony than negative cells in the stem cell medium. Moreover, these marker-positive cells have clear tendency to generate larger tumors in mouse transplantation assay. Taken together, our data suggest that SP, CD9, CD24, and CD26 are CSC markers of MM and could be used as novel therapeutic targets.« less

Validation of a Seven-Factor Structure for the Motives for Playing Drinking Games Measure.

PubMed

Zamboanga, Byron L; Audley, Shannon; Olthuis, Janine V; Blumenthal, Heidemarie; Tomaso, Cara C; Bui, Ngoc; Borsari, Brian

2017-04-01

Playing drinking games can be characterized as a high-risk drinking activity because games are typically designed to promote heavy alcohol consumption. While research suggests that young adults are motivated to play drinking games for a variety of reasons (e.g., for thrills/fun, for the competition), the Motives for Playing Drinking Games measure has received limited empirical attention. We examined the psychometric properties of this measure with a confirmation sample of young adults recruited from Amazon's MTurk ( N = 1,809, ages 18-25 years, 47% men; 41% not currently enrolled in college) and a validation sample of college students ( N = 671; ages 18-23 years; 26% men). Contrary to the 8-factor model obtained by Johnson and Sheets in a study published in 2004, examination of the factor structure with our confirmation sample yielded a revised 7-factor model that was invariant across race/ethnicity and college student status. This model was also validated with the college student sample. In the confirmation sample, enhancement/thrills and sexual pursuit motives for playing drinking games were positively associated with gaming frequency/consumption and negative gaming consequences. Furthermore, conformity motives for playing drinking games were positively associated with negative gaming consequences, while competition motives were positively associated with gaming frequency. These findings have significant implications for research and prevention/intervention efforts.

Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins.

PubMed

Pang, Yuan-Ping

2016-09-01

Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2-9 ± 1 Å 2 for Cα and 7.3 ± 0.9-9.6 ± 0.2 Å 2 for Cγ, when the sampling was done for each of these proteins over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations with AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive to a priori prediction of crystallographic B-factors of a folded globular protein.

Evaluation of PMS-PCR technology for detection of Mycobacterium avium subsp. paratuberculosis directly from bovine fecal specimens.

PubMed

Salgado, M; Steuer, P; Troncoso, E; Collins, M T

2013-12-27

Mycobacterium avium subsp. paratuberculosis (MAP) causes paratuberculosis, or Johne's disease, in animals. Diagnosis of MAP infection is challenging because of the pathogen's fastidious in vitro growth requirements and low-level intermittent shedding in feces during the preclinical phase of the infection. Detection of these "low-shedders" is important for effective control of paratuberculosis as these animals serve as sources of infection for susceptible calves. Magnetic separation technology, used in combination with culture or molecular methods for the isolation and detection of pathogenic bacteria, enhances the analytical sensitivity and specificity of detection methods. The aim of the present study was to evaluate peptide-mediated magnetic separation (PMS) capture technology coupled with IS900 PCR using the Roche real-time PCR system (PMS-PCR), in comparison with fecal culture using BACTEC-MGIT 960 system, for detection of MAP in bovine fecal samples. Among the 351 fecal samples 74.9% (263/351) were PMS-PCR positive while only 12.3% (43/351) were MGIT culture-positive (p=0.0001). All 43 MGIT culture-positive samples were also positive by PMS-PCR. Mean PMS-PCR crossing-point (Cp) values for the 13 fecal samples with the highest number of MAP, based on time to detection, (26.3) were significantly lower than for the 17 fecal samples with <100 MAP per 2g feces (30.06) (p<0.05). PMS-PCR technology provided results in a shorter time and yielded a higher number of positive results than MGIT culture. Earlier and faster detection of animals shedding MAP by PMS-PCR should significantly strengthen control efforts for MAP-infected cattle herds by helping to limit infection transmission at earlier stages of the infection. Copyright © 2013 Elsevier B.V. All rights reserved.

Novel and classical human astroviruses in stool and cerebrospinal fluid: comprehensive screening in a tertiary care hospital, Switzerland.

PubMed

Cordey, Samuel; Vu, Diem-Lan; Zanella, Marie-Celine; Turin, Lara; Mamin, Aline; Kaiser, Laurent

2017-09-20

Classical human astroviruses (HAstV) are the third most common cause of non-bacterial acute gastroenteritis. Due to the lack of routine molecular assays, novel HAstV are underdiagnosed and the magnitude of their contribution to clinical disease remains unknown. To better understand their prevalence and the susceptible patient profile, we conducted a comprehensive screening of novel and classical HAstV in stool and cerebrospinal fluid (CSF) samples collected for clinical care in a tertiary care hospital using a specially designed rRT-PCR panel for the detection of novel (MLB1-3 and VA1-4) and classical HAstV. Of the 654 stool samples, 20 were positive for HAstV, and the novel (n=10; 3 MLB1, 4 MLB2; 3 VA2) and classical (n=10) serotypes were equally prevalent. None of the 105 CSF samples were positive. Investigating the patient profile, we found a higher prevalence (P=0.0002) of both novel and classical HAstV in pediatric stool samples (3.4% and 3%, respectively) compared with adult stool samples (0.5% and 0.7%, respectively). Furthermore, all novel and classical HAstV-positive pediatric subjects were ≤four years old, demonstrating similar susceptible populations. Forty-five percent of positive patients were immunocompromised (novel: 40%, classical: 50%). A comparison of novel and classical HAstV-positive cases showed a lower viral load for novel HAstV (P=0.0007) with significantly more upper respiratory symptoms (70% of subjects; P=0.02); this observation may suggest a unique pathogenic pathway. This study confirms the clinical and epidemiological relevance of novel HAstV and identifies a target population in which routine screening may yield clinically valuable information.

[Determination of the survival of Trypanosoma evansi in equine blood, using the microhematocrit method].

PubMed

Monzón, C M; Jara, G A; Hoyos, C B

1995-09-01

The microhaematocrit (MH) technique was used to study the survival of Trypanosoma evansi in blood from two herds of naturally-infected horses. A comparison was made between samples treated with ethylenediaminetetraacetic acid and sodium citrate (alone or with 1% glucose), and sent to the laboratory packed in ice. In general, the number of samples yielding positive results by the MH technique showed the least variation during the first 24-36 h after sample collection. Survival varied with the anticoagulant used, but it declined rapidly from 48 h after collection, although live parasites were still observed in up to 10% of samples until the seventh day. On the basis of the results obtained, the authors recommend the use of sodium citrate in treating equine blood samples for the parasitological diagnosis of T. evansi.

Evaluation of OMNIgene®•SPUTUM-stabilised sputum for long-term transport and Xpert® MTB/RIF testing in Nepal.

PubMed

Maharjan, B; Kelly-Cirino, C D; Weirich, A; Curry, P S; Hoffman, H; Avsar, K; Shrestha, B

2016-12-01

German Nepal TB Project, National Tuberculosis Reference Laboratory, Kathmandu, Nepal. To evaluate whether transporting samples in OMNIgene®•SPUTUM (OM-S) reagent from a peripheral collection site to a central laboratory in Nepal can improve tuberculosis (TB) detection and increase the sensitivity of Xpert® MTB/RIF testing. One hundred sputum samples were split manually. Each portion was assigned to the OM-S group (OM-S added at collection, airline-couriered without cold chain, no other processing required) or the standard-of-care (SOC) group (samples airline-couriered on ice, sodium hydroxide + N-acetyl-L-cysteine processing required at the laboratory). Smear microscopy and Xpert testing were performed. Transport time was 2-13 days. Overall smear results were comparable (respectively 58% and 56% smear-negative results in the OM-S and SOC groups). The rate of smear-positive, Mycobacterium tuberculosis-positive (MTB+) sample detection was identical for both treatment groups, at 95%. More smear-negative MTB+ samples were detected in the OM-S group (17% vs. 13%, P = 0.0655). Sputum samples treated with OM-S can undergo multiday ambient-temperature transport and yield comparable smear and Xpert results to those of SOC samples. Further investigation with larger sample sizes is required to assess whether treating sputum samples with OM-S could increase the sensitivity of Xpert testing in smear-negative samples.

Electromagnetic Navigation Diagnostic Bronchoscopy

PubMed Central

Gildea, Thomas R.; Mazzone, Peter J.; Karnak, Demet; Meziane, Moulay; Mehta, Atul C.

2006-01-01

Rationale: Electromagnetic navigation bronchoscopy using superDimension/Bronchus System is a novel method to increase diagnostic yield of peripheral and mediastinal lung lesions. Objectives: A prospective, open label, single-center, pilot study was conducted to determine the ability of electromagnetic navigation bronchoscopy to sample peripheral lung lesions and mediastinal lymph nodes with standard bronchoscopic instruments and demonstrate safety. Methods: Electromagnetic navigation bronchoscopy was performed using the superDimension/Bronchus system consisting of electromagnetic board, position sensor encapsulated in the tip of a steerable probe, extended working channel, and real-time reconstruction of previously acquired multiplanar computed tomography images. The final distance of the steerable probe to lesion, expected error based on the actual and virtual markers, and procedure yield was gathered. Measurements: 60 subjects were enrolled between December 2004 and September 2005. Mean navigation times were 7 ± 6 min and 2 ± 2 min for peripheral lesions and lymph nodes, respectively. The steerable probe tip was navigated to the target lung area in all cases. The mean peripheral lesions and lymph nodes size was 22.8 ± 12.6 mm and 28.1 ± 12.8 mm. Yield was determined by results obtained during the bronchoscopy per patient. Results: The yield/procedure was 74% and 100% for peripheral lesions and lymph nodes, respectively. A diagnosis was obtained in 80.3% of bronchoscopic procedures. A definitive diagnosis of lung malignancy was made in 74.4% of subjects. Pneumothorax occurred in two subjects. Conclusion: Electromagnetic navigation bronchoscopy is a safe method for sampling peripheral and mediastinal lesions with high diagnostic yield independent of lesion size and location. PMID:16873767

Mobile chemical detector (AP2C+SP4E) as an aid for medical decision making in the battlefield.

PubMed

Eisenkraft, Arik; Markel, Gal; Simovich, Shirley; Layish, Ido; Hoffman, Azik; Finkelstein, Arseny; Rotman, Eran; Dushnitsky, Tsvika; Krivoy, Amir

2007-09-01

The combination of the AP2C unit with the SP4E kit composes a lightweight mobile detector of chemical warfare agents (CWA), such as nerve and mustard agents, with both vapor- and liquid-sampling capabilities. This apparatus was recently introduced into our military medical units as an aid for detection of CWA on casualties. Importantly, critical information regarding the applicability in the battlefield was absent. In view of the serious consequences that might follow a proclamation of CWA recognition in battlefield, a high false-positive rate positions the utilization of this apparatus as a medical decision tool in question. We have therefore conducted a field experiment to test the false-positive rate as well as analyze possible factors leading to false-positive readings with this device. The experiment was carried out before and after a 4-day army field exercise, using a standard AP2C device, a SP4E surface sampling kit, and a specially designed medical sampling kit for casualties, intended for medical teams. Soldiers were examined at rest, after mild exercise, and after 4 days in the field. The readings with AP2C alone were compared to the combination of AP2C and SP4E and to the medical sampling kit. Various body fluids served as negative controls. Remarkably, we found a false-positive rate of 57% at rest and after mild exercise, and an even higher rate of 64% after the 4-day field exercise with the AP2C detector alone, as compared to almost no false-positive readings with the combination of AP2C and SP4E. Strikingly, the medical sampling kit has yielded numerous false-positive readings, even in normal body fluids such as blood, urine, and saliva. We therefore see no place for using the medical sampling kit due to an unaccepted high rate of false-positive readings. Finally, we have designed an algorithm that uses the entire apparatus of AP2C and SP4E as a reliable validation tool for medical triage in the setting of exposure to nerve agents in the battlefield.

Mycobiome of the bat white nose syndrome affected caves and mines reveals diversity of fungi and local adaptation by the fungal pathogen Pseudogymnoascus (Geomyces) destructans.

PubMed

Zhang, Tao; Victor, Tanya R; Rajkumar, Sunanda S; Li, Xiaojiang; Okoniewski, Joseph C; Hicks, Alan C; Davis, April D; Broussard, Kelly; LaDeau, Shannon L; Chaturvedi, Sudha; Chaturvedi, Vishnu

2014-01-01

Current investigations of bat White Nose Syndrome (WNS) and the causative fungus Pseudogymnoascus (Geomyces) destructans (Pd) are intensely focused on the reasons for the appearance of the disease in the Northeast and its rapid spread in the US and Canada. Urgent steps are still needed for the mitigation or control of Pd to save bats. We hypothesized that a focus on fungal community would advance the understanding of ecology and ecosystem processes that are crucial in the disease transmission cycle. This study was conducted in 2010-2011 in New York and Vermont using 90 samples from four mines and two caves situated within the epicenter of WNS. We used culture-dependent (CD) and culture-independent (CI) methods to catalogue all fungi ('mycobiome'). CD methods included fungal isolations followed by phenotypic and molecular identifications. CI methods included amplification of DNA extracted from environmental samples with universal fungal primers followed by cloning and sequencing. CD methods yielded 675 fungal isolates and CI method yielded 594 fungal environmental nucleic acid sequences (FENAS). The core mycobiome of WNS comprised of 136 operational taxonomic units (OTUs) recovered in culture and 248 OTUs recovered in clone libraries. The fungal community was diverse across the sites, although a subgroup of dominant cosmopolitan fungi was present. The frequent recovery of Pd (18% of samples positive by culture) even in the presence of dominant, cosmopolitan fungal genera suggests some level of local adaptation in WNS-afflicted habitats, while the extensive distribution of Pd (48% of samples positive by real-time PCR) suggests an active reservoir of the pathogen at these sites. These findings underscore the need for integrated disease control measures that target both bats and Pd in the hibernacula for the control of WNS.

Prospective evaluation of SeptiFast Multiplex PCR in children with systemic inflammatory response syndrome under antibiotic treatment.

PubMed

Gies, Franziska; Tschiedel, Eva; Felderhoff-Müser, Ursula; Rath, Peter-Michael; Steinmann, Joerg; Dohna-Schwake, Christian

2016-08-08

Antimicrobially pre-treated children with systemic inflammation often pose a diagnostic challenge to the physician. We aimed to evaluate the additional use of SeptiFast multiplex polymerase chain reaction (PCR) to identify causative pathogens in children with suspected systemic bacterial or fungal infection. Prospective observational study in 39 children with systemic inflammatory response syndrome (SIRS) under empiric antibiotic treatment. Primary outcome was the rate of positive blood cultures (BC), compared to the rate of positive SeptiFast (SF) results. In total, 14 SF-samples yielded positive results, compared to 4 positive BC (p < 0.05). All blood cultures and 13 of 14 positive SF-tests were considered infection. Median time for positive BC was 2 days, and time to definite result was 6 days, compared to 12 h for SF. Antimicrobial therapy was adapted in 7 of the 14 patients with positive SeptiFast, and in 3 of the 4 patients with positive BC. Best predictive power for positive SF shown by receiver-operating characteristic was demonstrated for procalcitonin PCT (Area under the curve AUC: 0.79), compared to C-reactive protein CRP (AUC: 0.51) and leukocyte count (AUC: 0.46). A procalcitonin threshold of 0.89 ng/ml yielded a sensitivity of 0.82 and a specifity of 0.7. Children with a positive SeptiFast result on day 0 had a significantly higher risk to require treatment on the Pediatric Intensive Care Unit or to be deceased on day 30 (Odds-Ratio 8.62 (CI 1.44-51.72). The additional testing with SeptiFast in antimicrobially pre-treated children with systemic inflammation enhances the rate of pathogen detection. The influence of multiplex PCR on clinically relevant outcome parameters has to be further evaluated. ( DRKS00004694).

Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

PubMed Central

Browning, Brian L.; Yu, Zhaoxia

2009-01-01

We present a novel method for simultaneous genotype calling and haplotype-phase inference. Our method employs the computationally efficient BEAGLE haplotype-frequency model, which can be applied to large-scale studies with millions of markers and thousands of samples. We compare genotype calls made with our method to genotype calls made with the BIRDSEED, CHIAMO, GenCall, and ILLUMINUS genotype-calling methods, using genotype data from the Illumina 550K and Affymetrix 500K arrays. We show that our method has higher genotype-call accuracy and yields fewer uncalled genotypes than competing methods. We perform single-marker analysis of data from the Wellcome Trust Case Control Consortium bipolar disorder and type 2 diabetes studies. For bipolar disorder, the genotype calls in the original study yield 25 markers with apparent false-positive association with bipolar disorder at a p < 10−7 significance level, whereas genotype calls made with our method yield no associated markers at this significance threshold. Conversely, for markers with replicated association with type 2 diabetes, there is good concordance between genotype calls used in the original study and calls made by our method. Results from single-marker and haplotypic analysis of our method's genotype calls for the bipolar disorder study indicate that our method is highly effective at eliminating genotyping artifacts that cause false-positive associations in genome-wide association studies. Our new genotype-calling methods are implemented in the BEAGLE and BEAGLECALL software packages. PMID:19931040

Understanding the Changes in Global Crop Yields Through Changes in Climate and Technology

NASA Astrophysics Data System (ADS)

Najafi, Ehsan; Devineni, Naresh; Khanbilvardi, Reza M.; Kogan, Felix

2018-03-01

During the last few decades, the global agricultural production has risen and technology enhancement is still contributing to yield growth. However, population growth, water crisis, deforestation, and climate change threaten the global food security. An understanding of the variables that caused past changes in crop yields can help improve future crop prediction models. In this article, we present a comprehensive global analysis of the changes in the crop yields and how they relate to different large-scale and regional climate variables, climate change variables and technology in a unified framework. A new multilevel model for yield prediction at the country level is developed and demonstrated. The structural relationships between average yield and climate attributes as well as trends are estimated simultaneously. All countries are modeled in a single multilevel model with partial pooling to automatically group and reduce estimation uncertainties. El Niño-southern oscillation (ENSO), Palmer drought severity index (PDSI), geopotential height anomalies (GPH), historical carbon dioxide (CO2) concentration and country-based time series of GDP per capita as an approximation of technology measurement are used as predictors to estimate annual agricultural crop yields for each country from 1961 to 2013. Results indicate that these variables can explain the variability in historical crop yields for most of the countries and the model performs well under out-of-sample verifications. While some countries were not generally affected by climatic factors, PDSI and GPH acted both positively and negatively in different regions for crop yields in many countries.

Surface topography of 1€ coin measured by stereo-PIXE

NASA Astrophysics Data System (ADS)

Gholami-Hatam, E.; Lamehi-Rachti, M.; Vavpetič, P.; Grlj, N.; Pelicon, P.

2013-07-01

We demonstrate the stereo-PIXE method by measurement of surface topography of the relief details on 1€ coin. Two X-ray elemental maps were simultaneously recorded by two X-ray detectors positioned at the left and the right side of the proton microbeam. The asymmetry of the yields in the pixels of the two X-ray maps occurs due to different photon attenuation on the exit travel path of the characteristic X-rays from the point of emission through the sample into the X-ray detectors. In order to calibrate the inclination angle with respect to the X-ray asymmetry, a flat inclined surface model was at first applied for the sample in which the matrix composition and the depth elemental concentration profile is known. After that, the yield asymmetry in each image pixel was transferred into corresponding local inclination angle using calculated dependence of the asymmetry on the surface inclination. Finally, the quantitative topography profile was revealed by integrating the local inclination angle over the lateral displacement of the probing beam.

Questionnaire of core beliefs related to drug use and craving for assessment of relapse risk.

PubMed

Martínez-González, José Miguel; Vilar López, Raquel; Lozano-Rojas, Oscar; Verdejo-García, Antonio

2017-07-12

This study was aimed at designing a questionnaire for the assessment of addiction-related core beliefs and craving. The sample comprised 215 patients (85.8% males and 14.2% females) in treatment for dependence to alcohol (40%), cocaine (36.3%) and cannabis (23.7%). Descriptive statistics were used to characterize the sample. Variance, regression and factorial analyses were conducted to study the questionnaire structure and its relation with variables such as abstinence and craving. Items about drug-related beliefs yielded a four-factor structure: what patient think that they could not do without drug use, lack of withdrawal, conditions required to use drugs again, and use of drugs as the only way to feel good. Items related to craving yielded three factors: negative emotions as precipitants of drug use, positive emotions, and difficulties attributed to coping with craving. Furthermore, beliefs were more important to predict craving than abstinence time. The present questionnaire allows to assess a set of significant factors to design prevention relapse programs.

Evaluation of Procedures for Isolation of Nontuberculous Mycobacteria from Soil and Water

PubMed Central

Kamala, T.; Paramasivan, C. N.; Herbert, Daniel; Venkatesan, P.; Prabhakar, R.

1994-01-01

Six methods of decontamination each for the isolation of mycobacteria from soil and water were compared. On the basis of the results obtained, three of the six methods for soil and two of the six methods for water were further evaluated. For both soil and water samples, the method using 3% sodium lauryl sulfate in combination with 1% NaOH yielded more positives than the other methods. PMID:16349208

High prevalence of Legionella in non-passenger merchant vessels.

PubMed

Collins, S L; Stevenson, D; Mentasti, M; Shaw, A; Johnson, A; Crossley, L; Willis, C

2017-03-01

There is a paucity of information on the risk from potable water in non-passenger merchant vessels (NPMVs) particularly with regard to Legionella and other bacteria. This retrospective study examined water samples from 550 NPMVs docked in eight UK ports. A total of 1027 samples from 412 NPMVs were examined for total aerobic colony counts (ACC), coliforms, Escherichia coli and enterococci; 41% of samples yielded ACC above the action level (>1 × 103 c.f.u./ml) and 4·5% contained actionable levels (>1 c.f.u./100 ml) of faecal indicator bacteria. Eight hundred and three samples from 360 NPMVs were cultured specifically for Legionella and 58% of vessels proved positive for these organisms with 27% of samples showing levels greater than the UK upper action limit of 1 × 103 c.f.u./l. Cabin showers (49%) and hospital shower (45%) were frequently positive. A subset of 106 samples was analysed by quantitative polymerase chain reaction for Legionella and identified a further 11 Legionella-positive NPMVs, returning a negative predictive value of 100%. There was no correlation between NPMV age or size and any microbial parameters (P > 0·05). Legionella pneumophila serogroup 1 was isolated from 46% of NPMVs and sequence-based typing of 17 isolates revealed four sequence types (STs) previously associated with human disease. These data raise significant concerns regarding the management of microbial and Legionella risks on board NPMVs and suggest that better guidance and compliance are required to improve control.

Highly sensitive and specific detection of Giardia duodenalis, Entamoeba histolytica, and Cryptosporidium spp. in human stool samples by the BD MAX™ Enteric Parasite Panel.

PubMed

Parčina, Marijo; Reiter-Owona, Ingrid; Mockenhaupt, Frank P; Vojvoda, Valerija; Gahutu, Jean Bosco; Hoerauf, Achim; Ignatius, Ralf

2018-02-01

Detection of intestinal protozoan parasites by light microscopy is cumbersome, needs experienced personnel, and may lack sensitivity and/or specificity as compared with molecular-based stool assays. Here, we evaluated the BD MAX™ Enteric Parasite Panel, i.e., a multiplex real-time PCR assay for simultaneous detection of Giardia duodenalis, Entamoeba histolytica, and cryptosporidia (Cryptosporidium parvum and C. hominis), by examining 200 positive human stool samples (138 × G. duodenalis, 27 × E. histolytica, 35 × Cryptosporidium spp.) and 119 controls including 18 samples with E. dispar. The majority of the samples, i.e., 153/200 (76.5%) positive samples and 66/119 (55.5%) controls, were confirmed by multiplex in-house PCR detecting the same parasites as the BD MAX™ Enteric Parasite Panel. The BD MAX™ assay did not yield false-positive results. Sensitivity and specificity were 97.8% (95% CI, 93.3-99.4%) and 100% (95% CI, 97.4-100%) for G. duodenalis, 100% (95% CI, 84.5-100%) and 100% (95% CI, 98.4-100%) for E. histolytica, and 100% (95% CI, 87.7-100%) and 100% (95% CI, 98.3-100%) for cryptosporidia, and similar data were obtained when only the 219 PCR-confirmed samples were analyzed. Thus, the BD MAX™ Enteric Parasite Panel provides a highly sensitive and specific tool for the laboratory diagnosis of three predominant protozoan parasites causing enteritis.

Yield of Echocardiogram and Predictors of Positive Yield in Pediatric Patients: A Study in an Urban, Community-Based Outpatient Pediatric Cardiology Clinic.

PubMed

Billa, Ramya Deepthi; Szpunar, Susan; Zeinali, Lida; Anne, Premchand

2018-01-01

The yield of outpatient echocardiograms varies based on the indication for the echocardiogram and the age of the patient. The purpose of this study was to determine the cumulative yield of outpatient echocardiograms by age group and reason for the test. A secondary aim was to determine the predictors of a positive echocardiogram in an outpatient cardiology clinic at a large community teaching hospital. We retrospectively reviewed the charts of 891 patients who had a first-time echocardiogram between 2011 and 2015. Positive yield was defined as echocardiographic findings that explained the reason for the echocardiogram. The overall positive yield was 8.2%. Children between birth and 3 months of age had the highest yield (34.2%), and children between 12 and 18 years of age had the lowest yield (1%). Patients with murmurs (18.1%) had the highest yield compared with patients with other signs or symptoms. By age group and reason, the highest yields were as follows: 0 to 3 months of age, murmur (39.2%); 4 to 11 months of age, >1 symptom (50%); and 1 to 5 years of age, shortness of breath (66.7%). Based on our study, the overall yield of echocardiograms in the outpatient pediatric setting is low. Age and symptoms should be considered before ordering an echocardiogram.

Finding needles in a haystack: a methodology for identifying and sampling community-based youth smoking cessation programs.

PubMed

Emery, Sherry; Lee, Jungwha; Curry, Susan J; Johnson, Tim; Sporer, Amy K; Mermelstein, Robin; Flay, Brian; Warnecke, Richard

2010-02-01

Surveys of community-based programs are difficult to conduct when there is virtually no information about the number or locations of the programs of interest. This article describes the methodology used by the Helping Young Smokers Quit (HYSQ) initiative to identify and profile community-based youth smoking cessation programs in the absence of a defined sample frame. We developed a two-stage sampling design, with counties as the first-stage probability sampling units. The second stage used snowball sampling to saturation, to identify individuals who administered youth smoking cessation programs across three economic sectors in each county. Multivariate analyses modeled the relationship between program screening, eligibility, and response rates and economic sector and stratification criteria. Cumulative logit models analyzed the relationship between the number of contacts in a county and the number of programs screened, eligible, or profiled in a county. The snowball process yielded 9,983 unique and traceable contacts. Urban and high-income counties yielded significantly more screened program administrators; urban counties produced significantly more eligible programs, but there was no significant association between the county characteristics and program response rate. There is a positive relationship between the number of informants initially located and the number of programs screened, eligible, and profiled in a county. Our strategy to identify youth tobacco cessation programs could be used to create a sample frame for other nonprofit organizations that are difficult to identify due to a lack of existing directories, lists, or other traditional sample frames.

Chemometric investigation of light-shade effects on essential oil yield and morphology of Moroccan Myrtus communis L.

PubMed

Fadil, Mouhcine; Farah, Abdellah; Ihssane, Bouchaib; Haloui, Taoufik; Lebrazi, Sara; Zghari, Badreddine; Rachiq, Saâd

2016-01-01

To investigate the effect of environmental factors such as light and shade on essential oil yield and morphological traits of Moroccan Myrtus communis, a chemometric study was conducted on 20 individuals growing under two contrasting light environments. The study of individual's parameters by principal component analysis has shown that essential oil yield, altitude, and leaves thickness were positively correlated between them and negatively correlated with plants height, leaves length and leaves width. Principal component analysis and hierarchical cluster analysis have also shown that the individuals of each sampling site were grouped separately. The one-way ANOVA test has confirmed the effect of light and shade on essential oil yield and morphological parameters by showing a statistically significant difference between them from the shaded side to the sunny one. Finally, the multiple linear model containing main, interaction and quadratic terms was chosen for the modeling of essential oil yield in terms of morphological parameters. Sun plants have a small height, small leaves length and width, but they are thicker and richer in essential oil than shade plants which have shown almost the opposite. The highlighted multiple linear model can be used to predict essential oil yield in the studied area.

Genetic parameters of different measures of cheese yield and milk nutrient recovery from an individual model cheese-manufacturing process.

PubMed

Bittante, G; Cipolat-Gotet, C; Cecchinato, A

2013-01-01

Cheese yield (CY) is an important technological trait in the dairy industry, and the objective of this study was to estimate the genetic parameters of cheese yield in a dairy cattle population using an individual model-cheese production procedure. A total of 1,167 Brown Swiss cows belonging to 85 herds were sampled once (a maximum of 15 cows were sampled per herd on a single test day, 1 or 2 herds per week). From each cow, 1,500 mL of milk was processed according to the following steps: milk sampling and heating, culture addition, rennet addition, gelation-time recording, curd cutting, whey draining and sampling, wheel formation, pressing, salting in brine, weighing, and cheese sampling. The compositions of individual milk, whey, and curd samples were determined. Three measures of percentage cheese yield (%CY) were calculated: %CY(CURD), %CY(SOLIDS), and %CY(WATER), which represented the ratios between the weight of fresh curd, the total solids of the curd, and the water content of the curd, respectively, and the weight of the milk processed. In addition, 3 measures of daily cheese yield (dCY, kg/d) were defined, considering the daily milk yield. Three measures of nutrient recovery (REC) were computed: REC(FAT), REC(PROTEIN), and REC(SOLIDS), which represented the ratio between the weights of the fat, protein, and total solids in the curd, respectively, and the corresponding nutrient in the milk. Energy recovery, REC(ENERGY), represented the energy content of the cheese versus that in the milk. For statistical analysis, a Bayesian animal model was implemented via Gibbs sampling. The effects of parity (1 to ≥4), days in milk (6 classes), and laboratory vat (15 vats) were assigned flat priors; those of herd-test-date, animal, and residual were given Gaussian prior distributions. Intra-herd heritability estimates of %CY(CURD), %CY(SOLIDS), and %CY(WATER) ranged from 0.224 to 0.267; these were larger than the estimates obtained for milk yield (0.182) and milk fat content (0.122), and similar to that for protein content (0.275). Daily cheese yields showed heritability estimates similar to those of daily milk yield. The trait %CY(WATER) showed a highly positive genetic correlation with %CY(SOLIDS) (0.87), whereas their phenotypic correlation was moderate (0.37), and the fat and protein contents of milk showed high genetic correlations with %CY traits. The heritability estimates of REC(PROTEIN) and REC(FAT) were larger (0.490 and 0.208, respectively) than those obtained for the protein and fat contents of milk, and the genetic relationships between REC(PROTEIN) and REC(FAT) with milk protein and fat content were low or moderate; REC(PROTEIN) and REC(FAT) were moderately correlated with the %CY traits and highly correlated with REC(SOLIDS) and REC(ENERGY). Both REC(SOLIDS) and REC(ENERGY) were heritable (0.274 and 0.232), and showed high correlations with each other (0.96) and with the %CY traits (0.83 to 0.97). Together, these findings demonstrate the existence of economically important, genetically determined variability in cheese yield that does not depend solely upon the fat and protein contents of milk, but also relies on the ability of the coagulum to retain the highest possible proportions of the available protein, fat, and water. Exploitation of this interesting genetic variation does not seem to be feasible through direct measurement of the phenotype in cows at the population level. Instead, further research is warranted to examine possible means for indirect prediction, such as through assessing the mid-infrared spectra of milk samples. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Quantitation of Staphylococcus aureus in Seawater Using CHROMagar™ SA

PubMed Central

Pombo, David; Hui, Jennifer; Kurano, Michelle; Bankowski, Matthew J; Seifried, Steven E

2010-01-01

A microbiological algorithm has been developed to analyze beach water samples for the determination of viable colony forming units (CFU) of Staphylococcus aureus (S. aureus). Membrane filtration enumeration of S. aureus from recreational beach waters using the chromogenic media CHROMagar™SA alone yields a positive predictive value (PPV) of 70%. Presumptive CHROMagar™SA colonies were confirmed as S. aureus by 24-hour tube coagulase test. Combined, these two tests yield a PPV of 100%. This algorithm enables accurate quantitation of S. aureus in seawater in 72 hours and could support risk-prediction processes for recreational waters. A more rapid protocol, utilizing a 4-hour tube coagulase confirmatory test, enables a 48-hour turnaround time with a modest false negative rate of less than 10%. PMID:20222490

Towards ultrasensitive malaria diagnosis using surface enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Chen, Keren; Yuen, Clement; Aniweh, Yaw; Preiser, Peter; Liu, Quan

2016-02-01

We report two methods of surface enhanced Raman spectroscopy (SERS) for hemozoin detection in malaria infected human blood. In the first method, silver nanoparticles were synthesized separately and then mixed with lysed blood; while in the second method, silver nanoparticles were synthesized directly inside the parasites of Plasmodium falciparum. It was observed that the first method yields a smaller variation in SERS measurements and stronger correlation between the estimated contribution of hemozoin and the parasitemia level, which is preferred for the quantification of the parasitemia level. In contrast, the second method yields a higher sensitivity to a low parasitemia level thus could be more effective in the early malaria diagnosis to determine whether a given blood sample is positive.

High-resolution passive sampling of dissolved methane in the water column of lakes in Greenland

NASA Astrophysics Data System (ADS)

Goldman, A. E.; Cadieux, S. B.; White, J. R.; Pratt, L. M.

2013-12-01

Arctic lakes are important participants in the global carbon cycle, releasing methane in a warming climate and contributing to a positive feedback to climate change. In order to yield detailed methane budgets and understand the implications of warming on methane dynamics, high-resolution profiles revealing methane behavior within the water column need to be obtained. Single day sampling using disruptive techniques has the potential to result in biases. In order to obtain high-resolution, undisturbed profiles of methane concentration and isotopic composition, this study evaluates a passive sampling method over a multi-day equilibration period. Selected for this study were two small lakes (<1km2) within a narrow valley stretching between Russells Glacier and Søndre Strømfjord in southwestern Greenland, which are part of an ongoing study of a series of seven lakes. Commercially available, 150 mL, polyethylene Passive Diffusion Bags (PDB's) were deployed in July 2013 for five days at 0.5-meter depth intervals. PDB samples were compared to samples collected with a submersible, electric pump taken immediately before PBD deployment. Preliminary CH4 concentrations and carbon isotopes for one lake were obtained in the field using a Los Gatos Research Methane Carbon Isotope Analyzer. PDB sampling and pump sampling resulted in statistically similar concentrations (R2=0.89), ranging from 0.85 to 135 uM from PDB and 0.74 to 143 uM from pump sampling. In anoxic waters of the lake, where concentrations were high enough to yield robust isotopic results on the LGR MCIA, δ13C were also similar between the two methods, yielding -73‰ from PDB and -74‰ from pump sampling. Further investigation will produce results for a second lake and methane carbon and hydrogen isotopic composition for both lakes. Preliminary results for this passive sampling method are promising. We envision the use of this technique in future studies of dissolved methane and expect that it will provide a more finely resolved vertical profile, allowing for a more complete understanding of lacustrine methane dynamics.

A measurement of B0 meson properties using partially reconstructed B0 to D*- pi+ and B0 tp D*- lepton+ nu-lepton decays with the BABAR detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barrera, Barbara

The two B{sup 0} decay processes B{sup 0} {yields} D*{sup -} {pi}{sup +} and B{sup 0} {yields} D*{sup -} {ell}{sup +} {nu}{sub {ell}} have been studied by means of a partial reconstruction technique using a data sample collected with the BABAR detector at the PEP-II storage ring. To increase statistics, only the soft {pi}{sup -} from the decay D*{sup -} {yields} {pi}{sup -} D{sup 0} was used in association with either an oppositely-charged high-momentum pion or lepton. Events were then identified by exploiting the constraints from the simple kinematics of {Upsilon}(4S) decays. A clear signature is obtained in each case.more » The position of the B{sup 0} decay point was obtained from the reconstructed {pi}{sup +} ({ell}{sup +}){pi}{sup -} vertex. The position of the other {bar B}{sup 0} in the event was also determined. Taking advantage of the boost given to the {Upsilon}(4S) system by the asymmetric beam energies of PEP-II, the lifetime of the B{sup 0} meson has been measured from the separation distance between the two vertices along the beam direction.« less

Piecewise SALT sampling for estimating suspended sediment yields

Treesearch

Robert B. Thomas

1989-01-01

A probability sampling method called SALT (Selection At List Time) has been developed for collecting and summarizing data on delivery of suspended sediment in rivers. It is based on sampling and estimating yield using a suspended-sediment rating curve for high discharges and simple random sampling for low flows. The method gives unbiased estimates of total yield and...

When reality is out of focus: Can people tell whether their beliefs and judgments are correct or wrong?

PubMed

Koriat, Asher

2018-05-01

Can we tell whether our beliefs and judgments are correct or wrong? Results across many domains indicate that people are skilled at discriminating between correct and wrong answers, endorsing the former with greater confidence than the latter. However, it has not been realized that because of people's adaptation to reality, representative samples of items tend to favor the correct answer, yielding object-level accuracy (OLA) that is considerably better than chance. Across 16 experiments that used 2-alternative forced-choice items from several domains, the confidence/accuracy (C/A) relationship was positive for items with OLA >50%, but consistently negative across items with OLA <50%. A systematic sampling of items that covered the full range of OLA (0-100%) yielded a U-function relating confidence to OLA. The results imply that the positive C/A relationship that has been reported in many studies is an artifact of OLA being better than chance rather than representing a general ability to discriminate between correct and wrong responses. However, the results also support the ecological approach, suggesting that confidence is based on a frugal, "bounded" heuristic that has been specifically tailored to the ecological structure of the natural environment. This heuristic is used despite the fact that for items with OLA <50%, it yields confidence judgments that are counterdiagnostic of accuracy. Our ability to tell between correct and wrong judgments is confined to the probability structure of the world we live in. The results were discussed in terms of the contrast between systematic design and representative design. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Estimates of general combining ability in Hevea breeding at the Rubber Research Institute of Malaysia : I. Phases II and III A.

PubMed

Tan, H

1977-01-01

Estimates of general combining ability of parents for yield and girth obtained separately from seedlings and their corresponding clonal families in Phases II and IIIA of the RRIM breeding programme are compared. A highly significant positive correlation (r = 0.71***) is found between GCA estimates from seedling and clonal families for yield in Phase IIIA, but not in Phase II (r = -0.03(NS)) nor for girth (r= -0.27(NS)) in Phase IIIA. The correlations for Phase II yield and Phase IIIA girth, however, improve when the GCA estimates based on small sample size or reversed rankings are excluded.When the best selections (based on present clonal and seedling information) are compared, all five of the parents top-ranking for yield are common in Phase IIIA but only two parents are common for yield and girth in Phases II and IIIA respectively. However, only one parent for yield in Phase II and two parents for girth in Phase IIIA would, if selected on clonal performance, have been omitted from the top ranking selections made by previous workers using seedling information.These findings, therefore, justify the choice of parents based on GCA estimates for yield obtained from seedling performance. Similar justification cannot be offered for girth, for which analysis is confounded by uninterpretable site and seasonal effects.

In situ measurement of surface potential developed on MgO thin film surface under ion irradiation using ion scattering spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagatomi, T.; Kuwayama, T.; Takai, Y.

2009-11-15

The application of ion scattering spectroscopy (ISS) to the in situ measurement of the surface potential developed on an insulator surface under positive ion irradiation was investigated. The ISS spectra measured for a MgO film of 600 nm thickness on a Si substrate by the irradiation of 950 eV He{sup +} ions revealed that the surface is positively charged by approximately 180 V. For accurate measurement of the surface potential, a correction to take into account the angular deflection of primary ions induced by the high surface potential is required. The dependence of the surface potential on the sample temperaturemore » revealed that no charging is induced above 700 deg. C, indicating that accumulated charges can be removed by heating to 700 deg. C. From the measurement of the ion-induced secondary electron yield using a collector electrode located in front of the sample surface, the surface potential and ion-induced secondary electron yield were found to be strongly affected by the experimental setup. Secondary electrons produced by the impact of slow positive secondary ions, the maximum energy of which corresponds to the surface potential, play an important role when the bias voltage applied to the collector electrode is positively high for the present experimental setup. The surface potential developed on the surface of MgO films of 600 and 200 nm thickness was measured in situ, revealing that the amount of accumulated charges and the time required to attain the steady state of charging are slightly dependent on the beam current of primary ions and strongly dependent on the thickness of the MgO film. The present results confirmed that the application of ISS has high potential for investigating charging phenomena and the secondary electron emission from insulator surfaces under positive ion irradiation.« less

An External Matrix-Assisted Laser Desorption Ionization Source for Flexible FT-ICR Mass Spectrometry Imaging with Internal Calibration on Adjacent Samples

NASA Astrophysics Data System (ADS)

Smith, Donald F.; Aizikov, Konstantin; Duursma, Marc C.; Giskes, Frans; Spaanderman, Dirk-Jan; McDonnell, Liam A.; O'Connor, Peter B.; Heeren, Ron M. A.

2011-01-01

We describe the construction and application of a new MALDI source for FT-ICR mass spectrometry imaging. The source includes a translational X-Y positioning stage with a 10 × 10 cm range of motion for analysis of large sample areas, a quadrupole for mass selection, and an external octopole ion trap with electrodes for the application of an axial potential gradient for controlled ion ejection. An off-line LC MALDI MS/MS run demonstrates the utility of the new source for data- and position-dependent experiments. A FT-ICR MS imaging experiment of a coronal rat brain section yields ˜200 unique peaks from m/z 400-1100 with corresponding mass-selected images. Mass spectra from every pixel are internally calibrated with respect to polymer calibrants collected from an adjacent slide.

Accuracy and precision of Legionella isolation by US laboratories in the ELITE program pilot study.

PubMed

Lucas, Claressa E; Taylor, Thomas H; Fields, Barry S

2011-10-01

A pilot study for the Environmental Legionella Isolation Techniques Evaluation (ELITE) Program, a proficiency testing scheme for US laboratories that culture Legionella from environmental samples, was conducted September 1, 2008 through March 31, 2009. Participants (n=20) processed panels consisting of six sample types: pure and mixed positive, pure and mixed negative, pure and mixed variable. The majority (93%) of all samples (n=286) were correctly characterized, with 88.5% of samples positive for Legionella and 100% of negative samples identified correctly. Variable samples were incorrectly identified as negative in 36.9% of reports. For all samples reported positive (n=128), participants underestimated the cfu/ml by a mean of 1.25 logs with standard deviation of 0.78 logs, standard error of 0.07 logs, and a range of 3.57 logs compared to the CDC re-test value. Centering results around the interlaboratory mean yielded a standard deviation of 0.65 logs, standard error of 0.06 logs, and a range of 3.22 logs. Sampling protocol, treatment regimen, culture procedure, and laboratory experience did not significantly affect the accuracy or precision of reported concentrations. Qualitative and quantitative results from the ELITE pilot study were similar to reports from a corresponding proficiency testing scheme available in the European Union, indicating these results are probably valid for most environmental laboratories worldwide. The large enumeration error observed suggests that the need for remediation of a water system should not be determined solely by the concentration of Legionella observed in a sample since that value is likely to underestimate the true level of contamination. Published by Elsevier Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baird, K.; SLD Collaboration

The authors have measured production fractions and spectra for {pi}{sup {+-}}, K{sup {+-}} and p, and production spectra for K{sup 0} and {Lambda}{sup 0} in both hadronic Z{sup 0} decays and a Z{sup 0} {yields} light quark (uds) subset at SLD. The SLD Cherenkov Ring Imaging Detector was used to identify charged hadrons. The CCD vertex detector was used to select the enriched uds sample. For the global sample, the results are consistent with previous experiments. The authors observe a clear flavor dependence in production spectra, but only a small effect in hadron fractions and {xi} = ln(1/x{sub p}) peakmore » positions.« less

Utilizing hunter harvest effort to survey for wildlife disease: a case study of West Nile virus in greater sage-grouse

USGS Publications Warehouse

Dusek, Robert J.; Hagen, Christian A.; Franson, J. Christian; Budeau, David A.; Hofmeister, Erik K.

2014-01-01

Greater sage-grouse (Centrocercus urophasianus; sage-grouse) are highly susceptible to infection with West Nile virus (WNV), with substantial mortality reported in wild populations and in experimentally infected birds. Although sage-grouse are hunted throughout much of their range, they have also recently been considered for protection under the Endangered Species Act. We used blood samples collected on filter-paper strips during the 2006–2010 Oregon, USA, annual sage-grouse hunt to survey for specific WNV-neutralizing antibodies that indicate a previous infection with WNV. During this period, hunters submitted 1,880 blood samples from sage-grouse they harvested. Samples obtained were proportional for all 12 Oregon sage-grouse hunting units. Laboratory testing of 1,839 samples by the WNV epitope-blocking enzyme-linked immunosorbent assay (bELISA) followed by plaque reduction neutralization test on bELISA-positive samples yielded 19 (1%) and 1 (0.05%) positive samples, respectively. These data provided early baseline information for future comparisons regarding the prevalence of WNV-specific neutralizing antibodies in sage-grouse in Oregon. This methodology may provide other states where sage-grouse (or other species) populations are hunted and where WNV constitutes a species conservation concern with a viable option to track the relative prevalence of the virus in populations.

A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples

PubMed Central

Sebastiani, Paola; Zhao, Zhenming; Abad-Grau, Maria M; Riva, Alberto; Hartley, Stephen W; Sedgewick, Amanda E; Doria, Alessandro; Montano, Monty; Melista, Efthymia; Terry, Dellara; Perls, Thomas T; Steinberg, Martin H; Baldwin, Clinton T

2008-01-01

Background One of the challenges of the analysis of pooling-based genome wide association studies is to identify authentic associations among potentially thousands of false positive associations. Results We present a hierarchical and modular approach to the analysis of genome wide genotype data that incorporates quality control, linkage disequilibrium, physical distance and gene ontology to identify authentic associations among those found by statistical association tests. The method is developed for the allelic association analysis of pooled DNA samples, but it can be easily generalized to the analysis of individually genotyped samples. We evaluate the approach using data sets from diverse genome wide association studies including fetal hemoglobin levels in sickle cell anemia and a sample of centenarians and show that the approach is highly reproducible and allows for discovery at different levels of synthesis. Conclusion Results from the integration of Bayesian tests and other machine learning techniques with linkage disequilibrium data suggest that we do not need to use too stringent thresholds to reduce the number of false positive associations. This method yields increased power even with relatively small samples. In fact, our evaluation shows that the method can reach almost 70% sensitivity with samples of only 100 subjects. PMID:18194558

[Comparison of the CMV antigenemia test and CMV-DNA PCR results in solid organ transplant recipients].

PubMed

Özkarata, Emre; Özkarataş, Emre; Özbek, Ö Alpay; Avkan Oğuz, Vildan; Sayıner, A Arzu

2016-01-01

Cytomegalovirus (CMV) infection is among the most common important viral infections in solid organ transplant (SOT) recipients. Diagnostic tests for detecting CMV replication are widely used for this group of patients, however there is no clear agreement on the cut-off levels for interpretation of clinical decisions especially when the low level of viral load is detected. In this study, CMV pp65 antigenemia test results were compared with plasma CMV-DNA levels detected by quantitative real-time polymerase chain reaction (qPCR) in samples of kidney and liver transplant recipients in the Central Laboratory of Dokuz Eylul University Hospital between 2011 and 2013, and the correlation between these two tests and viral load equivalent to antigenemia positivity were determined. In the study, pp65 antigenemia and CMV-DNA qPCR results were evaluated retrospectively. The samples from the same patients were included if the time between antigenemia and CMV-DNA qPCR tests were less than 48 hours. SPSS v15.0 was used for correlation, regression and ROC curve analysis. The results of the 217 samples collected from 100 patients (59 male, 41 female; age range: 16-71, mean age: 46 ± 13 years), 36 liver and 64 kidney recipients were evaluated in the study. Of the patients 80% were CMV IgM negative, IgG positive; 1% was CMV IgG and IgM positive; 2% were CMV IgM and IgG negative, while for 17 patients serological results could not be reached. CMV pp65 antigenemia and CMV-DNA were both negative in 102 (47%) samples, while both were positive in 37 (17%) samples. The single sample from a case with CMV IgM and IgG positivity yielded negative results for both antigenemia and CMV-DNA tests. In 78 samples antigenemia were negative and CMV-DNA qPCR were positive, while there were no samples with antigenemia positive and qPCR negative. Mean values of antigenemia and qPCR tests were 23 positive cells/200.000 leukocytes (range: 1 to 230 positive cells) and 12.595 copies/ml (range: 180 to 106.311 copies/ml), respectively. There was a significant correlation between antigenemia and qPCR results among the samples that were positive by both assays (r= 0.785). ROC curve analysis showed that CMV viral load of 205 copies/ml in plasma corresponds to ≥ 1 pp65 antigen positive cells per 200.000 leukocytes (sensitivity: 91.7%, specificity: 90.3%). Higher analytical sensitivity of qPCR test can be explained by the results of CMV-DNA PCR positive and antigenemia negative samples. Non-existence of samples with antigen positive and PCR negative results supported this finding. ROC analysis showed that any sample with CMV-DNA qPCR result less than 205 copies/ml, could be accepted as pp65 antigenemia negative. This viral load value is valid only for the studied patient group and assays, therefore could be changed according to study population and tests.

Further support for association between GWAS variant for positive emotion and reward systems.

PubMed

Lancaster, T M; Ihssen, N; Brindley, L M; Linden, D E J

2017-01-31

A recent genome-wide association study (GWAS) identified a significant single-nucleotide polymorphism (SNP) for trait-positive emotion at rs322931 on chromosome 1, which was also associated with brain activation in the reward system of healthy individuals when observing positive stimuli in a functional magnetic resonance imaging (fMRI) study. In the current study, we aimed to further validate the role of variation at rs322931 in reward processing. Using a similar fMRI approach, we use two paradigms that elicit a strong ventral striatum (VS) blood oxygen-level dependency (BOLD) response in a sample of young, healthy individuals (N=82). In the first study we use a similar picture-viewing task to the discovery sample (positive>neutral stimuli) to replicate an effect of the variant on emotion processing. In the second study we use a probabilistic reversal learning procedure to identify reward processing during decision-making under uncertainly (reward>punishment). In a region of interest (ROI) analysis of the bilateral VS, we show that the rs322931 genotype was associated with BOLD in the left VS during the positive>neutral contrast (P ROI-CORRECTED =0.045) and during the reward>punishment contrast (P ROI-CORRECTED =0.018), although the effect of passive picture viewing was in the opposite direction from that reported in the discovery sample. These findings suggest that the recently identified GWAS hit may influence positive emotion via individual differences in activity in the key hubs of the brain's reward system. Furthermore, these effects may not be limited to the passive viewing of positive emotional scenes, but may also be observed during dynamic decision-making. This study suggests that future studies of this GWAS locus may yield further insight into the biological mechanisms of psychopathologies characterised by deficits in reward processing and positive emotion.

Impact of hydrogeological data on measures of uncertainty, site characterization and environmental performance metrics

NASA Astrophysics Data System (ADS)

de Barros, Felipe P. J.; Ezzedine, Souheil; Rubin, Yoram

2012-02-01

The significance of conditioning predictions of environmental performance metrics (EPMs) on hydrogeological data in heterogeneous porous media is addressed. Conditioning EPMs on available data reduces uncertainty and increases the reliability of model predictions. We present a rational and concise approach to investigate the impact of conditioning EPMs on data as a function of the location of the environmentally sensitive target receptor, data types and spacing between measurements. We illustrate how the concept of comparative information yield curves introduced in de Barros et al. [de Barros FPJ, Rubin Y, Maxwell R. The concept of comparative information yield curves and its application to risk-based site characterization. Water Resour Res 2009;45:W06401. doi:10.1029/2008WR007324] could be used to assess site characterization needs as a function of flow and transport dimensionality and EPMs. For a given EPM, we show how alternative uncertainty reduction metrics yield distinct gains of information from a variety of sampling schemes. Our results show that uncertainty reduction is EPM dependent (e.g., travel times) and does not necessarily indicate uncertainty reduction in an alternative EPM (e.g., human health risk). The results show how the position of the environmental target, flow dimensionality and the choice of the uncertainty reduction metric can be used to assist in field sampling campaigns.

The prevalence and potential fisheries consequences of Heterosporis sutherlandae in a Minnesota lake.

PubMed

Tomamichel, Megan M; Hodgins, Nathaniel C; Venturelli, Paul A; Phelps, Nicholas B D

2018-01-01

Heterosporis sutherlandae is an emerging microsporidian fish parasite in the Great Lakes region. H. sutherlandae forms lesions in the muscle tissue of fishes important to aquaculture and sport fishing. These lesions render the filet inedible and may have fitness consequences. We evaluated the prevalence and severity of H. sutherlandae among yellow perch (Perca flavescens) in a known-positive Minnesota lake, and used an equilibrium yield model to evaluate impacts on harvest. Twenty-eight percent of the 400 yellow perch sampled were infected with H. sutherlandae. Males were 1.5 times more likely to be infected than females and were more severely infected. The presence of the parasite did not vary with relative weight or age, but infection severity was highest among older individuals that were in better condition. These results suggest that males are more susceptible to infection, and that infection is not associated with maturity or a gape-limiting food source. These results also suggest that heterosporosis increases in severity with time or by increased exposure. Our equilibrium yield model found that a 10% increase in mortality due to H. sutherlandae could result in 30% and 10% reductions in yield and mean catch weight, respectively. The results of this study direct future field sampling and laboratory experiments to further understand and predict the impacts of this parasite.

Optimised cord blood sample selection for small‑scale CD34+ cell immunomagnetic isolation.

PubMed

Perdomo-Arciniegas, Ana-María; Vernot, Jean-Paul

2012-03-01

Haematopoietic stem cells (HSCs) are defined as multipotential cells, capable of self-renewal and reconstituting in vivo the haematopoietic compartment. The CD34 antigen is considered an important HSCs marker in humans. Immunomagnetic isolation, by targeting CD34 antigen, is widely used for human HSC separation. This method allows the enrichment of human HSCs that are present at low frequencies in umbilical cord blood (CB). Immunomagnetic CD34+-cell isolation reproducibility, regarding cell yield and purity, is affected by the CD34+ cell frequency and total cell numbers present in a given sample; CB HSC purification may thus yield variable results, which also depend on the volume and density fractionation-derived cell loss of a CB sample. The uncertainty of such an outcome and associated technical costs call for a cost-effective sample screening strategy. A correlation analysis using clinical and laboratory data from 59 CB samples was performed to establish predictive variables for CD34+-immunomagnetic HSCs isolation. This study described the positive association of CD34+-cell isolation with white and red cell numbers present after cell fractionation. Furthermore, purity has been correlated with lymphocyte percentages. Predictive variable cut-off values, which are particularly useful in situations involving low CB volumes being collected (such as prevalent late umbilical cord clamping clinical practice), were proposed for HSC isolation sampling. Using the simple and cost-effective CB sample screening criteria described here would lead to avoiding costly inefficient sample purification, thereby ensuring that pure CD34+ cells are obtained in the desired numbers following CD34 immunomagnetic isolation.

Estimating total suspended sediment yield with probability sampling

Treesearch

Robert B. Thomas

1985-01-01

The ""Selection At List Time"" (SALT) scheme controls sampling of concentration for estimating total suspended sediment yield. The probability of taking a sample is proportional to its estimated contribution to total suspended sediment discharge. This procedure gives unbiased estimates of total suspended sediment yield and the variance of the...

Positive mental health and well-being among a third level student population.

PubMed

Davoren, Martin P; Fitzgerald, Eimear; Shiely, Frances; Perry, Ivan J

2013-01-01

Much research on the health and well-being of third level students is focused on poor mental health leading to a dearth of information on positive mental health and well-being. Recently, the Warwick Edinburgh Mental Well-being scale (WEMWBS) was developed as a measurement of positive mental health and well-being. The aim of this research is to investigate the distribution and determinants of positive mental health and well-being in a large, broadly representative sample of third level students using WEMWBS. Undergraduate students from one large third level institution were sampled using probability proportional to size sampling. Questionnaires were distributed to students attending lectures in the randomly selected degrees. A total of 2,332 self-completed questionnaires were obtained, yielding a response rate of 51% based on students registered to relevant modules and 84% based on attendance. One-way ANOVAs and multivariate logistic regression were utilised to investigate factors associated with positive mental health and well-being. The sample was predominantly female (62.66%), in first year (46.9%) and living in their parents' house (42.4%) or in a rented house or flat (40.8%). In multivariate analysis adjusted for age and stratified by gender, no significant differences in WEMWBS score were observed by area of study, alcohol, smoking or drug use. WEMWBS scores were higher among male students with low levels of physical activity (p=0.04). Men and women reporting one or more sexual partners (p<0.001) were also more likely to report above average mental health and well-being. This is the first study to examine positive mental health and well-being scores in a third level student sample using WEMWBS. The findings suggest that students with a relatively adverse health and lifestyle profile have higher than average mental health and well-being. To confirm these results, this work needs to be replicated across other third level institutions.

The incremental value of troponin biomarkers in risk stratification of acute coronary syndromes: is the relationship multiplicative?

PubMed

Amin, Amit P; Nathan, Sandeep; Vassallo, Patricia; Calvin, James E

2009-05-20

To emphasize the importance of troponin in the context of a new score for risk stratifying acute coronary syndromes (ACS) patients. Although troponins have powerful prognostic value, current ACS scores do not fully capitalize this prognostic ability. Here, we weigh troponin status in a multiplicative manner to develop the TRACS score from previously published Rush score risk factors (RRF). 2,866 ACS patients (46.7% troponin positive) from 9 centers comprising the TRACS registry, were randomly split into derivation (n=1,422) and validation (n=1,444) cohorts. In the derivation sample, RRF sum was multiplied by 3 if troponins were positive to yield the TRACS score, which was grouped into five categories of 0-2, 3-5, 6-8, 9-11, 12-15 (multiples of 3). Predictive performance of this score to predict hospital death was ascertained in the validation sample. The TRACS score had ROC AUC of 0.71 in the validation cohort. Logistic regression, Kaplan-Meier analysis, likelihood-ratio and Bayesian Information Criterion (BIC) test indicated that weighing troponin status with 3 in the TRACS score improved the prediction of mortality. Hosmer-Lemeshow test indicated sound model fit. We demonstrate that weighing troponin as a multiple of 3 yields robust prognostication of hospital mortality in ACS patients, when used in the context of the TRACS score.

The Incremental Value of Troponin Biomarkers in Risk Stratification of Acute Coronary Syndromes: Is the Relationship Multiplicative?

PubMed Central

Amin, Amit P; Nathan, Sandeep; Vassallo, Patricia; Calvin, James E

2009-01-01

Structured Abstract Objective: To emphasize the importance of troponin in the context of a new score for risk stratifying acute coronary syndromes (ACS) patients. Although troponins have powerful prognostic value, current ACS scores do not fully capitalize this prognostic ability. Here, we weigh troponin status in a multiplicative manner to develop the TRACS score from previously published Rush score risk factors (RRF). Methods: 2,866 ACS patients (46.7% troponin positive) from 9 centers comprising the TRACS registry, were randomly split into derivation (n=1,422) and validation (n=1,444) cohorts. In the derivation sample, RRF sum was multiplied by 3 if troponins were positive to yield the TRACS score, which was grouped into five categories of 0-2, 3-5, 6-8, 9-11, 12-15 (multiples of 3). Predictive performance of this score to predict hospital death was ascertained in the validation sample. Results: The TRACS score had ROC AUC of 0.71 in the validation cohort. Logistic regression, Kaplan-Meier analysis, likelihood-ratio and Bayesian Information Criterion (BIC) test indicated that weighing troponin status with 3 in the TRACS score improved the prediction of mortality. Hosmer-Lemeshow test indicated sound model fit. Conclusions: We demonstrate that weighing troponin as a multiple of 3 yields robust prognostication of hospital mortality in ACS patients, when used in the context of the TRACS score. PMID:19557150

The yield of different pleural fluid volumes for Mycobacterium tuberculosis culture.

PubMed

von Groote-Bidlingmaier, Florian; Koegelenberg, Coenraad Frederik; Bolliger, Chris T; Chung, Pui Khi; Rautenbach, Cornelia; Wasserman, Elizabeth; Bernasconi, Maurizio; Friedrich, Sven Olaf; Diacon, Andreas Henri

2013-03-01

We prospectively compared the culture yields of two pleural fluid volumes (5 and 100 ml) inoculated in liquid culture medium in 77 patients of whom 58 (75.3%) were diagnosed with pleural tuberculosis. The overall fluid culture yield was high (60.3% of cases with pleural tuberculosis). The larger volume had a faster time to positivity (329 vs 376 h, p=0.055) but its yield was not significantly higher (53.5% vs 50%; p=0.75). HIV-positive patients were more likely to have positive cultures (78.9% vs 51.5%; p=0.002).

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

PubMed

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

2012-07-01

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

Absolute quantum yield measurement of powder samples.

PubMed

Moreno, Luis A

2012-05-12

Measurement of fluorescence quantum yield has become an important tool in the search for new solutions in the development, evaluation, quality control and research of illumination, AV equipment, organic EL material, films, filters and fluorescent probes for bio-industry. Quantum yield is calculated as the ratio of the number of photons absorbed, to the number of photons emitted by a material. The higher the quantum yield, the better the efficiency of the fluorescent material. For the measurements featured in this video, we will use the Hitachi F-7000 fluorescence spectrophotometer equipped with the Quantum Yield measuring accessory and Report Generator program. All the information provided applies to this system. Measurement of quantum yield in powder samples is performed following these steps: 1. Generation of instrument correction factors for the excitation and emission monochromators. This is an important requirement for the correct measurement of quantum yield. It has been performed in advance for the full measurement range of the instrument and will not be shown in this video due to time limitations. 2. Measurement of integrating sphere correction factors. The purpose of this step is to take into consideration reflectivity characteristics of the integrating sphere used for the measurements. 3. Reference and Sample measurement using direct excitation and indirect excitation. 4. Quantum Yield calculation using Direct and Indirect excitation. Direct excitation is when the sample is facing directly the excitation beam, which would be the normal measurement setup. However, because we use an integrating sphere, a portion of the emitted photons resulting from the sample fluorescence are reflected by the integrating sphere and will re-excite the sample, so we need to take into consideration indirect excitation. This is accomplished by measuring the sample placed in the port facing the emission monochromator, calculating indirect quantum yield and correcting the direct quantum yield calculation. 5. Corrected quantum yield calculation. 6. Chromaticity coordinates calculation using Report Generator program. The Hitachi F-7000 Quantum Yield Measurement System offer advantages for this application, as follows: High sensitivity (S/N ratio 800 or better RMS). Signal is the Raman band of water measured under the following conditions: Ex wavelength 350 nm, band pass Ex and Em 5 nm, response 2 sec), noise is measured at the maximum of the Raman peak. High sensitivity allows measurement of samples even with low quantum yield. Using this system we have measured quantum yields as low as 0.1 for a sample of salicylic acid and as high as 0.8 for a sample of magnesium tungstate. Highly accurate measurement with a dynamic range of 6 orders of magnitude allows for measurements of both sharp scattering peaks with high intensity, as well as broad fluorescence peaks of low intensity under the same conditions. High measuring throughput and reduced light exposure to the sample, due to a high scanning speed of up to 60,000 nm/minute and automatic shutter function. Measurement of quantum yield over a wide wavelength range from 240 to 800 nm. Accurate quantum yield measurements are the result of collecting instrument spectral response and integrating sphere correction factors before measuring the sample. Large selection of calculated parameters provided by dedicated and easy to use software. During this video we will measure sodium salicylate in powder form which is known to have a quantum yield value of 0.4 to 0.5.

Legionnaires' Disease Bacteria in power plant cooling systems: downtime report. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tyndall, R.L.; Solomon, J.A.; Christensen, S.W.

1985-04-01

Legionnaires' Disease Bacteria (Legionella) are a normal part of the aquatic community that, when aerosolized, can be pathogenic to man. The downtime study was designed to determine the degree to which Legionella populations are aerosolized during cleaning and maintenance operations in a closed-cycle steam-electric power plant. Both high-volume and impinger air samples were collected prior to and during downtime operations. Emphasis was placed on sampling inside or adjacent to water boxes, condensers, and cooling towers. Control air samples were taken upwind from the plant site. Water and sludge samples were also collected at various locations. In the laboratory, the concentrationsmore » of Groups A, B, and C Legionella were determined using the direct fluorescent antibody method. All positive air samples, and other selected air samples, were injected into guinea pigs to detect infectious Legionella. Legionella could be detected in only 12 of the 126 air samples collected. These were predominantly Group A Legionella (L. pneumophila, serogroups 1 to 6). All 12 positive samples had been collected in the vicinity of water boxes, condensers, detention ponds, and cooling towers during downtime operations where aerosolization of Legionella populations would be expected. None of the air samples yielded infectious Legionella when injected into guinea pigs. Detection of Legionella in air samples taken during downtime was significantly more likely than detection during normal operating conditions (p <0.01). 13 refs., 4 figs., 10 tabs.« less

Factors influencing polymerase chain reaction outcomes in patients with clinically suspected ocular tuberculosis.

PubMed

Balne, Praveen Kumar; Modi, Rohit Ramesh; Choudhury, Nuzhat; Mohan, Neha; Barik, Manas Ranjan; Padhi, Tapas Ranjan; Sharma, Savitri; Panigrahi, Satya Ranjan; Basu, Soumyava

2014-03-25

Polymerase chain reaction (PCR) assay can be a useful method for definitive diagnosis in paucibacillary infections such as ocular tuberculosis (TB). In this study, we have evaluated factors affecting PCR outcomes in patients with clinically suspected ocular TB. Patients with clinically suspected ocular TB were investigated by PCR of aqueous or vitreous samples. Three control groups were also tested: group 1 included culture-proven non-tuberculous endophthalmitis, group 2 culture-negative non-tuberculous endophthalmitis, and group 3 patients undergoing surgery for uncomplicated cataract. PCR targeted one or more of following targets: IS6110, MPB64, and protein b genes of Mycobacterium tuberculosis complex. Multiple regression analysis (5% level of significance) was done to evaluate the associations between positive PCR outcome and laterality of disease, tuberculin skin test (TST)/interferon-gamma release assay (IGRA), chest radiography, and type of sample (aqueous or vitreous). The main outcome measures were positive PCR by one or more gene targets, and factors influencing positive PCR outcomes. All 114 samples were tested for MPB64, 110 for protein b, and 88 for IS6110. MPB64 was positive in 70.2% (n = 80) of tested samples, protein b in 40.0% (n = 44), and IS6110 in only 9.1% (n = 8). DNA sequencing of amplicons from four randomly chosen PCR reactions showed homology for M. tuberculosis complex. Of the 80 PCR-positive patients, 71 completed a full course of antitubercular therapy, of which 65 patients (91.5%) had complete resolution of inflammation at final follow-up. Among controls, 12.5% (3 out of 24) in group 1 and 18.7% (6 out of 32) in group 2 also tested positive by PCR. No PCR-positive outcome was observed in control group 3 (n = 25). Multiple regression analysis revealed significant association of positive PCR outcome with bilateral presentation, but not with a positive TST/IGRA, chest radiography, or type of sample (aqueous/vitreous) used. Careful selection of gene targets can yield high PCR positivity in clinically suspected ocular TB. Bilateral disease presentation but not any evidence of latent systemic TB influences PCR outcomes. False-positive results may be seen in ocular inflammation unrelated to ocular TB.

Effect of Partial Replacement of Wheat Flour with High Quality Cassava Flour on the Chemical Composition, Antioxidant Activity, Sensory Quality, and Microbial Quality of Bread

PubMed Central

Eleazu, Chinedum; Eleazu, Kate; Aniedu, Chinyere; Amajor, John; Ikpeama, Ahamefula; Ebenzer, Ike

2014-01-01

In the current study, wheat flour was mixed with high quality cassava flour (HQCF) in several ratios: 90:10, 80:20, 70:30, and 60:40, and used to prepare 10%, 20%, 30%, and 40% National Root Crops Research Institute (NRCRI) cassava bread, respectively. 100% wheat bread was prepared as a control (100% wheat bread). Five bread samples were prepared per group. Antioxidant assays [i.e., 2,2-diphenyl- 1-picrylhydrazyl radical (DPPH) scavenging assay, reducing power assay] revealed that the bread samples had considerable antioxidant capacities. Substitution of wheat flour with HQCF at various concentrations resulted in dose dependent decreases in the mineral and protein contents of the resulting bread samples. The crude fiber content of the bread samples was minimal, while the carbohydrate content of the bread samples ranged from 43.86% to 48.64%. A 20% substitution of wheat flour with HQCF yielded bread samples with a general acceptability that was comparable to that of 100% wheat bread. The mean bacteria counts of the bread samples ranged from 2.0×103 CFU/mL to 1.4×104 CFU/mL, while the fungal counts ranged from 0 CFU/mL to 3×103 CFU/mL. There was a positive correlation between the DPPH antioxidant activities and the reducing powers of the bread samples (R2=0.871) and a positive correlation between the DPPH antioxidant activities and the flavonoid contents of the bread samples (R2=0.487). The higher microbial load of the NRCRI cassava bread samples indicates that these bread samples may have a shorter shelf life than the 100% wheat bread. The significant positive correlation between total flavonoid content and reducing power (R2=0.750) suggests that the flavonoids present in the lipophilic fractions of the bread samples could be responsible for the reductive capacities of the bread samples. PMID:25054110

Verification of false-positive blood culture results generated by the BACTEC 9000 series by eubacterial 16S rDNA and panfungal 18S rDNA directed polymerase chain reaction (PCR).

PubMed

Daxboeck, Florian; Dornbusch, Hans Jürgen; Krause, Robert; Assadian, Ojan; Wenisch, Christoph

2004-01-01

A small but significant proportion of blood cultures processed by the BACTEC 9000 series systems is signaled positive, while subsequent Gram's stain and culture on solid media yield no pathogens. In this study, 15 "false-positive" vials (7 aerobes, 8 anaerobes) from 15 patients were investigated for the presence of bacteria and fungi by eubacterial 16S rDNA and panfungal 18S rDNA amplification, respectively. All samples turned out negative by both methods. Most patients (7) had neutropenia, which does not support the theory that high leukocyte counts enhance the generation of false-positive results. In conclusion, the results of this study indicate that false-negative results generated by the BACTEC 9000 series are inherent to the automated detection and not due to the growth of fastidious organisms.

Prevalence of hepatitis C infection among intravenous drug users in Shanghai.

PubMed

Tao, Yan-Lin; Tang, Yu-Fan; Qiu, Jian-Ping; Cai, Xiao-Feng; Shen, Xiao-Ting; Wang, Ya-Xin; Zhao, Xue-Tao

2013-08-28

To characterize the prevalence of hepatitis C virus (HCV) infection among Chinese intravenous drug users (IDUs). A total of 432 adult IDUs (95 women and 337 men) in Shanghai were included in the study. The third-generation Elecsys Anti-HCV assay (Roche Diagnostics GmbH, Sandhofer Strasse 116, D-68305, Mannheim, Germany) was used to screen for antibodies against HCV. The RIBA strip, a supplemental anti-HCV test with high specificity, was performed on all of the samples that tested positive during the initial screening. All of the anti-HCV positive samples were analyzed with a Cobas TaqMan 48 Analyzer (Roche Diagnostics) for direct detection of HCV RNA. All of the HCV RNA-positive samples were sequenced for genotype determination. The preliminary screening identified 262 (60.6%) subjects who were seropositive for HCV. Of the 62 females and 200 males seropositive subjects, 16 (16.7%) and 65 (19.3%), respectively, were confirmed by RIBA, yielding an overall HCV seropositive rate of 18.8%. Four female (6.5%) and 14 male (7.0%) subjects tested positive for HCV RNA, indicating an active infection rate of 4.2% for the entire study population. The 18 HCV RNA-positive serum samples were genotyped. Seven individuals were genotype 1b, and four were genotype 1a. One individual each was infected with genotypes 2a, 2b and 3a. Four subjects were co-infected with multiple strains: two with genotypes 1a and 2a, and two with genotypes 1b and 2a. The active infection rate among HCV-seropositive individuals was 22.2%, which was significantly lower than most estimates. The prevalence of HCV is relatively low among IDUs in Shanghai, with a spontaneous recovery rate much higher than previous estimates.

Comparison of a standardized procedure with current laboratory practices for the detection of lupus anticoagulant in France. Working Group on Hemostasis of the Société Française de Biologie Clinique.

PubMed

1993-11-15

A multicenter study involving 13 laboratories was designed to compare a common procedure for screening lupus anticoagulants (LA) to the different practices currently in use in these laboratories. The common procedure combined 3 phospholipid-dependent assays, including mixing studies and a phospholipid neutralizing test. Due to the heterogeneity of LA expression, an abnormal result in at least one of the tests was sufficient to classify a sample as positive for LA. Consecutive samples referred for LA diagnosis were evaluated in parallel by each participant and the data found using the common procedure were analyzed independently according to mutually agreed cut-offs and criteria for sample classification. Within a period of 3 months, 535 samples were included, of which 147 were judged LA positive, 29 undetermined and 359 negative by the respective laboratories using their current practice. When using the common procedure, 149 plasmas were said to be positive, 38 undetermined and 348 negative. Absolute concordance occurred for 81% of the specimen population and absolute discordance (positive versus negative) for 7%. The level of agreement between the common procedure and the current practices, assessed by kappa indexes, indicated noticeable variations in the rates of detection from laboratory to laboratory. Among the different tests used in the common procedure, regular APTT was the least sensitive (about 50% detection) but none of the other tests alone recognized more than 73% of specimens from the LA positive population. This yield increased to about 90% with any combination of 2 sensitive tests.(ABSTRACT TRUNCATED AT 250 WORDS)

Validating a strategy for psychosocial phenotyping using a large corpus of clinical text.

PubMed

Gundlapalli, Adi V; Redd, Andrew; Carter, Marjorie; Divita, Guy; Shen, Shuying; Palmer, Miland; Samore, Matthew H

2013-12-01

To develop algorithms to improve efficiency of patient phenotyping using natural language processing (NLP) on text data. Of a large number of note titles available in our database, we sought to determine those with highest yield and precision for psychosocial concepts. From a database of over 1 billion documents from US Department of Veterans Affairs medical facilities, a random sample of 1500 documents from each of 218 enterprise note titles were chosen. Psychosocial concepts were extracted using a UIMA-AS-based NLP pipeline (v3NLP), using a lexicon of relevant concepts with negation and template format annotators. Human reviewers evaluated a subset of documents for false positives and sensitivity. High-yield documents were identified by hit rate and precision. Reasons for false positivity were characterized. A total of 58 707 psychosocial concepts were identified from 316 355 documents for an overall hit rate of 0.2 concepts per document (median 0.1, range 1.6-0). Of 6031 concepts reviewed from a high-yield set of note titles, the overall precision for all concept categories was 80%, with variability among note titles and concept categories. Reasons for false positivity included templating, negation, context, and alternate meaning of words. The sensitivity of the NLP system was noted to be 49% (95% CI 43% to 55%). Phenotyping using NLP need not involve the entire document corpus. Our methods offer a generalizable strategy for scaling NLP pipelines to large free text corpora with complex linguistic annotations in attempts to identify patients of a certain phenotype.

Validating a strategy for psychosocial phenotyping using a large corpus of clinical text

PubMed Central

Gundlapalli, Adi V; Redd, Andrew; Carter, Marjorie; Divita, Guy; Shen, Shuying; Palmer, Miland; Samore, Matthew H

2013-01-01

Objective To develop algorithms to improve efficiency of patient phenotyping using natural language processing (NLP) on text data. Of a large number of note titles available in our database, we sought to determine those with highest yield and precision for psychosocial concepts. Materials and methods From a database of over 1 billion documents from US Department of Veterans Affairs medical facilities, a random sample of 1500 documents from each of 218 enterprise note titles were chosen. Psychosocial concepts were extracted using a UIMA-AS-based NLP pipeline (v3NLP), using a lexicon of relevant concepts with negation and template format annotators. Human reviewers evaluated a subset of documents for false positives and sensitivity. High-yield documents were identified by hit rate and precision. Reasons for false positivity were characterized. Results A total of 58 707 psychosocial concepts were identified from 316 355 documents for an overall hit rate of 0.2 concepts per document (median 0.1, range 1.6–0). Of 6031 concepts reviewed from a high-yield set of note titles, the overall precision for all concept categories was 80%, with variability among note titles and concept categories. Reasons for false positivity included templating, negation, context, and alternate meaning of words. The sensitivity of the NLP system was noted to be 49% (95% CI 43% to 55%). Conclusions Phenotyping using NLP need not involve the entire document corpus. Our methods offer a generalizable strategy for scaling NLP pipelines to large free text corpora with complex linguistic annotations in attempts to identify patients of a certain phenotype. PMID:24169276

Determination of apparent quantum yield spectra of DMS photo-degradation in an in situ iron-induced Northeast Pacific Ocean bloom

NASA Astrophysics Data System (ADS)

Bouillon, René-Christian; Miller, William L.

2004-03-01

The wavelength dependence of the photochemical removal efficiency for DMS was studied for samples from an iron-induced bloom in the Northeastern Pacific Ocean. In July 2002, a 64 km2 patch of ocean was iron-fertilized near Ocean Station Papa (50°12'N 144°45'W). Only small changes in pseudo-first-order apparent quantum yield (AQY*DMS(λ)) were observed outside the iron-patch. However, inside the patch, AQY*DMS(λ) decreased considerably over the two weeks following the initial iron injection. A positive strong correlation was found between pseudo-first-order apparent quantum yield determined at 330 nm (AQY*DMS(330 nm)) and NO3- concentrations. We propose that NO3--photolysis has a substantial influence on DMS photo-degradation rates in oceanic waters. This finding demonstrates that in addition to control DMS production, marine phytoplankton could indirectly influence the DMS photochemical loss rate via its control on NO3- distribution.

Deconvolution of continuous paleomagnetic data from pass-through magnetometer: A new algorithm to restore geomagnetic and environmental information based on realistic optimization

NASA Astrophysics Data System (ADS)

Oda, Hirokuni; Xuan, Chuang

2014-10-01

development of pass-through superconducting rock magnetometers (SRM) has greatly promoted collection of paleomagnetic data from continuous long-core samples. The output of pass-through measurement is smoothed and distorted due to convolution of magnetization with the magnetometer sensor response. Although several studies could restore high-resolution paleomagnetic signal through deconvolution of pass-through measurement, difficulties in accurately measuring the magnetometer sensor response have hindered the application of deconvolution. We acquired reliable sensor response of an SRM at the Oregon State University based on repeated measurements of a precisely fabricated magnetic point source. In addition, we present an improved deconvolution algorithm based on Akaike's Bayesian Information Criterion (ABIC) minimization, incorporating new parameters to account for errors in sample measurement position and length. The new algorithm was tested using synthetic data constructed by convolving "true" paleomagnetic signal containing an "excursion" with the sensor response. Realistic noise was added to the synthetic measurement using Monte Carlo method based on measurement noise distribution acquired from 200 repeated measurements of a u-channel sample. Deconvolution of 1000 synthetic measurements with realistic noise closely resembles the "true" magnetization, and successfully restored fine-scale magnetization variations including the "excursion." Our analyses show that inaccuracy in sample measurement position and length significantly affects deconvolution estimation, and can be resolved using the new deconvolution algorithm. Optimized deconvolution of 20 repeated measurements of a u-channel sample yielded highly consistent deconvolution results and estimates of error in sample measurement position and length, demonstrating the reliability of the new deconvolution algorithm for real pass-through measurements.

[Value of specific 16S rDNA fragment of algae in diagnosis of drowning: an experiment with rabbits].

PubMed

Li, Peng; Xu, Qu-Yi; Chen, Ling; Liu, Chao; Zhao, Jian; Wang, Yu-Zhong; Yu, Zheng-Liang; Hu, Sun-Lin; Wang, Hui-Jun

2015-08-01

To establish a method for amplifying specific 16S rDNA fragment of algae related with drowning and test its value in drowning diagnosis. Thirty-five rabbits were randomly divided into 3 the drowning group (n=15), postmortem water immersion group (n=15, subjected to air embolism before seawater immersion), and control group(n=5, with air embolism only). Twenty samples of the liver tissues from human corpses found in water were also used, including 14 diatom-positive and 6 diatom-negative samples identified by microwave digestion-vacuum filtration-automated scanning electron microscopy (MD-VF-Auto SEM). Seven known species of algae served as the control algae (Melosira sp, Nitzschia sp, Synedra sp, Navicula sp, Microcystis sp, Cyclotella meneghiniana, and Chlorella sp). The total DNA was extracted from the tissues and algae to amplify the specific fragment of algae followed by 8% polyacrylamide gelelectrophoresis and sliver-staining. In the drowning group, algae was detected in the lungs (100%), liver (86%), and kidney (86%); algae was detected in the lungs in 2 rabbits in the postmortem group (13%) and none in the control group. The positivity rates of algae were significantly higher in the drowning group than in the postmortem group (P<0.05). Of the 20 tissue samples from human corps found in water, 15 were found positive for algae, including sample that had been identified as diatom-negative by MD-VF-Auto SEM. All the 7 control algae samples yielded positive results in PCR. The PCR-based method has a high sensitivity in algae detection for drowning diagnosis and allows simultaneous detection of multiple algae species related with drowning.

Evaluation of two 4th generation point-of-care assays for the detection of Human Immunodeficiency Virus infection.

PubMed

Stafylis, Chrysovalantis; Klausner, Jeffrey D

2017-01-01

Fourth generation assays detect simultaneously antibodies for HIV and the p24 antigen, identifying HIV infection earlier than previous generation tests. Previous studies have shown that the Alere Determine HIV-1/2 Combo has lower than anticipated performance in detecting antibodies for HIV and the p24 antigen. Furthermore, there are currently very few studies evaluating the performance of Standard Diagnostics BIOLINE HIV Ag/Ab Combo. To evaluate the performance of the Alere Determine HIV-1/2 Combo and the Standard Diagnostics BIOLINE HIV Ag/Ab Combo in a panel of frozen serum samples. The testing panel included 133 previously frozen serum specimens from the UCLA Clinical Microbiology & Immunoserology laboratory. Reference testing included testing for HIV antibodies by a 3rd generation enzyme immunoassay followed by HIV RNA detection. Antibody negative and RNA positive sera were also tested by a laboratory 4th generation HIV Ab/Ag enzyme immunoassay. Reference testing yielded 97 positives for HIV infection and 36 negative samples. Sensitivity of the Alere test was 95% (88-98%), while the SD Bioline sensitivity was 91% (83-96%). Both assays showed 100% (90-100%) specificity. No indeterminate or invalid results were recorded. Among 13 samples with acute infection (HIV RNA positive, HIV antibody negative), 12 were found positive by the first assay and 8 by the second. The antigen component of the Alere assay detected 10 acute samples, while the SD Bioline assay detected only one. Both rapid assays showed very good overall performance in detecting HIV infection in frozen serum samples, but further improvements are required to improve the performance in acute infection.

Six-year pilot study on nucleic acid testing for blood donations in China.

PubMed

Ye, Xianlin; Yang, Baocheng; Zhu, Weigang; Zheng, Xin; Du, Peng; Zeng, Jingfeng; Li, Chengyao

2013-10-01

A six-year pilot study on nucleic acid testing for HBV, HCV and HIV-1 has been undertaken on sero-negative plasmas in mini-pool and individual donation testing at Shenzhen Blood Center. Of 307,740 sero-negative blood samples, 95 of 102 HBV DNA yields were confirmed positive, 80/95 (84.2%) were classified as occult HBV infection (OBI) and 15 (15.8%) as window period cases. Amongst OBIs, 45% carried anti-HBc only, 41.3% anti-HBc and anti-HBs and 13.7% anti-HBs only. HBV DNA yield was 1:3239. One HCV WP and one HIV-1 infected donations were detected. High residual risk was found in current blood donations screening in China. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dual tuning in creative processes: Joint contributions of intrinsic and extrinsic motivational orientations.

PubMed

Gong, Yaping; Wu, Junfeng; Song, Lynda Jiwen; Zhang, Zhen

2017-05-01

Intrinsic and extrinsic motivational orientations often coexist and can serve important functions. We develop and test a model in which intrinsic and extrinsic motivational orientations interact positively to influence personal creativity goal. Personal creativity goal, in turn, has a positive relationship with incremental creativity and an inverted U-shaped relationship with radical creativity. In a pilot study, we validated the personal creativity goal measure using 180 (Sample 1) and 69 (Sample 2) employees from a consulting firm. In the primary study, we tested the overall model using a sample of 657 research and development employees and their direct supervisors from an automobile firm. The results support the hypothesized model and yield several new insights. Intrinsic and extrinsic motivational orientations synergize with each other to strengthen personal creativity goal. Personal creativity goal in turn benefits incremental and radical creativity, but only up to a certain point for the latter. In addition to its linear indirect relationship with incremental creativity, intrinsic motivational orientation has an inverted U-shaped indirect relationship with radical creativity via personal creativity goal. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

[A pseudo-outbreak of pharyngeal gonorrhoea related to a false-positive PCR-result].

PubMed

Verzijl, A; Berretty, P J M; Erceg, A; Krekels, G A M; Van den Brule, A J C; Boel, C H E

2007-03-24

Nucleic acid amplification tests, including the polymerase chain reaction (PCR), are sensitive and specific tests that are often used for diagnosing sexually transmitted diseases (STDs). A pseudo-outbreak of pharyngeal gonorrhoea in a group of prostitutes turned out to have been caused by false-positive test results due to commensal oropharyngeal Neisseria species. Specific molecular tests may yield erroneous results. When the results of an STD study have major consequences at a legal or social level, it is advisable, in consultation with a medical microbiologist, to take a sample for culture or to carry out a second molecular test aimed at a different part of the bacterial genome.

Further evidence for cosmological evolution of the fine structure constant.

PubMed

Webb, J K; Murphy, M T; Flambaum, V V; Dzuba, V A; Barrow, J D; Churchill, C W; Prochaska, J X; Wolfe, A M

2001-08-27

We describe the results of a search for time variability of the fine structure constant alpha using absorption systems in the spectra of distant quasars. Three large optical data sets and two 21 cm and mm absorption systems provide four independent samples, spanning approximately 23% to 87% of the age of the universe. Each sample yields a smaller alpha in the past and the optical sample shows a 4 sigma deviation: Delta alpha/alpha = -0.72+/-0.18 x 10(-5) over the redshift range 0.5

DOE Office of Scientific and Technical Information (OSTI.GOV)

Draganic, Z.D.; Draganic, I.G.; Shushtarian, M.J.

A study was made of the radiolytic behavior of dilute, neutral, oxygen-free aqueous solutions of CH/sub 3/CN and C/sub 2/H/sub 5/CN. Small-molecular products were identified as RCHO, NH/sub 3/, CO/sub 2/, and H/sub 2/. The decomposition of nitrile is followed by high yields of formation of the nonvolatile nitrogen-containing compounds, G(N). The ..gamma..-irradiated solutions exhibit a positive biuret reaction. Several amino acids were identified among radiolytic products, and glycine and alanine were found to be the most abundant for CH/sub 3/CN and C/sub 2/H/sub 5/CH, respectively. Their yields increased after strong acid hydrolysis of the irradiated samples. The free radicalsmore » formed by reactions of RCN with H, OH, and e/sub aq/- were found to be important for the phenomena observed. It is suggested that the positive biuret reaction, ir spectra, and the release of amino acids on acid hydrolysis provide some evidence on the formation of peptidic materials and might be of interest for the evaluation of the role that ionizing radiation might have played in prebiotic chemical evolution in aqueous media.« less

The magnetic polarity stratigraphy of the Mauch Chunk Formation, Pennsylvania

PubMed Central

Opdyke, Neil D.; DiVenere, Victor J.

2004-01-01

Three sections of Chesterian Mauch Chunk Formation in Pennsylvania have been studied paleomagnetically to determine a Late Mississippian magnetic polarity stratigraphy. The upper section at Lavelle includes a conglomerate with abundant red siltstone rip-up clasts that yielded a positive conglomerate test. All samples were subjected to progressive thermal demagnetization to temperatures as high as 700°C. Two components of magnetization were isolated: a synfolding “B” component and the prefolding “C” component. The conglomerate test is positive, indicating that the C component was acquired very early in the history of the sediment. A coherent pattern of magnetic polarity reversals was identified. Five magnetozones were identified in the upper Lavelle section, which yields a pattern that is an excellent match with the pattern of reversals obtained from the upper Mauch Chunk at the original type section of the Mississippian/Pennsylvanian boundary at Pottsville, PA. The frequency of reversals in the upper Mississippian, as identified in the Mauch Chunk Formation, is approximately one to two per million years, which is an average for field reversal through time. PMID:15353597

The magnetic polarity stratigraphy of the Mauch Chunk Formation, Pennsylvania.

PubMed

Opdyke, Neil D; DiVenere, Victor J

2004-09-14

Three sections of Chesterian Mauch Chunk Formation in Pennsylvania have been studied paleomagnetically to determine a Late Mississippian magnetic polarity stratigraphy. The upper section at Lavelle includes a conglomerate with abundant red siltstone rip-up clasts that yielded a positive conglomerate test. All samples were subjected to progressive thermal demagnetization to temperatures as high as 700 degrees C. Two components of magnetization were isolated: a synfolding "B" component and the prefolding "C" component. The conglomerate test is positive, indicating that the C component was acquired very early in the history of the sediment. A coherent pattern of magnetic polarity reversals was identified. Five magnetozones were identified in the upper Lavelle section, which yields a pattern that is an excellent match with the pattern of reversals obtained from the upper Mauch Chunk at the original type section of the Mississippian/Pennsylvanian boundary at Pottsville, PA. The frequency of reversals in the upper Mississippian, as identified in the Mauch Chunk Formation, is approximately one to two per million years, which is an average for field reversal through time.

Air and surface contamination patterns of meticillin-resistant Staphylococcus aureus on eight acute hospital wards.

PubMed

Creamer, E; Shore, A C; Deasy, E C; Galvin, S; Dolan, A; Walley, N; McHugh, S; Fitzgerald-Hughes, D; Sullivan, D J; Cunney, R; Coleman, D C; Humphreys, H

2014-03-01

Meticillin-resistant Staphylococcus aureus (MRSA) can be recovered from hospital air and from environmental surfaces. This poses a potential risk of transmission to patients. To investigate associations between MRSA isolates recovered from air and environmental surfaces with those from patients when undertaking extensive patient and environmental sampling. This was a prospective observational study of patients and their environment in eight wards of a 700-bed tertiary care hospital during 2010 and 2011. Sampling of patients, air and surfaces was carried out on all ward bays, with more extended environmental sampling in ward high-dependency bays and at particular times of the day. The genetic relatedness of isolates was determined by DNA microarray profiling and spa typing. MRSA was recovered from 30/706 (4.3%) patients and from 19/132 (14.4%) air samples. On 9/132 (6.8%) occasions both patient and air samples yielded MRSA. In 32 high-dependency bays, MRSA was recovered from 12/161 (7.4%) patients, 8/32 (25%) air samples, and 21/644 (3.3%) environmental surface samples. On 10/132 (7.6%) occasions, MRSA was isolated from air in the absence of MRSA-positive patients. Patient demographic data combined with spa typing and DNA microarray profiling revealed four likely transmission clusters, where patient and environmental isolates were deemed to be very closely related. Air sampling yielded MRSA on frequent occasions, especially in high-dependency bays. Environmental and air sampling combined with patient demographic data, spa typing and DNA microarray profiling indicated the presence of clusters that were not otherwise apparent. Copyright © 2014 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Personality traits measured by the Swedish universities Scales of Personality: factor structure and position within the five-factor model in an Estonian sample.

PubMed

Aluoja, Anu; Voogne, Helina; Maron, Eduard; Gustavsson, J Petter; Võhma, Ulle; Shlik, Jakov

2009-01-01

The study aims to test the reliability and validity of the Estonian version of the Swedish universities Scales of Personality (SSP), and to characterize the position of the SSP-measured traits within the basic personality dimensions of the five-factor model. A total of 529 participants completed the Estonian version of the SSP. A subsample of 197 persons completed the SSP together with the Revised NEO Personality Inventory (NEO-PI-R). The internal consistency of the SSP scales was satisfactory. Principal component analysis yielded three factors representing neuroticism, aggression and disinhibition. The factor solution obtained in the Estonian sample was similar to the original SSP study in the Swedish normative sample. NEO-PI-R Neuroticism had highest correlations with SSP neuroticism factor scales. Extraversion had strongest relationship with adventure seeking and low detachment. Agreeableness correlated positively with SSP social desirability and negatively to aggression-irritability scales. Conscientiousness facet Deliberation correlated with Impulsiveness. The Estonian SSP showed acceptable reliability and validity, which confirms that SSP is applicable in different social and cultural background. The SSP measures traits that correspond to the major personality models. The SSP characterizes three broad dimensions of personality, namely neuroticism, disinhibition and aggression, which are useful in assessment of personality correlates of mental disorders.

Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis.

PubMed

Mubemba, B; Thompson, P N; Odendaal, L; Coetzee, P; Venter, E H

2017-05-01

Rift Valley fever (RVF), caused by an arthropod borne Phlebovirus in the family Bunyaviridae, is a haemorrhagic disease that affects ruminants and humans. Due to the zoonotic nature of the virus, a biosafety level 3 laboratory is required for isolation of the virus. Fresh and frozen samples are the preferred sample type for isolation and acquisition of sequence data. However, these samples are scarce in addition to posing a health risk to laboratory personnel. Archived formalin-fixed, paraffin-embedded (FFPE) tissue samples are safe and readily available, however FFPE derived RNA is in most cases degraded and cross-linked in peptide bonds and it is unknown whether the sample type would be suitable as reference material for retrospective phylogenetic studies. A RT-PCR assay targeting a 490 nt portion of the structural G N glycoprotein encoding gene of the RVFV M-segment was applied to total RNA extracted from archived RVFV positive FFPE samples. Several attempts to obtain target amplicons were unsuccessful. FFPE samples were then analysed using next generation sequencing (NGS), i.e. Truseq ® (Illumina) and sequenced on the Miseq ® genome analyser (Illumina). Using reference mapping, gapped virus sequence data of varying degrees of shallow depth was aligned to a reference sequence. However, the NGS did not yield long enough contigs that consistently covered the same genome regions in all samples to allow phylogenetic analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Assessing Self-Efficacy for Coping with Cancer: Development and Psychometric Analysis of the Brief Version of the Cancer Behavior Inventory (CBI-B)

PubMed Central

Heitzmann, Carolyn A.; Merluzzi, Thomas V.; Jean-Pierre, Pascal; Roscoe, Joseph A.; Kirsh, Kenneth L.; Passik, Steven D.

2010-01-01

Introduction The Cancer Behavior Inventory-Brief Version (CBI-B), a 12-item measure of self-efficacy for coping with cancer derived from the longer 33-item version (CBI-L), was subjected to psychometric analysis. Method Participants consisted of three samples: 735 cancer patients from a multi-center CCOP study, 199 from central Indiana, and 370 from a national sample. Samples were mixed with respect to initial cancer diagnosis. Participants completed the CBI-B and measures of quality of life, optimism, life satisfaction, depression, and sickness impact. Results EFA with oblique rotation yielded four factors in the first sample: 1) Maintaining Independence and Positive Attitude; 2) Participating in Medical Care; 3) Coping and Stress Management; and 4) Managing Affect, which were confirmed in subsequent samples. Cronbach α coefficient for the 12-item CBI-B ranged from .84 to .88. Validity of the CBI-B was demonstrated by positive correlations with measures of quality of life and optimism and negative correlations with measures of depression and sickness impact. Discussion The CBI-B is a valid brief measure of self-efficacy for coping that could be easily integrated into clinical oncology research and practice and also be used in screening patients. PMID:11351373

Advancing Our Understanding of the Etiologies and Mutational Landscapes of Basal-Like, Luminal A, and Luminal B Breast Cancers

DTIC Science & Technology

2015-10-01

an additional 80 to 100 estrogen receptor positive (ER+) cases. In terms of the impact of this change on our specific aims, it impacts only Aims 1...This modification does not impact the work or budget of Dr. Chinnaiyan’s component of this project as there were never any plans to provide samples...increased speed and sequencing yield, months 7-60: We will optimize and incorporate improved methods for library construction, such as transposon based

Strength and Structure of Ga1-xInx as Alloys

DTIC Science & Technology

1986-04-01

fixtures were ordered and received. An existing furnace and retort will be used to surround the compression fixture. The sample will be positioned in a B203...oncerns the experimental measurement of the flow stress and hardness as a function of temperature and In content:. High mprare hardns testing is used ...approximately 1/3 of the hardness 4 value9 so the latter indicates expected trends for yield stress. flWI1AL WORK The hardess tester used in this study was

Time-of-flight measurement of ionic species generated during ablation for optimization of focusing condition at free-electron laser beamline

NASA Astrophysics Data System (ADS)

Senba, Y.; Nagasono, M.; Koyama, T.; Yumoto, H.; Ohashi, H.; Tono, K.; Togashi, T.; Inubushi, Y.; Sato, T.; Yabashi, M.; Ishikawa, T.

2013-03-01

Optimization of focusing conditions is important in free-electron laser applications. A time-of-flight mass analyzer has been designed and constructed for this purpose. The time-of-flight spectra of ionic species evolved from laser ablation of gold were measured. The yields of ionic species showed strong correlations with free-electron-laser intensity. This method conveniently allows for direct estimation of laser intensity on sample and determination of focusing position.

Teachers' instructional efficacy and teachers' efficacy toward integration of information technologies in the classroom.

PubMed

Dussault, Marc; Deaudelin, Colette; Brodeur, Monique

2004-06-01

The aim of the study was to investigate the relationship between teachers' instructional efficacy and their efficacy toward integration of technologies in the classroom. A sample of 309 French Canadian elementary school teachers volunteered and were administered a French Canadian version of the Teacher Efficacy Scale and Teachers' efficacy scale toward integration of technologies in the classroom. Analysis yielded, as expected, a positive and significant partial correlation between the two types of self-efficacy beliefs (.27 and .36).

High energy resolution with transparent ceramic garnet scintillators

NASA Astrophysics Data System (ADS)

Cherepy, N. J.; Seeley, Z. M.; Payne, S. A.; Beck, P. R.; Swanberg, E. L.; Hunter, S.; Ahle, L.; Fisher, S. E.; Melcher, C.; Wei, H.; Stefanik, T.; Chung, Y.-S.; Kindem, J.

2014-09-01

Breakthrough energy resolution, R(662keV) < 4%, has been achieved with an oxide scintillator, Cerium-doped Gadolinium Yttrium Gallium Aluminum Garnet, or GYGAG(Ce). Transparent ceramic GYGAG(Ce), has a peak emission wavelength of 550 nm that is better matched to Silicon photodetectors than to standard PMTs. We are therefore developing a spectrometer based on pixelated GYGAG(Ce) on a Silicon photodiode array that can provide R(662 keV) = 3.6%. In comparison, with large 1-2 in3 size GYGAG(Ce) ceramics we obtain R(662 keV) = 4.6% with PMT readout. We find that ceramic GYGAG(Ce) of a given stoichiometric chemical composition can exhibit very different scintillation properties, depending on sintering conditions and post-anneal treatments. Among the characteristics of transparent ceramic garnet scintillators that can be controlled by fabrication conditions are: scintillation decay components and their amplitudes, intensity and duration of afterglow, thermoluminescence glow curve peak positions and amplitudes, integrated light yield, light yield non-proportionality - as measured in the Scintillator Light Yield Non-Proportionality Characterization Instrument (SLYNCI), and energy resolution for gamma spectroscopy. Garnet samples exhibiting a significant fraction of Cerium dopant in the tetravalent valence also exhibit: faster overall scintillation decay, very low afterglow, high light yield, but poor light yield proportionality and degraded energy resolution.

Paleomagnetic results from Tertiary volcanic strata and intrusions, Absaroka Volcanic Supergroup, Yellowstone National Park and vicinity: Contributions to the North American apparent polar wander path

USGS Publications Warehouse

Harlan, S.S.; Morgan, L.A.

2010-01-01

We report paleomagnetic and rock magnetic data from volcanic, volcaniclastic, and intrusive rocks of the 55-44Ma Absaroka Volcanic Supergroup (AVS) exposed along the northeastern margin of Yellowstone National Park and adjacent areas. Demagnetization behavior and rock magnetic experiments indicate that the remanence in most samples is carried by low-Ti titanomagnetite, although high-coercivity phases are present in oxidized basalt flows. Paleomagnetic demagnetization and rock magnetic characteristics, the presence of normal and reverse polarity sites, consistency with previous results, and positive conglomerate tests suggest that the observed remanences are primary thermoremanent magnetizations of Eocene age (c. 50Ma). An in situ grand-mean for 22 individual site- or cooling-unit means from this study that yield acceptable data combined with published data from Independence volcano yields a declination of 347.6?? and inclination of 59.2?? (k=21.8, ??95=6.8??) and a positive reversal test. Averaging 21 virtual geomagnetic poles (VGPs) that are well-grouped yields a mean at 137.1??E, 82.5??N (K=17.6, A95=7.8??), similar to results previously obtained from published studies from the AVS. Combining the VGPs from our study with published data yields a combined AVS pole at 146.3??E, 83.1??N (K=13.5, A95=6.2??, N=42 VGPs). Both poles are indistinguishable from c. 50Ma cratonic and synthetic reference poles for North America, and demonstrate the relative stability of this part of the Cordillera with respect to the craton. ?? 2009 Elsevier B.V.

Sedimentation and Its Impacts/Effects on River System and Reservoir Water Quality: case Study of Mazowe Catchment, Zimbabwe

NASA Astrophysics Data System (ADS)

Tundu, Colleta; Tumbare, Michael James; Kileshye Onema, Jean-Marie

2018-04-01

Sediment delivery into water sources and bodies results in the reduction of water quantity and quality, increasing costs of water purification whilst reducing the available water for various other uses. The paper gives an analysis of sedimentation in one of Zimbabwe's seven rivers, the Mazowe Catchment, and its impact on water quality. The Revised Universal Soil Loss Equation (RUSLE) model was used to compute soil lost from the catchment as a result of soil erosion. The model was used in conjunction with GIS remotely sensed data and limited ground observations. The estimated annual soil loss in the catchment indicates soil loss ranging from 0 to 65 t ha yr-1. Bathymetric survey at Chimhanda Dam showed that the capacity of the dam had reduced by 39 % as a result of sedimentation and the annual sediment deposition into Chimhanda Dam was estimated to be 330 t with a specific yield of 226 t km-2 yr-1. Relationship between selected water quality parameters, TSS, DO, NO3, pH, TDS, turbidity and sediment yield for selected water sampling points and Chimhanda Dam was analyzed. It was established that there is a strong positive relationship between the sediment yield and the water quality parameters. Sediment yield showed high positive correlation with turbidity (0.63) and TDS (0.64). Water quality data from Chimhanda treatment plant water works revealed that the quality of water is deteriorating as a result of increase in sediment accumulation in the dam. The study concluded that sedimentation can affect the water quality of water sources.

A new method for ultrasound detection of interfacial position in gas-liquid two-phase flow.

PubMed

Coutinho, Fábio Rizental; Ofuchi, César Yutaka; de Arruda, Lúcia Valéria Ramos; Neves, Flávio; Morales, Rigoberto E M

2014-05-22

Ultrasonic measurement techniques for velocity estimation are currently widely used in fluid flow studies and applications. An accurate determination of interfacial position in gas-liquid two-phase flows is still an open problem. The quality of this information directly reflects on the accuracy of void fraction measurement, and it provides a means of discriminating velocity information of both phases. The algorithm known as Velocity Matched Spectrum (VM Spectrum) is a velocity estimator that stands out from other methods by returning a spectrum of velocities for each interrogated volume sample. Interface detection of free-rising bubbles in quiescent liquid presents some difficulties for interface detection due to abrupt changes in interface inclination. In this work a method based on velocity spectrum curve shape is used to generate a spatial-temporal mapping, which, after spatial filtering, yields an accurate contour of the air-water interface. It is shown that the proposed technique yields a RMS error between 1.71 and 3.39 and a probability of detection failure and false detection between 0.89% and 11.9% in determining the spatial-temporal gas-liquid interface position in the flow of free rising bubbles in stagnant liquid. This result is valid for both free path and with transducer emitting through a metallic plate or a Plexiglas pipe.

A New Method for Ultrasound Detection of Interfacial Position in Gas-Liquid Two-Phase Flow

PubMed Central

Coutinho, Fábio Rizental; Ofuchi, César Yutaka; de Arruda, Lúcia Valéria Ramos; Jr., Flávio Neves; Morales, Rigoberto E. M.

2014-01-01

Ultrasonic measurement techniques for velocity estimation are currently widely used in fluid flow studies and applications. An accurate determination of interfacial position in gas-liquid two-phase flows is still an open problem. The quality of this information directly reflects on the accuracy of void fraction measurement, and it provides a means of discriminating velocity information of both phases. The algorithm known as Velocity Matched Spectrum (VM Spectrum) is a velocity estimator that stands out from other methods by returning a spectrum of velocities for each interrogated volume sample. Interface detection of free-rising bubbles in quiescent liquid presents some difficulties for interface detection due to abrupt changes in interface inclination. In this work a method based on velocity spectrum curve shape is used to generate a spatial-temporal mapping, which, after spatial filtering, yields an accurate contour of the air-water interface. It is shown that the proposed technique yields a RMS error between 1.71 and 3.39 and a probability of detection failure and false detection between 0.89% and 11.9% in determining the spatial-temporal gas-liquid interface position in the flow of free rising bubbles in stagnant liquid. This result is valid for both free path and with transducer emitting through a metallic plate or a Plexiglas pipe. PMID:24858961

Methodological considerations of terrestrial laser scanning for vegetation monitoring in the sagebrush steppe

USGS Publications Warehouse

Anderson, Kyle E.; Glenn, Nancy; Spaete, Lucas; Shinneman, Douglas; Pilliod, David S.; Arkle, Robert; McIlroy, Susan; Derryberry, DeWayne R.

2017-01-01

Terrestrial laser scanning (TLS) provides fast collection of high-definition structural information, making it a valuable field instrument to many monitoring applications. A weakness of TLS collections, especially in vegetation, is the occurrence of unsampled regions in point clouds where the sensor’s line-of-sight is blocked by intervening material. This problem, referred to as occlusion, may be mitigated by scanning target areas from several positions, increasing the chance that any given area will fall within the scanner’s line-of-sight from at least one position. Because TLS collections are often employed in remote regions where the scope of sampling is limited by logistical factors such as time and battery power, it is important to design field protocols which maximize efficiency and support increased quantity and quality of the data collected. This study informs researchers and practitioners seeking to optimize TLS sampling methods for vegetation monitoring in dryland ecosystems through three analyses. First, we quantify the 2D extent of occluded regions based on the range from single scan positions. Second, we measure the efficacy of additional scan positions on the reduction of 2D occluded regions (area) using progressive configurations of scan positions in 1 ha plots. Third, we test the reproducibility of 3D sampling yielded by a 5-scan/ha sampling methodology using redundant sets of scans. Analyses were performed using measurements at analysis scales of 5 to 50 cm across the 1-ha plots, and we considered plots in grass and shrub-dominated communities separately. In grass-dominated plots, a center-scan configuration and 5 cm pixel size sampled at least 90% of the area up to 18 m away from the scanner. In shrub-dominated plots, sampling at least 90% of the area was only achieved within a distance of 12 m. We found that 3 and 5 scans/ha are needed to sample at least ~ 70% of the total area (1 ha) in the grass and shrub-dominated plots, respectively, using 5 cm pixels to measure sampling presence-absence. The reproducibility of 3D sampling provided by a 5 position scan layout across 1-ha plots was 50% (shrub) and 70% (grass) using a 5-cm voxel size, whereas at the 50-cm voxel scale, reproducibility of sampling was nearly 100% for all plot types. Future studies applying TLS in similar dryland environments for vegetation monitoring may use our results as a guide to efficiently achieve sampling coverage and reproducibility in datasets.

Methodological considerations of terrestrial laser scanning for vegetation monitoring in the sagebrush steppe.

PubMed

Anderson, Kyle E; Glenn, Nancy F; Spaete, Lucas P; Shinneman, Douglas J; Pilliod, David S; Arkle, Robert S; McIlroy, Susan K; Derryberry, DeWayne R

2017-10-23

Terrestrial laser scanning (TLS) provides fast collection of high-definition structural information, making it a valuable field instrument to many monitoring applications. A weakness of TLS collections, especially in vegetation, is the occurrence of unsampled regions in point clouds where the sensor's line-of-sight is blocked by intervening material. This problem, referred to as occlusion, may be mitigated by scanning target areas from several positions, increasing the chance that any given area will fall within the scanner's line-of-sight from at least one position. Because TLS collections are often employed in remote regions where the scope of sampling is limited by logistical factors such as time and battery power, it is important to design field protocols which maximize efficiency and support increased quantity and quality of the data collected. This study informs researchers and practitioners seeking to optimize TLS sampling methods for vegetation monitoring in dryland ecosystems through three analyses. First, we quantify the 2D extent of occluded regions based on the range from single scan positions. Second, we measure the efficacy of additional scan positions on the reduction of 2D occluded regions (area) using progressive configurations of scan positions in 1 ha plots. Third, we test the reproducibility of 3D sampling yielded by a 5-scan/ha sampling methodology using redundant sets of scans. Analyses were performed using measurements at analysis scales of 5 to 50 cm across the 1-ha plots, and we considered plots in grass and shrub-dominated communities separately. In grass-dominated plots, a center-scan configuration and 5 cm pixel size sampled at least 90% of the area up to 18 m away from the scanner. In shrub-dominated plots, sampling at least 90% of the area was only achieved within a distance of 12 m. We found that 3 and 5 scans/ha are needed to sample at least ~ 70% of the total area (1 ha) in the grass and shrub-dominated plots, respectively, using 5 cm pixels to measure sampling presence-absence. The reproducibility of 3D sampling provided by a 5 position scan layout across 1-ha plots was 50% (shrub) and 70% (grass) using a 5-cm voxel size, whereas at the 50-cm voxel scale, reproducibility of sampling was nearly 100% for all plot types. Future studies applying TLS in similar dryland environments for vegetation monitoring may use our results as a guide to efficiently achieve sampling coverage and reproducibility in datasets.

Detection of Mycobacterium tuberculosis in extrapulmonary biopsy samples using PCR targeting IS6110, rpoB, and nested-rpoB PCR Cloning

PubMed Central

Meghdadi, Hossein; Khosravi, Azar D.; Ghadiri, Ata A.; Sina, Amir H.; Alami, Ameneh

2015-01-01

Present study was aimed to examine the diagnostic utility of polymerase chain reaction (PCR) and nested PCR techniques for the detection of Mycobacterium tuberculosis (MTB) DNA in samples from patients with extra pulmonary tuberculosis (EPTB). In total 80 formalin-fixed, paraffin-embedded (FFPE) samples comprising 70 samples with definite diagnosis of EPTB and 10 samples from known non- EPTB on the basis of histopathology examination, were included in the study. PCR amplification targeting IS6110, rpoB gene and nested PCR targeting the rpoB gene were performed on the extracted DNAs from 80 FFPE samples. The strong positive samples were directly sequenced. For negative samples and those with weak band in nested-rpoB PCR, TA cloning was performed by cloning the products into the plasmid vector with subsequent sequencing. The 95% confidence intervals (CI) for the estimates of sensitivity and specificity were calculated for each method. Fourteen (20%), 34 (48.6%), and 60 (85.7%) of the 70 positive samples confirmed by histopathology, were positive by rpoB-PCR, IS6110-PCR, and nested-rpoB PCR, respectively. By performing TA cloning on samples that yielded weak (n = 8) or negative results (n = 10) in the PCR methods, we were able to improve their quality for later sequencing. All samples with weak band and 7 out of 10 negative samples, showed strong positive results after cloning. So nested-rpoB PCR cloning revealed positivity in 67 out of 70 confirmed samples (95.7%). The sensitivity of these combination methods was calculated as 95.7% in comparison with histopathology examination. The CI for sensitivity of the PCR methods were calculated as 11.39–31.27% for rpoB-PCR, 36.44–60.83% for IS6110- PCR, 75.29–92.93% for nested-rpoB PCR, and 87.98–99.11% for nested-rpoB PCR cloning. The 10 true EPTB negative samples by histopathology, were negative by all tested methods including cloning and were used to calculate the specificity of the applied methods. The CI for 100% specificity of each PCR method were calculated as 69.15–100%. Our results indicated that nested-rpoB PCR combined with TA cloning and sequencing is a preferred method for the detection of MTB DNA in EPTB samples with high sensitivity and specificity which confirm the histopathology results. PMID:26191059

Detection of Mycobacterium tuberculosis in extrapulmonary biopsy samples using PCR targeting IS6110, rpoB, and nested-rpoB PCR Cloning.

PubMed

Meghdadi, Hossein; Khosravi, Azar D; Ghadiri, Ata A; Sina, Amir H; Alami, Ameneh

2015-01-01

Present study was aimed to examine the diagnostic utility of polymerase chain reaction (PCR) and nested PCR techniques for the detection of Mycobacterium tuberculosis (MTB) DNA in samples from patients with extra pulmonary tuberculosis (EPTB). In total 80 formalin-fixed, paraffin-embedded (FFPE) samples comprising 70 samples with definite diagnosis of EPTB and 10 samples from known non- EPTB on the basis of histopathology examination, were included in the study. PCR amplification targeting IS6110, rpoB gene and nested PCR targeting the rpoB gene were performed on the extracted DNAs from 80 FFPE samples. The strong positive samples were directly sequenced. For negative samples and those with weak band in nested-rpoB PCR, TA cloning was performed by cloning the products into the plasmid vector with subsequent sequencing. The 95% confidence intervals (CI) for the estimates of sensitivity and specificity were calculated for each method. Fourteen (20%), 34 (48.6%), and 60 (85.7%) of the 70 positive samples confirmed by histopathology, were positive by rpoB-PCR, IS6110-PCR, and nested-rpoB PCR, respectively. By performing TA cloning on samples that yielded weak (n = 8) or negative results (n = 10) in the PCR methods, we were able to improve their quality for later sequencing. All samples with weak band and 7 out of 10 negative samples, showed strong positive results after cloning. So nested-rpoB PCR cloning revealed positivity in 67 out of 70 confirmed samples (95.7%). The sensitivity of these combination methods was calculated as 95.7% in comparison with histopathology examination. The CI for sensitivity of the PCR methods were calculated as 11.39-31.27% for rpoB-PCR, 36.44-60.83% for IS6110- PCR, 75.29-92.93% for nested-rpoB PCR, and 87.98-99.11% for nested-rpoB PCR cloning. The 10 true EPTB negative samples by histopathology, were negative by all tested methods including cloning and were used to calculate the specificity of the applied methods. The CI for 100% specificity of each PCR method were calculated as 69.15-100%. Our results indicated that nested-rpoB PCR combined with TA cloning and sequencing is a preferred method for the detection of MTB DNA in EPTB samples with high sensitivity and specificity which confirm the histopathology results.

Routine screening of blood donations at Qingdao central blood bank, China, for hepatitis B virus (HBV) DNA with a real-time, multiplex nucleic acid test for HBV, hepatitis C virus, and human immunodeficiency virus Types 1 and 2.

PubMed

Yang, Zhongsi; Xu, Lei; Liu, Li; Feng, Qiuxia; Zhang, Longmu; Ma, Weijuan; Saldanha, John; Wang, Mingmin; Zhao, Lin

2013-10-01

The Roche cobas TaqScreen MPX test was used to evaluate the rate of hepatitis B surface antigen (HBsAg)-negative donations that were hepatitis B virus (HBV) DNA reactive from June 2010 to January 2011 in Qingdao, China. HBsAg-negative samples from 65,800 voluntary blood donors were tested with the cobas TaqScreen MPX test in pools of 6 on the Roche cobas s 201 blood screening platform. Samples positive for HBV DNA and negative for HBsAg were quantitated with the Roche COBAS AmpliPrep/COBAS TaqMan HBV test. In addition, serologic tests for HBsAg, hepatitis B surface antibody, anti-hepatitis B core antigen (anti-HBc), anti-hepatitis B e antigen (anti-HBe), and hepatitis B e antigen (HBe) were done using the Roche electrochemiluminescence immunoassay. A total of 80 nucleic acid amplification technology (NAT) test-reactive pools were identified and 59 pools (74%) resolved to a reactive sample. All samples were HBV DNA reactive and the viral load in each sample was quantitated. The viral loads of the samples ranged from less than 20 to 34,600 IU/mL; 13 samples (22%) had viral loads of more than 20 IU/mL, 27 samples (45.8%) had viral loads of less than 20 IU/mL, and 19 samples (32.2%) had undetectable viral loads. Of the 59 NAT-reactive samples, 40 (67.8%) were anti-HBc positive. Fifteen of the 59 samples could not be confirmed as NAT reactive either by an alternative NAT test or by serology. The HBV NAT yield in blood donors in Qingdao is 0.06% (38/65,800). This study confirmed the value of NAT for interdicting HBV-positive donations and preventing transfusion-transmitted HBV infections. © 2013 American Association of Blood Banks.

Direct Solvothermal Liquefaction of Pennisetum purpureum Biomass to Produce Biocrude Using Ethanol Solvent

NASA Astrophysics Data System (ADS)

Adriane Ochiai, Mikael; Marrod Cruz, Salvador; Oporto, Louiellyn; de Leon, Rizalinda

2018-03-01

Direct solvothermal liquefaction was used in converting the lignocellulosic biomass, Pennisetum purpureum or Napier grass using ethanol as solvent. Liquefaction of Napier grass resulted in a dark and viscous bio-crude product and exhibited promising yields (34.6377% to 48.6267%). It was determined that the effects of temperature and residence time were statistically significant with the residence time having the greatest positive effect on yield. High yields of bio-crude from Napier grass seem to occur when solvothermal temperature, residence time increased and as solids ratio decreased. However, elemental analysis showed that the bio-crude produced needs to undergo deoxygenation (O: 14.25 - 49.42%) before mixing with petroleum. For the higher heating value (HHV), the parameters observed in the study were statistically insignificant, however, temperature was determined to have the greatest positive effect on HHV. It was observed that high HHV bio-crude were produced at high temperatures, low solids ratio, and low residence times. The acquired averages for the HHV (20.0333 MJ/kg to 29.7744 MJ/kg) were all higher than the HHV of the Napier grass sample used in the study (12.9394 MJ/kg). It was observed in the study, that even though solids ratio has the least effect on both responses, the choice of solids ratio is dependent on its interaction effects with the other parameters as its effects contribute to the observed responses.

Observations on Side-Swimming Rainbow Trout in Water Recirculation Aquaculture Systems

PubMed Central

Good, Christopher; Davidson, John; Kinman, Christin; Kenney, P. Brett; Bæverfjord, Grete; Summerfelt, Steven

2014-01-01

Abstract During a controlled 6-month study using six replicated water recirculation aquaculture systems (WRASs), it was observed that Rainbow Trout Oncorhynchus mykiss in all WRASs exhibited a higher-than-normal prevalence of side swimming (i.e., controlled, forward swimming but with misaligned orientation such that the fish's sagittal axis is approximately parallel to the horizontal plane). To further our understanding of this abnormality, a substudy was conducted wherein side swimmers and normally swimming fish were selectively sampled from each WRAS and growth performance (length, weight), processing attributes (fillet yield, visceral index, ventrum [i.e., thickness of the ventral “belly flap”] index), blood gas and chemistry parameters, and swim bladder morphology and positioning were compared. Side swimmers were found to be significantly smaller in length and weight and had less fillet yield but higher ventrum indices. Whole-blood analyses demonstrated that, among other things, side swimmers had significantly lower whole-blood pH and higher Pco 2. Side swimmers typically exhibited swim bladder malformations, although the positive predictive value of this subjective assessment was only 73%. Overall, this study found several anatomical and physiological differences between side-swimming and normally swimming Rainbow Trout. Given the reduced weight and fillet yield of market-age side swimmers, producers would benefit from additional research to reduce side-swimming prevalence in their fish stocks. Received March 20, 2014; accepted May 20, 2014 PMID:25250476

Enterobacteriaceae in dehydrated powdered infant formula manufactured in Indonesia and Malaysia.

PubMed

Estuningsih, Sri; Kress, Claudia; Hassan, Abdulwahed A; Akineden, Omer; Schneider, Elisabeth; Usleber, Ewald

2006-12-01

To determine the occurrence of Salmonella and Shigella in infant formula from Southeast Asia, 74 packages of dehydrated powdered infant follow-on formula (recommended age, > 4 months) from five different manufacturers, four from Indonesia and one from Malaysia, were analyzed. None of the 25-g test portions yielded Salmonella or Shigella. However, further identification of colonies growing on selective media used for Salmonella and Shigella detection revealed the frequent occurrence of several other Enterobacteriaceae species. A total of 35 samples (47%) were positive for Enterobacteriaceae. Ten samples (13.5%) from two Indonesian manufacturers yielded Enterobacter sakazakii. Other Enterobacteriaceae isolated included Pantoea spp. (n = 12), Escherichia hermanii (n = 10), Enterobacter cloacae (n = 8), Klebsiella pneumoniae subsp. pneumoniae (n = 3), Citrobacter spp. (n = 2), Serratia spp. (n = 2), and Escherichia coli (n = 2). To our knowledge, this is the first report to describe the contamination of dehydrated powdered infant formula from Indonesia with E. sakazakii and several other Enterobacteriaceae that could be opportunistic pathogens. Improper preparation and conservation of these products could result in a health risk for infants in Indonesia.

Positive organizational behavior and safety in the offshore oil industry: Exploring the determinants of positive safety climate.

PubMed

Hystad, Sigurd W; Bartone, Paul T; Eid, Jarle

2014-01-01

Much research has now documented the substantial influence of safety climate on a range of important outcomes in safety critical organizations, but there has been scant attention to the question of what factors might be responsible for positive or negative safety climate. The present paper draws from positive organizational behavior theory to test workplace and individual factors that may affect safety climate. Specifically, we explore the potential influence of authentic leadership style and psychological capital on safety climate and risk outcomes. Across two samples of offshore oil-workers and seafarers working on oil platform supply ships, structural equation modeling yielded results that support a model in which authentic leadership exerts a direct effect on safety climate, as well as an indirect effect via psychological capital. This study shows the importance of leadership qualities as well as psychological factors in shaping a positive work safety climate and lowering the risk of accidents.

Positive organizational behavior and safety in the offshore oil industry: Exploring the determinants of positive safety climate

PubMed Central

Hystad, Sigurd W.; Bartone, Paul T.; Eid, Jarle

2013-01-01

Much research has now documented the substantial influence of safety climate on a range of important outcomes in safety critical organizations, but there has been scant attention to the question of what factors might be responsible for positive or negative safety climate. The present paper draws from positive organizational behavior theory to test workplace and individual factors that may affect safety climate. Specifically, we explore the potential influence of authentic leadership style and psychological capital on safety climate and risk outcomes. Across two samples of offshore oil-workers and seafarers working on oil platform supply ships, structural equation modeling yielded results that support a model in which authentic leadership exerts a direct effect on safety climate, as well as an indirect effect via psychological capital. This study shows the importance of leadership qualities as well as psychological factors in shaping a positive work safety climate and lowering the risk of accidents. PMID:24454524

Endobronchial Ultrasound-guided Transbronchial Needle Aspiration Using 19-G Needle for Sarcoidosis.

PubMed

Balwan, Akshu

2018-05-16

Flexible bronchoscopy with endobronchial ultrasound (EBUS)-guided transbronchial needle aspiration (TBNA) is increasingly being used to obtain pathology specimens for diagnosis of sarcoidosis. There is wide variation in reported diagnostic yield in literature. New TBNA needles are available in the market but data are lacking about their diagnostic yield especially for sarcoidosis. This study reports the diagnostic yield of bronchoscopy with EBUS-TBNA using ViziShot FLEX 19-G needle in a series of patients with suspected sarcoidosis. This is a retrospective chart review for diagnostic yield of the 19-G EBUS-TBNA needle for suspected sarcoidosis. Eighty-six EBUS bronchoscopies were performed, 15 were done with clinical suspicion of sarcoidosis. The 19-G needle was used for all cases of suspected sarcoidosis. The procedure was diagnostic of sarcoidosis in 14 (93.3%) patients by TBNA with 1 nondiagnostic bronchoscopy. Procedural diagnostic yield was 93.3%. Eighty-five percent (28/33) of sampled lymph nodes were positive for noncaseating granulomas. The yield of transbronchial lung biopsy (TBLB) and endobronchial lung biopsy was 38% (5/13) and 43% (6/14), respectively. TBLB and endobronchial lung biopsy did not add to the diagnostic yield of the procedure. No significant adverse events were noted. This series reports a higher diagnostic yield than most other published studies and opens platform for direct comparison of each available needle. It also adds to the safety data for this larger needle. In addition, it raises doubt into utility of TBLB for diagnosis of sarcoidosis, which can increase the procedural complications.

Interrelationship and path coefficient analysis of yield components in F4 progenies of tef (Eragrostis tef).

PubMed

Debebe, Abel; Singh, Harijat; Tefera, Hailu

2014-01-01

This experiment was conducted at Debre Zeit and Akaki during 2004-2005 cropping season on F2-derived F4 bulk families of three crosses, viz, DZ-01-974 x DZ-01-2786, DZ-01-974 x DZ-Cr-37 and Alba x Kaye Murri. To estimate the correlations and path coefficients between yield and yield components, 63 F4 families were taken randomly from each of the three crosses. The 189 F4 families, five parents and two checks were space planted following in 14 x 14 simple lattice design. Study of associations among traits indicated that yield was positively associated with shoot biomass, harvest index, lodging index and panicle kernel weight at phenotypic level at Debre Zeit. At Akaki, yield had significant positive correlation with shoot biomass, harvest index, plant height, panicle length and panicle weight. At genotypic level, grain yield per plot exhibited positive association with harvest index, shoot biomass, lodging index and panicle kernel weight at Debre Zeit. By contrast, days to heading, days to maturity, plant height and panicle length showed negative association with yield. At Akaki, kernel yield per plot was positively correlated at genotypic level with all the traits considered where lodging index had the highest correlation followed by shoot biomass, panicle kernel weight and harvest index. Path coefficient analysis at both phenotypic and genotypic levels for both the locations suggested those shoot biomass and harvest indexes are the two important yield determining traits. These two traits might be useful in indirect selection for yield improvement in the material generated from the three crosses under consideration.

Confirmatory factor analysis of the School Refusal Assessment Scale – Revised in an African American community sample

PubMed Central

Lyon, Aaron R.

2010-01-01

The current study used confirmatory factor analysis techniques to investigate the construct validity of the child version of the School Refusal Assessment Scale – Revised (SRAS-R) in a community sample of low socioeconomic status, urban, African American fifth and sixth graders (n = 174). The SRAS-R is the best-researched measure of school refusal behavior in youth and typically yields four functional dimensions. Results of the investigation suggested that a modified version of the four-factor model, in which three items from the tangible reinforcement dimension are removed, may have construct validity in the current sample of youth. In addition, youth endorsement of the dimension measuring avoidance of social and/or evaluative situations was positively associated with unexcused absences. Implications for further psychometric research and early identification and prevention of problematic absenteeism in low-SES, ethnic minority community samples are highlighted. PMID:20567603

Quantifying ruminal nitrogen metabolism using the omasal sampling technique in cattle--a meta-analysis.

PubMed

Broderick, G A; Huhtanen, P; Ahvenjärvi, S; Reynal, S M; Shingfield, K J

2010-07-01

Mixed model analysis of data from 32 studies (122 diets) was used to evaluate the precision and accuracy of the omasal sampling technique for quantifying ruminal-N metabolism and to assess the relationships between nonammonia-N flow at the omasal canal and milk protein yield. Data were derived from experiments in cattle fed North American diets (n=36) based on alfalfa silage, corn silage, and corn grain and Northern European diets (n=86) composed of grass silage and barley-based concentrates. In all studies, digesta flow was quantified using a triple-marker approach. Linear regressions were used to predict microbial-N flow to the omasum from intake of dry matter (DM), organic matter (OM), or total digestible nutrients. Efficiency of microbial-N synthesis increased with DM intake and there were trends for increased efficiency with elevated dietary concentrations of crude protein (CP) and rumen-degraded protein (RDP) but these effects were small. Regression of omasal rumen-undegraded protein (RUP) flow on CP intake indicated that an average 32% of dietary CP escaped and 68% was degraded in the rumen. The slope from regression of observed omasal flows of RUP on flows predicted by the National Research Council (2001) model indicated that NRC predicted greater RUP supply. Measured microbial-N flow was, on average, 26% greater than that predicted by the NRC model. Zero ruminal N-balance (omasal CP flow=CP intake) was obtained at dietary CP and RDP concentrations of 147 and 106 g/kg of DM, corresponding to ruminal ammonia-N and milk urea N concentrations of 7.1 and 8.3mg/100mL, respectively. Milk protein yield was positively related to the efficiency of microbial-N synthesis and measured RUP concentration. Improved efficiency of microbial-N synthesis and reduced ruminal CP degradability were positively associated with efficiency of capture of dietary N as milk N. In conclusion, the results of this study indicate that the omasal sampling technique yields valuable estimates of RDP, RUP, and ruminal microbial protein supply in cattle. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Mass spectrometer calibration of Cosmic Dust Analyzer

NASA Astrophysics Data System (ADS)

Ahrens, Thomas J.; Gupta, Satish C.; Jyoti, G.; Beauchamp, J. L.

2003-02-01

The time-of-flight (TOF) mass spectrometer (MS) of the Cosmic Dust Analyzer (CDA) instrument aboard the Cassini spacecraft is expected to be placed in orbit about Saturn to sample submicrometer-diameter ring particles and impact ejecta from Saturn's satellites. The CDA measures a mass spectrum of each particle that impacts the chemical analyzer sector of the instrument. Particles impact a Rh target plate at velocities of 1-100 km/s and produce some 10-8 to 10-5 times the particle mass of positive valence, single-charged ions. These are analyzed via a TOF MS. Initial tests employed a pulsed N2 laser acting on samples of kamacite, pyrrhotite, serpentine, olivine, and Murchison meteorite induced bursts of ions which were detected with a microchannel plate and a charge sensitive amplifier (CSA). Pulses from the N2 laser (1011 W/cm2) are assumed to simulate particle impact. Using aluminum alloy as a test sample, each pulse produces a charge of ~4.6 pC (mostly Al+1), whereas irradiation of a stainless steel target produces a ~2.8 pC (Fe+1) charge. Thus the present system yields ~10-5% of the laser energy in resulting ions. A CSA signal indicates that at the position of the microchannel plate, the ion detector geometry is such that some 5% of the laser-induced ions are collected in the CDA geometry. Employing a multichannel plate detector in this MS yields for Al-Mg-Cu alloy and kamacite targets well-defined peaks at 24 (Mg+1), 27(Al+1), and 64 (Cu+1) and 56 (Fe+1), 58 (Ni+1), and 60 (Ni+1) dalton, respectively.

Paleosecular Variation of Plio-Pleistocene Lavas from the Loiyangalani Region of Kenya

NASA Astrophysics Data System (ADS)

Opdyke, N. D.; Kent, D. V.; Huang, K.; Foster, D.; Patel, J.

2008-12-01

The data reported here is part of a study of Pliocene-Pleistocene lavas in Kenya to document the paleosecular variation and time-averaged geomagnetic field direction near to the Equator. We sampled 32 sites (10 oriented cores each) in lavas to the south and the northeast of Loiyangalani that are mapped and dated as Plio-Pleistocene in age (less than ~5 Ma) and associated with Mt. Kulal and the Longipi eruption centers. The samples from this collection were returned to the US, sliced into samples and progressively demagnetized using alternating field demagnetization. The Loiyangalani sites yielded excellent results and are seemingly unaffected by lightning, which seems to be infrequent at this latitude, in this arid environment; all but one site gave acceptable data with an alpha95 of 10° or less. There are 17 reverse sites (Dec = 183.4°, Inc = 0.9°, alpha95 = 6.7°) and 15 normal sites (Dec = 358.4°, Inc = -1.2°, alpha95 = 4.7°). The reversal test is positive suggesting that the normal and reverse polarity populations both represent a reasonable time average. The site means were combined yielding an overall mean direction of Dec = 1.1°, Inc = -1.1°, alpha95 = 4.1°. The inclination is shallower than expected for a geocentric axial dipole field (delta I = -6°); accordingly, the site VGPs give a mean pole position at Lon = 205.1° E, Lat = 86.8° N, Alpha95 = 3°, which is significantly far-sided with respect to the geographic axis. The angular standard deviation of the VGPs is 9.3°, which is a relatively low angular dispersion compared to most PSVL models such as Model G.

Evaluation of the hyplex® TBC PCR test for detection of Mycobacterium tuberculosis complex in clinical samples

PubMed Central

2010-01-01

Background Tuberculosis (TB) is one of the major public health concerns worldwide. The detection of the pathogen Mycobacterium tuberculosis complex (MTBC) as early as possible has a great impact on the effective control of the spread of the disease. In our study, we evaluated the hyplex® TBC PCR test (BAG Health Care GmbH), a novel assay using a nucleic acid amplification technique (NAAT) with reverse hybridisation and ELISA read out for the rapid detection of M. tuberculosis directly in clinical samples. Results A total of 581 respiratory and non-respiratory specimens from our pneumological hospital and the National TB Institute of Uzbekistan were used for the evaluation of the PCR assay. Of these, 292 were classified as TB samples and 289 as non-TB samples based on the results of the TB cultures as reference method. The PCR results were initially used to optimise the cut-off value of the hyplex® TBC test system by means of a ROC analysis. The overall sensitivity of the assay was determined to be 83.1%. In smear-positive TB samples, the sensitivity of the hyplex® TBC PCR test was estimated to 93.4% versus 45.1% in smear-negative samples. The specificity of the test was 99.25%. Of the two specimens (0.75%) with false-positive PCR results, one yielded a culture positive for non-tuberculous mycobacteria. Based on the assumption of a prevalence of 8% TB positives among the samples in our diagnostic TB laboratory, the positive and negative predictive values were estimated to 90.4% and 98.5%, respectively. Conclusions The hyplex® TBC PCR test is an accurate NAAT assay for a rapid and reliable detection of M. tuberculosis in various respiratory and non-respiratory specimens. Compared to many other conventional NAAT assays, the hyplex® TBC PCR test is in a low price segment which makes it an attractive option for developing and emerging countries with high TB burdens. PMID:20356361

Contamination with HIV antibody may be responsible for false positive results in specimens tested on automated platforms running HIV 4th generation assays in a region of high HIV prevalence.

PubMed

Hardie, Diana Ruth; Korsman, Stephen N; Hsiao, Nei-Yuan; Morobadi, Molefi Daniel; Vawda, Sabeehah; Goedhals, Dominique

2017-01-01

In South Africa where the prevalence of HIV infection is very high, 4th generation HIV antibody/p24 antigen combo immunoassays are the tests of choice for laboratory based screening. Testing is usually performed in clinical pathology laboratories on automated analysers. To investigate the cause of false positive results on 4th generation HIV testing platforms in public sector laboratories, the performance of two automated platforms was compared in a clinical pathology setting, firstly on routine diagnostic specimens and secondly on known sero-negative samples. Firstly, 1181 routine diagnostic specimens were sequentially tested on Siemens and Roche automated 4th generation platforms. HIV viral load, western blot and follow up testing were used to determine the true status of inconclusive specimens. Subsequently, known HIV seronegative samples from a single donor were repeatedly tested on both platforms and an analyser was tested for surface contamination with HIV positive serum to identify how suspected specimen contamination could be occurring. Serial testing of diagnostic specimens yielded 163 weakly positive or discordant results. Only 3 of 163 were conclusively shown to indicate true HIV infection. Specimen contamination with HIV antibody was suspected, based on the following evidence: the proportion of positive specimens increased on repeated passage through the analysers; viral loads were low or undetectable and western blots negative or indeterminate on problem specimens; screen negative, 2nd test positive specimens tested positive when reanalysed on the screening assay; follow up specimens (where available) were negative. Similarly, an increasing number of known negative specimens became (repeatedly) sero-positive on serial passage through one of the analysers. Internal and external analyser surfaces were contaminated with HIV serum, evidence that sample splashes occur during testing. Due to the extreme sensitivity of these assays, contamination with minute amounts of HIV antibody can cause a negative sample to test positive. Better contamination control measures are needed on analysers used in clinical pathology environments, especially in regions where HIV sero-prevalence is high.

BACTERIAL PROFILE OF NECROTIC PULPS IN CHEETAH (ACINONYX JUBATUS) CANINE TEETH.

PubMed

Almansa Ruiz, José C; Bosman, Anna-Mari; Steenkamp, Gerhard

2016-03-01

The role of microbes and their antimicrobial susceptibilities in both acute and chronic infections of the dental pulp in humans has been well studied. Presently, no data are available on endodontic pathogens in cheetahs (Acinonyx jubatus). The aim of this study was to isolate and identify the bacteria found in the canine teeth of cheetahs, where the pulp was necrotic and exposed due to a complicated crown fracture. Thirty-six microbiologic samples were taken from root canals (RCs) of the canine teeth of 19 cheetahs: one pulp sample was taken from 10 cheetahs, four samples from 2 cheetahs, two samples from 3 cheetahs, and three samples from 4 cheetahs. Exposed pulps were cultured for aerobic and anaerobic bacteria; an additional screening with a 16S rRNA-specific polymerase chain reaction (PCR) was used for the last six samples. Antimicrobial susceptibility of isolates was determined by use of the Kirby-Bauer diffusion test. In total, 59 cultivable isolates belonging to 19 microbial species and 13 genera were recovered from the 36 RCs sampled. Only two samples yielded no cultivable bacteria. Thirty-two (54.49%) of the cultivable isolates were Gram positive and 27 (45.71%) were Gram negative. The maximum number of isolates cultivated from an individual RC was six. Facultative anaerobes (62.72%) were the most common bacteria of the RCs that yielded cultivable bacteria. Of the isolates, 28.81% were aerobic and 8.47% were strict anaerobes. The antimicrobials that showed the greatest efficacy in vitro against the different bacteria isolates were amikacin and gentamicin. The more common bacterial species isolated by PCR were anaerobes (60.8%), facultative anaerobes (30.2%), and aerobes (8.6%).

Characteristics of Aerococcus viridans isolated from bovine subclinical mastitis and its effect on milk SCC, yield, and composition.

PubMed

Sun, Meng; Gao, Jian; Ali, Tariq; Yu, Dan; Zhang, Shiyao; Khan, Saeed U; Fanning, Séamus; Han, Bo

2017-04-01

Aerococcus viridians (A. viridans), an environmental Gram-positive bacterium, has been documented to be associated with bovine mastitis. However, its exact role in bovine mastitis and the changes it brings about in milk characteristics are not yet known. The objectives of the current study were to describe the antibiotic resistance of A. viridans from bovine mastitis as well as the correlation between existence of this pathogen in udders and the somatic cell counts (SCC), daily milk yield, and composition of individual cow. One-year sampling for subclinical mastitis composite milk was conducted based on monthly DHI data from September 2013 to August 2014, in a commercial herd located in Beijing, China. All samples were cultured and pathogens were identified using microbiology method. A. viridians isolates were further identified by API identification system and 16S ribosomal RNA (rRNA) sequencing method. Kirby-Bauer disk diffusion method was used to test the antibiotic resistance of A. viridians against kinds of antimicrobial substance. SCC, milk yield, and milk composition data were from monthly Dairy Herd Improvement (DHI) results. Results showed that a total of 279 (16.67%) A. viridans isolates were identified from among 1674 bacterial isolates cultured from milk samples with high SCC. The incidence of mastitis caused by A. viridans was the highest (48-53%) during the summer season. Majority of the isolates were susceptible to most of antimicrobial compounds tested, especially to β-lactams, but were found to be resistant (50-90%) to aminoglycosides, sulfonamides, and tetracycline. The average SCC of the A. viridans infected cows was significantly higher (1000.0 × 10 3  cells/mL) (P < 0.01) as compared to healthy cows (72.4 × 10 3  cells/mL) and daily milk yield decreased (P > 0.05) by 1.86 kg/day. Reductions were also observed in fat content (P > 0.05), lactose (P < 0.01), and total solids (P > 0.05), whereas protein content increased significantly (P < 0.01) in milk samples of cows infected with A. viridans. The results of this study suggest that A. viridans could be considered as an emerging aetiological agent of bovine subclinical mastitis wherein it exerts an effect on SCC, milk yield, and composition.

Cytological Sampling Versus Forceps Biopsy During Percutaneous Transhepatic Biliary Drainage and Analysis of Factors Predicting Success

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tapping, C. R.; Byass, O. R.; Cast, J. E. I., E-mail: james.cast@hey.nhs.uk

Purpose: To assess the accuracy of cytological sampling and forceps biopsy in obstructing biliary lesions and to identify factors predictive of success. Methods: Consecutive patients (n = 119) with suspected malignant inoperable obstructive jaundice treated with percutaneous transhepatic biliary drainage during 7 years were included (60 male; mean age 72.5 years). All patients underwent forceps biopsy plus cytological sampling by washing the forceps device in cytological solution. Patient history, procedural and pathological records, and clinical follow-up were reviewed. Statistical analysis included chi-square test and multivariate regression analysis. Results: Histological diagnosis after forceps biopsy was more successful than cytology: Sensitivity wasmore » 78 versus 61%, and negative predictive value was 30 versus 19%. Cytology results were never positive when the forceps biopsy was negative. The cytological sample was negative and forceps sample positive in 2 cases of cholangiocarcinoma, 16 cases of pancreatic carcinoma, and 1 case of benign disease. Diagnostic accuracy was predicted by low bilirubin (p < 0.001), aspartate transaminase (p < 0.05), and white cell count (p {<=} 0.05). Conclusions: This technique is safe and effective and is recommended for histological diagnosis during PTBD in patients with inoperable malignant biliary strictures. Diagnostic yield is greater when bilirubin levels are low and there is no sepsis; histological diagnosis by way of forceps biopsy renders cytological sampling unnecessary.« less

Genetic parameters of coagulation properties, milk yield, quality, and acidity estimated using coagulating and noncoagulating milk information in Brown Swiss and Holstein-Friesian cows.

PubMed

Cecchinato, A; Penasa, M; De Marchi, M; Gallo, L; Bittante, G; Carnier, P

2011-08-01

The aim of this study was to estimate heritabilities of rennet coagulation time (RCT) and curd firmness (a(30)) and their genetic correlations with test-day milk yield, composition (fat, protein, and casein content), somatic cell score, and acidity (pH and titratable acidity) using coagulating and noncoagulating (NC) milk information. Data were from 1,025 Holstein-Friesian (HF) and 1,234 Brown Swiss (BS) cows, which were progeny of 54 HF and 58 BS artificial insemination sires, respectively. Milk coagulation properties (MCP) of each cow were measured once using a computerized renneting meter and samples not exhibiting coagulation within 31 min after rennet addition were classified as NC milk. For NC samples, RCT was unobserved. Multivariate analyses, using Bayesian methodology, were performed to estimate the genetic relationships of RCT or a(30) with the other traits and statistical inference was based on the marginal posterior distributions of parameters of concern. For analyses involving RCT, a right-censored Gaussian linear model was used and records of NC milk samples, being censored records, were included as unknown parameters in the model implementing a data augmentation procedure. Rennet coagulation time was more heritable [heritability (h(2))=0.240 and h(2)=0.210 for HF and BS, respectively] than a(30) (h(2)=0.148 and h(2)=0.168 for HF and BS, respectively). Milk coagulation properties were more heritable than a single test-day milk yield (h(2)=0.103 and h(2)=0.097 for HF and BS, respectively) and less heritable than milk composition traits whose heritability ranged from 0.275 to 0.275, with the only exception of fat content of BS milk (h(2)=0.108). A negative genetic correlation, lower than -0.85, was estimated between RCT and a(30) for both breeds. Genetic relationships of MCP with yield and composition were low or moderate and favorable. The genetic correlation of somatic cell score with RCT in BS cows was large and positive and even more positive were those of RCT with pH and titratable acidity in both breeds, ranging from 0.80 to 0.94. Including NC milk information in the data affected the estimated correlations and decreased the uncertainty associated with the estimation process. On the basis of the estimated heritabilities and genetic correlations, enhancement of MCP through selective breeding with no detrimental effects on yield and composition seems feasible in both breeds. Milk acidity may play a role as an indicator trait for indirect enhancement of MCP. Copyright © 2011 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Detection of Respiratory Viruses in Sputum from Adults by Use of Automated Multiplex PCR

PubMed Central

Walsh, Edward E.; Formica, Maria A.; Falsey, Ann R.

2014-01-01

Respiratory tract infections (RTI) frequently cause hospital admissions among adults. Diagnostic viral reverse transcriptase PCR (RT-PCR) of nose and throat swabs (NTS) is useful for patient care by informing antiviral use and appropriate isolation. However, automated RT-PCR systems are not amenable to utilizing sputum due to its viscosity. We evaluated a simple method of processing sputum samples in a fully automated respiratory viral panel RT-PCR assay (FilmArray). Archived sputum and NTS samples collected in 2008-2012 from hospitalized adults with RTI were evaluated. A subset of sputum samples positive for 10 common viruses by a uniplex RT-PCR was selected. A sterile cotton-tip swab was dunked in sputum, swirled in 700 μL of sterile water (dunk and swirl method) and tested by the FilmArray assay. Quantitative RT-PCR was performed on “dunked” sputum and NTS samples for influenza A (Flu A), respiratory syncytial virus (RSV), coronavirus OC43 (OC43), and human metapneumovirus (HMPV). Viruses were identified in 31% of 965 illnesses using a uniplex RT-PCR. The sputum sample was the only sample positive for 105 subjects, including 35% (22/64) of influenza cases and significantly increased the diagnostic yield of NTS alone (302/965 [31%] versus 197/965 [20%]; P = 0.0001). Of 108 sputum samples evaluated by the FilmArray assay using the dunk and swirl method, 99 (92%) were positive. Quantitative RT-PCR revealed higher mean viral loads in dunked sputum samples compared to NTS samples for Flu A, RSV, and HMPV (P = 0.0001, P = 0.006, and P = 0.011, respectively). The dunk and swirl method is a simple and practical method for reliably processing sputum samples in a fully automated PCR system. The higher viral loads in sputa may increase detection over NTS testing alone. PMID:25056335

Assessment of sewer source contamination of drinking water wells using tracers and human enteric viruses

USGS Publications Warehouse

Hunt, R.J.; Borchardt, M. A.; Richards, K.D.; Spencer, S. K.

2010-01-01

This study investigated the source, transport, and occurrence of human enteric viruses in municipal well water, focusing on sanitary sewer sources. A total of 33 wells from 14 communities were sampled once for wastewater tracers and viruses. Wastewater tracers were detected in four of these wells, and five wells were virus- positive by qRT-PCR. These results, along with exclusion of wells with surface water sources, were used to select three wells for additional investigation. Viruses and wastewater tracers were found in the groundwater at all sites. Some wastewater tracers, such as ionic detergents, flame retardants, and cholesterol, were considered unambiguous evidence of wastewater. Sampling at any given time may not show concurrent virus and tracer presence; however, given sufficient sampling over time, a relation between wastewater tracers and virus occurrence was identified. Presence of infectious viruses at the wellhead demonstrates that high-capacity pumping induced sufficiently short travel times for the transport of infectious viruses. Therefore, drinking-water wells are vulnerable to contaminants that travel along fast groundwater flowpaths even if they contribute a small amount of virus-laden water to the well. These results suggest that vulnerability assessments require characterization of "low yield-fast transport" in addition to traditional "high yield-slow transport", pathways. ?? 2010 American Chemical Society.

New Paleomagnetic Data from Upper Permian and Lower Triassic Volcanic Sequences from Hua Binh, Quynh Nhai, and Thuan Chau Localities, Northwest Veitnam and Their Bearing on the Accretion History of Southeast Asia

NASA Astrophysics Data System (ADS)

Geissman, J. W.; Chi, C. T.

2015-12-01

New paleomagnetic data from Upper Permian to Lower Triassic volcanic rocks sampled in NW Vietnam provide more quantitative constraints on the paleogeographic setting of crustal elements that comprise the Song Da Terrane, east of the Song Ma suture, between the South China block (SCB) and north Indochina. These include results from 12 sites (125 samples) from basalts of the Vien Nam Formation, exposed at Hoa Binh Dam; eight sites (74 samples) from basalts of the Cam Thuy Formation near Thuan Chau; and 19 sites (198 samples) from andesites and basalts of the Vien Nam Formation near Quynh Nhai. The collection is limited by the quality of exposures and quantity of independent flows. Most sites yield interpretable magnetizations in progressive demagnetization, and the response implies that characteristic remanent magnetization (ChRM) components are carried by low-titanium magnetite or hematite, or a combination of both; these are isolated from secondary components. Rock magnetic data and petrography support the retention of an early-acquired thermoremanent magnetization in most sites. The Vien Nam Formation mafic volcanic rocks yield a grand mean, in geographic coordinates, of D=33.8o, I=-28.4o ( a95 = 9.5o, k =30.3, N=9 accepted sites), and a pole position at Lat=41.1N, Long=239.8E and a paleolatitude at ~15o S during the Late Permian to Early Triassic. Permian basalts of the Cam Thuy Formation provide a grand mean, corrected for structural tilt, of D=216.1o, I=+10.5o, a95=8.9o, k=107.8, and N= 4, with a pole position at Lat=45.6N, Long=226.8E. Volcanic rocks at the Quynh Nhai locality likely yield the most robust paleofield determination, as the data set is of dual polarity and passes a reversal test. The tilt corrected grand mean (normal polarity) is D=48.3o, I=-10.0o, a95=8.0o, k=27.7, N = 13, and this in turn yields an inferred paleomagnetic pole at Lat=35.7N, Long=217.4E, and a paleolatitude of 5.1oS for the late Permian. Compared with the Late Permian-Early Triassic SCB apparent polar wander path, the data show that volcanic crustal elements of northwest Vietnam, east of the Song Ma suture zone, have been close to, but not unequivocally a coherent part of the SCB, since the Late Permian. Development of the parallel NW-SE striking Song Ma and Song Chay orogenic belts did not involve the closure of wide (> 500 km) ocean basins.

3T MR-guided in-bore transperineal prostate biopsy: A comparison of robotic and manual needle-guidance templates.

PubMed

Tilak, Gaurie; Tuncali, Kemal; Song, Sang-Eun; Tokuda, Junichi; Olubiyi, Olutayo; Fennessy, Fiona; Fedorov, Andriy; Penzkofer, Tobias; Tempany, Clare; Hata, Nobuhiko

2015-07-01

To demonstrate the utility of a robotic needle-guidance template device as compared to a manual template for in-bore 3T transperineal magnetic resonance imaging (MRI)-guided prostate biopsy. This two-arm mixed retrospective-prospective study included 99 cases of targeted transperineal prostate biopsies. The biopsy needles were aimed at suspicious foci noted on multiparametric 3T MRI using manual template (historical control) as compared with a robotic template. The following data were obtained: the accuracy of average and closest needle placement to the focus, histologic yield, percentage of cancer volume in positive core samples, complication rate, and time to complete the procedure. In all, 56 cases were performed using the manual template and 43 cases were performed using the robotic template. The mean accuracy of the best needle placement attempt was higher in the robotic group (2.39 mm) than the manual group (3.71 mm, P < 0.027). The mean core procedure time was shorter in the robotic (90.82 min) than the manual group (100.63 min, P < 0.030). Percentage of cancer volume in positive core samples was higher in the robotic group (P < 0.001). Cancer yields and complication rates were not statistically different between the two subgroups (P = 0.557 and P = 0.172, respectively). The robotic needle-guidance template helps accurate placement of biopsy needles in MRI-guided core biopsy of prostate cancer. © 2014 Wiley Periodicals, Inc.

Distribution of Salmonella serovars and phage types on 80 Ontario swine farms in 2004

PubMed Central

Farzan, Abdolvahab; Friendship, Robert M.; Dewey, Catherine E.; Muckle, Anne C.; Gray, Jeff T.; Funk, Julie

2008-01-01

The objective of this study was to describe the distribution of Salmonella spp. on Ontario grower–finisher pig farms. Eighty swine farms were visited from January through July 2004. On each farm, fecal samples were collected from 5 pens, 2 rectal samples and 1 pooled sample from fresh manure on the floor per pen. Salmonella was isolated from 91 (11%) of the 800 rectal samples and 73 (18%) of the 397 pooled samples. Overall, Salmonella was recovered from 37 (46%) of the 80 farms. On each positive farm, Salmonella was cultured from 1 to 7 pigs or 1 to 5 pens. Of the 37 farms, 18, 13, 5, and 1 yielded 1, 2, 3, and 4 serovars, respectively. The most common serovars were S. Typhimurium var. Copenhagen, S. Infantis, S. Typhimurium, S. Derby, S. Agona, S. Havana, and S. enterica subsp. I:Rough-O. The 3 most frequent phage types were PT 104, PT 104a, and PT 104b. There was a statistically fair agreement between samples collected directly from pigs and pooled pen samples in determining the Salmonella status at the pen and farm level (κ = 0.6, P < 0.0001). However, in 62 pens, Salmonella status, serovars, or phage types differed between the pig and pooled pen samples. The distribution of Salmonella on the swine farms in this study indicates that, in developing an intervention strategy, priority should be given to farms positive for S. Typhimurium var. Copenhagen. Also, the variation in Salmonella status between pig and pooled pen samples deserves consideration in a sampling strategy. PMID:18214155

Determination of Double Bond Positions in Polyunsaturated Fatty Acids Using the Photochemical Paternò-Büchi Reaction with Acetone and Tandem Mass Spectrometry.

PubMed

Murphy, Robert C; Okuno, Toshiaki; Johnson, Christopher A; Barkley, Robert M

2017-08-15

The positions of double bonds along the carbon chain of methylene interrupted polyunsaturated fatty acids are unique identifiers of specific fatty acids derived from biochemical reactions that occur in cells. It is possible to obtain direct structural information as to these double bond positions using tandem mass spectrometry after collisional activation of the carboxylate anions of an acetone adduct at each of the double bond positions formed by the photochemical Paternò-Büchi reaction with acetone. This reaction can be carried out by exposing a small portion of an inline fused silica capillary to UV photons from a mercury vapor lamp as the sample is infused into the electrospray ion source of a mass spectrometer. Collisional activation of [M - H] - yields a series of reverse Paternò-Büchi reaction product ions that essentially are derived from cleavage of the original carbon-carbon double bonds that yield an isopropenyl carboxylate anion corresponding to each double bond location. Aldehydic reverse Paternò-Büchi product ions are much less abundant as the carbon chain length and number of double bonds increase. The use of a mixture of D 0 /D 6 -acetone facilitates identification of these double bonds indicating product ions as shown for arachidonic acid. If oxygen is present in the solvent stream undergoing UV photoactivation, ozone cleavage ions are also observed without prior collisional activation. This reaction was used to determine the double bond positions in a 20:3 fatty acid that accumulated in phospholipids of RAW 264.7 cells cultured for 3 days.

Mycobiome of the Bat White Nose Syndrome Affected Caves and Mines Reveals Diversity of Fungi and Local Adaptation by the Fungal Pathogen Pseudogymnoascus (Geomyces) destructans

PubMed Central

Rajkumar, Sunanda S.; Li, Xiaojiang; Okoniewski, Joseph C.; Hicks, Alan C.; Davis, April D.; Broussard, Kelly; LaDeau, Shannon L.; Chaturvedi, Sudha; Chaturvedi, Vishnu

2014-01-01

Current investigations of bat White Nose Syndrome (WNS) and the causative fungus Pseudogymnoascus (Geomyces) destructans (Pd) are intensely focused on the reasons for the appearance of the disease in the Northeast and its rapid spread in the US and Canada. Urgent steps are still needed for the mitigation or control of Pd to save bats. We hypothesized that a focus on fungal community would advance the understanding of ecology and ecosystem processes that are crucial in the disease transmission cycle. This study was conducted in 2010–2011 in New York and Vermont using 90 samples from four mines and two caves situated within the epicenter of WNS. We used culture-dependent (CD) and culture-independent (CI) methods to catalogue all fungi (‘mycobiome’). CD methods included fungal isolations followed by phenotypic and molecular identifications. CI methods included amplification of DNA extracted from environmental samples with universal fungal primers followed by cloning and sequencing. CD methods yielded 675 fungal isolates and CI method yielded 594 fungal environmental nucleic acid sequences (FENAS). The core mycobiome of WNS comprised of 136 operational taxonomic units (OTUs) recovered in culture and 248 OTUs recovered in clone libraries. The fungal community was diverse across the sites, although a subgroup of dominant cosmopolitan fungi was present. The frequent recovery of Pd (18% of samples positive by culture) even in the presence of dominant, cosmopolitan fungal genera suggests some level of local adaptation in WNS-afflicted habitats, while the extensive distribution of Pd (48% of samples positive by real-time PCR) suggests an active reservoir of the pathogen at these sites. These findings underscore the need for integrated disease control measures that target both bats and Pd in the hibernacula for the control of WNS. PMID:25264864

Usefulness of the ARCHITECT Chagas® assay as a single test for the diagnosis of chronic Chagas disease.

PubMed

Pérez-Ayala, Ana; Fradejas, Isabel; Rebollo, Lourdes; Lora-Pablos, David; Lizasoain, Manuel; Herrero-Martínez, Juan María

2018-06-01

Imported Chagas disease (CD) is an emerging health problem in Europe due to immigration from endemic countries. Although WHO currently recommends two different serological methods to establish diagnosis, new tools like the ARCHITECT Chagas assay have potential for use as a single diagnostic test. Our objective was to determine an optimal signal-to-cut-off (S/CO) value for the ARCHITECT Chagas assay to diagnose CD with a single test. A retrospective study conducted at the 12 de Octubre University Hospital (Madrid, Spain). All patients with requests for Chagas screening between January 2014 and August 2017 were consecutively included. All samples were routinely tested with the ARCHITECT assay. Negative samples (S/CO < 0.8) required no further testing. Immunochromatographic testing (ICT) and/or indirect immunofluorescence (IFI) was used to confirm samples with S/CO ≥ 0.8. Receiver operator characteristic (ROC) curve analysis determined the ARCHITECT S/CO value that yielded 100% specificity and positive predictive value. SPSS software, version 22.0 was used for data analysis. A total of 4153 samples were analysed; 361 (8.69%) gave a reactive ARCHITECT Chagas result. 261/361 (72.3%) were women; median age was 38 years old (2-79). 92.8% were Bolivian. A total of 307 (85.0%) were confirmed as cases of Chagas; 52 (14.4%) were not infected; two (0.6%) were not evaluable. Seroprevalence was 7.39%. An S/CO ≥ 3.80 yielded 100% specificity (95% confidence interval [CI], 0.93-1.00) and 100% positive predictive value (95% CI, 0.99-1.00). Using S/CO ≥ 3.80, the ARCHITECT Chagas could be used as a single test for diagnosis of chronic CD in Bolivian immigrants. Patients with S/CO between 0.80 and 3.80 would require additional testing. © 2018 John Wiley & Sons Ltd.

Impact of cultivar selection and process optimization on ethanol yield from different varieties of sugarcane

PubMed Central

2014-01-01

Background The development of ‘energycane’ varieties of sugarcane is underway, targeting the use of both sugar juice and bagasse for ethanol production. The current study evaluated a selection of such ‘energycane’ cultivars for the combined ethanol yields from juice and bagasse, by optimization of dilute acid pretreatment optimization of bagasse for sugar yields. Method A central composite design under response surface methodology was used to investigate the effects of dilute acid pretreatment parameters followed by enzymatic hydrolysis on the combined sugar yield of bagasse samples. The pressed slurry generated from optimum pretreatment conditions (maximum combined sugar yield) was used as the substrate during batch and fed-batch simultaneous saccharification and fermentation (SSF) processes at different solid loadings and enzyme dosages, aiming to reach an ethanol concentration of at least 40 g/L. Results Significant variations were observed in sugar yields (xylose, glucose and combined sugar yield) from pretreatment-hydrolysis of bagasse from different cultivars of sugarcane. Up to 33% difference in combined sugar yield between best performing varieties and industrial bagasse was observed at optimal pretreatment-hydrolysis conditions. Significant improvement in overall ethanol yield after SSF of the pretreated bagasse was also observed from the best performing varieties (84.5 to 85.6%) compared to industrial bagasse (74.5%). The ethanol concentration showed inverse correlation with lignin content and the ratio of xylose to arabinose, but it showed positive correlation with glucose yield from pretreatment-hydrolysis. The overall assessment of the cultivars showed greater improvement in the final ethanol concentration (26.9 to 33.9%) and combined ethanol yields per hectare (83 to 94%) for the best performing varieties with respect to industrial sugarcane. Conclusions These results suggest that the selection of sugarcane variety to optimize ethanol production from bagasse can be achieved without adversely affecting juice ethanol and cane yield, thus maintaining first generation ethanol production levels while maximizing second generation ethanol production. PMID:24725458

Pretreatment to avoid positive RT-PCR results with inactivated viruses.

PubMed

Nuanualsuwan, Suphachai; Cliver, Dean O

2002-07-01

Enteric viruses that are important causes of human disease must often be detected by reverse transcription-polymerase chain reaction (RT-PCR), a method that commonly yields positive results with samples that contain only inactivated virus. This study was intended to develop a pretreatment for samples, so that inactivated viruses would not be detected by the RT-PCR procedure. Model viruses were human hepatitis A virus, vaccine poliovirus 1 and feline calicivirus as a surrogate for the Norwalk-like viruses. Each virus was inactivated (from an initial titer of approximately 10(3) PFU/ml) by ultraviolet light, hypochlorite or heating at 72 degrees C. Inactivated viruses, that were treated with proteinase K and ribonuclease for 30 min at 37 degrees C before RT-PCR, gave a negative result, which is to say that no amplicon was detected after the reaction was completed. This antecedent to the RT-PCR method may be applicable to other types of viruses, to viruses inactivated in other ways and to other molecular methods of virus detection.

Emergency department visual urinalysis versus laboratory urinalysis.

PubMed

Worrall, James C

2009-11-01

The primary objective of this study was to compare the results of nurse-performed urinalysis (NPU) interpreted visually in the emergency department (ED) with laboratory performed urinalysis (LPU) interpreted by reflectance photometry. This was a prospective observational study based on a convenience sample from my emergency practice. Emergency nurses, who were unaware of the study, performed usual dipstick analysis before sending the same urine sample to the laboratory for testing. Of 140 urinalyses performed during the study period, 124 were suitable for analysis. When compared with the reference standard LPU, the NPU had an overall sensitivity of 100% (95% confidence interval [CI] 95%-100%) and a specificity of 49% (95% CI 33%-65%) for the presence of any 1 of blood, leukocyte esterase, nitrites, protein, glucose or ketones in the urine. Of 20 falsely positive NPUs, 18 were a result of the nurse recording 1 or more components as "trace" positive. Although NPU does not yield identical results to LPU, a negative LPU is expected when the initial NPU in the ED is negative.

Sources of salmonellae in an uninfected commercially-processed broiler flock.

PubMed

Rigby, C E; Pettit, J R; Baker, M F; Bentley, A H; Salomons, M O; Lior, H

1980-07-01

Cultural monitoring was used to study the incidence and sources of salmonellae in a 4160 bird broiler flock during the growing period, transport and processing in a commercial plant. No salmonellae were isolated from any of 132 litter samples of 189 chickens cultured during the seven-week growing period, even though nest litter samples from four of the eight parent flocks yielded salmonellae and Salmonella worthington was isolated from the meat meal component of the grower ration. On arrival at the plant, 2/23 birds sampled carried S. infantis on their feathers, although intestinal cultures failed to yield salmonellae. Three of 18 processed carcasses samples yielded salmonellae (S. infantis, S. heidelberg, S. typhimurium var copenhagen). The most likely source of these salmonellae was the plastic transport crates, since 15/107 sampled before the birds were loaded yielded salmonellae (S. infantis, S. typhimurium). The crate washer at the plant did not reduce the incidence of Salmonella-contaminated crates, since 16/116 sampled after washing yielded salmonellae (S. infantis, S. typhimurium, S. heidelberg, S. schwarzengrund, S. albany).

Pathogens causing blood stream infections and their drug susceptibility profile in immunocompromised patients.

PubMed

Fayyaz, Muhammad; Mirza, Irfan Ali; Ikram, Aamer; Hussain, Aamir; Ghafoor, Tahir; Shujat, Umer

2013-12-01

To determine the types of pathogens causing blood stream infections and their drug susceptibility profile in immunocompromised patients. Cross-sectional, observational study. Department of Microbiology, Armed Forces Institute of Pathology, Rawalpindi, from January to September 2012. Blood culture bottles received from immunocompromised patients were dealt by two methods, brain heart infusion (BHI) broth based manual method and automated BACTEC system. The samples yielding positive growth from either of two methods were further analyzed. The identification of isolates was done with the help of biochemical reactions and rapid tests. Antimicrobial susceptibility of the isolates was carried out as per recommendations of Clinical and Laboratory Standards Institute (CLSI). Out of the 938 blood culture specimens received from immunocompromised patients, 188 (20%) yielded positive growth. Out of these, 89 (47.3%) isolates were Gram positive and Gram negative each, while 10 (5.3%) isolates were fungi (Candida spp.). In case of Gram positive isolates, 75 (84.3%) were Staphylococcus spp. and 51 (67%) were Methicillin resistant. Amongst Gram negative group 49 (55.1%) isolates were of enterobacteriaceae family, while 40 (44.9%) were non-lactose fermenters (NLF). In vitro antimicrobial susceptibility of Staphylococci revealed 100% susceptibility to vancomycin and linezolid. The enterobacteriaceae isolates had better susceptibility against amikacin 85.7% compared to tigecycline 61.2% and imipenem 59.2%. For NLF, the in vitro efficacy of aminoglycosides was 72.5%. The frequency of Gram positive and Gram negative organisms causing blood stream infections in immunocompromised patients was equal. Vancomycin in case of Gram positive and amikacin for Gram negative organisms revealed better in vitro efficacy as compared to other antibiotics.

Automated diagnostic kiosk for diagnosing diseases

DOEpatents

Regan, John Frederick; Birch, James Michael

2014-02-11

An automated and autonomous diagnostic apparatus that is capable of dispensing collection vials and collections kits to users interesting in collecting a biological sample and submitting their collected sample contained within a collection vial into the apparatus for automated diagnostic services. The user communicates with the apparatus through a touch-screen monitor. A user is able to enter personnel information into the apparatus including medical history, insurance information, co-payment, and answer a series of questions regarding their illness, which is used to determine the assay most likely to yield a positive result. Remotely-located physicians can communicate with users of the apparatus using video tele-medicine and request specific assays to be performed. The apparatus archives submitted samples for additional testing. Users may receive their assay results electronically. Users may allow the uploading of their diagnoses into a central databank for disease surveillance purposes.

DuPont Qualicon BAX System polymerase chain reaction assay. Performance Tested Method 100201.

PubMed

Tice, George; Andaloro, Bridget; Fallon, Dawn; Wallace, F Morgan

2009-01-01

A recent outbreak of Salmonella in peanut butter has highlighted the need for validation of rapid detection methods. A multilaboratory study for detecting Salmonella in peanut butter was conducted as part of the AOAC Research Institute Emergency Response Validation program for methods that detect outbreak threats to food safety. Three sites tested spiked samples from the same master mix according to the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA-BAM) method and the BAX System method. Salmonella Typhimurium (ATCC 14028) was grown in brain heart infusion for 24 h at 37 degrees C, then diluted to appropriate levels for sample inoculation. Master samples of peanut butter were spiked at high and low target levels, mixed, and allowed to equilibrate at room temperature for 2 weeks. Spike levels were low [1.08 most probable number (MPN)/25 g]; high (11.5 MPN/25 g) and unspiked to serve as negative controls. Each master sample was divided into 25 g portions and coded to blind the samples. Twenty portions of each spiked master sample and five portions of the unspiked sample were tested at each site. At each testing site, samples were blended in 25 g portions with 225 mL prewarmed lactose broth until thoroughly homogenized, then allowed to remain at room temperature for 55-65 min. Samples were adjusted to a pH of 6.8 +/- 0.2, if necessary, and incubated for 22-26 h at 35 degrees C. Across the three reporting laboratories, the BAX System detected Salmonella in 10/60 low-spike samples and 58/60 high-spike samples. The reference FDA-BAM method yielded positive results for 11/60 low-spike and 58/60 high-spike samples. Neither method demonstrated positive results for any of the 15 unspiked samples.

Sedimentation and occurrence and trends of selected chemical constituents in bottom sediment of 10 small reservoirs, Eastern Kansas

USGS Publications Warehouse

Juracek, Kyle E.

2004-01-01

Many municipalities in Kansas rely on small reservoirs as a source of drinking water and for recreational activities. Because of their significance to the community, management of the reservoirs and the associated basins is important to protect the reservoirs from degradation. Effective reservoir management requires information about water quality, sedimentation, and sediment quality. A combination of bathymetric surveying and bottom-sediment coring during 2002 and 2003 was used to investigate sediment deposition and the occurrence of selected nutrients (total nitrogen and total phosphorus), organic and total carbon, 26 trace elements, 15 organochlorine compounds, and 1 radionuclide in the bottom sediment of 10 small reservoirs in eastern Kansas. Original reservoir water-storage capacities ranged from 23 to 5,845 acre-feet. The mostly agricultural reservoir basins range in area from 0.6 to 14 square miles. The mean annual net volume of deposited sediment, estimated separately for several of the reservoirs, ranged from about 43,600 to about 531,000 cubic feet. The estimated mean annual net mass of deposited sediment ranged from about 1,360,000 to about 23,300,000 pounds. The estimated mean annual net sediment yields from the reservoir basins ranged from about 964,000 to about 2,710,000 pounds per square mile. Compared to sediment yield estimates provided by a statewide study published in 1965, the estimates determined in this study differed substantially and were typically smaller. A statistically significant positive correlation was determined for the relation between sediment yield and mean annual precipitation. Nutrient concentrations in the bottom sediment varied substantially among the 10 reservoirs. Median total nitrogen concentrations ranged from 1,400 to 3,700 milligrams per kilogram. Median total phosphorus concentrations ranged from 550 to 1,300 milligrams per kilogram. A statistically significant positive trend (that is, nutrient concentration increased toward the top of the sediment core) was indicated in one reservoir for total nitrogen and in two reservoirs for total phosphorus. Also, a possible positive trend for total nitrogen was indicated in two other reservoirs. These trends in nutrient concentrations may be related to a statewide increase in fertilizer use. Alternatively, the trends may be indicative of diagenesis (that is, postdepositional changes in the sediment caused by various processes including decomposition). Nutrient loads and yields also varied substantially among the five reservoirs for which loads and yields were estimated. Estimated mean annual net loads of total nitrogen deposited in the bottom sediment ranged from 4,080 to 49,100 pounds. Estimated mean annual net loads of total phosphorus deposited in the bottom sediment ranged from 1,120 to 20,800 pounds. Estimated mean annual net yields of total nitrogen from the basins ranged from 2,210 to 6,800 pounds per square mile. Estimated mean annual net yields of total phosphorus from the basins ranged from 598 to 2,420 pounds per square mile. Compared to nonenforceable sediment-quality guidelines adopted by the U.S. Environmental Protection Agency, bottom-sediment concentrations of arsenic, chromium, copper, and nickel in samples from all 10 reservoirs typically exceeded the threshold-effects levels (TELs) but were less than the probable-effects levels (PELs). TELs represent the concentrations above which toxic biological effects occasionally occur in aquatic organisms, whereas PELs represent the concentrations above which toxic biological effects usually or frequently occur. Concentrations of cadmium, lead, and zinc exceeded the TELs but were less than the PELs in sediment samples from about one-half of the reservoirs and were less than the TELs in samples from the remaining reservoirs. Mercury concentrations were less than the TEL (information only available for four reservoirs). Silver was not detected in the bottom sediment fro

Positive hysteresis of Ce-doped GAGG scintillator

NASA Astrophysics Data System (ADS)

Yanagida, Takayuki; Fujimoto, Yutaka; Koshimizu, Masanori; Watanabe, Kenichi; Sato, Hiroki; Yagi, Hideki; Yanagitani, Takagimi

2014-10-01

Positive hysteresis and radiation tolerance to high-dose radiation exposure were investigated for Ce 1% and 3% doped Gd3(Al, Ga)5O12 (Ce:GAGG) crystal scintillator on comparison with other garnet scintillators such Ce:YAG, Ce:LuAG, Pr:LuAG, and ceramic Ce:GAGG. When they were irradiated by several Gy 60Co γ-rays, Ce 1% doped GAGG crystal exhibited ∼20% light yield enhancement (positive hysteresis). This is the first time to observe positive hysteresis in Ce doped GAGG. On the other hand, other garnet materials did not show the positive hysteresis and their light yields were stable after 800 Gy irradiation except Pr:LuAG. The light yield of Pr:LuAG decreased largely. When irradiated Ce:GAGG which showed positive hysteresis was evaluated in Synchrotron facility (UVSOR), new excitation band was created around 60 nm.

RESPECT-ED: Rates of Pulmonary Emboli (PE) and Sub-Segmental PE with Modern Computed Tomographic Pulmonary Angiograms in Emergency Departments: A Multi-Center Observational Study Finds Significant Yield Variation, Uncorrelated with Use or Small PE Rates.

PubMed

Mountain, David; Keijzers, Gerben; Chu, Kevin; Joseph, Anthony; Read, Catherine; Blecher, Gabriel; Furyk, Jeremy; Bharat, Chrianna; Velusamy, Karthik; Munro, Andrew; Baker, Kylie; Kinnear, Frances; Mukherjee, Ahses; Watkins, Gina; Buntine, Paul; Livesay, Georgia; Fatovich, Daniel

2016-01-01

Overuse of CT Pulmonary Angiograms (CTPA) for diagnosing pulmonary embolism (PE), particularly in Emergency Departments (ED), is considered problematic. Marked variations in positive CTPA rates are reported, with American 4-10% yields driving most concerns. Higher resolution CTPA may increase sub-segmental PE (SSPE) diagnoses, which may be up to 40% false positive. Excessive use and false positives could increase harm vs. benefit. These issues have not been systematically examined outside America. To describe current yield variation and CTPA utilisation in Australasian ED, exploring potential factors correlated with variation. A retrospective multi-centre review of consecutive ED-ordered CTPA using standard radiology reports. ED CTPA report data were inputted onto preformatted data-sheets. The primary outcome was site level yield, analysed both intra-site and against a nominated 15.3% yield. Factors potentially associated with yield were assessed for correlation. Fourteen radiology departments (15 ED) provided 7077 CTPA data (94% ≥64-slice CT); PE were reported in 1028 (yield 14.6% (95%CI 13.8-15.4%; range 9.3-25.3%; site variation p <0.0001) with four sites significantly below and one above the 15.3% target. Admissions, CTPA usage, PE diagnosis rates and size of PE were uncorrelated with yield. Large PE (≥lobar) were 55% (CI: 52.1-58.2%) and SSPE 8.8% (CI: 7.1-10.5%) of positive scans. CTPA usage (0.2-1.5% adult attendances) was correlated (p<0.006) with PE diagnosis but not SSPE: large PE proportions. We found significant intra-site CTPA yield variation within Australasia. Yield was not clearly correlated with CTPA usage or increased small PE rates. Both SSPE and large PE rates were similar to higher yield historical cohorts. CTPA use was considerably below USA 2.5-3% rates. Higher CTPA utilisation was positively correlated with PE diagnoses, but without evidence of increased proportions of small PE. This suggests that increased diagnoses seem to be of clinically relevant sized PE.

Detection of bacteria and fungi in blood of patients with febrile neutropenia by real-time PCR with universal primers and probes.

PubMed

Teranishi, Hideto; Ohzono, Nanae; Inamura, Norikazu; Kato, Atsushi; Wakabayashi, Tokio; Akaike, Hiroto; Terada, Kihei; Ouchi, Kazunobu

2015-03-01

Febrile neutropenia is the main treatment-related cause of mortality in cancer patients. During June 2012 to April 2014, 97 blood culture samples were collected from patients receiving chemotherapy for hematological malignancy and cancer with febrile neutropenia episodes (FNEs). The samples were examined for the presence of bacteria and fungi using real-time PCR amplification and sequencing of 16S and 18S rRNA genes. Bacteria were identified in 20 of 97 samples (20.6%) by the real-time PCR assay and in 10 of 97 (10.3%) samples by blood culture. In 6 blood culture-positive samples, the real-time PCR assay detected the same type of bacteria. No fungi were detected by the real-time PCR assay or blood culture. During antibiotic therapy, all samples were negative by blood culture, but the real-time PCR assay yielded a positive result in 2 cases of 2 (100%). The bacterial DNA copy number was not well correlated with the serum C-reactive protein titer of patients with FNEs. We conclude that a real-time PCR assay could provide better detection of causative microbes' in a shorter time, and with a smaller blood sample than blood culture. Using a real-time PCR assay in combination with blood culture could improve microbiological documentation of FNEs. Copyright © 2014 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Genital mycoplasmas in semen samples of males attending a tertiary care hospital in Nigeria: any role in sperm count reduction?

PubMed

Agbakoba, N R; Adetosoye, A I; Ikechebelu, J I

2007-06-01

Semen samples from 54 married men attending the outpatient clinics for problems of infertility and routine semen analysis were examined for the presence of genital mycoplasmas. The mean age of the men was 36.1 years with a range of 25 55 years. Majority of the men 57.4% (31 of 54) were in their fourth decade of life (30 39 years). This age group also had the highest percentage 57.2% (8 of 14) of positive isolates of genital mycoplasmas on semen culture. A total of 21 organisms obtained from 14 (26.0%) positive samples were isolated. Mycoplasma and Ureaplasma spp. separately isolated from the samples yielded frequencies of 1 (1.9%) and 6 (11.1%) respectively and the remaining 7 (13.0%) samples were infected with both organisms. A breakdown of the mycoplasma species include 5 (23.8%) M. hominis, 2 (9.5%) M. fermentans and 1 (4.8%) M. penetrans. Apart from one isolate of M. hominis other Mycoplasma species were found in association with Ureaplasma species. Fifteen (71.4%) of the 21 isolates [8 (53.3%) ureaplasmas and 7 (46.7%) mycoplasmas] were isolated from samples with sperm counts less than 20 million/ml while the remaining 6 (21.6%) isolates [5 (83.3%) ureaplasmas and 1 (16.7) mycoplasma] were from samples with counts greater than 20 million/ml. This finding could indicate a possible influence of genital mycoplasmas especially mycoplasmas species on sperm count.

Interlaboratory Reproducibility and Proficiency Testing within the Human Papillomavirus Cervical Cancer Screening Program in Catalonia, Spain

PubMed Central

Ibáñez, R.; Félez-Sánchez, M.; Godínez, J. M.; Guardià, C.; Caballero, E.; Juve, R.; Combalia, N.; Bellosillo, B.; Cuevas, D.; Moreno-Crespi, J.; Pons, L.; Autonell, J.; Gutierrez, C.; Ordi, J.; de Sanjosé, S.

2014-01-01

In Catalonia, a screening protocol for cervical cancer, including human papillomavirus (HPV) DNA testing using the Digene Hybrid Capture 2 (HC2) assay, was implemented in 2006. In order to monitor interlaboratory reproducibility, a proficiency testing (PT) survey of the HPV samples was launched in 2008. The aim of this study was to explore the repeatability of the HC2 assay's performance. Participating laboratories provided 20 samples annually, 5 randomly chosen samples from each of the following relative light unit (RLU) intervals: <0.5, 0.5 to 0.99, 1 to 9.99, and ≥10. Kappa statistics were used to determine the agreement levels between the original and the PT readings. The nature and origin of the discrepant results were calculated by bootstrapping. A total of 946 specimens were retested. The kappa values were 0.91 for positive/negative categorical classification and 0.79 for the four RLU intervals studied. Sample retesting yielded systematically lower RLU values than the original test (P < 0.005), independently of the time elapsed between the two determinations (median, 53 days), possibly due to freeze-thaw cycles. The probability for a sample to show clinically discrepant results upon retesting was a function of the RLU value; samples with RLU values in the 0.5 to 5 interval showed 10.80% probability to yield discrepant results (95% confidence interval [CI], 7.86 to 14.33) compared to 0.85% probability for samples outside this interval (95% CI, 0.17 to 1.69). Globally, the HC2 assay shows high interlaboratory concordance. We have identified differential confidence thresholds and suggested the guidelines for interlaboratory PT in the future, as analytical quality assessment of HPV DNA detection remains a central component of the screening program for cervical cancer prevention. PMID:24574284

Three-dimensional cathodoluminescence characterization of a semipolar GaInN based LED sample

NASA Astrophysics Data System (ADS)

Hocker, Matthias; Maier, Pascal; Tischer, Ingo; Meisch, Tobias; Caliebe, Marian; Scholz, Ferdinand; Mundszinger, Manuel; Kaiser, Ute; Thonke, Klaus

2017-02-01

A semipolar GaInN based light-emitting diode (LED) sample is investigated by three-dimensionally resolved cathodoluminescence (CL) mapping. Similar to conventional depth-resolved CL spectroscopy (DRCLS), the spatial resolution perpendicular to the sample surface is obtained by calibration of the CL data with Monte-Carlo-simulations (MCSs) of the primary electron beam scattering. In addition to conventional MCSs, we take into account semiconductor-specific processes like exciton diffusion and the influence of the band gap energy. With this method, the structure of the LED sample under investigation can be analyzed without additional sample preparation, like cleaving of cross sections. The measurement yields the thickness of the p-type GaN layer, the vertical position of the quantum wells, and a defect analysis of the underlying n-type GaN, including the determination of the free charge carrier density. The layer arrangement reconstructed from the DRCLS data is in good agreement with the nominal parameters defined by the growth conditions.

Associations between pathogen-specific cases of subclinical mastitis and milk yield, quality, protein composition, and cheese-making traits in dairy cows.

PubMed

Bobbo, T; Ruegg, P L; Stocco, G; Fiore, E; Gianesella, M; Morgante, M; Pasotto, D; Bittante, G; Cecchinato, A

2017-06-01

The aim of this study was to investigate associations between pathogen-specific cases of subclinical mastitis and milk yield, quality, protein composition, and cheese-making traits. Forty-one multibreed herds were selected for the study, and composite milk samples were collected from 1,508 cows belonging to 3 specialized dairy breeds (Holstein Friesian, Brown Swiss, and Jersey) and 3 dual-purpose breeds of Alpine origin (Simmental, Rendena, and Grey Alpine). Milk composition [i.e., fat, protein, casein, lactose, pH, urea, and somatic cell count (SCC)] was analyzed, and separation of protein fractions was performed by reversed-phase high performance liquid chromatography. Eleven coagulation traits were measured: 5 traditional milk coagulation properties [time from rennet addition to milk gelation (RCT, min), curd-firming rate as the time to a curd firmness (CF) of 20 mm (k 20 , min), and CF at 30, 45, and 60 min from rennet addition (a 30 , a 45 , and a 60 , mm)], and 6 new curd firming and syneresis traits [potential asymptotical CF at an infinite time (CF P , mm), curd-firming instant rate constant (k CF , % × min -1 ), curd syneresis instant rate constant (k SR , % × min -1 ), modeled RCT (RCT eq , min), maximum CF value (CF max, mm), and time at CF max (t max , min)]. We also measured 3 cheese yield traits, expressing the weights of total fresh curd (%CY CURD ), dry matter (%CY SOLIDS ), and water (%CY WATER ) in the curd as percentages of the weight of the processed milk, and 4 nutrient recovery traits (REC PROTEIN , REC FAT , REC SOLIDS , and REC ENERGY ), representing the percentage ratio between each nutrient in the curd and milk. Milk samples with SCC > 100,000 cells/mL were subjected to bacteriological examination. All samples were divided into 7 clusters of udder health (UH) status: healthy (cows with milk SCC < 100,000 cells/mL and uncultured); culture-negative samples with low, medium, or high SCC; and culture-positive samples divided into contagious, environmental, and opportunistic intramammary infection (IMI). Data were analyzed using a linear mixed model. Significant variations in the casein to protein ratio and lactose content were observed in all culture-positive samples and in culture-negative samples with medium to high SCC compared to normal milk. No differences were observed among contagious, environmental, and opportunistic pathogens, suggesting an effect of inflammation rather than infection. The greatest impairment in milk quantity and composition, clotting ability, and cheese production was observed in the 2 UH status groups with the highest milk SCC (i.e., contagious IMI and culture-negative samples with high SCC), revealing a discrepancy between the bacteriological results and inflammatory status, and thus confirming the importance of SCC as an indicator of udder health and milk quality. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Estimating daily fat yield from a single milking on test day for herds with a robotic milking system.

PubMed

Peeters, R; Galesloot, P J B

2002-03-01

The objective of this study was to estimate the daily fat yield and fat percentage from one sampled milking per cow per test day in an automatic milking system herd, when the milking times and milk yields of all individual milkings are recorded by the automatic milking system. Multiple regression models were used to estimate the 24-h fat percentage when only one milking is sampled for components and milk yields and milking times are known for all milkings in the 24-h period before the sampled milking. In total, 10,697 cow test day records, from 595 herd tests at 91 Dutch herds milked with an automatic milking system, were used. The best model to predict 24-h fat percentage included fat percentage, protein percentage, milk yield and milking interval of the sampled milking, milk yield, and milking interval of the preceding milking, and the interaction between milking interval and the ratio of fat and protein percentage of the sampled milking. This model gave a standard deviation of the prediction error (SE) for 24-h fat percentage of 0.321 and a correlation between the predicted and actual 24-h fat percentage of 0.910. For the 24-h fat yield, we found SE = 90 g and correlation = 0.967. This precision is slightly better than that of present a.m.-p.m. testing schemes. Extra attention must be paid to correctly matching the sample jars and the milkings. Furthermore, milkings with an interval of less than 4 h must be excluded from sampling as well as milkings that are interrupted or that follow an interrupted milking. Under these restrictions (correct matching, interval of at least 4 h, and no interrupted milking), one sampled milking suffices to get a satisfactory estimate for the test-day fat yield.

Genetic correlations of mid-infrared-predicted milk fatty acid groups with milk production traits.

PubMed

Fleming, A; Schenkel, F S; Malchiodi, F; Ali, R A; Mallard, B; Sargolzaei, M; Jamrozik, J; Johnston, J; Miglior, F

2018-05-01

The objective of this research was to estimate the genetic correlations between milk mid-infrared-predicted fatty acid groups and production traits in first-parity Canadian Holsteins. Contents of short-chain, medium-chain, long-chain, saturated, and unsaturated fatty acid groupings in milk samples can be predicted using mid-infrared spectral data for cows enrolled in milk recording programs. Predicted fatty acid group contents were obtained for 49,127 test-day milk samples from 10,029 first-parity Holstein cows in 810 herds. Milk yield, fat and protein yield, fat and protein percentage, fat-to-protein ratio, and somatic cell score were also available for these test days. Genetic parameters were estimated for the fatty acid groups and production traits using multiple-trait random regression test day models by Bayesian methods via Gibbs sampling. Three separate 8- or 9-trait analyses were performed, including the 5 fatty acid groups with different combinations of the production traits. Posterior standard deviations ranged from <0.001 to 0.01. Average daily genetic correlations were negative and similar to each other for the fatty acid groups with milk yield (-0.62 to -0.59) and with protein yield (-0.32 to -0.25). Weak and positive average daily genetic correlations were found between somatic cell score and the fatty acid groups (from 0.25 to 0.36). Stronger genetic correlations with fat yield, fat and protein percentage, and fat-to-protein ratio were found with medium-chain and saturated fatty acid groups compared with those with long-chain and unsaturated fatty acid groups. Genetic correlations were very strong between the fatty acid groups and fat percentage, ranging between 0.88 for unsaturated and 0.99 for saturated fatty acids. Daily genetic correlations from 5 to 305 d in milk with milk, protein yield and percentage, and somatic cell score traits showed similar patterns for all fatty acid groups. The daily genetic correlations with fat yield at the beginning of lactation were decreasing for long-chain and unsaturated fatty acid groups and increasing for short-chain fatty acids. Genetic correlations between fat percentage and fatty acids were increasing at the beginning of lactation for short- and medium-chain and saturated fatty acids, but slightly decreasing for long-chain and unsaturated fatty acid groups. These results can be used in defining fatty acid traits and breeding objectives. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Designing occupancy studies when false-positive detections occur

USGS Publications Warehouse

Clement, Matthew

2016-01-01

1.Recently, estimators have been developed to estimate occupancy probabilities when false-positive detections occur during presence-absence surveys. Some of these estimators combine different types of survey data to improve estimates of occupancy. With these estimators, there is a tradeoff between the number of sample units surveyed, and the number and type of surveys at each sample unit. Guidance on efficient design of studies when false positives occur is unavailable. 2.For a range of scenarios, I identified survey designs that minimized the mean square error of the estimate of occupancy. I considered an approach that uses one survey method and two observation states and an approach that uses two survey methods. For each approach, I used numerical methods to identify optimal survey designs when model assumptions were met and parameter values were correctly anticipated, when parameter values were not correctly anticipated, and when the assumption of no unmodelled detection heterogeneity was violated. 3.Under the approach with two observation states, false positive detections increased the number of recommended surveys, relative to standard occupancy models. If parameter values could not be anticipated, pessimism about detection probabilities avoided poor designs. Detection heterogeneity could require more or fewer repeat surveys, depending on parameter values. If model assumptions were met, the approach with two survey methods was inefficient. However, with poor anticipation of parameter values, with detection heterogeneity, or with removal sampling schemes, combining two survey methods could improve estimates of occupancy. 4.Ignoring false positives can yield biased parameter estimates, yet false positives greatly complicate the design of occupancy studies. Specific guidance for major types of false-positive occupancy models, and for two assumption violations common in field data, can conserve survey resources. This guidance can be used to design efficient monitoring programs and studies of species occurrence, species distribution, or habitat selection, when false positives occur during surveys.

Biological sample collections from minors for genetic research: a systematic review of guidelines and position papers

PubMed Central

Hens, Kristien; Nys, Herman; Cassiman, Jean-Jacques; Dierickx, Kris

2009-01-01

Stored tissue samples are an important resource for epidemiological genetic research. Genetic research on biological material from minors can yield valuable information on the development and genesis of early-onset genetic disorders and the early interaction of environmental and genetic factors. The use of such tissue raises some specific ethical and governance questions, which are not completely covered by the discussion on biological materials from adults. We have retrieved 29 guidelines and position papers pertaining to the storage and use of biological tissue samples for genetic research, originating from 27 different organizations. Five documents have an international scope, three have an European scope and 21 have a national scope. We discovered that 11 of these documents did not contain a section on biological materials from minors. The content of the remaining 18 documents was categorized according to four themes: consent, principles of non-therapeutic research on vulnerable populations, ethics committee approval and difference between anonymous and identifiable samples. We found out that these themes are not consistently mentioned by each document, but that documents discussing the same themes were mostly in agreement with their recommendations. However, a systematic reflection on the ethical and policy issues arising from the participation of minors in biobank research is missing. PMID:19223929

Biological sample collections from minors for genetic research: a systematic review of guidelines and position papers.

PubMed

Hens, Kristien; Nys, Herman; Cassiman, Jean-Jacques; Dierickx, Kris

2009-08-01

Stored tissue samples are an important resource for epidemiological genetic research. Genetic research on biological material from minors can yield valuable information on the development and genesis of early-onset genetic disorders and the early interaction of environmental and genetic factors. The use of such tissue raises some specific ethical and governance questions, which are not completely covered by the discussion on biological materials from adults. We have retrieved 29 guidelines and position papers pertaining to the storage and use of biological tissue samples for genetic research, originating from 27 different organizations. Five documents have an international scope, three have an European scope and 21 have a national scope. We discovered that 11 of these documents did not contain a section on biological materials from minors. The content of the remaining 18 documents was categorized according to four themes: consent, principles of non-therapeutic research on vulnerable populations, ethics committee approval and difference between anonymous and identifiable samples. We found out that these themes are not consistently mentioned by each document, but that documents discussing the same themes were mostly in agreement with their recommendations. However, a systematic reflection on the ethical and policy issues arising from the participation of minors in biobank research is missing.

Novel genotype of Ehrlichia canis detected in samples of human blood bank donors in Costa Rica.

PubMed

Bouza-Mora, Laura; Dolz, Gaby; Solórzano-Morales, Antony; Romero-Zuñiga, Juan José; Salazar-Sánchez, Lizbeth; Labruna, Marcelo B; Aguiar, Daniel M

2017-01-01

This study focuses on the detection and identification of DNA and antibodies to Ehrlichia spp. in samples of blood bank donors in Costa Rica using molecular and serological techniques. Presence of Ehrlichia canis was determined in 10 (3.6%) out of 280 blood samples using polymerase chain reaction (PCR) targeting the ehrlichial dsb conserved gene. Analysis of the ehrlichial trp36 polymorphic gene in these 10 samples revealed substantial polymorphism among the E. canis genotypes, including divergent tandem repeat sequences. Nucleotide sequences of dsb and trp36 amplicons revealed a novel genotype of E. canis in blood bank donors from Costa Rica. Indirect immunofluorescence assay (IFA) detected antibodies in 35 (35%) of 100 serum samples evaluated. Thirty samples showed low endpoint titers (64-256) to E. canis, whereas five sera yielded high endpoint titers (1024-8192); these five samples were also E. canis-PCR positive. These findings represent the first report of the presence of E. canis in humans in Central America. Copyright © 2016 Elsevier GmbH. All rights reserved.

Supplementary effects of higher levels of various disaccharides on processing yield, quality properties and sensory attributes of Chinese - style pork jerky.

PubMed

Chen, Chih-Ming; Lin, Hsien-Tang

2017-12-01

This study evaluated the supplementary effect of higher concentrations of various disaccharides on processing yield, major physicochemical properties, and sensory attributes of Chinese-style pork jerky (CSPJ). CSPJ samples were prepared by marinating sliced ham (4 mm) with three dissaccharides, including sucrose, lactose, and maltose, at 0%, 15%, 18%, 21%, and 24%. Subsequently, the CSPJ samples were dried and roasted. The moisture content, water activity, crude protein, moisture-to-protein ratio, pH, processing yield, shear force, color, and sensory attributes of the CSPJ samples were evaluated. The quality characteristics of CSPJ samples prepared with sucrose were more acceptable. By contrast, CSPJ samples prepared with lactose showed the lowest scores. However, the processing yield and moisture content were the highest for CSPJ samples prepared with lactose, which may be associated with improved benefits for cost reduction. Furthermore, sucrose and lactose supplementation resulted in contrasting quality characteristics; for example, CSPJ samples with sucrose and maltose supplementation had higher sensory scores for color than samples with lactose supplementation. Additionally, most quality characteristics of CSPJ samples with sucrose supplementation contrasted with those of the samples with lactose supplementation; for example, the samples with sucrose supplementation had higher scores for sensory attributes than those with lactose supplementation. Sucrose supplementation up to 21% to 24% was associated with the highest overall acceptability scores (5.19 to 5.80), enhanced quality characteristics, increased processing yield, and reduced production cost.

Evaluation of BioFM liquid medium for culture of cerebrospinal fluid in tuberculous meningitis to identify Mycobacterium tuberculosis.

PubMed

Kashyap, R S; Ramteke, S S; Gaherwar, H M; Deshpande, P S; Purohit, H J; Taori, G M; Daginawala, H

2010-01-01

The present study was designed to evaluate the sensitivity and specificity of liquid culture medium (BioFM broth) for the diagnosis of tuberculous meningitis (TBM) in cerebrospinal fluid (CSF). CSF samples from 200 patients (TBM group = 150 and non-TBM group = 50) were tested for culture of Mycobacterium tuberculosis in BioFM liquid culture medium. Out of 150 TBM cases, 120 were found to be culture positive, indicating a sensitivity of 80% in BioFM broth within 2-3 weeks of inoculation. Positive cultures were also observed for CSF from 32 (64%) out of 50 non-TBM patients in BioFM liquid culture medium within 4 days of sample inoculation. Therefore, according to our study, BioFM broth system yielded 80% sensitivity [95% confidence interval (CI): 67-93%] and 36% specificity (95% CI: 57-98%) for TBM diagnosis. Our results indicate that although BioFM broth allows the detection of positive cultures within a shorter time, it has a high potential for contamination or for the coexistence of M. tuberculosis and non-tuberculous meningitis (NTM). This coexistence may go undetected or potentially lead to erroneous reporting of results.

Prevalence of bovine subclinical mastitis and isolation of its major causes in Bishoftu Town, Ethiopia.

PubMed

Birhanu, Misrak; Leta, Samson; Mamo, Gezahegne; Tesfaye, Shimelis

2017-12-21

A cross-sectional study was conducted from November 2015 to March 2016 to estimate the prevalence, to assess the risk factors and to isolate the major etiological agent of subclinical mastitis in Bishoftu town. The study was conducted on 262 cross breed lactating cows selected from 12 intensively managed dairy farms. California mastitis test (CMT) and bacteriological culture methods were used as diagnostic tools. From 262 cows examined, 105 (40.1%) and from 1048 quarters examined, 170 (16.1%) were positive for sub-clinical mastitis using CMT. All CMT positive samples were cultured for etiological agent identification. From 170 samples cultured, 153 were positive for known subclinical mastitis pathogens. The dominant bacteria isolated were Staphylococcus species from these Staphylococcus aureus (44.9%) was the major one followed by Streptococcus spp. (25.3%) and other gram negative enteric bacteria, Escherichia coli (8.8%). Age, body condition score, milk yield, and number of parity were considered as potential risk factors; among these, age and number of parity have statistically significance association with the occurrence of subclinical mastitis (P < 0.05) both in the CMT and the bacteriological tests.

Positive cell-free fetal DNA testing for trisomy 13 reveals confined placental mosaicism.

PubMed

Hall, April L; Drendel, Holli M; Verbrugge, Jennifer L; Reese, Angela M; Schumacher, Katherine L; Griffith, Christopher B; Weaver, David D; Abernathy, Mary P; Litton, Christian G; Vance, Gail H

2013-09-01

We report on a case in which cell-free fetal DNA was positive for trisomy 13 most likely due to confined placental mosaicism. Cell-free fetal DNA testing analyzes DNA derived from placental trophoblast cells and can lead to incorrect results that are not representative of the fetus. We sought to confirm commercial cell-free fetal DNA testing results by chorionic villus sampling and amniocentesis. These results were followed up by postnatal chromosome analysis of cord blood and placental tissue. First-trimester cell-free fetal DNA test results were positive for trisomy 13. Cytogenetic analysis of chorionic villus sampling yielded a mosaic karyotype of 47,XY,+13[10]/46,XY[12]. G-banded analysis of amniotic fluid was normal, 46,XY. Postnatal cytogenetic analysis of cord blood was normal. Karyotyping of tissues from four quadrants of the placenta demonstrated mosaicism for trisomy 13 in two of the quadrants and a normal karyotype in the other two. Our case illustrates several important aspects of this new testing methodology: that cell-free fetal DNA may not be representative of the fetal karyotype; that follow-up with diagnostic testing of chorionic villus sampling and/or amniotic fluid for abnormal test results should be performed; and that pretest counseling regarding the full benefits, limitations, and possible testing outcomes of cell-free fetal DNA screening is important.

The theory of polarization: From its origins to the modern day

NASA Astrophysics Data System (ADS)

Resta, Raffaele

Textbooks define macroscopic polarization P as the dipole of a bounded sample, divided by its volume, in the large sample limit. When instead we address unbounded samples within periodic boundary conditions (PBCs) the above definition cannot be adopted. The breakthrough came 25 years ago, when the focus was shifted from P itself to adiabatic changes in P, and it was soon realized that such changes take the form of a Berry phase of the electronic wavefunction. Even P itself can be defined, but it is not a vector: it is a lattice. Such exotic feature has outstanding physical consequences. For instance for an insulating centrosymmetric polymer P is a Z2 invariant: either P=e/2 mod e, or P=0 mod e: the Z2 class depends on the bulk, while the ``mod'' value depends on actual termination of the bounded sample. Besides P, other quantum-mechanical observables are based on the ``bare'' position r, which is not a legitimate operator within PBCs: foremost among them is orbital magnetization M. Here I express such observables in terms of a ``projected'' position operator r , which is legitimate for both bounded and unbounded samples, and yields very compact expressions for the relevant PBCs formulae. Besides P and M, I will also express in terms of r the anomalous Hall conductivity (for insulators and metals), and the Marzari-Vanderbilt gauge-invariant quadratic spread.

Salmonella Surveillance Among Great-Tailed Grackles (Quiscalus mexicanus) and Other Urban Bird Species in Eastern Texas.

PubMed

Grigar, Mary K; Cummings, Kevin J; Rodriguez-Rivera, Lorraine D; Rankin, Shelley C; Johns, Krista; Hamer, Gabriel L; Hamer, Sarah A

2016-12-01

Wild birds may play an important role in maintaining and transmitting Salmonella. Their ability to travel large distances and their proximity to human habitations could make them a vehicle for bridging Salmonella from wild and domestic animals to humans. To determine the potential public health risk presented by urban birds, we investigated the prevalence of Salmonella among great-tailed grackles (Quiscalus mexicanus) and other cohabiting urban bird species. Fecal samples were collected from 114 birds communally roosting in parking lots of retail locations in Brazos County, Texas, from February through July of 2015. Great-tailed grackles and European starlings (Sturnus vulgaris) were the predominant species sampled. Standard bacteriologic culture methods were used to isolate Salmonella from samples, and isolates were characterized by serotyping and antimicrobial susceptibility testing. Overall, 1.8% (2/114) of samples were confirmed positive for Salmonella. Both positive birds were great-tailed grackles sampled in June, yielding a 2.6% (2/76) apparent prevalence among this species. Isolates were serotyped as Salmonella Typhimurium and found to be pan-susceptible based on the National Antimicrobial Resistance Monitoring System (NARMS) panel of antimicrobial agents. The occurrence of Salmonella in great-tailed grackles represents a potential threat to public health, particularly considering their population size and tendency to congregate near human establishments such as grocery stores.

Comparison of different sampling techniques and of different culture methods for detection of group B streptococcus carriage in pregnant women.

PubMed

El Aila, Nabil A; Tency, Inge; Claeys, Geert; Saerens, Bart; Cools, Piet; Verstraelen, Hans; Temmerman, Marleen; Verhelst, Rita; Vaneechoutte, Mario

2010-09-29

Streptococcus agalactiae (group B streptococcus; GBS) is a significant cause of perinatal and neonatal infections worldwide. To detect GBS colonization in pregnant women, the CDC recommends isolation of the bacterium from vaginal and anorectal swab samples by growth in a selective enrichment medium, such as Lim broth (Todd-Hewitt broth supplemented with selective antibiotics), followed by subculture on sheep blood agar. However, this procedure may require 48 h to complete. We compared different sampling and culture techniques for the detection of GBS. A total of 300 swabs was taken from 100 pregnant women at 35-37 weeks of gestation. For each subject, one rectovaginal, one vaginal and one rectal ESwab were collected. Plating onto Columbia CNA agar (CNA), group B streptococcus differential agar (GBSDA) (Granada Medium) and chromID Strepto B agar (CA), with and without Lim broth enrichment, were compared. The isolates were confirmed as S. agalactiae using the CAMP test on blood agar and by molecular identification with tDNA-PCR or by 16S rRNA gene sequence determination. The overall GBS colonization rate was 22%. GBS positivity for rectovaginal sampling (100%) was significantly higher than detection on the basis of vaginal sampling (50%), but not significantly higher than for rectal sampling (82%). Direct plating of the rectovaginal swab on CNA, GBSDA and CA resulted in detection of 59, 91 and 95% of the carriers, respectively, whereas subculturing of Lim broth yielded 77, 95 and 100% positivity, respectively. Lim broth enrichment enabled the detection of only one additional GBS positive subject. There was no significant difference between GBSDA and CA, whereas both were more sensitive than CNA. Direct culture onto GBSDA or CA (91 and 95%) detected more carriers than Lim broth enrichment and subculture onto CNA (77%). One false negative isolate was observed on GBSDA, and three false positives on CA. In conclusion, rectovaginal sampling increased the number GBS positive women detected, compared to vaginal and/or rectal sampling. Direct plating on CA and/or GBSDA provided rapid detection of GBS that was at least as sensitive and specific as the CDC recommended method of Lim broth subcultured onto non chromogenic agar.

Lagos bat virus transmission in an Eidolon helvum bat colony, Ghana.

PubMed

Freuling, Conrad M; Binger, Tabea; Beer, Martin; Adu-Sarkodie, Yaw; Schatz, Juliane; Fischer, Melina; Hanke, Dennis; Hoffmann, Bernd; Höper, Dirk; Mettenleiter, Thomas C; Oppong, Samual K; Drosten, Christian; Müller, Thomas

2015-12-02

A brain sample of a straw-coloured fruit bat (Eidolon helvum) from Ghana without evident signs of disease tested positive by generic Lyssavirus RT-PCR and direct antigen staining. Sequence analysis confirmed the presence of a Lagos bat virus belonging to phylogenetic lineage A. Virus neutralization tests using the isolate with sera from the same group of bats yielded neutralizing antibodies in 74% of 567 animals. No cross-neutralization was observed against a different Lagos bat virus (lineage B). Copyright © 2015 Elsevier B.V. All rights reserved.

Sensitive and affordable diagnostic assay for the quantitative detection of anaplastic lymphoma kinase (ALK) alterations in patients with non-small cell lung cancer.

PubMed

Dama, Elisa; Tillhon, Micol; Bertalot, Giovanni; de Santis, Francesca; Troglio, Flavia; Pessina, Simona; Passaro, Antonio; Pece, Salvatore; de Marinis, Filippo; Dell'Orto, Patrizia; Viale, Giuseppe; Spaggiari, Lorenzo; Di Fiore, Pier Paolo; Bianchi, Fabrizio; Barberis, Massimo; Vecchi, Manuela

2016-06-14

Accurate detection of altered anaplastic lymphoma kinase (ALK) expression is critical for the selection of lung cancer patients eligible for ALK-targeted therapies. To overcome intrinsic limitations and discrepancies of currently available companion diagnostics for ALK, we developed a simple, affordable and objective PCR-based predictive model for the quantitative measurement of any ALK fusion as well as wild-type ALK upregulation. This method, optimized for low-quantity/-quality RNA from FFPE samples, combines cDNA pre-amplification with ad hoc generated calibration curves. All the models we derived yielded concordant predictions when applied to a cohort of 51 lung tumors, and correctly identified all 17 ALK FISH-positive and 33 of the 34 ALK FISH-negative samples. The one discrepant case was confirmed as positive by IHC, thus raising the accuracy of our test to 100%. Importantly, our method was accurate when using low amounts of input RNA (10 ng), also in FFPE samples with limited tumor cellularity (5-10%) and in FFPE cytology specimens. Thus, our test is an easily implementable diagnostic tool for the rapid, efficacious and cost-effective screening of ALK status in patients with lung cancer.

Lucerne transient streak virus; a Recently Detected Virus Infecting Alfafa (Medicago sativa) in Central Saudi Arabia.

PubMed

Raza, Ahmed; Al-Shahwan, Ibrahim M; Abdalla, Omer A; Al-Saleh, Mohammed A; Amer, Mahmoud A

2017-02-01

A survey was conducted to determine the status of Lucerne transient streak virus (LTSV) in three high-yielding alfalfa regions in central Saudi Arabia (Riyadh, Qassim, and Hail) during 2014. Three hundred and eight symptomatic alfalfa, and seven Sonchus oleraceus samples were collected. DAS-ELISA indicated that 59 of these samples were positive to LTSV. Two isolates of LTSV from each region were selected for molecular studies. RT-PCR confirmed the presence of LTSV in the selected samples using a specific primer pair. Percentage identity and homology tree comparisons revealed that all Saudi isolates were more closely related to each other but also closely related to the Canadian isolate-JQ782213 (97.1-97.6%) and the New Zealand isolate-U31286 (95.8-97.1%). Comparing Saudi isolates of LTSV with ten other sobemoviruses based on the coat protein gene sequences confirmed the distant relationship between them. Eleven out of fourteen plant species used in host range study were positive to LTSV. This is the first time to document that Trifolium alexandrinum , Nicotiana occidentalis , Chenopodium glaucum , and Lathyrus sativus are new host plant species for LTSV and that N. occidentalis being a good propagative host for it.

Guided percutaneous fine-needle aspiration biopsy of the liver

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, C.S.; McLoughlin, M.J.; Tao, L.C.

1981-04-01

Forty patients with suspected malignant disease of the liver underwent percutaneous fine-needle aspiration biopsy with radioisotope scintigraphic and fluoroscopic guidance. The needle was aimed at focal defects identified on the liver scan and several passes were made. When the scan was diffusely abnormal, the liver was widely sampled with multiple passes. Thirty patients were eventually considered to have malignant disease and aspiration biopsy was positive in 28 (93%) of these patients, including 25 of 26 with liver metastases (96%). There were two false-positive results and one minor complication. In 24 patients, conventional wide-bore needle biopsy was also performed. In thismore » group, 16 patients had a final diagnosis of hepatic malignancy. Aspiration biopsies were positive in 14 of these (87%) and conventional needle biopsies were positive in four (25%). Guided percutaneous fine-needle aspiration biopsy is recommended for pathologic diagnosis of hepatic malignancy because of its simplicity, high yield, and reasonable safety.« less

Calibrating SALT: a sampling scheme to improve estimates of suspended sediment yield

Treesearch

Robert B. Thomas

1986-01-01

Abstract - SALT (Selection At List Time) is a variable probability sampling scheme that provides unbiased estimates of suspended sediment yield and its variance. SALT performs better than standard schemes which are estimate variance. Sampling probabilities are based on a sediment rating function which promotes greater sampling intensity during periods of high...

Evaluation of Legionella Air Contamination in Healthcare Facilities by Different Sampling Methods: An Italian Multicenter Study.

PubMed

Montagna, Maria Teresa; De Giglio, Osvalda; Cristina, Maria Luisa; Napoli, Christian; Pacifico, Claudia; Agodi, Antonella; Baldovin, Tatjana; Casini, Beatrice; Coniglio, Maria Anna; D'Errico, Marcello Mario; Delia, Santi Antonino; Deriu, Maria Grazia; Guida, Marco; Laganà, Pasqualina; Liguori, Giorgio; Moro, Matteo; Mura, Ida; Pennino, Francesca; Privitera, Gaetano; Romano Spica, Vincenzo; Sembeni, Silvia; Spagnolo, Anna Maria; Tardivo, Stefano; Torre, Ida; Valeriani, Federica; Albertini, Roberto; Pasquarella, Cesira

2017-06-22

Healthcare facilities (HF) represent an at-risk environment for legionellosis transmission occurring after inhalation of contaminated aerosols. In general, the control of water is preferred to that of air because, to date, there are no standardized sampling protocols. Legionella air contamination was investigated in the bathrooms of 11 HF by active sampling (Surface Air System and Coriolis ® μ) and passive sampling using settling plates. During the 8-hour sampling, hot tap water was sampled three times. All air samples were evaluated using culture-based methods, whereas liquid samples collected using the Coriolis ® μ were also analyzed by real-time PCR. Legionella presence in the air and water was then compared by sequence-based typing (SBT) methods. Air contamination was found in four HF (36.4%) by at least one of the culturable methods. The culturable investigation by Coriolis ® μ did not yield Legionella in any enrolled HF. However, molecular investigation using Coriolis ® μ resulted in eight HF testing positive for Legionella in the air. Comparison of Legionella air and water contamination indicated that Legionella water concentration could be predictive of its presence in the air. Furthermore, a molecular study of 12 L. pneumophila strains confirmed a match between the Legionella strains from air and water samples by SBT for three out of four HF that tested positive for Legionella by at least one of the culturable methods. Overall, our study shows that Legionella air detection cannot replace water sampling because the absence of microorganisms from the air does not necessarily represent their absence from water; nevertheless, air sampling may provide useful information for risk assessment. The liquid impingement technique appears to have the greatest capacity for collecting airborne Legionella if combined with molecular investigations.

Evaluation of Legionella Air Contamination in Healthcare Facilities by Different Sampling Methods: An Italian Multicenter Study

PubMed Central

Montagna, Maria Teresa; De Giglio, Osvalda; Cristina, Maria Luisa; Napoli, Christian; Pacifico, Claudia; Agodi, Antonella; Baldovin, Tatjana; Casini, Beatrice; Coniglio, Maria Anna; D’Errico, Marcello Mario; Delia, Santi Antonino; Deriu, Maria Grazia; Guida, Marco; Laganà, Pasqualina; Liguori, Giorgio; Moro, Matteo; Mura, Ida; Pennino, Francesca; Privitera, Gaetano; Romano Spica, Vincenzo; Sembeni, Silvia; Spagnolo, Anna Maria; Tardivo, Stefano; Torre, Ida; Valeriani, Federica; Albertini, Roberto; Pasquarella, Cesira

2017-01-01

Healthcare facilities (HF) represent an at-risk environment for legionellosis transmission occurring after inhalation of contaminated aerosols. In general, the control of water is preferred to that of air because, to date, there are no standardized sampling protocols. Legionella air contamination was investigated in the bathrooms of 11 HF by active sampling (Surface Air System and Coriolis®μ) and passive sampling using settling plates. During the 8-hour sampling, hot tap water was sampled three times. All air samples were evaluated using culture-based methods, whereas liquid samples collected using the Coriolis®μ were also analyzed by real-time PCR. Legionella presence in the air and water was then compared by sequence-based typing (SBT) methods. Air contamination was found in four HF (36.4%) by at least one of the culturable methods. The culturable investigation by Coriolis®μ did not yield Legionella in any enrolled HF. However, molecular investigation using Coriolis®μ resulted in eight HF testing positive for Legionella in the air. Comparison of Legionella air and water contamination indicated that Legionella water concentration could be predictive of its presence in the air. Furthermore, a molecular study of 12 L. pneumophila strains confirmed a match between the Legionella strains from air and water samples by SBT for three out of four HF that tested positive for Legionella by at least one of the culturable methods. Overall, our study shows that Legionella air detection cannot replace water sampling because the absence of microorganisms from the air does not necessarily represent their absence from water; nevertheless, air sampling may provide useful information for risk assessment. The liquid impingement technique appears to have the greatest capacity for collecting airborne Legionella if combined with molecular investigations. PMID:28640202

Important vectors for Listeria monocytogenes transmission at farm dairies manufacturing fresh sheep and goat cheese from raw milk.

PubMed

Schoder, Dagmar; Melzner, Daniela; Schmalwieser, Alois; Zangana, Abdoulla; Winter, Petra; Wagner, Martin

2011-06-01

The aim of this study was to determine the transmission routs of Listeria spp. in dairy farms manufacturing fresh cheese made from ovine and caprine raw milk and to evaluate the impact of Listeria monocytogenes mastitis on raw milk contamination. Overall, 5,799 samples, including 835 environmental samples, 230 milk and milk product samples, and 4,734 aseptic half-udder foremilk samples were collected from 53 dairy farms in the dairy intensive area of Lower Austria. Farms were selected for the study because raw milk was processed to cheese that was sold directly to consumers. A total of 153 samples were positive for Listeria spp., yielding an overall prevalence of 2.6%; L. monocytogenes was found in 0.9% of the samples. Bulk tank milk, cheese, and half-udder samples were negative for Listeria spp. Because none of the sheep and goats tested positive from udder samples, L. monocytogenes mastitis was excluded as a significant source of raw milk contamination. L. monocytogenes was detected at 30.2% of all inspected farms. Swab samples from working boots and fecal samples had a significantly higher overall prevalence (P < 0.001) of L. monocytogenes (15.7 and 13.0%, respectively) than did swab samples from the milk processing environment (7.9%). A significant correlation was found between the prevalence of L. monocytogenes in the animal and in the milk processing environment and the silage feeding practices. Isolation of L. monocytogenes was three to seven times more likely from farms where silage was fed to animals throughout the year than from farms where silage was not fed to the animals.

Blood culture bottles are superior to conventional media for vitreous culture.

PubMed

Thariya, Patsuda; Yospaiboon, Yosanan; Sinawat, Suthasinee; Sanguansak, Thuss; Bhoomibunchoo, Chavakij; Laovirojjanakul, Wipada

2016-08-01

To compare blood culture bottles and conventional media for the vitreous culture in patients with clinically suspected infectious endophthalmitis. Retrospective comparative study at KKU Eye Center, Khon Kaen University. There were 342 patients with clinically suspected infectious endophthalmitis participated in the study. The vitreous specimens were inoculated in both blood culture bottles and on conventional culture media (blood agar, MacConkey agar, chocolate agar, Sabouraud dextrose agar and thioglycolate broth). The number of positive culture yields in both blood culture bottles and conventional media. Positive culture yields in both methods were found in 151 eyes (49.5%). There were 136 of 151 eyes (90.1%) with positive culture in blood culture bottles, whereas 99 of 151 eyes (65.6%) yielded positive cultures in conventional media. These findings were different with a statistical significance (P < 0.00001) and an odds ratio of 3.47 (95% confidence interval 1.92, 6.63). A combination of blood culture bottles and conventional media improved the yield. Blood culture bottles are superior to conventional media for vitreous culture in clinically suspected infectious endophthalmitis. Vitreous culture using blood culture bottles should be recommended as the primary method for microbiological diagnosis. A combination of both methods further improves the positive culture yield. © 2016 Royal Australian and New Zealand College of Ophthalmologists.

Identification of last interglacial deposits in eastern Beringia: a cautionary note from the Palisades, interior Alaska

USGS Publications Warehouse

Reyes, Alberto V.; Zazula, Grant D.; Kuzmina, Svetlana; Ager, Thomas A.; Froese, Duane G.

2011-01-01

Last interglacial sediments in unglaciated Alaska and Yukon (eastern Beringia) are commonly identified by palaeoecological indicators and stratigraphic position ~2-5m above the regionally prominent Old Crow tephra (124 + or - 10ka). We demonstrate that this approach can yield erroneous age assignments using data from a new exposure at the Palisades, a site in interior Alaska with numerous exposures of last interglacial sediments. Tephrochronology, stratigraphy, plant macrofossils, pollen and fossil insects from a prominent wood-rich organic silt unit are all consistent with a last interglacial age assignment. However, six 14C dates on plant and insect macrofossils from the organic silt range from non-finite to 4.0 14C ka BP, indicating that the organic silt instead represents a Holocene deposit with a mixed-age assemblage of organic material. In contrast, wood samples from presumed last interglacial organic-rich sediments elsewhere at the Palisades, in a similar stratigraphic position with respect to Old Crow tephra, yield non-finite 14C ages. Given that local permafrost thaw since the last interglaciation may facilitate reworking of older sediments into new stratigraphic positions, minimum constraining ages based on 14C dating or other methods should supplement age assignments for last interglacial sediments in eastern Beringia that are based on palaeoecology and stratigraphic association with Old Crow tephra.

Can the diagnosis of recurrent vulvovaginal candidosis be improved by use of vaginal lavage samples and cultures on chromogenic agar?

PubMed Central

Novikova, N; Rodrigues, A; Mårdh, P A

2002-01-01

OBJECTIVE: To investigate if introital and vaginal flushing samples inoculated on chromogenic agar could increase the recovery rate and rapid identification of Candida and non-albicans species, as compared to culture of posterior vaginal fornix samples on Sabouraud agar and speciation of isolates by biochemical tests. METHODS: Samples from the introitus and the posterior vaginal fornix and vaginal lavage samples were collected from 91 women with a history suggestive of recurrent vulvovaginal candidosis (RVVC), and with a suspected new attack of the condition. The specimens were cultured on Sabouraud and CHROMagar. Speciation of yeast isolates was made on the chromogenic agar by API 32C kits and by an atomized system (Vitek). RESULTS: Forty-six (51%) women were positive for Candida from one or more of the samples. The introital cultures were positive in 43 (47%) women, both on Sabouraud and chromogenic agar. From the posterior vaginal fomix, 42 (46%) women were positive on the Sabouraud and 43 (47%) on chromogenic agar cultures, while the vaginal lavage cultures yielded Candida on those two media in 40 (44%) and 41 (45%) cases, respectively. Candida albicans was the most frequent species recovered, from 40 (87%) cases, followed by C. krusei in 4 (9%), C. glabrata in 2 (4%), and C. parapsilosis in one case. There was only one woman who had a mixed yeast infection, by C. albicans and C. krusei. There was only one discrepancy in the speciation as demonstrated by mean of chromogenic agar and API 32C kit. CONCLUSIONS: Neither cultures of introital nor of vaginal lavage samples increases the detection rate of Candida in RVVC cases as compared to cultures of posterior vaginal fornix samples. Use of chromogenic agar is a convenient and reliable means to detect colonization by Candida and differentiate between C. albicans and non-albicans species. PMID:12530485

The Diagnostic Yield of Array Comparative Genomic Hybridization Is High Regardless of Severity of Intellectual Disability/Developmental Delay in Children.

PubMed

D'Arrigo, Stefano; Gavazzi, Francesco; Alfei, Enrico; Zuffardi, Orsetta; Montomoli, Cristina; Corso, Barbara; Buzzi, Erika; Sciacca, Francesca L; Bulgheroni, Sara; Riva, Daria; Pantaleoni, Chiara

2016-05-01

Microarray-based comparative genomic hybridization is a method of molecular analysis that identifies chromosomal anomalies (or copy number variants) that correlate with clinical phenotypes. The aim of the present study was to apply a clinical score previously designated by de Vries to 329 patients with intellectual disability/developmental disorder (intellectual disability/developmental delay) referred to our tertiary center and to see whether the clinical factors are associated with a positive outcome of aCGH analyses. Another goal was to test the association between a positive microarray-based comparative genomic hybridization result and the severity of intellectual disability/developmental delay. Microarray-based comparative genomic hybridization identified structural chromosomal alterations responsible for the intellectual disability/developmental delay phenotype in 16% of our sample. Our study showed that causative copy number variants are frequently found even in cases of mild intellectual disability (30.77%). We want to emphasize the need to conduct microarray-based comparative genomic hybridization on all individuals with intellectual disability/developmental delay, regardless of the severity, because the degree of intellectual disability/developmental delay does not predict the diagnostic yield of microarray-based comparative genomic hybridization. © The Author(s) 2015.

Psychosocial Benefits of Cooking Interventions: A Systematic Review.

PubMed

Farmer, Nicole; Touchton-Leonard, Katherine; Ross, Alyson

2018-04-01

Cooking interventions are used in therapeutic and rehabilitative settings; however, little is known about the influence of these interventions on psychosocial outcomes. This systematic review examines the research evidence regarding the influence of cooking interventions on psychosocial outcomes. A systematic review of the literature examined peer-reviewed research using Embase, PubMed, CINALH Plus, and PsychInfo with the following search terms: cooking, culinary, baking, food preparation, cookery, occupational therapy, mental health, mood, psychosocial, affect, confidence, self-confidence, self-esteem, socialization, and rehabilitation. Inclusion criteria were the following: adults, English, influence of cooking interventions on psychosocial outcomes. PRISMA guidelines were used. The search yielded 377 articles; and 11 ultimately met inclusion criteria and were reviewed. Generally, the quality of the research was weak due to nonrandomization, unvalidated research tools, and small sample sizes. However, inpatient and community-based cooking interventions yielded positive influences on socialization, self-esteem, quality of life, and affect. Finding benefits to cooking that extend beyond nutritional may be helpful in increasing motivation and frequency of cooking. This review suggests that cooking interventions may positively influence psychosocial outcomes, although this evidence is preliminary and limited. Further qualitative and rigorous quantitative research are needed to identify mechanisms by which cooking interventions may improve psychosocial outcomes.

Performance of Xpert MTB/RIF on Ascitic Fluid Samples for Detection of Abdominal Tuberculosis.

PubMed

Rufai, Syed Beenish; Singh, Sarman; Singh, Amit; Kumar, Parveen; Singh, Jitendra; Vishal, Anand

2017-01-01

Diagnosis of abdominal tuberculosis (TB) from ascitic fluid samples using routinely available diagnostic methods is challenging due to its paucibacillary nature. Although performance of Xpert MTB/RIF assay has been evaluated extensively on pulmonary samples, its performance on extrapulmonary samples is still under evaluation. The objective of this study was to find out the performance of Xpert MTB/RIF on ascitic fluid samples obtained from suspected cases of abdominal TB. Performance was compared with Mycobacterium growth indicator tube-960 (MGIT-960) culture and in-house multiplex polymerase chain reaction (PCR). The latter detects and differentiates Mycobacterium tuberculosis and nontuberculous mycobacteria simultaneously. Sixty-seven patients suspected of probable/possible abdominal TB were included in this observational, prospective study. All samples were tested by Ziehl-Neelsen staining, MGIT-960 culture, in-house multiplex PCR, and Xpert MTB/RIF assay. All 67 samples were smear negative. Seventeen (25.4%) were MGIT-960 culture positive while 12 (17.9%) were detected positive by the Xpert MTB/RIF assay and 9 (13.4%) by in-house multiplex PCR. Sensitivity and specificity of the Xpert MTB/RIF assay compared with the MGIT-960 culture were 70.6% (95%, confidence interval [CI]: 44.1-89.7) and 100% (95%, CI: 92.8-100) and that of in-house multiplex PCR were 52.9% (95%, CI: 30.9-73.8) and 100% (95%, CI: 92.8-100), respectively. Diagnostic yield of Xpert MTB/RIF assay on ascitic fluid samples was lower than MGIT-960 culture. We thus emphasize on the need for urgent discovery of new biomarkers for paucibacillary TB.

Percutaneous CT-Guided Biopsies of the Cervical Spine: Technique, Histopathologic and Microbiologic Yield, and Safety at a Single Academic Institution.

PubMed

Wiesner, E L; Hillen, T J; Long, J; Jennings, J W

2018-05-01

Cervical spine biopsies can be challenging due to the anatomy and the adjacent critical structures. Percutaneous image-guided biopsies can obviate the need for an open biopsy, however there have been few studies looking at the approaches, safety, and efficacy of percutaneous cervical spine biopsies. This retrospective study evaluated technical considerations, histopathologic and microbiologic yield, and safety in CT-guided cervical bone biopsies. A retrospective review of cervical bone and/or bone/disc biopsies performed from January 2010 to January 2017 was included in this study. Clinical diagnosis and indication, patient demographics, biopsy location, biopsy needle type, technical approach, lesion size, dose-length product, conscious sedation details, complications, and diagnostic histopathologic and/or microbiologic yield were recorded for each case and summarized. A total of 73 patients underwent CT-guided cervical bone biopsies. Fifty-three percent (39/73) were for clinical/imaging concern for infection and 47% (34/73) were for primary tumors or metastatic disease. Thirty-four percent (25/73) were of the inferior cervical spine (ie, C6 and C7). A sufficient sample was obtained for histopathologic and microbiologic analyses in 96% (70/73) of the biopsies. Forty-six percent (18/39) of those samples taken for infection had positive cultures. Two intraprocedural complications occurred in which the patients became hypotensive during the procedure without long-term complications. Percutaneous CT-guided biopsy of the cervical spine is an effective and safe procedure with high diagnostic yield and can obviate open procedures for histopathologic and microbiologic analyses of patients with clinical and imaging findings concerning for infection or primary and metastatic osseous lesions. © 2018 by American Journal of Neuroradiology.

Analysis of a repetitive DNA sequence from Bordetella pertussis and its application to the diagnosis of pertussis using the polymerase chain reaction.

PubMed Central

Glare, E M; Paton, J C; Premier, R R; Lawrence, A J; Nisbet, I T

1990-01-01

A tandemly repeated 1,046-base-pair (bp) ClaI DNA fragment from Bordetella pertussis was cloned into Escherichia coli by using the vector pUC19. This fragment, when isolated, hybridized strongly to DNA from all 100 clinical isolates of B. pertussis tested. It was shown to have homology to single-copy sequences in Bordetella bronchiseptica but not Bordetella parapertussis and did not hybridize to lysate blots of a wide range of other bacteria, including members of the closely related genera Pasteurella, Alcaligenes, and Haemophilus. The 1,046-bp fragment was sequenced, and complementary synthetic oligonucleotides flanking a 153-bp region within the repeated element were used as primers for specific amplification of this region using the polymerase chain reaction (PCR). This procedure was then applied to the rapid (5-h) detection of B. pertussis in nasopharyngeal secretions collected from 332 children with suspected pertussis. The test yielded positive results in a total of 98 samples, compared with 66 for culture and 33 for direct immunofluorescence (IF). All of the IF-positive samples were PCR positive, as were 63 of the samples from which B. pertussis was eventually cultured. Two hundred thirty-one specimens which were negative by IF and culture were also negative in the PCR assay. However, 33 culture- and IF-negative specimens were positive by PCR assay. Several of these specimens were collected from close contacts of culture-proven pertussis patients, were follow-up specimens from such patients, or were from patients with serological evidence of pertussis and therefore may be true-rather than false-positives. Images PMID:2229381

No evidence of persisting measles virus in peripheral blood mononuclear cells from children with autism spectrum disorder.

PubMed

D'Souza, Yasmin; Fombonne, Eric; Ward, Brian J

2006-10-01

Despite epidemiologic evidence to the contrary, claims of an association between measles-mumps-rubella vaccination and the development of autism have persisted. Such claims are based primarily on the identification of measles virus nucleic acids in tissues and body fluids by polymerase chain reaction. We sought to determine whether measles virus nucleic acids persist in children with autism spectrum disorder compared with control children. Peripheral blood mononuclear cells were isolated from 54 children with autism spectrum disorder and 34 developmentally normal children, and up to 4 real-time polymerase chain reaction assays and 2 nested polymerase chain reaction assays were performed. These assays targeted the nucleoprotein, fusion, and hemagglutinin genes of measles virus using previously published primer pairs with detection by SYBR green I. Our own real-time assay targeted the fusion gene using novel primers and an internal fluorescent probe. Positive reactions were evaluated rigorously, and amplicons were sequenced. Finally, anti-measles antibody titers were measured by enzyme immunoassay. The real-time assays based on previously published primers gave rise to a large number of positive reactions in both autism spectrum disorder and control samples. Almost all of the positive reactions in these assays were eliminated by evaluation of melting curves and amplicon band size. The amplicons for the remaining positive reactions were cloned and sequenced. No sample from either autism spectrum disorder or control groups was found to contain nucleic acids from any measles virus gene. In the nested polymerase chain reaction and in-house assays, none of the samples yielded positive results. Furthermore, there was no difference in anti-measles antibody titers between the autism and control groups. There is no evidence of measles virus persistence in the peripheral blood mononuclear cells of children with autism spectrum disorder.

Kr-86 Ion-Beam Irradiation of Hydrated DNA: Free Radical and Unaltered Base Yields

PubMed Central

Becker, David; Adhikary, Amitava; Tetteh, Smedley T.; Bull, Arthur W.; Sevilla, Michael D.

2012-01-01

This work reports an ESR and product analysis investigation of Kr-86 ion-beam irradiation of hydrated DNA at 77 K. The irradiation results in the formation and trapping of both base radicals and sugar phosphate radicals (DNA backbone radicals). The absolute yields (G, μmol/J) of the base radicals are smaller than the yields found in similarly prepared γ-irradiated DNA samples, and the relative yields of backbone radicals relative to base radicals are much higher than that found in γ-irradiated samples. From these results, we have elaborated our radiation chemical model of the track structure for ion-beam irradiated DNA as it applies to krypton ion-beams. The base radicals, which are trapped as ion radicals or reversibly protonated or deprotonated ion radicals, are formed almost entirely in the track penumbra, a region in which radiation chemical effects are similar to those found in γ-irradiated samples. By comparing the yields of base radicals in ion-beam samples to the yields of the same radicals in γ-irradiated samples, the partition of energy between the low-LET region (penumbra) and the core is experimentally determined. The neutral sugar and other backbone radicals, which are not as susceptible to recombination as are ion radicals, are formed largely in the track core. The backbone radicals show a linear dose response up to very high doses. Unaltered base release yields in Kr-86 irradiated hydrated DNA are equal to sugar radical yields within experimental error limits, consistent with radiation-chemical processes in which all base release originates with sugar radicals. Two phosphorus-centered radicals from fragmentation of the DNA backbone are found in low yields. PMID:23106211

Kr-86 ion-beam irradiation of hydrated DNA: free radical and unaltered base yields.

PubMed

Becker, David; Adhikary, Amitava; Tetteh, Smedley T; Bull, Arthur W; Sevilla, Michael D

2012-12-01

This work reports an ESR and product analysis investigation of Kr-86 ion-beam irradiation of hydrated DNA at 77 K. The irradiation results in the formation and trapping of both base radicals and sugar phosphate radicals (DNA backbone radicals). The absolute yields (G, μmol/J) of the base radicals are smaller than the yields found in similarly prepared γ-irradiated DNA samples, and the relative yields of backbone radicals relative to base radicals are much higher than that found in γ-irradiated samples. From these results, we have elaborated our radiation chemical model of the track structure for ion-beam irradiated DNA as it applies to krypton ion-beams. The base radicals, which are trapped as ion radicals or reversibly protonated or deprotonated ion radicals, are formed almost entirely in the track penumbra, a region in which radiation chemical effects are similar to those found in γ-irradiated samples. By comparing the yields of base radicals in ion-beam samples to the yields of the same radicals in γ-irradiated samples, the partition of energy between the low-LET region (penumbra) and the core is experimentally determined. The neutral sugar and other backbone radicals, which are not as susceptible to recombination as are ion radicals, are formed largely in the track core. The backbone radicals show a linear dose response up to very high doses. Unaltered base release yields in Kr-86 irradiated hydrated DNA are equal to sugar radical yields within experimental error limits, consistent with radiation-chemical processes in which all base release originates with sugar radicals. Two phosphorus-centered radicals from fragmentation of the DNA backbone are found in low yields.

Sampling in Developmental Science: Situations, Shortcomings, Solutions, and Standards.

PubMed

Bornstein, Marc H; Jager, Justin; Putnick, Diane L

2013-12-01

Sampling is a key feature of every study in developmental science. Although sampling has far-reaching implications, too little attention is paid to sampling. Here, we describe, discuss, and evaluate four prominent sampling strategies in developmental science: population-based probability sampling, convenience sampling, quota sampling, and homogeneous sampling. We then judge these sampling strategies by five criteria: whether they yield representative and generalizable estimates of a study's target population, whether they yield representative and generalizable estimates of subsamples within a study's target population, the recruitment efforts and costs they entail, whether they yield sufficient power to detect subsample differences, and whether they introduce "noise" related to variation in subsamples and whether that "noise" can be accounted for statistically. We use sample composition of gender, ethnicity, and socioeconomic status to illustrate and assess the four sampling strategies. Finally, we tally the use of the four sampling strategies in five prominent developmental science journals and make recommendations about best practices for sample selection and reporting.

Sampling in Developmental Science: Situations, Shortcomings, Solutions, and Standards

PubMed Central

Bornstein, Marc H.; Jager, Justin; Putnick, Diane L.

2014-01-01

Sampling is a key feature of every study in developmental science. Although sampling has far-reaching implications, too little attention is paid to sampling. Here, we describe, discuss, and evaluate four prominent sampling strategies in developmental science: population-based probability sampling, convenience sampling, quota sampling, and homogeneous sampling. We then judge these sampling strategies by five criteria: whether they yield representative and generalizable estimates of a study’s target population, whether they yield representative and generalizable estimates of subsamples within a study’s target population, the recruitment efforts and costs they entail, whether they yield sufficient power to detect subsample differences, and whether they introduce “noise” related to variation in subsamples and whether that “noise” can be accounted for statistically. We use sample composition of gender, ethnicity, and socioeconomic status to illustrate and assess the four sampling strategies. Finally, we tally the use of the four sampling strategies in five prominent developmental science journals and make recommendations about best practices for sample selection and reporting. PMID:25580049

[Correlation analysis between single nucleotide polymorphism of FGF5 gene and wool yield in rabbits].

PubMed

Li, Chun-Xiao; Jiang, Mei-Shan; Chen, Shi-Yi; Lai, Song-Jia

2008-07-01

Single nucleotide polymorphism (SNP) in exon 1 and 3 of fibroblast growth factor (FGF5) gene was studied by DNA sequencing in Yingjing angora rabbit, Tianfu black rabbit and California rabbit. A frameshift mutation (TCT insert) at base position 217 (site A) of exon 1 and a T/C missense mutation at base position 59 (site B) of exon 3 were found in Yingjing angora rabbit with a high frequency; a T/C same-sense mutation at base position 3 (site C) of exon 3 was found with similar frequency in three rabbit breeds. Least square analysis showed that different genotypes had no significant association with wool yield in site A, and had high significant association with wool yield in site B (P<0.01) and significant association with wool yield in site C (P<0.05). It was concluded from the results that FGF5 gene could be the potential major gene affecting wool yield or link with the major gene, and polymorphic loci B and C may be used as molecular markers for im-proving wool yield in angora rabbits.

Electron Emission Properties of Insulator Materials Pertinent to the International Space Station

NASA Technical Reports Server (NTRS)

Thomson, C. D.; Zavyalov, V.; Dennison, J. R.; Corbridge, Jodie

2004-01-01

We present the results of our measurements of the electron emission properties of selected insulating and conducting materials used on the International Space Station (ISS). Utah State University (USU) has performed measurements of the electron-, ion-, and photon-induced electron emission properties of conductors for a few years, and has recently extended our capabilities to measure electron yields of insulators, allowing us to significantly expand current spacecraft material charging databases. These ISS materials data are used here to illustrate our various insulator measurement techniques that include: i) Studies of electron-induced secondary and backscattered electron yield curves using pulsed, low current electron beams to minimize deleterious affects of insulator charging. ii) Comparison of several methods used to determine the insulator 1st and 2nd crossover energies. These incident electron energies induce unity total yield at the transition between yields greater than and less than one with either negative or positive charging, respectively. The crossover energies are very important in determining both the polarity and magnitude of spacecraft surface potentials. iii) Evolution of electron emission energy spectra as a function of insulator charging used to determine the surface potential of insulators. iv) Surface potential evolution as a function of pulsed-electron fluence to determine how quickly insulators charge, and how this can affect subsequent electron yields. v) Critical incident electron energies resulting in electrical breakdown of insulator materials and the effect of breakdown on subsequent emission, charging and conduction. vi) Charge-neutralization techniques such as low-energy electron flooding and UV light irradiation to dissipate both positive and negative surface potentials during yield measurements. Specific ISS materials being tested at USU include chromic and sulfuric anodized aluminum, RTV-silicone solar array adhesives, solar cell cover glasses, Kapton, and gold. Further details of the USU testing facilities, the instrumentation used for insulator measurements, and the NASA/SEE Charge Collector materials database are provided in other Spacecraft Charging Conference presentations (Dennison, 2003b). The work presented was supported in part by the NASA Space Environments and Effects (SEE) Program, the Boeing Corporation, and a NASA Graduate Fellowship. Samples were supplied by Boeing, the Environmental Effects Group at Marshall Space Flight Center, and Sheldahl, Inc.

DNA analysis of soil extracts can be used to investigate fine root depth distribution of trees

PubMed Central

Bithell, Sean L.; Tran-Nguyen, Lucy T. T.; Hearnden, Mark N.; Hartley, Diana M.

2015-01-01

Understanding the root distribution of trees by soil coring is time-consuming as it requires the separation of roots from soil and classification of roots into particular size classes. This labour-intensive process can limit sample throughput and therefore sampling intensity. We investigated the use of quantitative polymerase chain reaction (qPCR) on soil DNA extractions to determine live fine root DNA density (RDD, mg DNA m−2) for mango (Mangifera indica) trees. The specificity of the qPCR was tested against DNA extracted from 10 mango cultivars and 14 weed species. All mango cultivars and no weeds were detected. Mango DNA was successfully quantified from control soil spiked with mango roots and weed species. The DNA yield of mango root sections stored in moist soil at 23–28 °C declined after 15 days to low concentrations as roots decayed, indicating that dead root materials in moist soil would not cause false-positive results. To separate large roots from samples, a root separation method for field samples was used to target the root fragments remaining in sieved (minimum 2 mm aperture) soil for RDD comparisons. Using this method we compared the seasonal RDD values of fine roots for five mango rootstock cultivars in a field trial. The mean cultivar DNA yields by depth from root fragments in the sieved soil samples had the strongest relationship (adjusted multiple R2 = 0.9307, P < 0.001) with the dry matter (g m−2) of fine (diameter <0.64 mm) roots removed from the soil by sieving. This method provides a species-specific and rapid means of comparing the distribution and concentration of live fine roots of trees in orchards using soil samples up to 500 g. PMID:25552675

The effect of clinical outbreaks of salmonellosis on the prevalence of fecal Salmonella shedding among dairy cattle in New York.

PubMed

Cummings, Kevin J; Warnick, Lorin D; Elton, Mara; Gröhn, Yrjo T; McDonough, Patrick L; Siler, Julie D

2010-07-01

The objective of this study was to determine if the within-herd prevalence of fecal Salmonella shedding is higher in dairy herds with clinical outbreaks of disease, as compared to herds with subclinical infections only. Data were collected prospectively from dairy herds throughout New York that had at least 150 lactating cows and that received clinical service from participating veterinarians. After enrollment, Salmonella surveillance consisted of both environmental screening and disease monitoring within the herd. Herds positive by either environmental or fecal culture were sampled during three visits to estimate the within-herd prevalence of Salmonella. We characterized isolates by serovar and antimicrobial resistance pattern. Among 57 enrolled herds, 44 (77%) yielded Salmonella-positive samples during the study period; 27 (61%) of the positive herds had Salmonella isolated from environmental samples only, and 17 (39%) had one or more laboratory-confirmed clinical cases. The within-herd prevalence of fecal Salmonella shedding ranged from 0 to 53%. Salmonella Cerro was the predominant serovar, accounting for 56% of all isolates. Antimicrobial resistance ranged from zero to nine drugs, and 14 (32%) of the positive farms generated multidrug-resistant isolates. Herds with laboratory-confirmed clinical cases had a higher prevalence of fecal Salmonella shedding than herds that only generated positive environmental samples, as estimated by a Poisson regression model (prevalence ratio, 2.7; p = 0.01). An association between dairy herd outbreaks of salmonellosis and a higher prevalence of asymptomatic shedding should help guide strategies for reducing the public health threat of Salmonella, as the ability to recognize high-risk herds by clinical laboratory submissions presents an obvious opportunity to maximize food safety at the preharvest level. This is in contrast with other foodborne zoonotic pathogens, such as Campylobacter jejuni and Escherichia coli O157:H7, which occur widely in adult cattle without accompanying clinical disease.

The Effect of Clinical Outbreaks of Salmonellosis on the Prevalence of Fecal Salmonella Shedding Among Dairy Cattle in New York

PubMed Central

Warnick, Lorin D.; Elton, Mara; Gröhn, Yrjo T.; McDonough, Patrick L.; Siler, Julie D.

2010-01-01

Abstract The objective of this study was to determine if the within-herd prevalence of fecal Salmonella shedding is higher in dairy herds with clinical outbreaks of disease, as compared to herds with subclinical infections only. Data were collected prospectively from dairy herds throughout New York that had at least 150 lactating cows and that received clinical service from participating veterinarians. After enrollment, Salmonella surveillance consisted of both environmental screening and disease monitoring within the herd. Herds positive by either environmental or fecal culture were sampled during three visits to estimate the within-herd prevalence of Salmonella. We characterized isolates by serovar and antimicrobial resistance pattern. Among 57 enrolled herds, 44 (77%) yielded Salmonella-positive samples during the study period; 27 (61%) of the positive herds had Salmonella isolated from environmental samples only, and 17 (39%) had one or more laboratory-confirmed clinical cases. The within-herd prevalence of fecal Salmonella shedding ranged from 0 to 53%. Salmonella Cerro was the predominant serovar, accounting for 56% of all isolates. Antimicrobial resistance ranged from zero to nine drugs, and 14 (32%) of the positive farms generated multidrug-resistant isolates. Herds with laboratory-confirmed clinical cases had a higher prevalence of fecal Salmonella shedding than herds that only generated positive environmental samples, as estimated by a Poisson regression model (prevalence ratio, 2.7; p = 0.01). An association between dairy herd outbreaks of salmonellosis and a higher prevalence of asymptomatic shedding should help guide strategies for reducing the public health threat of Salmonella, as the ability to recognize high-risk herds by clinical laboratory submissions presents an obvious opportunity to maximize food safety at the preharvest level. This is in contrast with other foodborne zoonotic pathogens, such as Campylobacter jejuni and Escherichia coli O157:H7, which occur widely in adult cattle without accompanying clinical disease. PMID:20353290

Value of PCR for Detection of Toxoplasma gondii in Aqueous Humor and Blood Samples from Immunocompetent Patients with Ocular Toxoplasmosis

PubMed Central

Bou, Germán; Figueroa, Marta S.; Martí-Belda, Paloma; Navas, Enrique; Guerrero, Antonio

1999-01-01

Toxoplasma gondii infection is an important cause of chorioretinitis in the United States and Europe. Most cases of Toxoplasma chorioretinitis result from congenital infection. Patients are often asymptomatic during life, with a peak incidence of symptomatic illness in the second and third decades of life. Diagnosis is mainly supported by ophthalmological examination and a good response to installed therapy. However, establishment of a diagnosis by ophthalmological examination alone can be difficult in some cases. To determine the diagnostic value of PCR for the detection of T. gondii, 56 blood and 56 aqueous humor samples from 56 immunocompetent patients were examined. Fifteen patients with a diagnosis of ocular toxoplasmosis had increased serum anti-T. gondii immunoglobulin G levels but were negative for anti-T. gondii immunoglobulin M (group 1), and 41 patients were used as controls (group 2). Samples were taken before antiparasitic therapy was initiated, and only one blood sample and one aqueous humor sample were obtained for each patient. Single nested PCRs and Southern blot hybridization were performed with DNA extracted from these samples. The results obtained showed sensitivity and specificity values of 53.3 and 83%, respectively. Interestingly, among all patients with ocular toxoplasmosis, a positive PCR result with the aqueous humor sample was accompanied by a positive PCR result with the blood sample. This result suggests that ocular toxoplasmosis should not be considered a local event, as PCR testing of blood samples from patients with ocular toxoplasmosis yielded the same result as PCR testing of aqueous humor samples. PCR testing may be useful for discriminating between ocular toxoplasmosis and other ocular diseases, and also can avoid the problems associated with ocular puncture. PMID:10523535

Building a pantheoretical model of dehumanization with transgender men: Integrating objectification and minority stress theories.

PubMed

Velez, Brandon L; Breslow, Aaron S; Brewster, Melanie E; Cox, Robert; Foster, Aasha B

2016-10-01

With a national sample of 304 transgender men, the present study tested a pantheoretical model of dehumanization (Moradi, 2013) with hypotheses derived from objectification theory (Fredrickson & Roberts, 1997), minority stress theory (Meyer, 2003), and prior research regarding men's body image concerns. Specifically, we tested common objectification theory constructs (internalization of sociocultural standards of attractiveness [SSA], body surveillance, body satisfaction) as direct and indirect predictors of compulsive exercise. We also examined the roles of transgender-specific minority stress variables-antitransgender discrimination and transgender identity congruence-in the model. Results of a latent variable structural equation model yielded mixed support for the posited relations. The direct and indirect interrelations of internalization of SSA, body surveillance, and body satisfaction were consistent with prior objectification theory research, but only internalization of SSA yielded a significant direct relation with compulsive exercise. In addition, neither internalization of SSA nor body surveillance yielded significant indirect relations with compulsive exercise. However, antitransgender discrimination yielded predicted indirect relations with body surveillance, body satisfaction, and compulsive exercise, with transgender congruence playing a key mediating role in most of these relations. The implications of this pantheoretical model for research and practice with transgender men are discussed. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Rapid Determination of Salmonella in Samples of Egg Noodles, Cake Mixes, and Candies

PubMed Central

Banwart, George J.; Kreitzer, Madeleine J.

1969-01-01

A glass apparatus system was compared with a standard enrichment broth-selective agar method to test samples of egg noodles, cake mixes, and candy for the presence or absence of salmonellae. The glass apparatus system used fermentation of mannitol, production of H2S, or motility, in conjunction with a serological test of flagellar antigens, to detect salmonellae. No salmonellae were detected in 173 samples of food products. Of these samples, 171 were found to be Salmonella-negative after 48 hr with the glass apparatus system. After 72 hr, the standard Salmonella procedure yielded 38 samples which produced Salmonella false-positive results on selective agars. Inoculation of samples with cultures of Salmonella showed that approximately one inoculated cell could be detected after 48 hr of incubation with the glass apparatus. The standard Salmonella test requires a minimum of 72 hr for completion. Compared with the standard Salmonella test, the glass apparatus system is a more rapid and simple system that can be used to determine the presence or absence of Salmonella in these food products. Images PMID:5370460

Temperature influence on the fast pyrolysis of manure samples: char, bio-oil and gases production

NASA Astrophysics Data System (ADS)

Fernandez-Lopez, Maria; Anastasakis, Kostas; De Jong, Wiebren; Valverde, Jose Luis; Sanchez-Silva, Luz

2017-11-01

Fast pyrolysis characterization of three dry manure samples was studied using a pyrolyzer. A heating rate of 600°C/s and a holding time of 10 s were selected to reproduce industrial conditions. The effect of the peak pyrolysis temperature (600, 800 and 1000°C) on the pyrolysis product yield and composition was evaluated. Char and bio-oil were gravimetrically quantified. Scanning electron microscopy (SEM) was used to analyse the char structure. H2, CH4, CO and CO2 were measured by means of gas chromatography (GC). A decrease in the char yield and an increase of the gas yield were observed when temperature increased. From 800°C on, it was observed that the char yield of samples Dig R and SW were constant, which indicated that the primary devolatilization reactions stopped. This fact was also corroborated by GC analysis. The bio-oil yield slightly increased with temperature, showing a maximum of 20.7 and 27.8 wt.% for samples Pre and SW, respectively, whereas sample Dig R showed a maximum yield of 16.5 wt.% at 800°C. CO2 and CO were the main released gases whereas H2 and CH4 production increased with temperature. Finally, an increase of char porosity was observed with temperature.

Corn and soybean Landsat MSS classification performance as a function of scene characteristics

NASA Technical Reports Server (NTRS)

Batista, G. T.; Hixson, M. M.; Bauer, M. E.

1982-01-01

In order to fully utilize remote sensing to inventory crop production, it is important to identify the factors that affect the accuracy of Landsat classifications. The objective of this study was to investigate the effect of scene characteristics involving crop, soil, and weather variables on the accuracy of Landsat classifications of corn and soybeans. Segments sampling the U.S. Corn Belt were classified using a Gaussian maximum likelihood classifier on multitemporally registered data from two key acquisition periods. Field size had a strong effect on classification accuracy with small fields tending to have low accuracies even when the effect of mixed pixels was eliminated. Other scene characteristics accounting for variability in classification accuracy included proportions of corn and soybeans, crop diversity index, proportion of all field crops, soil drainage, slope, soil order, long-term average soybean yield, maximum yield, relative position of the segment in the Corn Belt, weather, and crop development stage.

Validation of the ANSR Salmonella method for detection of Salmonella spp. in selected foods and environmental samples.

PubMed

Mozola, Mark; Norton, Paul; Alles, Susan; Gray, R Lucas; Tolan, Jerry; Caballero, Oscar; Pinkava, Lisa; Hosking, Edan; Luplow, Karen; Rice, Jennifer

2013-01-01

ANSR Salmonella is a new molecular diagnostic assay for detection of Salmonella spp. in foods and environmental samples. The test is based on the nicking enzyme amplification reaction (NEAR) isothermal nucleic acid amplification technology. The assay platform features simple instrumentation, minimal labor, and, following a single-step 10-24 h enrichment (depending on sample type), an extremely short assay time of 30 min, including sample preparation. Detection is real-time using fluorescent molecular beacon probes. Inclusivity testing was performed using a panel of 113 strains of S. enterica and S. bongori, representing 109 serovars and all genetic subgroups. With the single exception of the rare serovar S. Weslaco, all serovars and genetic subgroups were detected. Exclusivity testing of 38 non-salmonellae, mostly Enterobacteriaceae, yielded no evidence of cross-reactivity. In comparative testing of chicken carcass rinse, raw ground turkey, raw ground beef, hot dogs, and oat cereal, there were no statistically significant differences in the number of positive results obtained with the ANSR and the U.S. Department of Agriculture-Food Safety and Inspection Service or U.S. Food and Drug Administration/Bacteriological Analytical Manual reference culture methods. In testing of swab or sponge samples from five different environmental surfaces, four trials showed no statistically significant differences in the number of positive results by the ANSR and the U.S. Food and Drug Administration/ Bacteriological Analytical Manual reference methods; in the trial with stainless steel surface, there were significantly more positive results by the ANSR method. Ruggedness experiments showed a high degree of assay robustness when deviations in reagent volumes and incubation times were introduced.

The use of PCR technique in the identification of Mycobacterium species responsible for bovine tuberculosis in cattle and buffaloes in Pakistan.

PubMed

Akhtar, Farah; Javed, Muhammad Tariq; Aziz-ur-Rehman; Khan, Muhammad Nisar; Akhtar, Pervez; Hussain, Sayed Misdaq; Aslam, Muhammad Sohaib; Kausar, Razia; Qamar, Mehwish; Cagiola, Monica

2015-08-01

Bovine tuberculosis is one of the important diseases of dairy and wild animals. The disease is prevalent all over the world, though developed countries have tremendously reduced the prevalence through eradication campaigns. The prevalence of disease in Pakistan on the basis of tuberculin testing or culture isolation of the organism has been reported previously. It is, however, important to use the latest diagnostic tools, i.e. PCR to confirm the type of Mycobacterium infecting the animals in Pakistan. Therefore, the present study was carried out to assess the utility of direct PCR on milk samples and nasal swabs to confirm the type of Mycobacterium infecting the animals. This study was carried out on 215 cattle and buffaloes of more than 2 years of age present at two livestock farms. The tuberculin results showed 22.5% prevalence at one farm and 25.9% at the other with an overall prevalence of 24.7%. The 92.5% of milk samples and/or nasal swabs showed positive PCR for Mycobacterium genus, 86.8% for Mycobacterium tuberculosis complex and 77.4% for Mycobacterium bovis. The M. bovis by PCR was detected in 13.2% of milk samples, 24.5% of nasal swabs and 39.6% of both milk samples + nasal swabs. The results suggested that there are 60% higher chance for a nasal swab to yield a positive PCR for M. bovis than the milk sample. It can be concluded from the present study that tuberculin testing is a useful method in studying the prevalence of disease as the PCR for Mycobacterium genus was positive in 92.5%, M. tuberculosis complex in 86.8% and Mycobacterium bovis in 77.4% cases.

Deployment of a Reverse Transcription Loop-Mediated Isothermal Amplification Test for Ebola Virus Surveillance in Remote Areas in Guinea.

PubMed

Kurosaki, Yohei; Magassouba, N'Faly; Bah, Hadja Aïssatou; Soropogui, Barré; Doré, Amadou; Kourouma, Fodé; Cherif, Mahamoud Sama; Keita, Sakoba; Yasuda, Jiro

2016-10-15

To strengthen the laboratory diagnostic capacity for Ebola virus disease (EVD) in the remote areas of Guinea, we deployed a mobile field laboratory and implemented reverse transcription loop-mediated isothermal amplification (RT-LAMP) for postmortem testing. We tested 896 oral swab specimens and 21 serum samples, using both RT-LAMP and reverse transcription-polymerase chain reaction (RT-PCR). Neither test yielded a positive result, and the results from RT-LAMP and RT-PCR were consistent. More than 95% of the samples were tested within 2 days of sample collection. These results highlight the usefulness of the RT-LAMP assay as an EVD diagnostic testing method in the field or remote areas. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

NASA Curiosity rover hits organic pay dirt on Mars

NASA Astrophysics Data System (ADS)

Voosen, Paul

2018-06-01

Since NASA's Curiosity rover landed on Mars in 2012, it has sifted samples of soil and ground-up rock for signs of organic molecules—the complex carbon chains that on Earth form the building blocks of life. Past detections have been so faint that they could be just contamination. Now, samples taken from two different drill sites on an ancient lakebed have yielded complex organic macromolecules that look strikingly similar to kerogen, the goopy fossilized building blocks of oil and gas on Earth. At a few dozen parts per million, the detected levels are 100 times higher than previous finds, but scientists still cannot say whether they have origins in biology or geology. The discovery positions scientists to begin searching for direct evidence of past life on Mars and bolsters the case for returning rock samples from the planet, an effort that begins with the Mars 2020 rover.

Biochar in vineyards: impact on soil quality and crop yield four years after the application

NASA Astrophysics Data System (ADS)

Ferreira, Carla; Verheijen, Frank; Puga, João; Keizer, Jacob; Ferreira, António

2017-04-01

Biochar is a recalcitrant organic carbon compound, created by biomass heating at high temperatures (300-1000°C) under low oxygen concentrations. Biochar application to agricultural soils has received increasing attention over the last years, due to its climate change mitigation and adaptation potential and reported improved soil properties and functions relevant to agronomic and environmental performance. Reported impacts are linked with increased cation exchange capacity, enhanced nutrient and water retention, and positive influences on soil microbial communities, which influence crop yields. Nevertheless, few studies have focused on mid-to-long term impacts of biochar application. This study investigated the impact of biochar on soil quality and crop yield four years after biochar application in a vineyard in North-Central Portugal. The site has a Mediterranean climate with a strong Atlantic Ocean influence, with mean annual rainfall and temperature of 1100 mm and 15°C, respectively. The soil is a relatively deep ( 80cm) sandy loam Cambisol, with gentle slopes (3°). The experimental design included three treatments: (i) control, without biochar; (ii) high biochar application rate (40 ton/ha); and (iii) biochar compost (40 ton/ha, 10% biochar). Three plots per treatment (2m×3m) were installed in March 2012, using a mini-rotavator (0-15cm depth). In May 2016, soil quality was also assessed through soil surveys and sampling. Penetration resistance was performed at the soil surface with a pocket penetrometer, and soil surface sampling rings were used for bulk density analyses (100 cm3). Bulked soil samples (0-30 cm) were collected in each plot for aggregate stability, microbial biomass (by chloroform fumigation extraction) and net mineralization rate (through photometric determination of non-incubated and incubated samples). Decomposition rate and litter stabilisation was assessed over a 3-month period through the Tea Bag Index (Keuskamp et al., 2013). The number, type and biomass of earthworms was recorded in each plot, at the soil surface (through excavation, 30cm×30cm×30cm) and sub-surface (using a mustard-tap water solution in the excavated hole). Crop yield was evaluated during harvesting (August 2016), through the number and weight of grape clusters. The potential impact of biochar on grape quality was investigated by total acidity, pH, potential alcoholic strength and total sugar in must analyses. Four years after the application, plots with high biochar showed lowest soil resistance, slightly lower bulk density, higher crop yield and must quality, than control plots. However, the soil of biochar plots also displayed slightly lower aggregate stability, microbial biomass, number and biodiversity of earthworms, although higher net-N mineralization, decomposition rate and litter stabilization. Plots with biochar and compost showed lowest earthworms, decomposition rate and litter stabilization, but highest crop yield that the other two treatments. Nevertheless, minor differences between three treatment plots suggest that potential impacts of biochar on soil quality and crop yield may persist during a relatively short period.

Instrumentation for Studies of Electron Emission and Charging From Insulators

NASA Technical Reports Server (NTRS)

Thomson, C. D.; Zavyalov, V.; Dennison, J. R.

2004-01-01

Making measurements of electron emission properties of insulators is difficult since insulators can charge either negatively or positively under charge particle bombardment. In addition, high incident energies or high fluences can result in modification of a material s conductivity, bulk and surface charge profile, structural makeup through bond breaking and defect creation, and emission properties. We discuss here some of the charging difficulties associated with making insulator-yield measurements and review the methods used in previous studies of electron emission from insulators. We present work undertaken by our group to make consistent and accurate measurements of the electron/ion yield properties for numerous thin-film and thick insulator materials using innovative instrumentation and techniques. We also summarize some of the necessary instrumentation developed for this purpose including fast response, low-noise, high-sensitivity ammeters; signal isolation and interface to standard computer data acquisition apparatus using opto-isolation, sample-and-hold, and boxcar integration techniques; computer control, automation and timing using Labview software; a multiple sample carousel; a pulsed, compact, low-energy, charge neutralization electron flood gun; and pulsed visible and UV light neutralization sources. This work is supported through funding from the NASA Space Environments and Effects Program and the NASA Graduate Research Fellowship Program.

Near-Unity Internal Quantum Efficiency of Luminescent Silicon Nanocrystals with Ligand Passivation.

PubMed

Sangghaleh, Fatemeh; Sychugov, Ilya; Yang, Zhenyu; Veinot, Jonathan G C; Linnros, Jan

2015-07-28

Spectrally resolved photoluminescence (PL) decays were measured for samples of colloidal, ligand-passivated silicon nanocrystals. These samples have PL emission energies with peak positions in the range ∼1.4-1.8 eV and quantum yields of ∼30-70%. Their ensemble PL decays are characterized by a stretched-exponential decay with a dispersion factor of ∼0.8, which changes to an almost monoexponential character at fixed detection energies. The dispersion factors and decay rates for various detection energies were extracted from spectrally resolved curves using a mathematical approach that excluded the effect of homogeneous line width broadening. Since nonradiative recombination would introduce a random lifetime variation, leading to a stretched-exponential decay for an ensemble, we conclude that the observed monoexponential decay in size-selected ensembles signifies negligible nonradiative transitions of a similar strength to the radiative one. This conjecture is further supported as extracted decay rates agree with radiative rates reported in the literature, suggesting 100% internal quantum efficiency over a broad range of emission wavelengths. The apparent differences in the quantum yields can then be explained by a varying fraction of "dark" or blinking nanocrystals.

RESPECT-ED: Rates of Pulmonary Emboli (PE) and Sub-Segmental PE with Modern Computed Tomographic Pulmonary Angiograms in Emergency Departments: A Multi-Center Observational Study Finds Significant Yield Variation, Uncorrelated with Use or Small PE Rates

PubMed Central

Chu, Kevin; Joseph, Anthony; Read, Catherine; Blecher, Gabriel; Furyk, Jeremy; Bharat, Chrianna; Velusamy, Karthik; Munro, Andrew; Baker, Kylie; Kinnear, Frances; Mukherjee, Ahses; Watkins, Gina; Buntine, Paul; Livesay, Georgia

2016-01-01

Introduction Overuse of CT Pulmonary Angiograms (CTPA) for diagnosing pulmonary embolism (PE), particularly in Emergency Departments (ED), is considered problematic. Marked variations in positive CTPA rates are reported, with American 4–10% yields driving most concerns. Higher resolution CTPA may increase sub-segmental PE (SSPE) diagnoses, which may be up to 40% false positive. Excessive use and false positives could increase harm vs. benefit. These issues have not been systematically examined outside America. Aims To describe current yield variation and CTPA utilisation in Australasian ED, exploring potential factors correlated with variation. Methods A retrospective multi-centre review of consecutive ED-ordered CTPA using standard radiology reports. ED CTPA report data were inputted onto preformatted data-sheets. The primary outcome was site level yield, analysed both intra-site and against a nominated 15.3% yield. Factors potentially associated with yield were assessed for correlation. Results Fourteen radiology departments (15 ED) provided 7077 CTPA data (94% ≥64-slice CT); PE were reported in 1028 (yield 14.6% (95%CI 13.8–15.4%; range 9.3–25.3%; site variation p <0.0001) with four sites significantly below and one above the 15.3% target. Admissions, CTPA usage, PE diagnosis rates and size of PE were uncorrelated with yield. Large PE (≥lobar) were 55% (CI: 52.1–58.2%) and SSPE 8.8% (CI: 7.1–10.5%) of positive scans. CTPA usage (0.2–1.5% adult attendances) was correlated (p<0.006) with PE diagnosis but not SSPE: large PE proportions. Discussion/ Conclusions We found significant intra-site CTPA yield variation within Australasia. Yield was not clearly correlated with CTPA usage or increased small PE rates. Both SSPE and large PE rates were similar to higher yield historical cohorts. CTPA use was considerably below USA 2.5–3% rates. Higher CTPA utilisation was positively correlated with PE diagnoses, but without evidence of increased proportions of small PE. This suggests that increased diagnoses seem to be of clinically relevant sized PE. PMID:27918576

Comparison of five assays for detection of Clostridium difficile toxin.

PubMed

Chapin, Kimberle C; Dickenson, Roberta A; Wu, Fongman; Andrea, Sarah B

2011-07-01

Performance characteristics of five assays for detection of Clostridium difficile toxin were compared using fresh stool samples from patients with C. difficile infection (CDI). Assays were performed simultaneously and according to the manufacturers' instructions. Patients were included in the study if they exhibited clinical symptoms consistent with CDI. Nonmolecular assays included glutamate dehydrogenase antigen tests, with positive findings followed by the Premier Toxin A and B Enzyme Immunoassay (GDH/EIA), and the C. Diff Quik Chek Complete test. Molecular assays (PCR) included the BD GeneOhm Cdiff Assay, the Xpert C. difficile test, and the ProGastro Cd assay. Specimens were considered true positive if results were positive in two or more assays. For each method, the Youden index was calculated and cost-effectiveness was analyzed. Of 81 patients evaluated, 26 (32.1%) were positive for CDI. Sensitivity of the BD GeneOhm Cdiff assay, the Xpert C. difficile test, the ProGastro Cd assay, C. Diff Quik Chek Complete test, and two-step GDH/EIA was 96.2%, 96.2%, 88.5%, 61.5%, and 42.3%, respectively. Specificity of the Xpert C. difficile test was 96.4%, and for the other four assays was 100%. Compared with nonmolecular methods, molecular methods detected 34.7% more positive specimens. Assessment of performance characteristics and cost-effectiveness demonstrated that the BD GeneOhm Cdiff assay yielded the best results. While costly, the Xpert C. difficile test required limited processing and yielded rapid results. Because of discordant results, specimen processing, and extraction equipment requirements, the ProGastro Cd assay was the least favored molecular assay. The GDH/EIA method lacked sufficient sensitivity to be recommended. Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Comparison of Five Assays for Detection of Clostridium difficile Toxin

PubMed Central

Chapin, Kimberle C.; Dickenson, Roberta A.; Wu, Fongman; Andrea, Sarah B.

2011-01-01

Performance characteristics of five assays for detection of Clostridium difficile toxin were compared using fresh stool samples from patients with C. difficile infection (CDI). Assays were performed simultaneously and according to the manufacturers' instructions. Patients were included in the study if they exhibited clinical symptoms consistent with CDI. Nonmolecular assays included glutamate dehydrogenase antigen tests, with positive findings followed by the Premier Toxin A and B Enzyme Immunoassay (GDH/EIA), and the C. Diff Quik Chek Complete test. Molecular assays (PCR) included the BD GeneOhm Cdiff Assay, the Xpert C. difficile test, and the ProGastro Cd assay. Specimens were considered true positive if results were positive in two or more assays. For each method, the Youden index was calculated and cost-effectiveness was analyzed. Of 81 patients evaluated, 26 (32.1%) were positive for CDI. Sensitivity of the BD GeneOhm Cdiff assay, the Xpert C. difficile test, the ProGastro Cd assay, C. Diff Quik Chek Complete test, and two-step GDH/EIA was 96.2%, 96.2%, 88.5%, 61.5%, and 42.3%, respectively. Specificity of the Xpert C. difficile test was 96.4%, and for the other four assays was 100%. Compared with nonmolecular methods, molecular methods detected 34.7% more positive specimens. Assessment of performance characteristics and cost-effectiveness demonstrated that the BD GeneOhm Cdiff assay yielded the best results. While costly, the Xpert C. difficile test required limited processing and yielded rapid results. Because of discordant results, specimen processing, and extraction equipment requirements, the ProGastro Cd assay was the least favored molecular assay. The GDH/EIA method lacked sufficient sensitivity to be recommended. PMID:21704273

Urinary shedding of pathogenic Leptospira in stray dogs and cats, Algiers: A prospective study.

PubMed

Zaidi, Sara; Bouam, Amar; Bessas, Amina; Hezil, Djamila; Ghaoui, Hicham; Ait-Oudhia, Khatima; Drancourt, Michel; Bitam, Idir

2018-01-01

Leptospirosis is an important worldwide zoonosis. This disease is caused by pathogenic species of the genus Leptospira which are maintained in the environment via chronic renal infection of carrier animals which can be asymptomatic excretors of the organisms in their urines and become a source of infection for humans and other hosts. The prevalence of animal leptospirosis in Algiers, Algeria, is unknown. Real-time PCR and standard PCR and sequencing were used to detect pathogenic Leptospira organisms in the urines of stray dogs and cats in Algiers. In the presence of appropriate controls, none of the 107 cat urine samples were positive while 5/104 (4.8%) canine urine samples (asymptomatic mixed-breed dogs, three females and two males) were positive in two real-time PCR assays targeting the rrs and hsp genes. The positivity of these samples was confirmed by partial PCR-sequencing of the rpoB gene which yielded 100% sequence similarity with Leptospira interrogans reference sequence. In this study, L. interrogans prevalence was significantly higher in dogs aged < one year (16.46% - 29.41%) than in adults (0%) (P value = 0.0001) and then in the overall dog population (2.68% - 4.8%) (P = 0.0007). These results suggest that dogs are maintenance hosts for zoonotic leptospirosis in Algiers, Algeria. To face this situation, effective canine vaccination strategies and raising public health awareness are mandatory. Further investigations incorporating a larger sample in more localities will be undertaken to document the epidemiology of urban animal leptospirosis in Algeria at large.

Correlation between molecular secondary ion yield and cluster ion sputtering for samples with different stopping powers

NASA Astrophysics Data System (ADS)

Heile, A.; Muhmann, C.; Lipinsky, D.; Arlinghaus, H. F.

2012-07-01

In static SIMS, the secondary ion yield, defined as detected ions per primary ion, can be increased by altering several primary ion parameters. For many years, no quantitative predictions could be made for the secondary ion yield enhancement of molecular ions. For thick samples of organic compounds, a power dependency of the secondary ion yield on the sputtering yield was shown. For this article, samples with thick molecular layers and (sub-)monolayers composed of various molecules were prepared on inorganic substrates such as silicon, silver, and gold, and subsequently analyzed. For primary ion bombardment, monoatomic (Ne+, Ar+, Ga+, Kr+, Xe+, Bi+) as well as polyatomic (Bin+, Bin++) primary ions were used within an energy range of 10-50 keV. The power dependency was found to hold true for the different samples; however, the exponent decreased with increasing stopping power. Based on these findings, a rule of thumb is proposed for the prediction of the lower limit of the secondary ion yield enhancement as a function of the primary ion species. Additionally, effects caused by the variation of the energy deposition are discussed, including the degree of molecular fragmentation and the non-linear increase of the secondary ion yield when polyatomic primary ions are used.

Structural characterization of phospholipids by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Marto, J A; White, F M; Seldomridge, S; Marshall, A G

1995-11-01

Matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance mass spectrometry provides for structural analysis of the principal biological phospholipids: glycerophosphatidylcholine, -ethanolamine, -serine, and -inositol. Both positive and negative molecular or quasimolecular ions are generated in high abundance. Isolated molecular ions may be collisionally activated in the source side of a dual trap mass analyzer, yielding fragments serving to identify the polar head group (positive ion mode) and fatty acid side chains (negative ion mode). Azimuthal quadrupolar excitation following collisionally activated dissociation refocuses productions close to the solenoid axis; subsequent transfer of product ions to the analyzer ion trap allows for high-resolution mass analysis. Cyro-cooling of the sample probe with liquid nitrogen greatly reduces matrix adduction encountered in the negative ion mode.

[Investigation of West Nile virus in central nervous system infections of unknown etiology in Ankara, Turkey].

PubMed

Ergünay, Koray; Aydoğan, Sibel; Menemenlioğlu, Dilek; Sener, Burçin; Lederer, Sabine; Steinhagen, Katja; Hasçelik, Gülşen; Pinar, Ahmet; Ozkul, Aykut; Us, Dürdal

2010-04-01

Arthropod-borne viral infections have recently gained considerable attention and importance as re-emerging infections in a global scale. West Nile Virus (WNV), a member of Flaviviridae, is an enveloped positive strand RNA virus that is usually transmitted to humans by the bite of Culicine mosquitoes. Although the majority of the human infections are asymptomatic, WNV may also cause febrile and neuro-invasive diseases. Seroprevalence data from Turkey indicate that WNV activity is present in Central Anatolia. In this study performed at Hacettepe University Hospital, paired serum and cerebrospinal fluid (CSF) samples from 87 adult patients with the preliminary diagnosis of aseptic meningitis/encephalitis of unknown etiology were evaluated retrospectively to identify WNV-related syndromes. Bacterial, fungal and mycobacterial cultures yielded negative results and Mycobacterium tuberculosis and Herpes simplex virus nucleic acid tests were also negative for the selected patients. Commercial enzyme-linked immunosorbent assay (ELISA)s and indirect immunofluorescence test (IIFT)s were employed for WNV IgM and IgG antibody detection (Anti-WNV Virus IgG/IgM ELISA, Anti-WNV Virus IgG/IgM IIFT; Euroimmun, Germany). Additional ELISA/IIFT assays were further performed for WNV antibody reactive samples to identify cross-reactions and/or infections with other flaviviruses and phleboviruses. All WNV antibody positive samples were also evaluated by a WNV real-time reverse-transcription polymerase chain reaction (RT-PCR) assay. WNV IgM and IgG antibodies were detected in %9.2 (8/87) and 3.4% (3/87) of the serum samples, respectively. All IgG reactive samples were negative for IgM. All sera with WNV antibody reactivity (n = 11) and the corresponding CSF samples were negative for viral RNA via RT-PCR. In 5 of the 8 WNV IgM positive subjects, sandfly fever virus IgM antibodies were detected, which was also accompanied by Dengue virus IgM positivity in one sample. In another case, intrathecal antibody synthesis against measles virus was demonstrated. Two cases (2/87; 2.3%) with WNV IgM positivity as the only serologic marker were identified as probable WNV infections and clinical features were discussed. In conclusion, in order to fully understand the impact of WNV and/or other flavivirus infections in Turkey, epidemiology and ecological features of these agents need to established.

Photostability of 6-MAM and morphine exposed to controlled UV irradiation in water and methanol solution: HRMS for the characterization of transformation products and comparison with the dry state.

PubMed

Miolo, Giorgia; Tucci, Marianna; Mazzoli, Alessandra; Ferrara, Santo Davide; Favretto, Donata

2016-07-15

The UVA and UVB light-induced behaviour of 6-monoacetylmorphine (6-MAM) and morphine, the main metabolites of heroin, was studied in methanol, aqueous solution and in the dry state. UVA and UVB irradiations were performed for different times (radiant energies of 20-300J/cm(2)). UV spectra of irradiated samples were compared with samples kept in the dark. To estimate the extent of photolysis, positive ion electrospray ionization experiments were performed on the irradiated samples by LC-HRMS. Tentative identification of photoproducts was performed on the basis of their elemental formula as calculated by HRMS results. Morphine and 6-MAM demonstrated to be quite stable under UVA light but very sensitive to UVB irradiation. In methanol solutions they undergo a similar pattern, both reaching 90% photodegradation after 100J/cm(2) of UVB, with a slightly faster kinetic for morphine at lower doses. In water, the yields of photodegradation are nearly one third lower than in methanol. In the solid state, the yield of photodegradation is lower than in solution. The structures of some UVB-induced degradation products are proposed. Photoaddition of the solvent and photooxidation seem the main pathways of phototransformation of these molecules. Moreover, both compounds revealed to generate singlet oxygen under UVB exposure. Copyright © 2016 Elsevier B.V. All rights reserved.

Extraction and physicochemical characterization of chitin and chitosan from Zophobas morio larvae in varying sodium hydroxide concentration.

PubMed

Soon, Chu Yong; Tee, Yee Bond; Tan, Choon Hui; Rosnita, Abdul Talib; Khalina, Abdan

2018-03-01

Large amount of sodium hydroxide (NaOH) is consumed to remove the protein content in chitin biomass during deproteinization. However, excessive NaOH concentration used might lead to the reduction of cost effectiveness during chitin extraction. Hence, the present study aimed to extract and evaluate the physicochemical properties of chitin and chitosan isolated from superworm (Zophobas morio) larvae using 0.5M-2.0M of NaOH. The extracted chitin and chitosan were subjected to Fourier Transform Infrared Spectroscopy (FT-IR), elemental analysis, Scanning Electron Microscope (SEM), Thermogravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC) and X-ray Diffraction (XRD). The 0.5M NaOH treatment resulted in the highest yield of chitin (5.43%), but produced the lowest yield (65.84%) of chitosan. The extracted chitin samples had relatively high degree of acetylation (DA) (82.39%-101.39%). Both chitin and chitosan showed smooth surface with tiny pores. The extracted chitin samples were confirmed as α-chitin based on the FT-IR and TGA. The chitin samples were amorphous with low degree of crystallinity. From TGA, the Chitosan 3 extracted was partially deacetylated. Both DPPH radical scavenging and ferric-chelating assay showed positive correlation with DD of chitosan isolates. However, the chitosan isolates were not fully dissolved, resulting in lower radical scavenging and ferric-chelating ability compared to commercial chitosan. Copyright © 2017. Published by Elsevier B.V.

Use of an Additional 19-G EBUS-TBNA Needle Increases the Diagnostic Yield of EBUS-TBNA.

PubMed

Garrison, Garth; Leclair, Timothy; Balla, Agnes; Wagner, Sarah; Butnor, Kelly; Anderson, Scott R; Kinsey, C Matthew

2018-06-12

Although endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) has an excellent diagnostic yield, there remain cases where the diagnosis is not obtained. We hypothesized that additional sampling with a 19-G EBUS-TBNA needle may increase diagnostic yield in a subset of cases where additional tissue sampling was required. Indications for use of the 19-G needle following 22-G sampling with rapid on-site cytologic examination were: (1) diagnostic uncertainty of the on-site cytopathologist (eg, nondiagnostic, probable lymphoma, etc.), (2) non-small cell lung cancer with probable need for molecular genetic and/or PD-L1 testing, or (3) need for a larger tissue sample for consideration of inclusion in a research protocol. A 19-G EBUS-TBNA needle was utilized following standard sampling with a 22-G needle in 48 patients (50 sites) during the same procedure. Although the diagnostic yield between the needles was equivalent, the concordance rate was only 83%. The 19-G determined a diagnosis in 4 additional patients (8%) and provided additional histopathologic information in 6 other cases (12%). Conversely, in 3 cases (6%) diagnostic information was provided only by the 22-G needle. Compared with 22-G EBUS-TBNA alone, sampling with both the 22- and 19-G EBUS needles resulted in an increase in diagnostic yield from 92% to 99% (P=0.045) and a number needed to sample of 13 patients to provide one additional diagnosis. There were no significant complications. In select cases where additional tissue may be needed, sampling with a 19-G EBUS needle following standard aspiration with a 22-G needle results in an increase in diagnostic yield.

Value of the oral swab for the molecular diagnosis of dogs in different stages of infection with Leishmania infantum.

PubMed

Aschar, Mariana; de Oliveira, Eveline Tozzi Braga; Laurenti, Marcia Dalastra; Marcondes, Mary; Tolezano, Jose Eduardo; Hiramoto, Roberto Mitsuyoshi; Corbett, Carlos Eduardo P; da Matta, Vania Lucia Ribeiro

2016-07-30

This study was based on the need to employ a sensitive and specific method with samples that could be easily collected for diagnosing dogs infected with Leishmania infantum. To this end, we used real time-PCR (qPCR) to assess the value of the oral swab (OS) in detecting infected sick dogs (SD; n=62), including, for the first time, the analysis of apparently healthy infected dogs (AD; n=30), both from endemic areas for visceral leishmaniasis (VL). For comparison, we also evaluated the performance of the conjunctival swab (CS), blood (BL), lymph node (LN) and serology. We detected the presence of Leishmania DNA in the oral cavity in 62 out of the 92 dogs studied. The OS positivity (67.4%) was equivalent to the CS (68.5%) (p>0.05), higher than BL (52.2%) (p≤0.05), and lower than LN (84.8%) (p≤0.05). OS and CS performed well in SD dogs (82.3% and 83.9%, respectively) but not in AD dogs (36.7% for both samples). BL showed the lowest positivity (52.2%) and provided equivalent results between AD (60.0%) and SD (48.4%) dogs (p>0.05). LN yielded the highest positivity (84.8%), and it was also higher in the SD population (93.5%) compared to the AD population (66.7%) (p≤0.05). Parasite load was high in LN, moderate in OS and CS, and low in BL, showing the relationship between the levels of parasitism and the positivity rates found in these samples. Serology was positive in 82.2% of the SD group and in 70% of the AD dogs (p>0.05). Among the 20 seronegative dogs, seven (35%) were positive in either OS or CS, and 12 (60%) were positive when both noninvasive samples were jointly considered. The OS/CS combination resulted in a significant increase of positivity (p≤0.05) for the AD dogs (from 36.7% to 63.4%), as well as OS/serology (80%) and OS/CS/serology (83.4%). For the SD population, positivity reached up to 95.2% with the same combinations, showing that combination of samples and/or tests is required for the identification of dogs infected with L. infantum and that the OS and CS combination based on qPCR notably improves the detection of both AD and SD dogs. In conclusion, OS proved to be a suitable sample for the molecular diagnosis of infected dogs with clinical signs of VL, but not for dogs with inapparent infection. For these, we recommend the combination of OS results with CS and/or serology in order to reach relevant positivity for L. infantum. Finally, another advantage of using OS or both noninvasive samples is the increased likelihood of diagnosing seronegative dogs. Copyright © 2016 Elsevier B.V. All rights reserved.

Improving the Yield of Histological Sampling in Patients With Suspected Colorectal Cancer During Colonoscopy by Introducing a Colonoscopy Quality Assurance Program.

PubMed

Gado, Ahmed; Ebeid, Basel; Abdelmohsen, Aida; Axon, Anthony

2011-08-01

Masses discovered by clinical examination, imaging or endoscopic studies that are suspicious for malignancy typically require biopsy confirmation before treatment is initiated. Biopsy specimens may fail to yield a definitive diagnosis if the lesion is extensively ulcerated or otherwise necrotic and viable tumor tissue is not obtained on sampling. The diagnostic yield is improved when multiple biopsy samples (BSs) are taken. A colonoscopy quality-assurance program (CQAP) was instituted in 2003 in our institution. The aim of this study was to determine the effect of instituting a CQAP on the yield of histological sampling in patients with suspected colorectal cancer (CRC) during colonoscopy. Initial assessment of colonoscopy practice was performed in 2003. A total of five patients with suspected CRC during colonoscopy were documented in 2003. BSs confirmed CRC in three (60%) patients and were nondiagnostic in two (40%). A quality-improvement process was instituted which required a minimum six BSs with adequate size of the samples from any suspected CRC during colonoscopy. A total of 37 patients for the period 2004-2010 were prospectively assessed. The diagnosis of CRC was confirmed with histological examination of BSs obtained during colonoscopy in 63% of patients in 2004, 60% in 2005, 50% in 2006, 67% in 2007, 100% in 2008, 67% in 2009 and 100% in 2010. The yield of histological sampling increased significantly ( p <0.02) from 61% in 2004-2007 to 92% in 2008-2010. The implementation of a quality assurance and improvement program increased the yield of histological sampling in patients with suspected CRC during colonoscopy.

MR-eyetracker: a new method for eye movement recording in functional magnetic resonance imaging.

PubMed

Kimmig, H; Greenlee, M W; Huethe, F; Mergner, T

1999-06-01

We present a method for recording saccadic and pursuit eye movements in the magnetic resonance tomograph designed for visual functional magnetic resonance imaging (fMRI) experiments. To reliably classify brain areas as pursuit or saccade related it is important to carefully measure the actual eye movements. For this purpose, infrared light, created outside the scanner by light-emitting diodes (LEDs), is guided via optic fibers into the head coil and onto the eye of the subject. Two additional fiber optical cables pick up the light reflected by the iris. The illuminating and detecting cables are mounted in a plastic eyepiece that is manually lowered to the level of the eye. By means of differential amplification, we obtain a signal that covaries with the horizontal position of the eye. Calibration of eye position within the scanner yields an estimate of eye position with a resolution of 0.2 degrees at a sampling rate of 1000 Hz. Experiments are presented that employ echoplanar imaging with 12 image planes through visual, parietal and frontal cortex while subjects performed saccadic and pursuit eye movements. The distribution of BOLD (blood oxygen level dependent) responses is shown to depend on the type of eye movement performed. Our method yields high temporal and spatial resolution of the horizontal component of eye movements during fMRI scanning. Since the signal is purely optical, there is no interaction between the eye movement signals and the echoplanar images. This reasonably priced eye tracker can be used to control eye position and monitor eye movements during fMRI.

Association of Beta2-Positive Clostridium perfringens Type A With Focal Duodenal Necrosis in Egg-Laying Chickens in the United States.

PubMed

França, M; Barrios, M A; Stabler, L; Zavala, Guillermo; Shivaprasad, H L; Lee, M D; Villegas, A M; Uzal, Francisco A

2016-03-01

Focal duodenal necrosis (FDN) is a poorly understood intestinal disease of egg layers, and has been associated with drops in egg production and decreased egg weights. The etiology of this disease is still unknown, but the condition has been associated with Clostridium colinum and Clostridium perfringens. In order to investigate the etiology, duodenal samples were taken from hens with FDN. The hens originated from table egg layer farms in three states. The samples were examined by histopathology, bacteriology, and immunohistochemistry. Macroscopically, all samples contained focal to multifocal, variably sized, reddened or brownish gray areas of mucosal erosion. Histopathology revealed mild to severe heterophilic and lymphoplasmacytic enteritis with loss of enterocytes at the villous tips, luminal fibrinonecrotic exudate, and variable numbers of Gram-positive and Gram-negative rod-shaped bacteria within the lesions in 16/30 samples. Clostridium perfringens was isolated by anaerobic bacteriology from 4/13 samples that had characteristic microscopic lesions of FDN. Polymerase chain reaction (PCR) revealed that all four isolates were Type A C. perfringens, positive for beta2 gene and negative for necrotic enteritis toxin B and enterotoxin genes. PCR for Clostridium colinum applied to DNA extracted from frozen intestinal samples yielded negative results in 14/14 duodenal samples. Immunohistochemistry (IHC) for 7C. perfringens, alpha and beta2 toxins stained a few to numerous long rod-shaped bacteria present in the lesions. IHC for alpha and beta2 toxins also stained enterocytes at the villous tips, inflammatory cells in the lamina propria, as well as degenerated and sloughed enterocytes present within the luminal exudate. These findings suggest that C. perfringens may play a role in the development of FDN. Experimental challenge studies with these isolates still need to be performed in order to reproduce the disease and fulfill Koch's postulates.

Digital droplet PCR (ddPCR) for the detection and quantification of HPV 16, 18, 33 and 45 - a short report.

PubMed

Lillsunde Larsson, Gabriella; Helenius, Gisela

2017-10-01

Human papilloma virus (HPV) infection is associated with several anogenital malignancies. Here, we set out to evaluate digital droplet PCR (ddPCR) as a tool for HPV 16, 18, 33 and 45 viral load quantification and, in addition, to compare the efficacy of the ddPCR assay for HPV 16 detection with that of quantitative real-time PCR (qPCR). Clinical samples, positive for HPV genotypes 16, 18, 33 and 45 were analyzed for viral load using ddPCR. Sample DNA was cleaved before droplet generation and PCR. Droplets positive for VIC and FAM fluorescence were read in a QX200 Droplet reader™ (BIO-RAD) after which the viral load was calculated using Quantasoft software. We found that DNAs extracted from formalin fixed paraffin embedded (FFPE) tissue samples yielded lower amplification signals compared to those obtained from liquid based cytology (LBC) samples, but they were clearly distinguishable from negative background signals. The viral limit of detection was 1.6 copies of HPV 16, 2.8 copies of HPV 18, 4.6 copies of HPV 33 and 1.6 copies of HPV 45. The mean inter-assay coefficients of variability (CV) for the assays ranged from 3.4 to 7.0%, and the mean intra-assay CV from 2.6 to 8.2%. The viral load in the different cohorts of tumor samples ranged from 154 to 340,200 copies for HPV 16, 244 to 31,300 copies for HPV 18 and 738 to 69,100 copies for HPV 33. One sample positive for HPV 45 contained 1331 viral copies. When comparing qPCR data with ddPCR copy number data, the qPCR values were found to be 1 to 31 times higher. Separation of fragments in nanodroplets may facilitate the amplification of fragmented human and viral DNA. The method of digital droplet PCR may, thus, provide a new and promising tool for evaluating the HPV viral load in clinical samples.

Utilization of flow cytometry for diagnosis of hematologic malignancies in Thailand: increasing trends and diagnostic yields in 7,982 samples.

PubMed

Promsuwicha, Orathai; Kankhao, Supattra; Songmuang, Wayuree; Auewarakul, Chirayu U

2014-12-01

Diagnosis of hematologic malignancies requires a multidisciplinary approach. Flow cytometry (FCM) has become an essential tool for immunophenotypic studies of malignant hematopoietic cells. To evaluate the utilization trend of FCM and its diagnostic yields for hematologic malignancy at a major teaching hospital in Thailand. FCM results of bone marrow (BM) and peripheral blood (PB) specimens during 2000-2013 were analyzed and compared to clinical diagnosis. Overall, 7,982 specimens were submitted for diagnostic FCM including 6,561 BM and 1,421 PB. The number of specimens analyzedwas 121, 142, 164, 299, 491, 431, 690, 611, 719, 744, 725, 863, 955 and 1,027, respectively, from 2000 to 2013. The most common clinical diagnoses requested for FCM were acute leukemia (5,911 cases, 74%) followed by lymphoma (1,419 cases, 17.8%), and chronic lymphocytic leukemia (CLL) (634 cases, 7.94%). The highest diagnostic yield of FCM was found in acute leukemia cases (69.71%) followed by CLL (35.33%). Only 15.43% of clinically suspected lymphoma cases were positive by FCM. Overutilization of PB (35.6% of cases) instead of BM for lymphoma staging significantly contributed to low diagnostic yields of lymphoma by FCM as circulating tumor cells may not be present in such cases. FCM has an increasing role in the diagnosis of hematologic malignancies in Thai patients over the past 14 years with the highest diagnostic yield in acute leukemia. Appropriate specimen types and study indications are required in order to reduce futility of costly diagnostic tests and improve diagnostic yields.

Detection of cfxA and cfxA2, the β-Lactamase Genes of Prevotella spp., in Clinical Samples from Dentoalveolar Infection by Real-Time PCR

PubMed Central

Iwahara, Kaori; Kuriyama, Tomoari; Shimura, Satoshi; Williams, David W.; Yanagisawa, Maki; Nakagawa, Kiyomasa; Karasawa, Tadahiro

2006-01-01

While most bacteria involved in dentoalveolar infection are highly susceptible to penicillin, some Prevotella strains exhibit resistance to this agent through the production of β-lactamase. The production of β-lactamase by Prevotella spp. is in turn associated with the expression of the genes cfxA and cfxA2. The aim of the present study was to determine the prevalence of cfxA and cfxA2 in Prevotella strains by use of real-time PCR and to assess the performance of this molecular method for the direct detection of the genes in 87 clinical samples (pus and root canal exudates) from dentoalveolar infection. Production of β-lactamase by each isolate was determined using a nitrocefin disk. β-Lactamase production was seen in 31% of Prevotella isolates, while all isolates of other species were β-lactamase negative. The penicillin resistance of isolates strongly correlated with the production of β-lactamase. Real-time PCR was found to detect the cfxA and cfxA2 genes from at least five cells per reaction mixture (5 × 103 CFU/ml of pus). Using real-time PCR, the presence of cfxA and cfxA2 was evident for all 48 β-lactamase-positive Prevotella strains. In contrast, neither β-lactamase-negative Prevotella (n = 91) or non-Prevotella (n = 31) strains were positive for the genes. In this study, 31 of the 87 samples yielded β-lactamase-positive Prevotella results, and cfxA and cfxA2 were detected in all 31 samples. Of the 56 culture-negative samples, 8 (14%) were positive for cfxA and cfxA2 by the real-time PCR. This sensitive and specific molecular method offers a rapid clinical test for aiding in the selection of an appropriate antibiotic for treatment of dentoalveolar infection. Although penicillin remains largely effective in the treatment of dentoalveolar infection, β-lactamase-stable antibiotics should be considered in cases in which β-lactamase-positive Prevotella strains are involved. PMID:16390966

Microbial flora of tears of orthokeratology patients, and microbial contamination of contact lenses and contact lens accessories.

PubMed

Boost, Maureen V; Cho, Pauline

2005-06-01

The purpose of this study is to determine if there are changes in the ocular flora of overnight orthokeratology (ortho-k) patients, and the levels of contamination of their lenses and lens accessories, and to correlate compliance with levels of contamination. Normal ocular flora of 41 subjects was determined twice before commencing ortho-k lens wear by culture of the lower conjunctiva. Further specimens were collected on six follow-up visits after beginning lens wear, as were samples from their lenses, cases, and suction holders. A questionnaire on lens care was administered after the fifth visit. Three subjects provided conjunctival samples yielding Staphylococcus aureus on one occasion before lens wear, one being positive for this organism after beginning lens wear. Of 38 subjects yielding no growth or only normal eye flora before use, 28 remained free of ocular pathogens after beginning lens wear. Only four subjects had positive cultures on more than one occasion after lens wear. There was no significant difference in isolation levels of pathogens with lens wear (p = 0.423). Lens culture of 54% of subjects yielded no growth or normal flora only; lenses of 16 subjects yielded potential pathogens, including three subjects contaminated on more than one occasion. Lens isolates did not match the organisms transiently colonizing the eye. Lens case, the most frequently contaminated item, was associated with lens contamination (p < 0.001), the same organism being isolated from both items in 11 subjects. Lens suction holder was less frequently contaminated. Neither lens case nor suction holder contamination was associated with isolates from the eye. Reported good compliance correlated with lack of contamination in all but one subject. The most frequent breaches in the lens care protocol were failure to clean, disinfect, and replace the lens case. Ocular flora was not altered by ortho-k lens wear over an extended period, and patients remained free of infection. Contaminants identified were generally of a transient nature. Most patients had significant contamination of at least one item, most frequently the lens case. Lens case isolates were significantly associated with those from the lens. The majority of patients reporting good compliance had low or no contamination of their lenses and accessories.

[Seropositivity of Borrelia burgdorferi in risky groups in Van region, Turkey].

PubMed

Parlak, Mehmet; Bayram, Yasemin; Çıkman, Aytekin; Ceylan, Nesrin; Berktaş, Mustafa

2015-07-01

Lyme borreliosis, which is more prevalent in the northern hemisphere, is the most common tick-borne contagious disease among people living in the North America and Europe. The causative agent of Lyme borreliosis, Borrelia burgdorferi, is transmitted by the bites of ticks of the genus Ixodes. In Turkey, the seroprevalence of Lyme disease is increased in regions where ticks and tick-bite cases are prevalent. The present study aimed to determine the seroprevalence of Lyme borreliosis in people at risk, living in the rural areas of Van province, which is located in the eastern region of Turkey. No previous study on this topic has been performed in our province. The study included a total of 446 subjects (mean age: 39.6±15.5 years), of them 139 were male and 307 were female, living in the rural areas of Van province between January 2012 and July 2012. The serum samples collected from participants after informed consent were screened for the presence of B.burgdorferi IgG antibodies by ELISA method. Western blot (WB) method was used for the confirmation of positive or borderline positive samples, and also for the investigation of IgM antibodies. During the study, the individuals from whom samples were taken, were questioned whether they have ever been exposed to tick or insect bite. B.burgdorferi IgG positivity was detected in 17 (3.8%) of the cases, whereas it was within the limit values in 14 cases. A total of 31 samples which yielded positive and borderline positive results were retested by WB and 4 (12.9%) were detected as positive while 10 (32.3%) of the samples were indeterminate. B.burgdorferi IgM antibody positivity was not detected in any of the samples. Considering the WB as reference method, the rate of B.burgdorferi IgG seropositivity was estimated as 0.9% (4/446). Three of these four cases were defined as tick or insect bites. The seroprevalence rate of B.burgdorferi detected in the present study was low as compared to the results of the other studies reported from Turkey. The reason of this result might be from the geographical characteristics and the differences of tick fauna in our region. As a result, it was concluded that our province is not endemic for Lyme borreliosis, however for the reduction of tick exposure, emphasis must be placed on preventive health services for the individuals at risk.

Technical note: a noninvasive method for measuring mammary apoptosis and epithelial cell activation in dairy animals using microparticles extracted from milk.

PubMed

Pollott, G E; Wilson, K; Jerram, L; Fowkes, R C; Lawson, C

2014-01-01

Milk production from dairy animals has been described in terms of 3 processes: the increase in secretory cell numbers in late pregnancy and early lactation, secretion rate of milk per cell, and the decline in cell numbers as lactation progresses. This latter process is thought to be determined by the level of programmed cell death (apoptosis) found in the animal. Until now, apoptosis has been measured by taking udder biopsies, using magnetic resonance imaging scans, or using animals postmortem. This paper describes an alternative, noninvasive method for estimating apoptosis by measuring microparticles in milk samples. Microparticles are the product of several processes in dairy animals, including apoptosis. Milk samples from 12 Holstein cows, at or past peak lactation, were collected at 5 monthly samplings. The samples (n=57) were used to measure the number of microparticles and calculate microparticle density for 4 metrics: annexin V positive and merocyanine 540 dye positive, for both and total particles, in both whole milk (WM) and spun milk. Various measures of milk production were also recorded for the 12 cows, including daily milk yield, fat and protein percentage in the milk, somatic cell count, and the days in milk when the samples were taken. A high correlation was found between the 4 WM microparticle densities and days in milk (0.46 to 0.64), and a moderate correlation between WM microparticle densities and daily milk yield (-0.33 to -0.44). No significant relationships were found involving spun milk samples, somatic cell count, or fat and protein percentage. General linear model analyses revealed differences between cows for both level of microparticle density and its rate of change in late lactation. Persistency of lactation was also found to be correlated with the WM microparticle traits (-0.65 to -0.32). As apoptosis is likely to be the major contributor to microparticle numbers in late lactation, this work found a noninvasive method for estimating apoptosis that gave promising results. Further investigation is required to find out the factors affecting microparticle production and how it changes throughout lactation. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Climatic and technological ceilings for Chinese rice stagnation based on yield gaps and yield trend pattern analysis.

PubMed

Zhang, Tianyi; Yang, Xiaoguang; Wang, Hesong; Li, Yong; Ye, Qing

2014-04-01

Climatic or technological ceilings could cause yield stagnation. Thus, identifying the principal reasons for yield stagnation within the context of the local climate and socio-economic conditions are essential for informing regional agricultural policies. In this study, we identified the climatic and technological ceilings for seven rice-production regions in China based on yield gaps and on a yield trend pattern analysis for the period 1980-2010. The results indicate that 54.9% of the counties sampled experienced yield stagnation since the 1980. The potential yield ceilings in northern and eastern China decreased to a greater extent than in other regions due to the accompanying climate effects of increases in temperature and decreases in radiation. This may be associated with yield stagnation and halt occurring in approximately 49.8-57.0% of the sampled counties in these areas. South-western China exhibited a promising scope for yield improvement, showing the greatest yield gap (30.6%), whereas the yields were stagnant in 58.4% of the sampled counties. This finding suggests that efforts to overcome the technological ceiling must be given priority so that the available exploitable yield gap can be achieved. North-eastern China, however, represents a noteworthy exception. In the north-central area of this region, climate change has increased the yield potential ceiling, and this increase has been accompanied by the most rapid increase in actual yield: 1.02 ton ha(-1) per decade. Therefore, north-eastern China shows a great potential for rice production, which is favoured by the current climate conditions and available technology level. Additional environmentally friendly economic incentives might be considered in this region. © 2013 John Wiley & Sons Ltd.

The firefighter coping self-efficacy scale: measure development and validation.

PubMed

Lambert, Jessica E; Benight, Charles C; Harrison, Erica; Cieslak, Roman

2012-01-01

The authors evaluated the psychometric properties of the Firefighter Coping Self-Efficacy (FFCSE) Scale, a new measure developed to assess firefighters' perceived competence in managing stressful and traumatic experiences encountered on the job. Two samples of firefighters completed the FFCSE Scale at two different time points. Exploratory factor analysis yielded a unidimensional structure, which was further supported with confirmatory factor analysis using a second sample. Internal consistency of the measure was excellent. Analysis of cross-sectional data indicated FFCSE was positively associated with measures of psychological well-being and social support, and negatively associated with work-related stress and psychological distress. FFCSE also uniquely contributed to the variance in psychological distress, over and above variables previously shown to be associated with distress among this population. Implications and suggestions for future research are discussed.

Concentrations, loads, and yields of particle-associated contaminants in urban creeks, Austin, Texas, 1999-2004

USGS Publications Warehouse

Mahler, B.J.; Van Metre, P.C.; Wilson, J.T.; Guilfoyle, A.L.; Sunvison, M.W.

2006-01-01

Concentrations, loads, and yields of particle-associated (hydrophobic) contaminants (PACs) in urban runoff in creeks in Austin, Texas, were characterized using an innovative approach: large-volume suspended-sediment sampling. This approach isolates suspended sediment from the water column in quantities sufficient for direct chemical analysis of PACs. During 1999-2004, samples were collected after selected rain events from each of five stream sites and Barton Springs for a study by the U.S. Geological Survey, in cooperation with the City of Austin. Sediment isolated from composited samples was analyzed for major elements, metals, organochlorine compounds, and polycyclic aromatic hydrocarbons (PAHs). In addition, at the Shoal Creek and Boggy Creek sites, individual samples for some events were analyzed to investigate within-event variation in sediment chemistry. Organochlorine compounds detected in suspended sediment included chlordane, dieldrin, DDD, DDE, DDT, and polychlorinated biphenyls (PCBs). Concentrations of PACs varied widely both within and between sites, with higher concentrations at the more urban sites and multiple nondetections at the least-urban sites. Within-site variation for metals and PAHs was smaller than between-site variation, and concentrations and yields of these and the organochlorine compounds correlated positively to the percentage of urban land use in the watershed. Loads of most PACs tested correlated significantly with suspended-sediment loads. Concentrations of most PACs correlated strongly with three measures of urban land use. Variation in suspended-sediment chemistry during runoff events was investigated at the Shoal and Boggy Creek sites. Five of the eight metals analyzed, dieldrin, chlordane, PCBs, and PAHs were detected at the highest concentrations in the first sample collected at the Shoal Creek site, a first-flush effect, but not at the Boggy Creek site. Temporal patterns in concentrations of DDT and its breakdown products varied from one event to the next. In spite of the first-flush effect in concentrations at the Shoal Creek site, most of the contaminant load was transported at peak discharge, when suspended-sediment concentration and load are maximum.

Effects of digestion, chemical separation, and deposition on Po-210 quantitative analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seiner, Brienne N.; Morley, Shannon M.; Beacham, Tere A.

Polonium-210 is a radioactive isotope often used to study sedimentation processes, food chains, aerosol behavior, and atmospheric circulations related to environmental sciences. Materials for the analysis of Po-210 range from tobacco leaves or cotton fibers, to soils and sediments. The purpose of this work was to determine polonium losses from a variety of sample types (soil, cotton fiber, and air filter) due to digestion technique, chemical separation, and deposition method for alpha energy analysis. Results demonstrated that yields from a perchloric acid wet-ash were similar to that from a microwave digestion. Both were greater than the dry-ash procedure. The poloniummore » yield from the perchloric acid wet ash was 87 ± 5%, the microwave digestion had a yield of 100 ± 7%, and the dry ash had a yield of 38 ± 5%. The chemical separation of polonium by an anion exchange resin was used only on the soil samples due to the complex nature of this sample. The yield of Po-209 tracer after chemical separation and deposition for alpha analysis was 83 ± 7% for the soil samples. Spontaneous deposition yields for the cotton and air filters were 87 ± 4% and 92 ± 6%, respectively. Based on the overall process yields for each sample type the amount of Po-210 was quantified using alpha energy analysis. The soil contained 0.18 ± 0.08 Bq/g, the cotton swipe contained 0.7 mBq/g, and the air filter contained 0.04 ± 0.02 mBq/g. High and robust yields of polonium are possible using a suitable digestion, separation, and deposition method.« less

Sputum color: potential implications for clinical practice.

PubMed

Johnson, Allen L; Hampson, David F; Hampson, Neil B

2008-04-01

Respiratory infections with sputum production are a major reason for physician visits, diagnostic testing, and antibiotic prescription in the United States. We sought to determine whether the simple characteristic of sputum color provides information that impacts resource utilization such as laboratory testing and prescription of antibiotics. Out-patient sputum samples submitted to the microbiology laboratory for routine analysis were assigned to one of 8 color categories (green, yellow-green, rust, yellow, red, cream, white, and clear), based on a key made from paint chip color samples. Subsequent Gram stain and culture results were compared to sputum color. Of 289 consecutive samples, 144 (50%) met standard Gram-stain criteria for being acceptable lower-respiratory-tract specimens. In the acceptable Gram-stain group, 60 samples had a predominant organism on Gram stain, and the culture yielded a consistent result in 42 samples (15% of the 289 total specimens). Yield at each level of analysis differed greatly by color. The yield from sputum colors green, yellow-green, yellow, and rust was much higher than the yield from cream, white, or clear. If out-patient sputum is cream, white, or clear, the yield from bacteriologic analysis is extremely low. This information can reduce laboratory processing costs and help minimize unnecessary antibiotic prescription.

Fission Product Library and Resource

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burke, J. T.; Padgett, S.

Fission product yields can be extracted from an irradiated sample by performing gamma ray spectroscopy on the whole sample post irradiation. There are several pitfalls to avoid when trying to determine a specific isotope's fission product yield.

Comparing diagnostic tests on benefit-risk.

PubMed

Pennello, Gene; Pantoja-Galicia, Norberto; Evans, Scott

2016-01-01

Comparing diagnostic tests on accuracy alone can be inconclusive. For example, a test may have better sensitivity than another test yet worse specificity. Comparing tests on benefit risk may be more conclusive because clinical consequences of diagnostic error are considered. For benefit-risk evaluation, we propose diagnostic yield, the expected distribution of subjects with true positive, false positive, true negative, and false negative test results in a hypothetical population. We construct a table of diagnostic yield that includes the number of false positive subjects experiencing adverse consequences from unnecessary work-up. We then develop a decision theory for evaluating tests. The theory provides additional interpretation to quantities in the diagnostic yield table. It also indicates that the expected utility of a test relative to a perfect test is a weighted accuracy measure, the average of sensitivity and specificity weighted for prevalence and relative importance of false positive and false negative testing errors, also interpretable as the cost-benefit ratio of treating non-diseased and diseased subjects. We propose plots of diagnostic yield, weighted accuracy, and relative net benefit of tests as functions of prevalence or cost-benefit ratio. Concepts are illustrated with hypothetical screening tests for colorectal cancer with test positive subjects being referred to colonoscopy.

The usefulness of carotid sinus massage in different patient groups.

PubMed

Kumar, Narasimhan Pradeep; Thomas, Alan; Mudd, Paul; Morris, Robert O; Masud, Tahir

2003-11-01

to determine the positive yield of carotid sinus massage in different patient groups: unexplained syncope, falls, dizziness and controls. observational study. teaching hospital. we studied consecutive patients over the age of 60 years referred to the 'falls clinic' with a history of unexplained syncope, unexplained falls and unexplained dizziness. We also studied asymptomatic control subjects recruited from a general practice register aged 60 years and over. All patients and control subjects underwent a full clinical assessment (comprehensive history and detailed clinical examination including supine and erect blood pressure measurements) and 12-lead electrocardiography. We performed carotid sinus massage in the supine position for 5 seconds separately on both sides followed by repeating the procedure in the upright positions using a motorised tilt table. Heart rate and blood pressure were recorded using a cardiac monitor and digital plethysmography respectively. The test was considered positive if carotid sinus massage produced asystole with more than a 3 second pause (cardioinhibitory type of carotid sinus syndrome), or a fall in systolic blood pressure of more than 50 mmHg in the absence of significant cardioinhibition (vasodepressor type of carotid sinus syndrome) or where there was evidence of both vasodepressor and cardio-inhibition as above (mixed type). we studied 44 asymptomatic control subjects and 221 symptomatic patients (130 with unexplained syncope, 41 with unexplained falls and 50 with unexplained dizziness). In the overall symptomatic patient group, the positive yield (any type of carotid sinus syndrome) was 17.6% (95% CI = 12.7-22.5). The positive yield in men (26.3% (95% CI = 16.4-36.2)) was twice that in women (13.1% (95% CI = 7.6-18.6)) (P = 0.014). Overall any type of carotid sinus syndrome was present in 22.3% (n = 29) of the syncope group, 17.1% (n = 7) in the unexplained fallers group and 6% (n = 3) in the dizziness group. We also found that no women with unexplained dizziness had a positive carotid sinus massage test. None of the controls demonstrated a positive response. None of the subjects suffered any complications during or after the test. the positive yield of carotid sinus massage in symptomatic patients was 17.6% with the yield in men being twice that in women. None of the asymptomatic control subjects demonstrated a positive response. The yields in unexplained syncope and unexplained falls patients were around 4-fold and 3-fold higher respectively than in unexplained dizziness patients. The positive yield in women with unexplained dizziness (without a definite history of syncope and falls) is zero. Hence, carotid sinus massage in older adults should particularly be targeted at patients with unexplained syncope and unexplained falls.

Petrography and geochemistry of selected lignite beds in the Gibbons Creek mine (Manning Formation, Jackson Group, Paleocene) of east-central Texas

USGS Publications Warehouse

Warwick, Peter D.; Crowley, Sharon S.; Ruppert, Leslie F.; Pontolillo, James

1997-01-01

This study examined the petrographic and geochemical characteristics of two lignite beds (3500 and 4500 beds, Manning Formation, Jackson Group, Eocene) that are mined at the Gibbons Creek mine in east-central Texas. The purpose of the study was to identify the relations among sample ash yield, coal petrography, and trace-element concentrations in lignite and adjoining rock layers of the Gibbons Creek mine. Particular interest was given to the distribution of 12 environmentally sensitive trace elements (As, Be, Cd, Cr, Co, Hg, Mn, Ni, Pb, Sb, Se, and U) that have been identified as potentially hazardous air pollutants (HAPs) in the United States Clean Air Act Amendments of 1990. Eleven lignite, floor, and rock parting samples were collected from incremental channel samples of the 3500 and 4500 beds that were exposed in a highwall of pit A3 at the Gibbons Creek mine. Short proximate and ultimate and forms of sulfur analyses were performed on all lignite samples, and lignite and rock samples were analyzed for 60 major, minor and trace elements. Representative splits of all lignite samples were ground and cast into pellets, and polished for petrographic analyses in blue-light fluorescence and reflected white light to determine liptinite, inertinite, and huminite maceral group percentages. The following observations summarize our results and conclusions about the geochemistry, petrography, and sedimentology of the 3500 and 4500 beds of the Gibbons Creek lignite deposit: (1) Weighted average dry (db) ash yield for the two beds is 29.7%, average total sulfur content is 2.6%, and average calorific value is 7832 Btu (18.22 MJ/kg). Ash yields are greatest in the lower bench (59.33% db) of the 3500 bed and in the upper bench of the 4500 bed (74.61% db). (2) For lignite samples (on a whole-coal basis), the distributions of two of the HAPs (Pb and Sb) are positively related to ash yield, probably indicating an inorganic affinity for these elements. By using cluster analysis we found that Be and Cd were poorly associated with ash yield, indicating a possible organic affinity, and that Ni, Se, Hg, U, and Pb cluster with most of the rare-earth elements. (3) The dominance of the crypto-eugelinite maceral subgroup over the crypto-humotelinite subgroup suggests that all Gibbons Creek lignites were subjected to peat-forming conditions (either biogenic or chemical) conducive to the degradation of wood cellular material into matrix gels, or that original plant material was not very woody and was prone to formation of matrix gels. The latter idea is supported by pollen studies of Gibbons Creek lignite beds; results indicate that the peat was derived in part from marsh plants low in wood tissue. (4) The occurrence of siliceous sponge spicules in the lower benches of the 3500 bed suggests the original peat in this part of the bed was deposited in standing, fresh water. (5) The petrographic data indicate that the upper sample interval of the 3500 bed contains more inertinite (3%) than the other samples studied. Increases in inertinite content in the upper part of the 3500 bed may have been associated with alteration of the peat by acids derived from the volcanic ash or could have been caused by fire, oxidation and drying, or biologic alteration of the peat in the paleo-mire.

Crack Damage Parameters and Dilatancy of Artificially Jointed Granite Samples Under Triaxial Compression

NASA Astrophysics Data System (ADS)

Walton, G.; Alejano, L. R.; Arzua, J.; Markley, T.

2018-06-01

A database of post-peak triaxial test results was created for artificially jointed planes introduced in cylindrical compression samples of a Blanco Mera granite. Aside from examining the artificial jointing effect on major rock and rock mass parameters such as stiffness, peak strength and residual strength, other strength parameters related to brittle cracking and post-yield dilatancy were analyzed. Crack initiation and crack damage values for both the intact and artificially jointed samples were determined, and these damage envelopes were found to be notably impacted by the presence of jointing. The data suggest that with increased density of jointing, the samples transition from a combined matrix damage and joint slip yielding mechanism to yield dominated by joint slip. Additionally, post-yield dilation data were analyzed in the context of a mobilized dilation angle model, and the peak dilation angle was found to decrease significantly when there were joints in the samples. These dilatancy results are consistent with hypotheses in the literature on rock mass dilatancy.

Evaluation of Flinders Technology Associates cards for storage and molecular detection of avian metapneumoviruses.

PubMed

Awad, Faez; Baylis, Matthew; Jones, Richard C; Ganapathy, Kannan

2014-01-01

The feasibility of using Flinders Technology Associates (FTA) cards for the molecular detection of avian metapneumovirus (aMPV) by reverse transcriptase-polymerase chain reaction (RT-PCR) was investigated. Findings showed that no virus isolation was possible from aMPV-inoculated FTA cards, confirming viral inactivation upon contact with the cards. The detection limits of aMPV from the FTA card and tracheal organ culture medium were 10(1.5) median ciliostatic doses/ml and 10(0.75) median ciliostatic doses/ml respectively. It was possible to perform molecular characterization of both subtypes A and B aMPV using inoculated FTA cards stored for up to 60 days at 4 to 6°C. Tissues of the turbinate, trachea and lung of aMPV-infected chicks sampled either by direct impression smears or by inoculation of the tissue homogenate supernatants onto the FTA cards were positive by RT-PCR. However, the latter yielded more detections. FTA cards are suitable for collecting and transporting aMPV-positive samples, providing a reliable and hazard-free source of RNA for molecular characterization.

Spin relaxation measurements of electrostatic bias in intermolecular exploration

NASA Astrophysics Data System (ADS)

Teng, Ching-Ling; Bryant, Robert G.

2006-04-01

We utilize the paramagnetic contribution to proton spin-lattice relaxation rate constants induced by freely diffusing charged paramagnetic centers to investigate the effect of charge on the intermolecular exploration of a protein by the small molecule. The proton NMR spectrum provided 255 resolved resonances that report how the explorer molecule local concentration varies with position on the surface. The measurements integrate over local dielectric constant variations, and, in principle, provide an experimental characterization of the surface free energy sampling biases introduced by the charge distribution on the protein. The experimental results for ribonuclease A obtained using positive, neutral, and negatively charged small nitroxide radicals are qualitatively similar to those expected from electrostatic calculations. However, while systematic electrostatic trends are apparent, the three different combinations of the data sets do not yield internally consistent values for the electrostatic contribution to the intermolecular free energy. We attribute this failure to the weakness of the electrostatic sampling bias for charged nitroxides in water and local variations in effective translational diffusion constant at the water-protein interface, which enters the nuclear spin relaxation equations for the nitroxide-proton dipolar coupling.

Profile of advanced nursing practice in Spain: A cross-sectional study.

PubMed

Sevilla Guerra, Sonia; Miranda Salmerón, Josep; Zabalegui, Adelaida

2018-03-01

In this study, we described the profile of advanced nursing practice in Spain. A cross-sectional study design was used to explore the extent and patterns of advanced nursing practice activity within the domains of expert care planning, integrated care, interprofessional collaboration, education, research, evidence-based practice, and professional leadership. Data were collected in 2015/2016. Purposive sampling yielded a sample of 165 specialist and expert nurses employed by a dual tertiary and community hospital in an urban setting. The study included specialist and expert nurses who had a higher practice profile than registered general nurses. The performance of activities according to age, current position, years of experience, nursing grade, and education was compared. Practice domains were more strongly influenced by the predictors of nursing position and professional career ladder. Age and experience predictors were found to be weak predictors of advanced practice domains. This study offers essential information of the nursing workforce, and clarifies both the advanced nursing practice profile and nomenclature in the context of study. © 2017 John Wiley & Sons Australia, Ltd.

Sensitivity and specificity of obesity diagnosis in pediatric ambulatory care in the United States.

PubMed

Walsh, Carolyn O; Milliren, Carly E; Feldman, Henry A; Taveras, Elsie M

2013-09-01

We examined the sensitivity and specificity of an obesity diagnosis in a nationally representative sample of pediatric outpatient visits. We used the 2005 to 2009 National Ambulatory Medical Care and National Hospital Ambulatory Medical Care surveys. We included visits with children 2 to 18 years, yielding a sample of 48 145 database visits. We determined 3 methods of identifying obesity: documented body mass index (BMI) ≥95th percentile; International Classification of Diseases, Ninth Revision (ICD-9) code; and positive answer to the question, "Does the patient now have obesity?" Using BMI as the gold standard, we calculated the sensitivity and specificity of a clinical obesity diagnosis. Among the 19.5% of children who were obese by BMI, 7.0% had an ICD-9 code and 15.2% had a positive response to questioning. The sensitivity of an obesity diagnosis was 15.4%, and the specificity was 99.2%. The sensitivity of the obesity diagnosis in pediatric ambulatory visits is low. Efforts are needed to increase identification of obese children.

Theory of mind in children with and without autism spectrum disorder: Associations with the sibling constellation.

PubMed

Matthews, Nicole L; Goldberg, Wendy A

2018-04-01

The two prior studies that have examined associations between the sibling constellation and theory of mind in autism spectrum disorder yielded discrepant findings. Thus, efforts to better understand the sibling-theory of mind link in autism spectrum disorder are necessary. This study examined a sample of prekindergarten- and kindergarten-aged (i.e. 4-6 years) typically developing children ( n = 39) and verbal children with autism spectrum disorder ( n = 61). Sibling presence, number of siblings, and having younger and older siblings were positively associated with theory of mind in typically developing children, but not in the full sample of children with autism spectrum disorder. However, in the subgroup of children with autism spectrum disorder without sibling recurrence, the presence of at least one older sibling was positively associated with theory of mind. Findings expand previous limited research on the sibling-theory of mind link in children with autism spectrum disorder by demonstrating a potential difference in the influence of the sibling constellation between children from simplex and multiplex families.

Raman spectroscopy based investigation of molecular changes associated with an early stage of dengue virus infection

NASA Astrophysics Data System (ADS)

Bilal, Maria; Bilal, Muhammad; Saleem, Muhammad; Khurram, Muhammad; Khan, Saranjam; Ullah, Rahat; Ali, Hina; Ahmed, Mushtaq; Shahzada, Shaista; Ullah Khan, Ehsan

2017-04-01

Raman spectroscopy based investigations of the molecular changes associated with an early stage of dengue virus infection (DENV) using a partial least squares (PLS) regression model is presented. This study is based on non-structural protein 1 (NS1) which appears after three days of DENV infection. In total, 39 blood sera samples were collected and divided into two groups. The control group contained samples which were the negative for NS1 and antibodies and the positive group contained those samples in which NS1 is positive and antibodies were negative. Out of 39 samples, 29 Raman spectra were used for the model development while the remaining 10 were kept hidden for blind testing of the model. PLS regression yielded a vector of regression coefficients as a function of Raman shift, which were analyzed. Cytokines in the region 775-875 cm-1, lectins at 1003, 1238, 1340, 1449 and 1672 cm-1, DNA in the region 1040-1140 cm-1 and alpha and beta structures of proteins in the region 933-967 cm-1 have been identified in the regression vector for their role in an early stage of DENV infection. Validity of the model was established by its R-square value of 0.891. Sensitivity, specificity and accuracy were 100% each and the area under the receiver operator characteristic curve was found to be 1.

Cell-wall properties contributing to improved deconstruction by alkaline pre-treatment and enzymatic hydrolysis in diverse maize (Zea mays L.) lines

PubMed Central

Li, Muyang; Heckwolf, Marlies; Crowe, Jacob D.; Williams, Daniel L.; Magee, Timothy D.; Kaeppler, Shawn M.; de Leon, Natalia; Hodge, David B.

2015-01-01

A maize (Zea mays L. subsp. mays) diversity panel consisting of 26 maize lines exhibiting a wide range of cell-wall properties and responses to hydrolysis by cellulolytic enzymes was employed to investigate the relationship between cell-wall properties, cell-wall responses to mild NaOH pre-treatment, and enzymatic hydrolysis yields. Enzymatic hydrolysis of the cellulose in the untreated maize was found to be positively correlated with the water retention value, which is a measure of cell-wall susceptibility to swelling. It was also positively correlated with the lignin syringyl/guaiacyl ratio and negatively correlated with the initial cell-wall lignin, xylan, acetate, and p-coumaric acid (pCA) content, as well as pCA released from the cell wall by pre-treatment. The hydrolysis yield following pre-treatment exhibited statistically significant negative correlations to the lignin content after pre-treatment and positive correlations to the solubilized ferulic acid and pCA. Several unanticipated results were observed, including a positive correlation between initial lignin and acetate content, lack of correlation between acetate content and initial xylan content, and negative correlation between each of these three variables to the hydrolysis yields for untreated maize. Another surprising result was that pCA release was negatively correlated with hydrolysis yields for untreated maize and, along with ferulic acid release, was positively correlated with the pre-treated maize hydrolysis yields. This indicates that these properties that may negatively contribute to the recalcitrance in untreated cell walls may positively contribute to their deconstruction by alkaline pre-treatment. PMID:25871649

Detection of Streptococcus pneumoniae and Haemophilus influenzae Type B by Real-Time PCR from Dried Blood Spot Samples among Children with Pneumonia: A Useful Approach for Developing Countries

PubMed Central

Selva, Laura; Benmessaoud, Rachid; Lanaspa, Miguel; Jroundi, Imane; Moraleda, Cinta; Acacio, Sozinho; Iñigo, Melania; Bastiani, Alien; Monsonis, Manuel; Pallares, Roman; Bassat, Quique; Muñoz-Almagro, Carmen

2013-01-01

Background Dried blood spot (DBS) is a reliable blood collection method for storing samples at room temperature and easily transporting them. We have previously validated a Real-Time PCR for detection of Streptococcus pneumoniae in DBS. The objective of this study was to apply this methodology for the diagnosis of S. pneumoniae and Haemophilus influenzae b (Hib) in DBS samples of children with pneumonia admitted to two hospitals in Mozambique and Morocco. Methods Ply and wzg genes of S. pneumoniae and bexA gene of Hib, were used as targets of Real-Time PCR. 329 DBS samples of children hospitalized with clinical diagnosis of pneumonia were tested. Results Real-Time PCR in DBS allowed for a significant increase in microbiological diagnosis of S. pneumoniae and Hib. When performing blood bacterial culture, only ten isolates of S. pneumoniae and none of Hib were detected (3·0% positivity rate, IC95% 1·4-5·5%). Real-Time PCR from DBS samples increased the detection yield by 4x fold, as 30 S. pneumoniae and 11 Hib cases were detected (12·4% positivity rate, IC95% 9·0-16·5%; P<0·001). Conclusion Real-Time PCR applied in DBS may be a valuable tool for improving diagnosis and surveillance of pneumonia caused by S. pneumoniae or Hib in developing countries. PMID:24116190

Developing a new diagnostic algorithm for human papilloma virus associated oropharyngeal carcinoma: an investigation of HPV DNA assays.

PubMed

Cohen, Natasha; Gupta, Michael; Doerwald-Munoz, Lilian; Jang, Dan; Young, James Edward Massey; Archibald, Stuart; Jackson, Bernard; Lee, Jenny; Chernesky, Max

2017-02-13

Human papilloma virus (HPV) has been implicated in the development of a large proportion of oropharyngeal squamous cell carcinoma (OPSCC). Current techniques used to diagnose HPV etiology require histopathologic analysis. We aim to investigate the diagnostic accuracy of a new application non-histopathologic diagnostic tests to help assist diagnosis of HPV-related oropharyngeal tumors. Patients with OPSCC with nodal metastasis were consecutively recruited from a multidisciplinary cancer clinic. Appropriate samples were collected and analyzed. The various tests examined included COBAS® 4800, Cervista® HR and Genotyping. These tests were compared to p16 staining, which was used as the diagnostic standard. StataIC 14.2 was used to perform analysis, including sensitivity, specificity and receiver operator characteristic [ROC] curves. The COBAS® FNA (area under ROC 0.863) and saliva (area under ROC 0.847) samples performed well in diagnosing HPV positive and negative tumors. Samples tested with Cervista® did not corroborate p16 status reliably. We were able to increase the diagnostic yield of the COBAS® FNA samples by applying the results of the saliva test to negative FNA samples which correctly identified 11 additional p16 positive tumors (area under ROC 0.915). Surrogate testing for HPV using alternate methods is feasible and closely predicts the results of standard diagnostic methods. In the future, these could minimize invasive procedures for diagnosing HPV-related oropharyngeal cancer, but also help to diagnose and treat patients with unknown primaries.

Evaluation of the Helicobacteraceae in the oral cavity of dogs.

PubMed

Craven, Melanie; Recordati, Camilla; Gualdi, Valentina; Pengo, Graziano; Luini, Mario; Scanziani, Eugenio; Simpson, Kenneth W

2011-11-01

To determine the Helicobacter spp present in the oral cavity of dogs and the relationship of those organisms with gastric Helicobacter spp to better define the potential for dog-human and dog-dog transmission. Saliva and dental plaque from 28 dogs and gastric biopsy specimens from a subset of 8 dogs. PCR-based screening for Helicobacter spp was conducted on samples obtained from the oral cavity of 28 dogs. Comparative analysis was conducted on Helicobacteraceae 16S rDNA clone libraries from the oral cavity and stomach of a subset of 8 dogs (5 vomiting and 3 healthy) that had positive PCR results for Helicobacter spp. Helicobacteraceae DNA was identified in the oral cavity of 24 of 28 dogs. Analysis of cloned 16S rDNA amplicons from 8 dogs revealed that Wolinella spp was the most common (8/8 dogs) and abundant (52/57 [91%] clones) member of the Helicobacteraceae family in the oral cavity. Only 2 of 8 dogs harbored Helicobacter spp in the oral cavity, and 1 of those was coinfected with Helicobacter heilmannii and Helicobacter felis in samples obtained from the stomach and saliva. Evaluation of oral cavity DNA with Wolinella-specific PCR primers yielded positive results for 16 of 20 other dogs (24/28 samples were positive for Wolinella spp). Wolinella spp rather than Helicobacter spp were the predominant Helicobacteraceae in the oral cavity of dogs. The oral cavity of dogs was apparently not a zoonotically important reservoir of Helicobacter spp that were non-Helicobacter pylori organisms.

Potential Impacts from Using Photoactive Roads as AN Air Quality Mitigation Strategy

NASA Astrophysics Data System (ADS)

Toro, C.; Jobson, B. T.; Shen, S.; Chung, S. H.; Haselbach, L.

2013-12-01

Mobile sources are major contributors to photochemical air pollution in urban areas. It has been proposed that the use of TiO2 coated roadways ('photoactive roads') could be an effective approach to reduce mobile source emissions by oxidizing NOx and VOC emissions at the roadway surface. However, studies have shown that formation of HONO and aldehydes can occur from some TiO2 treated surfaces during the photocatalytic oxidation of NOx and VOC, respectively. By changing the NOx-to-VOC ratio and generating photolabile HOx radical precursors, photoactive roads may enhance ozone formation rates in urban areas. In this work we present results that quantify NOx and VOC loss rates onto TiO2 treated asphalt and concrete samples, as well as HONO and aldehydes yields that result from the photocatalytic process. The treatment used a commercially available product. These objectives are relevant considering that the quantification of pollutant loss rates and yields of byproducts have not been determined for asphalt and that in the US more than 90% of the roadway surface is made of this material. Surface reaction probabilities (γ) and byproduct yields were determined using a CSTR photochemical chamber under varying conditions of water vapor and UV-A light intensity. Our results indicate that asphalt surfaces have a significantly higher molar yield of HONO compared to concrete surfaces with similar TiO2 loading. Concrete surfaces have reaction probabilities with NO one order of magnitude higher than asphalt samples. Fresh asphalt samples showed negligible photocatalytic activity, presumably due to absorption of TiO2 into the bitumen substrate. Laboratory-prepared asphalt samples with a higher degree of exposed aggregates showed increased HONO molar yields when compared to real-road asphalt samples, whose HONO molar yield was ~1%. Preliminary results for aldehydes formation showed similar molar yields between aged asphalt and concrete, even though aged asphalt samples had twice the TiO2 loading than concrete samples.

Certified Normal: Alzheimer’s Disease Biomarkers and Normative Estimates of Cognitive Functioning

PubMed Central

Hassenstab, Jason; Chasse, Rachel; Grabow, Perri; Benzinger, Tammie L.S.; Fagan, Anne M.; Xiong, Chengjie; Jasielec, Mateusz; Grant, Elizabeth; Morris, John C.

2016-01-01

Normative samples drawn from older populations may unintentionally include individuals with preclinical Alzheimer’s disease (AD) pathology, resulting in reduced means, increased variability, and overestimation of age-effects on cognitive performance. 264 cognitively normal (CDR=0) older adults were classified as biomarker-negative (“Robust Normal,” n=177) or biomarker-positive (“Preclinical Alzheimer’s Disease” (PCAD), n=87) based on amyloid imaging, cerebrospinal fluid biomarkers, and hippocampal volumes. PCAD participants performed worse than Robust Normals on nearly all cognitive measures. Removing PCAD participants from the normative sample yielded higher means and less variability on episodic memory, visuospatial ability, and executive functioning measures. These results were more pronounced in participants aged 75 and older. Notably, removing PCAD participants from the sample significantly reduced age effects across all cognitive domains. Applying norms from the Robust Normal sample to a separate cohort did not improve CDR classification when using standard deviation cutoff scores. Overall, removing individuals with biomarker evidence of preclinical AD improves normative sample quality and substantially reduces age-effects on cognitive performance, but provides no substantive benefit for diagnostic classifications. PMID:27255812

Identification of human remains from the Second World War mass graves uncovered in Bosnia and Herzegovina

PubMed Central

Marjanović, Damir; Hadžić Metjahić, Negra; Čakar, Jasmina; Džehverović, Mirela; Dogan, Serkan; Ferić, Elma; Džijan, Snježana; Škaro, Vedrana; Projić, Petar; Madžar, Tomislav; Rod, Eduard; Primorac, Dragan

2015-01-01

Aim To present the results obtained in the identification of human remains from World War II found in two mass graves in Ljubuški, Bosnia and Herzegovina. Methods Samples from 10 skeletal remains were collected. Teeth and femoral fragments were collected from 9 skeletons and only a femoral fragment from 1 skeleton. DNA was isolated from bone and teeth samples using an optimized phenol/chloroform DNA extraction procedure. All samples required a pre-extraction decalcification with EDTA and additional post-extraction DNA purification using filter columns. Additionally, DNA from 12 reference samples (buccal swabs from potential living relatives) was extracted using the Qiagen DNA extraction method. QuantifilerTM Human DNA Quantification Kit was used for DNA quantification. PowerPlex ESI kit was used to simultaneously amplify 15 autosomal short tandem repeat (STR) loci, and PowerPlex Y23 was used to amplify 23 Y chromosomal STR loci. Matching probabilities were estimated using a standard statistical approach. Results A total of 10 samples were processed, 9 teeth and 1 femoral fragment. Nine of 10 samples were profiled using autosomal STR loci, which resulted in useful DNA profiles for 9 skeletal remains. A comparison of established victims' profiles against a reference sample database yielded 6 positive identifications. Conclusion DNA analysis may efficiently contribute to the identification of remains even seven decades after the end of the World War II. The significant percentage of positively identified remains (60%), even when the number of the examined possible living relatives was relatively small (only 12), proved the importance of cooperation with the members of the local community, who helped to identify the closest missing persons’ relatives and collect referent samples from them. PMID:26088850

Identification of human remains from the Second World War mass graves uncovered in Bosnia and Herzegovina.

PubMed

Marjanović, Damir; Hadžić Metjahić, Negra; Čakar, Jasmina; Džehverović, Mirela; Dogan, Serkan; Ferić, Elma; Džijan, Snježana; Škaro, Vedrana; Projić, Petar; Madžar, Tomislav; Rod, Eduard; Primorac, Dragan

2015-06-01

To present the results obtained in the identification of human remains from World War II found in two mass graves in Ljubuški, Bosnia and Herzegovina. Samples from 10 skeletal remains were collected. Teeth and femoral fragments were collected from 9 skeletons and only a femoral fragment from 1 skeleton. DNA was isolated from bone and teeth samples using an optimized phenol/chloroform DNA extraction procedure. All samples required a pre-extraction decalcification with EDTA and additional post-extraction DNA purification using filter columns. Additionally, DNA from 12 reference samples (buccal swabs from potential living relatives) was extracted using the Qiagen DNA extraction method. QuantifilerTM Human DNA Quantification Kit was used for DNA quantification. PowerPlex ESI kit was used to simultaneously amplify 15 autosomal short tandem repeat (STR) loci, and PowerPlex Y23 was used to amplify 23 Y chromosomal STR loci. Matching probabilities were estimated using a standard statistical approach. A total of 10 samples were processed, 9 teeth and 1 femoral fragment. Nine of 10 samples were profiled using autosomal STR loci, which resulted in useful DNA profiles for 9 skeletal remains. A comparison of established victims' profiles against a reference sample database yielded 6 positive identifications. DNA analysis may efficiently contribute to the identification of remains even seven decades after the end of the World War II. The significant percentage of positively identified remains (60%), even when the number of the examined possible living relatives was relatively small (only 12), proved the importance of cooperation with the members of the local community, who helped to identify the closest missing persons' relatives and collect referent samples from them.

Matterwave interferometric velocimetry of cold Rb atoms

NASA Astrophysics Data System (ADS)

Carey, Max; Belal, Mohammad; Himsworth, Matthew; Bateman, James; Freegarde, Tim

2018-03-01

We consider the matterwave interferometric measurement of atomic velocities, which forms a building block for all matterwave inertial measurements. A theoretical analysis, addressing both the laboratory and atomic frames and accounting for residual Doppler sensitivity in the beamsplitter and recombiner pulses, is followed by an experimental demonstration, with measurements of the velocity distribution within a 20 ?K cloud of rubidium atoms. Our experiments use Raman transitions between the long-lived ground hyperfine states, and allow quadrature measurements that yield the full complex interferometer signal and hence discriminate between positive and negative velocities. The technique is most suitable for measurement of colder samples.

Matterwave interferometric velocimetry of cold Rb atoms

NASA Astrophysics Data System (ADS)

Carey, Max; Belal, Mohammad; Himsworth, Matthew; Bateman, James; Freegarde, Tim

2018-02-01

We consider the matterwave interferometric measurement of atomic velocities, which forms a building block for all matterwave inertial measurements. A theoretical analysis, addressing both the laboratory and atomic frames and accounting for residual Doppler sensitivity in the beamsplitter and recombiner pulses, is followed by an experimental demonstration, with measurements of the velocity distribution within a 20 $\\mu$K cloud of rubidium atoms. Our experiments use Raman transitions between the long-lived ground hyperfine states, and allow quadrature measurements that yield the full complex interferometer signal and hence discriminate between positive and negative velocities. The technique is most suitable for measurement of colder samples.

Pulsed source of ultra low-energy muons at RIKEN-RAL

NASA Astrophysics Data System (ADS)

Bakule, Pavel; Matsuda, Yasuyuki; Iwasaki, Masahiko; Miyake, Yasuhiro; Nagamine, Kanetada; Ikedo, Yutaka; Shimomura, Koichiro; Strasser, Patrick

2006-03-01

At RIKEN-RAL muon facility of the Rutherford Appleton Laboratory (UK) we have produced a pulsed LE-μ + beam with pulse duration of only 10 ns and performed μSR experiments to demonstrate the capability to measure high spin precession frequency signals. The yield of pulsed LE-μ + has been steadily improving over the past 3 years and currently rates of up to 20 μ + per second are observed at the sample position. The overall cooling efficiency from the surface muon beam is now comparable to moderating the muon beam to epithermal energies in simple van der Waals bound solids.

Revised paleomagnetic pole for the Sonoma Volcanics, California

USGS Publications Warehouse

Mankinen, E.A.

1989-01-01

Paleomagnetic sampling of the Miocene and Pliocene Sonoma Volcanics, northern California, was undertaken to supplement an earlier collection. Data from 25 cooling units yield positive fold and reversal tests, and a paleomagnetic pole located at 80.2??N., 069.2??E., with ??95 = 6.8??. This paleopole is significantly displaced (9.6?? ?? 5.3?? of latitude) to the farside of the geographic pole. A highly elliptical distribution of the data in both direction and VGP space indicates that incomplete averaging of geomagnetic secular variation is a more likely explanation for this anomaly than is northward translation of the volcanic field. -Author

Time and position resolution of the scintillator strips for a muon system at future colliders

DOE PAGES

Denisov, Dmitri; Evdokimov, Valery; Lukic, Strahinja

2016-03-31

In this study, prototype scintilator+WLS strips with SiPM readout for a muon system at future colliders were tested for light yield, time resolution and position resolution. Depending on the configuration, light yield of up to 36 photoelectrons per muon per SiPM has been observed, as well as time resolution of 0.45 ns and position resolution along the strip of 7.7 cm.

Analysis of false results in a series of 835 fine needle aspirates of breast lesions.

PubMed

Willis, S L; Ramzy, I

1995-01-01

To analyze cases of false diagnoses from a large series to help increase the accuracy of fine needle aspiration of palpable breast lesions. The results of FNA of 835 palpable breast lesions were analyzed to determine the reasons for false positive, false negative and false suspicious diagnoses. Of the 835 aspirates, 174 were reported as positive, 549 as negative and 66 as suspicious or atypical but not diagnostic of malignancy. Forty-six cases were considered unsatisfactory. Tissue was available for comparison in 286 cases. The cytologic diagnoses in these cases were reported as follows: positive, 125 (43.7%); suspicious, 33 (11.5%); atypical, 18 (6.2%); negative, 92 (32%); and unsatisfactory, 18 (6.2%). There was one false positive diagnosis, yielding a false positive rate of 0.8%. This lesion was a case of fibrocystic change with hyperplasia, focal fat necrosis and reparative atypia. There were 14 false negative cases, resulting in a false negative rate of 13.2%. Nearly all these cases were sampling errors and included infiltrating ductal carcinomas (9), ductal carcinomas in situ (2), infiltrating lobular carcinomas (2) and tubular carcinoma (1). Most of the suspicious and atypical lesions proved to be carcinomas (35/50). The remainder were fibroadenomas (6), fibrocystic change (4), gynecomastia (2), adenosis (2) and granulomatous mastitis (1). A positive diagnosis of malignancy by FNA is reliable in establishing the diagnosis and planning the treatment of breast cancer. The false-positive rate is very low, with only a single case reported in 835 aspirates. Most false negatives are due to sampling and not to interpretive difficulties. The category "suspicious but not diagnostic of malignancy" serves a useful purpose in management of patients with breast lumps.

Improving qPCR telomere length assays: Controlling for well position effects increases statistical power.

PubMed

Eisenberg, Dan T A; Kuzawa, Christopher W; Hayes, M Geoffrey

2015-01-01

Telomere length (TL) is commonly measured using quantitative PCR (qPCR). Although, easier than the southern blot of terminal restriction fragments (TRF) TL measurement method, one drawback of qPCR is that it introduces greater measurement error and thus reduces the statistical power of analyses. To address a potential source of measurement error, we consider the effect of well position on qPCR TL measurements. qPCR TL data from 3,638 people run on a Bio-Rad iCycler iQ are reanalyzed here. To evaluate measurement validity, correspondence with TRF, age, and between mother and offspring are examined. First, we present evidence for systematic variation in qPCR TL measurements in relation to thermocycler well position. Controlling for these well-position effects consistently improves measurement validity and yields estimated improvements in statistical power equivalent to increasing sample sizes by 16%. We additionally evaluated the linearity of the relationships between telomere and single copy gene control amplicons and between qPCR and TRF measures. We find that, unlike some previous reports, our data exhibit linear relationships. We introduce the standard error in percent, a superior method for quantifying measurement error as compared to the commonly used coefficient of variation. Using this measure, we find that excluding samples with high measurement error does not improve measurement validity in our study. Future studies using block-based thermocyclers should consider well position effects. Since additional information can be gleaned from well position corrections, rerunning analyses of previous results with well position correction could serve as an independent test of the validity of these results. © 2015 Wiley Periodicals, Inc.

Climate change impacts on crop yield: evidence from China.

PubMed

Wei, Taoyuan; Cherry, Todd L; Glomrød, Solveig; Zhang, Tianyi

2014-11-15

When estimating climate change impact on crop yield, a typical assumption is constant elasticity of yield with respect to a climate variable even though the elasticity may be inconstant. After estimating both constant and inconstant elasticities with respect to temperature and precipitation based on provincial panel data in China 1980-2008, our results show that during that period, the temperature change contributes positively to total yield growth by 1.3% and 0.4% for wheat and rice, respectively, but negatively by 12% for maize. The impacts of precipitation change are marginal. We also compare our estimates with other studies and highlight the implications of the inconstant elasticities for crop yield, harvest and food security. We conclude that climate change impact on crop yield would not be an issue in China if positive impacts of other socio-economic factors continue in the future. Copyright © 2014 Elsevier B.V. All rights reserved.

Fruit Wines Inhibitory Activity Against α-Glucosidase.

PubMed

Cakar, Uros; Grozdanic, Nada; Petrovic, Aleksandar; Pejin, Boris; Nastasijevic, Branislav; Markovic, Bojan; Dordevic, Brizita

2017-01-01

Fruit wines are well known for their profound health-promoting properties including both enzyme activations and inhibitions. They may act preventive in regard to diabetes melitus and other chronic diseases. Potential α-glucosidase inhibitory activity of fruit wines made from blueberry, black chokeberry, blackberry, raspberry and sour cherry was the subject of this study. In order to increase the alcohol content due to enriched extraction of total phenolics, sugar was added in the fruit pomace of the half of the examined fruit wine samples. Compared with acarbose used as a positive control (IC50 = 73.78 µg/mL), all fruit wine samples exhibited higher α-glucosidase inhibitory activity. Indeed, blueberry wine samples stood out, both prepared with IC50 = 24.14 µg/mL, lyophilised extract yield 3.23% and without IC50 = 46.39 µg/mL, lyophilised extract yield 2.89% and with addition of sugar before fermentation. Chlorogenic acid predominantly contributed to α-glucosidase inhibitory activity of the blueberry, black chokeberry and sour cherry wine samples. However, ellagic acid, a potent α-glucosidase inhibitor possessing a planar structure, only slightly affected the activity of the blueberry wine samples, due to the lower concentration. In addition to this, molecular docking study of chlorogenic acid pointed out the importance of binding energy (-8.5 kcal/mol) for the inhibition of the enzyme. In summary, fruit wines made from blueberry should be primarily taken into consideration as a medicinal food targeting diabetes mellitus type 2 in the early stage, if additional studies would confirm their therapeutic potential for the control of postprandial hyperglycemia. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A review and meta-analysis of affective judgments and physical activity in adult populations.

PubMed

Rhodes, Ryan E; Fiala, Bonnie; Conner, Mark

2009-12-01

Popular theories of health behavior have often been criticized for neglecting an affective component to behavioral engagement. This study reviewed affective judgment (AJ) constructs employed in physical activity research to assess the relationship with behavior. Studies were eligible if they included: (a) a measure of physical activity; (b) a distinct measure of AJ (e.g., affective attitude, enjoyment, intrinsic motivation); and (c) involved participants with a mean age of 18 years or older. Literature searches were concluded in September, 2009 among five key search engines. This search yielded a total of 10,631 potentially relevant records; of these, 102 passed the eligibility criteria. Random effects meta-analysis procedures with correction for sampling and measurement bias were employed in the analysis. Articles were published between 1989 and 2009, with sample sizes ranging from 15 to 6,739. Of the studies included, 82 were correlational and 20 were experimental, yielding 114 independent samples. The majority of the correlational samples reported a significant positive correlation between AJ and physical activity (83 out of 85), with a summary r of 0.42 (95% CI 0.37 to 0.46) that was invariant across the measures employed, study quality, population sampled and cultural variables. Experimental studies demonstrated that persuasive, information-based, and self-regulatory interventions failed to change AJ; by contrast, environmental and experiential interventions showed promise in their capability to influence AJ. The results point to a medium-effect size relationship between AJ and physical activity. Interventions that change AJ are scarce despite their potential for changing physical activity. Future experimental work designed to evaluate the causal impact ofAJ on physical activity is required.

Effect of Mesostructure and Fragmentation on Planar Shock Response of Dry Sand

NASA Astrophysics Data System (ADS)

Dwivedi, Sunil; Hatanpaa, Benjamin; Effs, Kijana; Ferri, Brian; Thadhani, Naresh

2017-06-01

The objective of the present work is to gain insight into the role of grain arrangements (mesostructure) and fragmentation on the shock response of dry sand under planar plate impact loading. Mesoscale simulations of the dry sand sample were carried out for initial porosities of 20% and 30% using CUBIT, LS-DYNA, and TECPLOT software. The mesostructure was varied as ordered (grains with edge contacts) and disordered (grains with point contacts) for the same porosity. The grain fragmentation was modeled by erosion method with erosion parameter of 0.5 and 0.75. The results show that computed Us-Up slope for 20% porosity with ordered mesostructure is negative at lower impact velocities and changes to positive when velocity is increased. However, the disordered mesostructure yields positive Us-Up slope at 20% porosity irrespective of the impact velocity. The Us-Up slope for 30% porous sand is positive irrespective of the mesostructure and impact velocity. More importantly, allowing grain fragmentation, the in-situ average longitudinal stress reduces from the computed Hugoniot stress by more than 25%. These results suggest the need for detailed simulations with varying mesostructure and more realistic fragmentation model as well experiments for a dry sand sample at lower porosities. Work supported by HDTRA-1-12-1-0004 and FA9550-12-1-0128 Grants.

On the Involvement of Single-Bond Rotation in the Primary Photochemistry of Photoactive Yellow Protein

PubMed Central

Stahl, Andreas D.; Hospes, Marijke; Singhal, Kushagra; van Stokkum, Ivo; van Grondelle, Rienk; Groot, Marie Louise; Hellingwerf, Klaas J.

2011-01-01

Prior experimental observations, as well as theoretical considerations, have led to the proposal that C4-C7 single-bond rotation may play an important role in the primary photochemistry of photoactive yellow protein (PYP). We therefore synthesized an analog of this protein's 4-hydroxy-cinnamic acid chromophore, (5-hydroxy indan-(1E)-ylidene)acetic acid, in which rotation across the C4-C7 single bond has been locked with an ethane bridge, and we reconstituted the apo form of the wild-type protein and its R52A derivative with this chromophore analog. In PYP reconstituted with the rotation-locked chromophore, 1), absorption spectra of ground and intermediate states are slightly blue-shifted; 2), the quantum yield of photochemistry is ∼60% reduced; 3), the excited-state dynamics of the chromophore are accelerated; and 4), dynamics of the thermal recovery reaction of the protein are accelerated. A significant finding was that the yield of the transient ground-state intermediate in the early phase of the photocycle was considerably higher in the rotation-locked samples than in the corresponding samples reconstituted with p-coumaric acid. In contrast to theoretical predictions, the initial photocycle dynamics of PYP were observed to be not affected by the charge of the amino acid residue at position 52, which was varied by 1), varying the pH of the sample between 5 and 10; and 2), site-directed mutagenesis to construct R52A. These results imply that C4-C7 single-bond rotation in PYP is not an alternative to C7=C8 double-bond rotation, in case the nearby positive charge of R52 is absent, but rather facilitates, presumably with a compensatory movement, the physiological Z/E isomerization of the blue-light-absorbing chromophore. PMID:21889456

Testing scale-dependent effects of seminatural habitats on farmland biodiversity.

PubMed

Dainese, Matteo; Luna, Diego Inclán; Sitzia, Tommaso; Marini, Lorenzo

2015-09-01

The effectiveness of conservation interventions for maximizing biodiversity benefits from agri-environment schemes (AESs) is expected to depend on the quantity of seminatural habitats in the surrounding landscape. To verify this hypothesis, we developed a hierarchical sampling design to assess the effects of field boundary type and cover of seminatural habitats in the landscape at two nested spatial scales. We sampled three types of field boundaries with increasing structural complexity (grass margin, simple hedgerow, complex hedgerow) in paired landscapes with the presence or absence of seminatural habitats (radius 0.5 km), that in turn, were nested within 15 areas with different proportions of seminatural habitats at a larger spatial scale (10 X 10 km). Overall, 90 field boundaries were sampled across a Mediterranean'region (northeastern Italy). We considered species richness response across three different taxonomic groups: vascular plants, butterflies, and tachinid flies. No interactions between type of field boundary and surrounding landscape were found at either 0.5 and 10 km, indicating that the quality of field boundary had the same effect irrespective of the cover of seminatural habitats. At the local scale, extended-width grass margins yielded higher plant species richness, while hedgerows yielded higher species richness of butterflies and tachinids. At the 0.5-km landscape scale, the effect of the proportion of seminatural habitats was neutral for plants and tachinids, while butterflies were positively related to the proportion of forest. At the 10-km landscape scale, only butterflies responded positively to the proportion of seminatural habitats. Our study confirmed the importance of testing multiple scales when considering species from different taxa and with different mobility. We showed that the quality of field boundaries at the local scale was an important factor in enhancing farmland biodiversity. For butterflies, AESs should focus particular attention on preservation'of forest patches in agricultural landscapes within 0.5 kin, as well as the conservation of seminatural habitats at a wider landscape scale.

Measuring and Modeling Suspended Sediment and Nutrient Yields from a Mixed-Land-Use Watershed of the Central U.S.

NASA Astrophysics Data System (ADS)

Zeiger, S. J.; Hubbart, J. A.

2016-12-01

A nested-scale watershed study design was used to monitor water quantity and quality of an impaired 3rd order stream in a rapidly urbanizing mixed-land-use watershed of the central USA. Grab samples were collected at each gauging site (n=836 samples x 5 gauging sites) and analyzed for suspended sediment, total phosphorus, and inorganic nitrogen species during the four year study period (2010 - 2013). Observed data were used to quantify relationships between climate, land use and pollutant loading. Additionally, Soil and Water Assessment Tool (SWAT) estimates of monthly stream flow, suspended sediment, total phosphorus, nitrate, nitrite, and ammonium were validated. Total annual precipitation ranged from approximately 650 mm during 2012 (extreme drought year) to 1350 mm during 2010 (record setting wet year) which caused significant (p<0.05) differences in annual pollutant yields (i.e. loads per unit area) that ranged from 115 to 174%. Multiple linear regression analyses showed significant (p<0.05) relationships between pollutant loading, annual total precipitation (positive correlate), urban land use (positive correlate), forested land use (negative correlate), and wetland land use (negative correlate). Results from SWAT model performance assessment indicated calibration was necessary to achieve Nash-Sutcliff Efficiency (NSE) values greater than 0.05 for monthly pollutant loads. Calibrating the SWAT model to multiple gauging sites within the watershed improved estimates of monthly stream flow (NSE=0.83), and pollutant loads (NSE>0.78). However, nitrite and ammonium loads were underestimated by more than four orders of magnitude (NSE<-0.16) indicating a critical need for improved nutrient cycling and routing routines. Results highlight the need for sampling regimens that capture the variability of climate and flow mediated pollutant transport, and the benefits of calibrating the SWAT model to multiple gauging sites in mixed-land-use watersheds.

[Effect of near infrared spectrum on the precision of PLS model for oil yield from oil shale].

PubMed

Wang, Zhi-Hong; Liu, Jie; Chen, Xiao-Chao; Sun, Yu-Yang; Yu, Yang; Lin, Jun

2012-10-01

It is impossible to use present measurement methods for the oil yield of oil shale to realize in-situ detection and these methods unable to meet the requirements of the oil shale resources exploration and exploitation. But in-situ oil yield analysis of oil shale can be achieved by the portable near infrared spectroscopy technique. There are different correlativities of NIR spectrum data formats and contents of sample components, and the different absorption specialities of sample components shows in different NIR spectral regions. So with the proportioning samples, the PLS modeling experiments were done by 3 formats (reflectance, absorbance and K-M function) and 4 regions of modeling spectrum, and the effect of NIR spectral format and region to the precision of PLS model for oil yield from oil shale was studied. The results show that the best data format is reflectance and the best modeling region is combination spectral range by PLS model method and proportioning samples. Therefore, the appropriate data format and the proper characteristic spectral region can increase the precision of PLS model for oil yield form oil shale.

Flammability Parameters of Candles

NASA Astrophysics Data System (ADS)

Balog, Karol; Kobetičová, Hana; Štefko, Tomáš

2017-06-01

The paper deals with the assessment of selected fire safety characteristics of candles. Weight loss of a candle during the burning process, candle burning rate, soot index, heat release rate and yield of carbon oxides were determined. Soot index was determined according to EN 15426: 2007 - Candles - Specification for Sooting Behavior. All samples met the prescribed amount of produced soot. Weight loss, heat release rate and the yield of carbon oxides were determined for one selected sample. While yield of CO increased during the measurement, the yield of CO2 decreased by half in 40 minutes.

Feedbacks between conservation and social-ecological systems

PubMed Central

Miller, Brian W.; Caplow, Susan C.; Leslie, Paul W.

2012-01-01

Robust ways to meet objectives of environmental conservation and social and economic development remain elusive. This struggle may in part be related to insufficient understanding of the feedbacks between conservation initiatives and social-ecological systems, specifically, the ways in which conservation initiatives result in social changes that have secondary effects on the environments targeted by conservation. To explore this idea we sampled peer-reviewed articles addressing the social and environmental dimensions of conservation and coded each paper according to its research focus and characterization of these feedbacks. The majority of articles in our sample focused either on the effect of conservation initiatives on people (e.g., relocation, employment) or the effect of people on the environment (e.g., fragmentation, conservation efficacy of traditional management systems). Few studies in our sample empirically addressed both the social dynamics resulting from conservation initiatives and subsequent environmental effects. In many cases, one was measured and the other was discussed anecdotally. Among the studies that describe feedbacks between social and environmental variables, there was more evidence of positive (amplifying) feedbacks between social and environmental outcomes (i.e., undesirable social outcomes yielded undesirable environmental effects, and desirable social outcomes yielded desirable environmental effects). The major themes within the sampled literature include conflict between humans and wild animals, social movements, adaptive comanagement, loss of traditional management systems, traditional ecological knowledge, human displacement and risks to livelihoods, and conservation and development. The narratives associated with each theme can serve as hypotheses for facilitating further discussion about conservation issues and for catalyzing future studies of the feedbacks between conservation and social-ecological systems. PMID:22443128

SPACE WARPS - I. Crowdsourcing the discovery of gravitational lenses

NASA Astrophysics Data System (ADS)

Marshall, Philip J.; Verma, Aprajita; More, Anupreeta; Davis, Christopher P.; More, Surhud; Kapadia, Amit; Parrish, Michael; Snyder, Chris; Wilcox, Julianne; Baeten, Elisabeth; Macmillan, Christine; Cornen, Claude; Baumer, Michael; Simpson, Edwin; Lintott, Chris J.; Miller, David; Paget, Edward; Simpson, Robert; Smith, Arfon M.; Küng, Rafael; Saha, Prasenjit; Collett, Thomas E.

2016-01-01

We describe SPACE WARPS, a novel gravitational lens discovery service that yields samples of high purity and completeness through crowdsourced visual inspection. Carefully produced colour composite images are displayed to volunteers via a web-based classification interface, which records their estimates of the positions of candidate lensed features. Images of simulated lenses, as well as real images which lack lenses, are inserted into the image stream at random intervals; this training set is used to give the volunteers instantaneous feedback on their performance, as well as to calibrate a model of the system that provides dynamical updates to the probability that a classified image contains a lens. Low-probability systems are retired from the site periodically, concentrating the sample towards a set of lens candidates. Having divided 160 deg2 of Canada-France-Hawaii Telescope Legacy Survey imaging into some 430 000 overlapping 82 by 82 arcsec tiles and displaying them on the site, we were joined by around 37 000 volunteers who contributed 11 million image classifications over the course of eight months. This stage 1 search reduced the sample to 3381 images containing candidates; these were then refined in stage 2 to yield a sample that we expect to be over 90 per cent complete and 30 per cent pure, based on our analysis of the volunteers performance on training images. We comment on the scalability of the SPACE WARPS system to the wide field survey era, based on our projection that searches of 105 images could be performed by a crowd of 105 volunteers in 6 d.

[Comparison of hot versus cold biopsy forceps in the diagnosis of endobronchial lesions].

PubMed

Firoozbakhsh, Shahram; Seifirad, Soroush; Safavi, Enayat; Dinparast, Reza; Taslimi, Shervin; Derakhshandeilami, Gholamreza

2011-11-01

Traditionally cold biopsy forceps were used for endobronchial biopsy, and recently electrocautery (hot) bronchoscopy biopsy forceps are introduced. It is hypothesized that hot biopsy forceps may decrease procedure related bleeding and also may decrease the quality of obtained samples. Patients with different indications for endobronchial biopsy during fiberoptic bronchoscopy underwent three hot and three cold biopsies with a random fashion. All biopsies were obtained with a single biopsy forceps with and without the application of an electrocoagulation current, set on soft coagulation mode (40W). A four point scale was used for quantification of bleeding. A single pathologist blinded to the patients' history was requested to review all samples. A three point scale was used to assess electrocoagulation damage. A total of 240 biopsies were obtained from 40 patients. Frequency of positive concordance between the two methods was 85%. The degree of electrocoagulation damage of the samples was as follows: grade 1=52.5%, grade 2=32.5%, and grade 3=15%. The average bleeding score following hot biopsy was significantly lower compared to the cold biopsy (P=.006). The concordance between diagnostic yield of hot and cold biopsies was 85%. There was no significant difference between the diagnostic yields of two biopsy methods (P=.687). Hot biopsy forceps significantly decreased the procedure related bleeding. The quality of samples was not impaired significantly. Regarding low prevalence of bleeding following endobronchial biopsy, routine use of hot bronchoscopy forceps is not reasonable. However, familiarity of bronchoscopists with this method may improve bronchoscopy safety. Copyright © 2011 SEPAR. Published by Elsevier Espana. All rights reserved.

Correlation and path coefficient analysis of quantitative characters in spine gourd (Momordica dioica Roxb.).

PubMed

Aliya, F; Begum, H; Reddy, M T; Sivaraj, N; Pandravada, S R; Narshimulu, G

2014-05-01

Fifty genotypes of spine gourd (Momordica dioica Roxb.) were evaluated in a randomized block design with two replications at the Vegetable Research Station, Rajendranagar, Hyderabad, Andhra Pradesh, India during kharif, 2012. Correlation and path coefficient analysis were carried out to study the character association and contribution, respectively for twelve quantitative characters namely vine length (m), number of stems per plant, days to first female flower appearance, first female flowering node, days to first fruit harvest, days to last fruit harvest, fruiting period (days), fruit length (cm), fruit width (cm), fruit weight (g), number of fruits per plant and fruit yield per plant (kg) for identification of the potential selection indices. Correlation and path coefficient analyses revealed that fruiting period and number of fruits per plant not only had positively significant correlation with fruit yield but also had positively high direct effect on it and are regarded as the main determinants of fruit yield. Days to first fruit harvest had positively moderate direct effect on fruit yield and its association was negatively significant, days to last fruit harvest had negatively high direct effect on fruit yield and its association was significant positively, hence restricted simultaneous selection can be made for days to first fruit harvest and days to last fruit harvest. The improvement in fruit yield can be effective if selection is based on days to first fruit harvest, days to last fruit harvest, fruiting period and number of fruits per plant.

Water-quality conditions, and constituent loads and yields in the Cambridge drinking-water source area, Massachusetts, water years 2005–07

USGS Publications Warehouse

Smith, Kirk P.

2013-01-01

The source water area for the drinking-water supply of the city of Cambridge, Massachusetts, encompasses major transportation corridors, as well as large areas of light industrial, commercial, and residential land use. Because of ongoing development in the drinking-water source area, the Cambridge water supply has the potential to be affected by a wide variety of contaminants. The U.S. Geological Survey (USGS) has monitored surface-water quality in the Hobbs Brook and Stony Brook Basins, which compose the drinking-water source area, since 1997 (water year 1997) through continuous monitoring and discrete sample collection and, since 2004, through systematic collection of streamwater samples during base-flow and stormflow conditions at five primary sampling stations in the drinking-water source area. Four primary sampling stations are on small tributaries in the Hobbs Brook and Stony Brook Basins; the fifth primary sampling station is on the main stem of Stony Brook and drains about 93 percent of the Cambridge drinking-water source area. Water samples also were collected at six secondary sampling stations, including Fresh Pond Reservoir, the final storage reservoir for the raw water supply. Storm runoff and base-flow concentrations of calcium (Ca), chloride (Cl), sodium (Na), and sulfate (SO4) were estimated from continuous records of streamflow and specific conductance for six monitoring stations, which include the five primary sampling stations. These data were used to characterize current water-quality conditions, estimate loads and yields, and describe trends in Cl and Na in the tributaries and main-stem streams in the Hobbs Brook and Stony Brook Basins. These data also were used to describe how streamwater quality is affected by various watershed characteristics and provide information to guide future watershed management. Water samples were analyzed for physical properties and concentrations of Ca, Cl, Na, and SO4, total nitrogen (TN), total phosphorus (TP), caffeine, and a suite of 59 polar pesticides. Values of physical properties and constituent concentrations varied widely, particularly in samples from tributaries. Median concentrations of Ca, Cl, Na, and SO4 in samples collected in the Hobbs Brook Basin (39.8, 392, 207, and 21.7 milligrams per liter (mg/L), respectively) were higher than those for the Stony Brook Basin (17.8, 87.7, 49.7, and 14.7 mg/L, respectively). These differences in major ion concentrations are likely related to the low percentages of developed land and impervious area in the Stony Brook Basin. Concentrations of dissolved Cl and Na in samples, and those estimated from continuous records of specific conductance (particularly during base flow), often were greater than the U.S. Environmental Protection Agency (USEPA) secondary drinking-water guideline for Cl (250 mg/L), the chronic aquatic-life guideline for Cl (230 mg/L), and the Commonwealth of Massachusetts, Executive Office of Energy and Environmental Affairs drinking-water guideline for Na (20 mg/L). Mean annual flow-weighted concentrations of Ca, Cl, and Na were generally positively correlated with the area of roadway land use in the subbasins. Correlations between mean annual concentrations of Ca and SO4 in base flow and total roadway, total impervious, and commercial-industrial land uses were statistically significant. Concentrations of TN (range of 0.42 to 5.13 mg/L in all subbasins) and TP (range of 0.006 to 0.80 mg/L in all subbasins) in tributary samples did not differ substantially between the Hobbs Brook and Stony Brook Basins. Concentrations of TN and TP in samples collected during water years 2004–07 exceeded proposed reference concentrations of 0.57 and 0.024 mg/L, in 94 and 56 percent of the samples, respectively. Correlations between annual flow-weighted concentrations of TN and percentages of recreational land use and water-body area were statistically significant; however, no significant relation was found between TP and available land-use information. The volume of streamflow affected water-quality conditions at the primary sampling stations. Turbidity and concentrations of TP were positively correlated with streamflow. In contrast, concentrations of major ions were negatively correlated with streamflow, indicating that these constituents were diluted during stormflows. Concentrations of TN were not correlated with streamflow. Twenty-five pesticides and caffeine were detected in water samples collected in the drinking-water source area and in raw water collected from the Cambridge water-treatment facility intake at the Fresh Pond Reservoir. Imidacloprid, norflurazon, and siduron were the most frequently detected pesticides with the frequency of detections ranging from about 24 to 41 percent. Caffeine was detected in about 37 percent of water samples at concentrations ranging from 0.003 to 1.82 micrograms per liter (μg/L). Although some of the detected pesticides degrade rapidly, norflurazon and siduron are relatively stable and are able to immigrate though the serial reservoir system. Concentrations of 2,4-D, carbaryl, imazaquin, MCPA (2-methyl-4-chlorophenoxyacetic acid), metsulfuron-methyl, norflurazon, siduron, and caffeine were detected more frequently in stormflow samples than in base-flow samples. Concentrations of pesticides did not exceed USEPA drinking-water guidelines or other health standards and were several orders of magnitude less than the lethal exposure level established for several fish species common to the drinking-water source area. Imidacloprid, an insecticide, was the only pesticide with a concentration exceeding available long-term aquatic-life guidelines. Several pesticides correlated significantly with the amount of recreational, residential, and commercial area in the tributary subbasins. Mean annual base-flow concentrations of caffeine correlated significantly with parking-lot land use. For most tributaries, about 70 percent of the annual loads of Ca, Cl, Na, and SO4 were associated with base flow. Upward temporal trends in annual loads of Cl and Na were identified on the basis of data for water years 1998 to 2008 for the outlet of the Cambridge Reservoir in the Hobbs Brook Basin; however, similar trends were not identified for the main stem of Stony Brook downstream from the reservoir. The proportions of the TN load attributed to base flow and stormflow were similar in each tributary. In contrast, more than 83 percent of the TP loads in the tributaries and about 73 percent of the TP load in main stem of Stony Brook were associated with stormflow. Mean annual yields of Ca, Cl, Na, and SO4 in the Stony Brook Reservoir watershed, which represents most of the drinking-water source area, were 14, 85, 46, and 9 metric tons per square kilometer, respectively. Mean annual yields among the individual tributary subbasins varied extensively. Mean annual yields for the respective constituents increased with an increase in roadway and parking-lot area in the tributary subbasins. Mean annual yields of TN in the tributary subbasins ranged from about 740 to more than 1,200 kilograms per square kilometer and exceeded the yield for the main stem of Stony Brook at USGS station 01104460 upstream from the Stony Brook Reservoir. Mean annual yields estimated for the herbicides 2,4-D and imidacloprid ranged from 34 to 310 grams per square kilometer (g/km2) and 3 to 170 g/km2, respectively. Annual loads for 2,4-D were entirely associated with stormflow. The largest annual load for imidacloprid was estimated for the main stem of Stony Brook; however, the highest annual yield for this pesticide, as well as for benomyl, carbaryl, metalaxyl, and propiconazole, was estimated for a tributary to the Stony Brook Reservoir that drains largely residential and recreational areas. Mean annual yields for the herbicide siduron ranged from 6.9 to 35 g/km2 with most of the loads associated with stormflow. Mean annual yields for the insecticide diuron ranged from 2.1 to 4.4 g/km2. Annual yields of caffeine ranged from 11 to 410 g/km2.

Hot-boning enhances cook yield of boneless skinless chicken thighs.

PubMed

Zhuang, H; Bowker, B C; Buhr, R J; Brambila, G Sanchez

2014-06-01

Three experiments were conducted to evaluate the effects of postmortem deboning time on cook yield of boneless skinless chicken thighs. In experiment 1, chicken thigh meat was deboned at 0.75 (hot-bone), 2, and 24 h postmortem (PM) and trimmed to obtain mainly iliotibialis muscle. Samples were cooked directly from a frozen state. Cook yield of the muscle was significantly influenced by PM deboning time. Hot-boned thighs exhibited a 7% greater cook yield than the samples deboned at 24 h. In experiment 2, boneless skinless chicken thighs were deboned at 0.3, 2, and 24 h PM and cooked directly from a fresh, never-frozen state at 24 h PM. Cook yield of the hot-boned thighs was significantly higher than those of the 2 and 24 h deboned samples, which did not differ from each other. In experiment 3, whole legs (thigh + drumstick) were cut from the carcass backbone at 0.3 (hot-cut), 2, and 24 h PM. Thighs were separated from the legs (drumsticks) at either the same time the whole legs were removed from the carcasses or at 24 h PM. Intact thighs (bone in) were cooked fresh at 24 h PM. Color of fresh thigh muscles, cook yield, and Warner-Bratzler shear force of cooked samples were measured. Cook yield of the thighs cut from the backbone before chilling was significantly higher than those cut from the carcasses at 2 and 24 h PM, which did not differ from each other. The PM time at which intact thighs were separated from the leg (drumstick) did not influence cook yield. These results demonstrate that postmortem deboning time can significantly affect cook yield of boneless skinless chicken thigh products. Deboning chicken thighs after chilling reduces the cook yield. Differences in the cook yield of thighs may also result from the removal of whole chicken legs from the carcass backbone. Poultry Science Association Inc.

Multiparametric comparison of chromogenic-based culture methods used to assess the microbiological quality of drinking water and the mFC method combined with a molecular confirmation procedure.

PubMed

Maheux, Andrée F; Dion-Dupont, Vanessa; Bisson, Marc-Antoine; Bouchard, Sébastien; Jubinville, Éric; Nkuranga, Martine; Rodrigue, Lynda; Bergeron, Michel G; Rodriguez, Manuel J

2015-03-01

MI agar and Colilert(®), as well as mFC agar combined with an Escherichia coli-specific molecular assay (mFC + E. coli rtPCR), were compared in terms of their sensitivity, ease of use, time to result and affordability. The three methods yielded a positive E. coli signal for 11.5, 10.8, and 11.5% of the 968 well water samples tested, respectively. One hundred and thirty-six (136) samples gave blue colonies on mFC agar and required confirmation. E. coli-specific rtPCR showed false-positive results in 23.5% (32/136) of cases. In terms of ease of use, Colilert was the simplest method to use while the MI method provided ease of use comparable to all membrane filtration methods. However, the mFC + E. coli rtPCR assay required highly trained employees for confirmation purposes. In terms of affordability, and considering contamination rate of well water samples tested, the Colilert method and the mFC + E. coli rtPCR assay were at least five times more costly than the MI agar method. Overall, compared with the other two methods tested, the MI agar method offers the most advantages to assess drinking water quality.

[Residues of chloramphenicol in the calf organism following parenteral administration of the Czechoslovak preparation Chronicin inj].

PubMed

Malíková, M; Habrda, J

1976-03-01

Using two biological methods the chloramphenicol content in various tissues of 11 calves aged 3--18 days was determined after a single-dose therapeutical administration of the Czechoslovak preparation of Chronicin inj. in the quantity of 12 mg kg-1 body mass. Of four test strains, solely Micrococcus flavus (ATCC 10240) strain proved suitable. Chloramphenicol was quantitatively determined by reading from transformed standard curves. An evalua tion of the two approximately equally sensitive methods yielded the following results: three days after the injection all calves were positive, at 5 and 10 days, one of three calves in each group was negativ similarly to both calves slaughtered 15 days post injection. The residues appeared most frequently in the liver, at the site of injection, and in the fore and hind musculature. Maximum detectable concentrations were recorded in the liver. Culinary and technological treatment of positive meat and liver samples revealed that 15 minutes' boiling and 30 minutes' roasting destroyed the microbiologically active chloramphenicol residues in the samples. Neither deep freezing nor salting was sufficient for residue inactivation, although in some samples a decrease in biological chloramphenicol activity by circa 20--30% was recorded. a preslaughter withdrawal time of 15 days is recommended.

Sensitive and affordable diagnostic assay for the quantitative detection of anaplastic lymphoma kinase (ALK) alterations in patients with non-small cell lung cancer

PubMed Central

Dama, Elisa; Tillhon, Micol; Bertalot, Giovanni; de Santis, Francesca; Troglio, Flavia; Pessina, Simona; Passaro, Antonio; Pece, Salvatore; de Marinis, Filippo; Dell'Orto, Patrizia; Viale, Giuseppe; Spaggiari, Lorenzo; Di Fiore, Pier Paolo; Bianchi, Fabrizio; Barberis, Massimo; Vecchi, Manuela

2016-01-01

Accurate detection of altered anaplastic lymphoma kinase (ALK) expression is critical for the selection of lung cancer patients eligible for ALK-targeted therapies. To overcome intrinsic limitations and discrepancies of currently available companion diagnostics for ALK, we developed a simple, affordable and objective PCR-based predictive model for the quantitative measurement of any ALK fusion as well as wild-type ALK upregulation. This method, optimized for low-quantity/−quality RNA from FFPE samples, combines cDNA pre-amplification with ad hoc generated calibration curves. All the models we derived yielded concordant predictions when applied to a cohort of 51 lung tumors, and correctly identified all 17 ALK FISH-positive and 33 of the 34 ALK FISH-negative samples. The one discrepant case was confirmed as positive by IHC, thus raising the accuracy of our test to 100%. Importantly, our method was accurate when using low amounts of input RNA (10 ng), also in FFPE samples with limited tumor cellularity (5–10%) and in FFPE cytology specimens. Thus, our test is an easily implementable diagnostic tool for the rapid, efficacious and cost-effective screening of ALK status in patients with lung cancer. PMID:27206799

Scanning electron microscope measurement of width and shape of 10nm patterned lines using a JMONSEL-modeled library.

PubMed

Villarrubia, J S; Vladár, A E; Ming, B; Kline, R J; Sunday, D F; Chawla, J S; List, S

2015-07-01

The width and shape of 10nm to 12 nm wide lithographically patterned SiO2 lines were measured in the scanning electron microscope by fitting the measured intensity vs. position to a physics-based model in which the lines' widths and shapes are parameters. The approximately 32 nm pitch sample was patterned at Intel using a state-of-the-art pitch quartering process. Their narrow widths and asymmetrical shapes are representative of near-future generation transistor gates. These pose a challenge: the narrowness because electrons landing near one edge may scatter out of the other, so that the intensity profile at each edge becomes width-dependent, and the asymmetry because the shape requires more parameters to describe and measure. Modeling was performed by JMONSEL (Java Monte Carlo Simulation of Secondary Electrons), which produces a predicted yield vs. position for a given sample shape and composition. The simulator produces a library of predicted profiles for varying sample geometry. Shape parameter values are adjusted until interpolation of the library with those values best matches the measured image. Profiles thereby determined agreed with those determined by transmission electron microscopy and critical dimension small-angle x-ray scattering to better than 1 nm. Published by Elsevier B.V.

Lucerne transient streak virus; a Recently Detected Virus Infecting Alfafa (Medicago sativa) in Central Saudi Arabia

PubMed Central

Raza, Ahmed; Al-Shahwan, Ibrahim M.; Abdalla, Omer A.; Al-Saleh, Mohammed A.; Amer, Mahmoud A.

2017-01-01

A survey was conducted to determine the status of Lucerne transient streak virus (LTSV) in three high-yielding alfalfa regions in central Saudi Arabia (Riyadh, Qassim, and Hail) during 2014. Three hundred and eight symptomatic alfalfa, and seven Sonchus oleraceus samples were collected. DAS-ELISA indicated that 59 of these samples were positive to LTSV. Two isolates of LTSV from each region were selected for molecular studies. RT-PCR confirmed the presence of LTSV in the selected samples using a specific primer pair. Percentage identity and homology tree comparisons revealed that all Saudi isolates were more closely related to each other but also closely related to the Canadian isolate-JQ782213 (97.1–97.6%) and the New Zealand isolate-U31286 (95.8–97.1%). Comparing Saudi isolates of LTSV with ten other sobemoviruses based on the coat protein gene sequences confirmed the distant relationship between them. Eleven out of fourteen plant species used in host range study were positive to LTSV. This is the first time to document that Trifolium alexandrinum, Nicotiana occidentalis, Chenopodium glaucum, and Lathyrus sativus are new host plant species for LTSV and that N. occidentalis being a good propagative host for it. PMID:28167887

The role of climatic variables in winter cereal yields: a retrospective analysis.

PubMed

Luo, Qunying; Wen, Li

2015-02-01

This study examined the effects of observed climate including [CO2] on winter cereal [winter wheat (Triticum aestivum), barley (Hordeum vulgare) and oat (Avena sativa)] yields by adopting robust statistical analysis/modelling approaches (i.e. autoregressive fractionally integrated moving average, generalised addition model) based on long time series of historical climate data and cereal yield data at three locations (Moree, Dubbo and Wagga Wagga) in New South Wales, Australia. Research results show that (1) growing season rainfall was significantly, positively and non-linearly correlated with crop yield at all locations considered; (2) [CO2] was significantly, positively and non-linearly correlated with crop yields in all cases except wheat and barley yields at Wagga Wagga; (3) growing season maximum temperature was significantly, negatively and non-linearly correlated with crop yields at Dubbo and Moree (except for barley); and (4) radiation was only significantly correlated with oat yield at Wagga Wagga. This information will help to identify appropriate management adaptation options in dealing with the risk and in taking the opportunities of climate change.

Kinetics of lipogenic genes expression in milk purified mammary epithelial cells (MEC) across lactation and their correlation with milk and fat yield in buffalo.

PubMed

Yadav, Poonam; Kumar, Parveen; Mukesh, Manishi; Kataria, R S; Yadav, Anita; Mohanty, A K; Mishra, B P

2015-04-01

Expression patterns of lipogenic genes (LPL, ABCG2, ACSS2, ACACA, SCD, BDH, LIPIN1, SREBF1, PPARα and PPARγ) were studied in milk purified MEC across different stages of lactation (15, 30, 45, 60, 90, 120 and 240 days relative to parturition) in buffalo. PPARα was the most abundant gene while ABCG2 and ACSS2 had moderate level of expression; whereas expression of SREBF and PPARγ was very low. The expression patterns of some genes (BDH1, ACSS2, and LIPIN1) across lactation were positively correlated with milk yield while negatively correlated with fat yield. SCD also showed weak correlation with milk yield (p, 0.53) and fat yield (p, -0.47). On the other hand, expression pattern of ACACA was negatively correlated with milk yield (p, -0.88) and positively correlated with fat yield (p, 0.62). Strong correlation was observed between genes involved in de novo milk fat synthesis (BDH1, ACSS2, LIPIN2 and SCD) and milk yield. Copyright © 2015 Elsevier Ltd. All rights reserved.

Seed Transmission of Soybean vein necrosis virus: The First Tospovirus Implicated in Seed Transmission.

PubMed

Groves, Carol; German, Thomas; Dasgupta, Ranjit; Mueller, Daren; Smith, Damon L

2016-01-01

Soybean vein necrosis virus (SVNV; genus Tospovirus; Family Bunyaviridae) is a negative-sense single-stranded RNA virus that has been detected across the United States and in Ontario, Canada. In 2013, a seed lot of a commercial soybean variety (Glycine max) with a high percentage of discolored, deformed and undersized seed was obtained. A random sample of this seed was planted in a growth room under standard conditions. Germination was greater than 90% and the resulting seedlings looked normal. Four composite samples of six plants each were tested by reverse transcription polymerase chain reaction (RT-PCR) using published primers complimentary to the S genomic segment of SVNV. Two composite leaflet samples retrieved from seedlings yielded amplicons with a size and sequence predictive of SVNV. Additional testing of twelve arbitrarily selected individual plants resulted in the identification of two SVNV positive plants. Experiments were repeated by growing seedlings from the same seed lot in an isolated room inside a thrips-proof cage to further eliminate any external source of infection. Also, increased care was taken to reduce any possible PCR contamination. Three positive plants out of forty-eight were found using these measures. Published and newly designed primers for the L and M RNAs of SVNV were also used to test the extracted RNA and strengthen the diagnosis of viral infection. In experiments, by three scientists, in two different labs all three genomic RNAs of SVNV were amplified in these plant materials. RNA-seq analysis was also conducted using RNA extracted from a composite seedling sample found to be SVNV-positive and a symptomatic sample collected from the field. This analysis revealed both sense and anti-sense reads from all three gene segments in both samples. We have shown that SVNV can be transmitted in seed to seedlings from an infected seed lot at a rate of 6%. To our knowledge this is the first report of seed-transmission of a Tospovirus.

Retrospective Species Identification of Microsporidian Spores in Diarrheic Fecal Samples from Human Immunodeficiency Virus/AIDS Patients by Multiplexed Fluorescence In Situ Hybridization▿

PubMed Central

Graczyk, Thaddeus K.; Johansson, Michael A.; Tamang, Leena; Visvesvara, Govinda S.; Moura, Laci S.; DaSilva, Alexandre J.; Girouard, Autumn S.; Matos, Olga

2007-01-01

In order to assess the applicability of multiplexed fluorescence in situ hybridization (FISH) assay for the clinical setting, we conducted retrospective analysis of 110 formalin-stored diarrheic stool samples from human immunodeficiency virus (HIV)/AIDS patients with intestinal microsporidiosis collected between 1992 and 2003. The multiplexed FISH assay identified microsporidian spores in 94 of 110 (85.5%) samples: 49 (52.1%) were positive for Enterocytozoon bieneusi, 43 (45.8%) were positive for Encephalitozoon intestinalis, 2 (2.1%) were positive for Encephalitozoon hellem, and 9 samples (9.6%) contained both E. bieneusi and E. intestinalis spores. Quantitative spore counts per ml of stool yielded concentration values from 3.5 × 103 to 4.4 × 105 for E. bieneusi (mean, 8.8 × 104/ml), 2.3 × 102 to 7.8 × 104 (mean, 1.5 × 104/ml) for E. intestinalis, and 1.8 × 102 to 3.6 × 102 for E. hellem (mean, 2.7 × 102/ml). Identification of microsporidian spores by multiplex FISH assay was more sensitive than both Chromotrope-2R and CalcoFluor White M2R stains; 85.5% versus 72.7 and 70.9%, respectively. The study demonstrated that microsporidian coinfection in HIV/AIDS patients with intestinal microsporidiosis is not uncommon and that formalin-stored fecal samples older than 10 years may not be suitable for retrospective analysis by techniques targeting rRNA. Multiplexed FISH assay is a reliable, quantitative fluorescence microscopy method for the simultaneous identification of E. bieneusi, E. intestinalis, and E. hellem, as well as Encephalitozoon cuniculi, spores in fecal samples and is a useful tool for assessing spore shedding intensity in intestinal microsporidiosis. The method can be used for epidemiological investigations and applied in clinical settings. PMID:17287331

Field Detection of Drugs of Abuse in Oral Fluid Using the Alere™ DDS®2 Mobile Test System with Confirmation by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS).

PubMed

Krotulski, Alex J; Mohr, Amanda L A; Friscia, Melissa; Logan, Barry K

2018-04-01

The collection and analysis of drugs in oral fluid (OF) at the roadside has become more feasible with the introduction of portable testing devices such as the Alere™ DDS®2 Mobile Test System (DDS®2). The objective of this study was to compare the on-site results for the DDS®2 to laboratory-based confirmatory assays with respect to detection of drugs of abuse in human subjects. As part of a larger Institutional Review Board approved study, two OF samples were collected from each participant at a music festival in Miami, FL, USA. One OF sample was field screened using the DDS®2, and a confirmatory OF sample was collected using the Quantisal™ OF collection device and submitted to the laboratory for testing. In total, 124 subjects participated in this study providing two contemporaneous OF samples. DDS®2 field screening yielded positive results for delta-9-tetrahydrocannabinol (THC) (n = 27), cocaine (n = 12), amphetamine (n = 3), methamphetamine (n = 3) and benzodiazepine (n = 1). No opiate-positive OF samples were detected. For cocaine, amphetamine, methamphetamine and benzodiazepines, the DDS®2 displayed sensitivity, specificity and accuracy of 100%. For THC, the DDS®2 displayed sensitivity of 90%, specificity of 100% and accuracy of 97.5%, when the threshold for confirmation matched that of the manufacturers advertised cut-off. When this confirmatory threshold was lowered to the analytical limit of detection (i.e., 1 ng/mL), apparent device performance for THC was poorer due to additional samples testing positive by confirmatory assay that had tested negative on the DDS®2, demonstrating a need for correlation between manufacturer cut-off and analytical reporting limit. These results from drug-using subjects demonstrate the value of field-based OF testing, and illustrate the significance of selecting an appropriate confirmation cut-off concentration with respect to performance evaluation and detection of drug use.

Insights into the Performance of SD Bioline Malaria Ag P.f/Pan Rapid Diagnostic Test and Plasmodium falciparum Histidine-Rich Protein 2 Gene Variation in Madagascar.

PubMed

Willie, Nigani; Mehlotra, Rajeev K; Howes, Rosalind E; Rakotomanga, Tovonahary A; Ramboarina, Stephanie; Ratsimbasoa, Arsène C; Zimmerman, Peter A

2018-06-01

Plasmodium falciparum histidine-rich protein 2 (PfHRP2) forms the basis of many current malaria rapid diagnostic tests (RDTs). However, the parasites lacking part or all of the pfhrp2 gene do not express the PfHRP2 protein and are, therefore, not identifiable by PfHRP2-detecting RDTs. We evaluated the performance of the SD Bioline Malaria Ag P.f/Pan RDT together with pfhrp2 variation in Madagascar. Genomic DNA isolated from 260 patient blood samples were polymerase chain reaction (PCR)-amplified for the parasite 18S rRNA and pfhrp2 genes. Post-PCR ligation detection reaction-fluorescent microsphere assay (LDR-FMA) was performed for the identification of parasite species. Plasmodium falciparum histidine-rich protein 2 amplicons were sequenced. Polymerase chain reaction diagnosis of patient samples showed that 29% (75/260) were infected and P. falciparum was present in 95% (71/75) of these PCR-positive samples. Comparing RDT and P. falciparum detection by LDR-FMA, eight samples were RDT negative but P. falciparum positive (false negatives), all of which were pfhrp2 positive. The sensitivity and specificity of the RDT were 87% and 90%, respectively. Seventy-three samples were amplified for pfhrp2 , from which nine randomly selected amplicons were sequenced, yielding 13 sequences. Amplification of pfhrp2 , combined with RDT analysis and P. falciparum detection by LDR-FMA, showed that there was no indication of pfhrp2 deletion. Sequence analysis of pfhrp2 showed that the correlation between pfhrp2 sequence structure and RDT detection rates was unclear. Although the observed absence of pfhrp2 deletion from the samples screened here is encouraging, continued monitoring of the efficacy of the SD Bioline Malaria Ag P.f/Pan RDT for malaria diagnosis in Madagascar is warranted.

Extraction of citral oil from lemongrass (Cymbopogon Citratus) by steam-water distillation technique

NASA Astrophysics Data System (ADS)

Alam, P. N.; Husin, H.; Asnawi, T. M.; Adisalamun

2018-04-01

In Indonesia, production of citral oil from lemon grass (Cymbopogon Cytratus) is done by a traditional technique whereby a low yield results. To improve the yield, an appropriate extraction technology is required. In this research, a steam-water distillation technique was applied to extract the essential oil from the lemongrass. The effects of sample particle size and bed volume on yield and quality of citral oil produced were investigated. The drying and refining time of 2 hours were used as fixed variables. This research results that minimum citral oil yield of 0.53% was obtained on sample particle size of 3 cm and bed volume of 80%, whereas the maximum yield of 1.95% on sample particle size of 15 cm and bed volume of 40%. The lowest specific gravity of 0.80 and the highest specific gravity of 0.905 were obtained on sample particle size of 8 cm with bed volume of 80% and particle size of 12 cm with bed volume of 70%, respectively. The lowest refractive index of 1.480 and the highest refractive index of 1.495 were obtained on sample particle size of 8 cm with bed volume of 70% and sample particle size of 15 cm with bed volume of 40%, respectively. The solubility of the produced citral oil in alcohol was 70% in ratio of 1:1, and the citral oil concentration obtained was around 79%.

Azimuthal resolution degradation due to ocean surface motion in focused arrays and SARS

NASA Astrophysics Data System (ADS)

1990-06-01

During the meeting at WHOI (5-18-90), a discussion arose of the ability of the focused array to simulate the R/v ratios typical of airborne and/or spaceborne SARs. In particular, the ability was questioned of the focused array to yield the same azimuthal resolution, rho, as the SAR. Although the focused array can be sampled to yield the same azimuthal resolution as the SAR, it is likely that the images generated by the focused array will not be identical to those produced by a SAR with the same azimuth resolution. For a true SAR, biases in the Doppler history of azimuthally traveling waves due to their along-track motion will cause shifts in their apparent position. This will cause waves which are physically at one location to shift over several pixel widths in the image. The limited swath width of the focused array will prevent if from observing scattered power from waves falling outside the swath, thus such waves will not affect the image formed within the swath, as would happen in the SAR. Thus, it is likely that the focused array will not yield the same image as a SAR having the same resolution.

Erosion Rates of Volcanic-ash Derived Soils in the Blue Mountains of Eastern Oregon, USA: A Comparison Across Sales in Space and Time.

NASA Astrophysics Data System (ADS)

Wondzell, S. M.; Clifton, C. F.; Harris, R. M.; Ritchie, J. C.

2007-12-01

We examined present day rates of erosion in the Blue Mountains of eastern Oregon to quantify background erosion rates to provide standards for assessing possible accelerated rates of erosion resulting from wild fire or from land-management activities such as prescribed fire. The Skookum Creek watersheds, where stream discharge and sediment yield have been recorded continuously since the watersheds were gauged in 1992, provided a watershed-scale estimate of erosion rates. We installed hillslope erosion plots on north- and south- facing slopes within the watersheds in 2002 and collected data for three years to estimate short-term, hillslope- scale erosion rates. We also collected soil samples and analyzed them for 137Cs to get a 40-yr time- integrated estimate of hillslope erosion rates. Our results showed large differences between whole-watershed sediment yields and hillslope erosion rates measured from plots, suggesting that episodic processes dominated sediment production and transport and therefore controlled watershed-scale sediment budgets. At the hillslope-scale, short-term erosion resulted primarily from digging by small mammals and trampling by elk. Visual observations at the plots suggested that annual down-slope sediment movement was usually less than one meter. There were no significant difference among slope positions, but erosion rates were significantly higher on south-facing aspects and positively correlated to the amount of bare ground. In contrast, the 137Cs data suggested that erosion rates differed with slope position. Higher erosion rates were measured in toe- and mid-slope positions, with little erosion occurring on upper slopes and ridge tops. We examine these results in light of the present-day pattern of surface soils resulting from redistribution of volcanic ash from upper- slope to lower-slope positions and the effects of disturbance, including wildfire and the preferential grazing of riparian and lower-slope positions by domestic livestock.

Assessment of microscopic and molecular tools for the diagnosis and follow-up of cryptosporidiosis in patients at risk.

PubMed

Le Govic, Y; Guyot, K; Certad, G; Deschildre, A; Novo, R; Mary, C; Sendid, B; Viscogliosi, E; Favennec, L; Dei-Cas, E; Fréalle, E; Dutoit, E

2016-01-01

Cryptosporidiosis is an important though underreported public health concern. Molecular tools might be helpful in improving its diagnosis. In this study, ZR Fecal DNA MiniPrep™ Kit (ZR) and NucliSens® easyMAG® (EM) were compared using four Cryptosporidium-seeded feces and 29 Cryptosporidium-positive stools. Thereafter, ZR was selected for prospective evaluation of Cryptosporidium detection by 18S rDNA and LAXER quantitative PCR (qPCR) in 69 stools from 56 patients after Cryptosporidium detection by glycerin, modified Ziehl-Neelsen (ZN) and auramine-phenol (AP) stainings. The combination of any of the two extraction methods with 18S qPCR yielded adequate detection of Cryptosporidium in seeded stools, but the ZR kit showed the best performance. All 29 Cryptosporidium-positive samples were positive with 18S qPCR, after both ZR and EM extraction. However, false-negative results were found with LAXER qPCR or nested PCR. Cryptosporidiosis was diagnosed in 7/56 patients. All the microscopic methods enabled the initial diagnosis, but Cryptosporidium was detected in 12, 13, and 14 samples from these seven patients after glycerin, ZN, and AP staining respectively. Among these samples, 14 and 12 were positive with 18S and LAXER qPCR respectively. In two patients, Cryptosporidium DNA loads were found to be correlated with clinical evolution. Although little known, glycerin is a sensitive method for the initial detection of Cryptosporidium. When combined with 18S qPCR, ZR extraction, which had not been evaluated so far for Cryptosporidium, was an accurate tool for detecting Cryptosporidium and estimating the oocyst shedding in the course of infection.

The Occurrence Rate of Hot Jupiters

NASA Astrophysics Data System (ADS)

Rampalli, Rayna; Catanzarite, Joseph; Batalha, Natalie M.

2017-01-01

As the first kind of exoplanet to be discovered, hot Jupiters have always been objects of interest. Despite being prevalent in radial velocity and ground-based surveys, they were found to be much rarer based on Kepler observations. These data show a pile-up at radii of 9-22 Rearth and orbital periods of 1-10 days. Computing accurate occurrence rates can lend insight into planet-formation and migration-theories. To get a more accurate look, the idea of reliability was introduced. Each hot Jupiter candidate was assigned a reliability based on its location in the galactic plane and likelihood of being a false positive. Numbers were updated if ground-based follow-up indicated a candidate was indeed a false positive. These reliabilities were introduced into an occurrence rate calculation and yielded about a 12% decrease in occurrence rate for each period bin examined and a 25% decrease across all the bins. To get a better idea of the cause behind the pileup, occurrence rates based on parent stellar metallicity were calculated. As expected from previous work, higher metallicity stars yield higher occurrence rates. Future work includes examining period distributions in both the high metallicity and low metallicity sample for a better understanding and confirmation of the pile-up effect.

Studies of a peatified angiosperm log cross section from Indonesia by nuclear magnetic resonance spectroscopy and analytical pyrolysis

USGS Publications Warehouse

Bates, A.L.; Hatcher, P.G.; Lerch, H. E.; Cecil, C.B.; Neuzil, S.G.; ,

1991-01-01

Samples from a 10 cm cross-sectional radius of a peatified angiosperm log from Sumatra, Indonesia, were examined by 13C nuclear magnetic resonance and pyrolysis-gas chromatography in order to understand chemical changes due to the peatification process. NMR results show degradation by selective loss of carbohydrates in all parts of the log section compared with fresh wood; however, the degree of degradation is less near the center of the log section. The degree of ring substitution of aromatic lignin monomeric units, as measured by dipolar dephasing NMR methods, appears to be less at the center of the log section than at the periphery. The methoxyl carbon content of lignin in the log is lower than in unaltered angiospermous lignin but does not appear to change as a function of either radial position or the degree of aromatic ring substitution. Pyrolysis-gas chromatography indicates higher yields of catechols in the outer areas relative to the heartwood. Other than the variations in catechol contents and in the yields of carbohydrate-derived pyrolysis products (e.g. levoglucosan, angelicalactones), the pyrolysis results do not show significant changes related to radial position, indicating that the lignin is not significantly altered across the log section. ?? 1991.

Psychometric properties of the mobility inventory for agoraphobia: convergent, discriminant, and criterion-related validity.

PubMed

Chambless, Dianne L; Sharpless, Brian A; Rodriguez, Dianeth; McCarthy, Kevin S; Milrod, Barbara L; Khalsa, Shabad-Ratan; Barber, Jacques P

2011-12-01

Aims of this study were (a) to summarize the psychometric literature on the Mobility Inventory for Agoraphobia (MIA), (b) to examine the convergent and discriminant validity of the MIA's Avoidance Alone and Avoidance Accompanied rating scales relative to clinical severity ratings of anxiety disorders from the Anxiety Disorders Interview Schedule (ADIS), and (c) to establish a cutoff score indicative of interviewers' diagnosis of agoraphobia for the Avoidance Alone scale. A meta-analytic synthesis of 10 published studies yielded positive evidence for internal consistency and convergent and discriminant validity of the scales. Participants in the present study were 129 people with a diagnosis of panic disorder. Internal consistency was excellent for this sample, α=.95 for AAC and .96 for AAL. When the MIA scales were correlated with interviewer ratings, evidence for convergent and discriminant validity for AAL was strong (convergent r with agoraphobia severity ratings=.63 vs. discriminant rs of .10-.29 for other anxiety disorders) and more modest but still positive for AAC (.54 vs. .01-.37). Receiver operating curve analysis indicated that the optimal operating point for AAL as an indicator of ADIS agoraphobia diagnosis was 1.61, which yielded sensitivity of .87 and specificity of .73. Copyright © 2011. Published by Elsevier Ltd.

Psychometric Properties of the Mobility Inventory for Agoraphobia: Convergent, Discriminant, and Criterion-Related Validity

PubMed Central

Chambless, Dianne L.; Sharpless, Brian A.; Rodriguez, Dianeth; McCarthy, Kevin S.; Milrod, Barbara L.; Khalsa, Shabad-Ratan; Barber, Jacques P.

2012-01-01

Aims of this study were (a) to summarize the psychometric literature on the Mobility Inventory for Agoraphobia (MIA), (b) to examine the convergent and discriminant validity of the MIA’s Avoidance Alone and Avoidance Accompanied rating scales relative to clinical severity ratings of anxiety disorders from the Anxiety Disorders Interview Schedule (ADIS), and (c) to establish a cutoff score indicative of interviewers’ diagnosis of agoraphobia for the Avoidance Alone scale. A meta-analytic synthesis of 10 published studies yielded positive evidence for internal consistency and convergent and discriminant validity of the scales. Participants in the present study were 129 people with a diagnosis of panic disorder. Internal consistency was excellent for this sample, α = .95 for AAC and .96 for AAL. When the MIA scales were correlated with interviewer ratings, evidence for convergent and discriminant validity for AAL was strong (convergent r with agoraphobia severity ratings = .63 vs. discriminant rs of .10-.29 for other anxiety disorders) and more modest but still positive for AAC (.54 vs. .01-.37). Receiver operating curve analysis indicated that the optimal operating point for AAL as an indicator of ADIS agoraphobia diagnosis was 1.61, which yielded sensitivity of .87 and specificity of .73. PMID:22035997

A review of the global relationship among freshwater fish, autotrophic activity, and regional climate

USGS Publications Warehouse

Deines, Andrew M.; Bunnell, David B.; Rogers, Mark W.; Beard, T. Douglas; Taylor, William W.

2015-01-01

The relationship between autotrophic activity and freshwater fish populations is an important consideration for ecologists describing trophic structure in aquatic communities, fisheries managers tasked with increasing sustainable fisheries development, and fish farmers seeking to maximize production. Previous studies of the empirical relationships of autotrophic activity and freshwater fish yield have found positive relationships but were limited by small sample sizes, small geographic scopes, and the inability to compare patterns among many types of measurement techniques. Individual studies and reviews have also lacked consistent consideration of regional climate factors which may inform relationships between fisheries and autotrophic activity. We compiled data from over 700 freshwater systems worldwide and used meta-analysis and linear models to develop a comprehensive global synthesis between multiple metrics of autotrophic activity, fisheries, and climate indicators. Our results demonstrate that multiple metrics of fish (i.e., catch per unit effort, yield, and production) increase with autotrophic activity across a variety of fisheries. At the global scale additional variation in this positive relationship can be ascribed to regional climate differences (i.e., temperature and precipitation) across systems. Our results provide a method and proof-of-concept for assessing inland fisheries production at the global scale, where current estimates are highly uncertain, and may therefore inform the continued sustainable use of global inland fishery resources.

[Identification of hepatitis B virus YMDD point mutation using peptide nucleic acid clamping PCR].

PubMed

Zhang, Yingying; He, Haitang; Yang, Jie; Hou, Jinlin

2013-06-01

To establish a peptide nucleic acid clamping PCR assay for detecting hepatitis B virus (HBV) drug resistance mutation. RtM204I (ATT) mutant, rtM204V (GTG) mutant and rtM204 (ATG) wild-type plasmids mixed at different ratios were detected for mutations by PNA clamping PCR assay and direct sequencing, and the sensitivity and specificity of the two methods were compared. Serum samples from 85 patients with chronic HBV infection were detected for drug resistance using the two methods. The sensitivity of PNA-PCR assay was 0.001% in a 10(5)-fold excess of wild-type HBV DNA with a detection limit of 10(1) copies. The sensitivity of direct sequencing was 10% with a detection limit of 10(4) copies. Mutants were detected in 73 of the 85 serum samples (85.9%), including YIDD in 40 samples, YVDD in 23 samples, and YIDD+YVDD in 10 samples. The agreement of PNA-PCR assay with direct sequencing was only 40% (34/85, YIDD in 21 samples, YVDD in 11 samples, and YIDD+YVDD in 2 samples). Neither of the two methods yielded positive results for the negative control samples, suggesting their good specificity. PNA-PCR assay appears to be a more sensitive and rapid assay for detection of HBV genotypic resistance.

Platelet-rich plasma in orthopedic therapy: a comparative systematic review of clinical and experimental data in equine and human musculoskeletal lesions.

PubMed

Brossi, Patrícia M; Moreira, Juliana J; Machado, Thaís S L; Baccarin, Raquel Y A

2015-04-22

This systematic review aimed to present and critically appraise the available information on the efficacy of platelet rich plasma (PRP) in equine and human orthopedic therapeutics and to verify the influence of study design and methodology on the assumption of PRP's efficacy. We searched Medline, PubMed, Embase, Bireme and Google Scholar without restrictions until July 2013. Randomized trials, human cohort clinical studies or case series with a control group on the use of PRP in tendons, ligaments or articular lesions were included. Equine clinical studies on the same topics were included independently of their design. Experimental studies relevant to the clarification of PRP's effects and mechanisms of action in tissues of interest, conducted in any animal species, were selected. This review included 123 studies. PRP's beneficial effects were observed in 46.7% of the clinical studies, while the absence of positive effects was observed in 43.3%. Among experimental studies, 73% yielded positive results, and 7.9% yielded negative results. The most frequent flaws in the clinical trials' designs were the lack of a true placebo group, poor product characterization, insufficient blinding, small sampling, short follow-up periods, and adoption of poor outcome measures. The methods employed for PRP preparation and administration and the selected outcome measures varied greatly. Poor study design was a common feature of equine clinical trials. From studies in which PRP had beneficial effects, 67.8% had an overall high risk of bias. From the studies in which PRP failed to exhibit beneficial effects, 67.8% had an overall low risk of bias. Most experimental studies revealed positive effects of PRP. Although the majority of equine clinical studies yielded positive results, the human clinical trials' results failed to corroborate these findings. In both species, beneficial results were more frequently observed in studies with a high risk of bias. The use of PRP in musculoskeletal lesions, although safe and promising, has still not shown strong evidence in clinical scenarios.

Inverted Apatite (U-Th)/He and Fission-track Dates from the Rae craton, Baffin Island, Canada and Implications for Apatite Radiation Damage-He Diffusivity Models

NASA Astrophysics Data System (ADS)

Ault, A. K.; Reiners, P. W.; Thomson, S. N.; Miller, G. H.

2015-12-01

Coupled apatite (U-Th)/He and fission-track (AFT) thermochronology data from the same sample can be used to decipher complex low temperature thermal histories and evaluate compatibility between these two methods. Existing apatite He damage-diffusivity models parameterize radiation damage annealing as fission-track annealing and yield inverted apatite He and AFT dates for samples with prolonged residence in the He partial retention zone. Apatite chemistry also impacts radiation damage and fission-track annealing, temperature sensitivity, and dates in both systems. We present inverted apatite He and AFT dates from the Rae craton, Baffin Island, Canada, that cannot be explained by apatite chemistry or existing damage-diffusivity and fission track models. Apatite He dates from 34 individual analyses from 6 samples range from 237 ± 44 Ma to 511 ± 25 Ma and collectively define a positive date-eU relationship. AFT dates from these same samples are 238 ± 15 Ma to 350 ± 20 Ma. These dates and associated track length data are inversely correlated and define the left segment of a boomerang diagram. Three of the six samples with 20-90 ppm eU apatite grains yield apatite He and AFT dates inverted by 300 million years. These samples have average apatite Cl chemistry of ≤0.02 wt.%, with no correlation between Cl content and Dpar. Thermal history simulations using geologic constraints, an apatite He radiation damage accumulation and annealing model, apatite He dates with the range of eU values, and AFT date and track length data, do not yield any viable time-temperature paths. Apatite He and AFT data modeled separately predict thermal histories with Paleozoic-Mesozoic peaks reheating temperatures differing by ≥15 °C. By modifying the parameter controlling damage annealing (Rmr0) from the canonical 0.83 to 0.5-0.6, forward models reproduce the apatite He date-eU correlation and AFT dates with a common thermal history. Results imply apatite radiation damage anneals at higher temperatures than fission-track damage and the impact on coupled apatite He and AFT dates is magnified for protracted cooling histories. Further experimental and field-based tests are important for refining radiation damage and fission-track annealing parameters for accurate interpretation of apatite He- and AFT-derived thermal histories.

Effects of organic fertilizers and biochar/organic fertilizer combinations on fertility and organic matter dynamics of a sandy soil in north-west Germany

NASA Astrophysics Data System (ADS)

Greenberg, Isabel; Kaiser, Michael; Polifka, Steven; Wiedner, Katja; Glaser, Bruno; Ludwig, Bernard

2017-04-01

Biochar and biochar/organic fertilizer combinations have been recommended as soil amendments to improve plant productivity and soil properties, as well as to increase soil organic C (OC) storage. However, these claims have been largely unverified by field experiments lasting several years. To address these issues, a field experiment was established in 2012 to analyze the effects of organic fertilizers and biochar/organic fertilizer combinations (five field replicates, fully randomized block design) on the fertility and organic matter dynamics of a sandy Cambisol. In 2016, samples were taken from the 0-10 cm and 10-30 cm soil depths of the following treatments: mineral fertilizer and maize digestate that were applied both individually and in combination with 1 t/ha or 40 t/ha biochar. Further treatments were compost and 10 t/ha composted biochar. The treatments were analyzed for the plant yield and the bulk soil samples were analyzed for the pH, cation exchange capacity (CEC), OC content, microbial biomass C and the distribution of aggregate-size fractions (i.e. >2 mm, 2 mm - 250 µm, 250 - 53 µm, <53 µm). The latter were also analyzed for OC content and by FTIR. In 2012, the combination of 40 t/ha biochar+digestate accounted for about 42% higher maize (Zea mays) yields (7.9 t/ha) than the mineral fertilization treatment. For winter rye (Secale cereale) in 2013, we detected the highest yield (10.4 t/ha) for the 10 t/ha composted biochar treatment. In 2014, the highest yield for blue lupine (Lupinus angustifolius) (1.84 t/ha) was detected for the 40 t/ha biochar+digestate treatment. The first data for the soil samples indicate that the 10 t/ha composted biochar and the compost treatment are most effective in increasing the CEC, and the microbial biomass C content of the soil, while pH was not significantly affected by any of the treatments. The bulk soil OC content of the treatments receiving 40 t/ha biochar+fertilizer (digestate or mineral), 10 t/ha composted biochar, and compost has been significantly increased by 43 to 88% in the 10-30 cm depth compared to the individual application of mineral fertilizer. The OC content of the water-stable macro- (2 mm - 250 µm) and micro-aggregates (250 - 53 µm) of the treatments receiving 40 t/ha biochar+fertilizer (digestate or mineral), 10 t/ha composted biochar, and compost was increased by 12 to 120% compared to the mineral fertilizer treatment. The magnitude of the demonstrated positive effect of biochar application on crop yield depends on the type and amount of the biochar+organic fertilizer mixture and the cultivated plant species. Besides benefiting biomass production, applications of 10 to 40 t/ha of biochar+fertilizer mixtures seem to result in increased bulk soil and aggregate protected OC contents, indicating a longer lasting positive effect on the OC storage and the structural stability of this sandy soil. Cost/benefit wise, the 10 t/ha composted biochar treatment seems to be most promising for improving soil properties and crop yield, while the compost treatment seems to be the best alternative for sandy soils where biochar is either unavailable or prohibitively expensive.

Comparison of diagnostic performances among bronchoscopic sampling techniques in the diagnosis of peripheral pulmonary lesions.

PubMed

Boonsarngsuk, Viboon; Kanoksil, Wasana; Laungdamerongchai, Sarangrat

2015-04-01

There are many sampling techniques dedicated to radial endobronchial ultrasound (R-EBUS) guided flexible bronchoscopy (FB). However, data regarding the diagnostic performances among bronchoscopic sampling techniques is limited. This study was conducted to compare the diagnostic yields among bronchoscopic sampling techniques in the diagnosis of peripheral pulmonary lesions (PPLs). A prospective study was conducted on 112 patients who were diagnosed with PPLs and underwent R-EBUS-guided FB between Oct 2012 and Sep 2014. Sampling techniques-including transbronchial biopsy (TBB), brushing cell block, brushing smear, rinsed fluid of brushing, and bronchoalveolar lavage (BAL)-were evaluated for the diagnosis. The mean diameter of the PPLs was 23.5±9.5 mm. The final diagnoses included 76 malignancies and 36 benign lesions. The overall diagnostic yield of R-EBUS-guided bronchoscopy was 80.4%; TBB gave the highest yield among the 112 specimens: 70.5%, 34.8%, 62.5%, 50.0% and 42.0% for TBB, brushing cell block, brushing smear, rinsed brushing fluid, and BAL fluid (BALF), respectively (P<0.001). TBB provided high diagnostic yield irrespective of the size and etiology of the PPLs. The combination of TBB and brushing smear achieved the maximum diagnostic yield. Of 31 infectious PPLs, BALF culture gave additional microbiological information in 20 cases. TBB provided the highest diagnostic yield; however, to achieve the highest diagnostic performance, TBB, brushing smear and BAL techniques should be performed together.

Performance of Chromogenic Candida agar and CHROMagar Candida in recovery and presumptive identification of monofungal and polyfungal vaginal isolates.

PubMed

Ozcan, Kadri; Ilkit, Macit; Ates, Aylin; Turac-Bicer, Aygul; Demirhindi, Hakan

2010-02-01

Chromogenic Candida agar (OCCA) is a novel medium facilitating isolation and identification of Candida albicans, C. tropicalis, and C. krusei, as well as indicating polyfungal population in clinical samples. We compare the performance of OCCA, to CHROMagar Candida (CAC) and Sabouraud chloramphenicol agar (SCA). Vaginal swab samples from 392 women were simultaneously inoculated onto three study media. A total of 161 (41.1%) were found to be positive for fungi of which 140 (87%) were monofungal, and 21 (13%) polyfungal. One-hundred and fifty-seven samples (97.5%) were positive on CAC, 156 (96.9%) on OCCA, 148 (91.9%) on SCA and 144 (89.4%) samples were positive on all three media. The yeasts were identified by conventional methods including germ tube test, microscopic morphology on cornmeal-Tween 80 agar, and the commercial API 20C AUX. The 182 isolates were C. albicans (n = 104), C. glabrata (n = 51), C. krusei (n = 7), C. tropicalis (n = 5), C. famata (n = 3), C. kefyr (n = 3), C. zeylanoides (n = 3), C. colliculosa (n = 2), and other species of Candida (n = 4). Among the 21 polyfungal populations, 20 (95.2%) were detected in OCCA, 14 (66.7%) in CAC, and 13 (61.9%) in CAC and OCCA (P <0.05). Most polyfungal populations (47.6%) yielded C. albicans + C. glabrata. The efficiency of both chromogenic media for C. albicans was >or=92.9% at 72 h. OCCA is more efficient and reliable for rapidly identifying C. albicans and polyfungal populations than CAC. However, CAC is more efficient for identifying C. krusei and C. tropicalis. A chromogenic agar with a higher isolation rate of yeasts and better detection of polyfungal populations than SCA, is suggested as a medium of first choice when available.

Hydrology, nutrient concentrations, and nutrient yields in nearshore areas of four lakes in northern Wisconsin, 1999-2001

USGS Publications Warehouse

Graczyk, David J.; Hunt, Randall J.; Greb, Steven R.; Buchwald, Cheryl A.; Krohelski, James T.

2003-01-01

The effects of shoreline development on water quality and nutrient yields in nearshore areas of four lakes in northern Wisconsin were investigated from October 1999 through September 2001. The study measured surface runoff and ground-water flows from paired developed (sites containing lawn, rooftops, sidewalks, and driveways) and undeveloped (mature and immature woods) catchments adjacent to four lakes in northern Wisconsin. Water samples from surface runoff and ground water were collected and analyzed for nutrients. Coupled with water volumes, loads and subsequent yields of selected constituents were computed for developed and undeveloped catchments. The median runoff from lawn surfaces ranged from 0.0019 to 0.059 inch over the catchment area. Median surface runoff estimates from the wooded catchments were an order of magnitude less than those from the lawn catchments. The increased water volumes from the lawn catchments resulted in greater nutrient loads and subsequent annual nutrient yields from the developed sites. Soil temperature and soil moisture were measured at two sites with mixed lawn and wooded areas. At both of these sites, the area covered with a lawn commonly was warmer than the wooded area. No consistent differences in soil moisture were found. A ground-water model was constructed to simulate the local flow systems at two of the paired catchments. Model simulations showed that much of the ground water delivered to the lake originated from distant areas that did not contribute runoff directly to the lake. Surface runoff and ground-water nutrient concentrations from the lawn and wooded catchments did not have apparent patterns. Some of the median concentrations from lawns were significantly different (at the 0.05 significance level) from those at wooded catchments. Water wells and piezometers were sampled for chemical analyses three times during the study period. Variability in the shallow ground-water chemistry over time in the lawn samples was larger than samples from the wooded areas and upgradient wells. Median nutrient yields in surface runoff from lawns always were greater than those from the wooded catchments. Runoff volumes were the most important factor in determining whether lawns or wooded catchments contribute more nutrients to the lake. The ground-water system had appreciable nutrient concentrations, and are likely an important pathway for nutrient transport to the lake. The nitrate plus nitrite nitrogen and total phosphorus yields to the ground-water system from a lawn catchment were approximately 3 to 4 times greater than those from the wooded catchment. There was no difference in the yields of dissolved inorganic phosphorus to the ground-water system from the lawn and wooded catchments. Study results demonstrate that choosing the appropriate landscape position for locating lawns in sloped areas (specifically, slopes that do not terminate at the lake or areas with intervening flat or buffer zones between lawn and lake) can help reduce the adverse effect of lawns on the shallow ground water and, ultimately, the lake. Additional information would be needed to extrapolate these results to a large drainage area of a lake.

The Effect of Preoperative Antimicrobial Prophylaxis on Intraoperative Culture Results in Patients with a Suspected or Confirmed Prosthetic Joint Infection: a Systematic Review

PubMed Central

Benito, Natividad; Soriano, Alex

2017-01-01

ABSTRACT Obtaining reliable cultures during revision arthroplasty is important to adequately diagnose and treat a prosthetic joint infection (PJI). The influence of antimicrobial prophylaxis on culture results remains unclear. Since withholding prophylaxis increases the risk for surgical site infections, clarification on this topic is critical. A systematic review was performed with the following research question: in patients who undergo revision surgery of a prosthetic joint, does preoperative antimicrobial prophylaxis affect the culture yield of intraoperative samples in comparison with nonpreoperative antimicrobial prophylaxis? Seven articles were included in the final analysis. In most studies, standard diagnostic culture techniques were used. In patients with a PJI, pooled analysis showed a culture yield of 88% (145/165) in the prophylaxis group versus 95% (344/362) in the nonprophylaxis group (P = 0.004). Subanalysis of patients with chronic PJIs showed positive cultures in 88% (78/89) versus 91% (52/57), respectively (P = 0.59). In patients with a suspected chronic infection, a maximum difference of 4% in culture yield between the prophylaxis and nonprophylaxis groups was observed. With the use of standard culture techniques, antimicrobial prophylaxis seems to affect cultures in a minority of patients. Along with the known risk of surgical site infections due to inadequate timing of antimicrobial prophylaxis, we discourage the postponement of prophylaxis until tissue samples are obtained in revision surgery. Future studies are necessary to conclude whether the small percentage of false-negative cultures after prophylaxis can be further reduced with the use of more-sensitive culture techniques, like sonication. PMID:28659322

Cell-wall properties contributing to improved deconstruction by alkaline pre-treatment and enzymatic hydrolysis in diverse maize (Zea mays L.) lines.

PubMed

Li, Muyang; Heckwolf, Marlies; Crowe, Jacob D; Williams, Daniel L; Magee, Timothy D; Kaeppler, Shawn M; de Leon, Natalia; Hodge, David B

2015-07-01

A maize (Zea mays L. subsp. mays) diversity panel consisting of 26 maize lines exhibiting a wide range of cell-wall properties and responses to hydrolysis by cellulolytic enzymes was employed to investigate the relationship between cell-wall properties, cell-wall responses to mild NaOH pre-treatment, and enzymatic hydrolysis yields. Enzymatic hydrolysis of the cellulose in the untreated maize was found to be positively correlated with the water retention value, which is a measure of cell-wall susceptibility to swelling. It was also positively correlated with the lignin syringyl/guaiacyl ratio and negatively correlated with the initial cell-wall lignin, xylan, acetate, and p-coumaric acid (pCA) content, as well as pCA released from the cell wall by pre-treatment. The hydrolysis yield following pre-treatment exhibited statistically significant negative correlations to the lignin content after pre-treatment and positive correlations to the solubilized ferulic acid and pCA. Several unanticipated results were observed, including a positive correlation between initial lignin and acetate content, lack of correlation between acetate content and initial xylan content, and negative correlation between each of these three variables to the hydrolysis yields for untreated maize. Another surprising result was that pCA release was negatively correlated with hydrolysis yields for untreated maize and, along with ferulic acid release, was positively correlated with the pre-treated maize hydrolysis yields. This indicates that these properties that may negatively contribute to the recalcitrance in untreated cell walls may positively contribute to their deconstruction by alkaline pre-treatment. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Cell-wall properties contributing to improved deconstruction by alkaline pre-treatment and enzymatic hydrolysis in diverse maize ( Zea mays L.) lines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Muyang; Heckwolf, Marlies; Crowe, Jacob D.

A maize (Zea mays L. subsp. mays) diversity panel consisting of 26 maize lines exhibiting a wide range of cell-wall properties and responses to hydrolysis by cellulolytic enzymes was employed to investigate the relationship between cell-wall properties, cell-wall responses to mild NaOH pre-treatment, and enzymatic hydrolysis yields. Enzymatic hydrolysis of the cellulose in the untreated maize was found to be positively correlated with the water retention value, which is a measure of cell-wall susceptibility to swelling. It was also positively correlated with the lignin syringyl/guaiacyl ratio and negatively correlated with the initial cell-wall lignin, xylan, acetate, and p-coumaric acid (pCA)more » content, as well as pCA released from the cell wall by pre-treatment. The hydrolysis yield following pre-treatment exhibited statistically significant negative correlations to the lignin content after pre-treatment and positive correlations to the solubilized ferulic acid and pCA. Several unanticipated results were observed, including a positive correlation between initial lignin and acetate content, lack of correlation between acetate content and initial xylan content, and negative correlation between each of these three variables to the hydrolysis yields for untreated maize. Also, another surprising result was that pCA release was negatively correlated with hydrolysis yields for untreated maize and, along with ferulic acid release, was positively correlated with the pre-treated maize hydrolysis yields. In conclusion, this indicates that these properties that may negatively contribute to the recalcitrance in untreated cell walls may positively contribute to their deconstruction by alkaline pre-treatment« less

Cell-wall properties contributing to improved deconstruction by alkaline pre-treatment and enzymatic hydrolysis in diverse maize ( Zea mays L.) lines

DOE PAGES

Li, Muyang; Heckwolf, Marlies; Crowe, Jacob D.; ...

2015-02-20

A maize (Zea mays L. subsp. mays) diversity panel consisting of 26 maize lines exhibiting a wide range of cell-wall properties and responses to hydrolysis by cellulolytic enzymes was employed to investigate the relationship between cell-wall properties, cell-wall responses to mild NaOH pre-treatment, and enzymatic hydrolysis yields. Enzymatic hydrolysis of the cellulose in the untreated maize was found to be positively correlated with the water retention value, which is a measure of cell-wall susceptibility to swelling. It was also positively correlated with the lignin syringyl/guaiacyl ratio and negatively correlated with the initial cell-wall lignin, xylan, acetate, and p-coumaric acid (pCA)more » content, as well as pCA released from the cell wall by pre-treatment. The hydrolysis yield following pre-treatment exhibited statistically significant negative correlations to the lignin content after pre-treatment and positive correlations to the solubilized ferulic acid and pCA. Several unanticipated results were observed, including a positive correlation between initial lignin and acetate content, lack of correlation between acetate content and initial xylan content, and negative correlation between each of these three variables to the hydrolysis yields for untreated maize. Also, another surprising result was that pCA release was negatively correlated with hydrolysis yields for untreated maize and, along with ferulic acid release, was positively correlated with the pre-treated maize hydrolysis yields. In conclusion, this indicates that these properties that may negatively contribute to the recalcitrance in untreated cell walls may positively contribute to their deconstruction by alkaline pre-treatment« less

Lack of latex allergen contamination of solutions withdrawn from vials with natural rubber stoppers.

PubMed

Thomsen, D J; Burke, T G

2000-01-01

The effect on latex allergen contamination and microbial growth of a latex-allergy precaution technique for preparing injectable products was studied. The study consisted of three parts: (1) preparation of 20 samples from vials with latex-containing stoppers in accordance with conventional guidelines, (2) preparation of 20 samples in accordance with latex-allergy precaution guidelines, and (3) preparation of 5 latex-free samples and 1 latex-contaminated sample as negative and positive controls, respectively. The conventional method involved swabbing a vial top with an alcohol prep pad, puncturing the dry natural rubber stopper with an 18-gauge needle attached to a latex-free syringe, and withdrawing the contents of the vial into the syringe. The latex-allergy precaution preparation technique was similar, except that the stopper was removed before the vial contents were withdrawn. There was essentially no difference in latex allergen concentrations between the two drug preparation methods. None of the samples prepared with the standard method supported any microbial growth. One sample prepared with the latex-allergy precaution method grew bacteria. Removal of the dry rubber stopper from vials did not yield solutions with less latex allergen than solutions prepared according to conventional guidelines.

Forgery at the Snite Museum of Art? Improving AMS Radiocarbon Dating at the University of Notre Dame

NASA Astrophysics Data System (ADS)

Troyer, Laura; Bagwell, Connor; Anderson, Tyler; Clark, Adam; Nelson, Austin; Skulski, Michael; Collon, Philippe

2017-09-01

The Snite Museum of Art recently obtained several donations of artifacts. Five of the pieces lack sufficient background information to prove authenticity and require further analysis to positively determine the artwork's age. One method to determine the artwork's age is radiocarbon dating via Accelerator Mass Spectrometry (AMS) performed at the University of Notre Dame's Nuclear Science Laboratory. Samples are prepared by combustion of a small amount of material and subsequent reduction to carbon into an iron powder matrix (graphitization). The graphitization procedure affects the maximum measurement rate, and a poor graphitization can be detrimental to the AMS measurement of the sample. Previous graphitization procedures resulted in a particle current too low or inconsistent to optimize AMS measurements. Thus, there was a desire to design and refine the graphitization system. The finalized process yielded physically darker samples and increased sample currents by two orders of magnitude. Additionally, the first testing of the samples was successful, yet analysis of the dates proved inconclusive. AMS measurements will be performed again to obtain better sampling statistics in the hopes of narrowing the reported date ranges. NSF and JINA-CEE.

Novel Babesia and Hepatozoon agents infecting non-volant small mammals in the Brazilian Pantanal, with the first record of the tick Ornithodoros guaporensis in Brazil.

PubMed

Wolf, Rafael William; Aragona, Mônica; Muñoz-Leal, Sebastián; Pinto, Leticia Borges; Melo, Andréia Lima Tomé; Braga, Isis Assis; Costa, Jackeliny dos Santos; Martins, Thiago Fernandes; Marcili, Arlei; Pacheco, Richard de Campos; Labruna, Marcelo B; Aguiar, Daniel Moura

2016-04-01

Taking into account the diversity of small terrestrial mammals of the Pantanal, the present study aimed to verify the occurrence of infection by Ehrlichia spp., Anaplasma spp., Rickettsia spp., Hepatozoon spp., Babesia spp. and parasitism by ticks in non-volant small mammals collected in the Brazilian Pantanal. Samples of blood, liver and spleen were collected from 64 captured animals, 22 marsupials and 42 rodents. Pathogen detection was performed by the use of genus-specific Polymerase Chain Reaction (PCR) assays. Ticks collected from the animals consisted of Amblyomma sculptum and Amblyomma triste nymphs, and Ornithodoros guaporensis larvae. None of the vertebrate samples (blood, liver, or spleen) yielded detectable DNA of Rickettsia spp. or Ehrlichia spp. The blood of the rodent Hylaeamys megacephalus yielded an Anaplasma sp. genotype (partial 16S rRNA gene) 99% similar to multiple Anaplasma spp. genotypes around the world. The blood of three rodents of the species Calomys callosus were positive for a novel Hepatozoon sp. agent, phylogenetically related (18S rDNA gene) to distinct Hepatozoon genotypes that have been detected in rodents from different parts of the world. One marsupial (Monodelphis domestica) and three rodents (Thrichomys pachyurus) were positive to novel piroplasmid genotypes, phylogenetically (18S rDNA gene) related to Theileria bicornis, Cytauxzoon manul, and Cytauxzoon felis. The present study provides the first molecular detection of Hepatozoon sp. and piroplasmids in small mammals in Brazil. Additionally, we expanded the distribution of O. guaporensis to Brazil, since this tick species was previously known to occur only in Bolivia. Copyright © 2016 Elsevier GmbH. All rights reserved.

The effect of biomass densification on structural sugar release and yield in biofuel feedstock and feedstock blends

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolfrum, Edward J.; Nagle, Nicholas J.; Ness, Ryan M.

In this work, we examined the behavior of feedstock blends and the effect of a specific feedstock densification strategy (pelleting) on the release and yield of structural carbohydrates in a laboratory-scale dilute acid pretreatment (PT) and enzymatic hydrolysis (EH) assay. We report overall carbohydrate release and yield from the two-stage PT-EH assay for five single feedstocks (two corn stovers, miscanthus, switchgrass, and hybrid poplar) and three feedstock blends (corn stover-switchgrass, corn stover-switchgrass-miscanthus, and corn stover-switchgrass-hybrid poplar). We first examined the experimental results over time to establish the robustness of the PT-EH assay, which limits the precision of the experimental results.more » The use of two different control samples in the assay enabled us to identify (and correct for) a small bias in the EH portion of the combined assay for some runs. We then examined the effect of variable pretreatment reaction conditions (residence time, acid loading, and reactor temperature) on the conversion of a single feedstock (single-pass corn stover, CS-SP) in order to establish the range of pretreatment reaction conditions likely to provide optimal conversion data. Finally, we applied the assay to the 16 materials (8 feedstocks in 2 formats, loose and pelleted) over a more limited range of pretreatment experimental conditions. The four herbaceous feedstocks behaved similarly, while the hybrid poplar feedstock required higher pretreatment temperatures for optimal results. As expected, the yield data for three blended feedstocks were the average of the yield data for the individual feedstocks. As a result, the pelleting process appears to provide a slightly positive effect on overall total sugar yield.« less

The effect of biomass densification on structural sugar release and yield in biofuel feedstock and feedstock blends

DOE PAGES

Wolfrum, Edward J.; Nagle, Nicholas J.; Ness, Ryan M.; ...

2017-01-13

In this work, we examined the behavior of feedstock blends and the effect of a specific feedstock densification strategy (pelleting) on the release and yield of structural carbohydrates in a laboratory-scale dilute acid pretreatment (PT) and enzymatic hydrolysis (EH) assay. We report overall carbohydrate release and yield from the two-stage PT-EH assay for five single feedstocks (two corn stovers, miscanthus, switchgrass, and hybrid poplar) and three feedstock blends (corn stover-switchgrass, corn stover-switchgrass-miscanthus, and corn stover-switchgrass-hybrid poplar). We first examined the experimental results over time to establish the robustness of the PT-EH assay, which limits the precision of the experimental results.more » The use of two different control samples in the assay enabled us to identify (and correct for) a small bias in the EH portion of the combined assay for some runs. We then examined the effect of variable pretreatment reaction conditions (residence time, acid loading, and reactor temperature) on the conversion of a single feedstock (single-pass corn stover, CS-SP) in order to establish the range of pretreatment reaction conditions likely to provide optimal conversion data. Finally, we applied the assay to the 16 materials (8 feedstocks in 2 formats, loose and pelleted) over a more limited range of pretreatment experimental conditions. The four herbaceous feedstocks behaved similarly, while the hybrid poplar feedstock required higher pretreatment temperatures for optimal results. As expected, the yield data for three blended feedstocks were the average of the yield data for the individual feedstocks. As a result, the pelleting process appears to provide a slightly positive effect on overall total sugar yield.« less

Peer relationships and adolescents' academic and non-academic outcomes: same-sex and opposite-sex peer effects and the mediating role of school engagement.

PubMed

Liem, Gregory Arief D; Martin, Andrew J

2011-06-01

The literature has documented theoretical/conceptual models delineating the facilitating role of peer relationships in academic and non-academic outcomes. However, the mechanisms through which peer relationships link to those outcomes is an area requiring further research. The study examined the role of adolescents' perceptions of their relationships with same-sex and opposite-sex peers in predicting their academic performance and general self-esteem and the potentially mediating role of school engagement in linking these perceived peer relationships with academic and non-academic outcomes. The sample comprised 1,436 high-school students (670 boys, 756 girls; 711 early adolescents, 723 later adolescents). Self-report measures and objective achievement tests were used. Structural equation modelling (SEM) was performed to test the hypothesized model and its invariance across gender and age groups. Perceived same-sex peer relationships yielded positive direct and indirect links with academic performance and general self-esteem. Perceived opposite-sex peer relationships yielded positive direct and indirect links with general self-esteem and an indirect positive link with academic performance, but mediation via school engagement was not as strong as that of perceived same-sex peer relationships. These findings generalized across gender and age groups. Adolescents' same-sex and opposite-sex peer relationships seem to positively impact their academic performance and general self-esteem in distinct ways. It appears that school engagement plays an important role in mediating these peer relationship effects, particularly those of same-sex peer relationships, on academic and non-academic functioning. Implications for psycho-educational theory, measurement, and practice are discussed. ©2011 The British Psychological Society.

Primary Endoscopic Transnasal Transsphenoidal Surgery for Magnetic Resonance Image-Positive Cushing Disease: Outcomes of a Series over 14 Years.

PubMed

Kuo, Chao-Hung; Yen, Yu-Shu; Wu, Jau-Ching; Chen, Yu-Chun; Huang, Wen-Cheng; Cheng, Henrich

2015-09-01

There are scant data of endoscopic transsphenoidal surgery (ETS) with adjuvant therapies of Cushing disease (CD). To report the remission rate, secondary management, and outcomes of a series of CD patients. Patients with CD with magnetic resonance imaging (MRI)-positive adenoma who underwent ETS as the first and primary treatment were included. The diagnostic criteria were a combination of 24-hour urine-free cortisol, elevated serum cortisol levels, or other tests (e.g., inferior petrosal sinus sampling). All clinical and laboratory evaluations and radiological examinations were reviewed. Forty consecutive CD patients, with an average age of 41.0 years, were analyzed with a mean follow-up of 40.2 ± 29.6 months. These included 22 patients with microadenoma and 18 with macroadenoma, including 9 cavernous invasions. The overall remission rate of CD after ETS was 72.5% throughout the entire follow-up. Patients with microadenoma or noninvasive macroadenoma had a higher remission rate than those who had macroadenoma with cavernous sinus invasion (81.8% or 77.8% vs. 44.4%, P = 0.02). After ETS, the patients who had adrenocorticotropic hormone-positive adenoma had a higher remission rate than those who had not (76.5% vs. 50%, P = 0.03). In the 11 patients who had persistent/recurrent CD after the first ETS, 1 underwent secondary ETS, 8 received gamma-knife radiosurgery (GKRS), and 2 underwent both. At the study end point, two (5%) of these CD patients had persistent CD and were under the medication of ketoconazole. For MRI-positive CD patients, primary (i.e., the first) ETS yielded an overall remission rate of 72.5%. Adjuvant therapies, including secondary ETS, GKRS, or both, yielded an ultimate remission rate of 95%. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparative analysis of vaginal microbiota sampling using 16S rRNA gene analysis.

PubMed

Virtanen, Seppo; Kalliala, Ilkka; Nieminen, Pekka; Salonen, Anne

2017-01-01

Molecular methods such as next-generation sequencing are actively being employed to characterize the vaginal microbiota in health and disease. Previous studies have focused on characterizing the biological variation in the microbiota, and less is known about how factors related to sampling contribute to the results. Our aim was to investigate the impact of a sampling device and anatomical sampling site on the quantitative and qualitative outcomes relevant for vaginal microbiota research. We sampled 10 Finnish women representing diverse clinical characteristics with flocked swabs, the Evalyn® self-sampling device, sterile plastic spatulas and a cervical brush that were used to collect samples from fornix, vaginal wall and cervix. Samples were compared on DNA and protein yield, bacterial load, and microbiota diversity and species composition based on Illumina MiSeq sequencing of the 16S rRNA gene. We quantified the relative contributions of sampling variables versus intrinsic variables in the overall microbiota variation, and evaluated the microbiota profiles using several commonly employed metrics such as alpha and beta diversity as well as abundance of major bacterial genera and species. The total DNA yield was strongly dependent on the sampling device and to a lesser extent on the anatomical site of sampling. The sampling strategy did not affect the protein yield or the bacterial load. All tested sampling methods produced highly comparable microbiota profiles based on MiSeq sequencing. The sampling method explained only 2% (p-value = 0.89) of the overall microbiota variation, markedly surpassed by intrinsic factors such as clinical status (microscopy for bacterial vaginosis 53%, p = 0.0001), bleeding (19%, p = 0.0001), and the variation between subjects (11%, p-value 0.0001). The results indicate that different sampling strategies yield comparable vaginal microbiota composition and diversity. Hence, past and future vaginal microbiota studies employing different sampling strategies should be comparable in the absence of other technical confounders. The Evalyn® self-sampling device performed equally well compared to samples taken by a clinician, and hence offers a good-quality microbiota sample without the need for a gynecological examination. The amount of collected sample as well as the DNA and protein yield varied across the sampling techniques, which may have practical implications for study design.

Comparative analysis of vaginal microbiota sampling using 16S rRNA gene analysis

PubMed Central

Kalliala, Ilkka; Nieminen, Pekka; Salonen, Anne

2017-01-01

Background Molecular methods such as next-generation sequencing are actively being employed to characterize the vaginal microbiota in health and disease. Previous studies have focused on characterizing the biological variation in the microbiota, and less is known about how factors related to sampling contribute to the results. Our aim was to investigate the impact of a sampling device and anatomical sampling site on the quantitative and qualitative outcomes relevant for vaginal microbiota research. We sampled 10 Finnish women representing diverse clinical characteristics with flocked swabs, the Evalyn® self-sampling device, sterile plastic spatulas and a cervical brush that were used to collect samples from fornix, vaginal wall and cervix. Samples were compared on DNA and protein yield, bacterial load, and microbiota diversity and species composition based on Illumina MiSeq sequencing of the 16S rRNA gene. We quantified the relative contributions of sampling variables versus intrinsic variables in the overall microbiota variation, and evaluated the microbiota profiles using several commonly employed metrics such as alpha and beta diversity as well as abundance of major bacterial genera and species. Results The total DNA yield was strongly dependent on the sampling device and to a lesser extent on the anatomical site of sampling. The sampling strategy did not affect the protein yield or the bacterial load. All tested sampling methods produced highly comparable microbiota profiles based on MiSeq sequencing. The sampling method explained only 2% (p-value = 0.89) of the overall microbiota variation, markedly surpassed by intrinsic factors such as clinical status (microscopy for bacterial vaginosis 53%, p = 0.0001), bleeding (19%, p = 0.0001), and the variation between subjects (11%, p-value 0.0001). Conclusions The results indicate that different sampling strategies yield comparable vaginal microbiota composition and diversity. Hence, past and future vaginal microbiota studies employing different sampling strategies should be comparable in the absence of other technical confounders. The Evalyn® self-sampling device performed equally well compared to samples taken by a clinician, and hence offers a good-quality microbiota sample without the need for a gynecological examination. The amount of collected sample as well as the DNA and protein yield varied across the sampling techniques, which may have practical implications for study design. PMID:28723942

Genetic parameters for milk mineral content and acidity predicted by mid-infrared spectroscopy in Holstein-Friesian cows.

PubMed

Toffanin, V; Penasa, M; McParland, S; Berry, D P; Cassandro, M; De Marchi, M

2015-05-01

The aim of the present study was to estimate genetic parameters for calcium (Ca), phosphorus (P) and titratable acidity (TA) in bovine milk predicted by mid-IR spectroscopy (MIRS). Data consisted of 2458 Italian Holstein-Friesian cows sampled once in 220 farms. Information per sample on protein and fat percentage, pH and somatic cell count, as well as test-day milk yield, was also available. (Co)variance components were estimated using univariate and bivariate animal linear mixed models. Fixed effects considered in the analyses were herd of sampling, parity, lactation stage and a two-way interaction between parity and lactation stage; an additive genetic and residual term were included in the models as random effects. Estimates of heritability for Ca, P and TA were 0.10, 0.12 and 0.26, respectively. Positive moderate to strong phenotypic correlations (0.33 to 0.82) existed between Ca, P and TA, whereas phenotypic weak to moderate correlations (0.00 to 0.45) existed between these traits with both milk quality and yield. Moderate to strong genetic correlations (0.28 to 0.92) existed between Ca, P and TA, and between these predicted traits with both fat and protein percentage (0.35 to 0.91). The existence of heritable genetic variation for Ca, P and TA, coupled with the potential to predict these components for routine cow milk testing, imply that genetic gain in these traits is indeed possible.

Bacterial subclinical mastitis and its effect on milk yield in low-input dairy goat herds.

PubMed

Gelasakis, A I; Angelidis, A S; Giannakou, R; Filioussis, G; Kalamaki, M S; Arsenos, G

2016-05-01

The objectives of this study were (1) to record the major pathogens associated with subclinical mastitis (SCM), (2) to calculate their incidence during the milking period, and (3) to estimate the effect of SCM on daily milk yield (DMY) for goats reared under low-input management schemes. Dairy goats (n=590) of Skopelos and indigenous Greek breeds from 4 herds were randomly selected for the study. The study included monthly monitoring, milk yield recording, and bacteriological analyses of milk of individual goats during the course of 2 successive milking periods. Incidence and cumulative incidence were calculated for SCM cases. Moreover, 2 mixed linear regression models were built to assess the effects of (1) SCM and (2) different pathogens isolated from SCM cases, on DMY. The estimated incidence and cumulative incidence of SCM for the first and the second year of the study were 69.5 and 96.4 new cases of SCM/1,000 goat-months, and 24.1 and 31.7%, respectively. A total of 755 milk samples were subjected to microbiological examination, resulting in 661 positive cultures. Coagulase-negative and coagulase-positive staphylococci were isolated from 50.2 and 34.5% of the positive cultures, respectively. The incidence of infections (new infections per 1,000 goat-months) for the first and the second year of the study were 34 and 53 for coagulase-negative staphylococci, 23 and 28 for coagulase-positive staphylococci, 3 and 5 for Streptococcus/Enterococcus spp., and 5.5 and 9.1 for gram-negative bacteria. Goats with SCM had lower DMY when compared with goats without SCM (ca. 47g/d, corresponding to a 5.7% decrease in DMY). In particular, goats with SCM due to coagulase-positive staphylococci infection produced approximately 80g/d less milk (a reduction of ca. 9.7%) compared with uninfected ones, whereas SCM due to gram-negative bacteria resulted in approximately 15% reduction in DMY. Investigating the epidemiology of SCM and its effects on production traits is critical for the establishment of effective preventive measures against SCM and for the assessment of the sustainability of production in low-input dairy goat herds. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The effect of thermal and ultrasonic treatment on amino acid composition, radical scavenging and reducing potential of hydrolysates obtained from simulated gastrointestinal digestion of cowpea proteins.

PubMed

Quansah, Joycelyn K; Udenigwe, Chibuike C; Saalia, Firibu K; Yada, Rickey Y

2013-03-01

The effect of thermal and ultrasonic treatment of cowpea proteins (CP) on amino acid composition, radical scavenging and reducing potential of hydrolysates (CPH) obtained from in vitro simulated gastrointestinal digestion of CP was evaluated. Hydrolysis of native and treated CP with gastrointestinal pepsin and pancreatin yielded CPH that displayed antioxidant activities based on oxygen radical scavenging capacity (ORAC), ferric reducing antioxidant power (FRAP) and superoxide radical scavenging activity (SRSA). CPH derived from the treated CP yielded higher ORAC values than CPH from untreated proteins. However, lower significant FRAP and SRSA values were observed for these samples compared to untreated CPH (p < 0.05). Amino acid analysis indicated that CP processing decreased total sulphur-containing amino acids in the hydrolysates, particularly cysteine. The amount of cysteine appeared to be positively related to FRAP and SRSA values of CPH samples, but not ORAC. The results indicated that thermal and ultrasonic processing of CP can reduce the radical scavenging and reducing potential of the enzymatic hydrolysates possibly due to the decreased amounts of cysteine. Since the hydrolysates were generated with gastrointestinal enzymes, it is possible that the resulting compounds are produced to exert some health functions during normal consumption of cowpea.

Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding.

PubMed

Lee, Michael S; Olson, Mark A

2011-06-28

Temperature-based replica exchange (T-ReX) enhances sampling of molecular dynamics simulations by autonomously heating and cooling simulation clients via a Metropolis exchange criterion. A pathological case for T-ReX can occur when a change in state (e.g., folding to unfolding of a protein) has a large energetic difference over a short temperature interval leading to insufficient exchanges amongst replica clients near the transition temperature. One solution is to allow the temperature set to dynamically adapt in the temperature space, thereby enriching the population of clients near the transition temperature. In this work, we evaluated two approaches for adapting the temperature set: a method that equalizes exchange rates over all neighbor temperature pairs and a method that attempts to induce clients to visit all temperatures (dubbed "current maximization") by positioning many clients at or near the transition temperature. As a test case, we simulated the 57-residue SH3 domain of alpha-spectrin. Exchange rate equalization yielded the same unfolding-folding transition temperature as fixed-temperature ReX with much smoother convergence of this value. Surprisingly, the current maximization method yielded a significantly lower transition temperature, in close agreement with experimental observation, likely due to more extensive sampling of the transition state.

A Comparison of Yield Studies of Slash Pine in Old-Field Plantations

Treesearch

F.A. Bennett; R. L. Barnes; J.L. Clutter; C.E. McGee

1970-01-01

This report compares three yield studies of slash pine in old-field plantation. Similarities and differences in yield are disccssed. Within the range of sample data common to all studies, yield estimates are similar; major difierences occur only in extrapolated values.

Modeling abundance effects in distance sampling

USGS Publications Warehouse

Royle, J. Andrew; Dawson, D.K.; Bates, S.

2004-01-01

Distance-sampling methods are commonly used in studies of animal populations to estimate population density. A common objective of such studies is to evaluate the relationship between abundance or density and covariates that describe animal habitat or other environmental influences. However, little attention has been focused on methods of modeling abundance covariate effects in conventional distance-sampling models. In this paper we propose a distance-sampling model that accommodates covariate effects on abundance. The model is based on specification of the distance-sampling likelihood at the level of the sample unit in terms of local abundance (for each sampling unit). This model is augmented with a Poisson regression model for local abundance that is parameterized in terms of available covariates. Maximum-likelihood estimation of detection and density parameters is based on the integrated likelihood, wherein local abundance is removed from the likelihood by integration. We provide an example using avian point-transect data of Ovenbirds (Seiurus aurocapillus) collected using a distance-sampling protocol and two measures of habitat structure (understory cover and basal area of overstory trees). The model yields a sensible description (positive effect of understory cover, negative effect on basal area) of the relationship between habitat and Ovenbird density that can be used to evaluate the effects of habitat management on Ovenbird populations.

Anaerobic co-digestion of sewage sludge and molasses

NASA Astrophysics Data System (ADS)

Kalemba, Katarzyna; Barbusiński, Krzysztof

2017-11-01

The efficiency of simultaneous digestion of sewage sludge and by-product of refining sugar beets (molasses) was investigated. The study was conducted for 28 days under mesophilic conditions. 0.5%, 1%, 1.5%, 2% and 3% (m/m) of molasses was added to the mixture of sludge. The result of the study showed that addition of molasses had positive effect the biogas production. The biggest biogas yield was achieved in sample with 0.5% of molasses (95.69 mL/g VS). In this sample biogas production increased by 21% in comparison with reference sample (without molasses). The biggest methane content (73%) was also observed in the sample with 0.5% of molasses. For comparison in reference sample was produced biogas with 70% content of methane. The dose over 0.5% of molasses caused inhibition of fermentation process. The minimal degree (38%) of degradation of organic matter was achieved in reference sample (38.53%) and in sample with 0.5% of molasses (39.71%) but in other samples was in the range of 35.61-36.76 % (from 3% to 1%, respectively). Digestion process have adverse effect on dewatering properties of sludge. Before co-digestion capillary suction time was from 31 s to 55 s, and after process increased from 36 s to 556 s (from 0% to 3% of molasses, respectively).

Shock Response of Commercial Purity Polycrystalline Magnesium Under Uniaxial Strain at Elevated Temperatures

NASA Astrophysics Data System (ADS)

Wang, Tianxue; Zuanetti, Bryan; Prakash, Vikas

2017-12-01

In the present paper, results of plate impact experiments designed to investigate the onset of incipient plasticity in commercial purity polycrystalline magnesium (99.9%) under weak uniaxial strain compression and elevated temperatures up to melt are presented. The dynamic stress at yield and post yield of magnesium, as inferred from the measured normal component of the particle velocity histories at the free (rear) surface of the target plate, are observed to decrease progressively with increasing test temperatures in the range from 23 to 500 °C. At (higher) test temperatures in the range 500-610 °C, the rate of decrease of dynamic stress with temperature at yield and post-yield in the sample is observed to weaken. At still higher test temperatures (617 and 630 °C), a dramatic increase in dynamic yield as well as flow stress is observed indicating a change in dominant mechanism of plastic deformation as the sample approaches the melt point of magnesium at strain rates of 105/s. In addition to these measurements at the wavefront, the plateau region of the free surface particle velocity profiles indicates that the longitudinal (plastic) impedance of the magnesium samples decreases continuously as the sample temperatures are increased from room to 610 °C, and then reverses trend (indicating increasing material longitudinal impedance/strength) as the sample temperatures are increased to 617 and 630 °C. Electron back scattered diffraction analysis of the as-received and annealed pre-test magnesium samples reveal grain coarsening as well as grain re-orientation to a different texture during the heating process of the samples.

Normative data on development of neural and behavioral mechanisms underlying attention orienting toward social-emotional stimuli: An exploratory study

PubMed Central

Lindstrom, Kara; Guyer, Amanda E.; Mogg, Karin; Bradley, Brendan P.; Fox, Nathan A.; Ernst, Monique; Nelson, Eric E.; Leibenluft, Ellen; Britton, Jennifer C.; Monk, Christopher S.; Pine, Daniel S.; Bar-Haim, Yair

2009-01-01

The ability of positive and negative facial signals to influence attention orienting is crucial to social functioning. Given the dramatic developmental change in neural architecture supporting social function, positive and negative facial cues may influence attention orienting differently in relatively young or old individuals. However, virtually no research examines such age-related differences in the neural circuitry supporting attention orienting to emotional faces. We examined age-related correlations in attention-orienting biases to positive and negative face emotions in a healthy sample (N=37; 9-40 years old) using functional magnetic resonance imaging and a dot-probe task. The dot-probe task in an fMRI setting yields both behavioral and neural indices of attention biases towards or away from an emotional cue (happy or angry face). In the full sample, angry-face attention bias scores did not correlate with age, and age did not correlate with brain activation to angry faces. However, age did positively correlate with attention bias towards happy faces; age also negatively correlated with left cuneus and left caudate activation to a happy-bias fMRI contrast. Secondary analyses suggested age-related changes in attention bias to happy faces. The tendency in younger children to direct attention away from happy faces (relative to neutral faces) was diminished in the older age groups, in tandem with increasing neural deactivation. Implications for future work on developmental changes in attention-emotion processing are discussed. PMID:19631626

Induced sputum and bronchoscopy in the diagnosis of pulmonary tuberculosis

PubMed Central

McWilliams, T; Wells, A; Harrison, A; Lindstrom, S; Cameron, R; Foskin, E

2002-01-01

Background: Previous studies suggest that bronchoscopy and a single induced sputum sample are equally effective for diagnosing pulmonary tuberculosis. Methods: In a prospective study of subjects with possibly active pulmonary tuberculosis, the diagnostic yield of three induced sputum tests was compared with that of bronchoscopy. Subjects either produced no sputum or (acid fast) smear negative sputum. Bronchoscopy was only performed if at least two induced sputum samples were smear negative. Results: Of 129 subjects who completed all tests, 27 (21%) had smear negative and culture positive specimens, 14 (52%) on bronchoscopy and 26 (96%) on induced sputum (p<0.005). One patient was culture positive on bronchoscopy alone compared with 13 on induced sputum alone; 13 were culture positive on both tests. Induced sputum positivity was strikingly more prevalent when chest radiographic appearances showed any features of active tuberculosis (20/63, 32%) than when appearances suggested inactivity (1/44, 2%; p<0.005). Induced sputum costs were about one third those of bronchoscopy, and the ratio of costs of the two tests per case of tuberculosis diagnosed could be as much as 1:6. Conclusions: In subjects investigated for possibly active or inactive tuberculosis who produce no sputum or have smear negative sputum, the most cost effective strategy is to perform three induced sputum tests without bronchoscopy. Induced sputum testing carries a high risk of nosocomial tuberculosis unless performed in respiratory isolation conditions. The cost benefits shown could be lost if risk management measures are not observed. PMID:12454293

Breakfast Clubs: Starting the Day in a Positive Way

PubMed Central

Graham, Pamela Louise; Russo, Riccardo; Defeyter, Margaret Anne

2015-01-01

Breakfast clubs are widely promoted as having a beneficial impact on children’s behavior at the start of the school day, which can be conducive to their learning within the classroom. However, the few available studies that have considered the impact of breakfast club attendance on children’s behavior have yielded mixed results and no studies to date have directly observed children’s behavior within the breakfast club setting. Using a combination of real-time observation and filmed breakfast club footage, the aims of the current study were to: (1) devise a set of observational criteria appropriate for use in the breakfast club setting; (2) investigate the occurrence of both positive and negative behaviors. A sample of 30 children aged between 3 and 11 years were recruited from 3, opportunistically sampled primary school breakfast clubs in the North East of England, UK. The behaviors they displayed within the breakfast club setting on two separate days were observed and coded for subsequent analysis. Results of the investigation showed that children’s behavior could be classified into three positive and three negative behavioral categories. Using these categories to code children’s behavior as they engaged in breakfast club showed that children displayed more positive than negative behaviors within the breakfast club setting and this was the case regardless of the type of activity (i.e., quiet or boisterous) children were involved in. Findings are discussed in relation to breakfast club policy, implementation, and evaluation. PMID:26217653

(I Can't Get No) Saturation: A simulation and guidelines for sample sizes in qualitative research.

PubMed

van Rijnsoever, Frank J

2017-01-01

I explore the sample size in qualitative research that is required to reach theoretical saturation. I conceptualize a population as consisting of sub-populations that contain different types of information sources that hold a number of codes. Theoretical saturation is reached after all the codes in the population have been observed once in the sample. I delineate three different scenarios to sample information sources: "random chance," which is based on probability sampling, "minimal information," which yields at least one new code per sampling step, and "maximum information," which yields the largest number of new codes per sampling step. Next, I use simulations to assess the minimum sample size for each scenario for systematically varying hypothetical populations. I show that theoretical saturation is more dependent on the mean probability of observing codes than on the number of codes in a population. Moreover, the minimal and maximal information scenarios are significantly more efficient than random chance, but yield fewer repetitions per code to validate the findings. I formulate guidelines for purposive sampling and recommend that researchers follow a minimum information scenario.

Synthesis of crystalline Ce-activated garnet phosphor powders and technique to characterize their scintillation light yield

NASA Astrophysics Data System (ADS)

Gordienko, E.; Fedorov, A.; Radiuk, E.; Mechinsky, V.; Dosovitskiy, G.; Vashchenkova, E.; Kuznetsova, D.; Retivov, V.; Dosovitskiy, A.; Korjik, M.; Sandu, R.

2018-04-01

This work reports on a process of preparation of garnet phosphor powders and a technique for light yield evaluation of strongly light scattering samples. Powders of scintillation compounds could be used as individual materials or as samples for express tests of scintillation properties. However, estimation of their light yield (LY) is complicated by strong light scattering of this kind of materials. Ce3+-activated yttrium-aluminum and gallium-gadolinium-aluminum garnet phosphor powders, Y3Al5O12 (YAG:Ce) and Gd3Ga3Al2O12 (GGAG:Ce), were obtained using a modified coprecipitation technique. Ga tends to residue in mother liquor in ammonia media, but the modification allows to avoid the loss of components. We propose an approach for sample preparation and LY measurement setup with alpha particles excitation, allowing to decrease light scattering influence and to estimate a light yield of powder samples. This approach is used to evaluate the obtained powders.

Unravelling the secrets of Cs controlled secondary ion formation: Evidence of the dominance of site specific surface chemistry, alloying and ionic bonding

NASA Astrophysics Data System (ADS)

Wittmaack, Klaus

2013-03-01

Exposure of ion bombarded solids to Cs gives rise to a very strong enhancement of the yields of negatively charged secondary ions and, concurrently, to a lowering of positive ion yields. The phenomena have been explored in a large number of experimental and theoretical studies but attempts to clarify the mechanism of ion formation were not as successful as assumed. This review examines the state of the art in Cs controlled secondary ion mass spectrometry (SIMS) in great detail, with due consideration of low-energy alkali-ion scattering. In very basic studies on alkali induced secondary ion yield changes, sub-monolayer quantities of Cs or Li were deposited on the sample surface, followed by low-fluence ion bombardment, to avoid significant damage. If SIMS is applied to characterise the composition of solid materials, the simplest approach to achieving sample erosion as well as high negative-ion yields is bombardment with primary ions of Cs. Two other methods of sample loading with Cs provide more flexibility, (i) exposure to a collimated beam of Cs vapour and concurrent bombardment with high-energy non-Cs ions and (ii) the mixed-beam approach involving quasi-simultaneous bombardment with Cs and Xe ions. Both concepts have the advantage that undesirable sample overload with Cs can be avoided. High Cs concentrations reduce the formation probability of target specific molecular ions and lower the yields of all types of positive secondary ions, including Cs+, M+, X+, MCs+ and XCs+ (M and X denoting matrix and impurity elements). Quantitative SIMS analysis using MCs+ and XCs+ ions appears feasible, provided the Cs coverage is kept below about 5%. The semi-classical model of resonant charge transfer, also known as the tunnelling model, has long been considered a solid framework for the interpretation of Cs and Li based SIMS data. The model predicts ionisation probabilities for cases in which, at shallow distances from the surface, the affinity (ionisation) level of the departing atom is shifted below (above) the Fermi level. Ion yields should be controlled by the work function (WF) of the sample, Φ, and the normal velocity of the ejected ions. To explore the predicted velocity dependence, the performance characteristics of the employed SIMS instrument need to be known. The Cs induced negative-ion yield enhancement observed with pure metal and alloy targets often exceeded five orders of magnitude, with enhancement factors essentially independent of the emission energy. This absence of a velocity dependence is at variance with the predictions of the tunnelling model. Previous theoretical attempts to model the Φ-dependence and the apparent velocity effect for the overrated case of O-emission from Li and Cs exposed oxidised metal surfaces must be considered a meander. The experimental data, recorded with a quadrupole based instrument of inadequate extraction geometry, may alternatively be rationalised in terms of alkali induced changes in the energy spectrum of sputtered atoms. Another important finding is that secondary ion yield changes do not correlate with the absolute magnitude of the (macroscopic) WF but often with WF changes, ΔΦ. The frequently used method of determining ΔΦ in situ from the shift of the leading edge of secondary ion energy spectra rests on the assumption, taken for granted or not even appreciated, that Cs induced yield changes are independent of the ion's emission velocity. Hence the approach is only applicable if the tunnelling model is not valid. The local character of alkali induced WF changes, which might provide a route to an understanding of previously unexplained phenomena, has been explored using photoemission of adsorbed inert gases, scanning tunneling microscopy and low-energy ion scattering spectrometry. At room temperature, the Cs coverage is limited to one layer of adatoms. Close similarities are identified between WF changes generated by Cs vapour deposition and by bombardment with Cs ions. This finding implies that sub-monolayer quantities of Cs adatoms grow at the surface of Cs bombarded samples. The process has been studied in-situ by medium-energy ion scattering spectrometry. The stationary Cs coverage, NCs, is controlled by the efficiency of active transport of implanted atoms to the surface, the bulk retention properties of the sample and the cross section for sputtering of adatoms. Unearthing immobile implanted Cs atoms by sputter erosion usually provides only a minor contribution to the stationary coverage. Cs adatoms are mobile; the time required for final adatom rearrangement may be on the order of minutes at room temperature. Exposure of Cs bombarded samples to oxygen gives rise to oxidation of the substrate as well as to the formation of oxide layers of complex composition. Intercalation should be taken into account as a possible route of alkali transport into analysed samples. An important aspect ignored in prior work is that the alkali coverage required to produce a certain WF change is five to seven times higher if Li is deposited instead of Cs. Studies involving the use of Li thus provide no advantage compared to Cs. Furthermore, migration of the tiny Li atoms into the sample and metallisation effects aggrevate data interpretation. Literature data for ΔΦ (NCs), measured using Cs vapour deposition, can be converted to calibration curves, NCs (ΔΦ), for calculating the coverage established in implantation studies, a method referred to as ΔΦ→NCs conversion. This concept may be carried even further, as shown convincingly for silicon, the material examined most frequently in basic SIMS studies: Si- ion fractions, P(Si-), derived from yields measured under vastly different conditions of Cs supply, exhibit essentially the same ΔΦ dependence. Inverting the data one can produce calibration functions for ΔΦ versus P(Si-), denoted P(Si-)→ΔΦ, or, more generally, P(M-)→ΔΦ conversion. On this basis, transient yields measured during Cs implantation can be evaluated as a function of Cs coverage. The summarised results imply that secondary ions are commonly not formed by charge transfer between an escaping atom and the electronic system of the sample but are already emitted as ions. The probability of ion formation appears to be controlled by the local ionic character of the alkali-target atom bonds, i.e., by the difference in electronegativity between the involved elements as well as by the electron affinity and the ionisation potential of the departing atom. This idea is supported by the finding that Si- yields exhibit the same very strong dependence on Cs coverage as Si+ and O- yields on the oxygen fraction in oxygen loaded Si. Most challenging to theoreticians is the finding that the ionisation probability is independent of the emission velocity of sputtered ions. This phenomenon cannot be rationalised along established routes of thinking. Different concepts need to be explored. An old, somewhat exotic idea takes account of the heavy perturbation created for a very short period of time at the site of ion emission (dynamic randomisation). Molecular dynamics simulations are desirable to clarify the issue. Ultimately it may be possible to describe all phenomena of enhanced or suppressed secondary ion formation, produced either by surface loading with alkali atoms or by enforced surface oxidation, on the basis of a single universal model. There is plenty of room for exciting new studies.

Tests of Scintillator+WLS Strips for Muon System at Future Colliders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Denisov, Dmitri; Evdokimov, Valery; Lukić, Strahinja

2015-10-11

Prototype scintilator+WLS strips with SiPM readout for muon system at future colliders were tested for light yield, time resolution and position resolution. Depending on the configuration, light yield of up to 36 photoelectrons per muon per SiPM has been achieved, as well as time resolution of 0.5 ns and position resolution of ~ 7 cm.

Occurrence of Legionella in wastewater treatment plants linked to wastewater characteristics.

PubMed

Caicedo, C; Beutel, S; Scheper, T; Rosenwinkel, K H; Nogueira, R

2016-08-01

In recent years, the occurrence of Legionella in wastewater treatment plants (WWTP) has often been reported. However, until now there is limited knowledge about the factors that promote Legionella's growth in such systems. The aim of this study was to investigate the chemical wastewater parameters that might be correlated to the concentration of Legionella spp. in WWTP receiving industrial effluents. For this purpose, samples were collected at different processes in three WWTP. In 100 % of the samples taken from the activated sludge tanks Legionella spp. were detected at varying concentrations (4.8 to 5.6 log GU/mL) by the quantitative real-time polymerase chain reaction method, but not by the culture method. Statistical analysis with various parameters yielded positive correlations of Legionella spp. concentration with particulate chemical oxygen demand, Kjeldahl nitrogen and protein concentration. Amino acids were quantified in wastewater and activated sludge samples at concentrations that may not support the growth of Legionella, suggesting that in activated sludge tanks this bacterium multiplied in protozoan hosts.

Comparative Analysis of Recruitment Strategies in a Study of Men Who Have Sex with Men (MSM) in Metropolitan Detroit.

PubMed

Iott, Bradley E; Veinot, Tiffany C; Loveluck, Jimena; Kahle, Erin; Golson, Leon; Benton, Akilah

2018-02-22

HIV/AIDS-related research requires recruitment of representative samples of MSM; yet, we know little about the comparative yield, diversity and cost-benefit tradeoffs between different recruitment venues. We compared 11 recruitment venues used for nine HIV prevention-related focus groups with MSM in Metropolitan Detroit. Of the 64 participants, 24 were clients recruited via an HIV/AIDS-focused nonprofit, 20 from Grindr advertisements, 6 from university-student email lists, and 5 from flyers/palmcards. Significantly more African-American, low-income and HIV-positive participants were recruited via the nonprofit. The best cost-benefit tradeoffs were for organizational Facebook posts, email groups, personal networking, and nonprofit recruitment. Grindr increased the size of the sample, though at greater expense. Facebook and Scruff advertisements and gay bar outreach represented greater costs than benefits. Only 11.6% of Grindr respondents attended the focus groups. A mix of online and offline recruitment venues can generate a large and diverse sample of MSM, but venue performance is uneven.

Number of pins in two-stage stratified sampling for estimating herbage yield

Treesearch

William G. O' Regan; C. Eugene Conrad

1975-01-01

In a two-stage stratified procedure for sampling herbage yield, plots are stratified by a pin frame in stage one, and clipped. In stage two, clippings from selected plots are sorted, dried, and weighed. Sample size and distribution of plots between the two stages are determined by equations. A way to compute the effect of number of pins on the variance of estimated...

Tick-borne haemoparasites and Anaplasmataceae in domestic dogs in Zambia.

PubMed

Qiu, Yongjin; Kaneko, Chiho; Kajihara, Masahiro; Ngonda, Saasa; Simulundu, Edgar; Muleya, Walter; Thu, May June; Hang'ombe, Mudenda Bernard; Katakura, Ken; Takada, Ayato; Sawa, Hirofumi; Simuunza, Martin; Nakao, Ryo

2018-05-01

Tick-borne diseases (TBDs), including emerging and re-emerging infectious diseases, are important threats to human and animal health worldwide. Indeed, the number of reported human and animal infectious cases of novel TBD agents has increased in recent decades. However, TBDs tend to be neglected, especially in resource-limited countries that often have limited diagnostic capacity. The aim of this molecular survey was to detect and characterise tick-borne pathogens (Babesia, Theileria, and Hepatozoon parasites and Anaplasmataceae bacteria) in domestic dogs in Zambia. In total, 247 canine peripheral blood samples were collected in Lusaka, Mazabuka, Monze, and Shangombo. Conventional PCR to detect the selected pathogens was performed using DNA extracted from canine blood. One hundred eleven samples were positive for protozoa and 5 were positive for Anaplasmataceae. Sequencing of thirty-five randomly selected protozoa-positive samples revealed the presence of Babesia rossi, Babesia vogeli, and Hepatozoon canis 18S rDNA. Based on these sequences, a multiplex PCR system was developed to yield PCR products with different amplicons, the size of which depended on the parasite species; thus, each species could be identified without the need for sequence analysis. Approximately 40% of dogs were positive for H. canis. In particular, the positive rate (75.2%) of H. canis infection was significantly higher in Shangombo than in other sampling sites. Multiplex PCR assay detected B. rossi and B. vogeli infections in five and seven dogs, respectively, indicating that this approach is useful for detecting parasites with low prevalence. Sequencing analysis of gltA and groEL genes of Anaplasmataceae revealed that two and one dogs in Lusaka were infected with Anaplasma platys and Ehrlichia canis, respectively. The data indicated that Zambian dogs were infected with multiple tick-borne pathogens such as H. canis, B. rossi, B. vogeli, A. platys, E. canis and uncharacterized Ehrlichia sp. Since some of these parasites are zoonotic, concerted efforts are needed to raise awareness of, and control, these tick-borne pathogens. Copyright © 2018 Elsevier GmbH. All rights reserved.

Caffeine expectancy: instrument development in the Rasch measurement framework.

PubMed

Heinz, Adrienne J; Kassel, Jon D; Smith, Everett V

2009-09-01

Although caffeine is the most widely consumed psychoactive drug in the world, the mechanisms associated with consumption are not well understood. Nonetheless, outcome expectancies for caffeine use are thought to underlie caffeine's reinforcing properties. To date, however, there is no available, sufficient measure by which to assess caffeine expectancy. Therefore, the current study sought to develop such a measure employing Rasch measurement models. Unlike traditional measurement development techniques, Rasch analyses afford dynamic and interactive control of the analysis process and generate helpful information to guide instrument construction. A 5-stage developmental process is described, ultimately yielding a 37-item Caffeine Expectancy Questionnaire (CEQ) comprised of 4 factors representing "withdrawal symptoms," "positive effects," "acute negative effects," and "mood effects." Initial evaluation of the CEQ yielded sufficient evidence for various aspects of validity. Although additional research with more heterogeneous samples is required to further assess the measure's reliability and validity, the CEQ demonstrates potential with regard to its utility in experimental laboratory research and clinical application. 2009 APA, all rights reserved.

Effects of bagasse microfibrillated cellulose and cationic polyacrylamide on key properties of bagasse paper.

PubMed

Djafari Petroudy, Seyed Rahman; Syverud, Kristin; Chinga-Carrasco, Gary; Ghasemain, Ali; Resalati, Hossein

2014-01-01

This study explores the benefits of using bagasse microfibrillated cellulose (MFC) in bagasse paper. Two different types of MFC were produced from DED bleached soda bagasse pulp. The MFC was added to soda bagasse pulp furnishes in different amounts. Cationic polyacrylamide (C-PAM) was selected as retention aid. The results show that addition of MFC increased the strength of paper as expected. Interestingly, 1% MFC in combination with 0.1% C-PAM yielded similar drainage time as the reference pulp, which did not contain MFC. In addition, the samples containing 1% MFC and 0.1% C-PAM yielded (i) a significant increment of the tensile index, (ii) a minor decrease of opacity and (iii) preserved Gurley porosity. Hence, this study proves that small fractions of MFC in combination with adequate retention aids can have positive effects with respect to paper properties, which is most interesting from an industrial point of view. Copyright © 2013 Elsevier Ltd. All rights reserved.

IR and NMR studies of hierarchical material obtained by the treatment of zeolite Y by ammonia solution

NASA Astrophysics Data System (ADS)

Gackowski, Mariusz; Kuterasiński, Łukasz; Podobiński, Jerzy; Sulikowski, Bogdan; Datka, Jerzy

2018-03-01

Ammonia treatment of ultrastable zeolite Y has a great impact on its features. XRD showed a partial loss of crystallinity coupled with a loss of long-distance zeolite ordering. However, a typical short-range zeolite ordering, in the light of 29Si NMR studies, was largely preserved. 27Al MAS NMR spectra evidenced that most of Al was located in zeolitic tetrahedral positions, but some of them adopted a distorted configuration. Evolution of zeolites acidity was followed quantitatively by using IR. In particular, such studies revealed the presence of strongly acidic Sisbnd OHsbnd Al groups. IR studies suggest also heterogeneity of these OH groups. The heterogeneity of Sisbnd OHsbnd Al groups was a consequence of the less ordered structure of zeolites treated with ammonia solutions. It was also found that the treatment with ammonia solutions yields hierarchical material. The samples revealed promising catalytic properties in the liquid phase isomerization of α-pinene. Zeolites desilicated with ammonia may constitute an inexpensive route yielding viable hierarchical catalysts.

Impact of Brazilian red propolis extract on blood metabolites, milk production, and lamb performance of Santa Inês ewes.

PubMed

Morsy, Amr S; Soltan, Yosra A; Sallam, Sobhy M A; Alencar, Severino M; Abdalla, Adibe L

2016-06-01

Twenty Santa Inês ewes used to evaluate effects of oral administration of Brazilian red propolis extract on blood metabolites, milk production, and lamb performance were randomly grouped (n = 10 ewes/group) to control without propolis administration and propolis treated (3 g red propolis extract/ewe/day) 21 days before expected lambing date. Blood samples were collected weekly, and daily milk yield was recorded twice weekly until 7 weeks postpartum. Propolis administration increased (P < 0.05) total leukocyte counts, protein, and globulin and glucose concentrations, decreased (P < 0.05) somatic cell counts, and enhanced (P < 0.05) yields of milk, fat, protein, and lactose. Propolis supplementation increased (P < 0.05) average daily gain and milk conversion ratio but had no effect on lamb birth and weaning weights. The prepartum administration of propolis extract supported positively the transition of ewes from pregnancy to lactation with health benefits achieved for both of ewes and lambs performances.

Photoactive roadways: Determination of CO, NO and VOC uptake coefficients and photolabile side product yields on TiO2 treated asphalt and concrete

NASA Astrophysics Data System (ADS)

Toro, C.; Jobson, B. T.; Haselbach, L.; Shen, S.; Chung, S. H.

2016-08-01

This work reports uptake coefficients and by-product yields of ozone precursors onto two photocatalytic paving materials (asphalt and concrete) treated with a commercial TiO2 surface application product. The experimental approach used a continuously stirred tank reactor (CSTR) and allowed for testing large samples with the same surface morphology encountered with real urban surfaces. The measured uptake coefficient (γgeo) and surface resistances are useful for parametrizing dry deposition velocities in air quality model evaluation of the impact of photoactive surfaces on urban air chemistry. At 46% relative humidity, the surface resistance to NO uptake was ∼1 s cm-1 for concrete and ∼2 s cm-1 for a freshly coated older roadway asphalt sample. HONO and NO2 were detected as side products from NO uptake to asphalt, with NO2 molar yields on the order of 20% and HONO molar yields ranging between 14 and 33%. For concrete samples, the NO2 molar yields increased with the increase of water vapor, ranging from 1% to 35% and HONO was not detected as a by-product. Uptake of monoaromatic VOCs to the asphalt sample set displayed a dependence on the compound vapor pressure, and was influenced by competitive adsorption from less volatile VOCs. Formaldehyde and acetaldehyde were detected as byproducts, with molar yields ranging from 5 to 32%.

DNA Yield From Tissue Samples in Surgical Pathology and Minimum Tissue Requirements for Molecular Testing.

PubMed

Austin, Melissa C; Smith, Christina; Pritchard, Colin C; Tait, Jonathan F

2016-02-01

Complex molecular assays are increasingly used to direct therapy and provide diagnostic and prognostic information but can require relatively large amounts of DNA. To provide data to pathologists to help them assess tissue adequacy and provide prospective guidance on the amount of tissue that should be procured. We used slide-based measurements to establish a relationship between processed tissue volume and DNA yield by A260 from 366 formalin-fixed, paraffin-embedded tissue samples submitted for the 3 most common molecular assays performed in our laboratory (EGFR, KRAS, and BRAF). We determined the average DNA yield per unit of tissue volume, and we used the distribution of DNA yields to calculate the minimum volume of tissue that should yield sufficient DNA 99% of the time. All samples with a volume greater than 8 mm(3) yielded at least 1 μg of DNA, and more than 80% of samples producing less than 1 μg were extracted from less than 4 mm(3) of tissue. Nine square millimeters of tissue should produce more than 1 μg of DNA 99% of the time. We conclude that 2 tissue cores, each 1 cm long and obtained with an 18-gauge needle, will almost always provide enough DNA for complex multigene assays, and our methodology may be readily extrapolated to individual institutional practice.

Measuring oxygen yields of a thermal conversion/elemental analyzer-isotope ratio mass spectrometer for organic and inorganic materials through injection of CO.

PubMed

Yin, Xijie; Chen, Zhigang

2014-12-01

The thermal conversion/elemental analyzer-isotope ratio mass spectrometer (TC/EA-IRMS) is widely used to measure the δ(18) O value of various substances. A premise for accurate δ(18) O measurement is that the oxygen in the sample can be converted into carbon monoxide (CO) quantitatively or at least proportionally. Therefore, a precise method to determine the oxygen yield of TC/EA-IRMS measurements is needed. Most studies have used the CO peak area obtained from a known amount of a solid reference material (for example, benzoic acid) to calibrate the oxygen yield of the sample. Although it was assumed that the oxygen yield of the solid reference material is 100%, no direct evidence has been provided. As CO is the analyte gas for δ(18) O measurement by IRMS, in this study, we use a six-port valve to inject CO gas into the TC/EA. The CO is carried to the IRMS by the He carrier gas and the CO peak area is measured by the IRMS. The CO peak area thus obtained from a known amount of the injected CO is used to calibrate the oxygen yield of the sample. The oxygen yields of commonly used organic and inorganic reference materials such as benzoic acid (C6 H5 COOH), silver phosphate (Ag3 PO4 ), calcium carbonate (CaCO3 ) and silicon dioxide (SiO2 ) are investigated at different reactor temperatures and sample sizes. We obtained excellent linear correlation between the peak area for the injected CO and its oxygen atom amount. C6 H5 COOH has the highest oxygen yield, followed by Ag3 PO4 , CaCO3 and SiO2 . The oxygen yields of TC/EA-IRMS are less than 100% for both organic and inorganic substances, but the yields are relatively stable at the specified reactor temperature and for a given quantity of sample. Copyright © 2014 John Wiley & Sons, Ltd.

Nanoscale Roughness of Faults Explained by the Scale-Dependent Yield Stress of Geologic Materials

NASA Astrophysics Data System (ADS)

Thom, C.; Brodsky, E. E.; Carpick, R. W.; Goldsby, D. L.; Pharr, G.; Oliver, W.

2017-12-01

Despite significant differences in their lithologies and slip histories, natural fault surfaces exhibit remarkably similar scale-dependent roughness over lateral length scales spanning 7 orders of magnitude, from microns to tens of meters. Recent work has suggested that a scale-dependent yield stress may result in such a characteristic roughness, but experimental evidence in favor of this hypothesis has been lacking. We employ an atomic force microscope (AFM) operating in intermittent-contact mode to map the topography of the Corona Heights fault surface. Our experiments demonstrate that the Corona Heights fault exhibits isotropic self-affine roughness with a Hurst exponent of 0.75 +/- 0.05 at all wavelengths from 60 nm to 10 μm. If yield stress controls roughness, then the roughness data predict that yield strength varies with length scale as λ-0.25 +/ 0.05. To test the relationship between roughness and yield stress, we conducted nanoindentation tests on the same Corona Heights sample and a sample of the Yair Fault, a carbonate fault surface that has been previously characterized by AFM. A diamond Berkovich indenter tip was used to indent the samples at a nominally constant strain rate (defined as the loading rate divided by the load) of 0.2 s-1. The continuous stiffness method (CSM) was used to measure the indentation hardness (which is proportional to yield stress) and the elastic modulus of the sample as a function of depth in each test. For both samples, the yield stress decreases with increasing size of the indents, a behavior consistent with that observed for many engineering materials and recently for other geologic materials such as olivine. The magnitude of this "indentation size effect" is best described by a power-law with exponents of -0.12 +/- 0.06 and -0.18 +/- 0.08 for the Corona Heights and Yair Faults, respectively. These results demonstrate a link between surface roughness and yield stress, and suggest that fault geometry is the physical manifestation of a scale-dependent yield stress.

Antimicrobial resistance of Listeria monocytogenes isolated from dairy-based food products.

PubMed

Harakeh, Steve; Saleh, Imane; Zouhairi, Omar; Baydoun, Elias; Barbour, Elie; Alwan, Nisreen

2009-06-15

In this study Listeria monocytogenes (L. monocytogenes) was isolated from three traditionally consumed Lebanese dairy-based food products. One hundred and sixty four samples (45 samples of Baladi cheese, 36 samples of Shankleesh and 83 of Kishk) were collected from the Bekaa Valley in the Northeast region of Lebanon. Suspected Listeria colonies were selected and initially identified by using standard biochemical tests. Initial identification of the positive L. monocytogenes colonies was confirmed at the molecular level by Polymerase Chain Reaction (n=30) and the confirmed isolates were evaluated for their susceptibility to 10 commonly used antimicrobials. All of the 30 isolates were confirmed to be L. monocytogenes yielding a PCR product of approximately 660 base pairs (bp). L. monocytogenes was detected in 26.67%, 13.89% and 7.23% of the Baladi cheese, Shankleesh and Kishk samples, respectively. The highest resistance in L. monocytogenes isolates was noted against oxacillin (93.33%) followed by penicillin (90%). The results provide an indication of the contamination levels of dairy-based foods in Lebanon and highlight the emergence of multi-drug resistant Listeria in the environment.

Population diversity of ammonium oxidizers investigated by specific PCR amplification

USGS Publications Warehouse

Ward, B.B.; Voytek, M.A.; Witzel, K.-P.

1997-01-01

The species composition of ammonia-oxidizing bacteria in aquatic environments was investigated using PCR primers for 16S rRNA genes to amplify specific subsets of the total ammonia-oxidizer population. The specificity of the amplification reactions was determined using total genomic DNA from known nitrifying strains and non-nitrifying strains identified as having similar rDNA sequences. Specificity of amplification was determined both for direct amplification, using the nitrifier specific primers, and with nested amplification, in which the nitrifier primers were used to reamplify a fragment obtained from direct amplification with Eubacterial universal primers. The present level of specificity allows the distinction between Nitrosomonas europaea, Nitrosomonas sp. (marine) and the other known ammonia-oxidizers in the beta subclass of the Proteobacteria. Using total DNA extracted from natural samples, we used direct amplification to determine presence/absence of different species groups. Species composition was found to differ among depths in vertical profiles of lake samples and among samples and enrichments from various other aquatic environments. Nested PCR yielded several more positive reactions, which implies that nitrifier DNA was present in most samples, but often at very low levels.

Prevalence and concentration of Campylobacter in rumen contents and feces in pasture and feedlot-fed cattle.

PubMed

Krueger, Nathan A; Anderson, Robin C; Krueger, Wimberley K; Horne, Willy J; Wesley, Irene V; Callaway, Todd R; Edrington, Tom S; Carstens, Gordon E; Harvey, Roger B; Nisbet, David J

2008-10-01

Campylobacter are important human foodborne pathogens known to colonize the gastrointestinal tract of cattle. The incidence of Campylobacter in cattle may be seasonal and may vary among age groups and type (beef versus dairy). Less is known about other factors that could influence the prevalence, colonization site, and shedding of Campylobacter in cattle. The objectives of this study were to evaluate the prevalence and enumerate Campylobacter at two sites along the digestive tract of beef and dairy type cattle consuming either grass or feedlot diets. In an initial study, Campylobacter was not recovered from rumen samples of any of 10 ruminally cannulated (six dairy and four beef type) pasture-reared cattle and there was no difference (p > 0.05) between cattle types on fecal Campylobacter recovery, with 50% of each type yielding culture-positive feces (overall mean +/- SE, 0.75 +/- 0.001 SEM log(10) colony-forming units [CFU]/g feces). When calculated from Campylobacter culture-positive animals only, mean fecal concentrations were 1.50 +/- 0.001 SEM log(10) CFU/g. In a follow-up study with feedlot and pasture-reared cattle (n = 18 head each), 78% of rumen and 94% of fecal samples from pastured cattle were positive for Campylobacter while 50% of the rumen and 72% of the fecal samples were positive in concentrate-fed animals. Overall mean concentration of Campylobacter was greater in feces than ruminal fluid (p < 0.05). When only Campylobacter-positive animals were analyzed, concentrations recovered from feces were higher (p < 0.05) in concentrate-fed than in pasture-fed cattle (4.29 vs. 3.34 log(10) CFU/g, respectively; SEM = 0.29). Our results suggest that the rumen environment and its microbial population are less favorable for the growth of Campylobacter and that concentrate diets may provide a more hospitable lower gastrointestinal tract for Campylobacter.