Application of magnetohydrodynamic actuation to continuous flow chemistry.

PubMed

West, Jonathan; Karamata, Boris; Lillis, Brian; Gleeson, James P; Alderman, John; Collins, John K; Lane, William; Mathewson, Alan; Berney, Helen

2002-11-01

Continuous flow microreactors with an annular microchannel for cyclical chemical reactions were fabricated by either bulk micromachining in silicon or by rapid prototyping using EPON SU-8. Fluid propulsion in these unusual microchannels was achieved using AC magnetohydrodynamic (MHD) actuation. This integrated micropumping mechanism obviates the use of moving parts by acting locally on the electrolyte, exploiting its inherent conductive nature. Both silicon and SU-8 microreactors were capable of MHD actuation, attaining fluid velocities of the order of 300 microm s(-1) when using a 500 mM KCl electrolyte. The polymerase chain reaction (PCR), a thermocycling process, was chosen as an illustrative example of a cyclical chemistry. Accordingly, temperature zones were provided to enable a thermal cycle during each revolution. With this approach, fluid velocity determines cycle duration. Here, we report device fabrication and performance, a model to accurately describe fluid circulation by MHD actuation, and compatibility issues relating to this approach to chemistry.

Novel approach based on one-tube nested PCR and a lateral flow strip for highly sensitive diagnosis of tuberculous meningitis.

PubMed

Sun, Yajuan; Chen, Jiajun; Li, Jia; Xu, Yawei; Jin, Hui; Xu, Na; Yin, Rui; Hu, Guohua

2017-01-01

Rapid and sensitive detection of Mycobacterium tuberculosis (M. Tb) in cerebrospinal fluid is crucial in the diagnosis of tuberculous meningitis (TBM), but conventional diagnostic technologies have limited sensitivity and specificity or are time-consuming. In this work, a novel, highly sensitive molecular diagnostic method, one-tube nested PCR-lateral flow strip test (OTNPCR-LFST), was developed for detecting M. tuberculosis. This one-tube nested PCR maintains the sensitivity of conventional two-step nested PCR and reduces both the chance of cross-contamination and the time required for analysis. The PCR product was detected by a lateral flow strip assay, which provided a basis for migration of the test to a point-of-care (POC) microfluidic format. The developed assay had an improved sensitivity compared with traditional PCR, and the limit of detection was up to 1 fg DNA isolated from M. tuberculosis. The assay was also specific for M. tuberculosis, and no cross-reactions were found in other non-target bacteria. The application of this technique to clinical samples was successfully evaluated, and OTNPCR-LFST showed 89% overall sensitivity and 100% specificity for TBM patients. This one-tube nested PCR-lateral flow strip assay is useful for detecting M. tuberculosis in TBM due to its rapidity, high sensitivity and simple manipulation.

Evaluation of Reference Genes for Quantitative Real-Time PCR Analysis of the Gene Expression in Laticifers on the Basis of Latex Flow in Rubber Tree (Hevea brasiliensis Muell. Arg.)

PubMed Central

Chao, Jinquan; Yang, Shuguang; Chen, Yueyi; Tian, Wei-Min

2016-01-01

Latex exploitation-caused latex flow is effective in enhancing latex regeneration in laticifer cells of rubber tree. It should be suitable for screening appropriate reference gene for analysis of the expression of latex regeneration-related genes by quantitative real-time PCR (qRT-PCR). In the present study, the expression stability of 23 candidate reference genes was evaluated on the basis of latex flow by using geNorm and NormFinder algorithms. Ubiquitin-protein ligase 2a (UBC2a) and ubiquitin-protein ligase 2b (UBC2b) were the two most stable genes among the selected candidate references in rubber tree clones with differential duration of latex flow. The two genes were also high-ranked in previous reference gene screening across different tissues and experimental conditions. By contrast, the transcripts of latex regeneration-related genes fluctuated significantly during latex flow. The results suggest that screening reference gene during latex flow should be an efficient and effective clue for selection of reference genes in qRT-PCR. PMID:27524995

Flow-through PCR on a 3D qiandu-shaped polydimethylsiloxane (PDMS) microdevice employing a single heater: toward microscale multiplex PCR.

PubMed

Wu, Wenming; Loan, Kieu The Loan; Lee, Nae Yoon

2012-05-07

Consistent temperature control in an on-chip flow-through polymerase chain reaction (PCR) employing two or more heaters is one of the main obstacles for device miniaturization and integration when realizing micro total analysis systems (μTAS), and also leads to operational complexity. In this study, we propose a qiandu (right triangular prism)-shaped polydimethylsiloxane (PDMS) microdevice with serpentine microchannels fabricated on its slanted plane, and apply the device for an on-chip flow-through PCR employing a single heater. The inclined nature of the qiandu-shaped microdevice enables the formation of a surface temperature gradient along the slanted plane of the microdevice in a height-dependent manner by the use of a single heater, and enables liquid to traverse over wide ranges of temperatures, including the three temperature zones--denaturation, annealing, and extension temperatures--required in a typical PCR. The feasibility of the qiandu-shaped PDMS microdevice as a versatile platform for performing a flow-through PCR was examined by employing multiple templates and varying the inclination angle of the device. In addition, the potential of performing a multiplex PCR using a single qiandu-shaped PDMS microdevice was explored. A 409 bp long gene fragment effective as a marker for diagnosing lung cancer and a 230 bp long gene fragment from a plasmid vector were simultaneously amplified in less than 25 min on a single microdevice, paving the way for a microscale, multiplex PCR on a single device employing a single heater.

Novel approach based on one-tube nested PCR and a lateral flow strip for highly sensitive diagnosis of tuberculous meningitis

PubMed Central

Sun, Yajuan; Chen, Jiajun; Li, Jia; Xu, Yawei; Jin, Hui; Xu, Na; Yin, Rui

2017-01-01

Rapid and sensitive detection of Mycobacterium tuberculosis (M. Tb) in cerebrospinal fluid is crucial in the diagnosis of tuberculous meningitis (TBM), but conventional diagnostic technologies have limited sensitivity and specificity or are time-consuming. In this work, a novel, highly sensitive molecular diagnostic method, one-tube nested PCR-lateral flow strip test (OTNPCR-LFST), was developed for detecting M. tuberculosis. This one-tube nested PCR maintains the sensitivity of conventional two-step nested PCR and reduces both the chance of cross-contamination and the time required for analysis. The PCR product was detected by a lateral flow strip assay, which provided a basis for migration of the test to a point-of-care (POC) microfluidic format. The developed assay had an improved sensitivity compared with traditional PCR, and the limit of detection was up to 1 fg DNA isolated from M. tuberculosis. The assay was also specific for M. tuberculosis, and no cross-reactions were found in other non-target bacteria. The application of this technique to clinical samples was successfully evaluated, and OTNPCR-LFST showed 89% overall sensitivity and 100% specificity for TBM patients. This one-tube nested PCR-lateral flow strip assay is useful for detecting M. tuberculosis in TBM due to its rapidity, high sensitivity and simple manipulation. PMID:29084241

Guar gum coupled microscale ZVI for in situ treatment of CAHs: continuous-flow column study.

PubMed

Velimirovic, Milica; Simons, Queenie; Bastiaens, Leen

2014-01-30

A column study was performed under in situ conditions to evaluate to which extend the inactivation of the microscale zerovalent iron (mZVI) by guar gum occurs under continuous flow conditions. Five aquifer containing columns were set up under different conditions. Efficient removal of trichloroethene was observed for the column amended by mZVI. Stabilization of the mZVI with guar gum led to slightly reduced activity. More reduced reactivity was observed in the poisoned column containing guar gum stabilized mZVI. This confirms that soil microorganisms can degrade guar gum and that subsequent removal of the oligosaccharides by the groundwater flow (flushing effect) can reactivate the mZVI. After more than six months of continuous operation the columns were dismantled. DNA-based qPCR analysis revealed that mZVI does not significantly affect the bacterial community, while guar gum stabilized mZVI particles can even induce bacterial growth. Overall, this study suggests that the temporarily decreased mZVI reactivity due to guar gum, has a rather limited impact on the performance of in situ reactive zones. The presence of guar gum slightly reduced the reactivity of iron, but also slowed down the iron corrosion rate which prolongs the life time of reactive zone. Copyright © 2013 Elsevier B.V. All rights reserved.

Droplet-based micro oscillating-flow PCR chip

NASA Astrophysics Data System (ADS)

Wang, Wei; Li, Zhi-Xin; Luo, Rong; Lü, Shu-Hai; Xu, Ai-Dong; Yang, Yong-Jun

2005-08-01

Polymerase chain reactions (PCR), thermally activated chemical reactions which are widely used for nucleic acid amplification, have recently received much attention in microelectromechanical systems and micro total analysis systems because a wide variety of DNA/RNA molecules can be enriched by PCR for further analyses. In the present work, a droplet-based micro oscillating-flow PCR chip was designed and fabricated by the silicon microfabrication technique. Three different temperature zones, which were stable at denaturation, extension and annealing temperatures and isolated from each other by a thin-wall linkage, were integrated with a single, simple and straight microchannel to form the chip's basic functional structure. The PCR mixture was injected into the chip as a single droplet and flowed through the three temperature zones in the main microchannel in an oscillating manner to achieve the temperature maintenance and transitions. The chip's thermal performance was theoretically analyzed and numerically simulated. The results indicated that the time needed for the temperature of the droplet to change to the target value is less than 1 s, and the root mean square error of temperature is less than 0.2 °C. A droplet of 1 µl PCR mixture with standard HPV (Human Papilloma Virus)-DNA sample inside was amplified by the present chip and the results were analyzed by slab gel electrophoresis with separation of DNA markers in parallel. The electrophoresis results demonstrated that the micro oscillating-flow PCR chip successfully amplified the HPV-DNA, with a processing time of about 15 min which is significantly reduced compared to that for the conventional PCR instrument.

Evaluation of droplet digital PCR for quantification of residual leucocytes in red blood cell concentrates.

PubMed

Doescher, A; Loges, U; Petershofen, E K; Müller, T H

2017-11-01

Enumeration of residual white blood cells in leucoreduced blood components is essential part of quality control. Digital PCR has substantially facilitated quantitative PCR and was thus evaluated for measurements of leucocytes. Target for quantification of leucocytes by digital droplet PCR was the blood group gene RHCE. The SPEF1 gene was added as internal control for the entire assay starting with automated DNA extraction. The sensitivity of the method was determined by serial dilutions of standard samples. Quality control samples were analysed within 24 h, 7 days and 6 months after collection. Routine samples from leucodepleted red blood cell concentrates (n = 150) were evaluated in parallel by flow-cytometry (LeucoCount) and by digital PCR. Digital PCR reliably detected at least 0·4 leucocytes per assay. The mean difference between PCR and flow-cytometric results from 150 units was -0·01 (±1·0). DNA samples were stable for up to at least six months. PCR measurement of leucocytes in samples from plasma and platelet concentrates also provided valid results in a pilot study. Droplet digital PCR to enumerate leucocytes offers an alternative for quality control of leucoreduced blood products. Sensitivity, specificity and reproducibility are comparable to flow-cytometry. The option to collect samples over an extended period of time and the automatization introduce attractive features for routine quality control. © 2017 International Society of Blood Transfusion.

Identification of residual leukemic cells by flow cytometry in childhood B-cell precursor acute lymphoblastic leukemia: verification of leukemic state by flow-sorting and molecular/cytogenetic methods.

PubMed

Øbro, Nina F; Ryder, Lars P; Madsen, Hans O; Andersen, Mette K; Lausen, Birgitte; Hasle, Henrik; Schmiegelow, Kjeld; Marquart, Hanne V

2012-01-01

Reduction in minimal residual disease, measured by real-time quantitative PCR or flow cytometry, predicts prognosis in childhood B-cell precursor acute lymphoblastic leukemia. We explored whether cells reported as minimal residual disease by flow cytometry represent the malignant clone harboring clone-specific genomic markers (53 follow-up bone marrow samples from 28 children with B-cell precursor acute lymphoblastic leukemia). Cell populations (presumed leukemic and non-leukemic) were flow-sorted during standard flow cytometry-based minimal residual disease monitoring and explored by PCR and/or fluorescence in situ hybridization. We found good concordance between flow cytometry and genomic analyses in the individual flow-sorted leukemic (93% true positive) and normal (93% true negative) cell populations. Four cases with discrepant results had plausible explanations (e.g. partly informative immunophenotype and antigen modulation) that highlight important methodological pitfalls. These findings demonstrate that with sufficient experience, flow cytometry is reliable for minimal residual disease monitoring in B-cell precursor acute lymphoblastic leukemia, although rare cases require supplementary PCR-based monitoring.

Overexpression of TGF-β1 enhances chondrogenic differentiation and proliferation of human synovium-derived stem cells

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

Kim, Yong Il; Ryu, Jae-Sung; Yeo, Jee Eun

2014-08-08

Highlights: • Continuous TGF-β1 overexpression in hSD-MSCs did not influence their phenotypes. • Retroviral-mediated transduction of TGFB1 in hSD-MSCs enhances cell proliferation. • TGF-β1 overexpression did not effect to adipo- or osteogenic potential of hSD-MSCs. • TGF-β1 overexpression in hSD-MSCs could stimulate and accelerate chondrogenesis. - Abstract: Transforming growth factor-beta (TGF-β) superfamily proteins play a critical role in proliferation, differentiation, and other functions of mesenchymal stem cells (MSCs). During chondrogenic differentiation of MSCs, TGF-β up-regulates chondrogenic gene expression by enhancing the expression of the transcription factor SRY (sex-determining region Y)-box9 (Sox9). In this study, we investigated the effect of continuousmore » TGF-β1 overexpression in human synovium-derived MSCs (hSD-MSCs) on immunophenotype, differentiation potential, and proliferation rate. hSD-MSCs were transduced with recombinant retroviruses (rRV) encoding TGF-β1. The results revealed that continuous overexpression of TGF-β1 did not affect their phenotype as evidenced by flow cytometry and reverse transcriptase PCR (RT-PCR). In addition, continuous TGF-β1 overexpression strongly enhanced cell proliferation of hSD-MSCs compared to the control groups. Also, induction of chondrogenesis was more effective in rRV-TGFB-transduced hSD-MSCs as shown by RT-PCR for chondrogenic markers, toluidine blue staining and glycosaminoglycan (GAG)/DNA ratio. Our data suggest that overexpression of TGF-β1 positively enhances the proliferation and chondrogenic potential of hSD-MSCs.« less

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification.

PubMed

Guan, Weihua; Chen, Liben; Rane, Tushar D; Wang, Tza-Huei

2015-09-03

We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification

PubMed Central

Guan, Weihua; Chen, Liben; Rane, Tushar D.; Wang, Tza-Huei

2015-01-01

We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples. PMID:26333806

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification

NASA Astrophysics Data System (ADS)

Guan, Weihua; Chen, Liben; Rane, Tushar D.; Wang, Tza-Huei

2015-09-01

We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.

Comparison of methods for in-house screening of HLA-B*57:01 to prevent abacavir hypersensitivity in HIV-1 care.

PubMed

De Spiegelaere, Ward; Philippé, Jan; Vervisch, Karen; Verhofstede, Chris; Malatinkova, Eva; Kiselinova, Maja; Trypsteen, Wim; Bonczkowski, Pawel; Vogelaers, Dirk; Callens, Steven; Ruelle, Jean; Kabeya, Kabamba; De Wit, Stephane; Van Acker, Petra; Van Sandt, Vicky; Emonds, Marie-Paule; Coucke, Paul; Sermijn, Erica; Vandekerckhove, Linos

2015-01-01

Abacavir is a nucleoside reverse transcriptase inhibitor used as part of combination antiretroviral therapy in HIV-1-infected patients. Because this drug can cause a hypersensitivity reaction that is correlated with the presence of the HLA-B*57:01 allotype, screening for the presence of HLA-B*57:01 is recommended before abacavir initiation. Different genetic assays have been developed for HLA-B*57:01 screening, each with specific sensitivity, turnaround time and assay costs. Here, a new real-time PCR (qPCR) based analysis is described and compared to sequence specific primer PCR with capillary electrophoresis (SSP PCR CE) on 149 patient-derived samples, using sequence specific oligonucleotide hybridization combined with high resolution SSP PCR as gold standard. In addition to these PCR based methods, a complementary approach was developed using flow cytometry with an HLA-B17 specific monoclonal antibody as a pre-screening assay to diminish the number of samples for genetic testing. All three assays had a maximum sensitivity of >99. However, differences in specificity were recorded, i.e. 84.3%, 97.2% and >99% for flow cytometry, qPCR and SSP PCR CE respectively. Our data indicate that the most specific and sensitive of the compared methods is the SSP PCR CE. Flow cytometry pre-screening can substantially decrease the number of genetic tests for HLA-B*57:01 typing in a clinical setting.

Towards rapid prototyped convective microfluidic DNA amplification platform

NASA Astrophysics Data System (ADS)

Ajit, Smrithi; Praveen, Hemanth Mithun; Puneeth, S. B.; Dave, Abhishek; Sesham, Bharat; Mohan, K. N.; Goel, Sanket

2017-02-01

Today, Polymerase Chain Reaction (PCR) based DNA amplification plays an indispensable role in the field of biomedical research. Its inherent ability to exponentially amplify sample DNA has proven useful for the identification of virulent pathogens like those causing Multiple Drug-Resistant Tuberculosis (MDR-TB). The intervention of Microfluidics technology has revolutionized the concept of PCR from being a laborious and time consuming process into one that is faster, easily portable and capable of being multifunctional. The Microfluidics based PCR outweighs its traditional counterpart in terms of flexibility of varying reaction rate, operation simplicity, need of a fraction of volume and capability of being integrated with other functional elements. The scope of the present work involves the development of a real-time continuous flow microfluidic device, fabricated by 3D printing-governed rapid prototyping method, eventually leading to an automated and robust platform to process multiple DNA samples for detection of MDRTB-associated mutations. The thermal gradient characteristic to the PCR process is produced using peltier units appropriate to the microfluidic environment fully monitored and controlled by a low cost controller driven by a Data Acquisition System. The process efficiency achieved in the microfluidic environment in terms of output per cycle is expected to be on par with the traditional PCR and capable of earning the additional advantages of being faster and minimizing the handling.

Telomere content measurement in human hematopoietic cells: Comparative analysis of qPCR and Flow-FISH techniques.

PubMed

Wand, Taylor; Fang, Mike; Chen, Christina; Hardy, Nathan; McCoy, J Philip; Dumitriu, Bogdan; Young, Neal S; Biancotto, Angélique

2016-10-01

Abnormal telomere lengths have been linked to cancer and other hematologic disorders. Determination of mean telomere content (MTC) is traditionally performed by Southern blotting and densitometry, giving a mean telomere restriction fragment (TRF) value for the total cell population studied. Here, we compared a quantitative Polymerase Chain Reaction approach (qPCR) and a flow cytometric approach, fluorescence in situ hybridization (Flow-FISH), to evaluate telomere content distribution in total patient peripheral blood mononuclear cells or specific cell populations. Flow-FISH is based on in situ hybridization using a fluorescein-labeled peptide nucleic acid (PNA) (CCCTAA) 3 probe and DNA staining with propidium iodide. We showed that both qPCR and Flow-FISH provide a robust measurement, with Flow-FISH measuring a relative content longer than qPCR at a single cell approach and that TRF2 fluorescence intensity did not correlate with MTC. Both methods showed comparable telomere content reduction with age, and the rate of relative telomere loss was similar. Published 2016 Wiley Periodicals Inc. This article is a US government work and, as such, is in the public domain in the United States of America. Published 2016 Wiley Periodicals Inc. This article is a US government work and, as such, is in the public domain in the United States of America.

Prognostic value of bone marrow involvement by clonal immunoglobulin gene rearrangements in follicular lymphoma

PubMed Central

Berget, Ellen; Helgeland, Lars; Liseth, Knut; Løkeland, Turid; Molven, Anders; Vintermyr, Olav Karsten

2014-01-01

Aims We aimed to evaluate the prognostic value of routine use of PCR amplification of immunoglobulin gene rearrangements in bone marrow (BM) staging in patients with follicular lymphoma (FL). Methods Clonal rearrangements were assessed by immunoglobulin heavy and light-chain gene rearrangement analysis in BM aspirates from 96 patients diagnosed with FL and related to morphological detection of BM involvement in biopsies. In 71 patients, results were also compared with concurrent flow cytometry analysis. Results BM involvement was detected by PCR in 34.4% (33/96) of patients. The presence of clonal rearrangements by PCR was associated with advanced clinical stage (I–III vs IV; p<0.001), high FL International Prognostic Index (FLIPI) score (0–1, 2 vs ≥3; p=0.003), and detection of BM involvement by morphology and flow cytometry analysis (p<0.001 for both). PCR-positive patients had a significantly poorer survival than PCR-negative patients (p=0.001, log-rank test). Thirteen patients positive by PCR but without morphologically detectable BM involvement, had significantly poorer survival than patients with negative morphology and negative PCR result (p=0.002). The poor survival associated with BM involvement by PCR was independent of the FLIPI score (p=0.007, Cox regression). BM involvement by morphology or flow cytometry did not show a significant impact on survival. Conclusions Our results showed that routine use of PCR-based clonality analysis significantly improved the prognostic impact of BM staging in patients with FL. BM involvement by PCR was also an independent adverse prognostic factor. PMID:25233852

Brazilian Red Propolis Induces Apoptosis-Like Cell Death and Decreases Migration Potential in Bladder Cancer Cells

PubMed Central

Begnini, Karine Rech; Moura de Leon, Priscila Marques; Thurow, Helena; Schultze, Eduarda; Campos, Vinicius Farias; Borsuk, Sibele; Dellagostin, Odir Antônio; Savegnago, Lucielli; Moura, Sidnei; Padilha, Francine F.; Pêgas Henriques, João Antonio; Seixas, Fabiana Kömmling

2014-01-01

Natural products continue to be an invaluable resource of anticancer drug discovery in recent years. Propolis is known for its biological activities such as antimicrobial and antitumor effects. This study assessed the effects of Brazilian red propolis (BRP) on apoptosis and migration potential in human bladder cancer cells. The effect of BRP ethanolic extract (25, 50, and 100 μg/mL) on 5637 cells was determined by MTT, LIVE/DEAD, and migration (scratch assay) assays. Apoptosis induction was investigated through flow cytometry and gene expression profile was investigated by qRT-PCR. Results showed cytotoxicity on MTT and LIVE/DEAD assays, with IC50 values of 95 μg/mL in 24 h of treatment. Cellular migration of 5637 cells was significantly inhibited through lower doses of BRP ethanolic extract (25 and 50 μg/mL). Flow cytometry analyses showed that BRP induced cytotoxicity through apoptosis-like mechanisms in 5637 cells and qRT-PCR revealed increased levels of Bax/Bcl-2 ratio, p53, AIF, and antioxidant enzymes genes. Data suggest that BRP may be a potential source of drugs to bladder cancer treatment. PMID:25530785

Brazilian red propolis induces apoptosis-like cell death and decreases migration potential in bladder cancer cells.

PubMed

Begnini, Karine Rech; Moura de Leon, Priscila Marques; Thurow, Helena; Schultze, Eduarda; Campos, Vinicius Farias; Martins Rodrigues, Fernanda; Borsuk, Sibele; Dellagostin, Odir Antônio; Savegnago, Lucielli; Roesch-Ely, Mariana; Moura, Sidnei; Padilha, Francine F; Collares, Tiago; Pêgas Henriques, João Antonio; Seixas, Fabiana Kömmling

2014-01-01

Natural products continue to be an invaluable resource of anticancer drug discovery in recent years. Propolis is known for its biological activities such as antimicrobial and antitumor effects. This study assessed the effects of Brazilian red propolis (BRP) on apoptosis and migration potential in human bladder cancer cells. The effect of BRP ethanolic extract (25, 50, and 100 μg/mL) on 5637 cells was determined by MTT, LIVE/DEAD, and migration (scratch assay) assays. Apoptosis induction was investigated through flow cytometry and gene expression profile was investigated by qRT-PCR. Results showed cytotoxicity on MTT and LIVE/DEAD assays, with IC50 values of 95 μg/mL in 24 h of treatment. Cellular migration of 5637 cells was significantly inhibited through lower doses of BRP ethanolic extract (25 and 50 μg/mL). Flow cytometry analyses showed that BRP induced cytotoxicity through apoptosis-like mechanisms in 5637 cells and qRT-PCR revealed increased levels of Bax/Bcl-2 ratio, p53, AIF, and antioxidant enzymes genes. Data suggest that BRP may be a potential source of drugs to bladder cancer treatment.

Micropumps, microvalves, and micromixers within PCR microfluidic chips: Advances and trends.

PubMed

Zhang, Chunsun; Xing, Da; Li, Yuyuan

2007-01-01

This review surveys the advances of microvalves, micropumps, and micromixers within PCR microfluidic chips over the past ten years. First, the types of microvalves in PCR chips are discussed, including active and passive microvalves. The active microvalves are subdivided into mechanical (thermopneumatic and shape memory alloy), non-mechanical (hydrogel, sol-gel, paraffin, and ice), and external (modular built-in, pneumatic, and non-pneumatic) microvalves. The passive microvalves also include mechanical (in-line polymerized gel and passive plug) and non-mechanical (hydrophobic) microvalves. The review then discusses mechanical (piezoelectric, pneumatic, and thermopneumatic) and non-mechanical (electrokinetic, magnetohydrodynamic, electrochemical, acoustic-wave, surface tension and capillary, and ferrofluidic magnetic) micropumps in PCR chips. Next, different micromixers within PCR chips are presented, including passive (Y/T-type flow, recirculation flow, and drop) and active (electrokinetically-driven, acoustically-driven, magnetohydrodynamical-driven, microvalves/pumps) micromixers. Finally, general discussions on microvalves, micropumps, and micromixers for PCR chips are given. The microvalve/micropump/micromixers allow high levels of PCR chip integration and analytical throughput.

Correlation of Leukocyte Telomere Length Measurement Methods in Patients with Dyskeratosis Congenita and in Their Unaffected Relatives.

PubMed

Khincha, Payal P; Dagnall, Casey L; Hicks, Belynda; Jones, Kristine; Aviv, Abraham; Kimura, Masayuki; Katki, Hormuzd; Aubert, Geraldine; Giri, Neelam; Alter, Blanche P; Savage, Sharon A; Gadalla, Shahinaz M

2017-08-13

Several methods have been employed to measure telomere length (TL) in human studies. It has been difficult to directly compare the results from these studies because of differences in the laboratory techniques and output parameters. We compared TL measurements (TLMs) by the three most commonly used methods, quantitative polymerase chain reaction (qPCR), flow cytometry with fluorescence in situ hybridization (flow FISH) and Southern blot, in a cohort of patients with the telomere biology disorder dyskeratosis congenita (DC) and in their unaffected relatives (controls). We observed a strong correlation between the Southern blot average TL and the flow FISH total lymphocyte TL in both the DC patients and their unaffected relatives ( R ² of 0.68 and 0.73, respectively). The correlation between the qPCR average TL and that of the Southern blot method was modest ( R ² of 0.54 in DC patients and of 0.43 in unaffected relatives). Similar results were noted when comparing the qPCR average TL and the flow FISH total lymphocyte TL ( R ² of 0.49 in DC patients and of 0.42 in unaffected relatives). In conclusion, the strengths of the correlations between the three widely used TL assays (qPCR, flow FISH, and Southern blot) were significantly different. Careful consideration is warranted when selecting the method of TL measurement for research and for clinical studies.

Generation of human-to-pig chimerism to induce tolerance through transcutaneous in utero injection of cord blood-derived mononuclear cells or human bone marrow mesenchymals cells in a preclinical program of liver xenotransplantation: preliminary results.

PubMed

Abellaneda, J M; Ramis, G; Martínez-Alarcón, L; Majado, M J; Quereda, J J; Herrero-Medrano, J M; Mendonça, L; García-Nicolás, O; Reus, M; Insausti, C; Ríos, A; López-Navas, A; González, M R; Pallarés, F J; Munoz, A; Ramírez, P; Parrilla, P

2012-01-01

Using a percutaneous ecoguided injection system to obtain chimeric piglets through a less invasive and traumatic technique than previously reported. The two types of human cells included umbilical cord blood mononuclear elements and mesenchymal stem cells cultured from bone marrow. Four sows at gestational day 50 were anesthetized. A needle was inserted through the skin and uterine wall to reach the peritoneal cavity of the fetuses under continuous ultrasound guidance. Fourteen piglets were injected with various cell concentrations. All sows carried pregnancies to term yielding 69 piglets, among which 67 were alive and two mummified. Two piglets died during the first 48 hours of life. Chimerism was detected using flow cytometry and by quantitative polymerase chain reaction (q-PCR) to detect Alu gene in blood or tissues samples. The analysis detected blood chimerism in 13 piglets (21%) by flow cytometry and the presence of the human Alu gene in 33 (51%) by q-PCR. The results suggest cell trafficking between littermates after in utero injection. Transcutaneous echo-guided injection succeeded to produce chimeric piglets without disadvantages to the sow or the fetuses and avoiding abortions or fetal death. Copyright © 2012 Elsevier Inc. All rights reserved.

Evaluation of the C.Diff Quik Chek Complete Assay, a new glutamate dehydrogenase and A/B toxin combination lateral flow assay for use in rapid, simple diagnosis of clostridium difficile disease.

PubMed

Sharp, Susan E; Ruden, Lila O; Pohl, Julie C; Hatcher, Patricia A; Jayne, Linda M; Ivie, W Michael

2010-06-01

The diagnosis of Clostridium difficile infection continues to be a challenge for many clinical microbiology laboratories. A new lateral flow assay, the C.Diff Quik Chek Complete assay, which tests for the presence of both glutamate dehydrogenase (GDH) and C. difficile toxins A and B, was evaluated for its ability to diagnose C. difficile disease. The results of this assay were compared to those of both PCR and toxigenic culture. The results showed that this assay allows 88% of specimens to be accurately screened as either positive (both tests positive) or negative (both tests negative) for the presence of toxigenic C. difficile in less than 30 min and with minimal hands-on time. Use of a random-access PCR for the analysis of specimens with discrepant results (one test positive and the other negative) allows the easy, rapid, and highly sensitive (100%; 95% confidence interval [CI], 89.6 to 100%) and specific (99.6%; 95% CI, 97.3 to 99.9%) diagnosis of C. difficile disease. The use of this algorithm would save institutional costs, curtail unnecessary isolation days, reduce the nosocomial transmission of disease, and increase the quality of care for patients.

Evaluation of the C.Diff Quik Chek Complete Assay, a New Glutamate Dehydrogenase and A/B Toxin Combination Lateral Flow Assay for Use in Rapid, Simple Diagnosis of Clostridium difficile Disease▿

PubMed Central

Sharp, Susan E.; Ruden, Lila O.; Pohl, Julie C.; Hatcher, Patricia A.; Jayne, Linda M.; Ivie, W. Michael

2010-01-01

The diagnosis of Clostridium difficile infection continues to be a challenge for many clinical microbiology laboratories. A new lateral flow assay, the C.Diff Quik Chek Complete assay, which tests for the presence of both glutamate dehydrogenase (GDH) and C. difficile toxins A and B, was evaluated for its ability to diagnose C. difficile disease. The results of this assay were compared to those of both PCR and toxigenic culture. The results showed that this assay allows 88% of specimens to be accurately screened as either positive (both tests positive) or negative (both tests negative) for the presence of toxigenic C. difficile in less than 30 min and with minimal hands-on time. Use of a random-access PCR for the analysis of specimens with discrepant results (one test positive and the other negative) allows the easy, rapid, and highly sensitive (100%; 95% confidence interval [CI], 89.6 to 100%) and specific (99.6%; 95% CI, 97.3 to 99.9%) diagnosis of C. difficile disease. The use of this algorithm would save institutional costs, curtail unnecessary isolation days, reduce the nosocomial transmission of disease, and increase the quality of care for patients. PMID:20375230

Evaluation of detection methods for screening meat and poultry products for the presence of foodborne pathogens.

PubMed

Bohaychuk, Valerie M; Gensler, Gary E; King, Robin K; Wu, John T; McMullen, Lynn M

2005-12-01

Rapid and molecular technologies such as enzyme-linked immunosorbent assay (ELISA), PCR, and lateral flow immunoprecipitation can reduce the time and labor involved in screening food products for the presence of pathogens. These technologies were compared with conventional culture methodology for the detection of Salmonella, Campylobacter, Listeria, and Escherichia coli O157:H7 inoculated in raw and processed meat and poultry products. Recommended protocols were modified so that the same enrichment broths used in the culture methods were also used in the ELISA, PCR, and lateral flow immunoprecipitation assays. The percent agreement between the rapid technologies and culture methods ranged from 80 to 100% depending on the pathogen detected and the method used. ELISA, PCR, and lateral flow immunoprecipitation all performed well, with no statistical difference, compared with the culture method for the detection of E. coli O157:H7. ELISA performed better for the detection of Salmonella, with sensitivity and specificity rates of 100%. PCR performed better for the detection of Campylobacter jejuni, with 100% agreement to the culture method. PCR was highly sensitive for the detection of all the foodborne pathogens tested except Listeria monocytogenes. Although the lateral flow immunoprecipitation tests were statistically different from the culture methods for Salmonella and Listeria because of false-positive results, the tests did not produce any false negatives, indicating that this method would be suitable for screening meat and poultry products for these pathogens.

Flow cytometric detection of human immunodeficiency virus type 1 proviral DNA by the polymerase chain reaction incorporating digoxigenin- or fluorescein-labeled dUTP

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

Yang, Gang; Olson, J.C.; Pu, R.

1995-10-01

Serological assays are routinely used in the laboratory diagnosis of human immunodeficiency virus type-1 (HrV-1) infection, but the polymerase chain reaction (PCR) is ultimately the most sensitive and direct method for establishing definitive diagnosis. As an alternative to the conventional radioactive PCR procedure we have developed and evaluated a pair of rapid nonradioisotopic flow cytometric detection methods. Using heminested PCR we directly incorporated fluorescein-12-dUTP (fluo-dUTP) or digoxigenin-11-dUTP (dig-dUTP) into the PCR-amplicons. The labeled amplicons were hybridized with biotinylated antisense and sense probes, followed by capture of the hybrid DNA using streptavidin-coated beads which were finally analyzed in a flow cytometermore » by (1) direct detection of the fluorescence intensity of the amplicons incorporating fluo-dUTP and (2) immunodetection of the amplicons incorporating dig-dUTP by anti-digoxigenin IgG labeled with fluorescein isothiocyanate (FITC). Although both assays were functionally comparable with radiolabeled probe in reliably detecting as low as five copies of HIV-1 proviral DNA sequences, the immunodetection of dig-dUTP consistently yielded higher mean channel fluorescence and gave a stable signal over an extended period of 12-14 weeks. In testing a panel of 20 pedigreed PBMC specimens from blood donors with or without HIV-1 infection, the results of both flow cytometric assays were identical with those of the conventional radioactive procedure. Therefore, we conclude that the dig-dUTP incorporation in amplicons, hybridization with a pair of sense-antisense biotinylated probes and immunodetection of hybrids by flow cytometric analyses is the nonisotopic method of choice for PCR-diagnosis of HIV-1 infection. 21 refs., 2 figs., 4 tabs.« less

On-chip quantitative detection of pathogen genes by autonomous microfluidic PCR platform.

PubMed

Tachibana, Hiroaki; Saito, Masato; Shibuya, Shogo; Tsuji, Koji; Miyagawa, Nobuyuki; Yamanaka, Keiichiro; Tamiya, Eiichi

2015-12-15

Polymerase chain reaction (PCR)-based genetic testing has become a routine part of clinical diagnoses and food testing. In these fields, rapid, easy-to-use, and cost-efficient PCR chips are expected to be appeared for providing such testing on-site. In this study, a new autonomous disposable plastic microfluidic PCR chip was created, and was utilized for quantitative detection of pathogenic microorganisms. To control the capillary flow of the following solution in the PCR microchannel, a driving microchannel was newly designed behind the PCR microchannel. This allowed the effective PCR by simply dropping the PCR solution onto the inlet without any external pumps. In order to achieve disposability, injection-molded cyclo-olefin polymer (COP) of a cost-competitive plastic was used for the PCR chip. We discovered that coating the microchannel walls with non-ionic surfactant produced a suitable hydrophilic surface for driving the capillary flow through the 1250-mm long microchannel. As a result, quantitative real-time PCR with the lowest initial concentration of human, Escherichia coli (E. coli), and pathogenic E. coli O157 genomic DNA of 4, 0.0019, 0.031 pg/μl, respectively, was successfully achieved in less than 18 min. Our results indicate that the platform presented in this study provided a rapid, easy-to-use, and low-cost real-time PCR system that could be potentially used for on-site gene testing. Copyright © 2015 Elsevier B.V. All rights reserved.

Impact of Two Measures of Micrometastatic Disease on Clinical Outcomes in Patients with Newly Diagnosed Ewing Sarcoma: A Report from the Children’s Oncology Group

PubMed Central

Vo, Kieuhoa T.; Edwards, Jeremy V.; Epling, C. Lorrie; Sinclair, Elizabeth; Hawkins, Douglas S.; Grier, Holcombe E.; Janeway, Katherine A.; Barnette, Phillip; McIlvaine, Elizabeth; Krailo, Mark D.; Barkauskas, Donald A.; Matthay, Katherine K.; Womer, Richard B.; Gorlick, Richard G.; Lessnick, Stephen L.; Mackall, Crystal L.; DuBois, Steven G.

2016-01-01

Purpose Flow cytometry and RT-PCR can detect occult Ewing sarcoma (ES) cells in the blood and bone marrow (BM). These techniques were used to evaluate the prognostic significance of micrometastatic disease in ES. Experimental Design Newly diagnosed patients with ES were enrolled on two prospective multi-center studies. In the flow cytometry cohort, patients were defined as “positive” for BM micrometastatic disease if their CD99+/CD45− values were above the upper limit in 22 control patients. In the PCR cohort, RT-PCR on blood or BM samples classified the patients as “positive” or “negative” for EWSR1/FLI1 translocations. The association between micrometastatic disease burden with clinical features and outcome was assessed. Co-expression of IGF-1R on detected tumor cells was performed in a subset of flow cytometry samples. Results The median total BM CD99+CD45− percent was 0.0012% (range 0–1.10%) in the flow cytometry cohort, with 14/109 (12.8%) of ES patients defined as “positive.” In the PCR cohort, 19.6% (44/225) patients were “positive” for any EWSR1/FLI1 translocation in blood or BM. There were no differences in baseline clinical features or event-free or overall survival between patients classified as “positive” vs. “negative” by either method. CD99+CD45− cells had significantly higher IGF-1R expression compared to CD45+ hematopoietic cells (mean geometric mean fluorescence intensity 982.7 vs. 190.9; p<0.001). Conclusion The detection of micrometastatic disease at initial diagnosis by flow cytometry or RT-PCR is not associated with outcome in newly diagnosed patients with ES. Flow cytometry provides a tool to characterize occult micrometastatic tumor cells for proteins of interest. PMID:26861456

A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics

PubMed Central

Chan, Kamfai; Wong, Pui-Yan; Yu, Peter; Hardick, Justin; Wong, Kah-Yat; Wilson, Scott A.; Wu, Tiffany; Hui, Zoe; Gaydos, Charlotte; Wong, Season S.

2016-01-01

The ability to make rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a great step forward in global health. Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. Unfortunately, most commercial thermal cyclers are expensive and need continuous electrical power supply, so they are not suitable for uses in low-resource settings. We have previously reported a low-cost and simple approach to amplify DNA using vacuum insulated stainless steel thermoses food cans, which we have named it thermos thermal cycler or TTC. Here, we describe the use of an improved set up to enable the detection of viral RNA targets by reverse-transcription PCR (RT-PCR), thus expanding the TTC’s ability to identify highly infectious, RNA virus-based diseases in low resource settings. The TTC was successful in demonstrating high-speed and sensitive detection of DNA or RNA targets of sexually transmitted diseases, HIV/AIDS, Ebola hemorrhagic fever, and dengue fever. Our innovative TTC costs less than $200 to build and has a capacity of at least eight tubes. In terms of speed, the TTC’s performance exceeded that of commercial thermal cyclers tested. When coupled with low-cost endpoint detection technologies such as nucleic acid lateral-flow assay or a cell-phone-based fluorescence detector, the TTC will increase the availability of on-site molecular diagnostics in low-resource settings. PMID:26872358

Characterization of incubation experiments and development of an enrichment culture capable of ammonium oxidation under iron-reducing conditions

NASA Astrophysics Data System (ADS)

Huang, S.; Jaffé, P. R.

2015-02-01

Incubation experiments were conducted using soil samples from a forested riparian wetland where we have previously observed anaerobic ammonium oxidation coupled to iron reduction. Production of both nitrite and ferrous iron was measured repeatedly during incubations when the soil slurry was supplied with either ferrihydrite or goethite and ammonium chloride. Significant changes in the microbial community were observed after 180 days of incubation as well as in a continuous flow membrane reactor, using 16S rRNA gene PCR-denaturing gradient gel electrophoresis, 454 pyrosequencing, and real-time quantitative PCR analysis. We be Acidimicrobiaceae bacterium A6), belonging to the Acidimicrobiaceae family, whose closest cultivated relative is Ferrimicrobium acidiphilum (with 92% identity) and Acidimicrobium ferrooxidans (with 90% identity), might play a key role in this anaerobic biological process that uses ferric iron as an electron acceptor while oxidizing ammonium to nitrite. After ammonium was oxidized to nitrite, nitrogen loss proceeded via denitrification and/or anammox.

Use of taxon-specific competitive-priming PCR to study host specificity, hybridization, and intergroup gene flow in intersterility groups of Heterobasidion annosum

Treesearch

M. Garbelotto; A. Ratcliff; T.D. Bruns; F.W. Cobb; W.J. Otrosina

1996-01-01

Two intersterility groups (ISGs) of the forest pathogen Heterobasidion annosum are found in California: S and P.We devised a polymerase chain reaction (PCR) method called taxon- specific competitive-priming (TSCP) PCR to differentiate the two ISGs.Using TSCP-PCR, we typed 537 live isolates and dry basidiocarps from 204 trees and 114 stumps from 60 sites in eight...

Improved assay to detect Plasmodium falciparum using an uninterrupted, semi-nested PCR and quantitative lateral flow analysis

PubMed Central

2013-01-01

Background A rapid, non-invasive, and inexpensive point-of-care (POC) diagnostic for malaria followed by therapeutic intervention would improve the ability to control infection in endemic areas. Methods A semi-nested PCR amplification protocol is described for quantitative detection of Plasmodium falciparum and is compared to a traditional nested PCR. The approach uses primers that target the P. falciparum dihydrofolate reductase gene. Results This study demonstrates that it is possible to perform an uninterrupted, asymmetric, semi-nested PCR assay with reduced assay time to detect P. falciparum without compromising the sensitivity and specificity of the assay using saliva as a testing matrix. Conclusions The development of this PCR allows nucleic acid amplification without the need to transfer amplicon from the first PCR step to a second reaction tube with nested primers, thus reducing both the chance of contamination and the time for analysis to < two hours. Analysis of the PCR amplicon yield was adapted to lateral flow detection using the quantitative up-converting phosphor (UCP) reporter technology. This approach provides a basis for migration of the assay to a POC microfluidic format. In addition the assay was successfully evaluated with oral samples. Oral fluid collection provides a simple non-invasive method to collect clinical samples. PMID:23433252

A comparison of methods to assess the antimicrobial activity of nanoparticle combinations on bacterial cells.

PubMed

Bankier, Claire; Cheong, Yuen; Mahalingam, Suntharavathanan; Edirisinghe, Mohan; Ren, Guogang; Cloutman-Green, Elaine; Ciric, Lena

2018-01-01

Bacterial cell quantification after exposure to antimicrobial compounds varies widely throughout industry and healthcare. Numerous methods are employed to quantify these antimicrobial effects. With increasing demand for new preventative methods for disease control, we aimed to compare and assess common analytical methods used to determine antimicrobial effects of novel nanoparticle combinations on two different pathogens. Plate counts of total viable cells, flow cytometry (LIVE/DEAD BacLight viability assay) and qPCR (viability qPCR) were used to assess the antimicrobial activity of engineered nanoparticle combinations (NPCs) on Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa) bacteria at different concentrations (0.05, 0.10 and 0.25 w/v%). Results were analysed using linear models to assess the effectiveness of different treatments. Strong antimicrobial effects of the three NPCs (AMNP0-2) on both pathogens could be quantified using the plate count method and flow cytometry. The plate count method showed a high log reduction (>8-log) for bacteria exposed to high NPC concentrations. We found similar antimicrobial results using the flow cytometry live/dead assay. Viability qPCR analysis of antimicrobial activity could not be quantified due to interference of NPCs with qPCR amplification. Flow cytometry was determined to be the best method to measure antimicrobial activity of the novel NPCs due to high-throughput, rapid and quantifiable results.

A Point-of-Need infrared mediated PCR platform with compatible lateral flow strip for HPV detection.

PubMed

Liu, Wenjia; Zhang, Mingfang; Liu, Xiaoyan; Sharma, Alok; Ding, Xianting

2017-10-15

With the increasing need of monitoring the epidemiology of serious infectious diseases, food hygiene, food additives and pesticide residues, it is urgent to develop portable, easy-to-use, inexpensive and rapid molecular diagnostic tools. Herein, we demonstrate a prototype of IR mediated Conducting Oil and CarbOn Nanotube circUlaTing PCR (IR-COCONUT PCR) platform for nucleic acid amplification. The presented platform offers a new solution for miniaturized PCR instruments with non-contact heaters by using conducting oil and carbon nanotube as a medium in IR mediated PCR. This novel platform offers accurate and flexible control of temperature through the integration of PID (proportional-integral-derivative) algorithms to manipulate the duty cycle of the voltage signals of IR LED and a peristaltic pump. The ramping rate of the introduced platform in current study is 1.5°C/s for heating speed and -2.0°C/s for cooling speed. This platform fulfills 30 thermal cycles within 50min which is a match to the conventional bench-top PCR thermo cyclers. For demonstration purpose, human papillomavirus (HPV) patient cervical swab specimens were examined. Downstream lateral flow strip (LFS) was also developed to quantity the PCR products from the IR-COCONUT PCR device within 25min. This PCR platform together with the compatible LFS shows great potential for in-field and Point-of-Need (PoN) testing of genetic or contagious diseases. Copyright © 2017 Elsevier B.V. All rights reserved.

Miniaturized devices towards an integrated lab-on-a-chip platform for DNA diagnostics

NASA Astrophysics Data System (ADS)

Kaprou, G.; Papadakis, G.; Kokkoris, G.; Papadopoulos, V.; Kefala, I.; Papageorgiou, D.; Gizeli, E.; Tserepi, A.

2015-06-01

Microfluidics is an emerging technology enabling the development of Lab-on-a-chip (LOC) systems for clinical diagnostics, drug discovery and screening, food safety and environmental analysis. LOC systems integrate and scale down one or several laboratory functions on a single chip of a few mm2 to cm2 in size, and account for many advantages on biochemical analyses, such as low sample and reagent consumption, low cost, reduced analysis time, portability and point-of-need compatibility. Currently, available nucleic acid diagnostic tests take advantage of Polymerase Chain Reaction (PCR) that allows exponential amplification of portions of nucleic acid sequences that can be used as indicators for the identification of various diseases. Here, we present a comparison between static chamber and continuous flow miniaturized PCR devices, in terms of energy consumption for devices fabricated on the same material stack, with identical sample volume and channel dimensions. The comparison is implemented by a computational study coupling heat transfer in both solid and fluid, mass conservation of species, and joule heating. Based on the conclusions of this study, we develop low-cost and fast DNA amplification devices for both PCR and isothermal amplification, and we implement them in the detection of mutations related to breast cancer. The devices are fabricated by mass production amenable technologies on printed circuit board (PCB) substrates, where copper facilitates the incorporation of on-chip microheaters, defining the thermal zones necessary for PCR or isothermal amplification methods.

Promising Nucleic Acid Lateral Flow Assay Plus PCR for Shiga Toxin-Producing Escherichia coli.

PubMed

Terao, Yoshitaka; Takeshita, Kana; Nishiyama, Yasutaka; Morishita, Naoki; Matsumoto, Takashi; Morimatsu, Fumiki

2015-08-01

Shiga toxin (Stx)-producing Escherichia coli (STEC) is a frequent cause of foodborne infections, and methods for rapid and reliable detection of STEC are needed. A nucleic acid lateral flow assay (NALFA) plus PCR was evaluated for detecting STEC after enrichment. When cell suspensions of 45 STEC strains, 14 non-STEC strains, and 13 non-E. coli strains were tested with the NALFA plus PCR, all of the STEC strains yielded positive results, and all of the non-STEC and non-E. coli strains yielded negative results. The lower detection limit for the STEC strains ranged from 0.1 to 1 pg of genomic DNA (about 20 to 200 CFU) per test, and the NALFA plus PCR was able to detect Stx1- and Stx2-producing E. coli strains with similar sensitivities. The ability of the NALFA plus PCR to detect STEC in enrichment cultures of radish sprouts, tomato, raw ground beef, and beef liver inoculated with 10-fold serially diluted STEC cultures was comparable to that of a real-time PCR assay (at a level of 100 to 100,000 CFU/ml in enrichment culture). The bacterial inoculation test in raw ground beef revealed that the lower detection limit of the NALFA plus PCR was also comparable to that obtained with a real-time PCR assay that followed the U.S. Department of Agriculture guidelines. Although further evaluation is required, these results suggest that the NALFA plus PCR is a specific and sensitive method for detecting STEC in a food manufacturing plant.

A review on microscale polymerase chain reaction based methods in molecular diagnosis, and future prospects for the fabrication of fully integrated portable biomedical devices.

PubMed

Lee, Nae Yoon

2018-05-08

Since the advent of microfabrication technology and soft lithography, the lab-on-a-chip concept has emerged as a state-of-the-art miniaturized tool for conducting the multiple functions associated with micro total analyses of nucleic acids, in series, in a seamless manner with a miniscule volume of sample. The enhanced surface-to-volume ratio inside a microchannel enables fast reactions owing to increased heat dissipation, allowing rapid amplification. For this reason, PCR has been one of the first applications to be miniaturized in a portable format. However, the nature of the basic working principle for microscale PCR, such as the complicated temperature controls and use of a thermal cycler, has hindered its total integration with other components into a micro total analyses systems (μTAS). This review (with 179 references) surveys the diverse forms of PCR microdevices constructed on the basis of different working principles and evaluates their performances. The first two main sections cover the state-of-the-art in chamber-type PCR microdevices and in continuous-flow PCR microdevices. Methods are then discussed that lead to microdevices with upstream sample purification and downstream detection schemes, with a particular focus on rapid on-site detection of foodborne pathogens. Next, the potential for miniaturizing and automating heaters and pumps is examined. The review concludes with sections on aspects of complete functional integration in conjunction with nanomaterial based sensing, a discussion on future prospects, and with conclusions. Graphical abstract In recent years, thermocycler-based PCR systems have been miniaturized to palm-sized, disposable polymer platforms. In addition, operational accessories such as heaters and mechanical pumps have been simplified to realize semi-automatted stand-alone portable biomedical diagnostic microdevices that are directly applicable in the field. This review summarizes the progress made and the current state of this field.

Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities

PubMed Central

Bokulich, Nicholas A.

2013-01-01

Ultra-high-throughput sequencing (HTS) of fungal communities has been restricted by short read lengths and primer amplification bias, slowing the adoption of newer sequencing technologies to fungal community profiling. To address these issues, we evaluated the performance of several common internal transcribed spacer (ITS) primers and designed a novel primer set and work flow for simultaneous quantification and species-level interrogation of fungal consortia. Primer comparison and validation were predicted in silico and by sequencing a “mock community” of mixed yeast species to explore the challenges of amplicon length and amplification bias for reconstructing defined yeast community structures. The amplicon size and distribution of this primer set are smaller than for all preexisting ITS primer sets, maximizing sequencing coverage of hypervariable ITS domains by very-short-amplicon, high-throughput sequencing platforms. This feature also enables the optional integration of quantitative PCR (qPCR) directly into the HTS preparatory work flow by substituting qPCR with these primers for standard PCR, yielding quantification of individual community members. The complete work flow described here, utilizing any of the qualified primer sets evaluated, can rapidly profile mixed fungal communities and capably reconstructed well-characterized beer and wine fermentation fungal communities. PMID:23377949

Sizing up arthropod genomes: an evaluation of the impact of environmental variation on genome size estimates by flow cytometry and the use of qPCR as a method of estimation.

PubMed

Gregory, T Ryan; Nathwani, Paula; Bonnett, Tiffany R; Huber, Dezene P W

2013-09-01

A study was undertaken to evaluate both a pre-existing method and a newly proposed approach for the estimation of nuclear genome sizes in arthropods. First, concerns regarding the reliability of the well-established method of flow cytometry relating to impacts of rearing conditions on genome size estimates were examined. Contrary to previous reports, a more carefully controlled test found negligible environmental effects on genome size estimates in the fly Drosophila melanogaster. Second, a more recently touted method based on quantitative real-time PCR (qPCR) was examined in terms of ease of use, efficiency, and (most importantly) accuracy using four test species: the flies Drosophila melanogaster and Musca domestica and the beetles Tribolium castaneum and Dendroctonus ponderosa. The results of this analysis demonstrated that qPCR has the tendency to produce substantially different genome size estimates from other established techniques while also being far less efficient than existing methods.

A disposable, self-contained PCR chip.

PubMed

Kim, Jitae; Byun, Doyoung; Mauk, Michael G; Bau, Haim H

2009-02-21

A disposable, self-contained polymerase chain reaction (PCR) chip with on-board stored, just-on-time releasable, paraffin-passivated, dry reagents is described. During both storage and sample preparation, the paraffin immobilizes and protects the stored reagents. Fluid flow through the reactor leaves the reagents undisturbed. Prior to the amplification step, the chamber is filled with target analyte suspended in water. Upon heating the PCR chamber to the DNA's denaturation temperature, the paraffin melts and moves out of the way, and the reagents are released and hydrated. To better understand the reagent release process, a scaled up model of the reactor was constructed and the paraffin migration was visualized. Experiments were carried out with a 30 microl reactor demonstrating detectable amplification (with agarose gel electrophoresis) of 10 fg ( approximately 200 copies) of lambda DNA template. The in-reactor storage and on-time release of the PCR reagents reduce the number of needed operations and significantly simplifies the flow control that would, otherwise, be needed in lab-on-chip devices.

A Disposable, Self-Contained PCR Chip

PubMed Central

Kim, Jitae; Byun, Doyoung; Mauk, Michael G.; Bau, Haim H.

2009-01-01

A disposable, self-contained polymerase chain reaction (PCR) chip with on-board stored, just on time releasable, paraffin-passivated, dry reagents is described. During both storage and sample preparation, the paraffin immobilizes and protects the stored reagents. Fluid flow through the reactor leaves the reagents undisturbed. Prior to the amplification step, the chamber is filled with target analyte suspended in water. Upon heating the PCR chamber to the DNA’s denaturation temperature, the paraffin melts and moves out of the way, and the reagents are released and hydrated. To better understand the reagent release process, a scaled up model of the reactor was constructed and the paraffin migration was visualized. Experiments were carried out with a 30 μl reactor demonstrating detectable amplification (with agarose gel electrophoresis) of 10 fg (~200 copies) of lambda DNA template. The in-reactor storage and on-time release of the PCR reagents reduce the number of needed operations and significantly simplify the flow control that would, otherwise, be needed in lab-on-chip devices. PMID:19190797

Characterization of incubation experiments and development of an enrichment culture capable of ammonium oxidation under iron reducing conditions

NASA Astrophysics Data System (ADS)

Huang, S.; Jaffé, P. R.

2014-08-01

Incubation experiments were conducted using soil samples from a forested riparian wetland where we have previously observed anaerobic ammonium oxidation coupled to iron reduction. Production of both nitrite and ferrous iron were measured repeatedly during incubations when the soil slurry was supplied with either ferrihydrite or goethite and ammonium chloride. Significant changes in the microbial community were observed after 180 days of incubation as well as in a continuous flow membrane reactor, using 16S rRNA gene PCR-denaturing gradient gel electrophoresis, 454-pyrosequencing, and real-time quantitative PCR analysis. We believe that one of the dominant microbial species in our system (an uncultured Acidimicrobiaceae bacterium A6), belonging to the Acidimicrobiaceae family, whose closest cultivated relative is Ferrimicrobium acidiphilum (with 92% identity) and Acidimicrobium ferrooxidans (with 90% identity), might play a key role in this anaerobic biological process that uses ferric iron as an electron acceptor while oxidizing ammonium to nitrite. After ammonium was oxidized to nitrite, nitrogen loss proceeded via denitrification and/or anammox.

Rapid Identification and Quantification of Aureococcus anophagefferens by qPCR Method (Taqman) in the Qinhuangdao Coastal Area: A Region for Recurrent Brown Tide Breakout in China.

PubMed

Wang, Li-Ping; Lei, Kun

2016-12-01

Since 2009, Aureococcus anophagefferens has caused brown tide to occur recurrently in Qinhuangdao coastal area, China. Because the algal cells of A. anophagefferens are so tiny (~3 µm) that it is very hard to identify exactly under a microscope for natural water samples, it is very urgent to develop a method for efficient and continuous monitoring. Here specific primers and Taqman probe are designed to develop a real-time quantitative PCR (qPCR) method for identification and quantification continually. The algal community and cell abundance of A. anophagefferens in the study area (E 119°20'-119°50' and N 39°30'-39°50') from April to October in 2013 are detected by pyrosequencing, and are used to validate the specification and precision of qPCR method for natural samples. Both pyrosequencing and qPCR shows that the targeted cells are present only in May, June and July, and the cell abundance are July > June > May. Although there are various algal species including dinoflagellata, diatom, Cryptomonadales, Chrysophyceae and Chlorophyta living in the natural seawater simultaneously, no disturbance happens to qPCR method. This qPCR method could detect as few as 10 targeted cells, indicating it is able to detect the algal cells at pre-bloom levels. Therefore, qPCR with Taqman probe provides a powerful and sensitive method to monitor the brown tide continually in Qinhuangdao coastal area, China. The results provide a necessary technology support for forecasting the brown tide initiation, in China.

Correlation between unstimulated salivary flow, pH and streptococcus mutans, analysed with real time PCR, in caries-free and caries-active children.

PubMed

Abbate, G M; Borghi, D; Passi, A; Levrini, L

2014-03-01

Evaluate the correlations between unstimulated salivary flow, pH and level of S. mutans, analysed through real time PCR, in caries-free and caries-active children. Thirty healthy children were divided into 2 groups: test group (DMFT/dmft ≥ 3 and at least 1 active caries lesion) and control group (DMFT/dmft=0). Un-stimulated saliva was collected, pH was measured and S. mutans and total bacterial amount were evaluated with real-time PCR analysis. Unstimulated salivary flow in the test group was significantly lower (p = 0.0269) compared to group control. The level of S. mutans was higher in the test group (p = 0.176), and an inverse correlation was recorded between total bacterial amount and un-stimulated salivary flow (p = 0.063). In the control group a positive relationship was found between total bacterial amount and S. mutans (p = 0.045) and an inverse correlation between pH and S. mutans (p = 0.088). A t-test and a linear regression analysis were performed. A higher salivary flow and an increased salivary pH seem to represent protective factors against caries in children, while high levels of S. mutans are correlated with caries active lesions. Caries risk assessment should be performed considering all parameters involved in the development of the disease.

A vertically-stacked, polymer, microfluidic point mutation analyzer: Rapid, high accuracy detection of low-abundance K-ras mutations

PubMed Central

Han, Kyudong; Lee, Tae Yoon; Nikitopoulos, Dimitris E.; Soper, Steven A.; Murphy, Michael C.

2011-01-01

Recognition of point mutations in the K-ras gene can be used for the clinical management of several types of cancers. Unfortunately, several assay and hardware concerns must be addressed to allow users not well-trained in performing molecular analyses the opportunity to undertake these measurements. To provide for a larger user-base for these types of molecular assays, a vertically-stacked microfluidic analyzer with a modular architecture and process automation was developed. The analyzer employed a primary PCR coupled to an allele-specific ligase detection reaction (LDR). Each functional device, including continuous flow thermal reactors for the PCR and LDR, passive micromixers and ExoSAP-IT® purification, was designed and tested. Individual devices were fabricated in polycarbonate using hot embossing and assembled using adhesive bonding for system assembly. The system produced LDR products from a DNA sample in ~1 h, an 80% reduction in time compared to conventional bench-top instrumentation. Purifying the post-PCR products with the ExoSAP-IT® enzyme led to optimized LDR performance minimizing false positive signals and producing reliable results. Mutant alleles in genomic DNA were quantified to the level of 0.25 ng of mutant DNA in 50 ng of wild-type DNA for a 25 μL sample, equivalent to DNA from 42 mutant cells. PMID:21771577

DETECTION AND IDENTIFICATION OF PATHOGENIC CANDIDA SPECIES IN WATER USING FLOW CYTOMETRY COUPLED WITH TAQMAN PCR

EPA Science Inventory

As the incidence of human fungal infection increases, the ability to detect and identify pathogenic fungi in potential environmental reservoirs becomes increasingly important for disease control. PCR based assays are widely used for diagnostic purposes, but may be inadequate for...

Migration pattern of hepatitis A virus genotype IA in North-Central Tunisia.

PubMed

Beji-Hamza, Abir; Taffon, Stefania; Mhalla, Salma; Lo Presti, Alessandra; Equestre, Michele; Chionne, Paola; Madonna, Elisabetta; Cella, Eleonora; Bruni, Roberto; Ciccozzi, Massimo; Aouni, Mahjoub; Ciccaglione, Anna Rita

2015-02-08

Hepatitis A virus (HAV) epidemiology in Tunisia has changed from high to intermediate endemicity in the last decades. However, several outbreaks continue to occur. The last reported sequences from Tunisian HAV strains date back to 2006. In order to provide an updated overview of the strains currently circulating in Tunisia, a large-scale molecular analysis of samples from hepatitis A cases was performed, the first in Tunisia. Biological samples were collected from patients with laboratory confirmed hepatitis A: 145 sera samples in Tunis, Monastir, Sousse and Kairouan from 2008 to 2013 and 45 stool samples in Mahdia in 2009. HAV isolates were characterised by nested RT-PCR (VP1/2A region) and sequencing. The sequences finally obtained from 81 samples showed 78 genotype IA and 3 genotype IB isolates. A Tunisian genotype IA sequence dataset, including both the 78 newly obtained IA sequences and 51 sequences retrieved from GenBank, was used for phylogenetic investigation, including analysis of migration pattern among six towns. Virus gene flow from Sfax and Monastir was directed to all other towns; in contrast, the gene flows from Sousse, Tunis, Mahdia and Kairouan were directed to three, two, one and no towns, respectively. Several different HAV strains co-circulate in Tunisia, but the predominant genotype still continues to be IA (78/81, 96% isolates). A complex gene flow (migration) of HAV genotype IA was observed, with Sfax and Monastir showing gene flows to all other investigated towns. This approach coupled to a wider sampling can prove useful to investigate the factors underlying the spread of HAV in Tunisia and, thus, to implement appropriate preventing measures.

Usefullness of IGH/TCR PCR studies in lymphoproliferative disorders with inconclusive clonality by flow cytometry.

PubMed

Ribera, Jordi; Zamora, Lurdes; Juncà, Jordi; Rodríguez, Inés; Marcé, Silvia; Cabezón, Marta; Millá, Fuensanta

2013-07-25

In up to 5-15% of studies of lymphoproliferative disorders (LPD) flow cytometry (FCM) or immunomorphologic methods cannot discriminate malignant from reactive processes. The aim of this work was to determine the usefulness of PCR for solving these diagnostic uncertainties. We analyzed IGH and TCRγ genes by PCR in 106 samples with inconclusive FCM results. A clonal result was registered in 36/106 studies, with a LPD being confirmed in 27 (75%) of these cases. Specifically, 9/9 IGH clonal and 16/25 TCRγ clonal results were finally diagnosed with LPD. Additionally, 2 clonal TCRγ samples with suspicion of undefined LPD were finally diagnosed with T LPD. Although polyclonal results were obtained in 47 of the cases studied (38 IGH and 9 TCRγ), hematologic neoplasms were diagnosed in 4/38 IGH polyclonal and in 1/9 TCRγ polyclonal studies. There were also 14 PCR polyclonal results (4 IGH, 10 TCRγ), albeit non-conclusive. Of these, 2/4 were eventually diagnosed with B-cell lymphoma and 3/10 with T-cell LPD. In 8 IGH samples the results of PCR techniques were non-informative but in 3/8 cases a B lymphoma was finally confirmed. We concluded that PCR is a useful technique to identify LPD when FCM is inconclusive. A PCR clonal B result is indicative of malignancy but IGH polyclonal and non-conclusive results do not exclude lymphoid neoplasms. Interpretation of T-cell clonality should be based on all the available clinical and analytical data. © 2013 Clinical Cytometry Society. Copyright © 2013 Clinical Cytometry Society.

Recombinase polymerase amplification combined with a lateral flow dipstick for discriminating between infectious Penaeus stylirostris densovirus and virus-related sequences in shrimp genome.

PubMed

Jaroenram, Wansadaj; Owens, Leigh

2014-11-01

Penaeus stylirostris densovirus (PstDV) is an important shrimp pathogen that causes mortality in P. stylirostris and runt deformity syndrome (RDS) in Penaeus vannamei and Penaeus monodon. Recently, PstDV-related sequences were found in the genome of P. monodon and P. vannamei. This led to false positive results by PCR-based detection system. Here, a more efficient detection platform based on recombinase polymerase amplification (RPA) and a lateral flow dipstick (LFD) was developed for detecting PstDV. Under the optimal conditions, 30 min at 37°C for RPA followed by 5 min at room temperature for LFD, the protocol was 10 times more sensitive than the Saksmerphrome et al's interim 3-tube nested PCR and showed no cross-reaction with other shrimp viruses. It also reduced false positive results arising from viral inserts to ∼5% compared to 76-78% by the IQ2000™ nested PCR kit and the 309F/R PCR protocol currently recommended by World Organization for Animal Health (OIE) for PstDV detection. Together with simplicity and portability, the protocol serves as an alternative tool to PCR for primarily screening PstDV, which is suitable for both laboratory and field application. Copyright © 2014 Elsevier B.V. All rights reserved.

Intracellular flow cytometry may be combined with good quality and high sensitivity RT-qPCR analysis.

PubMed

Sandstedt, Mikael; Jonsson, Marianne; Asp, Julia; Dellgren, Göran; Lindahl, Anders; Jeppsson, Anders; Sandstedt, Joakim

2015-12-01

Flow cytometry (FCM) has become a well-established method for analysis of both intracellular and cell-surface proteins, while quantitative RT-PCR (RT-qPCR) is used to determine gene expression with high sensitivity and specificity. Combining these two methods would be of great value. The effects of intracellular staining on RNA integrity and RT-qPCR sensitivity and quality have not, however, been fully examined. We, therefore, intended to assess these effects further. Cells from the human lung cancer cell line A549 were fixed, permeabilized and sorted by FCM. Sorted cells were analyzed using RT-qPCR. RNA integrity was determined by RNA quality indicator analysis. A549 cells were then mixed with cells of the mouse cardiomyocyte cell line HL-1. A549 cells were identified by the cell surface marker ABCG2, while HL-1 cells were identified by intracellular cTnT. Cells were sorted and analyzed by RT-qPCR. Finally, cell cultures from human atrial biopsies were used to evaluate the effects of fixation and permeabilization on RT-qPCR analysis of nonimmortalized cells stored prior to analysis by FCM. A large amount of RNA could be extracted even when cells had been fixed and permeabilized. Permeabilization resulted in increased RNA degradation and a moderate decrease in RT-qPCR sensitivity. Gene expression levels were also affected to a moderate extent. Sorted populations from the mixed A549 and HL-1 cell samples showed gene expression patterns that corresponded to FCM data. When samples were stored before FCM sorting, the RT-qPCR analysis could still be performed with high sensitivity and quality. In summary, our results show that intracellular FCM may be performed with only minor impairment of the RT-qPCR sensitivity and quality when analyzing sorted cells; however, these effects should be considered when comparing RT-qPCR data of not fixed samples with those of fixed and permeabilized samples. © 2015 International Society for Advancement of Cytometry.

Does melatonin influence the apoptosis in rat uterus of animals exposed to continuous light?

PubMed

Ferreira, Cecília S; Carvalho, Kátia C; Maganhin, Carla C; Paiotti, Ana P R; Oshima, Celina T F; Simões, Manuel J; Baracat, Edmund C; Soares, José M

2016-02-01

Melatonin has been described as a protective agent against cell death and oxidative stress in different tissues, including in the reproductive system. However, the information on the action of this hormone in rat uterine apoptosis is low. Our objective was to evaluate the effects of melatonin on mechanisms of cell death in uterus of rats exposed to continuous light stress. Twenty adult Wistar rats were divided into two groups: GContr (vehicle control) and GExp which were treated with melatonin (0.4 mg/mL), both were exposed to continuous light for 90 days. The uterus was removed and processed for quantitative real time PCR (qRT-PCR), using PCR-array plates of the apoptosis pathway; for immunohistochemistry and TUNEL. The results of qRT-PCR of GEXP group showed up-regulation of 13 and 7, pro-apoptotic and anti-apoptotic genes, respectively, compared to GContr group. No difference in pro-apoptotic proteins (Bax, Fas and Faslg) expression was observed by immunohistochemistry, although the number of TUNEL-positive cells was lower in the group treated with melatonin compared to the group not treated with this hormone. Our data suggest that melatonin influences the mechanism and decreases the apoptosis in uterus of rats exposed to continuous light.

Evaluation of DNA extraction methods and their clinical application for direct detection of causative bacteria in continuous ambulatory peritoneal dialysis culture fluids from patients with peritonitis by using broad-range PCR.

PubMed

Kim, Si Hyun; Jeong, Haeng Soon; Kim, Yeong Hoon; Song, Sae Am; Lee, Ja Young; Oh, Seung Hwan; Kim, Hye Ran; Lee, Jeong Nyeo; Kho, Weon-Gyu; Shin, Jeong Hwan

2012-03-01

The aims of this study were to compare several DNA extraction methods and 16S rDNA primers and to evaluate the clinical utility of broad-range PCR in continuous ambulatory peritoneal dialysis (CAPD) culture fluids. Six type strains were used as model organisms in dilutions from 10(8) to 10(0) colony-forming units (CFU)/mL for the evaluation of 5 DNA extraction methods and 5 PCR primer pairs. Broad-range PCR was applied to 100 CAPD culture fluids, and the results were compared with conventional culture results. There were some differences between the various DNA extraction methods and primer sets with regard to the detection limits. The InstaGene Matrix (Bio-Rad Laboratories, USA) and Exgene Clinic SV kits (GeneAll Biotechnology Co. Ltd, Korea) seem to have higher sensitivities than the others. The results of broad-range PCR were concordant with the results from culture in 97% of all cases (97/100). Two culture-positive cases that were broad-range PCR-negative were identified as Candida albicans, and 1 PCR-positive but culture-negative sample was identified as Bacillus circulans by sequencing. Two samples among 54 broad-range PCR-positive products could not be sequenced. There were differences in the analytical sensitivity of various DNA extraction methods and primers for broad-range PCR. The broad-range PCR assay can be used to detect bacterial pathogens in CAPD culture fluid as a supplement to culture methods.

Localization of male-specifically expressed MROS genes of Silene latifolia by PCR on flow-sorted sex chromosomes and autosomes.

PubMed

Kejnovský, E; Vrána, J; Matsunaga, S; Soucek, P; Siroký, J; Dolezel, J; Vyskot, B

2001-07-01

The dioecious white campion Silene latifolia (syn. Melandrium album) has heteromorphic sex chromosomes, XX in females and XY in males, that are larger than the autosomes and enable their separation by flow sorting. The group of MROS genes, the first male-specifically expressed genes in dioecious plants, was recently identified in S. latifolia. To localize the MROS genes, we used the flow-sorted X chromosomes and autosomes as a template for PCR with internal primers. Our results indicate that the MROS3 gene is located in at least two copies tandemly arranged on the X chromosome with additional copy(ies) on the autosome(s), while MROS1, MROS2, and MROS4 are exclusively autosomal. The specificity of PCR products was checked by digestion with a restriction enzyme or reamplification using nested primers. Homology search of databases has shown the presence of five MROS3 homologues in A. thaliana, four of them arranged in two tandems, each consisting of two copies. We conclude that MROS3 is a low-copy gene family, connected with the proper pollen development, which is present not only in dioecious but also in other dicot plant species.

Analysis of PCR Thermocycling by Rayleigh-Bénard Convection

NASA Astrophysics Data System (ADS)

Sharma, Ruchi; Ugaz, Victor

2004-03-01

In previous studies, we demonstrated a novel device employing the circulatory flow field established by Rayleigh-Bénard convection to perform amplification of a 295 base target region from a human genomic DNA template inside a 35 uL cylindrical cavity using the polymerase chain reaction (PCR) [Krishnan, Ugaz & Burns, Science, Vol. 298, 2002, p. 793]. This design eliminates the need for dynamic external temperature control required in conventional thermocyclers that repeatedly heat and cool static sample volumes to denaturation, annealing, and extension temperatures. In this paper, we extend these studies by demonstrating the design and operation of a multiwell convective flow device capable of achieving amplification of a 191 base pair fragment associated with membrane channel proteins M1 and M2 of the influenza-A virus in as little as 15 minutes with performance comparable to a conventional thermocycler. We also study the effect of initial template concentration and observe no degradation in performance over four orders of magnitude of initial template loading dilution, consistent with conventional thermocycler results. These results illustrate the ability of convective flow PCR systems to achieve performance equal to or exceeding conventional thermocycling hardware, and demonstrate their suitability for use in rapid biodetection assays.

Flow Cytometric Immunobead Assay for Detection of BCR-ABL1 Fusion Proteins in Chronic Myleoid Leukemia: Comparison with FISH and PCR Techniques

PubMed Central

Recchia, Anna Grazia; Caruso, Nadia; Bossio, Sabrina; Pellicanò, Mariavaleria; De Stefano, Laura; Franzese, Stefania; Palummo, Angela; Abbadessa, Vincenzo; Lucia, Eugenio; Gentile, Massimo; Vigna, Ernesto; Caracciolo, Clementina; Agostino, Antolino; Galimberti, Sara; Levato, Luciano; Stagno, Fabio; Molica, Stefano; Martino, Bruno; Vigneri, Paolo; Di Raimondo, Francesco; Morabito, Fortunato

2015-01-01

Chronic Myeloid Leukemia (CML) is characterized by a balanced translocation juxtaposing the Abelson (ABL) and breakpoint cluster region (BCR) genes. The resulting BCR-ABL1 oncogene leads to increased proliferation and survival of leukemic cells. Successful treatment of CML has been accompanied by steady improvements in our capacity to accurately and sensitively monitor therapy response. Currently, measurement of BCR-ABL1 mRNA transcript levels by real-time quantitative PCR (RQ-PCR) defines critical response endpoints. An antibody-based technique for BCR-ABL1 protein recognition could be an attractive alternative to RQ-PCR. To date, there have been no studies evaluating whether flow-cytometry based assays could be of clinical utility in evaluating residual disease in CML patients. Here we describe a flow-cytometry assay that detects the presence of BCR-ABL1 fusion proteins in CML lysates to determine the applicability, reliability, and specificity of this method for both diagnosis and monitoring of CML patients for initial response to therapy. We show that: i) CML can be properly diagnosed at onset, (ii) follow-up assessments show detectable fusion protein (i.e. relative mean fluorescent intensity, rMFI%>1) when BCR-ABL1IS transcripts are between 1–10%, and (iii) rMFI% levels predict CCyR as defined by FISH analysis. Overall, the FCBA assay is a rapid technique, fully translatable to the routine management of CML patients. PMID:26111048

Development of a novel lateral flow assay for detection of African swine fever in blood.

PubMed

Sastre, P; Gallardo, C; Monedero, A; Ruiz, T; Arias, M; Sanz, A; Rueda, P

2016-09-15

African swine fever (ASF) is a viral infectious disease of domestic and wild suids of all breeds and ages, causing a wide range of hemorrhagic syndromes and frequently characterized by high mortality. The disease is endemic in Sub-Saharan Africa and Sardinia. Since 2007, it has also been present in different countries of Eastern Europe, where control measures have not been effective so far. The continued spread poses a serious threat to the swine industry worldwide. In the absence of vaccine, early detection of infected animals is of paramount importance for control of the outbreak, to prevent the transmission of the virus to healthy animals and subsequent spreading of the disease. Current laboratory diagnosis is mainly based on virological methods (antigen and genome detection) and serodiagnosis. In the present work, a Lateral Flow Assay (LFA) for antigen detection has been developed and evaluated. The test is based on the use of a MAb against VP72 protein of ASFV, the major viral capsid protein and highly immunogenic. First experiments using VP72 viral and recombinant protein or inactivated culture virus showed promising results with a sensitivity similar to that of a commercially available Antigen-ELISA. Moreover, these strips were tested with blood from experimentally infected pigs and field animals and the results compared with those of PCR and Antigen-ELISA. For the experimentally infected samples, there was an excellent correlation between the LFA and the ELISA, while the PCR always showed to be more sensitive (38 % positive samples by PCR versus 27 % by LFA). The LFA was demonstrated to be positive for animals with circulating virus levels exceeding 10(4) HAU. With the field samples, once again, the PCR detected more positives than either the Antigen-ELISA or LFA, although here the number of positive samples scored by the LFA exceeded the values obtained with the Antigen-ELISA, showing 60 % positivity vs 48 % for the ELISA. For the two groups of sera, the specificity was close to 100 % indicating that hardly any false positive samples were found. The newly developed LFA allows rapid and reliable detection of ASFV, at field and laboratory level, providing a new useful tool for control programs and in situations where laboratory support and skilled personnel are limited.

Cryptosporidium Source Tracking in the Potomac River Watershed

EPA Science Inventory

To better characterize the presence of Cryptosporidium in the Potomac River watershed, a PCR-based genotyping tool was used to analyze 64 base-flow and 28 storm-flow samples from five sites within the watershed. These sites included two water treatment plant intakes as well as t...

Cryptosporidium source tracking in the Potomac River watershed - MCEARD

EPA Science Inventory

To better characterize Cryptosporidium in the Potomac River watershed, a PCR-based genotyping tool was used to analyze 64 base-flow and 28 storm-flow samples from five sites within the watershed. These sites included two water treatment plant intakes as well as three upstream si...

Influence of PCR reagents on DNA polymerase extension rates measured on real-time PCR instruments.

PubMed

Montgomery, Jesse L; Wittwer, Carl T

2014-02-01

Radioactive DNA polymerase activity methods are cumbersome and do not provide initial extension rates. A simple extension rate assay would enable study of basic assumptions about PCR and define the limits of rapid PCR. A continuous assay that monitors DNA polymerase extension using noncovalent DNA dyes on common real-time PCR instruments was developed. Extension rates were measured in nucleotides per second per molecule of polymerase. To initiate the reaction, a nucleotide analog was heat activated at 95 °C for 5 min, the temperature decreased to 75 °C, and fluorescence monitored until substrate exhaustion in 30-90 min. The assay was linear with time for over 40% of the reaction and for polymerase concentrations over a 100-fold range (1-100 pmol/L). Extension rates decreased continuously with increasing monovalent cation concentrations (lithium, sodium, potassium, cesium, and ammonium). Melting-temperature depressors had variable effects. DMSO increased rates up to 33%, whereas glycerol had little effect. Betaine, formamide, and 1,2-propanediol decreased rates with increasing concentrations. Four common noncovalent DNA dyes inhibited polymerase extension. Heat-activated nucleotide analogs were 92% activated after 5 min, and hot start DNA polymerases were 73%-90% activated after 20 min. Simple DNA extension rate assays can be performed on real-time PCR instruments. Activity is decreased by monovalent cations, DNA dyes, and most melting temperature depressors. Rational inclusion of PCR components on the basis of their effects on polymerase extension is likely to be useful in PCR, particularly rapid-cycle or fast PCR.

Accurate Quantification of T Cells by Measuring Loss of Germline T-Cell Receptor Loci with Generic Single Duplex Droplet Digital PCR Assays.

PubMed

Zoutman, Willem H; Nell, Rogier J; Versluis, Mieke; van Steenderen, Debby; Lalai, Rajshri N; Out-Luiting, Jacoba J; de Lange, Mark J; Vermeer, Maarten H; Langerak, Anton W; van der Velden, Pieter A

2017-03-01

Quantifying T cells accurately in a variety of tissues of benign, inflammatory, or malignant origin can be of great importance in a variety of clinical applications. Flow cytometry and immunohistochemistry are considered to be gold-standard methods for T-cell quantification. However, these methods require fresh, frozen, or fixated cells and tissue of a certain quality. In addition, conventional and droplet digital PCR (ddPCR), whether followed by deep sequencing techniques, have been used to elucidate T-cell content by focusing on rearranged T-cell receptor (TCR) genes. These approaches typically target the whole TCR repertoire, thereby supplying additional information about TCR use. We alternatively developed and validated two novel generic single duplex ddPCR assays to quantify T cells accurately by measuring loss of specific germline TCR loci and compared them with flow cytometry-based quantification. These assays target sequences between the Dδ2 and Dδ3 genes (TRD locus) and Dβ1 and Jβ1.1 genes (TRB locus) that become deleted systematically early during lymphoid differentiation. Because these ddPCR assays require small amounts of DNA instead of freshly isolated, frozen, or fixated material, initially unanalyzable (scarce) specimens can be assayed from now on, supplying valuable information about T-cell content. Our ddPCR method provides a novel and sensitive way for quantifying T cells relatively fast, accurate, and independent of the cellular context. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Validation of a HLA-A2 tetramer flow cytometric method, IFNgamma real time RT-PCR, and IFNgamma ELISPOT for detection of immunologic response to gp100 and MelanA/MART-1 in melanoma patients

PubMed Central

Xu, Yuanxin; Theobald, Valerie; Sung, Crystal; DePalma, Kathleen; Atwater, Laura; Seiger, Keirsten; Perricone, Michael A; Richards, Susan M

2008-01-01

Background HLA-A2 tetramer flow cytometry, IFNγ real time RT-PCR and IFNγ ELISPOT assays are commonly used as surrogate immunological endpoints for cancer immunotherapy. While these are often used as research assays to assess patient's immunologic response, assay validation is necessary to ensure reliable and reproducible results and enable more accurate data interpretation. Here we describe a rigorous validation approach for each of these assays prior to their use for clinical sample analysis. Methods Standard operating procedures for each assay were established. HLA-A2 (A*0201) tetramer assay specific for gp100209(210M) and MART-126–35(27L), IFNγ real time RT-PCR and ELISPOT methods were validated using tumor infiltrating lymphocyte cell lines (TIL) isolated from HLA-A2 melanoma patients. TIL cells, specific for gp100 (TIL 1520) or MART-1 (TIL 1143 and TIL1235), were used alone or spiked into cryopreserved HLA-A2 PBMC from healthy subjects. TIL/PBMC were stimulated with peptides (gp100209, gp100pool, MART-127–35, or influenza-M1 and negative control peptide HIV) to further assess assay performance characteristics for real time RT-PCR and ELISPOT methods. Validation parameters included specificity, accuracy, precision, linearity of dilution, limit of detection (LOD) and limit of quantification (LOQ). In addition, distribution was established in normal HLA-A2 PBMC samples. Reference ranges for assay controls were established. Results The validation process demonstrated that the HLA-A2 tetramer, IFNγ real time RT-PCR, and IFNγ ELISPOT were highly specific for each antigen, with minimal cross-reactivity between gp100 and MelanA/MART-1. The assays were sensitive; detection could be achieved at as few as 1/4545–1/6667 cells by tetramer analysis, 1/50,000 cells by real time RT-PCR, and 1/10,000–1/20,000 by ELISPOT. The assays met criteria for precision with %CV < 20% (except ELISPOT using high PBMC numbers with %CV < 25%) although flow cytometric assays and cell based functional assays are known to have high assay variability. Most importantly, assays were demonstrated to be effective for their intended use. A positive IFNγ response (by RT-PCR and ELISPOT) to gp100 was demonstrated in PBMC from 3 melanoma patients. Another patient showed a positive MART-1 response measured by all 3 validated methods. Conclusion Our results demonstrated the tetramer flow cytometry assay, IFNγ real-time RT-PCR, and INFγ ELISPOT met validation criteria. Validation approaches provide a guide for others in the field to validate these and other similar assays for assessment of patient T cell response. These methods can be applied not only to cancer vaccines but to other therapeutic proteins as part of immunogenicity and safety analyses. PMID:18945350

Development of a PCR/LDR/flow-through hybridization assay using a capillary tube, probe DNA-immobilized magnetic beads and chemiluminescence detection.

PubMed

Hommatsu, Manami; Okahashi, Hisamitsu; Ohta, Keisuke; Tamai, Yusuke; Tsukagoshi, Kazuhiko; Hashimoto, Masahiko

2013-01-01

A polymerase chain reaction (PCR)/ligase detection reaction (LDR)/flow-through hybridization assay using chemiluminescence (CL) detection was developed for analyzing point mutations in gene fragments with high diagnostic value for colorectal cancers. A flow-through hybridization format using a capillary tube, in which probe DNA-immobilized magnetic beads were packed, provided accelerated hybridization kinetics of target DNA (i.e. LDR product) to the probe DNA. Simple fluid manipulations enabled both allele-specific hybridization and the removal of non-specifically bound DNA in the wash step. Furthermore, the use of CL detection greatly simplified the detection scheme, since CL does not require a light source for excitation of the fluorescent dye tags on the LDR products. Preliminary results demonstrated that this analytical system could detect both homozygous and heterozygous mutations, without the expensive instrumentation and cumbersome procedures required by conventional DNA microarray-based methods.

Parallelized CCHE2D flow model with CUDA Fortran on Graphics Process Units

USDA-ARS?s Scientific Manuscript database

This paper presents the CCHE2D implicit flow model parallelized using CUDA Fortran programming technique on Graphics Processing Units (GPUs). A parallelized implicit Alternating Direction Implicit (ADI) solver using Parallel Cyclic Reduction (PCR) algorithm on GPU is developed and tested. This solve...

Flow cytometric detection method for DNA samples

DOEpatents

Nasarabadi, Shanavaz [Livermore, CA; Langlois, Richard G [Livermore, CA; Venkateswaran, Kodumudi S [Round Rock, TX

2011-07-05

Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM.TM. on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA.TM., on the 5' end.

Flow cytometric detection method for DNA samples

DOEpatents

Nasarabadi, Shanavaz [Livermore, CA; Langlois, Richard G [Livermore, CA; Venkateswaran, Kodumudi S [Livermore, CA

2006-08-01

Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM, on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA, on the 5' end.

Rapid authentication of Cordyceps by lateral flow dipstick.

PubMed

Wong, Yuk-Lau; Wong, Ka-Lok; Shaw, Pang-Chui

2015-01-01

Cordyceps (Dongchongxiacao), a valuable traditional Chinese medicine, is composed of the fruiting body of Ophiocordyceps sinensis (Family: Ophiocordycipitaceae) on a caterpillar of ghost-moth species (Family: Hepialidae). Owing to its multiple potential functions, Cordyceps are in great demand and represent significant economic value. Adulterants or substitutes named Cordyceps or Chongcao from related fungi have been reported. In this study, polymerase chain reaction (PCR) coupled with a lateral flow dipstick (LFD) system was developed to distinguish genuine herb O. sinensis from its common adulterant Cordyceps gunnii and Cordyceps militaris. Specific primers (EF-CS-F1-Biotin, EF-CG-F1-Biotin and EF-CM-F1- Biotin) were designed to differentiate the three Cordyceps species. Internal control (EF-F1-b-DIG and EF-R1-FITC) was included to minimize the false signal due to PCR inhibitors or DNA degradation. LFD was then successfully employed for speedy and accurate detection of the respective PCR products. Copyright © 2015 Elsevier B.V. All rights reserved.

Effectiveness of evaluating tumor vascularization using 3D power Doppler ultrasound with high-definition flow technology in the prediction of the response to neoadjuvant chemotherapy for T2 breast cancer: a preliminary report

NASA Astrophysics Data System (ADS)

Shia, Wei-Chung; Chen, Dar-Ren; Huang, Yu-Len; Wu, Hwa-Koon; Kuo, Shou-Jen

2015-10-01

The aim of this study was to evaluate the effectiveness of advanced ultrasound (US) imaging of vascular flow and morphological features in the prediction of a pathologic complete response (pCR) and a partial response (PR) to neoadjuvant chemotherapy for T2 breast cancer. Twenty-nine consecutive patients with T2 breast cancer treated with six courses of anthracycline-based neoadjuvant chemotherapy were enrolled. Three-dimensional (3D) power Doppler US with high-definition flow (HDF) technology was used to investigate the blood flow in and morphological features of the tumors. Six vascularity quantization features, three morphological features, and two vascular direction features were selected and extracted from the US images. A support vector machine was used to evaluate the changes in vascularity after neoadjuvant chemotherapy, and pCR and PR were predicted on the basis of these changes. The most accurate prediction of pCR was achieved after the first chemotherapy cycle, with an accuracy of 93.1% and a specificity of 85.5%, while that of a PR was achieved after the second cycle, with an accuracy of 79.31% and a specificity of 72.22%. Vascularity data can be useful to predict the effects of neoadjuvant chemotherapy. Determination of changes in vascularity after neoadjuvant chemotherapy using 3D power Doppler US with HDF can generate accurate predictions of the patient response, facilitating early decision-making.

Kolmogorov-Smirnov statistical test for analysis of ZAP-70 expression in B-CLL, compared with quantitative PCR and IgV(H) mutation status.

PubMed

Van Bockstaele, Femke; Janssens, Ann; Piette, Anne; Callewaert, Filip; Pede, Valerie; Offner, Fritz; Verhasselt, Bruno; Philippé, Jan

2006-07-15

ZAP-70 has been proposed as a surrogate marker for immunoglobulin heavy-chain variable region (IgV(H)) mutation status, which is known as a prognostic marker in B-cell chronic lymphocytic leukemia (CLL). The flow cytometric analysis of ZAP-70 suffers from difficulties in standardization and interpretation. We applied the Kolmogorov-Smirnov (KS) statistical test to make analysis more straightforward. We examined ZAP-70 expression by flow cytometry in 53 patients with CLL. Analysis was performed as initially described by Crespo et al. (New England J Med 2003; 348:1764-1775) and alternatively by application of the KS statistical test comparing T cells with B cells. Receiver-operating-characteristics (ROC)-curve analyses were performed to determine the optimal cut-off values for ZAP-70 measured by the two approaches. ZAP-70 protein expression was compared with ZAP-70 mRNA expression measured by a quantitative PCR (qPCR) and with the IgV(H) mutation status. Both flow cytometric analyses correlated well with the molecular technique and proved to be of equal value in predicting the IgV(H) mutation status. Applying the KS test is reproducible, simple, straightforward, and overcomes a number of difficulties encountered in the Crespo-method. The KS statistical test is an essential part of the software delivered with modern routine analytical flow cytometers and is well suited for analysis of ZAP-70 expression in CLL. (c) 2006 International Society for Analytical Cytology.

Development of a recombinase polymerase amplification combined with lateral-flow dipstick assay for detection of bovine ephemeral fever virus.

PubMed

Hou, Peili; Zhao, Guimin; Wang, Hongmei; He, Chengqiang; Huan, Yanjun; He, Hongbin

2018-04-01

Bovine ephemeral fever virus (BEFV), identified as the causative pathogen of bovine ephemeral fever (BEF), is responsible for increasing numbers of epidemics/outbreaks and has a significant harmful effect on the livestock industry. Therefore, a rapid detection assay is imperative for BEFV diagnosis. In this study, we described the development of lateral-flow dipstick isothermal recombinase polymerase amplification (LFD-RPA) assays for detection of BEFV. RPA primers and LF probes were designed by targeting the specific G gene, and the amplification product can be visualized on a simple lateral flow dipstick with the naked eyes. The amplification reaction was performed at 38 °C for 20 min and LFD incubation time within 5 min. The detection limit of this assay was 8 copies per reaction, and there was no cross-reactivity with other bovine infectious viruses such as bovine viral diarrhea virus, infectious bovine rhinotracheitis virus, bovine respiratory syncytial virus, bovine coronavirus, bovine parainfluenza virus type 3, bovine vesicular stomatitis virus. In addition, the assay was performed with total 128 clinical specimens and the diagnostic results were compared with conventional RT-PCR, real-time quantative(q) PCR. The result showed that the coincidence rate of BEFV LFD-RPA and real-time qPCR was 96.09% (123/128), which was higher than conventional RT-PCR. The RPA combined with LFD assay probably provides a rapid and sensitive alternative for diagnosis of BEFV infections outbreak. Copyright © 2018 Elsevier Ltd. All rights reserved.

Early Detection of NSCLC Using Stromal Markers in Peripheral Blood

DTIC Science & Technology

2016-09-01

circulating myeloid cells, flow cytometry, RNA -sequencing, expression profiling. 3. ACCOMPLISHMENTS:  What were the major goals of the project...Subtask 2: Flow cytometry sorting of circulating myeloid cells. Subtask 3: RNA -Sequencing Subtask 4: RNA -seq data analysis Subtask 5: Feasible RT-PCR...accomplished the patient recruitment, flow cytometry sorting of circulating myeloid cells, RNA -sequencing of the samples. During the RNA - seq data analysis, we

Using Flow Characteristics in Three-Dimensional Power Doppler Ultrasound Imaging to Predict Complete Responses in Patients Undergoing Neoadjuvant Chemotherapy.

PubMed

Shia, Wei-Chung; Huang, Yu-Len; Wu, Hwa-Koon; Chen, Dar-Ren

2017-05-01

Strategies are needed for the identification of a poor response to treatment and determination of appropriate chemotherapy strategies for patients in the early stages of neoadjuvant chemotherapy for breast cancer. We hypothesize that power Doppler ultrasound imaging can provide useful information on predicting response to neoadjuvant chemotherapy. The solid directional flow of vessels in breast tumors was used as a marker of pathologic complete responses (pCR) in patients undergoing neoadjuvant chemotherapy. Thirty-one breast cancer patients who received neoadjuvant chemotherapy and had tumors of 2 to 5 cm were recruited. Three-dimensional power Doppler ultrasound with high-definition flow imaging technology was used to acquire the indices of tumor blood flow/volume, and the chemotherapy response prediction was established, followed by support vector machine classification. The accuracy of pCR prediction before the first chemotherapy treatment was 83.87% (area under the ROC curve [AUC] = 0.6957). After the second chemotherapy treatment, the accuracy of was 87.9% (AUC = 0.756). Trend analysis showed that good and poor responders exhibited different trends in vascular flow during chemotherapy. This preliminary study demonstrates the feasibility of using the vascular flow in breast tumors to predict chemotherapeutic efficacy. © 2017 by the American Institute of Ultrasound in Medicine.

Blood grouping based on PCR methods and agarose gel electrophoresis.

PubMed

Sell, Ana Maria; Visentainer, Jeane Eliete Laguila

2015-01-01

The study of erythrocyte antigens continues to be an intense field of research, particularly after the development of molecular testing methods. More than 300 specificities have been described by the International Society for Blood Transfusion as belonging to 33 blood group systems. The polymerase chain reaction (PCR) is a central tool for red blood cells (RBC) genotyping. PCR and agarose gel electrophoresis are low cost, easy, and versatile in vitro methods for amplifying defined target DNA (RBC polymorphic region). Multiplex-PCR, AS-PCR (Specific Allele Polymerase Chain Reaction), and RFLP-PCR (Restriction Fragment Length Polymorphism-Polymerase Chain Reaction) techniques are usually to identify RBC polymorphisms. Furthermore, it is an easy methodology to implement. This chapter describes the PCR methodology and agarose gel electrophoresis to identify the polymorphisms of the Kell, Duffy, Kidd, and MNS blood group systems.

Development of a monoclonal antibody-based flow-through immunoassay (FTA) for detection of white spot syndrome virus (WSSV) in black tiger shrimp Penaeus monodon.

PubMed

Patil, R; Shankar, K M; Kumar, B T N; Kulkarni, A; Patil, P; Moger, N

2013-09-01

A flow-through immunoassay (FTA), an improved version of immunodot, was developed using a nitrocellulose membrane baked onto adsorbent pads enclosed in a plastic cassette to detect white spot syndrome virus (WSSV) in shrimp. Sharp purple dots developed with WSSV against the white background of the nitrocellulose membrane. The detection limits of WSSV by the FTA and immunodot were 0.312 and 1.2 μg mL(-1) crude WSSV protein, respectively. The FTA could be completed in 8-10 min compared with 90 min for immunodot. The FTA was 100 times more sensitive than 1-step polymerase chain reaction (PCR) and in between that of the 1- and 2-step PCR protocol recommended by the Office of International Epizootics (OIE). In experimental, orally infected shrimp post-larvae, WSSV was first detected 14, 16 and 18 h post-infection (hpi) by FTA, immunodot and one-step PCR, respectively. The FTA detected WSSV 2 and 4 h earlier than immunodot and one-step PCR, respectively. The FTA was more sensitive (25/27) than one-step PCR (23/27) and immunodot (23/27) for the detection of WSSV from white spot disease outbreak ponds. The reagent components of the FTA were stable giving expected results for 6 m at 4-8 °C. The FTA is available as a rapid test kit called 'RapiDot' for the early detection of WSSV under field conditions. © 2013 John Wiley & Sons Ltd.

Recombinase Polymerase Amplification Compared to Real-Time Polymerase Chain Reaction Test for the Detection of Fasciola hepatica in Human Stool

PubMed Central

Cabada, Miguel M.; Malaga, Jose L.; Castellanos-Gonzalez, Alejandro; Bagwell, Kelli A.; Naeger, Patrick A.; Rogers, Hayley K.; Maharsi, Safa; Mbaka, Maryann; White, A. Clinton

2017-01-01

Fasciola hepatica is the most widely distributed trematode infection in the world. Control efforts may be hindered by the lack of diagnostic capacity especially in remote endemic areas. Polymerase chain reaction (PCR)–based methods offer high sensitivity and specificity but require expensive technology. However, the recombinase polymerase amplification (RPA) is an efficient isothermal method that eliminates the need for a thermal cycler and has a high deployment potential to resource-limited settings. We report on the characterization of RPA and PCR tests to detect Fasciola infection in clinical stool samples with low egg burdens. The sensitivity of the RPA and PCR were 87% and 66%, respectively. Both tests were 100% specific showing no cross-reactivity with trematode, cestode, or nematode parasites. In addition, RPA and PCR were able to detect 47% and 26% of infections not detected by microscopy, respectively. The RPA adapted to a lateral flow platform was more sensitive than gel-based detection of the reaction products. In conclusion, the Fasciola RPA is a highly sensitive and specific test to diagnose chronic infection using stool samples. The Fasciola RPA lateral flow has the potential for deployment to endemic areas after further characterization. PMID:27821691

Inhibition of Breast Cancer-Induced Angiogenesis by a Diverged Homeobox Gene

DTIC Science & Technology

2006-05-01

and then harvested for flow cytometry using appropriate antibodies. Ad.Gax blocked the expression of VCAM-1, E-selectin, and ICAM-1. DOD Idea Award...solution. Bands were visualized by chemiluminescence using the ECL-Plus reagent (Amersham, Piscataway, NJ). Flow Cytometry Cells were harvested after...33), all of whose down-regulation we have confirmed using real time quantitative RT-PCR, Western blot, and flow cytometry (Fig. 5). Moreover, Gax

Marine Viral Pathogens.

DTIC Science & Technology

1998-05-13

coccolithophorid Emiliania huxleyi. Experiments are continuing to determine whether the pathogens are viral. We have continued the development of PCR primers... Emiliania huxleyi; further work will be required to determine if the pathogen is viral. We have also continued methodological work to improve our ability

Single-pair fluorescence resonance energy transfer analysis of mRNA transcripts for highly sensitive gene expression profiling in near real time.

PubMed

Peng, Zhiyong; Young, Brandon; Baird, Alison E; Soper, Steven A

2013-08-20

Expression analysis of mRNAs transcribed from certain genes can be used as important sources of biomarkers for in vitro diagnostics. While the use of reverse transcription quantitative PCR (RT-qPCR) can provide excellent analytical sensitivity for monitoring transcript numbers, more sensitive approaches for expression analysis that can report results in near real-time are needed for many critical applications. We report a novel assay that can provide exquisite limits-of-quantitation and consists of reverse transcription (RT) followed by a ligase detection reaction (LDR) with single-pair fluorescence resonance energy transfer (spFRET) to provide digital readout through molecular counting. For this assay, no PCR was employed, which enabled short assay turnaround times. To facilitate implementation of the assay, a cyclic olefin copolymer (COC) microchip, which was fabricated using hot embossing, was employed to carry out the LDR in a continuous flow format with online single-molecule detection following the LDR. As demonstrators of the assay's utility, MMP-7 mRNA was expression profiled from several colorectal cancer cell lines. It was found that the RT-LDR/spFRET assay produced highly linear calibration plots even in the low copy number regime. Comparison to RT-qPCR indicated a better linearity over the low copy number range investigated (10-10,000 copies) with an R(2) = 0.9995 for RT-LDR/spFRET and R(2) = 0.98 for RT-qPCR. In addition, differentiating between copy numbers of 10 and 50 could be performed with higher confidence using RT-LDR/spFRET. To demonstrate the short assay turnaround times obtainable using the RT-LDR/spFRET assay, a two thermal cycle LDR was carried out on amphiphysin gene transcripts that can serve as important diagnostic markers for ischemic stroke. The ability to supply diagnostic information on possible stroke events in short turnaround times using RT-LDR/spFRET will enable clinicians to treat patients effectively with appropriate time-sensitive therapeutics.

Single-Pair Fret Analysis of mRNA Transcripts for Highly Sensitive Gene Expression Profiling in Near Real Time

PubMed Central

Peng, Zhiyong; Young, Brandon; Baird, Alison E.; Soper, Steven A.

2013-01-01

Expression analysis of mRNAs transcribed from certain genes can be used as important sources of biomarkers for in vitro diagnostics. While the use of reverse transcription quantitative PCR (RT-qPCR) can provide excellent analytical sensitivity for monitoring transcript numbers, more sensitive approaches for expression analysis that can report results in near real-time are needed for many critical applications. We report a novel assay that can provide exquisite limits-of-quantitation and consists of reverse transcription (RT) followed by a ligase detection reaction (LDR) with single-pair fluorescence resonance energy transfer (spFRET) to provide digital readout through molecular counting. For this assay, no PCR was employed, which enabled short assay turnaround times. To facilitate implementation of the assay, a cyclic olefin copolymer (COC) microchip, which was fabricated using hot embossing, was employed to carry out the LDR in a continuous flow format with on-line single-molecule detection following the LDR. As demonstrators of the assay's utility, MMP-7 mRNA was expression profiled from several colorectal cancer cell lines. It was found that the RT-LDR/spFRET assay produced highly linear calibration plots even in the low copy number regime. Comparison to RT-qPCR indicated a better linearity over the low copy number range investigated (10 − 10,000 copies) with an R2 = 0.9995 for RT-LDR/spFRET and R2 = 0.98 for RT-qPCR. In addition, differentiating between copy numbers of 10 and 50 could be performed with higher confidence using RT-LDR/spFRET. To demonstrate the short assay turnaround times obtainable using the RT-LDR/spFRET assay, a 2 thermal cycle LDR was carried out on amphiphysin gene transcripts that can serve as important diagnostic markers for ischemic stroke. The ability to supply diagnostic information on possible stroke events in short turnaround times using RT-LDR/spFRET will enable clinicians to treat patients effectively with appropriate time-sensitive therapeutics. PMID:23869556

Tumor Metabolism and Blood Flow as Assessed by PET Varies by Tumor Subtype in Locally Advanced Breast Cancer

PubMed Central

Specht, Jennifer M.; Kurland, Brenda F.; Montgomery, Susan K.; Dunnwald, Lisa K.; Doot, Robert K.; Gralow, Julie R.; Ellis, Georgina K.; Linden, Hannah M.; Livingston, Robert B.; Allison, Kimberly H.; Schubert, Erin K.; Mankoff, David A.

2010-01-01

Purpose Dynamic PET imaging can identify patterns of breast cancer metabolism and perfusion in patients receiving neoadjuvant chemotherapy (NC) that are predictive of response. This analysis examines tumor metabolism and perfusion by tumor subtype. Experimental Design Tumor subtype was defined by immunohistochemistry (IHC) in 71 patients with LABC undergoing NC. Subtype was defined as luminal (ER/PR positive), triple-negative (TN; ER/PR negative, HER2 negative) and HER2 (ER/PR negative, HER2 over-expressing). Metabolic rate (MRFDG) and blood flow (BF) were calculated from PET imaging prior to NC. Pathologic complete response (pCR) to NC was classified as pCR versus other. Results Twenty-five (35%) of 71 patients had TN tumors, 6 (8%) were HER2 and 40 (56%) were luminal. MRFDG for TN tumors was on average 67% greater than for luminal tumors (95% CI 9% – 156%), and average MRFDG/BF ratio was 53% greater in TN compared to luminal tumors (95% CI 9% – 114%) (p < 0.05 for both). Average blood flow levels did not differ by subtype (p = 0.73). Most luminal tumors showed relatively low MRFDG and BF (and did not achieve pCR); high MRFDG was generally matched with high BF in luminal tumors, and predicted pCR. This was not true in TN tumors. Conclusions The relationship between breast tumor metabolism and perfusion differed by subtype. The high MRFDG/BF ratio that predicts poor response to NC was more common in TN tumors. Metabolism and perfusion measures may identify subsets of tumors susceptible and resistant to NC and may help direct targeted therapy. PMID:20460489

Lab-on-a-chip nucleic-acid analysis towards point-of-care applications

NASA Astrophysics Data System (ADS)

Kopparthy, Varun Lingaiah

Recent infectious disease outbreaks, such as Ebola in 2013, highlight the need for fast and accurate diagnostic tools to combat the global spread of the disease. Detection and identification of the disease-causing viruses and bacteria at the genetic level is required for accurate diagnosis of the disease. Nucleic acid analysis systems have shown promise in identifying diseases such as HIV, anthrax, and Ebola in the past. Conventional nucleic acid analysis systems are still time consuming, and are not suitable for point-ofcare applications. Miniaturized nucleic acid systems has shown great promise for rapid analysis, but they have not been commercialized due to several factors such as footprint, complexity, portability, and power consumption. This dissertation presents the development of technologies and methods for a labon-a-chip nucleic acid analysis towards point-of-care applications. An oscillatory-flow PCR methodology in a thermal gradient is developed which provides real-time analysis of nucleic-acid samples. Oscillating flow PCR was performed in the microfluidic device under thermal gradient in 40 minutes. Reverse transcription PCR (RT-PCR) was achieved in the system without an additional heating element for incubation to perform reverse transcription step. A novel method is developed for the simultaneous pattering and bonding of all-glass microfluidic devices in a microwave oven. Glass microfluidic devices were fabricated in less than 4 minutes. Towards an integrated system for the detection of amplified products, a thermal sensing method is studied for the optimization of the sensor output. Calorimetric sensing method is characterized to identify design considerations and optimal parameters such as placement of the sensor, steady state response, and flow velocity for improved performance. An understanding of these developed technologies and methods will facilitate the development of lab-on-a-chip systems for point-of-care analysis.

Application of real-time PCR (qPCR) for characterization of microbial populations and type of milk in dairy food products.

PubMed

Agrimonti, Caterina; Bottari, Benedetta; Sardaro, Maria Luisa Savo; Marmiroli, Nelson

2017-09-08

Dairy foods represent an important sector of the food market for their nutritional qualities and their organoleptic characteristics, which are often linked to tradition and to region. These products are typically protected by labels such as PDO (Protected Designation of Origin) and PGI (Protected Geographical Indication). Real-time PCR (qPCR) is a fundamental tool in "Food Genomics;" a discipline concerned with the residual DNA in food, which, alongside traditional physical and chemical methods, is frequently used to determine product safety, quality and authenticity. Compared to conventional or "end-point" PCR, qPCR incorporates continuous monitoring of reaction progress, thereby enabling quantification of target DNA. This review describes qPCR applications to the analysis of microbiota, and to the identification of the animal species source of milk from which dairy products have been made. These are important aspects for ensuring safety and authenticity. The various applications of qPCR are discussed, as well as advantages and disadvantages in comparison with other analytical methods.

Biological behaviour of human umbilical artery smooth muscle cell grown on nickel-free and nickel-containing stainless steel for stent implantation

PubMed Central

Li, Liming; An, Liwen; Zhou, Xiaohang; Pan, Shuang; Meng, Xin; Ren, Yibin; Yang, Ke; Guan, Yifu

2016-01-01

To evaluate the clinical potential of high nitrogen nickel-free austenitic stainless steel (HNNF SS), we have compared the cellular and molecular responses of human umbilical artery smooth muscle cells (HUASMCs) to HNNF SS and 316L SS (nickel-containing austenitic 316L stainless steel). CCK-8 analysis and flow cytometric analysis were used to assess the cellular responses (proliferation, apoptosis, and cell cycle), and quantitative real-time PCR (qRT-PCR) was used to analyze the gene expression profiles of HUASMCs exposed to HNNF SS and 316L SS, respectively. CCK-8 analysis demonstrated that HUASMCs cultured on HNNF SS proliferated more slowly than those on 316L SS. Flow cytometric analysis revealed that HNNF SS could activate more cellular apoptosis. The qRT-PCR results showed that the genes regulating cell apoptosis and autophagy were up-regulated on HNNF SS. Thus, HNNF SS could reduce the HUASMC proliferation in comparison to 316L SS. The findings furnish valuable information for developing new biomedical materials for stent implantation. PMID:26727026

Ease fabrication of PCR modular chip for portable DNA detection kit

NASA Astrophysics Data System (ADS)

Whulanza, Yudan; Aditya, Rifky; Arvialido, Reyhan; Utomo, Muhammad S.; Bachtiar, Boy M.

2017-02-01

Engineering a lab-on-a-chip (LoC) to perform the DNA polymerase chain reaction (PCR) for malaria detection is the ultimate goal of this study. This paper investigates the ability to fabricate an LoC kit using conventional method to achieve the lowest production cost by using existing fabrication process. It has been known that majority of LoC was made of polydimethylsiloxane (PDMS) which in this study was realized through a contact mold process. CNC milling process was utilized to create channel features in the range of 150-250 µm on the mold. Characterization on the milling process was done to understand the shrinkage/contraction between mold to product, roughness and also angle of contact of PDMS surface. Ultimately, this paper also includes analysis on flow measurement and heat distribution of an assembled LoC PCR kit. The results show that the achieved dimension of microchannel is 227 µm wide with a roughness of 0.01 µm. The flow measurement indicates a deviation with simulation in the range of 10%. A heat distribution through the kit is achieved following the three temperature zones as desired.

Detection of Neisseria meningitidis in cerebrospinal fluid using a multiplex PCR and the Luminex detection technology.

PubMed

Møller, Jens Kjølseth

2012-01-01

Rapid clinical and laboratory diagnoses are the foundation for a successful management of serious infections with Neisseria meningitidis. A species-specific multiplex polymerase chain reaction (PCR) coupled with fluidic microarrays using microbeads (the Luminex xMAP™ Technology) can detect pathogens most frequently found in the cerebrospinal fluid of patients. The Luminex suspension array system uniquely combines flow cytometry, microspheres, laser technology, digital signal processing, and traditional chemistry. In this method, the reaction is carried out in one vessel, in which distinctly color-coded bead sets, each conjugated with a different specific nucleic acid reactant, are hybridized with the PCR products, and a reporter molecule is used to quantify the interaction. The flow-based Luminex array reader identifies each reaction (bead set) after excitation by a red classification laser. Reporter signals from each reaction are simultaneously quantified by fluorescence generated by a green reporter laser. This nonculture, multiplex assay may prove to be an important tool for optimal laboratory diagnosis, not only of meningococcal meningitis, but also of meningitis caused by other bacterial or viral pathogens.

Biological behaviour of human umbilical artery smooth muscle cell grown on nickel-free and nickel-containing stainless steel for stent implantation

NASA Astrophysics Data System (ADS)

Li, Liming; An, Liwen; Zhou, Xiaohang; Pan, Shuang; Meng, Xin; Ren, Yibin; Yang, Ke; Guan, Yifu

2016-01-01

To evaluate the clinical potential of high nitrogen nickel-free austenitic stainless steel (HNNF SS), we have compared the cellular and molecular responses of human umbilical artery smooth muscle cells (HUASMCs) to HNNF SS and 316L SS (nickel-containing austenitic 316L stainless steel). CCK-8 analysis and flow cytometric analysis were used to assess the cellular responses (proliferation, apoptosis, and cell cycle), and quantitative real-time PCR (qRT-PCR) was used to analyze the gene expression profiles of HUASMCs exposed to HNNF SS and 316L SS, respectively. CCK-8 analysis demonstrated that HUASMCs cultured on HNNF SS proliferated more slowly than those on 316L SS. Flow cytometric analysis revealed that HNNF SS could activate more cellular apoptosis. The qRT-PCR results showed that the genes regulating cell apoptosis and autophagy were up-regulated on HNNF SS. Thus, HNNF SS could reduce the HUASMC proliferation in comparison to 316L SS. The findings furnish valuable information for developing new biomedical materials for stent implantation.

Bayes to the Rescue: Continuous Positive Airway Pressure Has Less Mortality Than High-Flow Oxygen.

PubMed

Modesto I Alapont, Vicent; Khemani, Robinder G; Medina, Alberto; Del Villar Guerra, Pablo; Molina Cambra, Alfred

2017-02-01

The merits of high-flow nasal cannula oxygen versus bubble continuous positive airway pressure are debated in children with pneumonia, with suggestions that randomized controlled trials are needed. In light of a previous randomized controlled trial showing a trend for lower mortality with bubble continuous positive airway pressure, we sought to determine the probability that a new randomized controlled trial would find high-flow nasal cannula oxygen superior to bubble continuous positive airway pressure through a "robust" Bayesian analysis. Sample data were extracted from the trial by Chisti et al, and requisite to "robust" Bayesian analysis, we specified three prior distributions to represent clinically meaningful assumptions. These priors (reference, pessimistic, and optimistic) were used to generate three scenarios to represent the range of possible hypotheses. 1) "Reference": we believe bubble continuous positive airway pressure and high-flow nasal cannula oxygen are equally effective with the same uninformative reference priors; 2) "Sceptic on high-flow nasal cannula oxygen": we believe that bubble continuous positive airway pressure is better than high-flow nasal cannula oxygen (bubble continuous positive airway pressure has an optimistic prior and high-flow nasal cannula oxygen has a pessimistic prior); and 3) "Enthusiastic on high-flow nasal cannula oxygen": we believe that high-flow nasal cannula oxygen is better than bubble continuous positive airway pressure (high-flow nasal cannula oxygen has an optimistic prior and bubble continuous positive airway pressure has a pessimistic prior). Finally, posterior empiric Bayesian distributions were obtained through 100,000 Markov Chain Monte Carlo simulations. In all three scenarios, there was a high probability for more death from high-flow nasal cannula oxygen compared with bubble continuous positive airway pressure (reference, 0.98; sceptic on high-flow nasal cannula oxygen, 0.982; enthusiastic on high-flow nasal cannula oxygen, 0.742). The posterior 95% credible interval on the difference in mortality identified a future randomized controlled trial would be extremely unlikely to find a mortality benefit for high-flow nasal cannula oxygen over bubble continuous positive airway pressure, regardless of the scenario. Interpreting these findings using the "range of practical equivalence" framework would recommend rejecting the hypothesis that high-flow nasal cannula oxygen is superior to bubble continuous positive airway pressure for these children. For children younger than 5 years with pneumonia, high-flow nasal cannula oxygen has higher mortality than bubble continuous positive airway pressure. A future randomized controlled trial in this population is unlikely to find high-flow nasal cannula oxygen superior to bubble continuous positive airway pressure.

Simple Repeat-Primed PCR Analysis of the Myotonic Dystrophy Type 1 Gene in a Clinical Diagnostics Environment

PubMed Central

Dryland, Philippa A.; Doherty, Elaine; Love, Jennifer M.; Love, Donald R.

2013-01-01

Myotonic dystrophy type 1 is an autosomal dominant neuromuscular disorder that is caused by the expansion of a CTG trinucleotide repeat in the DMPK gene. The confirmation of a clinical diagnosis of DM-1 usually involves PCR amplification of the CTG repeat-containing region and subsequent sizing of the amplification products in order to deduce the number of CTG repeats. In the case of repeat hyperexpansions, Southern blotting is also used; however, the latter has largely been superseded by triplet repeat-primed PCR (TP-PCR), which does not yield a CTG repeat number but nevertheless provides a means of stratifying patients regarding their disease severity. We report here a combination of forward and reverse TP-PCR primers that allows for the simple and effective scoring of both the size of smaller alleles and the presence or absence of expanded repeat sequences. In addition, the CTG repeat-containing TP-PCR forward primer can target both the DM-1 and Huntington disease genes, thereby streamlining the work flow for confirmation of clinical diagnoses in a diagnostic laboratory. PMID:26317000

Neoadjuvant chemotherapy in breast cancer: prediction of pathologic response with PET/CT and dynamic contrast-enhanced MR imaging--prospective assessment.

PubMed

Tateishi, Ukihide; Miyake, Mototaka; Nagaoka, Tomoaki; Terauchi, Takashi; Kubota, Kazunori; Kinoshita, Takayuki; Daisaki, Hiromitsu; Macapinlac, Homer A

2012-04-01

To clarify whether fluorine 18 ((18)F) fluorodeoxyglucose (FDG) positron emission tomography (PET)/computed tomography (CT) and dynamic contrast-enhanced (DCE) magnetic resonance (MR) imaging performed after two cycles of neoadjuvant chemotherapy (NAC) can be used to predict pathologic response in breast cancer. Institutional human research committee approval and written informed consent were obtained. Accuracy after two cycles of NAC for predicting pathologic complete response (pCR) was examined in 142 women (mean age, 57 years: range, 43-72 years) with histologically proved breast cancer between December 2005 and February 2009. Quantitative PET/CT and DCE MR imaging were performed at baseline and after two cycles of NAC. Parameters of PET/CT and of blood flow and microvascular permeability at DCE MR were compared with pathologic response. Patients were also evaluated after NAC by using Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 based on DCE MR measurements and European Organization for Research and Treatment of Cancer (EORTC) criteria and PET Response Criteria in Solid Tumors (PERCIST) 1.0 based on PET/CT measurements. Multiple logistic regression analyses were performed to examine continuous variables at PET/CT and DCE MR to predict pCR, and diagnostic accuracies were compared with the McNemar test. Significant decrease from baseline of all parameters at PET/CT and DCE MR was observed after NAC. Therapeutic response was obtained in 24 patients (17%) with pCR and 118 (83%) without pCR. Sensitivity, specificity, and accuracy to predict pCR were 45.5%, 85.5%, and 82.4%, respectively, with RECIST and 70.4%, 95.7%, and 90.8%, respectively, with EORTC and PERCIST. Multiple logistic regression revealed three significant independent predictors of pCR: percentage maximum standardized uptake value (%SUV(max)) (odds ratio [OR], 1.22; 95% confidence interval [CI]: 1.11, 1.34; P < .0001), percentage rate constant (%k(ep)) (OR, 1.07; CI: 1.03, 1.12; P = .002), and percentage area under the time-intensity curve over 90 seconds (%AUC(90)) (OR, 1.04; CI: 1.01, 1.07; P = .048). When diagnostic accuracies are compared, PET/CT is superior to DCE MR for the prediction of pCR (%SUV(max) [90.1%] vs %κ(ep) [83.8%] or %AUC(90) [76.8%]; P < .05). The sensitivities of %SUV(max) (66.7%), %k(ep) (51.7%), and %AUC(90) (50.0%) at (18)F-FDG PET/CT and DCE MR after two cycles of NAC are not acceptable, but the specificities (96.4%, 92.0%, and 95.2%, respectively) are high for stratification of pCR cases in breast cancer. © RSNA, 2012.

Use of flow cytometry, fluorescence microscopy, and PCR-based techniques to assess intraspecific and interspecific matings of Armillaria species

Treesearch

Mee-Sook Kim; Ned B. Klopfenstein; Geral I. McDonald; Kathiravetpillai Arumuganathan

2001-01-01

For assessments of intraspecific mating using flow cytometry and fluorescence microscopy, two compatible basidiospore-derived isolates were selected from each of four parental basidiomata of North American Biological Species (NABS) X. The nuclear status in NABS X varied with basidiospore-derived isolates. Nuclei within basidiospore-derived isolates existed as haploids...

Introducing Undergraduate Students to Real-Time PCR

ERIC Educational Resources Information Center

Hancock, Dale; Funnell, Alister; Jack, Briony; Johnston, Jill

2010-01-01

An experiment is conducted, which in four 3 h laboratory sessions, introduces third year undergraduate Biochemistry students to the technique of real-time PCR in a biological context. The model used is a murine erythroleukemia cell line (MEL cells). These continuously cycling, immature red blood cells, arrested at an early stage in erythropoiesis,…

A Rapid and Low-Cost PCR Thermal Cycler for Low Resource Settings.

PubMed

Wong, Grace; Wong, Isaac; Chan, Kamfai; Hsieh, Yicheng; Wong, Season

2015-01-01

Many modern molecular diagnostic assays targeting nucleic acids are typically confined to developed countries or to the national reference laboratories of developing-world countries. The ability to make technologies for the rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a revolutionary step forward in global health. Many molecular assays are also developed based on polymerase chain reactions (PCR), which require thermal cyclers that are relatively heavy (>20 pounds) and need continuous electrical power. The temperature ramping speed of most economical thermal cyclers are relatively slow (2 to 3 °C/s) so a polymerase chain reaction can take 1 to 2 hours. Most of all, these thermal cyclers are still too expensive ($2k to $4k) for low-resource setting uses. In this article, we demonstrate the development of a low-cost and rapid water bath based thermal cycler that does not require active temperature control or continuous power supply during PCR. This unit costs $130 to build using commercial off-the-shelf items. The use of two or three vacuum-insulated stainless-steel Thermos food jars containing heated water (for denaturation and annealing/extension steps) and a layer of oil on top of the water allow for significantly stabilized temperatures for PCR to take place. Using an Arduino-based microcontroller, we automate the "archaic" method of hand-transferring PCR tubes between water baths. We demonstrate that this innovative unit can deliver high speed PCR (17 s per PCR cycle) with the potential to go beyond the 1,522 bp long amplicons tested in this study and can amplify from templates down to at least 20 copies per reaction. The unit also accepts regular PCR tubes and glass capillary tubes. The PCR efficiency of our thermal cycler is not different from other commercial thermal cyclers. When combined with a rapid nucleic acid detection approach, the thermos thermal cycler (TTC) can enable on-site molecular diagnostics in low-resource settings.

Diagnostic evaluation of a multiplexed RT-PCR microsphere array assay for the detection of foot-and-mouth disease virus and look-alike disease viruses

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

Hindson, B J; Reid, S M; Baker, B R

2007-07-26

A high-throughput multiplexed assay was developed for the differential laboratory diagnosis of foot-and-mouth disease virus (FMDV) from viruses which cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses using multiplexed reverse transcription PCR (mRT-PCR) amplification coupled with a microsphere hybridization array and flow-cytometric detection. Two of the seventeen primer-probe sets included in this multiplex assay were adopted from previously characterized real-time RT-PCR (rRT-PCR) assays for FMDV. The diagnostic accuracy of the mRT-PCR was evaluated using 287 field samples, including 248 (true positive n= 213, true negative n=34) from suspect cases of foot-and-mouthmore » disease collected from 65 countries between 1965 and 2006 and 39 true negative samples collected from healthy animals. The mRT-PCR assay results were compared with two singleplex rRT-PCR assays, using virus isolation with antigen-ELISA as the reference method. The diagnostic sensitivity of the mRT-PCR assay for FMDV was 93.9% [95% C.I. 89.8-96.4%], compared to 98.1% [95% C.I. 95.3-99.3%] for the two singleplex rRT-PCR assays used in combination. In addition, the assay could reliably differentiate between FMDV and other vesicular viruses such as swine vesicular disease virus and vesicular exanthema of swine virus. Interestingly, the mRT-PCR detected parapoxvirus (n=2) and bovine viral diarrhea virus (n=2) in clinical samples, demonstrating the screening potential of this mRT-PCR assay to identify viruses in FMDV-negative material not previously recognized using focused single-target rRT-PCR assays.« less

Low-flow characteristics of Indiana streams

USGS Publications Warehouse

Fowler, K.K.; Wilson, J.T.

1996-01-01

Knowledge of low-flow characteristics of streams is essential for management of water resources. Low-flow characteristics are presented for 229 continuous-record, streamflow-gaging stations and 285 partial-record stations in Indiana. Low- flow-frequency characteristics were computed for 210 continuous-record stations that had at least 10 years of record, and flow-duration curves were computed for all continuous-record stations. Low-flow-frequency and flow-duration analyses are based on available streamflow records through September 1993. Selected low-flow-frequency curves were computed for annual low flows and seasonal low flows. The four seasons are represented by the 3-month groups of March-May, June-August, September-November, and December- February. The 7-day, 10-year and the 7-day, 2 year low flows were estimated for 285 partial-record stations, which are ungaged sites where streamflow measurements were made at base flow. The same low-flow characteristics were estimated for 19 continuous-record stations where less than 10 years of record were available. Precipitation and geology directly influence the streams in Indiana. Streams in the northern, glaciated part of the State tend to have higher sustained base flows than those in the nonglaciated southern part. Flow at several of the continuous-record gaging stations is affected by some form of regulation or diversion. Low-flow characteristics for continuous-record stations at which flow is affected by regulation are determined using the period of record affected by regulation; natural flows prior to regulation are not used.

Long-Term Effects of Residual Chlorine on Pseudomonas aeruginosa in Simulated Drinking Water Fed With Low AOC Medium

PubMed Central

Mao, Guannan; Song, Yuhao; Bartlam, Mark; Wang, Yingying

2018-01-01

Residual chlorine is often required to remain present in public drinking water supplies during distribution to ensure water quality. It is essential to understand how bacteria respond to long-term chlorine exposure, especially with the presence of assimilable organic carbon (AOC). This study aimed to investigate the effects of chlorination on Pseudomonas aeruginosa in low AOC medium by both conventional plating and culture-independent methods including flow cytometry (FCM) and quantitative PCR (qPCR). In a simulated chlorinated system using a bioreactor, membrane damage and DNA damage were measured by FCM fluorescence fingerprint. The results indicated membrane permeability occurred prior to DNA damage in response to chlorination. A regrowth of P. aeruginosa was observed when the free chlorine concentration was below 0.3 mg/L. The bacterial response to long-term exposure to a constant low level of free chlorine (0.3 mg/L) was subsequently studied in detail. Both FCM and qPCR data showed a substantial reduction during initial exposure (0–16 h), followed by a plateau where the cell concentration remained stable (16–76 h), until finally all bacteria were inactivated with subsequent continuous chlorine exposure (76–124 h). The results showed three-stage inactivation kinetics for P. aeruginosa at a low chlorine level with extended exposure time: an initial fast inactivation stage, a relatively stable middle stage, and a final stage with a slower rate than the initial stage. A series of antibiotic resistance tests suggested long-term exposure to low chlorine level led to the selection of antibiotic-resistant P. aeruginosa. The combined results suggest that depletion of residual chlorine in low AOC medium systems could reactivate P. aeruginosa, leading to a possible threat to drinking water safety. PMID:29774019

Acetyl group availability influences phosphocreatine degradation even during intense muscle contraction

PubMed Central

Timmons, James A; Constantin-Teodosiu, Dumitru; Poucher, Simon M; Greenhaff, Paul L

2004-01-01

We previously established that activation of the pyruvate dehydrogenase complex (PDC) using dichloroacetate (DCA) reduced the reliance on substrate-level phosphorylation (SLP) at the onset of exercise, with normal and reduced blood flow. PDC activation also reduced fatigue development during contraction with reduced blood flow. Since these observations, several studies have re-evaluated our observations. One study demonstrated a performance benefit without a reduction in SLP, raising a question mark over PDC's role in the regulation of ATP regeneration and our interpretation of fatigue mechanisms. Using a model of muscle contraction similar to the conflicting study (i.e. tetanic rather than twitch stimulation), we re-examined this question. Using canine skeletal muscle, one group was infused with saline while the other was pretreated with 300 mg (kg body mass)−1 DCA. Muscle biopsies were taken at rest, peak tension (1 min) and after 6 min of tetanic electrical stimulation (75 ms on−925 ms off per second) and blood flow was limited to 25% of normal values observed during contraction. DCA reduced phosphocreatine (PCr) degradation by 40% during the first minute of contraction, but did not prevent the almost complete depletion of PCr stores at 6 min, while muscle fatigue did not differ between the two groups. During intermittent tetanic stimulation PCr degradation was 75% greater than with our previous 3 Hz twitch contraction protocol, despite a similar rate of oxygen consumption at 6 min. Thus, in the present study enhanced acetyl group availability altered the time course of PCr utilization but did not prevent the decline towards depletion. Consistent with our earlier conclusions, DCA pretreatment reduces muscle fatigue only when SLP is attenuated. The present study and our met-analysis indicates that enhanced acetyl group availability results in a readily measurable reduction in SLP when the initial rate of PCr utilization is ∼1 mmol (kg dry mass)−1 s−1 or less (depending on intrinsic mitochondrial capacity). When measured early during an uninterrupted period of muscle contraction, acetyl group availability is likely to influence SLP under any condition where mitochondria are responsible for a significant proportion of ATP regeneration. PMID:15498812

Macro and micro diversity of Clostridium difficile isolates from diverse sources and geographical locations.

PubMed

Stabler, Richard A; Dawson, Lisa F; Valiente, Esmeralda; Cairns, Michelle D; Martin, Melissa J; Donahue, Elizabeth H; Riley, Thomas V; Songer, J Glenn; Kuijper, Ed J; Dingle, Kate E; Wren, Brendan W

2012-01-01

Clostridium difficile has emerged rapidly as the leading cause of antibiotic-associated diarrheal disease, with the temporal and geographical appearance of dominant PCR ribotypes such as 017, 027 and 078. Despite this continued threat, we have a poor understanding of how or why particular variants emerge and the sources of strains that dominate different human populations. We have undertaken a breadth genotyping study using multilocus sequence typing (MLST) analysis of 385 C. difficile strains from diverse sources by host (human, animal and food), geographical locations (North America, Europe and Australia) and PCR ribotypes. Results identified 18 novel sequence types (STs) and 3 new allele sequences and confirmed the presence of five distinct clonal lineages generally associated with outbreaks of C. difficile infection in humans. Strains of animal and food origin were found of both ST-1 and ST-11 that are frequently associated with human disease. An in depth MLST analysis of the evolutionary distant ST-11/PCR ribotype 078 clonal lineage revealed that ST-11 can be found in alternative but closely related PCR ribotypes and PCR ribotype 078 alleles contain mutations generating novel STs. PCR ribotype 027 and 017 lineages may consist of two divergent subclades. Furthermore evidence of microdiversity was present within the heterogeneous clade 1. This study helps to define the evolutionary origin of dominant C. difficile lineages and demonstrates that C. difficile is continuing to evolve in concert with human activity.

Ultrafast, sensitive and large-volume on-chip real-time PCR for the molecular diagnosis of bacterial and viral infections.

PubMed

Houssin, Timothée; Cramer, Jérémy; Grojsman, Rébecca; Bellahsene, Lyes; Colas, Guillaume; Moulet, Hélène; Minnella, Walter; Pannetier, Christophe; Leberre, Maël; Plecis, Adrien; Chen, Yong

2016-04-21

To control future infectious disease outbreaks, like the 2014 Ebola epidemic, it is necessary to develop ultrafast molecular assays enabling rapid and sensitive diagnoses. To that end, several ultrafast real-time PCR systems have been previously developed, but they present issues that hinder their wide adoption, notably regarding their sensitivity and detection volume. An ultrafast, sensitive and large-volume real-time PCR system based on microfluidic thermalization is presented herein. The method is based on the circulation of pre-heated liquids in a microfluidic chip that thermalize the PCR chamber by diffusion and ultrafast flow switches. The system can achieve up to 30 real-time PCR cycles in around 2 minutes, which makes it the fastest PCR thermalization system for regular sample volume to the best of our knowledge. After biochemical optimization, anthrax and Ebola simulating agents could be respectively detected by a real-time PCR in 7 minutes and a reverse transcription real-time PCR in 7.5 minutes. These detections are respectively 6.4 and 7.2 times faster than with an off-the-shelf apparatus, while conserving real-time PCR sample volume, efficiency, selectivity and sensitivity. The high-speed thermalization also enabled us to perform sharp melting curve analyses in only 20 s and to discriminate amplicons of different lengths by rapid real-time PCR. This real-time PCR microfluidic thermalization system is cost-effective, versatile and can be then further developed for point-of-care, multiplexed, ultrafast and highly sensitive molecular diagnoses of bacterial and viral diseases.

The assembly and use of continuous flow systems for chemical synthesis.

PubMed

Britton, Joshua; Jamison, Timothy F

2017-11-01

The adoption of and opportunities in continuous flow synthesis ('flow chemistry') have increased significantly over the past several years. Continuous flow systems provide improved reaction safety and accelerated reaction kinetics, and have synthesised several active pharmaceutical ingredients in automated reconfigurable systems. Although continuous flow platforms are commercially available, systems constructed 'in-lab' provide researchers with a flexible, versatile, and cost-effective alternative. Herein, we describe the assembly and use of a modular continuous flow apparatus from readily available and affordable parts in as little as 30 min. Once assembled, the synthesis of a sulfonamide by reacting 4-chlorobenzenesulfonyl chloride with dibenzylamine in a single reactor coil with an in-line quench is presented. This example reaction offers the opportunity to learn several important skills including reactor construction, charging of a back-pressure regulator, assembly of stainless-steel syringes, assembly of a continuous flow system with multiple junctions, and yield determination. From our extensive experience of single-step and multistep continuous flow synthesis, we also describe solutions to commonly encountered technical problems such as precipitation of solids ('clogging') and reactor failure. Following this protocol, a nonspecialist can assemble a continuous flow system from reactor coils, syringes, pumps, in-line liquid-liquid separators, drying columns, back-pressure regulators, static mixers, and packed-bed reactors.

Evaluation of Cytokine Synthesis in Human Whole Blood by Enzyme Linked Immunoassay (ELISA), Reverse Transcriptase Polymerase Chain Reaction (RT-PCR), and Flow Cytometry

DTIC Science & Technology

2007-05-08

deoxynucleotide triphosphates, from Sigma. Sequences for glyceraldehyde-3-phosphate dehydrogenase ( G3PDH ), IL-8,and TNF-a were amplified with primer...This was accomplished by normalizing all samples to the mRNA for the moderately expressed housekeeping function glyceraldehyde-3 -phosphate...without and with isolation of cells before reverse transcription and PCR. G3PDH mRNA target amplifies at 983 base pairs. The 630 base pair band is the

Diagnostic evaluation of a multiplexed RT-PCR microsphere array assay for the detection of foot-and-mouth and look-alike disease viruses

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

Hindson, B J; Baker, B R; Bentley Tammero, L F

2007-09-18

A high-throughput multiplexed assay (Multiplex Version 1.0) was developed for the differential laboratory diagnosis of foot-and-mouth disease virus (FMDV) from viruses which cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses using multiplexed reverse transcription PCR (mRT-PCR) amplification coupled with a microsphere hybridization array and flow-cytometric detection. Two of the seventeen primer-probe sets included in this multiplex assay were adopted from previously characterized real-time RT-PCR (rRT-PCR) assays for FMDV. The diagnostic accuracy of the mRT-PCR was evaluated using 287 field samples, including 248 (true positive n= 213, true negative n=34) from suspectmore » cases of foot-and-mouth disease collected from 65 countries between 1965 and 2006 and 39 true negative samples collected from healthy animals. The mRT-PCR assay results were compared with two singleplex rRT-PCR assays, using virus isolation with antigen-ELISA as the reference method. The diagnostic sensitivity of the mRT-PCR assay for FMDV was 93.9% [95% C.I. 89.8-96.4%], compared to 98.1% [95% C.I. 95.3-99.3%] for the two singleplex rRTPCR assays used in combination. In addition, the assay could reliably differentiate between FMDV and other vesicular viruses such as swine vesicular disease virus and vesicular exanthema of swine virus. Interestingly, the mRT-PCR detected parapoxvirus (n=2) and bovine viral diarrhea virus (n=2) in clinical samples, demonstrating the screening potential of this mRT-PCR assay to identify viruses in FMDV-negative material not previously recognized using focused single-target rRT-PCR assays.« less

Comparison of Associations of Urine Protein-Creatinine Ratio Versus Albumin-Creatinine Ratio With Complications of CKD: A Cross-sectional Analysis

PubMed Central

Fisher, Herrick; Hsu, Chi-yuan; Vittinghoff, Eric; Lin, Feng; Bansal, Nisha

2013-01-01

Background Urine albumin-creatinine ratio (ACR) and protein-creatinine ratio (PCR) are important markers of kidney damage and are utilized for prognosis in persons with chronic kidney disease (CKD). Despite how commonly these measurements are done in clinical practice, relatively few studies have directly compared the performance of these two measures with regard to associations with clinical outcomes, which may inform clinicians about which measure of urinary protein excretion is best. We studied the association of ACR and PCR with common complications of CKD. Study Design Cross-sectional study. Setting & Participants 3,481 participants with CKD in the Chronic Renal Insufficiency Cohort (CRIC) study. Predictors ACR and PCR. Outcomes We examined the association between ACR and PCR with measures of common CKD complications: serum hemoglobin, bicarbonate, parathyroid hormone, phosphorus, potassium and albumin. Measurements Restricted cubic spline analyses adjusted for estimated glomerular filtration rate (eGFR; calculated by the MDRD [Modification of Diet in Renal Disease] Study Equation) were performed to study the continuous association with our predictors with each outcome. Results Mean eGFR was 43 ± 13 (SD) ml/min/1.73 m2 and median levels of PCR and ACR were 140 and 46 mg/g, respectively. In continuous analyses adjusted for eGFR, higher ACR and PCR were comparable and both were associated with lower levels of serum hemoglobin, bicarbonate, and albumin and higher levels of parathyroid hormone, phosphorus, and potassium. Across all outcomes, the associations of ACR and PCR were comparable with only small, absolute differences in the outcome measure. Similar associations were seen in patients with diabetes mellitus. Limitations Participants largely had moderate CKD with low levels of ACR and PCR, so results may not be generalizable to all CKD populations. Conclusions In persons with CKD, ACR and PCR are relatively comparable in their associations with common complications of CKD. Thus routine measurement of PCR may provide similar information as ACR in managing immediate complications of CKD. PMID:24041612

Advances in PCR technology.

PubMed

Lauerman, Lloyd H

2004-12-01

Since the discovery of the polymerase chain reaction (PCR) 20 years ago, an avalanche of scientific publications have reported major developments and changes in specialized equipment, reagents, sample preparation, computer programs and techniques, generated through business, government and university research. The requirement for genetic sequences for primer selection and validation has been greatly facilitated by the development of new sequencing techniques, machines and computer programs. Genetic libraries, such as GenBank, EMBL and DDBJ continue to accumulate a wealth of genetic sequence information for the development and validation of molecular-based diagnostic procedures concerning human and veterinary disease agents. The mechanization of various aspects of the PCR assay, such as robotics, microfluidics and nanotechnology, has made it possible for the rapid advancement of new procedures. Real-time PCR, DNA microarray and DNA chips utilize these newer techniques in conjunction with computer and computer programs. Instruments for hand-held PCR assays are being developed. The PCR and reverse transcription-PCR (RT-PCR) assays have greatly accelerated the speed and accuracy of diagnoses of human and animal disease, especially of the infectious agents that are difficult to isolate or demonstrate. The PCR has made it possible to genetically characterize a microbial isolate inexpensively and rapidly for identification, typing and epidemiological comparison.

Alpha-environmental continuous air monitor inlet

DOEpatents

Rodgers, John C.

2003-01-01

A wind deceleration and protective shroud that provides representative samples of ambient aerosols to an environmental continuous air monitor (ECAM) has a cylindrical enclosure mounted to an input on the continuous air monitor, the cylindrical enclosure having shrouded nozzles located radially about its periphery. Ambient air flows, often along with rainwater flows into the nozzles in a sampling flow generated by a pump in the continuous air monitor. The sampling flow of air creates a cyclonic flow in the enclosure that flows up through the cylindrical enclosure until the flow of air reaches the top of the cylindrical enclosure and then is directed downward to the continuous air monitor. A sloped platform located inside the cylindrical enclosure supports the nozzles and causes any moisture entering through the nozzle to drain out through the nozzles.

Continuation Power Flow with Variable-Step Variable-Order Nonlinear Predictor

NASA Astrophysics Data System (ADS)

Kojima, Takayuki; Mori, Hiroyuki

This paper proposes a new continuation power flow calculation method for drawing a P-V curve in power systems. The continuation power flow calculation successively evaluates power flow solutions through changing a specified value of the power flow calculation. In recent years, power system operators are quite concerned with voltage instability due to the appearance of deregulated and competitive power markets. The continuation power flow calculation plays an important role to understand the load characteristics in a sense of static voltage instability. In this paper, a new continuation power flow with a variable-step variable-order (VSVO) nonlinear predictor is proposed. The proposed method evaluates optimal predicted points confirming with the feature of P-V curves. The proposed method is successfully applied to IEEE 118-bus and IEEE 300-bus systems.

Rapid detection of methicillin-resistant Staphylococcus aureus in pork using a nucleic acid-based lateral flow immunoassay.

PubMed

Zhang, Hongwei; Ma, Luyao; Ma, Lina; Hua, Marti Z; Wang, Shuo; Lu, Xiaonan

2017-02-21

Methicillin-resistant Staphylococcus aureus (MRSA) is considered as one of the leading causes of food poisonings worldwide. Due to the high prevalence and extensive challenges in clinical treatment, a rapid and accurate detection method is required to differentiate MRSA from other S. aureus isolated from foods. Since the methicillin resistance of S. aureus is due to the acquisition of the mecA gene from staphylococcal chromosome cassette, the presence of the mecA gene is interpreted as a marker for the identification of MRSA. In this study, a low-cost lateral flow immunoassay (LFI) strip was used to detect the mecA amplicons subsequent to polymerase chain reaction (PCR). The specificity of this PCR-LFI assay was tested between MRSA and methicillin-susceptive S. aureus. Both the test line and control line were shown up on the LFI strip for MRSA, whereas only the control line developed for methicillin-susceptive S. aureus. The detection limit of PCR-LFI assay was 20fg for genomic DNA (100 times more sensitive than gel electrophoresis) and 2×10 0 CFU per 100g of pork products after enrichment at 37°C for 48h. The total detection time of using LFI was 3min, which was faster than the conventional electrophoresis (~45min). With the performance of PCR-LFI, 7 out of 42 S. aureus isolates were identified to be MRSA from imported pork products, which was consistent to the standardized minimum inhibitory concentration assay. This mecA-based PCR-LFI strip can be used for rapid and accurate detection of MRSA isolated from commercial pork products. Copyright © 2016. Published by Elsevier B.V.

Use of flow cytometry and PCR analysis to detect 5-carboxyfluoroscein-stained obligate intracellular bacteria Lawsonia intracellularis invasion of McCoy cells.

PubMed

Obradovic, Milan; Pasternak, J Alex; Ng, Siew Hon; Wilson, Heather L

2016-07-01

In this study, we describe a method to quantify invasion of obligate intracellular bacteria, Lawsonia intracellularis, inside McCoy cells. In immunological research, the cell-permeable fluorescent dye 5'-carboxyfluoroscein succidyl ester (CFSE) is commonly used to quantify eukaryotic cellular proliferation. Instead of using it in this traditional way, we stained L. intracellularis with CFSE dye prior to infection of McCoy cells. Flow cytometry was performed to quantify the percentage of eukaryotic cells which had taken up or were associated with fluorescent bacteria. As obligate intracellular bacteria, they cannot replicate outside of eukaryotic cells and thus qPCR analysis was used to quantify bacterial growth. Indirectly, PCR analysis confirmed invasion rather than adherence to the McCoy cell surface. Fluorescent activated cell sorting (FACS) was used to sort the CFSE(+) (i.e. infected) McCoy cells from the CFSE(-) (i.e. non-infected) McCoy cells and confocal microscopy was used to confirm bacterial invasion and cytosolic localization of CFSE-L. intracellularis. To show that this approach could be used in conjunction with functional assays, we investigated the effect that serum antibodies had on CFSE-bacterial invasion and growth. Instead of blocking invasion, rabbit hyperimmune serum augmented invasion of the bacteria inside McCoy cells and qPCR analysis confirmed bacterial growth over the course of 5days. We conclude that CFSE-labeling of bacteria and qPCR can be used to track and quantify bacterial invasion and may be a valuable tool for studying the invasive properties of bacteria, especially if commercial antibodies are not available. This approach may be adapted for use in other obligate intracellular bacteria and intracellular pathogens. Copyright © 2016 Elsevier B.V. All rights reserved.

Genetic variability and discrimination of low doses of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification assay as a field-friendly molecular tool.

PubMed

Ozlati, Maryam; Spotin, Adel; Shahbazi, Abbas; Mahami-Oskouei, Mahmoud; Hazratian, Teimour; Adibpor, Mohammad; Ahmadpour, Ehsan; Dolatkhah, Afsaneh; Khoshakhlagh, Paria

2016-12-01

Aim: One of the main diagnostic problems of conventional polymerase chain reaction (PCR) is indiscrimination of low parasitic loads in soil samples. The aim of this study is to determine the genetic diversity and identification of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification (LAMP) assay. A total of 180 soil samples were collected from various streets and public parks of northwest Iran. The DNA of recovered Toxocara eggs were extracted and amplified by PCR and LAMP following ZnSO 4 flotation technique. The amplicons of internal transcribed spacer-2 gene were sequenced to reveal the heterogeneity traits of Toxocara spp. In addition, Toxocara canis sequences of southwest Iran were directly retrieved to compare gene flow between two distinct populations. Toxocara spp. eggs were found in 57, 14 and 77 of soil samples using the microscopy, PCR and LAMP (detection limit 1-3 eggs/200 g soil), respectively. 7.7% of isolates were identified as T. canis by PCR method, while LAMP was able to detect 27.2%, 15.5% and 12.2% as Toxocara cati , T. canis and mixed infections, respectively. The kappa coefficient between LAMP and microscopy indicated a strong agreement (0.765) but indicated a faint agreement among LAMP-PCR (0.203) and PCR-microscopy (0.308) methods. A pairwise fixation index ( F st) as a degree of gene flow was generally low (0.02156) among Toxocara populations of northwest and southwest Iran. The statistically significant F st value indicates that the T. canis populations are not genetically well differentiated between northwest and southwest Iran. This shows that here is possibly an epidemiological drift due to the transfer of alleles. The LAMP assay because of its shorter reaction time, more sensitivity, and simultaneous detection of environmental contamination to be appears as valuable field diagnosis compared to PCR. Therefore, the detection of low Toxocara spp. loads from public area soils will help to expand epidemiological understanding of toxocariasis and establishing preventive strategies in resource-limited endemic of Iran.

Genetic variability and discrimination of low doses of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification assay as a field-friendly molecular tool

PubMed Central

Ozlati, Maryam; Spotin, Adel; Shahbazi, Abbas; Mahami-Oskouei, Mahmoud; Hazratian, Teimour; Adibpor, Mohammad; Ahmadpour, Ehsan; Dolatkhah, Afsaneh; Khoshakhlagh, Paria

2016-01-01

Abstract: Aim: One of the main diagnostic problems of conventional polymerase chain reaction (PCR) is indiscrimination of low parasitic loads in soil samples. The aim of this study is to determine the genetic diversity and identification of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification (LAMP) assay. Materials and Methods: A total of 180 soil samples were collected from various streets and public parks of northwest Iran. The DNA of recovered Toxocara eggs were extracted and amplified by PCR and LAMP following ZnSO4 flotation technique. The amplicons of internal transcribed spacer-2 gene were sequenced to reveal the heterogeneity traits of Toxocara spp. In addition, Toxocara canis sequences of southwest Iran were directly retrieved to compare gene flow between two distinct populations. Results: Toxocara spp. eggs were found in 57, 14 and 77 of soil samples using the microscopy, PCR and LAMP (detection limit 1-3 eggs/200 g soil), respectively. 7.7% of isolates were identified as T. canis by PCR method, while LAMP was able to detect 27.2%, 15.5% and 12.2% as Toxocara cati, T. canis and mixed infections, respectively. The kappa coefficient between LAMP and microscopy indicated a strong agreement (0.765) but indicated a faint agreement among LAMP-PCR (0.203) and PCR-microscopy (0.308) methods. A pairwise fixation index (Fst) as a degree of gene flow was generally low (0.02156) among Toxocara populations of northwest and southwest Iran. Conclusions: The statistically significant Fst value indicates that the T. canis populations are not genetically well differentiated between northwest and southwest Iran. This shows that here is possibly an epidemiological drift due to the transfer of alleles. The LAMP assay because of its shorter reaction time, more sensitivity, and simultaneous detection of environmental contamination to be appears as valuable field diagnosis compared to PCR. Therefore, the detection of low Toxocara spp. loads from public area soils will help to expand epidemiological understanding of toxocariasis and establishing preventive strategies in resource-limited endemic of Iran. PMID:28096624

Analysis of gene expression in small numbers of purified hemopoietic progenitor cells by RT-PCR.

PubMed

Ziegler, B L; Lamping, C P; Thoma, S J; Fliedner, T M

1995-05-01

Primitive hemopoietic stem cells represent the most probable targets for genetic alterations due to exposure to ionizing irradiation or chemical carcinogens. We have applied a two-step protocol for the purification of CD34+HLA-DR-/low hemopoietic progenitor cells from cord blood (CB). CD34+ cells were isolated by monoclonal antibody (mAb) against CD34 (My10) and immunomagnetic beads. Beads were cleaved off the CD34+ cells by enzymatic treatment with chymopapain. Due to chymopapain-resistance of epitopes recognized by the used mAbs purity control of CD34+ cells and separation into CD34+HLA-DR-/low and CD34+HLA-DR+ subsets could be performed by using flow cytometry. Two miniaturized procedures were applied to isolate poly(A)+ mRNA for the reverse transcription polymerase chain reaction (RT-PCR) from small numbers of CD34+HLA-DR-/low cells. In five experiments, the mean purity of immunomagnetically isolated CD34+ cells was 93.8% +/- 3.9. Flow cytometry sorting of CD34+ cells resulted in pure CD34+HLA-DR-/low populations (purity > 98.8%; range 98.8% to 99.9%; viability > 96%) with an average yield of 2600 +/- 800 cells/5 x 10(7) low density CB cells. By RT-PCR using both poly(A)+ mRNA isolation procedures, sequences corresponding to CD34 and beta 2-microglobulin were amplified from as few as 20 cells. Furthermore, a sequence-independent RT-PCR (SIP-RT-PCR) was applied to amplify the cDNA derived from five erythroblasts isolated from a burst-forming unit-erythroid (BFU-E). Upon hybridization, full-length c-fos message was detected in the SIP-RT-PCR amplified material. Our data demonstrate that gene expression can be detected at the transcriptional level in small numbers of hemopoietic progenitor cells. In addition, the SIP-RT-PCR may allow the amplification of unique mRNA species when subtractive hybridization procedures are performed. The presented data should be useful to analyze gene expression in rare subsets of radiation-exposed immature hemopoietic stem/progenitor cells.

A Novel Isothermal Assay of Borrelia burgdorferi by Recombinase Polymerase Amplification with Lateral Flow Detection.

PubMed

Liu, Wei; Liu, Hui-Xin; Zhang, Lin; Hou, Xue-Xia; Wan, Kang-Lin; Hao, Qin

2016-08-03

A novel isothermal detection for recombinase polymerase amplification with lateral flow (LF-RPA) was established for Borrelia burgdorferi (B. burgdorferi) detection in this study. This assay with high sensitivity and specificity can get a visible result without any additional equipment in 30 min. We designed a pair of primers according to recA gene of B. burgdorferi strains and a methodology evaluation was performed. The results showed that the RPA assay based on the recA gene was successfully applied in B. burgdorferi detection, and its specific amplification was only achieved from the genomic DNA of B. burgdorferi. The detection limit of the new assay was about 25 copies of the B. burgdorferi genomic DNA. Twenty Lyme borreliosis patients' serum samples were detected by LF-RPA assay, real-time qPCR and nested-PCR. Results showed the LF-RPA assay is more effective than nested-PCR for its shorter reaction time and considerably higher detection rate. This method is of great value in clinical rapid detection for Lyme borreliosis. Using the RPA assay might be a megatrend for DNA detection in clinics and endemic regions.

Development of Nested PCR-Based Specific Markers for Detection of Peach Rosette Mosaic Virus in Plant Quarantine.

PubMed

Lee, S; Kim, C S; Shin, Y G; Kim, J H; Kim, Y S; Jheong, W H

2016-03-01

The Peach rosette mosaic virus (PRMV) is a plant pathogen of the genus Nepovirus, and has been designated as a controlled quarantine virus in Korea. In this study, a specific reverse transcription (RT)-PCR marker set, nested PCR marker set, and modified-plasmid positive control were developed to promptly and accurately diagnose PRMV at plant-quarantine sites. The final selected PRMV-specific RT-PCR marker was PRMV-N10/C70 (967 bp), and the nested PCR product of 419 bp was finally amplified. The modified-plasmid positive control, in which the SalI restriction-enzyme region (GTCGAC) was inserted, verified PRMV contamination in a comparison with the control, enabling a more accurate diagnosis. It is expected that the developed method will continuously contribute to the plant-quarantine process in Korea.

Heated, humidified high-flow nasal cannula therapy: yet another way to deliver continuous positive airway pressure?

PubMed

Kubicka, Zuzanna J; Limauro, Joseph; Darnall, Robert A

2008-01-01

The goal was to estimate the level of delivered continuous positive airway pressure by measuring oral cavity pressure with the mouth closed in infants of various weights and ages treated with heated, humidified high-flow nasal cannula at flow rates of 1-5 L/minute. We hypothesized that clinically relevant levels of continuous positive airway pressure would not be achieved if a nasal leak is maintained. After performing bench measurements and demonstrating that oral cavity pressure closely approximated levels of traditionally applied nasal continuous positive airway pressure, we successfully measured oral cavity pressure during heated, humidified, high-flow nasal cannula treatment in 27 infants. Small (outer diameter: 0.2 cm) cannulae were used for all infants, and flow rates were left as ordered by providers. Bench measurements showed that, for any given leak size, there was a nearly linear relationship between flow rate and pressure. The highest pressure achieved was 4.5 cmH2O (flow rate: 8 L/minute; leak: 3 mm). In our study infants (postmenstrual age: 29.1-44.7 weeks; weight: 835-3735 g; flow rate: 1-5 L/minute), no pressure was generated with the mouth open at any flow rate. With the mouth closed, the oral cavity pressure was related to both flow rate and weight. For infants of < or = 1500 g, there was a linear relationship between flow rate and oral cavity pressure. Oral cavity pressure can estimate the level of continuous positive airway pressure. Continuous positive airway pressure generated with heated, humidified, high-flow nasal cannula treatment depends on the flow rate and weight. Only in the smallest infants with the highest flow rates, with the mouth fully closed, can clinically significant but unpredictable levels of continuous positive airway pressure be achieved. We conclude that heated, humidified high-flow nasal cannula should not be used as a replacement for delivering continuous positive airway pressure.

Ibrutinib plus Venetoclax for the Treatment of Mantle-Cell Lymphoma.

PubMed

Tam, Constantine S; Anderson, Mary Ann; Pott, Christiane; Agarwal, Rishu; Handunnetti, Sasanka; Hicks, Rodney J; Burbury, Kate; Turner, Gillian; Di Iulio, Juliana; Bressel, Mathias; Westerman, David; Lade, Stephen; Dreyling, Martin; Dawson, Sarah-Jane; Dawson, Mark A; Seymour, John F; Roberts, Andrew W

2018-03-29

Both the BTK inhibitor ibrutinib and the BCL2 inhibitor venetoclax are active as monotherapy in the treatment of mantle-cell lymphoma. Complete response rates of 21% have been observed for each agent when administered as long-term continuous therapy. Preclinical models predict synergy in combination. We conducted a single-group, phase 2 study of daily oral ibrutinib and venetoclax in patients, as compared with historical controls. Patients commenced ibrutinib monotherapy at a dose of 560 mg per day. After 4 weeks, venetoclax was added in stepwise, weekly increasing doses to 400 mg per day. Both drugs were continued until progression or an unacceptable level of adverse events. The primary end point was the rate of complete response at week 16. Minimal residual disease (MRD) was assessed by flow cytometry in bone marrow and by allele-specific oligonucleotide-polymerase chain reaction (ASO-PCR) in blood. The study included 24 patients with relapsed or refractory mantle-cell lymphoma (23 patients) or previously untreated mantle-cell lymphoma (1 patient). Patients were 47 to 81 years of age, and the number of previous treatments ranged from none to six. Half the patients had aberrations of TP53, and 75% had a high-risk prognostic score. The complete response rate according to computed tomography at week 16 was 42%, which was higher than the historical result of 9% at this time point with ibrutinib monotherapy (P<0.001). The rate of complete response as assessed by positron-emission tomography was 62% at week 16 and 71% overall. MRD clearance was confirmed by flow cytometry in 67% of the patients and by ASO-PCR in 38%. In a time-to-event analysis, 78% of the patients with a response were estimated to have an ongoing response at 15 months. The tumor lysis syndrome occurred in 2 patients. Common side effects were generally low grade and included diarrhea (in 83% of the patients), fatigue (in 75%), and nausea or vomiting (in 71%). In this study involving historical controls, dual targeting of BTK and BCL2 with ibrutinib and venetoclax was consistent with improved outcomes in patients with mantle-cell lymphoma who had been predicted to have poor outcomes with current therapy. (Funded by Janssen and others; AIM ClinicalTrials.gov number, NCT02471391 .).

Archaeal enrichment in the hypoxic zone in the northern Gulf of Mexico.

PubMed

Gillies, Lauren E; Thrash, J Cameron; deRada, Sergio; Rabalais, Nancy N; Mason, Olivia U

2015-10-01

Areas of low oxygen have spread exponentially over the past 40 years, and are cited as a key stressor on coastal ecosystems. The world's second largest coastal hypoxic (≤ 2 mg of O2 l(-1)) zone occurs annually in the northern Gulf of Mexico. The net effect of hypoxia is the diversion of energy flow away from higher trophic levels to microorganisms. This energy shunt is consequential to the overall productivity of hypoxic water masses and the ecosystem as a whole. In this study, water column samples were collected at 39 sites in the nGOM, 21 of which were hypoxic. Analysis of the microbial community along a hypoxic to oxic dissolved oxygen gradient revealed that the relative abundance (iTag) of Thaumarchaeota species 16S rRNA genes (> 40% of the microbial community in some hypoxic samples), the absolute abundance (quantitative polymerase chain reaction; qPCR) of Thaumarchaeota 16S rRNA genes and archaeal ammonia-monooxygenase gene copy number (qPCR) were significantly higher in hypoxic samples. Spatial interpolation of the microbial and chemical data revealed a continuous, shelfwide band of low dissolved oxygen waters that were dominated by Thaumarchaeota (and Euryarchaeota), amoA genes and high concentrations of phosphate in the nGOM, thus implicating physicochemical forcing on microbial abundance. © 2015 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Flow through PCR module of BioBriefcase

NASA Astrophysics Data System (ADS)

Arroyo, E.; Wheeler, E. K.; Shediac, R.; Hindson, B.; Nasarabadi, S.; Vrankovich, G.; Bell, P.; Bailey, C.; Sheppod, T.; Christian, A. T.

2005-11-01

The BioBriefcase is an integrated briefcase-sized aerosol collection and analysis system for autonomous monitoring of the environment, which is currently being jointly developed by Lawrence Livermore and Sandia National Laboratories. This poster presents results from the polymerase chain reaction (PCR) module of the system. The DNA must be purified after exiting the aerosol collector to prevent inhibition of the enzymatic reaction. Traditional solid-phase extraction results in a large loss of sample. In this flow-through system, we perform sample purification, concentration and amplification in one reactor, which minimizes the loss of material. The sample from the aerosol collector is mixed with a denaturation solution prior to flowing through a capillary packed with silica beads. The DNA adheres to the silica beads allowing the environmental contaminants to be flushed to waste while effectively concentrating the DNA on the silica matrix. The adhered DNA is amplified while on the surface of the silica beads, resulting in a lower limit of detection than an equivalent eluted sample. Thus, this system is beneficial since more DNA is available for amplification, less reagents are utilized, and contamination risks are reduced.

Integrated microfluidic system with automatic sampling for permanent molecular and antigen-based detection of CBRNE-related pathogens

NASA Astrophysics Data System (ADS)

Becker, Holger; Schattschneider, Sebastian; Klemm, Richard; Hlawatsch, Nadine; Gärtner, Claudia

2015-03-01

The continuous monitoring of the environment for lethal pathogens is a central task in the field of biothreat detection. Typical scenarios involve air-sampling in locations such as public transport systems or large public events and a subsequent analysis of the samples by a portable instrument. Lab-on-a-chip technologies are one of the promising technological candidates for such a system. We have developed an integrated microfluidic system with automatic sampling for the detection of CBRNE-related pathogens. The chip contains a two-pronged analysis strategy, on the one hand an immunological track using antibodies immobilized on a frit and a subsequent photometric detection, on the other hand a molecular biology approach using continuous-flow PCR with a fluorescence end-point detection. The cartridge contains two-component molded rotary valve to allow active fluid control and switching between channels. The accompanying instrument contains all elements for fluidic and valve actuation, thermal control, as well as the two detection modalities. Reagents are stored in dedicated reagent packs which are connected directly to the cartridge. With this system, we have been able to demonstrate the detection of a variety of pathogen species.

Cloning of gene-encoded stem bromelain on system coming from Pichia pastoris as therapeutic protein candidate

NASA Astrophysics Data System (ADS)

Yusuf, Y.; Hidayati, W.

2018-01-01

The process of identifying bacterial recombination using PCR, and restriction, and then sequencing process was done after identifying the bacteria. This research aimed to get a yeast cell of Pichia pastoris which has an encoder gene of stem bromelain enzyme. The production of recombinant stem bromelain enzymes using yeast cells of P. pastoris can produce pure bromelain rod enzymes and have the same conformation with the enzyme’s conformation in pineapple plants. This recombinant stem bromelain enzyme can be used as a therapeutic protein in inflammatory, cancer and degenerative diseases. This study was an early stage of a step series to obtain bromelain rod protein derived from pineapple made with genetic engineering techniques. This research was started by isolating the RNA of pineapple stem which was continued with constructing cDNA using reserve transcriptase-PCR technique (RT-PCR), doing the amplification of bromelain enzyme encoder gene with PCR technique using a specific premiere couple which was designed. The process was continued by cloning into bacterium cells of Escherichia coli. A vector which brought the encoder gene of stem bromelain enzyme was inserted into the yeast cell of P. pastoris and was continued by identifying the yeast cell of P. pastoris which brought the encoder gene of stem bromelain enzyme. The research has not found enzyme gene of stem bromelain in yeast cell of P. pastoris yet. The next step is repeating the process by buying new reagent; RNase inhibitor, and buying liquid nitrogen.

21 CFR 862.2150 - Continuous flow sequential multiple chemistry analyzer for clinical use.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Continuous flow sequential multiple chemistry..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Laboratory Instruments § 862.2150 Continuous flow sequential multiple chemistry...

An efficient and more sustainable one-step continuous-flow multicomponent synthesis approach to chromene derivatives

EPA Science Inventory

A simple and rapid one-step continuous-flow synthesis route has been developed for the preparation of chromene derivatives from the reaction of aromatic aldehydes, α-cyanomethylene compounds and naphthols. In this contribution, a one-step continuous-flow protocol in a continuous ...

21 CFR 862.2150 - Continuous flow sequential multiple chemistry analyzer for clinical use.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Continuous flow sequential multiple chemistry..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Laboratory Instruments § 862.2150 Continuous flow sequential multiple chemistry...

21 CFR 862.2150 - Continuous flow sequential multiple chemistry analyzer for clinical use.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Continuous flow sequential multiple chemistry..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Laboratory Instruments § 862.2150 Continuous flow sequential multiple chemistry...

21 CFR 862.2150 - Continuous flow sequential multiple chemistry analyzer for clinical use.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Continuous flow sequential multiple chemistry..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Laboratory Instruments § 862.2150 Continuous flow sequential multiple chemistry...

21 CFR 862.2150 - Continuous flow sequential multiple chemistry analyzer for clinical use.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Continuous flow sequential multiple chemistry..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Laboratory Instruments § 862.2150 Continuous flow sequential multiple chemistry...

78 FR 65306 - Best Practices for Continuous Monitoring of Temperature and Flow in Wadeable Streams

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-31

... Practices for Continuous Monitoring of Temperature and Flow in Wadeable Streams AGENCY: Environmental... Monitoring of Temperature and Flow in Wadeable Streams'' (EPA/600/R-13/170). The EPA also is announcing that... Development. The report describes best practices for the deployment of continuous temperature and flow sensors...

On-chip isothermal, chemical cycling polymerase chain reaction (ccPCR)

NASA Astrophysics Data System (ADS)

Persat, Alexandre; Santiago, Juan

2008-11-01

We demonstrate a novel ccPCR technique for microfluidic DNA amplification where temperature is held constant in space and time. The polymerase chain reaction is a platform of choice for biological assays and typically based on a three-step thermal cycling: DNA denaturation, primers annealing and extension by an enzyme. We here demonstrate a novel technique where high concentration chemical denaturants (solvents) denature DNA. We leverage the high electrophoretic mobility of DNA and the electrical neutrality of denaturants to achieve chemical cycling. We focus DNA with isotachophoresis (ITP); a robust electrophoretic preconcentration technique which generates strong electric field gradients and protects the sample from dispersion. We apply a pressure-driven flow to balance electromigration velocity and keep the DNA sample stationary in a microchannel. We drive the DNA through a series of high denaturant concentration zones. DNA denatures at high denaturant concentration. At low denaturant concentration, the enzyme creates complementary strands. DNA reaction kinetics are slower than buffer reactions involved in ITP. We demonstrate successful ccPCR amplification for detection of E. Coli. The ccPCR has the potential for simpler chemistry than traditional PCR.

A Rapid and Low-Cost PCR Thermal Cycler for Low Resource Settings

PubMed Central

Wong, Grace; Wong, Isaac; Chan, Kamfai; Hsieh, Yicheng; Wong, Season

2015-01-01

Background Many modern molecular diagnostic assays targeting nucleic acids are typically confined to developed countries or to the national reference laboratories of developing-world countries. The ability to make technologies for the rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a revolutionary step forward in global health. Many molecular assays are also developed based on polymerase chain reactions (PCR), which require thermal cyclers that are relatively heavy (>20 pounds) and need continuous electrical power. The temperature ramping speed of most economical thermal cyclers are relatively slow (2 to 3°C/s) so a polymerase chain reaction can take 1 to 2 hours. Most of all, these thermal cyclers are still too expensive ($2k to $4k) for low-resource setting uses. Methodology/Principal Findings In this article, we demonstrate the development of a low-cost and rapid water bath based thermal cycler that does not require active temperature control or continuous power supply during PCR. This unit costs $130 to build using commercial off-the-shelf items. The use of two or three vacuum-insulated stainless-steel Thermos food jars containing heated water (for denaturation and annealing/extension steps) and a layer of oil on top of the water allow for significantly stabilized temperatures for PCR to take place. Using an Arduino-based microcontroller, we automate the “archaic” method of hand-transferring PCR tubes between water baths. Conclusions/Significance We demonstrate that this innovative unit can deliver high speed PCR (17 s per PCR cycle) with the potential to go beyond the 1,522 bp long amplicons tested in this study and can amplify from templates down to at least 20 copies per reaction. The unit also accepts regular PCR tubes and glass capillary tubes. The PCR efficiency of our thermal cycler is not different from other commercial thermal cyclers. When combined with a rapid nucleic acid detection approach, the thermos thermal cycler (TTC) can enable on-site molecular diagnostics in low-resource settings. PMID:26146999

Effect of intermittent shear stress on corneal epithelial cells using an in vitro flow culture model.

PubMed

Hampel, Ulrike; Garreis, Fabian; Burgemeister, Fabian; Eßel, Nicole; Paulsen, Friedrich

2018-04-27

The aim of this study was to establish and to evaluate an in vitro model for culturing human telomerase-immortalized corneal epithelial (hTCEpi) cells under adjustable medium flow mimicking the movements of the tear film on the ocular surface. Using an IBIDI pump system, cells were cultured under unidirectional, continuous or oscillating, discontinuous medium flow. Cell surface and cytoskeletal architecture were investigated by scanning electron microscopy and immunofluorescence. Gene expression of e-cadherin, occludin, tight junction protein (TJP), desmoplakin, desmocollin and mucins was investigated by real-time PCR. Protein expression of desmoplakin, TJP, occludin and e-cadherin was analyzed by western blot and localization was detected by immunofluorescence. Rose bengal staining was used to assess mucin (MUC) barrier integrity. MUC1, -4 and -16 proteins were localized by immunofluorescence. Medium flow-induced shear stress dramatically changed cellular morphology of hTCEpi. Cells subjected to discontinuous shear stress displayed the typical flattened, polygonal cell shape of the superficial layer of stratified squamous epithelia. Cell surfaces showed less bulging under shear stress and less extracellular gaps. The mRNA expression of E-cadherin, occludin and TJP were increased under oscillatory medium flow. Desmoplakin and occludin protein were upregulated under oscillatory shear stress. Stress fiber formation was not aligned to flow direction. MUC1, -4, and -16 protein were localized under all culture conditions, a regulation on mRNA expression was not detectable. Rose Bengal uptake was diminished under unidirectional conditions. Our findings suggest that shear stress as it occurs at the ocular surface during blinking exerts marked effects on corneal epithelial cells, such as changes in cellular morphology and expression of cell junctions. The described model may be useful for in vitro investigations of ocular surface epithelia as it represents a much more physiologic reproduction of the in vivo situation than the commonly applied static culture conditions. Copyright © 2018. Published by Elsevier Inc.

Continuous Flow Science in an Undergraduate Teaching Laboratory: Photocatalytic Thiol-Ene Reaction Using Visible Light

ERIC Educational Resources Information Center

Santandrea, Jeffrey; Kairouz, Vanessa; Collins, Shawn K.

2018-01-01

An undergraduate teaching laboratory experiment involving a continuous flow, photocatalytic thiol-ene reaction using visible-light irradiation is described that allows students to explore concepts of green chemistry, photochemistry, photocatalysis, and continuous flow chemistry.

Quantification of mRNA expression by competitive PCR using non-homologous competitors containing a shifted restriction site

PubMed Central

Watzinger, Franz; Hörth, Elfriede; Lion, Thomas

2001-01-01

Despite the recent introduction of real-time PCR methods, competitive PCR techniques continue to play an important role in nucleic acid quantification because of the significantly lower cost of equipment and consumables. Here we describe a shifted restriction-site competitive PCR (SRS-cPCR) assay based on a modified type of competitor. The competitor fragments are designed to contain a recognition site for a restriction endonuclease that is also present in the target sequence to be quantified, but in a different position. Upon completion of the PCR, the amplicons are digested in the same tube with a single restriction enzyme, without the need to purify PCR products. The generated competitor- and target-specific restriction fragments display different sizes, and can be readily separated by electrophoresis and quantified by image analysis. Suboptimal digestion affects competitor- and target-derived amplicons to the same extent, thus eliminating the problem of incorrect quantification as a result of incomplete digestion of PCR products. We have established optimized conditions for a panel of 20 common restriction endonucleases permitting efficient digestion in PCR buffer. It is possible, therefore, to find a suitable restriction site for competitive PCR in virtually any sequence of interest. The assay presented is inexpensive, widely applicable, and permits reliable and accurate quantification of nucleic acid targets. PMID:11376164

Laboratory Tests of Multiplex Detection of PCR Amplicons Using the Luminex 100 Flow Analyzer

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

Venkateswaran, K.S.; Nasarabadi, S.; Langlois, R.G.

2000-05-05

Lawrence Livermore National Laboratory (LLNL) demonstrated the power of flow cytometry in detecting the biological agents simulants at JFT III. LLNL pioneered in the development of advanced nucleic acid analyzer (ANM) for portable real time identification. Recent advances in flow cytometry provide a means for multiplexed nucleic acid detection and immunoassay of pathogenic microorganisms. We are presently developing multiplexed immunoassays for the simultaneous detection of different simulants. Our goal is to build an integrated instrument for both nucleic acid analysis and immuno detection. In this study we evaluated the Luminex LX 100 for concurrent identification of more than one PCRmore » amplified product. ANAA has real-time Taqman fluorescent detection capability for rapid identification of field samples. However, its multiplexing ability is limited by the combination of available fluorescent labels. Hence integration of ANAA with flow cytometry can give the rapidity of ANAA amplification and the multiplex capability of flow cytometry. Multiplexed flow cytometric analysis is made possible using a set of fluorescent latex microsphere that are individually identified by their red and infrared fluorescence. A green fluorochrome is used as the assay signal. Methods were developed for the identification of specific nucleic acid sequences from Bacillus globigii (Bg), Bacillus thuringensis (Bt) and Erwinia herbicola (Eh). Detection sensitivity using different reporter fluorochromes was tested with the LX 100, and also different assay formats were evaluated for their suitability for rapid testing. A blind laboratory trial was carried out December 22-27, 1999 to evaluate bead assays for multiplex identification of Bg and Bt PCR products. This report summarizes the assay development, fluorochrome comparisons, and the results of the blind trial conducted at LLNL for the laboratory evaluation of the LX 100 flow analyzer.« less

Simultaneous detection of multiple HPV DNA via bottom-well microfluidic chip within an infra-red PCR platform.

PubMed

Liu, Wenjia; Warden, Antony; Sun, Jiahui; Shen, Guangxia; Ding, Xianting

2018-03-01

Portable Polymerase Chain Reaction (PCR) devices combined with microfluidic chips or lateral flow stripes have shown great potential in the field of point-of-need testing (PoNT) as they only require a small volume of patient sample and are capable of presenting results in a short time. However, the detection for multiple targets in this field leaves much to be desired. Herein, we introduce a novel PCR platform by integrating a bottom-well microfluidic chip with an infra-red (IR) excited temperature control method and fluorescence co-detection of three PCR products. Microfluidic chips are utilized to partition different samples into individual bottom-wells. The oil phase in the main channel contains multi-walled carbon nanotubes which were used as a heat transfer medium that absorbs energy from the IR-light-emitting diode (LED) and transfers heat to the water phase below. Cyclical rapid heating and cooling necessary for PCR are achieved by alternative power switching of the IR-LED and Universal Serial Bus (USB) mini-fan with a pulse width modulation scheme. This design of the IR-LED PCR platform is economic, compact, and fully portable, making it a promising application in the field of PoNT. The bottom-well microfluidic chip and IR-LED PCR platform were combined to fulfill a three-stage thermal cycling PCR for 40 cycles within 90 min for Human Papilloma Virus (HPV) detection. The PCR fluorescent signal was successfully captured at the end of each cycle. The technique introduced here has broad applications in nucleic acid amplification and PoNT devices.

Residual eDNA detection sensitivity assessed by quantitative real-time PCR in a river ecosystem.

PubMed

Balasingham, Katherine D; Walter, Ryan P; Heath, Daniel D

2017-05-01

Several studies have demonstrated that environmental DNA (eDNA) can be used to detect the presence of aquatic species, days to weeks after the target species has been removed. However, most studies used eDNA analysis in lentic systems (ponds or lakes), or in controlled laboratory experiments. While eDNA degrades rapidly in all aquatic systems, it also undergoes dilution effects and physical destruction in flowing systems, complicating detection in rivers. However, some eDNA (i.e. residual eDNA) can be retained in aquatic systems, even those subject to high flow regimes. Our goal was to determine residual eDNA detection sensitivity using quantitative real-time polymerase chain reaction (qRT-PCR), in a flowing, uncontrolled river after the eDNA source was removed from the system; we repeated the experiment over 2 years. Residual eDNA had the strongest signal strength at the original source site and was detectable there up to 11.5 h after eDNA source removal. Residual eDNA signal strength decreased as sampling distance downstream from the eDNA source site increased, and was no longer detectable at the source site 48 h after the eDNA source water was exhausted in both experiments. This experiment shows that residual eDNA sampled in surface water can be mapped quantitatively using qRT-PCR, which allows a more accurate spatial identification of the target species location in lotic systems, and relative residual eDNA signal strength may allow the determination of the timing of the presence of target species. © 2016 John Wiley & Sons Ltd.

Influence of Rack Design and Disease Prevalence on Detection of Rodent Pathogens in Exhaust Debris Samples from Individually Ventilated Caging Systems.

PubMed

Bauer, Beth A; Besch-Williford, Cynthia; Livingston, Robert S; Crim, Marcus J; Riley, Lela K; Myles, Matthew H

2016-11-01

Sampling of bedding debris within the exhaust systems of ventilated racks may be a mechanism for detecting murine pathogens in colony animals. This study examined the effectiveness of detecting pathogens by PCR analysis of exhaust debris samples collected from ventilated racks of 2 different rack designs, one with unfiltered air flow from within the cage to the air-exhaust pathway, and the other had a filter between the cage and the air-exhaust pathway. For 12 wk, racks were populated with either 1 or 5 cages of mice (3 mice per cage) infected with one of the following pathogens: mouse norovirus (MNV), mouse parvovirus (MPV), mouse hepatitis virus (MHV), Helicobacter spp., Pasteurella pneumotropica, pinworms, Entamoeba muris, Tritrichomonas muris, and fur mites. Pathogen shedding by infected mice was monitored throughout the study. In the filter-containing rack, PCR testing of exhaust plenums yielded negative results for all pathogens at all time points of the study. In the rack with open air flow, pathogens detected by PCR analysis of exhaust debris included MHV, Helicobacter spp., P. pneumotropica, pinworms, enteric protozoa, and fur mites; these pathogens were detected in racks housing either 1 or 5 cages of infected mice. Neither MPV nor MNV was detected in exhaust debris, even though prolonged viral shedding was confirmed. These results demonstrate that testing rack exhaust debris from racks with unfiltered air flow detected MHV, enteric bacteria and parasites, and fur mites. However, this method failed to reliably detect MNV or MPV infection of colony animals.

Influence of Rack Design and Disease Prevalence on Detection of Rodent Pathogens in Exhaust Debris Samples from Individually Ventilated Caging Systems

PubMed Central

Bauer, Beth A; Besch-Williford, Cynthia; Livingston, Robert S; Crim, Marcus J; Riley, Lela K; Myles, Matthew H

2016-01-01

Sampling of bedding debris within the exhaust systems of ventilated racks may be a mechanism for detecting murine pathogens in colony animals. This study examined the effectiveness of detecting pathogens by PCR analysis of exhaust debris samples collected from ventilated racks of 2 different rack designs, one with unfiltered air flow from within the cage to the air-exhaust pathway, and the other had a filter between the cage and the air-exhaust pathway. For 12 wk, racks were populated with either 1 or 5 cages of mice (3 mice per cage) infected with one of the following pathogens: mouse norovirus (MNV), mouse parvovirus (MPV), mouse hepatitis virus (MHV), Helicobacter spp., Pasteurella pneumotropica, pinworms, Entamoeba muris, Tritrichomonas muris, and fur mites. Pathogen shedding by infected mice was monitored throughout the study. In the filter-containing rack, PCR testing of exhaust plenums yielded negative results for all pathogens at all time points of the study. In the rack with open air flow, pathogens detected by PCR analysis of exhaust debris included MHV, Helicobacter spp., P. pneumotropica, pinworms, enteric protozoa, and fur mites; these pathogens were detected in racks housing either 1 or 5 cages of infected mice. Neither MPV nor MNV was detected in exhaust debris, even though prolonged viral shedding was confirmed. These results demonstrate that testing rack exhaust debris from racks with unfiltered air flow detected MHV, enteric bacteria and parasites, and fur mites. However, this method failed to reliably detect MNV or MPV infection of colony animals. PMID:27931317

Evaluation of lateral flow devices for identification of infected poultry by testing swab and feather specimens during H5N1 highly pathogenic avian influenza outbreaks in Vietnam

PubMed Central

Slomka, Marek J.; To, Thanh L.; Tong, Hien H.; Coward, Vivien J.; Mawhinney, Ian C.; Banks, Jill; Brown, Ian H.

2011-01-01

Please cite this paper as: Slomka et al. (2012) Evaluation of lateral flow devices for identification of infected poultry by testing swab and feather specimens during H5N1 highly pathogenic avian influenza outbreaks in Vietnam. Influenza and Other Respiratory Viruses 6(5), 318–327. Background  Evaluation of two commercial lateral flow devices (LFDs) for avian influenza (AI) detection in H5N1 highly pathogenic AI infected poultry in Vietnam. Objectives  Determine sensitivity and specificity of the LFDs relative to a validated highly sensitive H5 RRT PCR. Methods  Swabs (cloacal and tracheal) and feathers were collected from 46 chickens and 48 ducks (282 clinical specimens) and tested by both LFDs and H5 RRT PCR. A subset of 59 chicken and 34 duck specimens was also tested by virus isolation (VI), the ‘gold standard’. Results  Twenty‐six chickens and 15 ducks were shown to be infected by at least one RRT PCR positive clinical specimen per bird. Bird‐level sensitivity for the Anigen LFD was 84·6% for chickens and 53·3% for ducks, and for the Quickvue LFD 65·4% for chickens and 33·3% for ducks. Comparison of the three clinical specimens revealed that chicken feathers were the most sensitive with 84% and 56% sensitivities for Anigen and Quickvue respectively. All 21 RRT PCR positive swabs from ducks were negative by both LFDs. However, duck feather testing gave sensitivities of 53·3% and 33·3% for Anigen and Quickvue respectively. Specificity was 100% for both LFDs in all investigations. Conclusions  Although LFDs were less sensitive than AI RRT PCR and VI, high titre viral shedding in H5N1 highly pathogenic avian influenza (HPAI) infected and diseased chickens is sufficient for a proportion of birds to be identified as AI infected by LFDs. Feathers were the optimal specimen for LFD testing in such diseased HPAI scenarios, particularly for ducks where swab testing by LFDs failed to identify any infected birds. However, specimens should be forwarded to the laboratory for confirmation by more sensitive diagnostic techniques. PMID:22151025

Alternative electron flows (water-water cycle and cyclic electron flow around PSI) in photosynthesis: molecular mechanisms and physiological functions.

PubMed

Miyake, Chikahiro

2010-12-01

An electron flow in addition to the major electron sinks in C(3) plants [both photosynthetic carbon reduction (PCR) and photorespiratory carbon oxidation (PCO) cycles] is termed an alternative electron flow (AEF) and functions in the chloroplasts of leaves. The water-water cycle (WWC; Mehler-ascorbate peroxidase pathway) and cyclic electron flow around PSI (CEF-PSI) have been studied as the main AEFs in chloroplasts and are proposed to play a physiologically important role in both the regulation of photosynthesis and the alleviation of photoinhibition. In the present review, I discuss the molecular mechanisms of both AEFs and their functions in vivo. To determine their physiological function, accurate measurement of the electron flux of AEFs in vivo are required. Methods to assay electron flux in CEF-PSI have been developed recently and their problematic points are discussed. The common physiological function of both the WWC and CEF-PSI is the supply of ATP to drive net CO(2) assimilation. The requirement for ATP depends on the activities of both PCR and PCO cycles, and changes in both WWC and CEF-PSI were compared with the data obtained in intact leaves. Furthermore, the fact that CEF-PSI cannot function independently has been demonstrated. I propose a model for the regulation of CEF-PSI by WWC, in which WWC is indispensable as an electron sink for the expression of CEF-PSI activity.

A two-year follow-up study of the PCV2 status of a Danish pig herd that was initially assumed to be PCV2-free.

PubMed

Kristensen, Charlotte S; Hjulsager, Charlotte K; Larsen, Lars E

2015-01-01

A longitudinal study was carried out to investigate whether a herd that had previously tested negative for porcine circovirus type 2 (PCV2) by polymerase chain reaction (PCR) was free of PCV2 or whether the negative profiles indicate that the level of PCV2 varies over time. In eight Danish herds that had initially tested negative for PCV2 by quantitative polymerase chain reaction (PCR), additional sampling was performed. Only one of the herds was still PCV2-negative in the additional sampling and was included in the study. The herd was a finishing herd, subclinically infected with PCV2, but vaccinated against PCV2 to improve performance. The herd was monitored by taking blood samples every seventh week over a period of two years and was not found to be continuously negative for PCV2 by PCR. The first time PCV2 was detected by PCR, in May 2010, PCV2 vaccination had been withdrawn from the herd, and at the same time the herd was infected with porcine reproductive and respiratory syndrome virus (PRRS). The PCV2-negative status, measured by PCR, was obtained in the first sampling after the PCV2 vaccination had been reintroduced. When PCV2 vaccination was withdrawn again in September 2011, the herd tested positive for PCV2 by PCR, and this time it continued to be PCV2-positive, even though PCV2 vaccination had been reintroduced. A Danish finishing herd that appeared to be PCV2-free from the start of a period of two years was not free of PCV2 during the entire period.

Microfluidic system for the identification of bacterial pathogens causing urinary tract infections

NASA Astrophysics Data System (ADS)

Becker, Holger; Hlawatsch, Nadine; Haraldsson, Tommy; van der Wijngaart, Wouter; Lind, Anders; Malhotra-Kumar, Surbi; Turlej-Rogacka, Agata; Goossens, Herman

2015-03-01

Urinary tract infections (UTIs) are among the most common bacterial infections and pose a significant healthcare burden. The growing trend in antibiotic resistance makes it mandatory to develop diagnostic kits which allow not only the determination of a pathogen but also the antibiotic resistances. We have developed a microfluidic cartridge which takes a direct urine sample, extracts the DNA, performs an amplification using batch-PCR and flows the sample over a microarray which is printed into a microchannel for fluorescence detection. The cartridge is injection-molded out of COP and contains a set of two-component injection-molded rotary valves to switch between input and to isolate the PCR chamber during thermocycling. The hybridization probes were spotted directly onto a functionalized section of the outlet microchannel. We have been able to successfully perform PCR of E.coli in urine in this chip and perform a fluorescence detection of PCR products. An upgraded design of the cartridge contains the buffers and reagents in blisters stored on the chip.

Verification of a computational cardiovascular system model comparing the hemodynamics of a continuous flow to a synchronous valveless pulsatile flow left ventricular assist device.

PubMed

Gohean, Jeffrey R; George, Mitchell J; Pate, Thomas D; Kurusz, Mark; Longoria, Raul G; Smalling, Richard W

2013-01-01

The purpose of this investigation is to use a computational model to compare a synchronized valveless pulsatile left ventricular assist device with continuous flow left ventricular assist devices at the same level of device flow, and to verify the model with in vivo porcine data. A dynamic system model of the human cardiovascular system was developed to simulate the support of a healthy or failing native heart from a continuous flow left ventricular assist device or a synchronous pulsatile valveless dual-piston positive displacement pump. These results were compared with measurements made during in vivo porcine experiments. Results from the simulation model and from the in vivo counterpart show that the pulsatile pump provides higher cardiac output, left ventricular unloading, cardiac pulsatility, and aortic valve flow as compared with the continuous flow model at the same level of support. The dynamic system model developed for this investigation can effectively simulate human cardiovascular support by a synchronous pulsatile or continuous flow ventricular assist device.

Verification of a computational cardiovascular system model comparing the hemodynamics of a continuous flow to a synchronous valveless pulsatile flow left ventricular assist device

PubMed Central

Gohean, Jeffrey R.; George, Mitchell J.; Pate, Thomas D.; Kurusz, Mark; Longoria, Raul G.; Smalling, Richard W.

2012-01-01

The purpose of this investigation is to utilize a computational model to compare a synchronized valveless pulsatile left ventricular assist device to continuous flow left ventricular assist devices at the same level of device flow, and to verify the model with in vivo porcine data. A dynamic system model of the human cardiovascular system was developed to simulate support of a healthy or failing native heart from a continuous flow left ventricular assist device or a synchronous, pulsatile, valveless, dual piston positive displacement pump. These results were compared to measurements made during in vivo porcine experiments. Results from the simulation model and from the in vivo counterpart show that the pulsatile pump provides higher cardiac output, left ventricular unloading, cardiac pulsatility, and aortic valve flow as compared to the continuous flow model at the same level of support. The dynamic system model developed for this investigation can effectively simulate human cardiovascular support by a synchronous pulsatile or continuous flow ventricular assist device. PMID:23438771

Enhancement of expression of survivin promoter-driven CD/TK double suicide genes by the nuclear matrix attachment region in transgenic gastric cancer cells.

PubMed

Niu, Ying; Li, Jian-Sheng; Luo, Xian-Run

2014-01-25

This work aimed to study a novel transgenic expression system of the CD/TK double suicide genes enhanced by the nuclear matrix attachment region (MAR) for gene therapy. The recombinant vector pMS-CD/TK containing the MAR-survivin promoter-CD/TK cassette was developed and transfected into human gastric cancer SGC-7901 cells. Expression of the CD/TK genes was detected by quantitative real-time PCR (qPCR) and Western blot. Cell viability and apoptosis were measured using the methyl thiazolyl tetrazolium (MTT) assay and flow cytometry. When the MAR fragment was inserted into the upstream of the survivin promoter, the qPCR result showed that the expression of the CD/TK genes significantly increased 7.7-fold in the transgenic SGC-7901 cells with plasmid pMS-CD/TK compared with that without MAR. MTT and flow cytometry analyses indicated that treatment with the prodrugs (5-FC+GCV) significantly decreased the cellular survival rate and enhanced the cellular apoptosis in the SGC-7901 cells. The expression of the CD/TK double suicide genes driven by the survivin promoter can be enhanced by the MAR fragment in human gastric cancer cells. Copyright © 2013 Elsevier B.V. All rights reserved.

Organic loading rate and food-to-microorganism ratio shape prokaryotic diversity in a demo-scale up-flow anaerobic sludge blanket reactor treating domestic wastewater.

PubMed

Cardinali-Rezende, Juliana; Araújo, Juliana C; Almeida, Paulo G S; Chernicharo, Carlos A L; Sanz, José L; Chartone-Souza, Edmar; Nascimento, Andréa M A

2013-12-01

We investigated the microbial community in an up-flow anaerobic sludge blanket (UASB) reactor treating domestic wastewater (DW) during two different periods of organic loading rate (OLR) and food-to-microorganism (F/M) ratio. 16S rDNA clone libraries were generated, and quantitative real-time PCR (qPCR) analyses were performed. Fluctuations in the OLR and F/M ratio affected the abundance and the composition of the UASB prokaryotic community, mainly at the species level, as well as the performance of the UASB reactor. The qPCR analysis suggested that there was a decrease in the bacterial cell number during the rainy season, when the OLR and F/M ratio were lower. However, the bacterial diversity was higher during this time, suggesting that the community degraded more diversified substrates. The diversity and the abundance of the archaeal community were higher when the F/M ratio was lower. Shifts in the methanogenic community composition might have influenced the route of methane production, with methane produced by acetotrophic methanogens (dry season), and by hydrogenotrophic, methylotrophic and acetotrophic methanogens (rainy season). This study revealed higher levels of bacterial diversity, metabolic specialization and chemical oxygen demand removal efficiency of the DW UASB reactor during the rainy season.

Chip-based sequencing nucleic acids

DOEpatents

Beer, Neil Reginald

2014-08-26

A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

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

PubMed

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

2013-09-01

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

Development of a Stable Cell Line, Overexpressing Human T-cell Immunoglobulin Mucin 1

PubMed Central

Ebrahimi, Mina; Kazemi, Tohid; Ganjalikhani-hakemi, Mazdak; Majidi, Jafar; khanahmad, Hossein; Rahimmanesh, Ilnaz; Homayouni, Vida; Kohpayeh, Shirin

2015-01-01

Background Recent researches have demonstrated that human T-cell immunoglobulin mucin 1 (TIM-1) glycoprotein plays important roles in regulation of autoimmune and allergic diseases, as well as in tumor immunity and response to viral infections. Therefore, targeting TIM-1 could be a potential therapeutic approach against such diseases. Objectives In this study, we aimed to express TIM-1 protein on Human Embryonic kidney (HEK) 293T cell line in order to have an available source of the TIM-1 antigen. Materials and Methods The cDNA was synthesized after RNA extraction from peripheral blood mononuclear cells (PBMC) and TIM-1 cDNA was amplified by PCR with specific primers. The PCR product was cloned in pcDNA™3.1/Hygro (+) and transformed in Escherichia coli TOP 10 F’. After cloning, authenticity of DNA sequence was checked and expressed in HEK 293T cells. Finally, expression of TIM-1 was analyzed by flow cytometry and real-time PCR. Results The result of DNA sequencing demonstrated correctness of TIM-1 DNA sequence. The flow cytometry results indicated that TIM-1 was expressed in about 90% of transfected HEK 293T cells. The real-time PCR analysis showed TIM-1 mRNA expression increased 195-fold in transfected cells compared with un-transfected cells. Conclusions Findings of present study demonstrated the successful cloning and expression of TIM-1 on HEK 293T cells. These cells could be used as an immunogenic source for production of specific monoclonal antibodies, nanobodies and aptamers against human TIM-1. PMID:28959306

Mycophenolate mofetil prevents the delayed T cell response after pilocarpine-induced status epilepticus in mice

PubMed Central

Engelmann, Robby; Sellmann, Tina; Köhling, Rüdiger; Müller-Hilke, Brigitte

2017-01-01

Growing clinical and laboratory evidence corroborates a role for the immune system in the pathophysiology of epilepsy. In order to delineate the immune response following pilocarpine-induced status epilepticus (SE) in the mouse, we monitored the kinetics of leukocyte presence in the hippocampus over the period of four weeks. SE was induced following a ramping protocol of pilocarpine injection into 4–5 weeks old C57BL/6 mice. Brains were removed at days 1–4, 14 or 28 after SE, and the hippocampi were analyzed via flow cytometry, via quantitative reverse transcriptase PCR (qRT-PCR) and via immunohistochemistry. Epileptogenesis was confirmed by Timm staining of mossy fiber sprouting in the inner molecular layer of the dentate gyrus. The flow cytometry data revealed a biphasic immune response following pilocarpine-induced SE with a transient increase in activated CD11b+ and F4/80+ macrophages within the first four days replaced by an increase in CD3+ T-lymphocytes around day 28. This delayed T cell response was confirmed via qRT-PCR and via immunohistochemistry. In addition, qRT-PCR data could show that the delayed T cell response was associated with an increased CD8/CD4 ratio indicating a cytotoxic T cell response after SE. Intriguingly, early intervention with mycophenolate mofetil administration on days 0–3 after SE prevented this delayed T cell response. These results show an orchestrated immunological sequela and provide evidence that the delayed T cell response is sensitive to early immunomodulatory intervention. PMID:29182639

Assessment of real-time PCR based methods for quantification of pollen-mediated gene flow from GM to conventional maize in a field study.

PubMed

Pla, Maria; La Paz, José-Luis; Peñas, Gisela; García, Nora; Palaudelmàs, Montserrat; Esteve, Teresa; Messeguer, Joaquima; Melé, Enric

2006-04-01

Maize is one of the main crops worldwide and an increasing number of genetically modified (GM) maize varieties are cultivated and commercialized in many countries in parallel to conventional crops. Given the labeling rules established e.g. in the European Union and the necessary coexistence between GM and non-GM crops, it is important to determine the extent of pollen dissemination from transgenic maize to other cultivars under field conditions. The most widely used methods for quantitative detection of GMO are based on real-time PCR, which implies the results are expressed in genome percentages (in contrast to seed or grain percentages). Our objective was to assess the accuracy of real-time PCR based assays to accurately quantify the contents of transgenic grains in non-GM fields in comparison with the real cross-fertilization rate as determined by phenotypical analysis. We performed this study in a region where both GM and conventional maize are normally cultivated and used the predominant transgenic maize Mon810 in combination with a conventional maize variety which displays the characteristic of white grains (therefore allowing cross-pollination quantification as percentage of yellow grains). Our results indicated an excellent correlation between real-time PCR results and number of cross-fertilized grains at Mon810 levels of 0.1-10%. In contrast, Mon810 percentage estimated by weight of grains produced less accurate results. Finally, we present and discuss the pattern of pollen-mediated gene flow from GM to conventional maize in an example case under field conditions.

Unified approach for incompressible flows

NASA Astrophysics Data System (ADS)

Chang, Tyne-Hsien

1993-12-01

An unified approach for solving both compressible and incompressible flows was investigated in this study. The difference in CFD code development between incompressible and compressible flows is due to the mathematical characteristics. However, if one can modify the continuity equation for incompressible flows by introducing pseudocompressibility, the governing equations for incompressible flows would have the same mathematical characters as compressible flows. The application of a compressible flow code to solve incompressible flows becomes feasible. Among numerical algorithms developed for compressible flows, the Centered Total Variation Diminishing (CTVD) schemes possess better mathematical properties to damp out the spurious oscillations while providing high-order accuracy for high speed flows. It leads us to believe that CTVD schemes can equally well solve incompressible flows. In this study, the governing equations for incompressible flows include the continuity equation and momentum equations. The continuity equation is modified by adding a time-derivative of the pressure term containing the artificial compressibility. The modified continuity equation together with the unsteady momentum equations forms a hyperbolic-parabolic type of time-dependent system of equations. The continuity equation is modified by adding a time-derivative of the pressure term containing the artificial compressibility. The modified continuity equation together with the unsteady momentum equations forms a hyperbolic-parabolic type of time-dependent system of equations. Thus, the CTVD schemes can be implemented. In addition, the boundary conditions including physical and numerical boundary conditions must be properly specified to obtain accurate solution. The CFD code for this research is currently in progress. Flow past a circular cylinder will be used for numerical experiments to determine the accuracy and efficiency of the code before applying this code to more specific applications.

Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems: applications and considerations.

PubMed

Kim, Jaai; Lim, Juntaek; Lee, Changsoo

2013-12-01

Quantitative real-time PCR (qPCR) has been widely used in recent environmental microbial ecology studies as a tool for detecting and quantifying microorganisms of interest, which aids in better understandings of the complexity of wastewater microbial communities. Although qPCR can be used to provide more specific and accurate quantification than other molecular techniques, it does have limitations that must be considered when applying it in practice. This article reviews the principle of qPCR quantification and its applications to microbial ecology studies in various wastewater treatment environments. Here we also address several limitations of qPCR-based approaches that can affect the validity of quantification data: template nucleic acid quality, nucleic acid extraction efficiency, specificity of group-specific primers and probes, amplification of nonviable DNA, gene copy number variation, and limited number of sequences in the database. Even with such limitations, qPCR is reportedly among the best methods for quantitatively investigating environmental microbial communities. The application of qPCR is and will continue to be increasingly common in studies of wastewater treatment systems. To obtain reliable analyses, however, the limitations that have often been overlooked must be carefully considered when interpreting the results. Copyright © 2013 Elsevier Inc. All rights reserved.

Early diagnosis of typhoid fever by nested PCR for flagellin gene of Salmonella enterica serotype Typhi.

PubMed

Khan, S; Harish, B N; Menezes, G A; Acharya, N S; Parija, S C

2012-11-01

Typhoid fever caused by Salmonella Typhi continues to be a major health problem in spite of the use of antibiotics and the development of newer antibacterial drugs. Inability to make an early laboratory diagnosis and resort to empirical therapy, often lead to increased morbidity and mortality in cases of typhoid fever. This study was aimed to optimize a nested PCR for early diagnosis of typhoid fever and using it as a diagnostic tool in culture negative cases of suspected typhoid fever. Eighty patients with clinical diagnosis of typhoid fever and 40 controls were included in the study. The blood samples collected were subjected to culture, Widal and nested PCR targeting the flagellin gene of S. Typhi. The sensitivity of PCR on blood was found to be 100 per cent whereas the specificity was 76.9 per cent. The positive predictive value (PPV) of PCR was calculated to be 76.9 per cent with an accuracy of 86 per cent. None of the 40 control samples gave a positive PCR. Due to its high sensitivity and specificity nested PCR can be used as a useful tool to diagnose clinically suspected, culture negative cases of typhoid fever.

Continuous Flow Science in an Undergraduate Teaching Laboratory: Bleach-Mediated Oxidation in a Biphasic System

ERIC Educational Resources Information Center

Kairouz, Vanessa; Collins, Shawn K.

2018-01-01

An undergraduate teaching laboratory experiment involving a continuous flow, bleach-mediated oxidation of aldehydes under biphasic conditions was developed that allowed students to explore concepts of mixing or mass transport, solvent sustainability, biphasic reactions, phase transfer catalysis, and continuous flow chemistry.

Applications of Continuous-Flow Photochemistry in Organic Synthesis, Material Science, and Water Treatment.

PubMed

Cambié, Dario; Bottecchia, Cecilia; Straathof, Natan J W; Hessel, Volker; Noël, Timothy

2016-09-14

Continuous-flow photochemistry in microreactors receives a lot of attention from researchers in academia and industry as this technology provides reduced reaction times, higher selectivities, straightforward scalability, and the possibility to safely use hazardous intermediates and gaseous reactants. In this review, an up-to-date overview is given of photochemical transformations in continuous-flow reactors, including applications in organic synthesis, material science, and water treatment. In addition, the advantages of continuous-flow photochemistry are pointed out and a thorough comparison with batch processing is presented.

Rapid Sample Processing for Detection of Food-Borne Pathogens via Cross-Flow Microfiltration

PubMed Central

Li, Xuan; Ximenes, Eduardo; Amalaradjou, Mary Anne Roshni; Vibbert, Hunter B.; Foster, Kirk; Jones, Jim; Liu, Xingya; Bhunia, Arun K.

2013-01-01

This paper reports an approach to enable rapid concentration and recovery of bacterial cells from aqueous chicken homogenates as a preanalytical step of detection. This approach includes biochemical pretreatment and prefiltration of food samples and development of an automated cell concentration instrument based on cross-flow microfiltration. A polysulfone hollow-fiber membrane module having a nominal pore size of 0.2 μm constitutes the core of the cell concentration instrument. The aqueous chicken homogenate samples were circulated within the cross-flow system achieving 500- to 1,000-fold concentration of inoculated Salmonella enterica serovar Enteritidis and naturally occurring microbiota with 70% recovery of viable cells as determined by plate counting and quantitative PCR (qPCR) within 35 to 45 min. These steps enabled 10 CFU/ml microorganisms in chicken homogenates or 102 CFU/g chicken to be quantified. Cleaning and sterilizing the instrument and membrane module by stepwise hydraulic and chemical cleaning (sodium hydroxide and ethanol) enabled reuse of the membrane 15 times before replacement. This approach begins to address the critical need for the food industry for detecting food pathogens within 6 h or less. PMID:24014538

Sensitivity of a real-time PCR method for the detection of transgenes in a mixture of transgenic and non-transgenic seeds of papaya (Carica papaya L.).

PubMed

Nageswara-Rao, Madhugiri; Kwit, Charles; Agarwal, Sujata; Patton, Mariah T; Skeen, Jordan A; Yuan, Joshua S; Manshardt, Richard M; Stewart, C Neal

2013-09-01

Genetically engineered (GE) ringspot virus-resistant papaya cultivars 'Rainbow' and 'SunUp' have been grown in Hawai'i for over 10 years. In Hawai'i, the introduction of GE papayas into regions where non-GE cultivars are grown and where feral non-GE papayas exist have been accompanied with concerns associated with transgene flow. Of particular concern is the possibility of transgenic seeds being found in non-GE papaya fruits via cross-pollination. Development of high-throughput methods to reliably detect the adventitious presence of such transgenic material would benefit both the scientific and regulatory communities. We assessed the accuracy of using conventional qualitative polymerase chain reaction (PCR) as well as real-time PCR-based assays to quantify the presence of transgenic DNA from bulk samples of non-GE papaya seeds. In this study, an optimized method of extracting high quality DNA from dry seeds of papaya was standardized. A reliable, sensitive real-time PCR method for detecting and quantifying viral coat protein (cp) transgenes in bulk seed samples utilizing the endogenous papain gene is presented. Quantification range was from 0.01 to 100 ng/μl of GE-papaya DNA template with a detection limit as low as 0.01% (10 pg). To test this system, we simulated transgene flow using known quantities of GE and non-GE DNA and determined that 0.038% (38 pg) GE papaya DNA could be detected using real-time PCR. We also validated this system by extracting DNA from known ratios of GE seeds to non-GE seeds of papaya followed by real-time PCR detection and observed a reliable detection limit of 0.4%. This method for the quick and sensitive detection of transgenes in bulked papaya seed lots using conventional as well as real-time PCR-based methods will benefit numerous stakeholders. In particular, this method could be utilized to screen selected fruits from maternal non-GE papaya trees in Hawai'i for the presence of transgenic seed at typical regulatory threshold levels. Incorporation of subtle differences in primers and probes for variations in cp worldwide should allow this method to be utilized elsewhere when and if deregulation of transgenic papaya occurs.

Sensitivity of a real-time PCR method for the detection of transgenes in a mixture of transgenic and non-transgenic seeds of papaya (Carica papaya L.)

PubMed Central

2013-01-01

Background Genetically engineered (GE) ringspot virus-resistant papaya cultivars ‘Rainbow’ and ‘SunUp’ have been grown in Hawai’i for over 10 years. In Hawai’i, the introduction of GE papayas into regions where non-GE cultivars are grown and where feral non-GE papayas exist have been accompanied with concerns associated with transgene flow. Of particular concern is the possibility of transgenic seeds being found in non-GE papaya fruits via cross-pollination. Development of high-throughput methods to reliably detect the adventitious presence of such transgenic material would benefit both the scientific and regulatory communities. Results We assessed the accuracy of using conventional qualitative polymerase chain reaction (PCR) as well as real-time PCR-based assays to quantify the presence of transgenic DNA from bulk samples of non-GE papaya seeds. In this study, an optimized method of extracting high quality DNA from dry seeds of papaya was standardized. A reliable, sensitive real-time PCR method for detecting and quantifying viral coat protein (cp) transgenes in bulk seed samples utilizing the endogenous papain gene is presented. Quantification range was from 0.01 to 100 ng/μl of GE-papaya DNA template with a detection limit as low as 0.01% (10 pg). To test this system, we simulated transgene flow using known quantities of GE and non-GE DNA and determined that 0.038% (38 pg) GE papaya DNA could be detected using real-time PCR. We also validated this system by extracting DNA from known ratios of GE seeds to non-GE seeds of papaya followed by real-time PCR detection and observed a reliable detection limit of 0.4%. Conclusions This method for the quick and sensitive detection of transgenes in bulked papaya seed lots using conventional as well as real-time PCR-based methods will benefit numerous stakeholders. In particular, this method could be utilized to screen selected fruits from maternal non-GE papaya trees in Hawai’i for the presence of transgenic seed at typical regulatory threshold levels. Incorporation of subtle differences in primers and probes for variations in cp worldwide should allow this method to be utilized elsewhere when and if deregulation of transgenic papaya occurs. PMID:24004548

Quantitative PCR and Digital PCR for Detection of Ascaris lumbricoides Eggs in Reclaimed Water

PubMed Central

Santísima-Trinidad, Ana Belén; Bornay-Llinares, Fernando Jorge; Martín González, Marcos; Pascual Valero, José Antonio; Ros Muñoz, Margarita

2017-01-01

The reuse of reclaimed water from wastewater depuration is a widespread and necessary practice in many areas around the world and must be accompanied by adequate and continuous quality control. Ascaris lumbricoides is one of the soil-transmitted helminths (STH) with risk for humans due to its high infectivity and an important determinant of transmission is the inadequacy of water supplies and sanitation. The World Health Organization (WHO) recommends a limit equal to or lower than one parasitic helminth egg per liter, to reuse reclaimed water for unrestricted irrigation. We present two new protocols of DNA extraction from large volumes of reclaimed water. Quantitative PCR (qPCR) and digital PCR (dPCR) were able to detect low amounts of A. lumbricoides eggs. By using the first extraction protocol, which processes 500 mL of reclaimed water, qPCR can detect DNA concentrations as low as one A. lumbricoides egg equivalent, while dPCR can detect DNA concentrations as low as five A. lumbricoides egg equivalents. By using the second protocol, which processes 10 L of reclaimed water, qPCR was able to detect DNA concentrations equivalent to 20 A. lumbricoides eggs. This fact indicated the importance of developing new methodologies to detect helminth eggs with higher sensitivity and precision avoiding possible human infection risks. PMID:28377928

Methods used to compute low-flow frequency characteristics for continuous-record streamflow stations in Minnesota, 2006

USGS Publications Warehouse

Winterstein, Thomas A.; Arntson, Allan D.; Mitton, Gregory B.

2007-01-01

The 1-, 7-, and 30-day low-flow series were determined for 120 continuous-record streamflow stations in Minnesota having at least 20 years of continuous record. The 2-, 5-, 10-, 50-, and 100-year statistics were determined for each series by fitting a log Pearson type III distribution to the data. The methods used to determine the low-flow statistics and to construct the plots of the low-flow frequency curves are described. The low-flow series and the low-flow statistics are presented in tables and graphs.

A fluorometric lateral flow assay for visual detection of nucleic acids using a digital camera readout.

PubMed

Magiati, Maria; Sevastou, Areti; Kalogianni, Despina P

2018-06-04

A fluorometric lateral flow assay has been developed for the detection of nucleic acids. The fluorophores phycoerythrin (PE) and fluorescein isothiocyanate (FITC) were used as labels, while a common digital camera and a colored vinyl-sheet, acting as a cut-off optical filter, are used for fluorescence imaging. After DNA amplification by polymerase chain reaction (PCR), the biotinylated PCR product is hybridized to its complementary probe that carries a poly(dA) tail at 3΄ edge and then applied to the lateral flow strip. The hybrids are captured to the test zone of the strip by immobilized poly(dT) sequences and detected by streptavidin-fluorescein and streptavidin-phycoerythrin conjugates, through streptavidin-biotin interaction. The assay is widely applicable, simple, cost-effective, and offers a large multiplexing potential. Its performance is comparable to assays based on the use of streptavidin-gold nanoparticles conjugates. As low as 7.8 fmol of a ssDNA and 12.5 fmol of an amplified dsDNA target were detectable. Graphical abstract Schematic presentation of a fluorometric lateral flow assay based on fluorescein and phycoerythrin fluorescent labels for the detection of single-stranded (ssDNA) and double-stranded DNA (dsDNA) sequences and using a digital camera readout. SA: streptavidin, BSA: Bovine Serum Albumin, B: biotin, FITC: fluorescein isothiocyanate, PE: phycoerythrin, TZ: test zone, CZ: control zone.

Continuous and Pulsatile Pediatric Ventricular Assist Device Hemodynamics with a Viscoelastic Blood Model

PubMed Central

Good, Bryan C.; Deutsch, Steven; Manning, Keefe B.

2015-01-01

Purpose To investigate the effects of pulsatile and continuous pediatric ventricular assist (PVAD) flow and pediatric blood viscoelasticity on hemodynamics in a pediatric aortic graft model. Methods Hemodynamic parameters of pulsatility, along with velocity and wall shear stress (WSS), are analyzed and compared between Newtonian and viscoelastic blood models at a range of physiological pediatric hematocrits using computational fluid dynamics. Results Both pulsatile and continuous PVAD flow lead to a decrease in pulsatility (surplus hemodynamic energy (SHE), ergs/cm3) compared to healthy aortic flow but with continuous PVAD pulsatility up to 2.4 times lower than pulsatile PVAD pulsatility at each aortic outlet. Significant differences are also seen between the two flow modes in velocity and WSS. The higher velocity jet during systole with pulsatile flow leads to higher WSSs at the anastomotic toe and at the aortic branch bifurcations. The lower velocity but continuous flow jet leads to a much different flow field and higher WSSs into diastole. Under a range of physiological pediatric hematocrit (20-60%), both velocity and WSS can vary significantly with the higher hematocrit blood model generally leading to higher peak WSSs but also lower WSSs in regions of flow separation. Conclusions The large decrease in pulsatility seen from continuous PVAD flow could lead to complications in pediatric vascular development while the high WSSs during peak systole from pulsatile PVAD flow could lead to blood damage. Both flow modes lead to similar regions prone to intimal hyperplasia (IH) resulting from low time-averaged WSS (TAWSS) and high oscillatory shear index (OSI). PMID:26643646

Effect of the load size on the efficiency of microwave heating under stop flow and continuous flow conditions.

PubMed

Patil, Narendra G; Rebrov, Evgeny V; Eränen, Kari; Benaskar, Faysal; Meuldijk, Jan; Mikkola, Jyri-Pekka; Hessel, Volker; Hulshof, Lumbertus A; Murzin, Dmitry Yu; Schouten, Jaap C

2012-01-01

A novel heating efficiency analysis of the microwave heated stop-flow (i.e. stagnant liquid) and continuous-flow reactors has been presented. The thermal losses to the surrounding air by natural convection have been taken into account for heating efficiency calculation of the microwave heating process. The effect of the load diameter in the range of 4-29 mm on the heating efficiency of ethylene glycol was studied in a single mode microwave cavity under continuous flow and stop-flow conditions. The variation of the microwave absorbing properties of the load with temperature was estimated. Under stop-flow conditions, the heating efficiency depends on the load diameter. The highest heating efficiency has been observed at the load diameter close to the half wavelength of the electromagnetic field in the corresponding medium. Under continuous-flow conditions, the heating efficiency increased linearly. However, microwave leakage above the propagation diameter restricted further experimentation at higher load diameters. Contrary to the stop-flow conditions, the load temperature did not raise monotonously from the inlet to outlet under continuous-flow conditions. This was due to the combined effect of lagging convective heat fluxes in comparison to volumetric heating. This severely disturbs the uniformity of the electromagnetic field in the axial direction and creates areas of high and low field intensity along the load Length decreasing the heating efficiency as compared to stop-flow conditions.

Development of a CMOS-compatible PCR chip: comparison of design and system strategies

NASA Astrophysics Data System (ADS)

Erill, Ivan; Campoy, Susana; Rus, José; Fonseca, Luis; Ivorra, Antoni; Navarro, Zenón; Plaza, José A.; Aguiló, Jordi; Barbé, Jordi

2004-11-01

In the last decade research in chips for DNA amplification through the polymerase chain reaction (PCR) has been relatively abundant, but has taken very diverse approaches, leaving little common ground for a straightforward comparison of results. Here we report the development of a line of PCR chips that is fully compatible with complementary-metal-oxide-semiconductor (CMOS) technology and its revealing use as a general platform to test and compare a wide range of experimental parameters involved in PCR-chip design and operation. Peltier-heated and polysilicon thin-film driven PCR chips have been produced and directly compared in terms of efficiency, speed and power consumption, showing that thin-film systems run faster and more efficiently than Peltier-based ones, but yield inferior PCR products. Serpentine-like chamber designs have also been compared with standard rectangular designs and with the here reported rhomboidal chamber shape, showing that serpentine-like chambers do not have detrimental effects in PCR efficiency when using non-flow-through schemes, and that chamber design has a strong impact on sample insertion/extraction yields. With an accurate temperature control (±0.2 °C) we have optimized reaction kinetics to yield sound PCR amplifications of 25 µl mixtures in 20 min and with 24.4 s cycle times, confirming that a titrated amount of bovine albumin serum (BSA, 2.5 µg µl-1) is essential to counteract polymerase adsorption at chip walls. The reported use of a CMOS-compatible technological process paves the way for an easy adaption to foundry requirements and for a scalable integration of electro-optic detection and control circuitry.

Combined use of reverse transcriptase polymerase chain reaction and flow cytometry to study minimal residual disease in Philadelphia positive acute lymphoblastic leukemia.

PubMed

Muñoz, L; López, O; Martino, R; Brunet, S; Bellido, M; Rubiol, E; Sierra, J; Nomdedéu, J F

2000-07-01

The Philadelphia chromosome in acute lymphoblastic leukemia (Ph+ ALL) is associated with a poor prognosis given the high frequency of chemoresistance and leukemia relapse. Minimal residual disease (MRD) detection before cytogenetic and hematologic relapse could be useful in early therapy. The most suitable methods for detecting MRD in Ph+ ALL are flow cytometry (FC) and reverse transcriptase polymerase chain reaction (RT-PCR). However, since both techniques carry the risk of false-negative results the combined use of these two techniques could overcome this problem. We report our experience using this approach in 47 bone marrow samples obtained from 10 Ph+ ALL patients. Twenty-seven marrow aspirates were taken from patients in clinical remission (CR). The samples were considered positive for MRD by FC when two conditions were met: 1) detection of an abnormal B-cell differentiation pattern and 2) presence of more than 1x10(-3) cells coexpressing CD22/CD34/CD45 or CD66/CD34/CD10. After FC analysis, RNA was purified using standard methods. FC was positive in 23/27 samples in CR (sensitivity 85%). RT-PCR was successfully performed in 23 samples in CR. RT-PCR was positive in 18/23 samples (sensitivity 78%). There were 5 samples with discordant results. FC was positive in 3 samples with a negative RT-PCR and FC was negative in 2 samples with a positive RT. All the 10 patients relapsed and only 1 is currently alive after an allogeneic stem cell transplantation (alloSCT). The median (range) time from MRD detection to relapse in patients treated with chemotherapy was 42 (39-71) days. These data suggest that RT-PCR may be negative despite the presence of neoplastic cells identified by their immunophenotypic traits. We conclude that immunologic and molecular techniques can be used in tandem for monitoring MRD in Ph+ ALL.

Evaluation of lateral flow devices for identification of infected poultry by testing swab and feather specimens during H5N1 highly pathogenic avian influenza outbreaks in Vietnam.

PubMed

Slomka, Marek J; To, Thanh L; Tong, Hien H; Coward, Vivien J; Mawhinney, Ian C; Banks, Jill; Brown, Ian H

2012-09-01

Evaluation of two commercial lateral flow devices (LFDs) for avian influenza (AI) detection in H5N1 highly pathogenic AI infected poultry in Vietnam. Determine sensitivity and specificity of the LFDs relative to a validated highly sensitive H5 RRT PCR. Swabs (cloacal and tracheal) and feathers were collected from 46 chickens and 48 ducks (282 clinical specimens) and tested by both LFDs and H5 RRT PCR. A subset of 59 chicken and 34 duck specimens was also tested by virus isolation (VI), the 'gold standard'. Twenty-six chickens and 15 ducks were shown to be infected by at least one RRT PCR positive clinical specimen per bird. Bird-level sensitivity for the Anigen LFD was 84·6% for chickens and 53·3% for ducks, and for the Quickvue LFD 65·4% for chickens and 33·3% for ducks. Comparison of the three clinical specimens revealed that chicken feathers were the most sensitive with 84% and 56% sensitivities for Anigen and Quickvue respectively. All 21 RRT PCR positive swabs from ducks were negative by both LFDs. However, duck feather testing gave sensitivities of 53·3% and 33·3% for Anigen and Quickvue respectively. Specificity was 100% for both LFDs in all investigations. Although LFDs were less sensitive than AI RRT PCR and VI, high titre viral shedding in H5N1 highly pathogenic avian influenza (HPAI) infected and diseased chickens is sufficient for a proportion of birds to be identified as AI infected by LFDs. Feathers were the optimal specimen for LFD testing in such diseased HPAI scenarios, particularly for ducks where swab testing by LFDs failed to identify any infected birds. However, specimens should be forwarded to the laboratory for confirmation by more sensitive diagnostic techniques. © 2011 Blackwell Publishing Ltd.

Establishment and application of cross-priming isothermal amplification coupled with lateral flow dipstick (CPA-LFD) for rapid and specific detection of red-spotted grouper nervous necrosis virus.

PubMed

Su, Zi Dan; Shi, Cheng Yin; Huang, Jie; Shen, Gui Ming; Li, Jin; Wang, Sheng Qiang; Fan, Chao

2015-09-26

Red-spotted grouper nervous necrosis virus (RGNNV) is an important pathogen that causes diseases in many species of fish in marine aquaculture. The larvae and juveniles are more easily infected by RGNNV and the cumulative mortality is as high as 100 % after being infected with RGNNV. This virus imposes a serious threat to aquaculture of grouper fry. This study aimed to establish a simple, accurate and highly sensitive method for rapid detection of RGNNV on the spot. In this study, the primers specifically targeting RGNNV were designed and cross-priming isothermal amplification (CPA) system was established. The product amplified by CPA was detected through visualization with lateral flow dipstick (LFD). Three important parameters, including the amplification temperature, the concentration of dNTPs and the concentration of Mg(2+) for the CPA system, were optimized. The sensitivity and specificity of this method for RGNNV were tested and compared with those of the conventional RT-PCR and real-time quantitative RT-PCR (qRT-PCR). The optimized conditions for the CPA amplification system were determined as follows: the optimal amplification temperature, the optimized concentration of dNTPs and the concentration for Mg(2+) were 69 °C, 1.2 mmol/L and 5 mmol/L, respectively. The lowest limit of detection (LLOD) of this method for RGNNV was 10(1) copies/μL of RNA sample, which was 10 times lower than that of conventional RT-PCR and comparable to that of RT-qPCR. This method was specific for RGNNV in combination with SJNNV and had no cross-reactions with 8 types of virus and bacterial strains tested. This method was successfully applied to detect RGNNV in fish samples. This study established a CPA-LFD method for detection of RGNNV. This method is simple and rapid with high sensitivity and good specificity and can be widely applied for rapid detection of this virus on the spot.

40 CFR Table 5 to Subpart Hhhhhhh... - Operating Parameters, Operating Limits and Data Monitoring, Recording and Compliance Frequencies...

Code of Federal Regulations, 2013 CFR

2013-07-01

... conductivity Continuous Every 15 minutes 3-hour block average. Regenerative Adsorber Regeneration stream flow. Minimum total flow per regeneration cycle Continuous N/A Total flow for each regeneration cycle. Adsorber bed temperature. Maximum temperature Continuously after regeneration and within 15 minutes of...

40 CFR Table 5 to Subpart Hhhhhhh... - Operating Parameters, Operating Limits and Data Monitoring, Recording and Compliance Frequencies...

Code of Federal Regulations, 2014 CFR

2014-07-01

... conductivity Continuous Every 15 minutes 3-hour block average. Regenerative Adsorber Regeneration stream flow. Minimum total flow per regeneration cycle Continuous N/A Total flow for each regeneration cycle. Adsorber bed temperature. Maximum temperature Continuously after regeneration and within 15 minutes of...

Asymmetric reactions in continuous flow

PubMed Central

Mak, Xiao Yin; Laurino, Paola

2009-01-01

Summary An overview of asymmetric synthesis in continuous flow and microreactors is presented in this review. Applications of homogeneous and heterogeneous asymmetric catalysis as well as biocatalysis in flow are discussed. PMID:19478913

Novel molecular diagnostic tools for malaria elimination: a review of options from the point of view of high-throughput and applicability in resource limited settings.

PubMed

Britton, Sumudu; Cheng, Qin; McCarthy, James S

2016-02-16

As malaria transmission continues to decrease, an increasing number of countries will enter pre-elimination and elimination. To interrupt transmission, changes in control strategies are likely to require more accurate identification of all carriers of Plasmodium parasites, both symptomatic and asymptomatic, using diagnostic tools that are highly sensitive, high throughput and with fast turnaround times preferably performed in local health service settings. Currently available immunochromatographic lateral flow rapid diagnostic tests and field microscopy are unlikely to consistently detect infections at parasite densities less than 100 parasites/µL making them insufficiently sensitive for detecting all carriers. Molecular diagnostic platforms, such as PCR and LAMP, are currently available in reference laboratories, but at a cost both financially and in turnaround time. This review describes the recent progress in developing molecular diagnostic tools in terms of their capacity for high throughput and potential for performance in non-reference laboratories for malaria elimination.

Real-time PCR machine system modeling and a systematic approach for the robust design of a real-time PCR-on-a-chip system.

PubMed

Lee, Da-Sheng

2010-01-01

Chip-based DNA quantification systems are widespread, and used in many point-of-care applications. However, instruments for such applications may not be maintained or calibrated regularly. Since machine reliability is a key issue for normal operation, this study presents a system model of the real-time Polymerase Chain Reaction (PCR) machine to analyze the instrument design through numerical experiments. Based on model analysis, a systematic approach was developed to lower the variation of DNA quantification and achieve a robust design for a real-time PCR-on-a-chip system. Accelerated lift testing was adopted to evaluate the reliability of the chip prototype. According to the life test plan, this proposed real-time PCR-on-a-chip system was simulated to work continuously for over three years with similar reproducibility in DNA quantification. This not only shows the robustness of the lab-on-a-chip system, but also verifies the effectiveness of our systematic method for achieving a robust design.

Deriving Global Convection Maps From SuperDARN Measurements

NASA Astrophysics Data System (ADS)

Gjerloev, J. W.; Waters, C. L.; Barnes, R. J.

2018-04-01

A new statistical modeling technique for determining the global ionospheric convection is described. The principal component regression (PCR)-based technique is based on Super Dual Auroral Radar Network (SuperDARN) observations and is an advanced version of the PCR technique that Waters et al. (https//:doi.org.10.1002/2015JA021596) used for the SuperMAG data. While SuperMAG ground magnetic field perturbations are vector measurements, SuperDARN provides line-of-sight measurements of the ionospheric convection flow. Each line-of-sight flow has a known azimuth (or direction), which must be converted into the actual vector flow. However, the component perpendicular to the azimuth direction is unknown. Our method uses historical data from the SuperDARN database and PCR to determine a fill-in model convection distribution for any given universal time. The fill-in data process is driven by a list of state descriptors (magnetic indices and the solar zenith angle). The final solution is then derived from a spherical cap harmonic fit to the SuperDARN measurements and the fill-in model. When compared with the standard SuperDARN fill-in model, we find that our fill-in model provides improved solutions, and the final solutions are in better agreement with the SuperDARN measurements. Our solutions are far less dynamic than the standard SuperDARN solutions, which we interpret as being due to a lack of magnetosphere-ionosphere inertia and communication delays in the standard SuperDARN technique while it is inherently included in our approach. Rather, we argue that the magnetosphere-ionosphere system has inertia that prevents the global convection from changing abruptly in response to an interplanetary magnetic field change.

Recombinase polymerase amplification (RPA) combined with lateral flow (LF) strip for detection of Toxoplasma gondii in the environment.

PubMed

Wu, Y D; Xu, M J; Wang, Q Q; Zhou, C X; Wang, M; Zhu, X Q; Zhou, D H

2017-08-30

Toxoplasma gondii infects all warm-blooded vertebrates, resulting in a great threat to human health and significant economic loss to the livestock industry. Ingestion of infectious oocysts of T. gondii from the environment is the major source of transmission. Detection of T. gondii oocysts by existing methods is laborious, time-consuming and expensive. The objective of the present study was to develop a recombinase polymerase amplification (RPA) method combined with a lateral flow (LF) strip for detection of T. gondii oocysts in the soil and water. The DNA of T. gondii oocysts was amplified by a pair of specific primers based on the T. gondii B1 gene over 15min at a constant temperature ranging from 30°C to 45°C using RPA. The amplification product was visualized by the lateral flow (LF) strip within 5min using the specific probe added to the RPA reaction system. The sensitivity of the established assay was 10 times higher than that of nested PCR with a lower detection limit of 0.1 oocyst per reaction, and there was no cross-reactivity with other closely related protozoan species. Fifty environmental samples were further assessed for the detection validity of the LF-RPA assay (B1-LF-RPA) and compared with nested PCR based on the B1 gene sequence. The B1-LF-RPA and nested PCR both showed that 5 out of the 50 environmental samples were positive. The B1-LF-RPA method was also proven to be sufficiently tolerant of existing inhibitors in the environment. In addition, the advantages of simple operation, speediness and cost-effectiveness make B1-LF-RPA a promising molecular detection tool for T. gondii. Copyright © 2017 Elsevier B.V. All rights reserved.

Applications of immobilized catalysts in continuous flow processes.

PubMed

Kirschning, Andreas; Jas, Gerhard

2004-01-01

As part of the dramatic changes associated with automation in pharmaceutical and agrochemical research laboratories, the search for new technologies has become a major topic in the chemical community. Commonly, high-throughput chemistry is still carried out in batches whereas flow-through processes are rather restricted to production processes, despite the fact that the latter concept allows facile automation, reproducibility, safety, and process reliability. Indeed, methods and technologies are missing that allow rapid transfer from the research level to process development. Continuous flow processes are considered as a universal lever to overcome these restrictions and only recently, joint efforts between synthetic and polymer chemists and chemical engineers have resulted in the first continuous flow devices and microreactors which allow rapid preparation of compounds with minimum workup. Importantly, more and more developments combine the use of immobilized reagents and catalysts with the concept of structured continuous flow reactors. Consequently, the present article focuses on this new research field, which is located at the interface of continuous flow processes and solid-phase-bound catalysts.

High performance concentration method for viruses in drinking water.

PubMed

Kunze, Andreas; Pei, Lu; Elsässer, Dennis; Niessner, Reinhard; Seidel, Michael

2015-09-15

According to the risk assessment of the WHO, highly infectious pathogenic viruses like rotaviruses should not be present in large-volume drinking water samples of up to 90 m(3). On the other hand, quantification methods for viruses are only operable in small volumes, and presently no concentration procedure for processing such large volumes has been reported. Therefore, the aim of this study was to demonstrate a procedure for processing viruses in-line of a drinking water pipeline by ultrafiltration (UF) and consecutive further concentration by monolithic filtration (MF) and centrifugal ultrafiltration (CeUF) of viruses to a final 1-mL sample. For testing this concept, the model virus bacteriophage MS2 was spiked continuously in UF instrumentation. Tap water was processed in volumes between 32.4 m(3) (22 h) and 97.7 m(3) (72 h) continuously either in dead-end (DE) or cross-flow (CF) mode. Best results were found by DE-UF over 22 h. The concentration of MS2 was increased from 4.2×10(4) GU/mL (genomic units per milliliter) to 3.2×10(10) GU/mL and from 71 PFU/mL to 2×10(8) PFU/mL as determined by qRT-PCR and plaque assay, respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of age and hypertension on α1-adrenoceptors in the major source arteries of the rat bladder and penis.

PubMed

Yono, Makoto; Tanaka, Takanori; Tsuji, Shigeki; Irie, Shin; Sakata, Yukikuni; Otani, Masayuki; Yoshida, Masaki; Latifpour, Jamshid

2011-11-16

α(1)-Adrenoceptors regulate blood pressure, regional vascular resistance and tissue blood flow. As aging and hypertension may impact pelvic arterial blood flow resulting in bladder and penile dysfunction, we investigated effects of age and hypertension on α(1)-adrenoceptors in the major source arteries of the rat bladder and penis. Using radioligand receptor binding, real-time reverse transcription-polymerase chain reaction (RT-PCR) and fluorescent microsphere infusion techniques, we compared 3 and 22-month-old male Fischer rats, and male normotensive Wistar-Kyoto (WKY) rats and spontaneously hypertensive rats (SHRs). Twenty-two-month-old rats and SHRs had significantly higher total α(1)-adrenoceptor density in the internal iliac artery and lower blood flow to the bladder and penis than 3-month-old and WKY rats, respectively. RT-PCR data showed an age and hypertension related increase in the expression of α(1B)-adrenoceptor mRNA in the internal iliac, vesical and internal pudendal arteries and a switch from α(1A) predominance in 3-month-old and WKY rats to α(1B)>α(1A) in 22-month-old rats and SHRs. Our data indicate the presence of age and hypertension related alterations in vascular α(1)-adrenoceptor subtype distribution and in blood flow to the rat bladder and penis. These findings suggest that pharmacological blockade of the vascular α(1B)-adrenoceptor, which could increase pelvic blood flow, may contribute to the improvement of bladder and penile dysfunctions in animal models for aging and hypertension. Copyright © 2011 Elsevier B.V. All rights reserved.

40 CFR 89.416 - Raw exhaust gas flow.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 20 2011-07-01 2011-07-01 false Raw exhaust gas flow. 89.416 Section 89.416 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED... Procedures § 89.416 Raw exhaust gas flow. The exhaust gas flow shall be determined by one of the methods...

40 CFR 89.416 - Raw exhaust gas flow.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Raw exhaust gas flow. 89.416 Section 89.416 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED... Procedures § 89.416 Raw exhaust gas flow. The exhaust gas flow shall be determined by one of the methods...

Microwave and continuous flow technologies in drug discovery.

PubMed

Sadler, Sara; Moeller, Alexander R; Jones, Graham B

2012-12-01

Microwave and continuous flow microreactors have become mainstream heating sources in contemporary pharmaceutical company laboratories. Such technologies will continue to benefit from design and engineering improvements, and now play a key role in the drug discovery process. The authors review the applications of flow- and microwave-mediated heating in library, combinatorial, solid-phase, metal-assisted, and protein chemistries. Additionally, the authors provide a description of the combination of microwave and continuous flow platforms, with applications in the preparation of radiopharmaceuticals and in drug candidate development. Literature reviewed is chiefly 2000 - 2012, plus key citations from earlier reports. With the advent of microwave irradiation, reactions that normally took days to complete can now be performed in a matter of minutes. Coupled with the introduction of continuous flow microreactors, pharmaceutical companies have an easy way to improve the greenness and efficiency of many synthetic operations. The combined force of these technologies offers the potential to revolutionize discovery and manufacturing processes.

Head-to-head comparison of the diagnostic accuracies of BD Veritor™ System RSV and Quidel® Sofia® RSV FIA systems for respiratory syncytial virus (RSV) diagnosis.

PubMed

Kanwar, Neena; Hassan, Ferdaus; Nguyen, Ashley; Selvarangan, Rangaraj

2015-04-01

Respiratory syncytial virus (RSV) is one of the most common causes of severe lower respiratory tract disease among infants and young children. BD Veritor™ System RSV (BD) and Quidel(®) Sofia(®) RSV FIA (QD) are the new generation lateral flow digital immunoassay (DIA) tests with an instrumented read for the qualitative detection of RSV viral antigens. To compare the diagnostic accuracies of BD and QD for RSV detection using fresh nasopharyngeal aspirates and nasopharyngeal swab specimens collected in universal transport media during 2013-2014 respiratory season. The two DIA tests were performed simultaneously on randomly selected specimens on a weekly basis during the RSV season until 200 fresh remnant specimens were enrolled. Real-time RT-PCR assay results were used to compare and evaluate the performance of both RSV DIA assays. Among 200 specimens tested, RSV real-time RT-PCR assay detected RSV in 104 samples, while QD detected 84 samples and BD detected 74 samples as positive. The overall sensitivity for detection of RSV in comparison to PCR was 71.15% (61.3-79.4) for BD and 80.77% (71.6-87.6) for QD system (P=0.36). The specificity was 100% (95.2-100) for both systems. The work flow analysis revealed that the overall specimen processing time was significantly lower for BD as compared with the QD assay. In comparison with the real-time PCR, the QD system showed a higher sensitivity than that of the BD system, but the difference did not reach statistical significance (P=0.36). Both BD and QD systems were found comparable in terms of specificity. Copyright © 2015 Elsevier B.V. All rights reserved.

Dynamic Changes of Smooth Muscle and Endothelial Markers in the Early Healing Process of Dacron Vascular Grafts in the Dog, Using RT-PCR.

PubMed

Ishida; Wu; Shi; Fujita; Sauvage; Hammond; Wijelath

2000-03-01

Previous studies of neointima formation on Dacron vascular grafts mainly focused on the late stages using immunohistochemistry staining for von Willebrand factor (vWF) and smooth muscle (SM) alpha-actin. However, it is impossible to use immunohistochemistry to study the early events of neointima formation, because graft samples lack sufficient cellular material. Therefore, we used reverse transcriptase-polymerase chain reaction (RT-PCR) to demonstrate dynamic changes of SM and endothelial markers during the early stages of neointima formation. Preclotted Dacron grafts were implanted in the descending thoracic aorta of 14 mongrel dogs. Specimens were retrieved at 1-4 weeks. Total RNAs were extracted from mid-portion of graft flow surfaces, and RT-PCR for vWF, SM myosin heavy chain (MHC), and SM alpha-actin were performed and expressed as a ratio to the ribosome s17 signal. SM MHC and vWF mRNA expression was low at 1-2 weeks but elevated at 3-4 weeks (P < 0.05). However, SM alpha-actin mRNA levels were expressed consistently throughout the study period. At 3-4 weeks, vWF mRNA expression was inversely correlated to thrombus formation on the graft flow surface. Increased expressions of SM MHC and vWF mRNA corresponded to the formation of neointima and an endothelial layer at the later stages. However, SM alpha-actin mRNA expression did not vary during the healing process. The application of RT-PCR should permit further studies of gene regulation in the early vascular graft healing process in vivo. This model can also be used to study the molecular events that are involved in SM cell differentiation.

T lymphocytes among HIV-infected and -uninfected infants: CD4/CD8 ratio as a potential tool in diagnosis of infection in infants under the age of 2 years.

PubMed

Zijenah, Lynn S; Katzenstein, David A; Nathoo, Kusum J; Rusakaniko, Simbarashe; Tobaiwa, Ocean; Gwanzura, Christine; Bikoue, Arsene; Nhembe, Margaret; Matibe, Petronella; Janossy, George

2005-02-01

BACKGROUND: Serologic tests for HIV infection in infants less than 18 months do not differentiate exposure and infection since maternally acquired IgG antibodies may be detected in infants. Thus, the gold standard for diagnosis of HIV-1 infection in infants under the age of 2 years is DNA or reverse transcriptase polymerase chain reaction. There is an urgent need to evaluate alternative and cost effective laboratory methods for early diagnosis of infant HIV-1 infection as well as identifying infected infants who may benefit from cotrimoxazole prophylaxis and/or initiation of highly active antiretroviral therapy. METHODS: Whole blood was collected in EDTA from 137 infants aged 0 to 18 months. DNA polymerase chain reaction was used as the reference standard for diagnosis of HIV-1 infection. T-cell subset profiles were determined by flow cytometry. RESULTS: Seventy-six infants were DNA PCR positive while 61 were negative. The median CD4 counts of PCR negative infants were significantly higher than those of the PCR positive infants, p < 0.001. The median CD4/CD8 ratio and the %CD4 of the PCR positive infants were both significantly lower than those of the negative infants, p < 0.001. The CD4/CD8 ratio had a >98% sensitivity for diagnosis of HIV-1 infection and a specificity of >98%. CONCLUSION: The CD4/CD8 ratio appears useful in identifying HIV-infected infants. The development of lower cost and more robust flow cytometric methods that provide both CD4/CD8 ratio and %CD4 may be cost-effective for HIV-1 diagnosis and identification of infants for cotrimoxazole prophylaxis and/or highly active antiretroviral therapy.

T lymphocytes among HIV-infected and -uninfected infants: CD4/CD8 ratio as a potential tool in diagnosis of infection in infants under the age of 2 years

PubMed Central

Zijenah, Lynn S; Katzenstein, David A; Nathoo, Kusum J; Rusakaniko, Simbarashe; Tobaiwa, Ocean; Gwanzura, Christine; Bikoue, Arsene; Nhembe, Margaret; Matibe, Petronella; Janossy, George

2005-01-01

Background Serologic tests for HIV infection in infants less than 18 months do not differentiate exposure and infection since maternally acquired IgG antibodies may be detected in infants. Thus, the gold standard for diagnosis of HIV-1 infection in infants under the age of 2 years is DNA or reverse transcriptase polymerase chain reaction. There is an urgent need to evaluate alternative and cost effective laboratory methods for early diagnosis of infant HIV-1 infection as well as identifying infected infants who may benefit from cotrimoxazole prophylaxis and/or initiation of highly active antiretroviral therapy. Methods Whole blood was collected in EDTA from 137 infants aged 0 to 18 months. DNA polymerase chain reaction was used as the reference standard for diagnosis of HIV-1 infection. T-cell subset profiles were determined by flow cytometry. Results Seventy-six infants were DNA PCR positive while 61 were negative. The median CD4 counts of PCR negative infants were significantly higher than those of the PCR positive infants, p < 0.001. The median CD4/CD8 ratio and the %CD4 of the PCR positive infants were both significantly lower than those of the negative infants, p < 0.001. The CD4/CD8 ratio had a >98% sensitivity for diagnosis of HIV-1 infection and a specificity of >98%. Conclusion The CD4/CD8 ratio appears useful in identifying HIV-infected infants. The development of lower cost and more robust flow cytometric methods that provide both CD4/CD8 ratio and %CD4 may be cost-effective for HIV-1 diagnosis and identification of infants for cotrimoxazole prophylaxis and/or highly active antiretroviral therapy. PMID:15683549

Flow cytometry and real-time quantitative PCR as tools for assessing plasmid persistence.

PubMed

Loftie-Eaton, Wesley; Tucker, Allison; Norton, Ann; Top, Eva M

2014-09-01

The maintenance of a plasmid in the absence of selection for plasmid-borne genes is not guaranteed. However, plasmid persistence can evolve under selective conditions. Studying the molecular mechanisms behind the evolution of plasmid persistence is key to understanding how plasmids are maintained under nonselective conditions. Given the current crisis of rapid antibiotic resistance spread by multidrug resistance plasmids, this insight is of high medical relevance. The conventional method for monitoring plasmid persistence (i.e., the fraction of plasmid-containing cells in a population over time) is based on cultivation and involves differentiating colonies of plasmid-containing and plasmid-free cells on agar plates. However, this technique is time-consuming and does not easily lend itself to high-throughput applications. Here, we present flow cytometry (FCM) and real-time quantitative PCR (qPCR) as alternative tools for monitoring plasmid persistence. For this, we measured the persistence of a model plasmid, pB10::gfp, in three Pseudomonas hosts and in known mixtures of plasmid-containing and -free cells. We also compared three performance criteria: dynamic range, resolution, and variance. Although not without exceptions, both techniques generated estimates of overall plasmid loss rates that were rather similar to those generated by the conventional plate count (PC) method. They also were able to resolve differences in loss rates between artificial plasmid persistence assays. Finally, we briefly discuss the advantages and disadvantages for each technique and conclude that, overall, both FCM and real-time qPCR are suitable alternatives to cultivation-based methods for routine measurement of plasmid persistence, thereby opening avenues for high-throughput analyses. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Rapid visual detection of Mycobacterium avium subsp. paratuberculosis by recombinase polymerase amplification combined with a lateral flow dipstick

PubMed Central

Zhao, Guimin; Wang, Hongmei; Hou, Peili; He, Chengqiang

2018-01-01

Paratuberculosis (Johne's disease) is a chronic debilitating disease of domestic and wild ruminants. However, widespread point-of-care testing is infrequent due to the lack of a robust method. The isothermal recombinase polymerase amplification (RPA) technique has applied for rapid diagnosis. Herein, RPA combined with a lateral flow dipstick (LFD) assay was developed to estimate DNA from Mycobacterium avium subsp. paratuberculosis. First, analytical specificity and sensitivity of the RPA-nfo primer and probe sets were assessed. The assay successfully detected M. paratuberculosis DNA in 30 min at 39℃ with a detection limit of up to eight copies per reaction, which was equivalent to that of the real-time quantitative polymerase chain reaction (qPCR) assay. The assay was specific, as it did not amplify genomes from five other Mycobacterium spp. or five pathogenic enteric bacteria. Six hundred-twelve clinical samples (320 fecal and 292 serum) were assessed by RPA-LFD, qPCR, and enzyme-linked immunosorbent assay, respectively. The RPA-LFD assay yielded 100% sensitivity, 97.63% specificity, and 98.44% concordance rate with the qPCR results. This is the first report utilizing an RPA-LFD assay to visualize and rapidly detect M. paratuberculosis. Our results show this assay should be a useful method for the diagnosis of paratuberculosis in resource-constrained settings. PMID:29284204

Molecular analysis of carbon monoxide-oxidizing bacteria associated with recent Hawaiian volcanic deposits.

PubMed

Dunfield, Kari E; King, Gary M

2004-07-01

Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity.

Molecular Analysis of Carbon Monoxide-Oxidizing Bacteria Associated with Recent Hawaiian Volcanic Deposits†

PubMed Central

Dunfield, Kari E.; King, Gary M.

2004-01-01

Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity. PMID:15240307

Rapid visual detection of Mycobacterium avium subsp. paratuberculosis by recombinase polymerase amplification combined with a lateral flow dipstick.

PubMed

Zhao, Guimin; Wang, Hongmei; Hou, Peili; He, Chengqiang; He, Hongbin

2018-03-31

Paratuberculosis (Johne's disease) is a chronic debilitating disease of domestic and wild ruminants. However, widespread point-of-care testing is infrequent due to the lack of a robust method. The isothermal recombinase polymerase amplification (RPA) technique has applied for rapid diagnosis. Herein, RPA combined with a lateral flow dipstick (LFD) assay was developed to estimate DNA from Mycobacterium avium subsp. paratuberculosis . First, analytical specificity and sensitivity of the RPA-nfo primer and probe sets were assessed. The assay successfully detected M. paratuberculosis DNA in 30 min at 39°C with a detection limit of up to eight copies per reaction, which was equivalent to that of the real-time quantitative polymerase chain reaction (qPCR) assay. The assay was specific, as it did not amplify genomes from five other Mycobacterium spp. or five pathogenic enteric bacteria. Six hundred-twelve clinical samples (320 fecal and 292 serum) were assessed by RPA-LFD, qPCR, and enzyme-linked immunosorbent assay, respectively. The RPA-LFD assay yielded 100% sensitivity, 97.63% specificity, and 98.44% concordance rate with the qPCR results. This is the first report utilizing an RPA-LFD assay to visualize and rapidly detect M. paratuberculosis . Our results show this assay should be a useful method for the diagnosis of paratuberculosis in resource-constrained settings.

Sensitive, microliter PCR with consensus degenerate primers for Epstein Barr virus amplification

PubMed Central

Oh, Kyudam; Pak, Nikita; Saunders, D. Curtis; Conrardy, Christina; Landers, James P.; Tong, Suxiang; Forest, Craig R.

2016-01-01

Sensitive identification of the etiology of viral diseases is key to implementing appropriate prevention and treatment. The gold standard for virus identification is the polymerase chain reaction (PCR), a technique that allows for highly specific and sensitive detection of pathogens by exponentially amplifying a specific region of DNA from as little as a single copy through thermocycling a biochemical cocktail. Today, molecular biology laboratories use commercial instruments that operate in 0.5–2 h/analysis using reaction volumes of 5–50 μL contained within polymer tubes or chambers. Towards reducing this volume and maintaining performance, we present a semi-quantitative, systematic experimental study of how PCR yield is affected by tube/chamber substrate, surface-area-to-volume ratio (SA:V), and passivation methods. We perform PCR experiments using traditional PCR tubes as well as using disposable polymer microchips with 1 μL reaction volumes thermocycled using water baths. We report the first oil encapsulation microfluidic PCR method without fluid flow and its application to the first microfluidic amplification of Epstein Barr virus using consensus degenerate primers, a powerful and broad PCR method to screen for both known and novel members of a viral family. The limit of detection is measured as 140 starting copies of DNA from a starting concentration of 3×105 copies/mL, regarded as an accepted sensitivity threshold for diagnostic purposes, and reaction specificity was improved as compared to conventional methods. Also notable, these experiments were conducted with conventional reagent concentrations, rather than commonly spiked enzyme and/or template mixtures. This experimental study of the effects of substrate, SA:V, and passivation, together with sensitive and specific microfluidic PCR with consensus degenerate primers represent advances towards lower cost and higher throughput pathogen screening. PMID:23080522

76 FR 41669 - Airworthiness Directives; B/E Aerospace, Continuous Flow Passenger Oxygen Mask Assembly, Part...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-15

... Airworthiness Directives; B/E Aerospace, Continuous Flow Passenger Oxygen Mask Assembly, Part Numbers 174006... to prevent the in-line flow indicators of the oxygen mask assembly from fracturing and separating, which could inhibit oxygen flow to the masks. This condition could consequently result in occupants...

Centrifugal Microfluidic System for Nucleic Acid Amplification and Detection.

PubMed

Miao, Baogang; Peng, Niancai; Li, Lei; Li, Zheng; Hu, Fei; Zhang, Zengming; Wang, Chaohui

2015-11-04

We report here the development of a rapid PCR microfluidic system comprising a double-shaft turntable and centrifugal-based disc that rapidly drives the PCR mixture between chambers set at different temperatures, and the bidirectional flow improved the space utilization of the disc. Three heating resistors and thermistors maintained uniform, specific temperatures for the denaturation, annealing, and extension steps of the PCR. Infrared imaging showed that there was little thermal interference between reaction chambers; the system enabled the cycle number and reaction time of each step to be independently adjusted. To validate the function and efficiency of the centrifugal microfluidic system, a 350-base pair target gene from the hepatitis B virus was amplified and quantitated by fluorescence detection. By optimizing the cycling parameters, the reaction time was reduced to 32 min as compared to 120 min for a commercial PCR machine. DNA samples with concentrations ranging from 10 to 10⁶ copies/mL could be quantitatively analyzed using this system. This centrifugal-based microfluidic platform is a useful system and possesses industrialization potential that can be used for portable diagnostics.

Centrifugal Microfluidic System for Nucleic Acid Amplification and Detection

PubMed Central

Miao, Baogang; Peng, Niancai; Li, Lei; Li, Zheng; Hu, Fei; Zhang, Zengming; Wang, Chaohui

2015-01-01

We report here the development of a rapid PCR microfluidic system comprising a double-shaft turntable and centrifugal-based disc that rapidly drives the PCR mixture between chambers set at different temperatures, and the bidirectional flow improved the space utilization of the disc. Three heating resistors and thermistors maintained uniform, specific temperatures for the denaturation, annealing, and extension steps of the PCR. Infrared imaging showed that there was little thermal interference between reaction chambers; the system enabled the cycle number and reaction time of each step to be independently adjusted. To validate the function and efficiency of the centrifugal microfluidic system, a 350-base pair target gene from the hepatitis B virus was amplified and quantitated by fluorescence detection. By optimizing the cycling parameters, the reaction time was reduced to 32 min as compared to 120 min for a commercial PCR machine. DNA samples with concentrations ranging from 10 to 106 copies/mL could be quantitatively analyzed using this system. This centrifugal-based microfluidic platform is a useful system and possesses industrialization potential that can be used for portable diagnostics. PMID:26556354

Experimental and theoretical investigation of the stability of stepwise pH gradients in continuous flow electrophoresis

NASA Technical Reports Server (NTRS)

Kuhn, Reinhard; Wagner, Horst; Mosher, Richard A.; Thormann, Wolfgang

1987-01-01

Isoelectric focusing in the continuous flow mode can be more quickly and economically performed by admitting a stepwise pH gradient composed of simple buffers instead of uniform mixtures of synthetic carrier ampholytes. The time-consuming formation of the pH gradient by the electric field is thereby omitted. The stability of a three-step system with arginine - morpholinoethanesulfonic acid/glycylglycine - aspartic acid is analyzed theoretically by one-dimensional computer simulation as well as experimentally at various flow rates in a continuous flow apparatus. Excellent agreement between experimental and theoretical data was obtained. This metastable configuration was found to be suitable for focusing of proteins under continuous flow conditions. The influence of various combinations of electrolytes and membranes between electrophoresis chamber and electrode compartments is also discussed.

High-bandwidth continuous-flow arc furnace

DOEpatents

Hardt, David E.; Lee, Steven G.

1996-01-01

A high-bandwidth continuous-flow arc furnace for stream welding applications includes a metal mass contained in a crucible having an orifice. A power source charges an electrode for generating an arc between the electrode and the mass. The arc heats the metal mass to a molten state. A pressurized gas source propels the molten metal mass through the crucible orifice in a continuous stream. As the metal is ejected, a metal feeder replenishes the molten metal bath. A control system regulates the electrode current, shielding gas pressure, and metal source to provide a continuous flow of molten metal at the crucible orifice. Independent control over the electrode current and shield gas pressure decouples the metal flow temperature and the molten metal flow rate, improving control over resultant weld characteristics.

High-bandwidth continuous-flow arc furnace

DOEpatents

Hardt, D.E.; Lee, S.G.

1996-08-06

A high-bandwidth continuous-flow arc furnace for stream welding applications includes a metal mass contained in a crucible having an orifice. A power source charges an electrode for generating an arc between the electrode and the mass. The arc heats the metal mass to a molten state. A pressurized gas source propels the molten metal mass through the crucible orifice in a continuous stream. As the metal is ejected, a metal feeder replenishes the molten metal bath. A control system regulates the electrode current, shielding gas pressure, and metal source to provide a continuous flow of molten metal at the crucible orifice. Independent control over the electrode current and shield gas pressure decouples the metal flow temperature and the molten metal flow rate, improving control over resultant weld characteristics. 4 figs.

Detection of the Dinozoans Pfiesteria piscicida and P. shumwayae: a review of detection methods and geographic distribution.

PubMed

Rublee, Parke A; Remington, David L; Schaefer, Eric F; Marshall, Michael M

2005-01-01

Molecular methods, including conventional PCR, real-time PCR, denaturing gradient gel electrophoresis, fluorescent fragment detection PCR, and fluorescent in situ hybridization, have all been developed for use in identifying and studying the distribution of the toxic dinoflagellates Pfiesteria piscicida and P. shumwayae. Application of the methods has demonstrated a worldwide distribution of both species and provided insight into their environmental tolerance range and temporal changes in distribution. Genetic variability among geographic locations generally appears low in rDNA genes, and detection of the organisms in ballast water is consistent with rapid dispersal or high gene flow among populations, but additional sequence data are needed to verify this hypothesis. The rapid development and application of these tools serves as a model for study of other microbial taxa and provides a basis for future development of tools that can simultaneously detect multiple targets.

Genetic variation in Indian populations of Scirpophaga incertulas as revealed by RAPD-PCR analysis.

PubMed

Kumar, L S; Sawant, A S; Gupta, V S; Ranjekar, P K

2001-02-01

Scirpophaga incertulas, commonly referred to as yellow stem borer, is a predominant pest of rice causing serious losses in its yield. Genetic variation among populations of Scirpophaga incertulas collected from 28 hotspot locations in India was examined using the randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). In all, 32 primers were used and 354 amplification products were observed. No RAPD-PCR bands diagnostic to the pest population from any specific region were identified. Cluster analysis using UPGMA showed that, with the exception of the pest population from Pattambi, all the populations cluster as one group with GD values in the range of 6-22%, suggesting that gene flow between populations is independent of geographic distance and appears to be unrestricted. The relatively high GD value of 48% exhibited by the pest population from Pattambi was the only exception.

HLA-targeted flow cytometric sorting of blood cells allows separation of pure and viable microchimeric cell populations.

PubMed

Drabbels, Jos J M; van de Keur, Carin; Kemps, Berit M; Mulder, Arend; Scherjon, Sicco A; Claas, Frans H J; Eikmans, Michael

2011-11-10

Microchimerism is defined by the presence of low levels of nonhost cells in a person. We developed a reliable method for separating viable microchimeric cells from the host environment. For flow cytometric cell sorting, HLA antigens were targeted with human monoclonal HLA antibodies (mAbs). Optimal separation of microchimeric cells (present at a proportion as low as 0.01% in artificial mixtures) was obtained with 2 different HLA mAbs, one targeting the chimeric cells and the other the background cells. To verify purity of separated cell populations, flow-sorted fractions of 1000 cells were processed for DNA analysis by HLA-allele-specific and Y-chromosome-directed real-time quantitative PCR assays. After sorting, PCR signals of chimeric DNA markers in the positive fractions were significantly enhanced compared with those in the presort samples, and they were similar to those in 100% chimeric control samples. Next, we demonstrate applicability of HLA-targeted FACS sorting after pregnancy by separating chimeric maternal cells from child umbilical cord mononuclear cells. Targeting allelic differences with anti-HLA mAbs with FACS sorting allows maximal enrichment of viable microchimeric cells from a background cell population. The current methodology enables reliable microchimeric cell detection and separation in clinical specimens.

Development of an improved PCR-ICT hybrid assay for direct detection of Legionellae and Legionella pneumophila from cooling tower water specimens.

PubMed

Horng, Yu-Tze; Soo, Po-Chi; Shen, Bin-Jon; Hung, Yu-Li; Lo, Kai-Yin; Su, Hsun-Pi; Wei, Jun-Rong; Hsieh, Shang-Chen; Hsueh, Po-Ren; Lai, Hsin-Chih

2006-06-01

A novelly improved polymerase chian reaction and immunochromatography test (PCR-ICT) hybrid assay comprising traditional multiplex-nested PCR and ICT, (a lateral-flow device) was developed for direct detection of Legionella bacteria from environmental cooling tower samples. The partial 16S rDNA (specific for Legionella spp.) and dnaJ (specific for Legionella pneumophila) genes from Legionella chromosome were first specifically amplified by multiplex-nested PCR, respectively, followed by detection using ICT strip. Reading of results was based on presence or absence of the two test lines on the strips. Presence of test line 1 indicated existence of Legionella spp. specific 16S rDNA and identified Legionella spp. Presence of test line 2 further indicated existence of dnaJ and thus specifically identified L. pneumophila. In contrast, for non-Legionellae bacteria no test line formation was observed. Results of direct detection of Legionella bacteria and L. pneumophila from water tower specimens by this assay showed 100% sensitivity, and 96.6% and 100% specificity, respectively compared with traditional culture, biochemical and serological identification methods. The PCR-ICT hybrid assay does not require sophisticated equipment and was proved to be practically useful in rapid and direct Legionellae detection from environmental water samples.

Investigation of the continuous flow of the sample solution on the performance of electromembrane extraction: Comparison with conventional procedure.

PubMed

Nojavan, Saeed; Sirani, Mahsa; Asadi, Sakine

2017-10-01

In this study, electromembrane extraction from a flowing sample solution, termed as continuous-flow electromembrane extraction, was developed and compared with conventional procedures for the determination of four basic drugs in real samples. Experimental parameters affecting the extraction efficiency were further studied and optimized. Under optimum conditions, linearity of continuous-flow procedure was within 8.0-500 ng/mL, while it was wider for conventional procedures (2.0-500 ng/mL). Moreover, repeatability (percentage relative standard deviation) was found to range between 5.6 and 10.4% (n = 3) for the continuous-flow procedure, with a better repeatability than that of conventional procedures (2.3-5.5% (n = 3)). Also, for the continuous-flow procedure, the estimated detection limit (signal-to-noise ratio = 3) was less than 2.4 ng/mL and extraction recoveries were within 8-10%, while the corresponding figures for conventional procedures were less than 0.6 ng/mL and 42-60%, respectively. Thus, the results showed that both continuous flow and conventional procedures were applicable for the extraction of model compounds. However, the conventional procedure was more convenient to use, and thus it was applied to determine sample drugs in real urine and wastewater samples. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Depth-Averaged 2-D Simulation for Coastal Barrier Breaching Processes

DTIC Science & Technology

2011-05-01

including bed change and variable flow density in the flow continuity and momentum equations. The model adopts the HLL approximate Riemann solver to handle...flow density in the flow continuity and momentum equations. The model adopts the HLL approximate Riemann solver to handle the mixed-regime flows near...18 547 Keulegan equation or the Bernoulli equation, and the breach morphological change is determined using simplified sediment transport models

An investigation of the basic physics of irrigation in urology and the role of automated pump irrigation in cystoscopy.

PubMed

Chang, Dwayne; Manecksha, Rustom P; Syrrakos, Konstantinos; Lawrentschuk, Nathan

2012-01-01

To investigate the effects of height, external pressure, and bladder fullness on the flow rate in continuous, non-continuous cystoscopy and the automated irrigation fluid pumping system (AIFPS). Each experiment had two 2-litre 0.9% saline bags connected to a continuous, non-continuous cystoscope or AIFPS via irrigation tubing. Other equipment included height-adjustable drip poles, uroflowmetry devices, and model bladders. In Experiment 1, saline bags were elevated to measure the increment in flow rate. In Experiment 2, saline bags were placed under external pressures to evaluate the effect on flow rate. In Experiment 3, flow rate changes in response to variable bladder fullness were measured. Elevating saline bags caused an increase in flow rates, however the increment slowed down beyond a height of 80 cm. Increase in external pressure on saline bags elevated flow rates, but inconsistently. A fuller bladder led to a decrease in flow rates. In all experiments, the AIFPS posted consistent flow rates. Traditional irrigation systems were susceptible to changes in height of irrigation solution, external pressure application, and bladder fullness thus creating inconsistent flow rates. The AIFPS produced consistent flow rates and was not affected by any of the factors investigated in the study.

Low-flow characteristics of streams in Virginia

USGS Publications Warehouse

Hayes, Donald C.

1991-01-01

Streamflow data were collected and low-flow characteristics computed for 715 gaged sites in Virginia Annual minimum average 7-consecutive-day flows range from 0 to 2,195 cubic feet per second for a 2-year recurrence interval and from 0 to 1,423 cubic feet per second for a 10-year recurrence interval. Drainage areas range from 0.17 to 7,320 square miles. Existing and discontinued gaged sites are separated into three types: long-term continuous-record sites, short-term continuous-record sites, and partial-record sites. Low-flow characteristics for long-term continuous-record sites are determined from frequency curves of annual minimum average 7-consecutive-day flows . Low-flow characteristics for short-term continuous-record sites are estimated by relating daily mean base-flow discharge values at a short-term site to concurrent daily mean discharge values at nearby long-term continuous-record sites having similar basin characteristics . Low-flow characteristics for partial-record sites are estimated by relating base-flow measurements to daily mean discharge values at long-term continuous-record sites. Information from the continuous-record sites and partial-record sites in Virginia are used to develop two techniques for estimating low-flow characteristics at ungaged sites. A flow-routing method is developed to estimate low-flow values at ungaged sites on gaged streams. Regional regression equations are developed for estimating low-flow values at ungaged sites on ungaged streams. The flow-routing method consists of transferring low-flow characteristics from a gaged site, either upstream or downstream, to a desired ungaged site. A simple drainage-area proration is used to transfer values when there are no major tributaries between the gaged and ungaged sites. Standard errors of estimate for108 test sites are 19 percent of the mean for estimates of low-flow characteristics having a 2-year recurrence interval and 52 percent of the mean for estimates of low-flow characteristics having a 10-year recurrence interval . A more complex transfer method must be used when major tributaries enter the stream between the gaged and ungaged sites. Twenty-four stream networks are analyzed, and predictions are made for 84 sites. Standard errors of estimate are 15 percent of the mean for estimates of low-flow characteristics having a 2-year recurrence interval and 22 percent of the mean for estimates of low-flow characteristics having a 10-year recurrence interval. Regional regression equations were developed for estimating low-flow values at ungaged sites on ungaged streams. The State was divided into eight regions on the basis of physiography and geographic grouping of the residuals computed in regression analyses . Basin characteristics that were significant in the regression analysis were drainage area, rock type, and strip-mined area. Standard errors of prediction range from 60 to139 percent for estimates of low-flow characteristics having a 2-year recurrence interval and 90 percent to 172 percent for estimates of low-flow characteristics having a 10-year recurrence interval.

SIMILARITY OF PARTICLE-ASSOCIATED AND FREE-LIVING BACTERIAL COMMUNITIES IN NORTHERN SAN FRANCISCO BAY, CALIFORNIA

EPA Science Inventory

We used denaturing gradient gel electrophoresis (DGGE) of 16S rDNA PCR amplicons to analyze the composition of Bacteria communities in samples collected during the summer, low flow season from northern San Francisco Bay, California. There were clear compositional differences in ...

Electrohydrodynamic effects in continuous flow electrophoresis

NASA Technical Reports Server (NTRS)

Rhodes, P. H.; Snyder, R. S.; Roberts, G. O.; Baygents, J. C.

1991-01-01

We demonstrate experimentally and theoretically the importance of electrohydrodynamic (EHD) flows in continuous-flow electrophoresis (CFE) separations. These flows are associated with variations in the conductivity or dielectric constant, and are quadratic in the field strength. They appear to be the main cause of extraneous and undesired flows in CFE which have degraded separation performance and have until now not been explained. We discuss the importance of EHD flows relative to other effects. We also describe possible techniques for reducing the associated degradation of CFE separations.

Diagnostic accuracy of PCR in gambiense sleeping sickness diagnosis, staging and post-treatment follow-up: a 2-year longitudinal study.

PubMed

Deborggraeve, Stijn; Lejon, Veerle; Ekangu, Rosine Ali; Mumba Ngoyi, Dieudonné; Pati Pyana, Patient; Ilunga, Médard; Mulunda, Jean Pierre; Büscher, Philippe

2011-02-22

The polymerase chain reaction (PCR) has been proposed for diagnosis, staging and post-treatment follow-up of sleeping sickness but no large-scale clinical evaluations of its diagnostic accuracy have taken place yet. An 18S ribosomal RNA gene targeting PCR was performed on blood and cerebrospinal fluid (CSF) of 360 T. brucei gambiense sleeping sickness patients and on blood of 129 endemic controls from the Democratic Republic of Congo. Sensitivity and specificity (with 95% confidence intervals) of PCR for diagnosis, disease staging and treatment failure over 2 years follow-up post-treatment were determined. Reference standard tests were trypanosome detection for diagnosis and trypanosome detection and/or increased white blood cell concentration in CSF for staging and detection of treatment failure. PCR on blood showed a sensitivity of 88.4% (84.4-92.5%) and a specificity of 99.2% (97.7-100%) for diagnosis, while for disease staging the sensitivity and specificity of PCR on cerebrospinal fluid were 88.4% (84.8-91.9%) and 82.9% (71.2-94.6%), respectively. During follow-up after treatment, PCR on blood had low sensitivity to detect treatment failure. In cerebrospinal fluid, PCR positivity vanished slowly and was observed until the end of the 2 year follow-up in around 20% of successfully treated patients. For T.b. gambiense sleeping sickness diagnosis and staging, PCR performed better than, or similar to, the current parasite detection techniques but it cannot be used for post-treatment follow-up. Continued PCR positivity in one out of five cured patients points to persistence of living or dead parasites or their DNA after successful treatment and may necessitate the revision of some paradigms about the pathophysiology of sleeping sickness.

Multiplex Real-Time PCR Assay for Rapid Detection of Methicillin-Resistant Staphylococci Directly from Positive Blood Cultures

PubMed Central

Wang, Hye-young; Kim, Sunghyun; Kim, Jungho; Park, Soon-Deok

2014-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) is the most prevalent cause of bloodstream infections (BSIs) and is recognized as a major nosocomial pathogen. This study aimed to evaluate a newly designed multiplex real-time PCR assay capable of the simultaneous detection of mecA, S. aureus, and coagulase-negative staphylococci (CoNS) in blood culture specimens. The Real-MRSA and Real-MRCoNS multiplex real-time PCR assays (M&D, Republic of Korea) use the TaqMan probes 16S rRNA for Staphylococcus spp., the nuc gene for S. aureus, and the mecA gene for methicillin resistance. The detection limit of the multiplex real-time PCR assay was 103 CFU/ml per PCR for each gene target. The multiplex real-time PCR assay was evaluated using 118 clinical isolates from various specimen types and a total of 350 positive blood cultures from a continuous monitoring blood culture system. The results obtained with the multiplex real-time PCR assay for the three targets were in agreement with those of conventional identification and susceptibility testing methods except for one organism. Of 350 positive bottle cultures, the sensitivities of the multiplex real-time PCR kit were 100% (166/166 cultures), 97.2% (35/36 cultures), and 99.2% (117/118 cultures) for the 16S rRNA, nuc, and mecA genes, respectively, and the specificities for all three targets were 100%. The Real-MRSA and Real-MRCoNS multiplex real-time PCR assays are very useful for the rapid accurate diagnosis of staphylococcal BSIs. In addition, the Real-MRSA and Real-MRCoNS multiplex real-time PCR assays could have an important impact on the choice of appropriate antimicrobial therapy, based on detection of the mecA gene. PMID:24648566

Effects of episodic sediment supply on bedload transport rate in mountain rivers. Detecting debris flow activity using continuous monitoring

NASA Astrophysics Data System (ADS)

Uchida, Taro; Sakurai, Wataru; Iuchi, Takuma; Izumiyama, Hiroaki; Borgatti, Lisa; Marcato, Gianluca; Pasuto, Alessandro

2018-04-01

Monitoring of sediment transport from hillslopes to channel networks as a consequence of floods with suspended and bedload transport, hyperconcentrated flows, debris and mud flows is essential not only for scientific issues, but also for prevention and mitigation of natural disasters, i.e. for hazard assessment, land use planning and design of torrent control interventions. In steep, potentially unstable terrains, ground-based continuous monitoring of hillslope and hydrological processes is still highly localized and expensive, especially in terms of manpower. In recent years, new seismic and acoustic methods have been developed for continuous bedload monitoring in mountain rivers. Since downstream bedload transport rate is controlled by upstream sediment supply from tributary channels and bed-external sources, continuous bedload monitoring might be an effective tool for detecting the sediments mobilized by debris flow processes in the upper catchment and thus represent an indirect method to monitor slope instability processes at the catchment scale. However, there is poor information about the effects of episodic sediment supply from upstream bed-external sources on downstream bedload transport rate at a single flood time scale. We have examined the effects of sediment supply due to upstream debris flow events on downstream bedload transport rate along the Yotagiri River, central Japan. To do this, we have conducted continuous bedload observations using a hydrophone (Japanese pipe microphone) located 6.4 km downstream the lower end of a tributary affected by debris flows. Two debris flows occurred during the two-years-long observation period. As expected, bedload transport rate for a given flow depth showed to be larger after storms triggering debris flows. That is, although the magnitude of sediment supply from debris flows is not large, their effect on bedload is propagating >6 km downstream at a single flood time scale. This indicates that continuous bedload observations could be effective for detecting sediment supply as a consequence of debris flow events.

Real-time PCR Machine System Modeling and a Systematic Approach for the Robust Design of a Real-time PCR-on-a-Chip System

PubMed Central

Lee, Da-Sheng

2010-01-01

Chip-based DNA quantification systems are widespread, and used in many point-of-care applications. However, instruments for such applications may not be maintained or calibrated regularly. Since machine reliability is a key issue for normal operation, this study presents a system model of the real-time Polymerase Chain Reaction (PCR) machine to analyze the instrument design through numerical experiments. Based on model analysis, a systematic approach was developed to lower the variation of DNA quantification and achieve a robust design for a real-time PCR-on-a-chip system. Accelerated lift testing was adopted to evaluate the reliability of the chip prototype. According to the life test plan, this proposed real-time PCR-on-a-chip system was simulated to work continuously for over three years with similar reproducibility in DNA quantification. This not only shows the robustness of the lab-on-a-chip system, but also verifies the effectiveness of our systematic method for achieving a robust design. PMID:22315563

Streamflow characteristics and trends in New Jersey, water years 1897-2003

USGS Publications Warehouse

Watson, Kara M.; Reiser, Robert G.; Nieswand, Steven P.; Schopp, Robert D.

2005-01-01

Streamflow statistics were computed for 111 continuous-record streamflow-gaging stations with 20 or more years of continuous record and for 500 low-flow partial-record stations, including 66 gaging stations with less than 20 years of continuous record. Daily mean streamflow data from water year 1897 through water year 2001 were used for the computations at the gaging stations. (The water year is the 12-month period, October 1 through September 30, designated by the calendar year in which it ends). The characteristics presented for the long-term continuous-record stations are daily streamflow, harmonic mean flow, flow frequency, daily flow durations, trend analysis, and streamflow variability. Low-flow statistics for gaging stations with less than 20 years of record and for partial-record stations were estimated by correlating base-flow measurements with daily mean flows at long-term (more than 20 years) continuous-record stations. Instantaneous streamflow measurements through water year 2003 were used to estimate low-flow statistics at the partial-record stations. The characteristics presented for partial-record stations are mean annual flow; harmonic mean flow; and annual and winter low-flow frequency. The annual 1-, 7-, and 30-day low- and high-flow data sets were tested for trends. The results of trend tests for high flows indicate relations between upward trends for high flows and stream regulation, and high flows and development in the basin. The relation between development and low-flow trends does not appear to be as strong as for development and high-flow trends. Monthly, seasonal, and annual precipitation data for selected long-term meteorological stations also were tested for trends to analyze the effects of climate. A significant upward trend in precipitation in northern New Jersey, Climate Division 1 was identified. For Climate Division 2, no general increase in average precipitation was observed. Trend test results indicate that high flows at undeveloped, unregulated sites have not been affected by the increase in average precipitation. The ratio of instantaneous peak flow to 3-day mean flow, ratios of flow duration, ratios of high-flow/low-flow frequency, and coefficient of variation were used to define streamflow variability. Streamflow variability was significantly greater among the group of gaging stations located outside the Coastal Plain than among the group of gaging stations located in the Coastal Plain.

Sequential continuous flow processes for the oxidation of amines and azides by using HOF·MeCN.

PubMed

McPake, Christopher B; Murray, Christopher B; Sandford, Graham

2012-02-13

The generation and use of the highly potent oxidising agent HOF·MeCN in a controlled single continuous flow process is described. Oxidations of amines and azides to corresponding nitrated systems by using fluorine gas, water and acetonitrile by sequential gas-liquid/liquid-liquid continuous flow procedures are reported. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

42 CFR 84.162 - Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air...

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 1 2011-10-01 2011-10-01 false Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air respirators; test requirements. 84.162 Section 84.162 Public....162 Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air...

42 CFR 84.162 - Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air...

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 1 2014-10-01 2014-10-01 false Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air respirators; test requirements. 84.162 Section 84.162 Public....162 Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air...

42 CFR 84.162 - Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air...

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 1 2013-10-01 2013-10-01 false Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air respirators; test requirements. 84.162 Section 84.162 Public....162 Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air...

42 CFR 84.162 - Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air...

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 1 2012-10-01 2012-10-01 false Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air respirators; test requirements. 84.162 Section 84.162 Public....162 Man test for gases and vapors; Type C respirators, continuous-flow class and Type CE supplied-air...

Phosphocreatine kinetics at the onset of contractions in skeletal muscle of MM creatine kinase knockout mice

NASA Technical Reports Server (NTRS)

Roman, Brian B.; Meyer, Ronald A.; Wiseman, Robert W.

2002-01-01

Phosphocreatine (PCr) depletion during isometric twitch stimulation at 5 Hz was measured by (31)P-NMR spectroscopy in gastrocnemius muscles of pentobarbital-anesthetized MM creatine kinase knockout (MMKO) vs. wild-type C57B (WT) mice. PCr depletion after 2 s of stimulation, estimated from the difference between spectra gated to times 200 ms and 140 s after 2-s bursts of contractions, was 2.2 +/- 0.6% of initial PCr in MMKO muscle vs. 9.7 +/- 1.6% in WT muscles (mean +/- SE, n = 7, P < 0.001). Initial PCr/ATP ratio and intracellular pH were not significantly different between groups, and there was no detectable change in intracellular pH or ATP in either group after 2 s. The initial difference in net PCr depletion was maintained during the first minute of continuous 5-Hz stimulation. However, there was no significant difference in the quasi-steady-state PCr level approached after 80 s (MMKO 36.1 +/- 3.5 vs. WT 35.5 +/- 4.4% of initial PCr; n = 5-6). A kinetic model of ATPase, creatine kinase, and adenylate kinase fluxes during stimulation was consistent with the observed PCr depletion in MMKO muscle after 2 s only if ADP-stimulated oxidative phosphorylation was included in the model. Taken together, the results suggest that cytoplasmic ADP more rapidly increases and oxidative phosphorylation is more rapidly activated at the onset of contractions in MMKO compared with WT muscles.

Tectonic and lithological controls on fluvial landscape development in central-eastern Portugal: Insights from long profile tributary stream analyses

NASA Astrophysics Data System (ADS)

Martins, António A.; Cabral, João; Cunha, Pedro P.; Stokes, Martin; Borges, José; Caldeira, Bento; Martins, A. Cardoso

2017-01-01

This study examines the long profiles of tributaries of the Tagus and Zêzere rivers in Portugal (West Iberia) in order to provide new insights into patterns, timing, and controls on drainage development during the Quaternary incision stage. The studied streams are incised into a relict culminant fluvial surface, abandoned at the beginning of the incision stage. The streams flow through a landscape with bedrock variations in lithology (mainly granites and metasediments) and faulted blocks with distinct uplift rates. The long profiles of the analyzed streams record an older transitory knickpoint/knickzone separating (1) an upstream relict graded profile, with lower steepness and higher concavity, that reflects a long period of quasi-equilibrium conditions reached after the beginning of the incision stage, and (2) a downstream rejuvenated long profile, with steeper gradient and lower concavity, particularly for the final reach, which is often convex. The rejuvenated reaches testify to the upstream propagation of several incision waves, interpreted as the response of each stream to increasing crustal uplift and prolonged periods of base-level lowering by the trunk drainages, coeval with low sea level conditions. The morphological configurations of the long profiles enabled spatial and relative temporal patterns of incisions to be quantified. The incision values of streams flowing on the Portuguese Central Range (PCR; ca. 380-150 m) are variable but generally higher than the incision values of streams flowing on the adjacent South Portugal Planation Surface (SPPS; ca. 220-110 m), corroborating differential uplift of the PCR relative to the SPPS. Owing to the fact that the relict graded profiles can be correlated with the Tagus River T1 terrace (1.1-0.9 My) present in the study area, incision rates can be estimated (1) for the streams located in the PCR, 0.38-0.15 m/ky and (2) for the streams flowing on the SPPS, 0.22-0.12 m/ky. The differential uplift inferred in the study area supports the neotectonic activity of the bordering faults, as proposed in previous studies based upon other geological evidence.

Comparison of Assays for Sensitive and Reproducible Detection of Cell Culture-Infectious Cryptosporidium parvum and Cryptosporidium hominis in Drinking Water

PubMed Central

Di Giovanni, George D.; Rochelle, Paul A.

2012-01-01

This study compared the three most commonly used assays for detecting Cryptosporidium sp. infections in cell culture: immunofluorescent antibody and microscopy assay (IFA), PCR targeting Cryptosporidium sp.-specific DNA, and reverse transcriptase PCR (RT-PCR) targeting Cryptosporidium sp.-specific mRNA. Monolayers of HCT-8 cells, grown in 8-well chamber slides or 96-well plates, were inoculated with a variety of viable and inactivated oocysts to assess assay performance. All assays detected infection with low doses of flow cytometry-enumerated Cryptosporidium parvum oocysts, including infection with one oocyst and three oocysts. All methods also detected infection with Cryptosporidium hominis. The RT-PCR assay, IFA, and PCR assay detected infection in 23%, 25%, and 51% of monolayers inoculated with three C. parvum oocysts and 10%, 9%, and 16% of monolayers inoculated with one oocyst, respectively. The PCR assay was the most sensitive, but it had the highest frequency of false positives with mock-infected cells and inactivated oocysts. IFA was the only infection detection assay that did not produce false positives with mock-infected monolayers. IFA was also the only assay that detected infections in all experiments with spiked oocysts recovered from Envirochek capsules following filtration of 1,000 liters of treated water. Consequently, cell culture with IFA detection is the most appropriate method for routine and sensitive detection of infectious Cryptosporidium parvum and Cryptosporidium hominis in drinking water. PMID:22038611

Low-Flow Characteristics and Regionalization of Low-Flow Characteristics for Selected Streams in Arkansas

USGS Publications Warehouse

Funkhouser, Jaysson E.; Eng, Ken; Moix, Matthew W.

2008-01-01

Water use in Arkansas has increased dramatically in recent years. Since 1990, the use of water for all purposes except power generation has increased 53 percent (4,004 cubic feet per second in 1990 to 6,113 cubic feet per second in 2005). The biggest users are agriculture (90 percent), municipal water supply (4 percent) and industrial supply (2 percent). As the population of the State continues to grow, so does the demand for the State's water resources. The low-flow characteristics of a stream ultimately affect its utilization by humans. Specific information on the low-flow characteristics of streams is essential to State water-management agencies such as the Arkansas Department of Environmental Quality, the Arkansas Natural Resources Commission, and the Arkansas Game and Fish Commission when dealing with problems related to irrigation, municipal and industrial water supplies, fish and wildlife conservation, and dilution of waste. Low-flow frequency data are of particular value to management agencies responsible for the development and management of the State's water resources. This report contains the low-flow characteristics for 70 active continuous-streamflow record gaging stations, 59 inactive continuous-streamflow record stations, and 101 partial-record gaging stations. These characteristics are the annual 7-day, 10-year low flow and the annual 7-day, 2-year low flow, and the seasonal, bimonthly, and monthly 7-day, 10-year low flow for the 129 active and inactive continuous-streamflow record and 101 partial-record gaging stations. Low-flow characteristics were computed on the basis of streamflow data for the period of record through September 2005 for the continuous-streamflow record and partial-record streamflow gaging stations. The low-flow characteristics of these continuous- and partial-record streamflow gaging stations were utilized in a regional regression analysis to produce equations for estimating the annual, seasonal, bimonthly, and monthly (November through April) 7-day, 10-year low flows and the annual 7-day, 2-year low flow for ungaged streams in the western two-thirds of Arkansas.

Using a tracer technique to identify the extent of non-ideal flows in the continuous mixing of non-Newtonian fluids

NASA Astrophysics Data System (ADS)

Patel, D.; Ein-Mozaffari, F.; Mehrvar, M.

2013-05-01

The identification of non-ideal flows in a continuous-flow mixing of non-Newtonian fluids is a challenging task for various chemical industries: plastic manufacturing, water and wastewater treatment, and pulp and paper manufacturing. Non-ideal flows such as channelling, recirculation, and dead zones significantly affect the performance of continuous-flow mixing systems. Therefore, the main objective of this paper was to develop an identification protocol to measure non-ideal flows in the continuous-flow mixing system. The extent of non-ideal flows was quantified using a dynamic model that incorporated channelling, recirculation, and dead volume in the mixing vessel. To estimate the dynamic model parameters, the system was excited using a frequency-modulated random binary input by injecting the saline solution (as a tracer) into the fresh feed stream prior to being pumped into the mixing vessel. The injection of the tracer was controlled by a computer-controlled on-off solenoid valve. Using the trace technique, the extent of channelling and the effective mixed volume were successfully determined and used as mixing quality criteria. Such identification procedures can be applied at various areas of chemical engineering in order to improve the mixing quality.

Utilization of Stop-flow Micro-tubing Reactors for the Development of Organic Transformations.

PubMed

Toh, Ren Wei; Li, Jie Sheng; Wu, Jie

2018-01-04

A new reaction screening technology for organic synthesis was recently demonstrated by combining elements from both continuous micro-flow and conventional batch reactors, coined stop-flow micro-tubing (SFMT) reactors. In SFMT, chemical reactions that require high pressure can be screened in parallel through a safer and convenient way. Cross-contamination, which is a common problem in reaction screening for continuous flow reactors, is avoided in SFMT. Moreover, the commercially available light-permeable micro-tubing can be incorporated into SFMT, serving as an excellent choice for light-mediated reactions due to a more effective uniform light exposure, compared to batch reactors. Overall, the SFMT reactor system is similar to continuous flow reactors and more superior than batch reactors for reactions that incorporate gas reagents and/or require light-illumination, which enables a simple but highly efficient reaction screening system. Furthermore, any successfully developed reaction in the SFMT reactor system can be conveniently translated to continuous-flow synthesis for large scale production.

Mathematical models of continuous flow electrophoresis: Electrophoresis technology

NASA Technical Reports Server (NTRS)

Saville, Dudley A.

1986-01-01

Two aspects of continuous flow electrophoresis were studied: (1) the structure of the flow field in continuous flow devices; and (2) the electrokinetic properties of suspended particles relevant to electrophoretic separations. Mathematical models were developed to describe flow structure and stability, with particular emphasis on effects due to buoyancy. To describe the fractionation of an arbitrary particulate sample by continuous flow electrophoresis, a general mathematical model was constructed. In this model, chamber dimensions, field strength, buffer composition, and other design variables can be altered at will to study their effects on resolution and throughput. All these mathematical models were implemented on a digital computer and the codes are available for general use. Experimental and theoretical work with particulate samples probed how particle mobility is related to buffer composition. It was found that ions on the surface of small particles are mobile, contrary to the widely accepted view. This influences particle mobility and suspension conductivity. A novel technique was used to measure the mobility of particles in concentrated suspensions.

Improved Bacterial and Viral Recoveries from 'Complex' Samples using Electrophoretically Assisted Acoustic Focusing

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

Ness, K; Rose, K; Jung, B

2008-03-27

Automated front-end sample preparation technologies can significantly enhance the sensitivity and reliability of biodetection assays [1]. We are developing advanced sample preparation technologies for biowarfare detection and medical point-of-care diagnostics using microfluidic systems with continuous sample processing capabilities. Here we report an electrophoretically assisted acoustic focusing technique to rapidly extract and enrich viral and bacterial loads from 'complex samples', applied in this case to human nasopharyngeal samples as well as simplified surrogates. The acoustic forces capture and remove large particles (> 2 {micro}m) such as host cells, debris, dust, and pollen from the sample. We simultaneously apply an electric fieldmore » transverse to the flow direction to transport small ({le} 2 {micro}m), negatively-charged analytes into a separate purified recovery fluid using a modified H-filter configuration [Micronics US Patent 5,716,852]. Hunter and O'Brien combined transverse electrophoresis and acoustic focusing to measure the surface charge on large particles, [2] but to our knowledge, our work is the first demonstration combining these two techniques in a continuous flow device. Marina et al. demonstrated superimposed dielectrophoresis (DEP) and acoustic focusing for enhanced separations [3], but these devices have limited throughput due to the rapid decay of DEP forces. Both acoustic standing waves and electric fields exert significant forces over the entire fluid volume in microchannels, thus allowing channels with larger dimensions (> 100 {micro}m) and high throughputs (10-100 {micro}L/min) necessary to process real-world volumes (1 mL). Previous work demonstrated acoustic focusing of microbeads [4] and biological species [5] in various geometries. We experimentally characterized our device by determining the biological size-cutoff where acoustic radiation pressure forces no longer transport biological particles. Figure 1 shows images of E.Coli ({approx}1 {micro}m) and yeast ({approx}4-5 {micro}m) flowing in a microchannel (200 {micro}m deep, 500 {micro}m wide) at a flow rate of 10 {micro}L/min. The E.Coli does not focus in the acoustic field while the yeast focuses at the channel centerline. This result suggests the acoustic size-cutoff for biological particles in our device lies between 2 and 3 {micro}m. Transverse electrophoresis has been explored extensively in electric field flow fractionation [6] and isoelectric focusing devices [7]. We demonstrated transverse electrophoretic transport of a wide variety of negatively-charged species, including fluorophores, beads, viruses, E.Coli, and yeast. Figure 2 shows the electromigration of a fluorescently labeled RNA virus (MS2) from the lower half of the channel to the upper half region with continuous flow. We demonstrated the effectiveness of our electrophoretically assisted acoustic focusing device by separating virus-like particles (40 nm fluorescent beads, selected to aid in visualization) from a high background concentration of yeast contaminants (see Figure 3). Our device allows for the efficient recovery of virus into a pre-selected purified buffer while background contaminants are acoustically captured and removed. We also tested the device using clinical nasopharyngeal samples, both washes and lavages, and demonstrated removal of unknown particulates (>2 ?m size) from the sample. Our future research direction includes spiking known amounts of bacteria and viruses into clinical samples and performing quantitative off-chip analysis (real-time PCR and flow cytometry).« less

Low-flow-frequency characteristics for continuous-record streamflow stations in Minnesota

USGS Publications Warehouse

Arntson, A.D.; Lorenz, D.L.

1987-01-01

Annual and summer (May 1 to September 30) low-flow frequency curves are presented for 175 continuous-record streamflow stations in Minnesota. The curves were developed for all stations with 10 or more years of continuous record. The 1-, 7-, and 30-day low-flow discharges at selected recurrence intervals obtained from these curves are listed. Low-flow characteristics can and will vary for a station depending upon the number of years of record and the period gaged. When comparing low-flow characteristics between two or more stations, it should be remembered that no provisions were made to use concurrent periods of record for stations along the same stream.

High-flow nasal prong oxygen therapy or nasopharyngeal continuous positive airway pressure for children with moderate-to-severe respiratory distress?*.

PubMed

ten Brink, Fia; Duke, Trevor; Evans, Janine

2013-09-01

The aim of this study was to compare the use of high-flow nasal prong oxygen therapy to nasopharyngeal continuous positive airway pressure in a PICU at a tertiary hospital; to understand the safety and effectiveness of high-flow nasal prong therapy; in particular, what proportion of children require escalation of therapy, whether any bedside monitoring data predict stability or need for escalation, and complications of the therapies. This was a prospective observational study of the first 6 months after the introduction of high-flow nasal prong oxygen therapy at the Royal Children's Hospital in Melbourne. Data were collected on all children who were managed with either high-flow nasal prong oxygen therapy or nasopharyngeal continuous positive airway pressure. The mode of respiratory support was determined by the treating medical staff. Data were collected on each patient before the use of high-flow nasal prong or nasopharyngeal continuous positive airway pressure, at 2 hours after starting the therapy, and the children were monitored and data collected until discharge from the ICU. Therapy was considered to be escalated if children on high-flow nasal prong required a more invasive form or higher level of respiratory support, including nasopharyngeal continuous positive airway pressure or mask bilevel positive airway pressure or endotracheal intubation and mechanical ventilation. Therapy was considered to be escalated if children on nasopharyngeal continuous positive airway pressure required bilevel positive airway pressure or intubation and mechanical ventilation. As the first mode of respiratory support, 72 children received high-flow nasal prong therapy and 37 received nasopharyngeal continuous positive airway pressure. Forty-four patients (61%) who received high-flow nasal prong first were weaned to low-flow oxygen or to room air and 21 (29%) required escalation of respiratory support, compared with children on nasopharyngeal continuous positive airway pressure: 21 (57%) weaned successfully and 9 (24%) required escalation. Repeated treatment and crossover were common in this cohort. Throughout the study duration, escalation to a higher level of respiratory support was needed in 26 of 100 high-flow nasal prong treatment episodes (26%) and in 10 of 55 continuous positive airway pressure episodes (18%; p = 0.27). The need for escalation could be predicted by two of failure of normalization of heart rate and respiratory rate, and if the FIO2 did not fall to lower than 0.5, 2 hours after starting high-flow nasal prong therapy. Nasopharyngeal continuous positive airway pressure was required for significantly longer periods than high-flow nasal prong (median 48 and 18 hours, respectively; p ≤ 0.001). High-flow nasal prong therapy is a safe form of respiratory support for children with moderate-to-severe respiratory distress, across a large range of diagnoses, whose increased work of breathing or hypoxemia is not relieved by standard oxygen therapy. About one quarter of all children will require escalation to another form of respiratory support. This can be predicted by simple bedside observations.

Mixing regime as a key factor to determine DON formation in drinking water biological treatment.

PubMed

Lu, Changqing; Li, Shuai; Gong, Song; Yuan, Shoujun; Yu, Xin

2015-11-01

Dissolved organic nitrogen (DON) can act as precursor of nitrogenous disinfection by-products formed during chlorination disinfection. The performances of biological fluidized bed (continuous stirred tank reactor, CSTR) and bio-ceramic filters (plug flow reactor, PFR) were compared in this study to investigate the influence of mixing regime on DON formation in drinking water treatment. In the shared influent, DON ranged from 0.71mgL(-1) to 1.20mgL(-1). The two biological fluidized bed reactors, named BFB1 (mechanical stirring) and BFB2 (air agitation), contained 0.12 and 0.19mgL(-1) DON in their effluents, respectively. Meanwhile, the bio-ceramic reactors, labeled as BCF1 (no aeration) and BCF2 (with aeration), had 1.02 and 0.81mgL(-1) DON in their effluents, respectively. Comparative results showed that the CSTR mixing regime significantly reduced DON formation. This particular reduction was further investigated in this study. The viable/total microbial biomass was determined with propidium monoazide quantitative polymerase chain reaction (PMA-qPCR) and qPCR, respectively. The results of the investigation demonstrated that the microbes in BFB2 had higher viability than those in BCF2. The viable bacteria decreased more sharply than the total bacteria along the media depth in BCF2, and DON in BCF2 accumulated in the deeper media. These phenomena suggested that mixing regime determined DON formation by influencing the distribution of viable, total biomass, and ratio of viable biomass to total biomass. Copyright © 2014 Elsevier Ltd. All rights reserved.

Continuous flow nitration in miniaturized devices

PubMed Central

2014-01-01

Summary This review highlights the state of the art in the field of continuous flow nitration with miniaturized devices. Although nitration has been one of the oldest and most important unit reactions, the advent of miniaturized devices has paved the way for new opportunities to reconsider the conventional approach for exothermic and selectivity sensitive nitration reactions. Four different approaches to flow nitration with microreactors are presented herein and discussed in view of their advantages, limitations and applicability of the information towards scale-up. Selected recent patents that disclose scale-up methodologies for continuous flow nitration are also briefly reviewed. PMID:24605161

Continuous detection and genetic diversity of human rotavirus A in sewage in eastern China, 2013-2014.

PubMed

Zhou, Nan; Lv, Dong; Wang, Suting; Lin, Xiaojuan; Bi, Zhenwang; Wang, Haiyan; Wang, Pei; Zhang, Huaning; Tao, Zexin; Hou, Peibin; Song, Yanyan; Xu, Aiqiang

2016-09-13

Rotavirus is the leading viral agent for pediatric gastroenteritis. However, the case-based surveillance for rotavirus is limited in China, and its circulation in the environment is not well investigated. From 2013 to 2014, rotavirus was detected in raw sewage samples of Jinan and Linyi by quantitative PCR (qPCR) and conventional reverse transcription PCR (RT-PCR). After sequenced and genotyped, sequences analysis was conducted. A total of 46 sewage samples were collected monthly for the detection of rotavirus, and rotavirus was positive in 43 samples (93.5 %, 43/46). By quantitative assessment, the concentrations of rotavirus in raw sewage ranged from 4.1 × 10(3) to 1.3 × 10(6) genome copies (GC)/L in Jinan, and from 1.5 × 10(3) to 3.0 × 10(5) GC/L in Linyi. A total of 318 sequences of 5 G-genotypes and 318 sequences of 5 P-genotypes were obtained. G9 (91.8 %, 292/318) and P[8] (56.0 %, 178/318) were the most common G- and P-genotype, respectively. Multiple transmission lineages were recognized in these genotypes. Interestingly, an intragenic recombination event between two G9 lineages was observed. This study provided the first report of comprehensive environmental surveillance for rotavirus in China. The results suggest that the concentration of rotavirus in raw sewage was high, and multiple rotavirus transmission lineages continuously co-circulated in Shandong.

Unified approach for incompressible flows

NASA Astrophysics Data System (ADS)

Chang, Tyne-Hsien

1995-07-01

A unified approach for solving incompressible flows has been investigated in this study. The numerical CTVD (Centered Total Variation Diminishing) scheme used in this study was successfully developed by Sanders and Li for compressible flows, especially for the high speed. The CTVD scheme possesses better mathematical properties to damp out the spurious oscillations while providing high-order accuracy for high speed flows. It leads us to believe that the CTVD scheme can equally well apply to solve incompressible flows. Because of the mathematical difference between the governing equations for incompressible and compressible flows, the scheme can not directly apply to the incompressible flows. However, if one can modify the continuity equation for incompressible flows by introducing pseudo-compressibility, the governing equations for incompressible flows would have the same mathematical characters as compressible flows. The application of the algorithm to incompressible flows thus becomes feasible. In this study, the governing equations for incompressible flows comprise continuity equation and momentum equations. The continuity equation is modified by adding a time-derivative of the pressure term containing the artificial compressibility. The modified continuity equation together with the unsteady momentum equations forms a hyperbolic-parabolic type of time-dependent system of equations. Thus, the CTVD schemes can be implemented. In addition, the physical and numerical boundary conditions are properly implemented by the characteristic boundary conditions. Accordingly, a CFD code has been developed for this research and is currently under testing. Flow past a circular cylinder was chosen for numerical experiments to determine the accuracy and efficiency of the code. The code has shown some promising results.

Unified approach for incompressible flows

NASA Technical Reports Server (NTRS)

Chang, Tyne-Hsien

1995-01-01

A unified approach for solving incompressible flows has been investigated in this study. The numerical CTVD (Centered Total Variation Diminishing) scheme used in this study was successfully developed by Sanders and Li for compressible flows, especially for the high speed. The CTVD scheme possesses better mathematical properties to damp out the spurious oscillations while providing high-order accuracy for high speed flows. It leads us to believe that the CTVD scheme can equally well apply to solve incompressible flows. Because of the mathematical difference between the governing equations for incompressible and compressible flows, the scheme can not directly apply to the incompressible flows. However, if one can modify the continuity equation for incompressible flows by introducing pseudo-compressibility, the governing equations for incompressible flows would have the same mathematical characters as compressible flows. The application of the algorithm to incompressible flows thus becomes feasible. In this study, the governing equations for incompressible flows comprise continuity equation and momentum equations. The continuity equation is modified by adding a time-derivative of the pressure term containing the artificial compressibility. The modified continuity equation together with the unsteady momentum equations forms a hyperbolic-parabolic type of time-dependent system of equations. Thus, the CTVD schemes can be implemented. In addition, the physical and numerical boundary conditions are properly implemented by the characteristic boundary conditions. Accordingly, a CFD code has been developed for this research and is currently under testing. Flow past a circular cylinder was chosen for numerical experiments to determine the accuracy and efficiency of the code. The code has shown some promising results.

Low-flow characteristics of Virginia streams

USGS Publications Warehouse

Austin, Samuel H.; Krstolic, Jennifer L.; Wiegand, Ute

2011-01-01

Low-flow annual non-exceedance probabilities (ANEP), called probability-percent chance (P-percent chance) flow estimates, regional regression equations, and transfer methods are provided describing the low-flow characteristics of Virginia streams. Statistical methods are used to evaluate streamflow data. Analysis of Virginia streamflow data collected from 1895 through 2007 is summarized. Methods are provided for estimating low-flow characteristics of gaged and ungaged streams. The 1-, 4-, 7-, and 30-day average streamgaging station low-flow characteristics for 290 long-term, continuous-record, streamgaging stations are determined, adjusted for instances of zero flow using a conditional probability adjustment method, and presented for non-exceedance probabilities of 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.05, 0.02, 0.01, and 0.005. Stream basin characteristics computed using spatial data and a geographic information system are used as explanatory variables in regional regression equations to estimate annual non-exceedance probabilities at gaged and ungaged sites and are summarized for 290 long-term, continuous-record streamgaging stations, 136 short-term, continuous-record streamgaging stations, and 613 partial-record streamgaging stations. Regional regression equations for six physiographic regions use basin characteristics to estimate 1-, 4-, 7-, and 30-day average low-flow annual non-exceedance probabilities at gaged and ungaged sites. Weighted low-flow values that combine computed streamgaging station low-flow characteristics and annual non-exceedance probabilities from regional regression equations provide improved low-flow estimates. Regression equations developed using the Maintenance of Variance with Extension (MOVE.1) method describe the line of organic correlation (LOC) with an appropriate index site for low-flow characteristics at 136 short-term, continuous-record streamgaging stations and 613 partial-record streamgaging stations. Monthly streamflow statistics computed on the individual daily mean streamflows of selected continuous-record streamgaging stations and curves describing flow-duration are presented. Text, figures, and lists are provided summarizing low-flow estimates, selected low-flow sites, delineated physiographic regions, basin characteristics, regression equations, error estimates, definitions, and data sources. This study supersedes previous studies of low flows in Virginia.

Electrohydrodynamics and other hydrodynamic phenomena in continuous flow electrophoresis

NASA Technical Reports Server (NTRS)

Saville, D. A.

1982-01-01

The process known as continuous flow electrophoresis employs an electric field to separate the constituents of particulate samples suspended in a liquid. Complications arise because the electric field generates temperature gradients due to Joule heating and derives an electrohydrodynamic crossflow. Several aspects of the flow are discussed including entrance effects, hydrodynamic stability and a flow restructuring due to the combined effects of buoyancy and the crossflow.

Increasing Sensitivity In Continuous-Flow Electrophoresis

NASA Technical Reports Server (NTRS)

Sharnez, Rizwan; Sammons, David W.

1994-01-01

Sensitivity of continuous-flow electrophoresis (CFE) chamber increased by introducing lateral gradients in concentration of buffer solution and thickness of chamber. Such gradients, with resulting enhanced separation, achieved in CFE chamber with wedge-shaped cross section and collateral flow. Enables improved separations of homogeneous components of mixtures of variety of biologically important substances.

[Analysis of FABP4 expression pattern in rump fat deposition and metabolism of Altay sheep].

PubMed

Ruixia, Xu; Lei, Gao; Weili, Zhao; Wei, Zhang; Guangchao, Song; Shangquan, Gan; Guoqing, Shi

2015-02-01

FABP4 (Fatty acid binding protein 4) is a hot candidate gene in fat deposition and lipid metabolism and participates in the transport and metabolism of intracellular free fatty acids. We aim to study the role of FABP4 in fat deposition and metabolism of the rump fat in Altay sheep. In this study, bioinformatics method was used to analyze the protein sequence homology among 10 species, and RT-PCR was employed to detect FABP4 tissue profiling of Altay sheep. An animal model simulating the rump fat deposition and metabolism of Altay sheep was established by continuous starvation, and qPCR and iTRAQ (isobaric tags for relative and absolute quantitation) were used to detecte FABP4 mRNA and protein expression changes in the control and continuous starvation groups, respectively. Sequence analysis showed that FABP4 protein sequence is highly conserved among species, suggesting an important biological function during evolution for FABP4. The RT-PCR result confirmed that FABP4 mRNA was highly expressed in intestinal and rump fat, suggesting that FABP4 plays an important physiological role in fat tissues. We did not find significant differences in FABP4 mRNA and protein between control and continuous starvation groups (P>0.05), which indicates that FABP4 may not be the key gene in fat deposition and metabolism in Altay sheep.The results above lay a foundation for further studies of FABP4 in rump or tail fat.

Multiplex qPCR for serodetection and serotyping of hepatitis viruses: A brief review.

PubMed

Irshad, Mohammad; Gupta, Priyanka; Mankotia, Dhananjay Singh; Ansari, Mohammad Ahmad

2016-05-28

The present review describes the current status of multiplex quantitative real time polymerase chain reaction (qPCR) assays developed and used globally for detection and subtyping of hepatitis viruses in body fluids. Several studies have reported the use of multiplex qPCR for the detection of hepatitis viruses, including hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), and hepatitis E virus (HEV). In addition, multiplex qPCR has also been developed for genotyping HBV, HCV, and HEV subtypes. Although a single step multiplex qPCR assay for all six hepatitis viruses, i.e., A to G viruses, is not yet reported, it may be available in the near future as the technologies continue to advance. All studies use a conserved region of the viral genome as the basis of amplification and hydrolysis probes as the preferred chemistries for improved detection. Based on a standard plot prepared using varying concentrations of template and the observed threshold cycle value, it is possible to determine the linear dynamic range and to calculate an exact copy number of virus in the specimen. Advantages of multiplex qPCR assay over singleplex or other molecular techniques in samples from patients with co-infection include fast results, low cost, and a single step investigation process.

Multiplex qPCR for serodetection and serotyping of hepatitis viruses: A brief review

PubMed Central

Irshad, Mohammad; Gupta, Priyanka; Mankotia, Dhananjay Singh; Ansari, Mohammad Ahmad

2016-01-01

The present review describes the current status of multiplex quantitative real time polymerase chain reaction (qPCR) assays developed and used globally for detection and subtyping of hepatitis viruses in body fluids. Several studies have reported the use of multiplex qPCR for the detection of hepatitis viruses, including hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), and hepatitis E virus (HEV). In addition, multiplex qPCR has also been developed for genotyping HBV, HCV, and HEV subtypes. Although a single step multiplex qPCR assay for all six hepatitis viruses, i.e., A to G viruses, is not yet reported, it may be available in the near future as the technologies continue to advance. All studies use a conserved region of the viral genome as the basis of amplification and hydrolysis probes as the preferred chemistries for improved detection. Based on a standard plot prepared using varying concentrations of template and the observed threshold cycle value, it is possible to determine the linear dynamic range and to calculate an exact copy number of virus in the specimen. Advantages of multiplex qPCR assay over singleplex or other molecular techniques in samples from patients with co-infection include fast results, low cost, and a single step investigation process. PMID:27239109

Molecular diagnosis of Plasmodium ovale by photo-induced electron transfer fluorogenic primers: PET-PCR

PubMed Central

Akerele, David; Ljolje, Dragan; Talundzic, Eldin; Udhayakumar, Venkatachalam

2017-01-01

Accurate diagnosis of malaria infections continues to be challenging and elusive, especially in the detection of submicroscopic infections. Developing new malaria diagnostic tools that are sensitive enough to detect low-level infections, user friendly, cost effective and capable of performing large scale diagnosis, remains critical. We have designed novel self-quenching photo-induced electron transfer (PET) fluorogenic primers for the detection of P. ovale by real-time PCR. In our study, a total of 173 clinical samples, consisting of different malaria species, were utilized to test this novel PET-PCR primer. The sensitivity and specificity were calculated using nested-PCR as the reference test. The novel primer set demonstrated a sensitivity of 97.5% and a specificity of 99.2% (95% CI 85.2–99.8% and 95.2–99.9% respectively). Furthermore, the limit of detection for P. ovale was found to be 1 parasite/μl. The PET-PCR assay is a new molecular diagnostic tool with comparable performance to other commonly used PCR methods. It is relatively easy to perform, and amiable to large scale malaria surveillance studies and malaria control and elimination programs. Further field validation of this novel primer will be helpful to ascertain the utility for large scale malaria screening programs. PMID:28640824

Molecular diagnosis of Plasmodium ovale by photo-induced electron transfer fluorogenic primers: PET-PCR.

PubMed

Akerele, David; Ljolje, Dragan; Talundzic, Eldin; Udhayakumar, Venkatachalam; Lucchi, Naomi W

2017-01-01

Accurate diagnosis of malaria infections continues to be challenging and elusive, especially in the detection of submicroscopic infections. Developing new malaria diagnostic tools that are sensitive enough to detect low-level infections, user friendly, cost effective and capable of performing large scale diagnosis, remains critical. We have designed novel self-quenching photo-induced electron transfer (PET) fluorogenic primers for the detection of P. ovale by real-time PCR. In our study, a total of 173 clinical samples, consisting of different malaria species, were utilized to test this novel PET-PCR primer. The sensitivity and specificity were calculated using nested-PCR as the reference test. The novel primer set demonstrated a sensitivity of 97.5% and a specificity of 99.2% (95% CI 85.2-99.8% and 95.2-99.9% respectively). Furthermore, the limit of detection for P. ovale was found to be 1 parasite/μl. The PET-PCR assay is a new molecular diagnostic tool with comparable performance to other commonly used PCR methods. It is relatively easy to perform, and amiable to large scale malaria surveillance studies and malaria control and elimination programs. Further field validation of this novel primer will be helpful to ascertain the utility for large scale malaria screening programs.

High clustering rates of multidrug-resistant Mycobacterium tuberculosis genotypes in Panama

PubMed Central

2013-01-01

Background Tuberculosis continues to be one of the leading causes of death worldwide and in the American region. Although multidrug-resistant tuberculosis (MDR-TB) remains a threat to TB control in Panama, few studies have focused in typing MDR-TB strains. The aim of our study was to characterize MDR Mycobacterium tuberculosis clinical isolates using PCR-based genetic markers. Methods From 2002 to 2004, a total of 231 Mycobacterium tuberculosis isolates from TB cases country-wide were screened for antibiotic resistance, and MDR-TB isolates were further genotyped by double repetitive element PCR (DRE-PCR), (GTG)5-PCR and spoligotyping. Results A total of 37 isolates (0.85%) were resistant to both isoniazid (INH) and rifampicin (RIF). Among these 37 isolates, only two (5.4%) were resistant to all five drugs tested. Dual genotyping using DRE-PCR and (GTG)5-PCR of MDR Mycobacterium tuberculosis isolates revealed eight clusters comprising 82.9% of the MDR-TB strain collection, and six isolates (17.1%) showed unique fingerprints. The spoligotyping of MDR-TB clinical isolates identified 68% as members of the 42 (LAM9) family genotype. Conclusion Our findings suggest that MDR Mycobacterium tuberculosis is highly clustered in Panama’s metropolitan area corresponding to Panama City and Colon City, and our study reveals the genotype distribution across the country. PMID:24053690

Zero entropy continuous interval maps and MMLS-MMA property

NASA Astrophysics Data System (ADS)

Jiang, Yunping

2018-06-01

We prove that the flow generated by any continuous interval map with zero topological entropy is minimally mean-attractable and minimally mean-L-stable. One of the consequences is that any oscillating sequence is linearly disjoint from all flows generated by all continuous interval maps with zero topological entropy. In particular, the Möbius function is linearly disjoint from all flows generated by all continuous interval maps with zero topological entropy (Sarnak’s conjecture for continuous interval maps). Another consequence is a non-trivial example of a flow having discrete spectrum. We also define a log-uniform oscillating sequence and show a result in ergodic theory for comparison. This material is based upon work supported by the National Science Foundation. It is also partially supported by a collaboration grant from the Simons Foundation (grant number 523341) and PSC-CUNY awards and a grant from NSFC (grant number 11571122).

Aerobic biodegradability of methyldiethanolamine (MDEA) used in natural gas sweetening plants in batch tests and continuous flow experiments.

PubMed

Fürhacker, M; Pressl, A; Allabashi, R

2003-09-01

Mixtures of different amines including tertiary amines (methyldiethanolamine, MDEA) are commonly used for the removal of CO2 from gas mixtures or in gas sweetening processes for the extraction of CO2 and H2S. The absorber solutions used can be released into the industrial waste water due to continuous substitution of degraded MDEA, periodically cleaning processes or an accidental spill. In this study, the aerobic biodegradability of MDEA was investigated in a standardised batch test and a continuous flow experiment (40 l/d). The results of the batch test indicated that the MDEA-solution was non-biodegradable during the test period of 28 days, whereas the continuous flow experiments showed biodegradation of more than 96% based on TOC-measurements. This was probably due to the adaptation of the microorganisms to this particular waste water contamination during continuous flow experiment.

The Applicability of TaqMan-Based Quantitative Real-Time PCR Assays for Detecting and Enumerating Cryptosporidium spp. Oocysts in the Environment

PubMed Central

Staggs, Sarah E.; Beckman, Erin M.; Keely, Scott P.; Mackwan, Reena; Ware, Michael W.; Moyer, Alan P.; Ferretti, James A.; Sayed, Abu; Xiao, Lihua; Villegas, Eric N.

2013-01-01

Quantitative real-time polymerase chain reaction (qPCR) assays to detect Cryptosporidium oocysts in clinical samples are increasingly being used to diagnose human cryptosporidiosis, but a parallel approach for detecting and identifying Cryptosporidium oocyst contamination in surface water sources has yet to be established for current drinking water quality monitoring practices. It has been proposed that Cryptosporidium qPCR-based assays could be used as viable alternatives to current microscopic-based detection methods to quantify levels of oocysts in drinking water sources; however, data on specificity, analytical sensitivity, and the ability to accurately quantify low levels of oocysts are limited. The purpose of this study was to provide a comprehensive evaluation of TaqMan-based qPCR assays, which were developed for either clinical or environmental investigations, for detecting Cryptosporidium oocyst contamination in water. Ten different qPCR assays, six previously published and four developed in this study were analyzed for specificity and analytical sensitivity. Specificity varied between all ten assays, and in one particular assay, which targeted the Cryptosporidium 18S rRNA gene, successfully detected all Cryptosporidium spp. tested, but also cross-amplified T. gondii, fungi, algae, and dinoflagellates. When evaluating the analytical sensitivity of these qPCR assays, results showed that eight of the assays could reliably detect ten flow-sorted oocysts in reagent water or environmental matrix. This study revealed that while a qPCR-based detection assay can be useful for detecting and differentiating different Cryptosporidium species in environmental samples, it cannot accurately measure low levels of oocysts that are typically found in drinking water sources. PMID:23805235

Clinical applicability and prognostic significance of molecular response assessed by fluorescent-PCR of immunoglobulin genes in multiple myeloma. Results from a GEM/PETHEMA study.

PubMed

Martinez-Lopez, Joaquin; Fernández-Redondo, Elena; García-Sánz, Ramón; Montalbán, María Angeles; Martínez-Sánchez, Pilar; Pavia, Bruno; Mateos, María Victoria; Rosiñol, Laura; Martín, Marisa; Ayala, Rosa; Martínez, Rafael; Blanchard, María Jesus; Alegre, Adrian; Besalduch, Joan; Bargay, Joan; Hernandez, Miguel T; Sarasquete, María Eugenia; Sanchez-Godoy, Pedro; Fernández, Manuela; Blade, Joan; San Miguel, Jesús F; Lahuerta, Juan Jose

2013-12-01

Minimal residual disease monitoring is becoming increasingly important in multiple myeloma (MM), but multiparameter flow cytometry (MFC) and allele-specific oligonucleotide polymerase chain reaction (ASO-PCR) techniques are not routinely available. This study investigated the prognostic influence of achieving molecular response assessed by fluorescent-PCR (F-PCR) in 130 newly diagnosed MM patients from Grupo Español Multidisciplinar de Melanoma (GEM)2000/GEM05 trials (NCT00560053, NCT00443235, NCT00464217) who achieved almost very good partial response after induction therapy. As a reference, we used the results observed with simultaneous MFC. F-PCR at diagnosis was performed on DNA using three different multiplex PCRs: IGH D-J, IGK V-J and KDE rearrangements. The applicability of F-PCR was 91·5%. After induction therapy, 64 patients achieved molecular response and 66 non-molecular response; median progression-free survival (PFS) was 61 versus 36 months, respectively (P = 0·001). Median overall survival (OS) was not reached (NR) in molecular response patients (5-year survival: 75%) versus 66 months in the non-molecular response group (P = 0·03). The corresponding PFS and OS values for patients with immunophenotypic versus non-immunophenotypic response were 67 versus 42 months (P = 0·005) and NR (5-year survival: 95%) versus 69 months (P = 0·004), respectively. F-PCR analysis is a rapid, affordable, and easily performable technique that, in some circumstances, may be a valid approach for minimal residual disease investigations in MM. © 2013 John Wiley & Sons Ltd.

Reduction of In-Stent Restenosis Risk on Nickel-Free Stainless Steel by Regulating Cell Apoptosis and Cell Cycle

PubMed Central

Li, Liming; Pan, Shuang; Zhou, Xiaohang; Meng, Xin; Han, Xiaoxi; Ren, Yibin; Yang, Ke; Guan, Yifu

2013-01-01

High nitrogen nickel-free austenitic stainless steel (HNNF SS) is one of the biomaterials developed recently for circumventing the in-stent restenosis (ISR) in coronary stent applications. To understand the ISR-resistance mechanism, we have conducted a comparative study of cellular and molecular responses of human umbilical vein endothelial cells (HUVECs) to HNNF SS and 316L SS (nickel-containing austenitic 316L stainless steel) which is the stent material used currently. CCK-8 analysis and flow cytometric analysis were used to assess the cellular responses (proliferation, apoptosis, and cell cycle), and quantitative real-time PCR (qRT-PCR) was used to analyze the gene expression profile of HUVECs exposed to HNNF SS and 316L SS, respectively. Flow cytometry analysis revealed that 316L SS could activate the cellular apoptosis more efficiently and initiate an earlier entry into the S-phase of cell cycle than HNNF SS. At the molecular level, qRT-PCR results showed that the genes regulating cell apoptosis and autophagy were overexpressed on 316L SS. Further examination indicated that nickel released from 316L SS triggered the cell apoptosis via Fas-Caspase8-Caspase3 exogenous pathway. These molecular mechanisms of HUVECs present a good model for elucidating the observed cellular responses. The findings in this study furnish valuable information for understanding the mechanism of ISR-resistance on the cellular and molecular basis as well as for developing new biomedical materials for stent applications. PMID:23638002

Bacterial biodiversity from an anaerobic up flow bioreactor with ANAMMOX activity inoculated with swine sludge

USDA-ARS?s Scientific Manuscript database

The present study aimed to identify organisms with ANAMMOX activity in a reactor maintained in a laboratory. Molecular methods as fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR) and cloning of 16S-rDNA genes probing for Planctomycetes were performed. Seventeen clones were ...

Improved detection of Bovine Viral Diarrhea Virus in Bovine lymphoid cell lines using PrimeFlow RNA assay

USDA-ARS?s Scientific Manuscript database

Bovine viral diarrhea virus (BVDV) infections, whether as acute, persistent or contributing to co-infections, result in significant losses for cattle producers. BVDV can be identified by real-time PCR and ELISA, detection and quantification of viral infection at the single cell level is extremely di...

Improved detection of bovine viral diarrhea virus in bovine lymphoid cell lines using PrimeFlow RNA assay

USDA-ARS?s Scientific Manuscript database

Bovine viral diarrhea virus (BVDV) infections, whether as acute, persistent or contributing to co-infections, result in significant losses for cattle producers. BVDV can be identified by real-time PCR and ELISA, detection and quantification of viral infection at the single cell level is extremely di...

Characterization of the maize pollen transcriptome: Validation of microarray results using quantitative real-time PCR

EPA Science Inventory

Pollen is the primary means of gene flow between plants and plant populations and plays a critical role in seed production. Pollen fitness can be defined as the ability of a particular pollen grain to outcompete other pollen present on the stigma and complete fertilization, thus ...

A rapid lateral-flow immunoassay for phytosanitary detection of Erwinia amylovora and on-site fire blight diagnosis.

PubMed

Braun-Kiewnick, A; Altenbach, D; Oberhänsli, T; Bitterlin, W; Duffy, B

2011-10-01

Fire blight is an invasive disease caused by Erwinia amylovora that threatens pome fruit production globally. Effective implementation of phytosanitary control measures depends upon rapid, reliable pathogen detection and disease diagnosis. We developed a lateral-flow immunoassay specific for E. amylovora with a detection limit of log 5.7 CFU/ml, typical of pathogen concentrations in symptomatic plant material. The simple assay had comparable sensitivity to standard culture plating, serum agglutination and nested PCR when validated for application in a phytosanitary laboratory as a confirmatory test of cultured isolates and for first-line diagnosis of phytosanitary samples that represent the full range of commercial, ornamental and forestry host species. On-site validation in ring-trials with local plant inspectors demonstrated robust and reliable detection (compared to subsequent plating and PCR analysis). The simplicity, inspector acceptance and facilitation of expedited diagnosis (from 2 days for laboratory submitted samples to 15 min with the immunoassay), offers a valuable tool for improved phytosanitary control of fire blight. Copyright © 2011 Elsevier B.V. All rights reserved.

Osteoinduction and survival of osteoblasts and bone-marrow stromal cells in 3D biphasic calcium phosphate scaffolds under static and dynamic culture conditions.

PubMed

Rath, Subha N; Strobel, Leonie A; Arkudas, Andreas; Beier, Justus P; Maier, Anne-Kathrin; Greil, Peter; Horch, Raymund E; Kneser, Ulrich

2012-10-01

In many tissue engineering approaches, the basic difference between in vitro and in vivo conditions for cells within three-dimensional (3D) constructs is the nutrition flow dynamics. To achieve comparable results in vitro, bioreactors are advised for improved cell survival, as they are able to provide a controlled flow through the scaffold. We hypothesize that a bioreactor would enhance long-term differentiation conditions of osteogenic cells in 3D scaffolds. To achieve this either primary rat osteoblasts or bone marrow stromal cells (BMSC) were implanted on uniform-sized biphasic calcium phosphate (BCP) scaffolds produced by a 3D printing method. Three types of culture conditions were applied: static culture without osteoinduction (Group A); static culture with osteoinduction (Group B); dynamic culture with osteoinduction (Group C). After 3 and 6 weeks, the scaffolds were analysed by alkaline phosphatase (ALP), dsDNA amount, SEM, fluorescent labelled live-dead assay, and real-time RT-PCR in addition to weekly alamarBlue assays. With osteoinduction, increased ALP values and calcium deposition are observed; however, under static conditions, a significant decrease in the cell number on the biomaterial is observed. Interestingly, the bioreactor system not only reversed the decreased cell numbers but also increased their differentiation potential. We conclude from this study that a continuous flow bioreactor not only preserves the number of osteogenic cells but also keeps their differentiation ability in balance providing a suitable cell-seeded scaffold product for applications in regenerative medicine. © 2012 The Authors Journal of Cellular and Molecular Medicine © 2012 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.

Efficient removal of antibiotics in surface-flow constructed wetlands, with no observed impact on antibiotic resistance genes.

PubMed

Berglund, Björn; Khan, Ghazanfar Ali; Weisner, Stefan E B; Ehde, Per Magnus; Fick, Jerker; Lindgren, Per-Eric

2014-04-01

Recently, there have been growing concerns about pharmaceuticals including antibiotics as environmental contaminants. Antibiotics of concentrations commonly encountered in wastewater have been suggested to affect bacterial population dynamics and to promote dissemination of antibiotic resistance. Conventional wastewater treatment processes do not always adequately remove pharmaceuticals causing environmental dissemination of low levels of these compounds. Using constructed wetlands as an additional treatment step after sewage treatment plants have been proposed as a cheap alternative to increase reduction of wastewater contaminants, however this means that the natural microbial community of the wetlands becomes exposed to elevated levels of antibiotics. In this study, experimental surface-flow wetlands in Sweden were continuously exposed to antibiotics of concentrations commonly encountered in wastewater. The aim was to assess the antibiotic removal efficiency of constructed wetlands and to evaluate the impact of low levels of antibiotics on bacterial diversity, resistance development and expression in the wetland bacterial community. Antibiotic concentrations were measured using liquid chromatography-mass spectrometry and the effect on the bacterial diversity was assessed with 16S rRNA-based denaturing gradient gel electrophoresis. Real-time PCR was used to detect and quantify antibiotic resistance genes and integrons in the wetlands, during and after the exposure period. The results indicated that the antibiotic removal efficiency of constructed wetlands was comparable to conventional wastewater treatment schemes. Furthermore, short-term treatment of the constructed wetlands with environmentally relevant concentrations (i.e. 100-2000 ng×l(-1)) of antibiotics did not significantly affect resistance gene concentrations, suggesting that surface-flow constructed wetlands are well-suited for wastewater treatment purposes. Copyright © 2014 Elsevier B.V. All rights reserved.

How to measure RNA expression in rare senescent cells expressing any specific protein such as p16Ink4a

PubMed Central

Jeyapalan, Jessie C.; Sedivy, John M.

2013-01-01

Here we describe a carefully optimized method for the preparation of high quality RNA by flow sorting of formaldehyde fixed senescent cells immunostained for any intracellular antigen. Replicative cellular senescence is a phenomenon of irreversible growth arrest triggered by the accumulation of a discrete number of cell divisions. The underlying cause of senescence due to replicative exhaustion is telomere shortening. We document here a spontaneous and apparently stochastic process that continuously generates senescent cells in cultures fully immortalized with telomerase. In the course of studying this phenomenon we developed a preparative fluorescence activated flow sorting method based on immunofluorescent staining of intracellular antigens that can also deliver RNA suitable for quantitative analysis of global gene expression. The protocols were developed using normal human diploid fibroblasts (HDF) and up to 5×107 cells could be conveniently processed in a single experiment. The methodology is based on formaldehyde crosslinking of cells, followed by permeabilization, antibody staining, flow sorting, reversal of the crosslinks, and recovery of the RNA. We explored key parameters such as crosslink reversal that affect the fragmentation of RNA. The recovered RNA is of high quality for downstream molecular applications based on short range sequence analysis, such qPCR, hybridization microarrays, and next generation sequencing. The RNA was analyzed by Affymetrix Gene Chip expression profiling and compared to RNA prepared by the direct lysis of cells. The correlation between the data sets was very high, indicating that the procedure does not introduce systematic changes in the mRNA transcriptome. The methods presented in this communication should be of interest to many investigators working in diverse model systems. PMID:23454889

How to measure RNA expression in rare senescent cells expressing any specific protein such as p16Ink4a.

PubMed

Jeyapalan, Jessie C; Sedivy, John M

2013-02-01

Here we describe a carefully optimized method for the preparation of high quality RNA by flow sorting of formaldehyde fixed senescent cells immunostained for any intracellular antigen. Replicative cellular senescence is a phenomenon of irreversible growth arrest triggered by the accumulation of a discrete number of cell divisions. The underlying cause of senescence due to replicative exhaustion is telomere shortening. We document here a spontaneous and apparently stochastic process that continuously generates senescent cells in cultures fully immortalized with telomerase. In the course of studying this phenomenon we developed a preparative fluorescence activated flow sorting method based on immunofluorescent staining of intracellular antigens that can also deliver RNA suitable for quantitative analysis of global gene expression. The protocols were developed using normal human diploid fibroblasts (HDF) and up to 5x107 cells could be conveniently processed in a single experiment. The methodology is based on formaldehyde crosslinking of cells, followed by permeabilization, antibody staining, flow sorting, reversal of the crosslinks, and recovery of the RNA. We explored key parameters such as crosslink reversal that affect the fragmentation of RNA. The recovered RNA is of high quality for downstream molecular applications based on short range sequence analysis, such qPCR, hybridization microarrays, and next generation sequencing. The RNA was analyzed by Affymetrix Gene Chip expression profiling and compared to RNA prepared by the direct lysis of cells. The correlation between the data sets was very high, indicating that the procedure does not introduce systematic changes in the mRNA transcriptome. The methods presented in this communication should be of interest to many investigators working in diverse model systems.

Pressurized tundish for controlling a continuous flow of molten metal

DOEpatents

Lewis, T.W.; Hamill, P.E. Jr.; Ozgu, M.R.; Padfield, R.C.; Rego, D.N.; Brita, G.P.

1990-07-24

A pressurized tundish for controlling a continuous flow of molten metal is characterized by having a pair of principal compartments, one being essentially unpressurized and receiving molten metal introduced thereto, and the other being adapted for maintaining a controlled gaseous pressure over the surface of the fluid metal therein, whereby, by controlling the pressure within the pressurized chamber, metal exiting from the tundish is made to flow continually and at a controlled rate. 1 fig.

Oscillatory multiphase flow strategy for chemistry and biology.

PubMed

Abolhasani, Milad; Jensen, Klavs F

2016-07-19

Continuous multiphase flow strategies are commonly employed for high-throughput parameter screening of physical, chemical, and biological processes as well as continuous preparation of a wide range of fine chemicals and micro/nano particles with processing times up to 10 min. The inter-dependency of mixing and residence times, and their direct correlation with reactor length have limited the adaptation of multiphase flow strategies for studies of processes with relatively long processing times (0.5-24 h). In this frontier article, we describe an oscillatory multiphase flow strategy to decouple mixing and residence times and enable investigation of longer timescale experiments than typically feasible with conventional continuous multiphase flow approaches. We review current oscillatory multiphase flow technologies, provide an overview of the advancements of this relatively new strategy in chemistry and biology, and close with a perspective on future opportunities.

Natural Length Scales Shape Liquid Phase Continuity in Unsaturated Flows

NASA Astrophysics Data System (ADS)

Assouline, S.; Lehmann, P. G.; Or, D.

2015-12-01

Unsaturated flows supporting soil evaporation and internal drainage play an important role in various hydrologic and climatic processes manifested at a wide range of scales. We study inherent natural length scales that govern these flow processes and constrain the spatial range of their representation by continuum models. These inherent length scales reflect interactions between intrinsic porous medium properties that affect liquid phase continuity, and the interplay among forces that drive and resist unsaturated flow. We have defined an intrinsic length scale for hydraulic continuity based on pore size distribution that controls soil evaporation dynamics (i.e., stage 1 to stage 2 transition). This simple metric may be used to delineate upper bounds for regional evaporative losses or the depth of soil-atmosphere interactions (in the absence of plants). A similar length scale governs the dynamics of internal redistribution towards attainment of field capacity, again through its effect on hydraulic continuity in the draining porous medium. The study provides a framework for guiding numerical and mathematical models for capillary flows across different scales considering the necessary conditions for coexistence of stationarity (REV), hydraulic continuity and intrinsic capillary gradients.

Numerical optimization using flow equations.

PubMed

Punk, Matthias

2014-12-01

We develop a method for multidimensional optimization using flow equations. This method is based on homotopy continuation in combination with a maximum entropy approach. Extrema of the optimizing functional correspond to fixed points of the flow equation. While ideas based on Bayesian inference such as the maximum entropy method always depend on a prior probability, the additional step in our approach is to perform a continuous update of the prior during the homotopy flow. The prior probability thus enters the flow equation only as an initial condition. We demonstrate the applicability of this optimization method for two paradigmatic problems in theoretical condensed matter physics: numerical analytic continuation from imaginary to real frequencies and finding (variational) ground states of frustrated (quantum) Ising models with random or long-range antiferromagnetic interactions.

Numerical optimization using flow equations

NASA Astrophysics Data System (ADS)

Punk, Matthias

2014-12-01

We develop a method for multidimensional optimization using flow equations. This method is based on homotopy continuation in combination with a maximum entropy approach. Extrema of the optimizing functional correspond to fixed points of the flow equation. While ideas based on Bayesian inference such as the maximum entropy method always depend on a prior probability, the additional step in our approach is to perform a continuous update of the prior during the homotopy flow. The prior probability thus enters the flow equation only as an initial condition. We demonstrate the applicability of this optimization method for two paradigmatic problems in theoretical condensed matter physics: numerical analytic continuation from imaginary to real frequencies and finding (variational) ground states of frustrated (quantum) Ising models with random or long-range antiferromagnetic interactions.

Value of PCR in sonication fluid for the diagnosis of orthopedic hardware-associated infections: Has the molecular era arrived?

PubMed

Renz, Nora; Cabric, Sabrina; Morgenstern, Christian; Schuetz, Michael A; Trampuz, Andrej

2018-04-01

Bone healing disturbance following fracture fixation represents a continuing challenge. We evaluated a novel fully automated polymerase chain reaction (PCR) assay using sonication fluid from retrieved orthopedic hardware to diagnose infection. In this prospective diagnostic cohort study, explanted orthopedic hardware materials from consecutive patients were investigated by sonication and the resulting sonication fluid was analyzed by culture (standard procedure) and multiplex PCR (investigational procedure). Hardware-associated infection was defined as visible purulence, presence of a sinus tract, implant on view, inflammation in peri-implant tissue or positive culture. McNemar's chi-squared test was used to compare the performance of diagnostic tests. For the clinical performance all pathogens were considered, whereas for analytical performance only microorganisms were considered for which primers are included in the PCR assay. Among 51 patients, hardware-associated infection was diagnosed in 38 cases (75%) and non-infectious causes in 13 patients (25%). The sensitivity for diagnosing infection was 66% for peri-implant tissue culture, 84% for sonication fluid culture, 71% (clinical performance) and 77% (analytical performance) for sonication fluid PCR, the specificity of all tests was >90%. The analytical sensitivity of PCR was higher for gram-negative bacilli (100%), coagulase-negative staphylococci (89%) and Staphylococcus aureus (75%) than for Cutibacterium (formerly Propionibacterium) acnes (57%), enterococci (50%) and Candida spp. (25%). The performance of sonication fluid PCR for diagnosis of orthopedic hardware-associated infection was comparable to culture tests. The additional advantage of PCR was short processing time (<5 h) and fully automated procedure. With further improvement of the performance, PCR has the potential to complement conventional cultures. Copyright © 2018 Elsevier Ltd. All rights reserved.

The effects of plant extracts on microbial community structure in a rumen-simulating continuous-culture system as revealed by molecular profiling.

PubMed

Ferme, D; Banjac, M; Calsamiglia, S; Busquet, M; Kamel, C; Avgustin, G

2004-01-01

An in vitro study in dual-flow continuous-culture fermentors was conducted with two different concentrations of monensin, cinnamaldehyde or garlic extract added to 1:1 forage-to-concentrate diet in order to determine their effects on selected rumen bacterial populations. Samples were subjected to total DNA extraction, restriction analysis of PCR amplified parts of 16S rRNA genes (ARDRA) and subsequent analysis of the restriction profiles by lab-on-chip technology with the Agilent's Bioanalyser 2100. Eub338-BacPre primer pair was used to select for the bacteria from the genera Bacteroides, Porphyromonas and Prevotella, especially the latter representing the dominant Gram-negative bacterial population in the rumen. Preliminary results of HaeIII restriction analysis show that the effects of monensin, cinnamaldehyde and garlic extract on the BacPre targeted ruminal bacteria are somewhat different in regard to targeted populations and to the nature of the effect. Garlic extract was found to trigger the most intensive changes in the structure of the BacPre targeted population. Comparison of the in silico restriction analysis of BacPre sequences deposited in different DNA databanks and of the results of performed amplified ribosomal DNA restriction analysis showed differences between the predicted and obtained HaeIII restriction profiles, and suggested the presence of novel, still unknown Prevotella populations in studied samples.

[Molecular characterization of heterozygous beta-thalassemia in Lanzarote, Spain].

PubMed

Calvo-Villas, José Manuel; de la Iglesia Iñigo, Silvia; Ropero Gradilla, Paloma; Zapata Ramos, María Francisca; Cuesta Tovar, Jorge; Sicilia Guillén, Francisco

2008-04-05

The aim of this study was to determine the molecular defects of heterozygous beta thalassaemia and to ascertain their distribution in Lanzarote. Molecular characterization was achieved by real time polymerase chain reaction (RT-PCR LightCycler, Roche), PCR-ARMS (PCR-amplification reaction mutations system) and DNA sequencing on an automated DNA sequencer. Two hundred forty-three heterozygous beta thalassaemia carriers were included between July 1991 and February 2007. RT-PCR detected the molecular defect in 81% of the beta thalassaemia chromosomes analyzed [113 codon CD 39 (C --> T); 41 IVS-1-nt-110 (G --> A), 25 IVS 1-nt-1 (G --> A) and 19 IVS 1-nt-6 (T --> C)]. The remaining 12 molecular defects included the deletion 619 bp (7.8%) and the mutations -28 (A --> G), IVS1-nt-2 (T --> G), CD 41/42 (-TTCT), CD 8/9 (+G), CD 51 (-C), CD 22 (G --> T) and CD 24 (T --> A), CD 67 (-TG) and the novel mutation CD 20/21-TGGA. The distribution of the mutations is similar to that found in the Mediterranean area. The increasing migratory flow received in the Canary Islands may explain the emergence of new mutations not reported before in our area.

Population structure of Angiostrongylus cantonensis (Nematoda: Metastrongylidae) in Thailand based on PCR-RAPD markers.

PubMed

Thaenkham, Urusa; Pakdee, Wallop; Nuamtanong, Supaporn; Maipanich, Wanna; Pubampen, Somchit; Sa-Nguankiat, Surapol; Komalamisra, Chalit

2012-05-01

Angiostrongylus cantonensis is the causative agent of angiostrongyliasis, which is widely distributed throughout the world. It can specifically infect many species of intermediate and definitive hosts. This study examined the genetic differentiation and population structure using the RAPD-PCR method of parasites obtained from 8 different geographical areas of Thailand. Based on 8 primers, high levels of genetic diversity and low levels of gene flow among populations were found. Using genetic distance and neighbor-joining dendrogram methods, A. cantonensis in Thailand could be divided into two groups with statistically significant genetic differentiation of the two populations. However, genotypic variations and haplotype relationships need to be further elucidated using other markers.

Gene cloning, expression and functional characterization of a proliferation-inducing ligand (APRIL) from hedgehog (Erinaceus europaeus).

PubMed

Cui, Xian-Wei; Xiao, Wen; Ji, Chen-Bo; Tian, Ai-Ying; Zhang, Jie; Zhang, Shuang-Quan

2012-05-01

Here we describe the identification of the hedgehog Erinaceus europaeus homologue of a proliferation-inducing ligand (APRIL) of the TNF family (designated heAPRIL). Hedgehog APRIL contains two cysteine residues (Cys(196) and Cys(211)), a furin protease cleavage site and a conserved putative N-glycosylation site (Asn(124)). Real-time quantitative PCR (qPCR) analysis revealed that heAPRIL could be detected in various tissues. MTT assays and flow cytometric analysis revealed that Nus-hesAPRIL and hesAPRIL could promote the survival/proliferation of splenic B cells. Laser scanning confocal microscopy analysis showed GFP-hesAPRIL could successfully bind to the APRIL receptors of lymphocytes.

Using multiple PCR and CE with chemiluminescence detection for simultaneous qualitative and quantitative analysis of genetically modified organism.

PubMed

Guo, Longhua; Qiu, Bin; Chi, Yuwu; Chen, Guonan

2008-09-01

In this paper, an ultrasensitive CE-CL detection system coupled with a novel double-on-column coaxial flow detection interface was developed for the detection of PCR products. A reliable procedure based on this system had been demonstrated for qualitative and quantitative analysis of genetically modified organism-the detection of Roundup Ready Soy (RRS) samples was presented as an example. The promoter, terminator, function and two reference genes of RRS were amplified with multiplex PCR simultaneously. After that, the multiplex PCR products were labeled with acridinium ester at the 5'-terminal through an amino modification and then analyzed by the proposed CE-CL system. Reproducibility of analysis times and peak heights for the CE-CL analysis were determined to be better than 0.91 and 3.07% (RSD, n=15), respectively, for three consecutive days. It was shown that this method could accurately and qualitatively detect RRS standards and the simulative samples. The evaluation in terms of quantitative analysis of RRS provided by this new method was confirmed by comparing our assay results with those of the standard real-time quantitative PCR (RT-QPCR) using SYBR Green I dyes. The results showed a good coherence between the two methods. This approach demonstrated the possibility for accurate qualitative and quantitative detection of GM plants in a single run.

[Zinc-dependent metalloprotease 1 promotes apoptosis of RAW264.7 macrophages].

PubMed

Li, Peng; He, Yonglin; Zhang, Jiming; Fang, Chencheng

2015-12-01

To construct the eukaryotic expression vector of zinc-dependent metalloprotease 1 (zmp1) gene from Bacillus Calmette-Guerin (BCG) and investigate its impact on the apoptosis of RAW264.7 macrophages. Zmp1 gene was amplified from the genome of BCG by PCR. The zmp1 gene fragment was inserted into multiple cloning sites of pEGFP-N1 to construct the eukaryotic expression vector pEGFP-N1-zmp1. The constructed pEGFP-N1-zmp1 was transfected into RAW264.7 cells by Lipofectamine(TM) 2000. The expression of green fluorescent protein (GFP) was observed by fluorescence microscopy. The zmp1 mRNA was detected by quantitative real-time PCR (qR-PCR). The effect of Zmp1 protein on the apoptosis of RAW264.7 macrophages was detected by flow cytometry (FCM). With zmp1 gene amplified by PCR, we successfully constructed the recombinant vector pEGFP-N1-zmp1 as demonstrated by restriction enzyme analysis and sequencing. GFP was seen in RAW264.7 cells 24 hours after transfected with the recombinant plasmid. As qRT-PCR showed, the expression level of zmp1 mRNA was up-regulated. The early apoptotic rate increased 48 hours after transfection. The increased expression of Zmp1 in RAW264.7 cells promotes the apoptosis of RAW264.7 cells.

Atomizing, continuous, water monitoring module

DOEpatents

Thompson, C.V.; Wise, M.B.

1997-07-08

A system for continuously analyzing volatile constituents of a liquid is described. The system contains a pump for continuously pumping the liquid to be tested at a predetermined flow rate into an extracting container through a liquid directing tube having an orifice at one end and positioned to direct the liquid into the extracting container at a flow rate sufficient to atomize the liquid within the extracting container. A continuous supply of helium carrier gas at a predetermined flow rate is directed through a tube into the extracting container and co-mingled with the atomized liquid to extract the volatile constituents contained within the atomized liquid. The helium containing the extracted volatile constituents flows out of the extracting container into a mass spectrometer for an analysis of the volatile constituents of the liquid. 3 figs.

Atomizing, continuous, water monitoring module

DOEpatents

Thompson, Cyril V.; Wise, Marcus B.

1997-01-01

A system for continuously analyzing volatile constituents of a liquid is described. The system contains a pump for continuously pumping the liquid to be tested at a predetermined flow rate into an extracting container through a liquid directing tube having an orifice at one end and positioned to direct the liquid into the extracting container at a flow rate sufficient to atomize the liquid within the extracting container. A continuous supply of helium carrier gas at a predetermined flow rate is directed through a tube into the extracting container and co-mingled with the atomized liquid to extract the volatile constituents contained within the atomized liquid. The helium containing the extracted volatile constituents flows out of the extracting container into a mass spectrometer for an analysis of the volatile constituents of the liquid.

Use of Length Heterogeneity PCR and Fatty Acid Methyl Ester Profiles To Characterize Microbial Communities in Soil†

PubMed Central

Ritchie, Nancy J.; Schutter, Mary E.; Dick, Richard P.; Myrold, David D.

2000-01-01

In length heterogeneity PCR (LH-PCR) a fluorescently labeled primer is used to determine the relative amounts of amplified sequences originating from different microorganisms. Labeled fragments are separated by gel electrophoresis and detected by laser-induced fluorescence with an automated gene sequencer. We used LH-PCR to evaluate the composition of the soil microbial community. Four soils, which differed in terms of soil type and/or crop management practice, were studied. Previous data for microbial biomass, nitrogen and carbon contents, and nitrogen mineralization rates suggested that the microbial characteristics of these soils were different. One site received two different treatments: no-till and conventional till perennial ryegrass. The other sites were no-till continuous grass plots at separate locations with different soil types. Community composition was characterized by assessing the natural length heterogeneity in eubacterial sequences amplified from the 5′ domain of the 16S rRNA gene and by determining fatty acid methyl ester (FAME) profiles. We found that LH-PCR results were reproducible. Both methods distinguished the three sites. The most abundant bacterial community members, based on cloned LH-PCR products, were members of the β subclass of the class Proteobacteria, the Cytophaga-Flexibacter-Bacteriodes group, and the high-G+C-content gram-positive bacterial group. Strong correlations were found between LH-PCR results and FAME results. We found that the LH-PCR method is an efficient, reliable, and highly reproducible method that should be a useful tool in future assessments of microbial community composition. PMID:10742258

KSC01pp0129

NASA Image and Video Library

2001-01-17

Workers in the Payload Changeout Room check the U.S. Lab Destiny as its moves from Atlantis’ payload bay into the PCR. Destiny will remain in the PCR while Atlantis rolls back to the Vehicle Assembly Building to allow workers to conduct inspections, continuity checks and X-ray analysis on the 36 solid rocket booster cables located inside each booster’s system tunnel. An extensive evaluation of NASA’s SRB cable inventory revealed conductor damage in four (of about 200) cables on the shelf. Shuttle managers decided to prove the integrity of the system tunnel cables already on Atlantis

KSC01pp0130

NASA Image and Video Library

2001-01-17

Workers in the Payload Changeout Room check the U.S. Lab Destiny as its moves from Atlantis’ payload bay into the PCR. Destiny will remain in the PCR while Atlantis rolls back to the Vehicle Assembly Building to allow workers to conduct inspections, continuity checks and X-ray analysis on the 36 solid rocket booster cables located inside each booster’s system tunnel. An extensive evaluation of NASA’s SRB cable inventory revealed conductor damage in four (of about 200) cables on the shelf. Shuttle managers decided to prove the integrity of the system tunnel cables already on Atlantis

Post-explant visualization of thrombi in outflow grafts and their junction to a continuous-flow total artificial heart using a high-definition miniaturized camera.

PubMed

Karimov, Jamshid H; Horvath, David; Sunagawa, Gengo; Byram, Nicole; Moazami, Nader; Golding, Leonard A R; Fukamachi, Kiyotaka

2015-12-01

Post-explant evaluation of the continuous-flow total artificial heart in preclinical studies can be extremely challenging because of the device's unique architecture. Determining the exact location of tissue regeneration, neointima formation, and thrombus is particularly important. In this report, we describe our first successful experience with visualizing the Cleveland Clinic continuous-flow total artificial heart using a custom-made high-definition miniature camera.

Low-flow characteristics of Indiana streams

USGS Publications Warehouse

Stewart, J.A.

1983-01-01

Knowledge of low-flow data for Indiana streams is essential to the planners and developers of water resources for municipal, industrial, and recreational uses in the State. Low-flow data for 219 continuous-record gaging stations through the 1978 water year and for some stations since then are presented in tables and curves. Flow-duration and low-flow-frequency data were estimated or determined for continuous-record stations having more than 10 years of record. In addition, low-flow-frequency data were estimated for 248 partial-record stations. Methods for estimating these data are included in the report. (USGS)

Detection of minute virus of mice using real time quantitative PCR in assessment of virus clearance during the purification of Mammalian cell substrate derived biotherapeutics.

PubMed

Zhan, Dejin; Roy, Margaret R; Valera, Christine; Cardenas, Jesse; Vennari, Joann C; Chen, Janice W; Liu, Shengjiang

2002-12-01

A real time quantitative PCR assay has been developed for detecting minute virus of mice (MVM). This assay directly quantifies PCR product by monitoring the increase of fluorescence intensity emitted during enzymatic hydrolysis of an oligonucleotide probe labelled covalently with fluorescent reporting and quenching dyes via Taq polymerase 5'-->3' exonuclease activity. The quantity of MVM DNA molecules in the samples was determined using a known amount of MVM standard control DNA fragment cloned into a plasmid (pCR-MVM). We have demonstrated that MVM TaqMan PCR assay is approximately 1000-fold more sensitive than the microplate infectivity assay with the lowest detection limit of approximately one particle per reaction. The reliable detection range is within 100 to 10(9) molecules per reaction with high reproducibility. The intra assay variation is <2.5%, and the inter assays variation is <6.5% when samples contain >100 particles/assay. When we applied the TaqMan PCR to MVM clearance studies done by column chromatography or normal flow viral filtration, we found that the virus removal factors were similar to that of virus infectivity assay. It takes about a day to complete entire assay processes, thus, the TaqMan PCR assay is at least 10-fold faster than the infectivity assay. Therefore, we concluded that this fast, specific, sensitive, and robust assay could replace the infectivity assay for virus clearance evaluation. Copyright 2002 The International Association for Biologicals. Published by Elsevier Science Ltd. All rights reserved.

Prenatal diagnosis using polymerase chain reaction on amniotic fluid for congenital toxoplasmosis.

PubMed

Romand, S; Wallon, M; Franck, J; Thulliez, P; Peyron, F; Dumon, H

2001-02-01

To evaluate sensitivity, specificity, and predictive values of a prenatal amniotic fluid (AF) polymerase chain reaction (PCR) test for diagnosis of congenital toxoplasmosis. A multicenter prospective study was done on 271 women with proved primary Toxoplasma infection during pregnancy and who had amniocentesis for prenatal diagnosis by PCR. Live-born infants were eligible for analysis only if a serologic follow-up could assess a definitive infection status. Of the 270 evaluable cases, 75 were congenitally infected, 48 of whom had a positive PCR at prenatal diagnosis. Overall sensitivity of PCR on AF was estimated at 64% (95% confidence interval [CI] 53.1%, 74.9%), negative predictive value of 87.8% (95% CI 83.5%, 92.1%), whereas specificity and positive predictive value were 100% (95% CIs 98%, 100% and 92.3%, 100%, respectively). Among cases with congenital toxoplasmosis, there were no significant differences between those with positive or negative PCR with regard to median gestational age at maternal infection, interval between maternal infection and amniocentesis, or duration of treatment before amniocentesis. However, sensitivity of PCR was found to be significantly higher for maternal infections that occurred between 17 and 21 weeks' gestation (P <.02). A negative PCR of AF cannot rule out congenital infection. In this case, continuation of treatment with spiramycin combined with ultrasonographic follow-up and postnatal follow-up are warranted. Our results also suggest presumptive treatment combining pyrimethamine and sulfonamides in case of maternal infection occurring late in pregnancy.

Comparative analysis of genetic diversity among Indian populations of Scirpophaga incertulas by ISSR-PCR and RAPD-PCR.

PubMed

Kumar, L S; Sawant, A S; Gupta, V S; Ranjekar, P K

2001-10-01

Genetic variation between 28 Indian populations of the rice pest, Scirpophaga incertulas was evaluated using inter-simple sequence repeats (ISSR)-PCR assay. Nine SSR primers gave rise to 79 amplification products of which 67 were polymorphic. A dendrogram constructed from this data indicates that there is no geographical bias to the clustering and that gene flow between populations appears to be relatively unrestricted, substantiating our earlier conclusion based on the RAPD (random amplified polymorphic DNA) data. The dendrograms obtained using each of these marker systems were poorly correlated with each other as determined by Mantel's test for matrix correlation. Estimates of expected heterozygosity and marker index for each of these marker systems suggests that both these marker systems are equally efficient in determining polymorphisms. Matrix correlation analyses suggest that reliable estimates of genetic variation among the S. incertulas pest populations can be obtained by using RAPDs alone or in combination with ISSRs, but ISSRs alone cannot be used for this purpose.

Studies with sample conductivity, insertion rates, and particle deflection in a continuous flow electrophoresis system

NASA Technical Reports Server (NTRS)

Williams, G., Jr.

1982-01-01

The continuous flow electrophoresis system makes electrophoresis possible in a free-flowing film of aqueous electrolyte medium. The sample continuously enters the electrolyte at the top of the chamber and is subjected to the action of a lateral dc field. This divides the sample into fractions since each component has a distinctive electrophoretic mobility. Tests were made using monodisperse polystyrene latex microspheres to determine optimum sample conductivity, insertion rates and optimum electric field applications as baseline data for future STS flight experiments. Optimum sample flow rates for the selected samples were determined to be approximately 26 micro-liters/min. Experiments with samples in deionized water yielded best results and voltages in the 20 V/cm to 30 V/cm range were optimum. Deflections of formaldehyde fixed turkey and bovine erythrocytes were determined using the continuous flow electrophoresis system. The effects of particle interactions on sample resolution and migration in the chamber was also evaluated.

Ethyl acetate as an acyl donor in the continuous flow kinetic resolution of (±)-1-phenylethylamine catalyzed by lipases.

PubMed

de Miranda, Amanda S; Miranda, Leandro S M; de Souza, Rodrigo O M A

2013-05-28

The synthesis of chiral amines is still a challenge for organic synthesis since optically pure amines are of great importance for the pharmaceutical and agrochemical industries. Among all the methodologies developed until now, chemoenzymatic dynamic kinetic resolution has proven to be useful for the preparation of enantioenriched primary chiral amines. In our continuous efforts toward the development of a continuous flow process, herein we report our results on the continuous flow kinetic resolution of (±)-1-phenylethylamine leading to the desired products with high enantiomeric ratios (>200) and short residence times (40 minutes) using ethyl acetate as the acyl donor.

S-phase arrest after vincristine treatment may promote hepatitis B virus replication

PubMed Central

Xu, Lei; Tu, Zeng; Xu, Ge; Hu, Jie-Li; Cai, Xue-Fei; Zhan, Xing-Xing; Wang, Yu-Wei; Huang, Yuan; Chen, Juan; Huang, Ai-Long

2015-01-01

AIM: To observe the effect of vincristine on hepatitis B virus (HBV) replication in vitro and to study its possible mechanisms. METHODS: Vincristine was added to the cultures of two cell lines stably expressing HBV. Then, the levels of hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), and hepatitis B core antigen (HBcAg) in the supernatants or cytoplasm were examined using by enzyme-linked immunosorbent assay and Western blot. The HBV pregenome RNA (pgRNA) was detected using reverse transcription-PCR and real-time fluorescent quantitative PCR (RT-qPCR), and viral DNA was detected using Southern blot and RT-qPCR. Cell proliferation after drug treatment was detected using the BrdU incorporation test and the trypan blue exclusion assay. Cell cycle and cell apoptosis were examined using flow cytometry and Western blot. RESULTS: Vincristine up-regulated HBV replication directly in vitro in a dose-dependent manner, and 24-h exposure to 0.1 μmol/L vincristine induced more than 4-fold and 3-fold increases in intracellular HBV DNA and the secretion of viral DNA, respectively. The expression of HBV pgRNA, intracellular HBsAg and HBcAg, and the secretion of HBeAg were also increased significantly after drug treatment. Most importantly, vincristine promoted the cell excretion of HBV nucleocapsids instead of HBV Dane particles, and the nucleocapsids are closely related to the HBV pathogenesis. Furthermore, vincristine inhibited the proliferation of cells stably expressing HBV. The higher the concentration of the drug, the more significant the inhibition of the cell proliferation and the stronger the HBV replication ability in cells. Flow cytometry indicated that cell cycle arrest at S-phase was responsible for the cell proliferation inhibition. CONCLUSION: Vincristine has a strong stimulatory effect on HBV replication and induces cell cycle arrest, and cell proliferation inhibition may be conducive to viral replication. PMID:25663769

The diagnostic accuracy of three rapid diagnostic tests for typhoid fever at Chittagong Medical College Hospital, Chittagong, Bangladesh.

PubMed

Maude, Rapeephan R; de Jong, Hanna K; Wijedoru, Lalith; Fukushima, Masako; Ghose, Aniruddha; Samad, Rasheda; Hossain, Mohammed Amir; Karim, Mohammed Rezaul; Faiz, Mohammed Abul; Parry, Christopher M

2015-10-01

To determine the diagnostic accuracy of three rapid diagnostic tests (RDTs) for typhoid fever in febrile hospitalised patients in Bangladesh. Febrile adults and children admitted to Chittagong Medical College Hospital, Bangladesh, were investigated with Bact/Alert(®) blood cultures and real-time PCR to detect Salmonella enterica Typhi and Paratyphi A and assays for Rickettsia, leptospirosis and dengue fever. Acute serum samples were examined with the LifeAssay (LA) Test-it™ Typhoid IgM lateral flow assay detecting IgM antibodies against S. Typhi O antigen, CTKBiotech Onsite Typhoid IgG/IgM Combo Rapid-test cassette lateral flow assay detecting IgG and IgM antibodies against S. Typhi O and H antigens and SD Bioline line assay for IgG and IgM antibodies against S. Typhi proteins. In 300 malaria smear-negative febrile patients [median (IQR) age of 13.5 (5-31) years], 34 (11.3%) had confirmed typhoid fever: 19 positive by blood culture for S. Typhi (three blood PCR positive) and 15 blood culture negative but PCR positive for S. Typhi in blood. The respective sensitivity and specificity of the three RDTs in patients using a composite reference standard of blood culture and/or PCR-confirmed typhoid fever were 59% and 61% for LifeAssay, 59% and 74% for the CTK IgM and/or IgG, and 24% and 96% for the SD Bioline RDT IgM and/or IgG. The LifeAssay RDT had a sensitivity of 63% and a specificity of 91% when modified with a positive cut-off of ≥2+ and analysed using a Bayesian latent class model. These typhoid RDTs demonstrated moderate diagnostic accuracies, and better tests are needed. © 2015 The Authors. Tropical Medicine & International Health Published by John Wiley & Sons Ltd.

Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis

PubMed Central

2010-01-01

Background In the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In this study, a genome-wide expression profiling approach (cDNA-AFLP), validated by quantitative real-time polymerase chain reaction (qPCR) were used to get insights into the role of differential gene expression on the ecological adaptation of the marine snail Littorina saxatilis. This gastropod displays two sympatric ecotypes (RB and SU) which are becoming one of the best studied systems for ecological speciation. Results Among the 99 transcripts shared between ecotypes, 12.12% showed significant differential expression. At least 4% of these transcripts still displayed significant differences after correction for multiple tests, highlighting that gene expression can differ considerably between subpopulations adapted to alternative habitats in the face of gene flow. One of the transcripts identified was Cytochrome c Oxidase subunit I (COI). In addition, 6 possible reference genes were validated to normalize and confirm this result using qPCR. α-Tubulin and histone H3.3 showed the more stable expression levels, being therefore chosen as the best option for normalization. The qPCR analysis confirmed a higher COI expression in SU individuals. Conclusions At least 4% of the transcriptome studied is being differentially expressed between ecotypes living in alternative habitats, even when gene flow is still substantial between ecotypes. We could identify a candidate transcript of such ecotype differentiation: Cytochrome c Oxidase Subunit I (COI), a mitochondrial gene involved in energy metabolism. Quantitative PCR was used to confirm the differences found in COI and its over-expression in the SU ecotype. Interestingly, COI is involved in the oxidative phosphorylation, suggesting an enhanced mitochondrial gene expression (or increased number of mitochondria) to improve energy supply in the ecotype subjected to the strongest wave action. PMID:21087461

Polystyrene latex separations by continuous flow electrophoresis on the Space Shuttle

NASA Technical Reports Server (NTRS)

Snyder, R. S.; Rhodes, P. H.; Miller, T. Y.; Micale, F. J.; Mann, R. V.

1986-01-01

The seventh mission of the Space Shuttle carried two NASA experiments in the McDonnell Douglas Astronautics Corporation continuous flow electrophoresis system. The objectives were to test the operation of continuous flow electrophoresis in a reduced gravity environment using stable particles with established electrokinetic properties and specifically to evaluate the influence of the electrical properties of the sample constituents on the resolution of the continuous flow electrophoretic device. Polystrene latex microspheres dispersed in a solution with three times the electrical conductivity of the curtain buffer separated with a significantly larger band spread compared to the second experiment under matched conductivity conditions. It is proposed that the sample of higher electrical conductivity distorted the electric field near the sample stream so that the polystyrene latex particles migrated toward the chamber walls where electroosmosis retarded and spread the sample.

40 CFR 75.33 - Standard missing data procedures for SO2, NOX, Hg, and flow rate.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Standard missing data procedures for... AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) CONTINUOUS EMISSION MONITORING Missing Data Substitution Procedures § 75.33 Standard missing data procedures for SO2, NOX, Hg, and flow rate. (a) Following initial...

40 CFR 75.33 - Standard missing data procedures for SO2, NOX, and flow rate.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 16 2011-07-01 2011-07-01 false Standard missing data procedures for... (CONTINUED) AIR PROGRAMS (CONTINUED) CONTINUOUS EMISSION MONITORING Missing Data Substitution Procedures § 75.33 Standard missing data procedures for SO2, NOX, and flow rate. (a) Following initial certification...

40 CFR 75.33 - Standard missing data procedures for SO2, NOX, and flow rate.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 17 2012-07-01 2012-07-01 false Standard missing data procedures for... (CONTINUED) AIR PROGRAMS (CONTINUED) CONTINUOUS EMISSION MONITORING Missing Data Substitution Procedures § 75.33 Standard missing data procedures for SO2, NOX, and flow rate. (a) Following initial certification...

40 CFR 75.33 - Standard missing data procedures for SO2, NOX, and flow rate.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 17 2013-07-01 2013-07-01 false Standard missing data procedures for... (CONTINUED) AIR PROGRAMS (CONTINUED) CONTINUOUS EMISSION MONITORING Missing Data Substitution Procedures § 75.33 Standard missing data procedures for SO2, NOX, and flow rate. (a) Following initial certification...

40 CFR 75.33 - Standard missing data procedures for SO2, NOX, and flow rate.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 17 2014-07-01 2014-07-01 false Standard missing data procedures for... (CONTINUED) AIR PROGRAMS (CONTINUED) CONTINUOUS EMISSION MONITORING Missing Data Substitution Procedures § 75.33 Standard missing data procedures for SO2, NOX, and flow rate. (a) Following initial certification...

The fluid mechanics of continuous flow electrophoresis in perspective

NASA Technical Reports Server (NTRS)

Saville, D. A.

1980-01-01

Buoyancy alters the flow in continuous flow electrophoresis chambers through the mechanism of hydrodynamic instability and, when the instability is supressed by careful cooling of the chamber boundaries, by restructuring the axial flow. The expanded roles of buoyancy follow upon adapting the size of the chamber and the electric field so as to fractionate certain sorts of cell populations. Scale-up problems, hydrodynamic stability and the altered flow fields are discussed to show how phenomena overlooked in the design and operations of narrow-gap devices take on an overwhelming importance in wide-gap chambers

Response of the Cardiovascular System to Vibration and Combined Stresses

DTIC Science & Technology

1975-08-31

Canines were chronically instrumented for continuous measurements of ascending aortic flow ( Zepeda ), left ventricular pressure (Konigsberg), circum- flex...different animals. Each dog was chronically instrumented for continuous measuremernt of ascending aortic flow ( Zepeda ), left ventricular pressure...vibration protocol as those animals restrained vertically. METHODS Canines (16 to 22 kg) were chronically instrumented with electromagnetic flow cuffs ( Zepeda

Flow-through polymerase chain reaction inside a seamless 3D helical microreactor fabricated utilizing a silicone tube and a paraffin mold.

PubMed

Wu, Wenming; Trinh, Kieu The Loan; Lee, Nae Yoon

2015-03-07

We introduce a new strategy for fabricating a seamless three-dimensional (3D) helical microreactor utilizing a silicone tube and a paraffin mold. With this method, various shapes and sizes of 3D helical microreactors were fabricated, and a complicated and laborious photolithographic process, or 3D printing, was eliminated. With dramatically enhanced portability at a significantly reduced fabrication cost, such a device can be considered to be the simplest microreactor, developed to date, for performing the flow-through polymerase chain reaction (PCR).

A novel method to measure regional muscle blood flow continuously using NIRS kinetics information

PubMed Central

Nioka, Shoko; Kime, Ryotaro; Sunar, Ulas; Im, Joohee; Izzetoglu, Meltem; Zhang, Jun; Alacam, Burak; Chance, Britton

2006-01-01

Background This article introduces a novel method to continuously monitor regional muscle blood flow by using Near Infrared Spectroscopy (NIRS). We demonstrate the feasibility of the new method in two ways: (1) by applying this new method of determining blood flow to experimental NIRS data during exercise and ischemia; and, (2) by simulating muscle oxygenation and blood flow values using these newly developed equations during recovery from exercise and ischemia. Methods Deoxy (Hb) and oxyhemoglobin (HbO2), located in the blood ofthe skeletal muscle, carry two internal relationships between blood flow and oxygen consumption. One is a mass transfer principle and the other describes a relationship between oxygen consumption and Hb kinetics in a two-compartment model. To monitor blood flow continuously, we transfer these two relationships into two equations and calculate the blood flow with the differential information of HbO2 and Hb. In addition, these equations are used to simulate the relationship between blood flow and reoxygenation kinetics after cuff ischemia and a light exercise. Nine healthy subjects volunteered for the cuff ischemia, light arm exercise and arm exercise with cuff ischemia for the experimental study. Results Analysis of experimental data of both cuff ischemia and light exercise using the new equations show greater blood flow (four to six times more than resting values) during recovery, agreeing with previous findings. Further, the simulation and experimental studies of cuff ischemia and light exercise agree with each other. Conclusion We demonstrate the accuracy of this new method by showing that the blood flow obtained from the method agrees with previous data as well as with simulated data. We conclude that this novel continuous blood flow monitoring method can provide blood flow information non-invasively with NIRS. PMID:16704736

Length polymorphism scanning is an efficient approach for revealing chloroplast DNA variation.

Treesearch

Matthew E. Horning; Richard C. Cronn

2006-01-01

Phylogeographic and population genetic screens of chloroplast DNA (cpDNA) provide insights into seedbased gene flow in angiosperms, yet studies are frequently hampered by the low mutation rate of this genome. Detection methods for intraspecific variation can be either direct (DNA sequencing) or indirect (PCR-RFLP), although no single method incorporates the best...

Ice flow in the Weddell Sea sector of West Antarctica as elucidated by radar-imaged internal layering

NASA Astrophysics Data System (ADS)

Bingham, R. G.; Rippin, D. M.; Karlsson, N. B.; Corr, H.; Ferraccioli, F.; Jordan, T. A.; Le Brocq, A.; Ross, N.; Wright, A.; Siegert, M. J.

2012-12-01

Radio-echo sounding (RES) across polar ice sheets reveals extensive, isochronous internal layers, whose stratigraphy, and especially their degree of continuity over multi-km distances, can inform us about both present ice flow and past ice-flow histories. Here, we bring together for the first time two recent advances in this field of cryospheric remote sensing to analyse ice flow into the Weddell Sea sector of West Antarctica. Firstly, we have developed a new quantitative routine for analysing the continuity of internal layers obtained over large areas of ice by airborne RES surveys - we term this routine the "Internal-Layering Continuity-Index (ILCI)". Secondly, in the austral season 2010-11 we acquired, by airborne RES survey, the first comprehensive dataset of deep internal layering across Institute and Möller Ice Streams, two of the more significant feeders of ice into the Filchner-Ronne Ice Shelf. Applying the ILCI to SAR-processed (migrated) RES profiles across Institute Ice Stream's catchment reveals two contrasting regions of internal-layering continuity behaviour. In the western portion of the catchment, where ice-stream tributaries incise deeply through the Ellsworth Subglacial Highlands, the continuity of internal layers is most disrupted across the present ice streams. We therefore interpret the ice-flow configuration in this western region as predominantly spatially stable over the lifetime of the ice. Further east, towards Möller Ice Stream, and towards the interior of the ice sheet, the ILCI does not closely match the present ice flow configuration, while across most of present-day Möller Ice Stream itself, the continuity of internal layers is generally low. We propose that the variation in continuity of internal layering across eastern Institute Ice Stream and the neighbouring Möller results primarily from two factors. Firstly, the noncorrespondence of some inland tributaries with internal-layering continuity acts as evidence for past spatial migration of those tributaries, with likely consequences for the relative positions of Institute and Möller Ice Streams over recent history. Secondly, the subglacial roughness, in part a function of the underlying geology across the region, imposes a strong influence on the continuity of the overlying deep internal layers, though whether it controls, or is a function of, ice flow, remains undetermined. We conclude that in the subglacially mountainous Ellsworth Subglacial Highlands sector, there is long-term stability in the spatial configuration of ice flow, but that elsewhere across Insitute and Möller Ice Streams, the ice-flow configuration has the potential to switch.

Renewable Wood Pulp Paper Reactor with Hierarchical Micro/Nanopores for Continuous-Flow Nanocatalysis.

PubMed

Koga, Hirotaka; Namba, Naoko; Takahashi, Tsukasa; Nogi, Masaya; Nishina, Yuta

2017-06-22

Continuous-flow nanocatalysis based on metal nanoparticle catalyst-anchored flow reactors has recently provided an excellent platform for effective chemical manufacturing. However, there has been limited progress in porous structure design and recycling systems for metal nanoparticle-anchored flow reactors to create more efficient and sustainable catalytic processes. In this study, traditional paper is used for a highly efficient, recyclable, and even renewable flow reactor by tailoring the ultrastructures of wood pulp. The "paper reactor" offers hierarchically interconnected micro- and nanoscale pores, which can act as convective-flow and rapid-diffusion channels, respectively, for efficient access of reactants to metal nanoparticle catalysts. In continuous-flow, aqueous, room-temperature catalytic reduction of 4-nitrophenol to 4-aminophenol, a gold nanoparticle (AuNP)-anchored paper reactor with hierarchical micro/nanopores provided higher reaction efficiency than state-of-the-art AuNP-anchored flow reactors. Inspired by traditional paper materials, successful recycling and renewal of AuNP-anchored paper reactors were also demonstrated while high reaction efficiency was maintained. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Redesigning flow injection after 40 years of development: Flow programming.

PubMed

Ruzicka, Jaromir Jarda

2018-01-01

Automation of reagent based assays, by means of Flow Injection (FI), is based on sample processing, in which a sample flows continuously towards and through a detector for quantification of the target analyte. The Achilles heel of this methodology, the legacy of Auto Analyzer®, is continuous reagent consumption, and continuous generation of chemical waste. However, flow programming, assisted by recent advances in precise pumping, combined with the lab-on-valve technique, allows the FI manifold to be designed around a single confluence point through which sample and reagents are sequentially directed by means of a series of flow reversals. This approach results in sample/reagent mixing analogous to the traditional FI, reduces sample and reagent consumption, and uses the stop flow technique for enhancement of the yield of chemical reactions. The feasibility of programmable Flow Injection (pFI) is documented by example of commonly used spectrophotometric assays of, phosphate, nitrate, nitrite and glucose. Experimental details and additional information are available in online tutorial http://www.flowinjectiontutorial.com/. Copyright © 2017 Elsevier B.V. All rights reserved.

The effect of small temperature gradients on flow in a continuous flow electrophoresis chamber

NASA Technical Reports Server (NTRS)

Rhodes, P. H.; Snyder, R. S.

1982-01-01

Continuous flow electrophoresis employs an electric field to separate biological cells suspended in a flowing liquid buffer solution. Good separations based on differences in electrophoretic mobility are obtained only when a unidirectional flow is maintained. The desired flow has a parabolic structure in the narrow dimension of the chamber and is uniform acros the width, except near the edges where the no-slip condition prevails. However, because of buoyancy, very small laterall or axial temperature gradients deform the flow significantly. The results of experiments conducted with a specially instrumented chamber show the origin and structure of the buoyancy-driven perturbations. It is found that very small temperature gradients can disturb the flow significantly, as was predicted by earlier theoretical work.

Shape complexes: the intersection of label orderings and star convexity constraints in continuous max-flow medical image segmentation

PubMed Central

Baxter, John S. H.; Inoue, Jiro; Drangova, Maria; Peters, Terry M.

2016-01-01

Abstract. Optimization-based segmentation approaches deriving from discrete graph-cuts and continuous max-flow have become increasingly nuanced, allowing for topological and geometric constraints on the resulting segmentation while retaining global optimality. However, these two considerations, topological and geometric, have yet to be combined in a unified manner. The concept of “shape complexes,” which combine geodesic star convexity with extendable continuous max-flow solvers, is presented. These shape complexes allow more complicated shapes to be created through the use of multiple labels and super-labels, with geodesic star convexity governed by a topological ordering. These problems can be optimized using extendable continuous max-flow solvers. Previous approaches required computationally expensive coordinate system warping, which are ill-defined and ambiguous in the general case. These shape complexes are demonstrated in a set of synthetic images as well as vessel segmentation in ultrasound, valve segmentation in ultrasound, and atrial wall segmentation from contrast-enhanced CT. Shape complexes represent an extendable tool alongside other continuous max-flow methods that may be suitable for a wide range of medical image segmentation problems. PMID:28018937

One-step synthesis of pyridines and dihydropyridines in a continuous flow microwave reactor

PubMed Central

Fusillo, Vincenzo; Jenkins, Robert L; Lubinu, M Caterina; Mason, Christopher

2013-01-01

Summary The Bohlmann–Rahtz pyridine synthesis and the Hantzsch dihydropyridine synthesis can be carried out in a microwave flow reactor or using a conductive heating flow platform for the continuous processing of material. In the Bohlmann–Rahtz reaction, the use of a Brønsted acid catalyst allows Michael addition and cyclodehydration to be carried out in a single step without isolation of intermediates to give the corresponding trisubstituted pyridine as a single regioisomer in good yield. Furthermore, 3-substituted propargyl aldehydes undergo Hantzsch dihydropyridine synthesis in preference to Bohlmann–Rahtz reaction in a very high yielding process that is readily transferred to continuous flow processing. PMID:24204407

Initial in vitro testing of a paediatric continuous-flow total artificial heart.

PubMed

Fukamachi, Kiyotaka; Karimov, Jamshid H; Horvath, David J; Sunagawa, Gengo; Byram, Nicole A; Kuban, Barry D; Moazami, Nader

2018-06-01

Mechanical circulatory support has become standard therapy for adult patients with end-stage heart failure; however, in paediatric patients with congenital heart disease, the options for chronic mechanical circulatory support are limited to paracorporeal devices or off-label use of devices intended for implantation in adults. Congenital heart disease and cardiomyopathy often involve both the left and right ventricles; in such cases, heart transplantation, a biventricular assist device or a total artificial heart is needed to adequately sustain both pulmonary and systemic circulations. We aimed to evaluate the in vitro performance of the initial prototype of our paediatric continuous-flow total artificial heart. The paediatric continuous-flow total artificial heart pump was downsized from the adult continuous-flow total artificial heart configuration by a scale factor of 0.70 (1/3 of total volume) to enable implantation in infants. System performance of this prototype was evaluated using the continuous-flow total artificial heart mock loop set to mimic paediatric circulation. We generated maps of pump performance and atrial pressure differences over a wide range of systemic vascular resistance/pulmonary vascular resistance and pump speeds. Performance data indicated left pump flow range of 0.4-4.7 l/min at 100 mmHg delta pressure. The left/right atrial pressure difference was maintained within ±5 mmHg with systemic vascular resistance/pulmonary vascular resistance ratios between 1.4 and 35, with/without pump speed modulation, verifying expected passive self-regulation of atrial pressure balance. The paediatric continuous-flow total artificial heart prototype met design requirements for self-regulation and performance; in vivo pump performance studies are ongoing.

Effect of Flow Rate Controller on Liquid Steel Flow in Continuous Casting Mold using Numerical Modeling

NASA Astrophysics Data System (ADS)

Gursoy, Kadir Ali; Yavuz, Mehmet Metin

2014-11-01

In continuous casting operation of steel, the flow through tundish to the mold can be controlled by different flow rate control systems including stopper rod and slide-gate. Ladle changes in continuous casting machines result in liquid steel level changes in tundishes. During this transient event of production, the flow rate controller opening is increased to reduce the pressure drop across the opening which helps to keep the mass flow rate at the desired level for the reduced liquid steel level in tundish. In the present study, computational fluid dynamic (CFD) models are developed to investigate the effect of flow rate controller on mold flow structure, and particularly to understand the effect of flow controller opening on meniscus flow. First, a detailed validation of the CFD models is conducted using available experimental data and the performances of different turbulence models are compared. Then, the constant throughput casting operations for different flow rate controller openings are simulated to quantify the opening effect on meniscus region. The results indicate that the meniscus velocities are significantly affected by the flow rate controller and its opening level. The steady state operations, specified as constant throughput casting, do not provide the same mold flow if the controller opening is altered. Thus, for quality and castability purposes, adjusting the flow controller opening to obtain the fixed mold flow structure is proposed. Supported by Middle East Technical University (METU) BAP (Scientific Research Projects) Coordination.

Comparison of non-invasive MRI measurements of cerebral blood flow in a large multisite cohort.

PubMed

Dolui, Sudipto; Wang, Ze; Wang, Danny Jj; Mattay, Raghav; Finkel, Mack; Elliott, Mark; Desiderio, Lisa; Inglis, Ben; Mueller, Bryon; Stafford, Randall B; Launer, Lenore J; Jacobs, David R; Bryan, R Nick; Detre, John A

2016-07-01

Arterial spin labeling and phase contrast magnetic resonance imaging provide independent non-invasive methods for measuring cerebral blood flow. We compared global cerebral blood flow measurements obtained using pseudo-continuous arterial spin labeling and phase contrast in 436 middle-aged subjects acquired at two sites in the NHLBI CARDIA multisite study. Cerebral blood flow measured by phase contrast (CBFPC: 55.76 ± 12.05 ml/100 g/min) was systematically higher (p < 0.001) and more variable than cerebral blood flow measured by pseudo-continuous arterial spin labeling (CBFPCASL: 47.70 ± 9.75). The correlation between global cerebral blood flow values obtained from the two modalities was 0.59 (p < 0.001), explaining less than half of the observed variance in cerebral blood flow estimates. Well-established correlations of global cerebral blood flow with age and sex were similarly observed in both CBFPCASL and CBFPC CBFPC also demonstrated statistically significant site differences, whereas no such differences were observed in CBFPCASL No consistent velocity-dependent effects on pseudo-continuous arterial spin labeling were observed, suggesting that pseudo-continuous labeling efficiency does not vary substantially across typical adult carotid and vertebral velocities, as has previously been suggested. Although CBFPCASL and CBFPC values show substantial similarity across the entire cohort, these data do not support calibration of CBFPCASL using CBFPC in individual subjects. The wide-ranging cerebral blood flow values obtained by both methods suggest that cerebral blood flow values are highly variable in the general population. © The Author(s) 2016.

Impact of monotherapy on HIV-1 reservoir, immune activation, and co-infection with Epstein-Barr virus

PubMed Central

Petrara, Maria Raffaella; Cattelan, Anna Maria; Sasset, Lolita; Freguja, Riccardo; Carmona, Francesco; Sanavia, Silvia; Zanchetta, Marisa; Del Bianco, Paola

2017-01-01

Objectives Although monotherapy (mART) effectiveness in maintaining viral suppression and CD4 cell count has been extensively examined in HIV-1-infected patients, its impact on HIV-1 reservoir, immune activation, microbial translocation and co-infection with Epstein-Barr Virus (EBV) is unclear. Methods This retrospective study involved 32 patients who switched to mART; patients were studied at baseline, 48 and 96 weeks after mART initiation. Thirty-two patients who continued combined antiretroviral therapy (cART) over the same period of time were included in the study. Markers of HIV-1 reservoir (HIV-1 DNA and intracellular HIV-1 RNA) were quantified by real-time PCR. Markers of T-(CD3+CD8+CD38+) and B-(CD19+CD80/86+ and CD19+CD10-CD21lowCD27+) cell activation were evaluated by flow cytometry. Plasma levels of microbial translocation markers were quantified by real-time PCR (16S ribosomal DNA and mitochondrial [mt]DNA) or by ELISA (LPS and sCD14). EBV was typed and quantified by multiplex real-time PCR. Results At baseline, no differences were found between mART and cART groups. Three (10%) mART-treated patients had a virological failure vs none in the cART group. Levels of HIV-1 DNA, intracellular HIV-1 RNA and EBV-DNA remained stable in the mART group, while decreased significantly in the cART group. Percentages of T- and B-activated cells significantly increased in the mART-treated patients, while remained at low levels in the cART-treated ones (p = 0.014 and p<0.001, respectively). Notably, levels of mtDNA remained stable in the cART group, but significantly rose in the mART one (p<0.001). Conclusions Long-term mART is associated with higher levels of T- and B-cell activation and, conversely to cART, does not reduce the size of HIV-1 reservoir and EBV co-infection. PMID:28926641

High-energy phosphate metabolism during incremental calf exercise in humans measured by 31 phosphorus magnetic resonance spectroscopy (31P MRS).

PubMed

Schocke, Michael F H; Esterhammer, Regina; Kammerlander, Christian; Rass, Anton; Kremser, Christian; Fraedrich, Gustav; Jaschke, Werner R; Greiner, Andreas

2004-01-01

Several previous 31 phosphorus magnetic resonance spectroscopy ((31)P MRS) studies performing incremental or progressive muscle exercises have observed that a decrease in pH is accompanied with an acceleration in phosphocreatine (PCr) hydrolysis. The purpose of this study was to investigate the relationship between PCr breakdown and pH during isotonic, exhaustive, incremental plantar flexion exercises. We included eight healthy, male volunteers into this study. Using a 1.5 Tesla MR scanner and a self-built exercise bench, we performed serial free induction decay (FID) (31)P MRS measurements with a time resolution of 1 min at rest, isotonic calf muscle exercise, and recovery. The exercise protocol consisted of 5-min intervals with 4.5, 6, 7.5, and 9 W workload followed by 9-min recovery. Changes in PCr and inorganic phosphate (Pi) were determined as percent changes in comparison to the baseline. In addition, pH values were calculated. This study obtained significant decreases in PCr corresponding to the gradual increases in workload. In each workload level that was succeeded by all volunteers, PCr hydrolysis passed into a steady state. After an early biphasic response, we detected a significant decrease in pH from the first to the second minute of the 6-W workload level followed by a further continuous decrease in pH up to the second minute of the recovery phase. The decrease in pH was not accompanied by acceleration in PCr hydrolysis. In conclusion, this study shows that PCr hydrolysis during incremental plantar flexion exercises passes into a steady state at different workload levels. The observed decrease in pH does not result in acceleration of PCr hydrolysis.

Development of a One-Step Multiplex PCR Assay for Differential Detection of Major Mycobacterium Species

PubMed Central

Chae, Hansong; Han, Seung Jung; Kim, Su-Young; Ki, Chang-Seok; Huh, Hee Jae; Yong, Dongeun

2017-01-01

ABSTRACT The prevalence of tuberculosis continues to be high, and nontuberculous mycobacterial (NTM) infection has also emerged worldwide. Moreover, differential and accurate identification of mycobacteria to the species or subspecies level is an unmet clinical need. Here, we developed a one-step multiplex PCR assay using whole-genome analysis and bioinformatics to identify novel molecular targets. The aims of this assay were to (i) discriminate between the Mycobacterium tuberculosis complex (MTBC) and NTM using rv0577 or RD750, (ii) differentiate M. tuberculosis (M. tuberculosis) from MTBC using RD9, (iii) selectively identify the widespread M. tuberculosis Beijing genotype by targeting mtbk_20680, and (iv) simultaneously detect five clinically important NTM (M. avium, M. intracellulare, M. abscessus, M. massiliense, and M. kansasii) by targeting IS1311, DT1, mass_3210, and mkan_rs12360. An initial evaluation of the multiplex PCR assay using reference strains demonstrated 100% specificity for the targeted Mycobacterium species. Analytical sensitivity ranged from 1 to 10 pg for extracted DNA and was 103 and 104 CFU for pure cultures and nonhomogenized artificial sputum cultures, respectively, of the targeted species. The accuracy of the multiplex PCR assay was further evaluated using 55 reference strains and 94 mycobacterial clinical isolates. Spoligotyping, multilocus sequence analysis, and a commercial real-time PCR assay were employed as standard assays to evaluate the multiplex PCR assay with clinical M. tuberculosis and NTM isolates. The PCR assay displayed 100% identification agreement with the standard assays. Our multiplex PCR assay is a simple, convenient, and reliable technique for differential identification of MTBC, M. tuberculosis, M. tuberculosis Beijing genotype, and major NTM species. PMID:28659320

Development of a One-Step Multiplex PCR Assay for Differential Detection of Major Mycobacterium Species.

PubMed

Chae, Hansong; Han, Seung Jung; Kim, Su-Young; Ki, Chang-Seok; Huh, Hee Jae; Yong, Dongeun; Koh, Won-Jung; Shin, Sung Jae

2017-09-01

The prevalence of tuberculosis continues to be high, and nontuberculous mycobacterial (NTM) infection has also emerged worldwide. Moreover, differential and accurate identification of mycobacteria to the species or subspecies level is an unmet clinical need. Here, we developed a one-step multiplex PCR assay using whole-genome analysis and bioinformatics to identify novel molecular targets. The aims of this assay were to (i) discriminate between the Mycobacterium tuberculosis complex (MTBC) and NTM using rv0577 or RD750, (ii) differentiate M. tuberculosis ( M. tuberculosis ) from MTBC using RD9, (iii) selectively identify the widespread M. tuberculosis Beijing genotype by targeting mtbk_20680 , and (iv) simultaneously detect five clinically important NTM ( M. avium , M. intracellulare , M. abscessus , M. massiliense , and M. kansasii ) by targeting IS 1311 , DT1, mass_3210 , and mkan_rs12360 An initial evaluation of the multiplex PCR assay using reference strains demonstrated 100% specificity for the targeted Mycobacterium species. Analytical sensitivity ranged from 1 to 10 pg for extracted DNA and was 10 3 and 10 4 CFU for pure cultures and nonhomogenized artificial sputum cultures, respectively, of the targeted species. The accuracy of the multiplex PCR assay was further evaluated using 55 reference strains and 94 mycobacterial clinical isolates. Spoligotyping, multilocus sequence analysis, and a commercial real-time PCR assay were employed as standard assays to evaluate the multiplex PCR assay with clinical M. tuberculosis and NTM isolates. The PCR assay displayed 100% identification agreement with the standard assays. Our multiplex PCR assay is a simple, convenient, and reliable technique for differential identification of MTBC, M. tuberculosis , M. tuberculosis Beijing genotype, and major NTM species. Copyright © 2017 American Society for Microbiology.

High sensitivity detection and sorting of infectious human immunodeficiency virus (HIV-1) particles by flow virometry

PubMed Central

Bonar, Micha M.; Tilton, John C.

2017-01-01

Detection of viruses by flow cytometry is complicated by their small size. Here, we characterized the ability of a standard (FACSAria II) and a sub-micron flow cytometer (A50 Micro) to resolve HIV-1 viruses. The A50 was superior at resolving small particles but did not reliably distinguish HIV-1, extracellular vesicles, and laser noise by light scatter properties alone. However, single fluorescent HIV-1 particles could readily be detected by both cytometers. Fluorescent particles were sorted and retained infectivity, permitting further exploration of the functional consequences of HIV-1 heterogeneity. Finally, flow cytometry had a limit of detection of 80 viruses/ml, nearly equal to PCR assays. These studies demonstrate the power of flow cytometry to detect and sort viral particles and provide a critical toolkit to validate methods to label wild-type HIV-1; quantitatively assess integrity and aggregation of viruses and virus-based therapeutics; and efficiently screen drugs inhibiting viral assembly and release. PMID:28235684

High sensitivity detection and sorting of infectious human immunodeficiency virus (HIV-1) particles by flow virometry.

PubMed

Bonar, Michał M; Tilton, John C

2017-05-01

Detection of viruses by flow cytometry is complicated by their small size. Here, we characterized the ability of a standard (FACSAria II) and a sub-micron flow cytometer (A50 Micro) to resolve HIV-1 viruses. The A50 was superior at resolving small particles but did not reliably distinguish HIV-1, extracellular vesicles, and laser noise by light scatter properties alone. However, single fluorescent HIV-1 particles could readily be detected by both cytometers. Fluorescent particles were sorted and retained infectivity, permitting further exploration of the functional consequences of HIV-1 heterogeneity. Finally, flow cytometry had a limit of detection of 80 viruses/ml, nearly equal to PCR assays. These studies demonstrate the power of flow cytometry to detect and sort viral particles and provide a critical toolkit to validate methods to label wild-type HIV-1; quantitatively assess integrity and aggregation of viruses and virus-based therapeutics; and efficiently screen drugs inhibiting viral assembly and release. Copyright © 2017 Elsevier Inc. All rights reserved.

Annular-Cross-Section CFE Chamber

NASA Technical Reports Server (NTRS)

Sharnez, Rizwan; Sammons, David W.

1994-01-01

Proposed continuous-flow-electrophoresis (CFE) chamber of annular cross section offers advantages over conventional CFE chamber, and wedge-cross-section chamber described in "Increasing Sensitivity in Continuous-Flow Electrophoresis" (MFS-26176). In comparison with wedge-shaped chamber, chamber of annular cross section virtually eliminates such wall effects as electro-osmosis and transverse gradients of velocity. Sensitivity enhanced by incorporating gradient maker and radial (collateral) flow.

40 CFR 75.16 - Special provisions for monitoring emissions from common, bypass, and multiple stacks for SO2...

Code of Federal Regulations, 2010 CFR

2010-07-01

... maintain an SO2 continuous emission monitoring system and flow monitoring system in the duct to the common... emission monitoring system and flow monitoring system in the common stack and combine emissions for the... continuous emission monitoring system and flow monitoring system in the duct to the common stack from each...

Effects of dialysate flow configurations in continuous renal replacement therapy on solute removal: computational modeling.

PubMed

Kim, Jeong Chul; Cruz, Dinna; Garzotto, Francesco; Kaushik, Manish; Teixeria, Catarina; Baldwin, Marie; Baldwin, Ian; Nalesso, Federico; Kim, Ji Hyun; Kang, Eungtaek; Kim, Hee Chan; Ronco, Claudio

2013-01-01

Continuous renal replacement therapy (CRRT) is commonly used for critically ill patients with acute kidney injury. During treatment, a slow dialysate flow rate can be applied to enhance diffusive solute removal. However, due to the lack of the rationale of the dialysate flow configuration (countercurrent or concurrent to blood flow), in clinical practice, the connection settings of a hemodiafilter are done depending on nurse preference or at random. In this study, we investigated the effects of flow configurations in a hemodiafilter during continuous venovenous hemodialysis on solute removal and fluid transport using computational fluid dynamic modeling. We solved the momentum equation coupling solute transport to predict quantitative diffusion and convection phenomena in a simplified hemodiafilter model. Computational modeling results showed superior solute removal (clearance of urea: 67.8 vs. 45.1 ml/min) and convection (filtration volume: 29.0 vs. 25.7 ml/min) performances for the countercurrent flow configuration. Countercurrent flow configuration enhances convection and diffusion compared to concurrent flow configuration by increasing filtration volume and equilibrium concentration in the proximal part of a hemodiafilter and backfiltration of pure dialysate in the distal part. In clinical practice, the countercurrent dialysate flow configuration of a hemodiafilter could increase solute removal in CRRT. Nevertheless, while this configuration may become mandatory for high-efficiency treatments, the impact of differences in solute removal observed in slow continuous therapies may be less important. Under these circumstances, if continuous therapies are prescribed, some of the advantages of the concurrent configuration in terms of simpler circuit layout and simpler machine design may overcome the advantages in terms of solute clearance. Different dialysate flow configurations influence solute clearance and change major solute removal mechanisms in the proximal and distal parts of a hemodiafilter. Advantages of each configuration should be balanced against the overall performance of the treatment and its simplicity in terms of treatment delivery and circuit handling procedures. Copyright © 2013 S. Karger AG, Basel.

Continuous-flow electrophoresis: Membrane-associated deviations of buffer pH and conductivity

NASA Technical Reports Server (NTRS)

Smolka, A. J. K.; Mcguire, J. K.

1978-01-01

The deviations in buffer pH and conductivity which occur near the electrode membranes in continuous-flow electrophoresis were studied in the Beckman charged particle electrophoresis system and the Hanning FF-5 preparative electrophoresis instrument. The nature of the membranes separating the electrode compartments from the electrophoresis chamber, the electric field strength, and the flow rate of electrophoresis buffer were all found to influence the formation of the pH and conductivity gradients. Variations in electrode buffer flow rate and the time of electrophoresis were less important. The results obtained supported the hypothesis that a combination of Donnan membrane effects and the differing ionic mobilities in the electrophoresis buffer was responsible for the formation of the gradients. The significance of the results for the design and stable operation of continuous-flow electrophoresis apparatus was discussed.

[Responses of sap flow to natural rainfall and continuous drought of tree species growing on bedrock outcrops].

PubMed

Zhang, Hui Ling; Ding, Ya Li; Chen, Hong Song; Wang, Ke Lin; Nie, Yun Peng

2018-04-01

This study focused on bedrock outcrops, a very common habitat in karst region of southwest China. To reveal the responses of plant transpiration to natural rainfall and continuous drought, two tree species typical to this habitat, Radermachera sinica and Triadica rotundifolia, were selected as test materials. A rainout shelter was used to simulate continuous drought. The sap flow dynamics were monitored using the method of Granier's thermal dissipation probe (TDP). Our results showed that sap flow density increased to different degrees after rain in different stages of the growing season. Sap flow density of the deciduous species T. rotundifolia was always higher than that of the semi-deciduous species R. sinica. After two months without rainfall input, both species exhibited no obvious decrease in sap flow density, indicating that rainfall was not the dominant source for their water uptake, at least in the short-term. Based on the regression relationships between sap flow density and meteorological factors before and after rainfall, as well as at different stages of continuous drought, we found that the dynamics of meteorological factors contributed little to plant transpiration. The basic transpiration characteristics of both species were not changed in the circumstance of natural rainfall and short-term continuous drought, which would be closely related to the special water storage environments of bedrock outcrops and the reliance on deep water sources by tree species.

Continuous flow measurements using fixed ultrasonic meters

USGS Publications Warehouse

Oltmann, Rick

1993-01-01

USGS has or soon will be installing four continuous flow-monitoring stations in the delta that will use ultrasonic velocity meters (DVM). Funding for the stations has been provided by USGS, DWR, USBR, and Contra Costa Water District.

The cryogenic wind tunnel for high Reynolds number testing. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Kilgore, R. A.

1974-01-01

Experiments performed at the NASA Langley Research Center in a cryogenic low-speed continuous-flow tunnel and in a cryogenic transonic continuous-flow pressure tunnel have demonstrated the predicted changes in Reynolds number, drive power, and fan speed with temperature, while operating with nitrogen as the test gas. The experiments have also demonstrated that cooling to cryogenic temperatures by spraying liquid nitrogen directly into the tunnel circuit is practical and that tunnel temperature can be controlled within very close limits. Whereas most types of wind tunnel could operate with advantage at cryogenic temperatures, the continuous-flow fan-driven tunnel is particularly well suited to take full advantage of operating at these temperatures. A continuous-flow fan-driven cryogenic tunnel to satisfy current requirements for test Reynolds number can be constructed and operated using existing techniques. Both capital and operating costs appear acceptable.

Monitoring patients with continuous-flow ventricular assist devices outside of the intensive care unit: novel challenges to bedside nursing.

PubMed

O'Shea, Genevieve; Teuteberg, Jeffrey J; Severyn, Donald A

2013-03-01

Ventricular assist devices provide therapeutic options for patients with severe heart failure who have exhausted available medical therapies. With restoration of organ perfusion with ventricular assist devices, the heart failure resolves and quality of life and functional status improve. The current generation of continuous-flow devices present novel challenges to the clinical assessment of patients by substantially reducing or nearly eliminating any palpable pulse. Patients therefore generally have inadequate arterial pulsatility for most noninvasive monitoring devices such as pulse oximeters or automated blood pressure cuffs to work accurately. This article describes the function of continuous-flow devices and how this function affects common monitoring options, as well as how to clinically assess recipients of continuous-flow devices to promptly identify those whose condition may be deteriorating or who may be receiving inadequate perfusion.

Electrowetting (EW)-based valve combined with hydrophilic teflon microfluidic guidance in controlling continuous fluid flow.

PubMed

Cheng, Ji-Yen; Hsiung, Lo-Chang

2004-12-01

Electrowetting (EW)-based techniques have been widely used in manipulating discrete liquid. However, few articles discussed the controlling of continuous fluid flow by using EW-based techniques. In this paper, an EW-based valve combined with plasma-modified Teflon surface, which serves as a microfluidic guidance, in controlling continuous fluid flow has been demonstrated. The plasma-modified Teflon surface is firstly demonstrated for confining continuous fluid flow. The EW-based microfluidic device possesses the functions of a valve and a microchannel without complex moving parts and grooved microchannels. The quantitative characteristics of the EW-based valve are also studied. Propylene carbonate (PC) is firstly demonstrated as the working liquid in the EW-based device because of its applications in parallel oligonucleotide synthesis. It is found that lower valve actuation voltage reduces the deterioration of the valve and improves the valve stability.

Continuous flow chemistry: a discovery tool for new chemical reactivity patterns.

PubMed

Hartwig, Jan; Metternich, Jan B; Nikbin, Nikzad; Kirschning, Andreas; Ley, Steven V

2014-06-14

Continuous flow chemistry as a process intensification tool is well known. However, its ability to enable chemists to perform reactions which are not possible in batch is less well studied or understood. Here we present an example, where a new reactivity pattern and extended reaction scope has been achieved by transferring a reaction from batch mode to flow. This new reactivity can be explained by suppressing back mixing and precise control of temperature in a flow reactor set up.

Characterization of bacterial community associated to biofilms of corroded oil pipelines from the southeast of Mexico.

PubMed

Neria-González, Isabel; Wang, En Tao; Ramírez, Florina; Romero, Juan M; Hernández-Rodríguez, César

2006-06-01

Microbial communities associated to biofilms promote corrosion of oil pipelines. The community structure of bacteria in the biofilm formed in oil pipelines is the basic knowledge to understand the complexity and mechanisms of metal corrosion. To assess bacterial diversity, biofilm samples were obtained from X52 steel coupons corroded after 40 days of exposure to normal operation and flow conditions. The biofilm samples were directly used to extract metagenomic DNA, which was used as template to amplify 16S ribosomal gene by PCR. The PCR products of 16S ribosomal gene were also employed as template for sulfate-reducing bacteria (SRB) specific nested-PCR and both PCR products were utilized for the construction of gene libraries. The V3 region of the 16S rRNA gene was also amplified to analyse the bacterial diversity by analysis of denaturing gradient gel electrophoresis (DGGE). Ribosomal library and DGGE profiles exhibited limited bacterial diversity, basically including Citrobacter spp., Enterobacter spp. and Halanaerobium spp. while Desulfovibrio alaskensis and a novel clade within the genus Desulfonatronovibrio were detected from the nested PCR library. The biofilm samples were also taken for the isolation of SRB. Desulfovibrio alaskensis and Desulfovibrio capillatus, as well as some strains related to Citrobacter were isolated. SRB consists in a very small proportion of the community and Desulfovibrio spp. were the relatively abundant groups among the SRB. This is the first study directly exploring bacterial diversity in corrosive biofilms associated to steel pipelines subjected to normal operation conditions.

A quantitative PCR method for assessing the presence of Pasteurella testudinis DNA in nasal lavage samples from the desert tortoise (Gopherus agassizii).

PubMed

duPre', S A; Tracy, C R; Sandmeier, F C; Hunter, K W

2012-12-01

Pasteurella testudinis has been associated with upper respiratory tract disease (URTD) in the threatened desert tortoise (Gopherus agassizii). Our goal was to develop a sensitive and specific qPCR method for detecting DNA from P. testudinis in nasal lavage fluid collected from desert tortoises in the field. Probes for 16S ribosomal RNA and RNA polymerase β-subunit (rpoB) genes were designed. A standard curve generated with DNA extracted from known numbers of bacterial cells determined by flow cytometry revealed a lower detection limit of 50 fg/ml (10 bacteria/ml). The nasal lavage fluid contained no interfering substances, and the qPCR method did not recognize normal flora DNA. The nasal lavage samples from 20 desert tortoises captured in Clark County, Nevada, USA in 2007 and housed at the Desert Tortoise Conservation Center, were all positive for P. testudinis DNA by qPCR. Another set of 19 lavage samples collected in 2010 from wild desert tortoises in the Mojave Desert were tested and 84% were positive for P. testudinis DNA. Fully validated, this qPCR method will provide a means of determining colonization rate. When used in conjunction with serological methods and clinical evaluations, both infection rate and disease rate can be determined for this potential URTD pathogen. This new assay provides an important tool for managing the threatened populations of the Mojave Desert tortoise. Copyright © 2012 Elsevier B.V. All rights reserved.

Comparative quantification of human intestinal bacteria based on cPCR and LDR/LCR

PubMed Central

Tang, Zhou-Rui; Li, Kai; Zhou, Yu-Xun; Xiao, Zhen-Xian; Xiao, Jun-Hua; Huang, Rui; Gu, Guo-Hao

2012-01-01

AIM: To establish a multiple detection method based on comparative polymerase chain reaction (cPCR) and ligase detection reaction (LDR)/ligase chain reaction (LCR) to quantify the intestinal bacterial components. METHODS: Comparative quantification of 16S rDNAs from different intestinal bacterial components was used to quantify multiple intestinal bacteria. The 16S rDNAs of different bacteria were amplified simultaneously by cPCR. The LDR/LCR was examined to actualize the genotyping and quantification. Two beneficial (Bifidobacterium, Lactobacillus) and three conditionally pathogenic bacteria (Enterococcus, Enterobacterium and Eubacterium) were used in this detection. With cloned standard bacterial 16S rDNAs, standard curves were prepared to validate the quantitative relations between the ratio of original concentrations of two templates and the ratio of the fluorescence signals of their final ligation products. The internal controls were added to monitor the whole detection flow. The quantity ratio between two bacteria was tested. RESULTS: cPCR and LDR revealed obvious linear correlations with standard DNAs, but cPCR and LCR did not. In the sample test, the distributions of the quantity ratio between each two bacterial species were obtained. There were significant differences among these distributions in the total samples. But these distributions of quantity ratio of each two bacteria remained stable among groups divided by age or sex. CONCLUSION: The detection method in this study can be used to conduct multiple intestinal bacteria genotyping and quantification, and to monitor the human intestinal health status as well. PMID:22294830

Comparative quantification of human intestinal bacteria based on cPCR and LDR/LCR.

PubMed

Tang, Zhou-Rui; Li, Kai; Zhou, Yu-Xun; Xiao, Zhen-Xian; Xiao, Jun-Hua; Huang, Rui; Gu, Guo-Hao

2012-01-21

To establish a multiple detection method based on comparative polymerase chain reaction (cPCR) and ligase detection reaction (LDR)/ligase chain reaction (LCR) to quantify the intestinal bacterial components. Comparative quantification of 16S rDNAs from different intestinal bacterial components was used to quantify multiple intestinal bacteria. The 16S rDNAs of different bacteria were amplified simultaneously by cPCR. The LDR/LCR was examined to actualize the genotyping and quantification. Two beneficial (Bifidobacterium, Lactobacillus) and three conditionally pathogenic bacteria (Enterococcus, Enterobacterium and Eubacterium) were used in this detection. With cloned standard bacterial 16S rDNAs, standard curves were prepared to validate the quantitative relations between the ratio of original concentrations of two templates and the ratio of the fluorescence signals of their final ligation products. The internal controls were added to monitor the whole detection flow. The quantity ratio between two bacteria was tested. cPCR and LDR revealed obvious linear correlations with standard DNAs, but cPCR and LCR did not. In the sample test, the distributions of the quantity ratio between each two bacterial species were obtained. There were significant differences among these distributions in the total samples. But these distributions of quantity ratio of each two bacteria remained stable among groups divided by age or sex. The detection method in this study can be used to conduct multiple intestinal bacteria genotyping and quantification, and to monitor the human intestinal health status as well.

Impact of cyclic mechanical stimulation on the expression of extracellular matrix proteins in human primary rotator cuff fibroblasts.

PubMed

Lohberger, Birgit; Kaltenegger, Heike; Stuendl, Nicole; Rinner, Beate; Leithner, Andreas; Sadoghi, Patrick

2016-12-01

Mechanical stimulation plays an important role in the development and remodelling of tendons. The aim of the study was to evaluate the effects of mechanical stimulation on the expression of extracellular matrix proteins in human primary rotator cuff (RC) fibroblasts. RC fibroblasts were isolated from patients with degenerative RC tears and characterized using flow cytometry and immunohistochemistry. Cells were stimulated using the Flexcell FX5K™ Tension System. The stimulation regime was a uniaxial sinusoidal waveform with 10 % elongation and a frequency of 0.5 Hz, whereby each cycle consists of 10-s strain and 30-s relaxation. Data were normalized to mechanically unstimulated control groups for every experimental condition. RT-qPCR was performed to determine relative mRNA levels, and collagen production was measured by a colorimetric assay. The positive expression of CD91 and CD10, and negativity for CD45 and CD4 confirmed the fibroblast phenotype of RC primary cells. RT-qPCR revealed that 10 % continuous cyclic strain for 7 and 14 days induced a significant increase in the mRNA expression both on the matrix metalloproteinases MMP1, MMP3, MMP13, and MMP14 and on the extracellular matrix proteins decorin, tenascin-C, and scleraxis. Furthermore, mechanically stimulated groups produced significantly higher amounts of total collagen. These results may contribute to a better understanding of strain-induced tendon remodelling and will form the basis for the correct choice of applied force in rehabilitation after orthopaedic surgery. These findings underline the fact that early passive motion of the joint in order to induce remodelling of the tendon should be included within a rehabilitation protocol for rotator cuff repair.

High-throughput continuous flow synthesis of nickel nanoparticles for the catalytic hydrodeoxygenation of guaiacol

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

Roberts, Emily J.; Habas, Susan E.; Wang, Lu

2016-11-07

The translation of batch chemistries to high-throughput continuous flow methods dresses scaling, automation, and reproducibility concerns associated with the implementation of colloidally prepared nanoparticle (NP) catalysts for industrial catalytic processes. Nickel NPs were synthesized by the high-temperature amine reduction of a Ni2+ precursor using a continuous millifluidic (mF) flow method, achieving yields greater than 60%. The resulting Ni NP catalysts were compared against catalysts prepared in a batch reaction under conditions analogous to the continuous flow conditions with respect to total reaction volume, time, and temperature and by traditional incipient wetness (IW) impregnation for the hydrodeoxygenation (HDO) of guaiacol undermore » ex situ catalytic fast pyrolysis conditions. Compared to the IW method, the colloidally prepared NPs displayed increased morphological control and narrowed size distributions, and the NPs prepared by both methods showed similar size, shape, and crystallinity. The Ni NP catalyst synthesized by the continuous flow method exhibited similar H-adsorption site densities, site-time yields, and selectivities towards deoxygenated products as compared to the analogous batch reaction, and outperformed the IW catalyst with respect to higher selectivity to lower oxygen content products and a 6.9-fold slower deactivation rate. These results demonstrate the utility of synthesizing colloidal Ni NP catalysts using continuous flow methods while maintaining the catalytic properties displayed by the batch equivalent. Finally, this methodology can be extended to other catalytically relevant base metals for the high-throughput synthesis of metal NPs for the catalytic production of biofuels.« less

Cryotherapy Treatment After Unicompartmental and Total Knee Arthroplasty: A Review.

PubMed

Chughtai, Morad; Sodhi, Nipun; Jawad, Michael; Newman, Jared M; Khlopas, Anton; Bhave, Anil; Mont, Michael A

2017-12-01

Cryotherapy is widely utilized to enhance recovery after knee surgeries. However, the outcome parameters often vary between studies. Therefore, the purpose of this review is to compare (1) no cryotherapy vs cryotherapy; (2) cold pack cryotherapy vs continuous flow device cryotherapy; (3) various protocols of application of these cryotherapy methods; and (4) cost-benefit analysis in patients who had unicompartmental knee arthroplasty (UKA) or total knee arthroplasty (TKA). A search for "knee" and "cryotherapy" using PubMed, EBSCO Host, and SCOPUS was performed, yielding 187 initial reports. After selecting for RCTs relevant to our study, 16 studies were included. Of the 8 studies that compared the immediate postoperative outcomes between patients who did and did not receive cryotherapy, 5 studies favored cryotherapy (2 cold packs and 3 continuous cold flow devices). Of the 6 studies comparing the use of cold packs and continuous cold flow devices in patients who underwent UKA or TKA, 3 favor the use of continuous flow devices. There was no difference in pain, postoperative opioid consumption, or drain output between 2 different temperature settings of continuous cold flow device. The optimal device to use may be one that offers continuous circulating cold flow, as there were more studies demonstrating better outcomes. In addition, the pain relieving effects of cryotherapy may help minimize pain medication use, such as with opioids, which are associated with numerous potential side effects as well as dependence and addiction. Meta-analysis on the most recent RCTs should be performed next. Copyright © 2017 Elsevier Inc. All rights reserved.

chipPCR: an R package to pre-process raw data of amplification curves.

PubMed

Rödiger, Stefan; Burdukiewicz, Michał; Schierack, Peter

2015-09-01

Both the quantitative real-time polymerase chain reaction (qPCR) and quantitative isothermal amplification (qIA) are standard methods for nucleic acid quantification. Numerous real-time read-out technologies have been developed. Despite the continuous interest in amplification-based techniques, there are only few tools for pre-processing of amplification data. However, a transparent tool for precise control of raw data is indispensable in several scenarios, for example, during the development of new instruments. chipPCR is an R: package for the pre-processing and quality analysis of raw data of amplification curves. The package takes advantage of R: 's S4 object model and offers an extensible environment. chipPCR contains tools for raw data exploration: normalization, baselining, imputation of missing values, a powerful wrapper for amplification curve smoothing and a function to detect the start and end of an amplification curve. The capabilities of the software are enhanced by the implementation of algorithms unavailable in R: , such as a 5-point stencil for derivative interpolation. Simulation tools, statistical tests, plots for data quality management, amplification efficiency/quantification cycle calculation, and datasets from qPCR and qIA experiments are part of the package. Core functionalities are integrated in GUIs (web-based and standalone shiny applications), thus streamlining analysis and report generation. http://cran.r-project.org/web/packages/chipPCR. Source code: https://github.com/michbur/chipPCR. stefan.roediger@b-tu.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Molecular Cloning of Secreted Luciferases from Marine Planktonic Copepods.

PubMed

Takenaka, Yasuhiro; Ikeo, Kazuho; Shigeri, Yasushi

2016-01-01

Secreted luciferases isolated from copepod crustaceans are frequently used for nondisruptive reporter-gene assays, such as the continuous, automated and/or high-throughput monitoring of gene expression in living cells. All known copepod luciferases share highly conserved amino acid residues in two similar, repeated domains in the sequence. The similarity in the domains are ideal nature for designing PCR primers to amplify cDNA fragments of unidentified copepod luciferases from bioluminescent copepod crustaceans. Here, we introduce how to establish a cDNA encoding novel copepod luciferases from a copepod specimen by PCR with degenerated primers.

Microchip Module for Blood Sample Preparation and Nucleic Acid Amplification Reactions

PubMed Central

Yuen, Po Ki; Kricka, Larry J.; Fortina, Paolo; Panaro, Nicholas J.; Sakazume, Taku; Wilding, Peter

2001-01-01

A computer numerical control-machined plexiglas-based microchip module was designed and constructed for the integration of blood sample preparation and nucleic acid amplification reactions. The microchip module is comprised of a custom-made heater-cooler for thermal cycling, a series of 254 μm × 254 μm microchannels for transporting human whole blood and reagents in and out of an 8–9 μL dual-purpose (cell isolation and PCR) glass-silicon microchip. White blood cells were first isolated from a small volume of human whole blood (<3 μL) in an integrated cell isolation–PCR microchip containing a series of 3.5-μm feature-sized “weir-type” filters, formed by an etched silicon dam spanning the flow chamber. A genomic target, a region in the human coagulation Factor V gene (226-bp), was subsequently directly amplified by microchip-based PCR on DNA released from white blood cells isolated on the filter section of the microchip mounted onto the microchip module. The microchip module provides a convenient means to simplify nucleic acid analyses by integrating two key steps in genetic testing procedures, cell isolation and PCR and promises to be adaptable for additional types of integrated assays. PMID:11230164

A scalable self-priming fractal branching microchannel net chip for digital PCR.

PubMed

Zhu, Qiangyuan; Xu, Yanan; Qiu, Lin; Ma, Congcong; Yu, Bingwen; Song, Qi; Jin, Wei; Jin, Qinhan; Liu, Jinyu; Mu, Ying

2017-05-02

As an absolute quantification method at the single-molecule level, digital PCR has been widely used in many bioresearch fields, such as next generation sequencing, single cell analysis, gene editing detection and so on. However, existing digital PCR methods still have some disadvantages, including high cost, sample loss, and complicated operation. In this work, we develop an exquisite scalable self-priming fractal branching microchannel net digital PCR chip. This chip with a special design inspired by natural fractal-tree systems has an even distribution and 100% compartmentalization of the sample without any sample loss, which is not available in existing chip-based digital PCR methods. A special 10 nm nano-waterproof layer was created to prevent the solution from evaporating. A vacuum pre-packaging method called self-priming reagent introduction is used to passively drive the reagent flow into the microchannel nets, so that this chip can realize sequential reagent loading and isolation within a couple of minutes, which is very suitable for point-of-care detection. When the number of positive microwells stays in the range of 100 to 4000, the relative uncertainty is below 5%, which means that one panel can detect an average of 101 to 15 374 molecules by the Poisson distribution. This chip is proved to have an excellent ability for single molecule detection and quantification of low expression of hHF-MSC stem cell markers. Due to its potential for high throughput, high density, low cost, lack of sample and reagent loss, self-priming even compartmentalization and simple operation, we envision that this device will significantly expand and extend the application range of digital PCR involving rare samples, liquid biopsy detection and point-of-care detection with higher sensitivity and accuracy.

Prognostic value of minimal residual disease (MRD) in acute myeloid leukemia (AML) with favorable cytogenetics [t(8;21) and inv(16)].

PubMed

Perea, G; Lasa, A; Aventín, A; Domingo, A; Villamor, N; Queipo de Llano, M Paz; Llorente, A; Juncà, J; Palacios, C; Fernández, C; Gallart, M; Font, L; Tormo, M; Florensa, L; Bargay, J; Martí, J M; Vivancos, P; Torres, P; Berlanga, J J; Badell, I; Brunet, S; Sierra, J; Nomdedéu, J F

2006-01-01

Most patients with acute myeloid leukemia (AML) and t(8;21) or inv(16) have a good prognosis with current anthracycline- and cytarabine-based protocols. Tandem analysis with flow cytometry (FC) and real-time RT-PCR (RQ-PCR) was applied to 55 patients, 28 harboring a t(8;21) and 27 an inv(16), including one case with a novel CBFbeta/MYH11 transcript. A total of 31% (n=17) of CR patients relapsed: seven with t(8;21) and 10 with inv(16). The mean amount of minimal residual disease (MRD) detected by FC in relapsed and nonrelapsed patients was markedly different: 0.3 vs 0.08% (P=0.002) at the end of treatment. The mean number of fusion transcript copies/ ABL x 10(4) also differed between relapsed and non-relapsed patients: 2385 vs 122 (P=0.001) after induction, 56 vs 7.6 after intensification (P=0.0001) and 75 vs 3.3 (P=0.0001) at the end of chemotherapy. Relapses were more common in patients with FC MRD level >0.1% at the end of treatment than in patients with < or = 0.1%: cumulative incidence of relapse (CIR) was 67 and 21% (P=0.03), respectively. Likewise, using RQ-PCR, a cutoff level of >10 copies at the end of treatment correlated with a high risk of relapse: CIR was 75% for patients with RQ-PCR >10 compared to 21% for patients with RQ-PCR levels < or = 10 (P=0.04). Combined use of FC and RQ-PCR may improve MRD detection, and provide useful clinical information on relapse kinetics in AML patients.

Distinction between asymptomatic monoclonal B-cell lymphocytosis with cyclin D1 overexpression and mantle cell lymphoma: from molecular profiling to flow cytometry.

PubMed

Espinet, Blanca; Ferrer, Ana; Bellosillo, Beatriz; Nonell, Lara; Salar, Antonio; Fernández-Rodríguez, Concepción; Puigdecanet, Eulàlia; Gimeno, Javier; Garcia-Garcia, Mar; Vela, Maria Carmen; Luño, Elisa; Collado, Rosa; Navarro, José Tomás; de la Banda, Esmeralda; Abrisqueta, Pau; Arenillas, Leonor; Serrano, Cristina; Lloreta, Josep; Miñana, Belén; Cerutti, Andrea; Florensa, Lourdes; Orfao, Alberto; Sanz, Ferran; Solé, Francesc; Dominguez-Sola, David; Serrano, Sergio

2014-02-15

According to current diagnostic criteria, mantle cell lymphoma (MCL) encompasses the usual, aggressive variants and rare, nonnodal cases with monoclonal asymptomatic lymphocytosis, cyclin D1-positive (MALD1). We aimed to understand the biology behind this clinical heterogeneity and to identify markers for adequate identification of MALD1 cases. We compared 17 typical MCL cases with a homogeneous group of 13 untreated MALD1 cases (median follow-up, 71 months). We conducted gene expression profiling with functional analysis in five MCL and five MALD1. Results were validated in 12 MCL and 8 MALD1 additional cases by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and in 24 MCL and 13 MALD1 cases by flow cytometry. Classification and regression trees strategy was used to generate an algorithm based on CD38 and CD200 expression by flow cytometry. We found 171 differentially expressed genes with enrichment of neoplastic behavior and cell proliferation signatures in MCL. Conversely, MALD1 was enriched in gene sets related to immune activation and inflammatory responses. CD38 and CD200 were differentially expressed between MCL and MALD1 and confirmed by flow cytometry (median CD38, 89% vs. 14%; median CD200, 0% vs. 24%, respectively). Assessment of both proteins allowed classifying 85% (11 of 13) of MALD1 cases whereas 15% remained unclassified. SOX11 expression by qRT-PCR was significantly different between MCL and MALD1 groups but did not improve the classification. We show for the first time that MALD1, in contrast to MCL, is characterized by immune activation and driven by inflammatory cues. Assessment of CD38/CD200 by flow cytometry is useful to distinguish most cases of MALD1 from MCL in the clinical setting. MALD1 should be identified and segregated from the current MCL category to avoid overdiagnosis and unnecessary treatment. ©2013 AACR

Distinction between Asymptomatic Monoclonal B-cell Lymphocytosis with Cyclin D1 Overexpression and Mantle Cell Lymphoma: From Molecular Profiling to Flow Cytometry

PubMed Central

Espinet, Blanca; Ferrer, Ana; Bellosillo, Beatriz; Nonell, Lara; Salar, Antonio; Fernández-Rodríguez, Concepción; Puigdecanet, Eulàlia; Gimeno, Javier; Garcia-Garcia, Mar; Carmen Vela, Maria; Luño, Elisa; Collado, Rosa; Navarro, José Tomás; de la Banda, Esmeralda; Abrisqueta, Pau; Arenillas, Leonor; Serrano, Cristina; Lloreta, Josep; Miñana, Belén; Cerutti, Andrea; Florensa, Lourdes; Orfao, Alberto; Sanz, Ferran; Solé, Francesc; Dominguez-Sola, David; Serrano, Sergio

2015-01-01

Purpose According to current diagnostic criteria, mantle cell lymphoma (MCL) encompasses the usual, aggressive variants and rare, nonnodal cases with monoclonal asymptomatic lymphocytosis, cyclin D1–positive (MALD1). We aimed to understand the biology behind this clinical heterogeneity and to identify markers for adequate identification of MALD1 cases. Experimental Design We compared 17 typical MCL cases with a homogeneous group of 13 untreated MALD1 cases (median follow-up, 71 months). We conducted gene expression profiling with functional analysis in five MCL and five MALD1. Results were validated in 12 MCL and 8 MALD1 additional cases by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and in 24 MCL and 13 MALD1 cases by flow cytometry. Classification and regression trees strategy was used to generate an algorithm based on CD38 and CD200 expression by flow cytometry. Results We found 171 differentially expressed genes with enrichment of neoplastic behavior and cell proliferation signatures in MCL. Conversely, MALD1 was enriched in gene sets related to immune activation and inflammatory responses. CD38 and CD200 were differentially expressed between MCL and MALD1 and confirmed by flow cytometry (median CD38, 89% vs. 14%; median CD200, 0% vs. 24%, respectively). Assessment of both proteins allowed classifying 85% (11 of 13) of MALD1 cases whereas 15% remained unclassified. SOX11 expression by qRT-PCR was significantly different between MCL and MALD1 groups but did not improve the classification. Conclusion We show for the first time that MALD1, in contrast to MCL, is characterized by immune activation and driven by inflammatory cues. Assessment of CD38/CD200 by flow cytometry is useful to distinguish most cases of MALD1 from MCL in the clinical setting. MALD1 should be identified and segregated from the current MCL category to avoid overdiagnosis and unnecessary treatment. PMID:24352646

Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams

Treesearch

Stephen F. Jane; Taylor M. Wilcox; Kevin S. McKelvey; Michael K. Young; Michael K. Schwartz; Winsor H. Lowe; Benjamin H. Letcher; Andrew R. Whiteley

2014-01-01

Environmental DNA (eDNA) detection has emerged as a powerful tool for monitoring aquatic organisms, but much remains unknown about the dynamics of aquatic eDNA over a range of environmental conditions. DNA concentrations in streams and rivers will depend not only on the equilibrium between DNA entering the water and DNA leaving the system through degradation, but also...

Food-borne pathogens of animal origin-diagnosis, prevention, control and their zoonotic significance: a review.

PubMed

Dhama, K; Rajagunalan, S; Chakraborty, S; Verma, A K; Kumar, A; Tiwari, R; Kapoor, S

2013-10-15

The term food borne diseases or food-borne illnesses or more commonly food poisoning are used to denote gastrointestinal complications that occur following recent consumption of a particular food or drink. Millions of people suffer worldwide every year and the situation is quiet grave in developing nations creating social and economic strain. The food borne pathogens include various bacteria viz., Salmonella, Campylobacter, Escherichia coli, Listeria monocytogenes, Yersinia enterocolitica, Staphylococcus, Arcobacter, Clostridium perfringens, Cl. botulinum and Bacillus cereus and helminths viz., Taenia. They also include protozoa viz., Trichinella, Sarcocystis, Toxoplasma gondii and Cryptosporidium parvum. The zoonotic potential and the ability to elaborate toxins by many of the microbes causing fatal intoxication are sufficient to understand the seriousness of the situation. The viral agents being host specific their transmission to humans through food of animal origin is not yet confirmed although these animal viruses are similar to that of viruses infecting human. Food-borne bacteria; protozoa and helminthes have complex distribution pattern in the environment and inside the host system. This along with complexity of the maintenance chain and life cycle (of parasites) has made it difficult for epidemiologist and diagnostician to undertake any immediate safety measures against them. Serological and molecular diagnostic tests viz. ELISA, Latex agglutination test, Lateral flow assays, Immunomagnetic separation assays, molecular assays viz. Polymerase Chain Reaction (PCR), multiplex PCR, immuno-PCR, Realtime PCR, Random Amplified Polymorphic DNA (RAPD)-PCR, DNA microarrays and probes are widely used. Along with these LAMP assays, Capillary Electrophoresis-Single Strand Confirmation polymorphism (CE-SSCP); Flow cytometry, FISH, Biosensors, Direct epifluorescent filter technique, nanotechnology based methods and sophisticated tools (ultrasonography, magnetic resonance imaging and chlonangio-pancreatography) have aided in the diagnosis greatly. Most of the food-borne illnesses are self-limiting but in many instances antibiotics are recommended. With the increased drug resistance however use of chicken immunoglobulin, bacteriophage therapy, probiotics and herbs are gaining much importance these days. Adoption of proper prevention and control measures (including cooking procedures; hygiene, strict adherence to HACCP principles, public awareness and disease surveillance and monitoring) are the need of hour. All these have been discussed vividly in this review to help epidemiologists, diagnosticians, clinicians and above all common people so as to enable them avoid negligence regarding such serious issue.

Study of NGEP expression in androgen sensitive prostate cancer cells: A potential target for immunotherapy

PubMed Central

Mohsenzadegan, Monireh; Tajik, Nader; Madjd, Zahra; Shekarabi, Mehdi; Farajollahi, Mohammad M

2015-01-01

Background: Prostate cancer is one of the leading causes of cancer deaths among men. New gene expressed in prostate (NGEP), is a prostate-specific gene expressed only in normal prostate and prostate cancer tissue. Because of its selective expression in prostate cancer cell surface, NGEP is a potential immunotherapeutic target. To target the NGEP in prostate cancer, it is essential to investigate its expression in prostate cancer cells. Methods: In the present study, we investigated NGEP expression in LNCaP and DU145 cells by real time and RT-PCR, flow cytometric and immunocytochemical analyses. Results: Real time and RT-PCR analyses of NGEP expression showed that NGEP was expressed in the LNCaP cells but not in DU145 cells. The detection of NGEP protein by flow cytometric and immunocytochemistry analyses indicated that NGEP protein was weakly expressed only in LNCaP cell membrane. Conclusion: Our results demonstrate that LNCaP cell line is more suitable than DU145 for NGEP expression studies; however, its low-level expression is a limiting issue. NGEP expression may be increased by androgen supplementation of LNCaP cell culture medium. PMID:26000254

Development and standardization of a monoclonal antibody-based rapid flow-through immunoassay for the detection of Aphanomyces invadans in the field

PubMed Central

Adil, B; Naveen Kumar, B. T.; Patil, Rajreddy; Ballyaya, Abhiman; Ramesh, K. S.; Poojary, Sathish Rama; Byadgi, Omkar V.; Siriyappagouder, Prabhugouda

2013-01-01

A monoclonal antibody-based flow-through immunoassay (FTA) was developed using a nitrocellulose membrane placed on the top of adsorbent pads enclosed in a plastic cassette with a test zone at the center. The FTA could be completed within 10 min. Clear purple dots against a white background indicated the presence of Aphanomyces (A.) invadans. The FTA limit of detection was 7 µg/mL for A. invadans compared to 56 µg/mL for the immunodot. FTA and polymerase chain reaction (PCR) could detect A. invadans in fish tissue homogenates at a 10-11 dilution compared to a 10-8 dilution by immunodot. In fish suffering from natural cases of epizootic ulcerative syndrome (EUS) collected from Mangalore, India, FTA and PCR could detect A. invadans in 100% of the samples compared to 89.04% detected by immunodot. FTA reagents were stable and produced expected results for 4 months when stored at 4~8℃. This rapid test could serve as simple and cost-effective on-site screening tool to detect A. invadans in fish from EUS outbreak areas and in ports during the shipment of live or frozen fish. PMID:23820211

Loop-Mediated Isothermal Amplification-Lateral-Flow Dipstick (LAMP-LFD) to detect Toxoplasma gondii oocyst in ready-to-eat salad.

PubMed

Lalle, Marco; Possenti, Alessia; Dubey, Jitender P; Pozio, Edoardo

2018-04-01

The apicomplexan parasite Toxoplasma gondii is the causative agent of toxoplasmosis, a foodborne zoonosis with a global distribution and estimated to cause up to 20% of the total foodborne disease burden in Europe. Association between T. gondii infection and the consumption of unwashed raw fruits and vegetables contaminated with oocysts has been reported and the increasing habit to eat pre-washed ready-to-eat salads poses a new potential risk for consumers. It is therefore important to trace the occurrence of potential contamination with this parasite to guarantee the safety of ready-to-eat vegetables. Detection of T. gondii in vegetables by molecular techniques has been achieved but low sensitivity (PCR) or expensive equipments (qPCR) limit routine applicability. Here, we describe the development and validation of a sensitive and robust method relying on a LAMP assay, targeting the 529 bp locus, to detect T. gondii oocysts down to 25 oocysts/50 g in ready-to-eat baby lettuce. The LAMP has been also adapted for a faster visualization of the result by a lateral flow dipstick chromatographic detection method. Copyright © 2017 Elsevier Ltd. All rights reserved.

Immunohaematological and rheological parameters in canine visceral leishmaniasis.

PubMed

Silva, José Nivaldo da; Cotrim, Aron Carlos; Conceição, Luciana Auxiliadora Viebrantz da; Marins, Camila Moreira Ferreira; Marchi, Patricia Gelli Feres de; Honorio-França, Adenilda Cristina; Almeida, Arleana do Bom Parto Ferreira de; França, Eduardo Luzía; Sousa, Valéria Régia Franco

2018-05-24

The aim of this study was to find correlations between haematological and rheological parameters in canine visceral leishmaniasis (CLV). Enrolled dogs with CVL (n=31) had a confirmed diagnosis using the rapid test Dual Path Platform (TR DPP®) kit and Polymerase Chain Reaction (PCR) assay. A control group (n=31) comprised healthy dogs with negative results for the TR DPP® kit and PCR assay. Haematological parameters and total protein, albumin, globulin, and antibody were assessed. The rheological properties of the blood samples were also determined. Erythrocytes, haematocrit and platelet values of dogs in the CVL group were found to be lower than those of the control group. The total protein, globulin and IgG concentrations were higher in serum samples from the CVL group. The blood flow curve demonstrated increased shear rates in the CVL group. The viscosity of the blood from the infected animals was lower than in the healthy dogs. A positive correlation was found between erythrocyte numbers and blood viscosity. These data suggest that changes in the flow curve and viscosity of blood as well as the erythrocyte values may be a viable low-cost alternative for the monitoring of dogs with visceral leishmaniasis.

Immune gene expression for diverse haemocytes derived from pacific white shrimp, Litopenaeus vannamei.

PubMed

Yang, Chih-Chiu; Lu, Chung-Lun; Chen, Sherwin; Liao, Wen-Liang; Chen, Shiu-Nan

2015-05-01

In this study, diverse haemocytes from Pacific white shrimp Litopenaeus vannamei were spread by flow cytometer sorting system. Using the two commonly flow cytometric parameters FSC and SSC, the haemocytes could be divided into three populations. Microscopy observation of L. vannamei haemocytes in anticoagulant buffer revealed three morphologically distinct cell types designated as granular cell, hyaline cell and semigranular cell. Immune genes, which includes prophenoloxidase (proPO), lipopolysaccharide-β-glucan binding protein (LGBP), peroxinectin, crustin, lysozyme, penaeid-3a and transglutaminase (TGase), expressed from different haemocyte were analysed by quantitative real time PCR (qPCR). Results from the mRNA expression was estimated by relative level of each gene to β-actin gene. Finally, the seven genes could be grouped by their dominant expression sites. ProPO, LGBP and peroxinectin were highly expressed in granular cells, while LGBP, crustin, lysozyme and P-3a were highly expressed in semigranular cells and TGase was highly expressed in hyaline cells. In this study, L. vannamei haemocytes were firstly grouped into three different types and the immune related genes expression in grouped haemocytes were estimated. Copyright © 2015 Elsevier Ltd. All rights reserved.

Seasonal and regional diversity of maple sap microbiota revealed using community PCR fingerprinting and 16S rRNA gene clone libraries.

PubMed

Filteau, Marie; Lagacé, Luc; LaPointe, Gisèle; Roy, Denis

2010-04-01

An arbitrary primed community PCR fingerprinting technique based on capillary electrophoresis was developed to study maple sap microbial community characteristics among 19 production sites in Québec over the tapping season. Presumptive fragment identification was made with corresponding fingerprint profiles of bacterial isolate cultures. Maple sap microbial communities were subsequently compared using a representative subset of 13 16S rRNA gene clone libraries followed by gene sequence analysis. Results from both methods indicated that all maple sap production sites and flow periods shared common microbiota members, but distinctive features also existed. Changes over the season in relative abundance of predominant populations showed evidence of a common pattern. Pseudomonas (64%) and Rahnella (8%) were the most abundantly and frequently represented genera of the 2239 sequences analyzed. Janthinobacterium, Leuconostoc, Lactococcus, Weissella, Epilithonimonas and Sphingomonas were revealed as occasional contaminants in maple sap. Maple sap microbiota showed a low level of deep diversity along with a high variation of similar 16S rRNA gene sequences within the Pseudomonas genus. Predominance of Pseudomonas is suggested as a typical feature of maple sap microbiota across geographical regions, production sites, and sap flow periods.

Development and Practical Use of RT-PCR for Seed-transmitted Prune dwarf virus in Quarantine

PubMed Central

Lee, Siwon; Shin, Yong-Gil

2014-01-01

Among imported plants, seeds are the items that have many latent pathogens and are difficult to inspect. Also, they are the import and export items whose market is expected to expand. The biggest problem with seeds is viruses. Prune dwarf virus (PDV) is the virus that is commonly inspected in Prunus cerasifera, P. persica, P. armeniaca, P. mandshurica, P. cerasus, P. avium or P. serotina seeds. In this study, two RT-PCR primer sets, which can promptly and specifically diagnose plant quarantine seed-transmitted PDV, were developed; and nested PCR primers, where products amplify 739 and 673 nucleotides (nt), and an nested PCR-product, 305 nt, can be obtained as these products are amplified again, were developed. Also, a modified-positive control plasmid was developed, where the restriction enzyme XhoI, which can identify the contamination of samples from the control, was inserted. The method developed in this study has detected PDV in 18 cases since 2007, and is expected to continuously contribute to the plant quarantine in Korea. PMID:25289000

Population structure of wild bananas, Musa balbisiana, in China determined by SSR fingerprinting and cpDNA PCR-RFLP.

PubMed

Ge, X J; Liu, M H; Wang, W K; Schaal, B A; Chiang, T Y

2005-04-01

Both demographic history and dispersal mechanisms influence the apportionment of genetic diversity among plant populations across geographical regions. In this study, phylogeography and population structure of wild banana, Musa balbisiana, one of the progenitors of cultivated bananas and plantains in China were investigated by an analysis of genetic diversity of simple sequence repeat (SSR) fingerprint markers and cpDNA PCR-RFLP. A chloroplast DNA (cpDNA) genealogy of 21 haplotypes identified two major clades, which correspond to two geographical regions separated by the Beijiang and Xijiang rivers, suggesting a history of vicariance. Significant genetic differentiation was detected among populations with cpDNA markers, a result consistent with limited seed dispersal in wild banana mediated by foraging of rodents. Nuclear SSR data also revealed significant geographical structuring in banana populations. In western China, however, there was no detected phylogeograpahical pattern, possibly due to frequent pollen flow via fruit bats. In contrast, populations east of the Beijiang River and the population of Hainan Island, where long-range soaring pollinators are absent, are genetically distinct. Colonization-extinction processes may have influenced the evolution of Musa populations, which have a metapopulation structure and are connected by migrating individuals. Effective gene flow via pollen, estimated from the nuclear SSR data, is 3.65 times greater than gene flow via seed, estimated from cpDNA data. Chloroplast and nuclear DNAs provide different insights into phylogeographical patterns of wild banana populations and, taken together, can inform conservation practices.

Preparation of genomic DNA from a single species of uncultured magnetotactic bacterium by multiple-displacement amplification.

PubMed

Arakaki, Atsushi; Shibusawa, Mie; Hosokawa, Masahito; Matsunaga, Tadashi

2010-03-01

Magnetotactic bacteria comprise a phylogenetically diverse group that is capable of synthesizing intracellular magnetic particles. Although various morphotypes of magnetotactic bacteria have been observed in the environment, bacterial strains available in pure culture are currently limited to a few genera due to difficulties in their enrichment and cultivation. In order to obtain genetic information from uncultured magnetotactic bacteria, a genome preparation method that involves magnetic separation of cells, flow cytometry, and multiple displacement amplification (MDA) using phi29 polymerase was used in this study. The conditions for the MDA reaction using samples containing 1 to 100 cells were evaluated using a pure-culture magnetotactic bacterium, "Magnetospirillum magneticum AMB-1," whose complete genome sequence is available. Uniform gene amplification was confirmed by quantitative PCR (Q-PCR) when 100 cells were used as a template. This method was then applied for genome preparation of uncultured magnetotactic bacteria from complex bacterial communities in an aquatic environment. A sample containing 100 cells of the uncultured magnetotactic coccus was prepared by magnetic cell separation and flow cytometry and used as an MDA template. 16S rRNA sequence analysis of the MDA product from these 100 cells revealed that the amplified genomic DNA was from a single species of magnetotactic bacterium that was phylogenetically affiliated with magnetotactic cocci in the Alphaproteobacteria. The combined use of magnetic separation, flow cytometry, and MDA provides a new strategy to access individual genetic information from magnetotactic bacteria in environmental samples.

The synthesis of active pharmaceutical ingredients (APIs) using continuous flow chemistry

PubMed Central

2015-01-01

Summary The implementation of continuous flow processing as a key enabling technology has transformed the way we conduct chemistry and has expanded our synthetic capabilities. As a result many new preparative routes have been designed towards commercially relevant drug compounds achieving more efficient and reproducible manufacture. This review article aims to illustrate the holistic systems approach and diverse applications of flow chemistry to the preparation of pharmaceutically active molecules, demonstrating the value of this strategy towards every aspect ranging from synthesis, in-line analysis and purification to final formulation and tableting. Although this review will primarily concentrate on large scale continuous processing, additional selected syntheses using micro or meso-scaled flow reactors will be exemplified for key transformations and process control. It is hoped that the reader will gain an appreciation of the innovative technology and transformational nature that flow chemistry can leverage to an overall process. PMID:26425178

The synthesis of active pharmaceutical ingredients (APIs) using continuous flow chemistry.

PubMed

Baumann, Marcus; Baxendale, Ian R

2015-01-01

The implementation of continuous flow processing as a key enabling technology has transformed the way we conduct chemistry and has expanded our synthetic capabilities. As a result many new preparative routes have been designed towards commercially relevant drug compounds achieving more efficient and reproducible manufacture. This review article aims to illustrate the holistic systems approach and diverse applications of flow chemistry to the preparation of pharmaceutically active molecules, demonstrating the value of this strategy towards every aspect ranging from synthesis, in-line analysis and purification to final formulation and tableting. Although this review will primarily concentrate on large scale continuous processing, additional selected syntheses using micro or meso-scaled flow reactors will be exemplified for key transformations and process control. It is hoped that the reader will gain an appreciation of the innovative technology and transformational nature that flow chemistry can leverage to an overall process.

The synthesis of cadmium sulfide nanoplatelets using a novel continuous flow sonochemical reactor

DOE PAGES

Palanisamy, Barath; Paul, Brian; Chang, Chih -hung

2015-01-21

A continuous flow sonochemical reactor was developed capable of producing metastable cadmium sulfide (CdS) nanoplatelets with thicknesses at or below 10 nm. The continuous flow sonochemical reactor included the passive in-line micromixing of reagents prior to sonochemical reaction. Synthesis results were compared with those from reactors involving batch conventional heating and batch ultrasound-induced heating. The continuous sonochemical synthesis was found to result in high aspect ratio hexagonal platelets of CdS possessing cubic crystal structures with thicknesses well below 10 nm. The unique shape and crystal structure of the nanoplatelets are suggestive of high localized temperatures within the sonochemical process. Asmore » a result, the particle size uniformity and product throughput are much higher for the continuous sonochemical process in comparison to the batch sonochemical process and conventional synthesis processes.« less

Using Selective Drainage Methods to Extract Continuous Surface Flow from 1-Meter Lidar-Derived Digital Elevation Data

USGS Publications Warehouse

Poppenga, Sandra K.; Worstell, Bruce B.; Stoker, Jason M.; Greenlee, Susan K.

2010-01-01

Digital elevation data commonly are used to extract surface flow features. One source for high-resolution elevation data is light detection and ranging (lidar). Lidar can capture a vast amount of topographic detail because of its fine-scale ability to digitally capture the surface of the earth. Because elevation is a key factor in extracting surface flow features, high-resolution lidar-derived digital elevation models (DEMs) provide the detail needed to consistently integrate hydrography with elevation, land cover, structures, and other geospatial features. The U.S. Geological Survey has developed selective drainage methods to extract continuous surface flow from high-resolution lidar-derived digital elevation data. The lidar-derived continuous surface flow network contains valuable information for water resource management involving flood hazard mapping, flood inundation, and coastal erosion. DEMs used in hydrologic applications typically are processed to remove depressions by filling them. High-resolution DEMs derived from lidar can capture much more detail of the land surface than courser elevation data. Therefore, high-resolution DEMs contain more depressions because of obstructions such as roads, railroads, and other elevated structures. The filling of these depressions can significantly affect the DEM-derived surface flow routing and terrain characteristics in an adverse way. In this report, selective draining methods that modify the elevation surface to drain a depression through an obstruction are presented. If such obstructions are not removed from the elevation data, the filling of depressions to create continuous surface flow can cause the flow to spill over an obstruction in the wrong location. Using this modified elevation surface improves the quality of derived surface flow and retains more of the true surface characteristics by correcting large filled depressions. A reliable flow surface is necessary for deriving a consistently connected drainage network, which is important in understanding surface water movement and developing applications for surface water runoff, flood inundation, and erosion. Improved methods are needed to extract continuous surface flow features from high-resolution elevation data based on lidar.

Quant. PCR and bDNA - the search for the truth continues as high viral load are linked to high beta 2 microglobulin levels.

PubMed

1998-01-01

Controversy exists over whether numbers obtained from Quant. PCR & bDNA tests actually represent the HIV virus; however, a researcher is collecting evidence to determine whether both tests have the same prognostic value as the beta 2 microglobulin tests. There is enough evidence to show that beta 2 microglobulin levels correlate directly with high viral loads. The researcher speculates that Quant. PCR or bDNA measures the combined effects of both HIV and HHV-6A infection in destroying cells. To help resolve this and other issues, volunteers with Chronic Fatigue Immune Dysfunction Syndrome (CFIDS) and active HHV-6A infection are being sought. Volunteers will be asked to use Norvir after which its effectiveness against HHV-6A infection will be determined. CFIDS patients will show a viral load for HIV even though they do not have the virus; the research speculates that if the PCR test for HIV is non-detectable in HHV-6A related cases, it will prove that Quant PCR is not measuring HHV-6A titers in persons with AIDS. Other diagnostic tests are available to patients. Five of these tests are briefly summarized and responses to patient questions regarding viral load issues and therapy are included.

The LAM-PCR Method to Sequence LV Integration Sites.

PubMed

Wang, Wei; Bartholomae, Cynthia C; Gabriel, Richard; Deichmann, Annette; Schmidt, Manfred

2016-01-01

Integrating viral gene transfer vectors are commonly used gene delivery tools in clinical gene therapy trials providing stable integration and continuous gene expression of the transgene in the treated host cell. However, integration of the reverse-transcribed vector DNA into the host genome is a potentially mutagenic event that may directly contribute to unwanted side effects. A comprehensive and accurate analysis of the integration site (IS) repertoire is indispensable to study clonality in transduced cells obtained from patients undergoing gene therapy and to identify potential in vivo selection of affected cell clones. To date, next-generation sequencing (NGS) of vector-genome junctions allows sophisticated studies on the integration repertoire in vitro and in vivo. We have explored the use of the Illumina MiSeq Personal Sequencer platform to sequence vector ISs amplified by non-restrictive linear amplification-mediated PCR (nrLAM-PCR) and LAM-PCR. MiSeq-based high-quality IS sequence retrieval is accomplished by the introduction of a double-barcode strategy that substantially minimizes the frequency of IS sequence collisions compared to the conventionally used single-barcode protocol. Here, we present an updated protocol of (nr)LAM-PCR for the analysis of lentiviral IS using a double-barcode system and followed by deep sequencing using the MiSeq device.

Radar-imaged internal layering in the Weddell Sea sector of West Antarctica

NASA Astrophysics Data System (ADS)

Bingham, Robert G.; Rippin, David M.; Karlsson, Nanna B.; Corr, Hugh F. J.; Ferraccioli, Fausto; Jordan, Tom A.; Le Brocq, Anne M.; Ross, Neil; Wright, Andrew P.; Siegert, Martin J.

2013-04-01

Radio-echo sounding (RES) across polar ice sheets reveals extensive, isochronous internal layers, whose stratigraphy, and especially their degree of continuity over multi-km distances, can inform us about both present ice flow and past ice-flow histories. Here, we bring together for the first time two recent advances in this field of cryospheric remote sensing to analyse ice flow into the Weddell Sea sector of West Antarctica. Firstly, we have developed a new quantitative routine for analysing the continuity of internal layers obtained over large areas of ice by airborne RES surveys - we term this routine the "Internal-Layering Continuity-Index (ILCI)". Secondly, in the austral season 2010-11 we acquired, by airborne RES survey, the first comprehensive dataset of deep internal layering across Institute and Möller Ice Streams, two of the more significant feeders of ice into the Filchner-Ronne Ice Shelf. Applying the ILCI to SAR-processed (migrated) RES profiles across Institute Ice Stream's catchment reveals two contrasting regions of internal-layering continuity behaviour. In the western portion of the catchment, where ice-stream tributaries incise deeply through the Ellsworth Subglacial Highlands, the continuity of internal layers is most disrupted across the present ice streams. We therefore interpret the ice-flow configuration in this western region as predominantly spatially stable over the lifetime of the ice. Further east, towards Möller Ice Stream, and towards the interior of the ice sheet, the ILCI does not closely match the present ice flow configuration, while across most of present-day Möller Ice Stream itself, the continuity of internal layers is generally low. We propose that the variation in continuity of internal layering across eastern Institute Ice Stream and the neighbouring Möller results primarily from two factors. Firstly, the noncorrespondence of some inland tributaries with internal-layering continuity acts as evidence for past spatial migration of those tributaries, with likely consequences for the relative positions of Institute and Möller Ice Streams over recent history. Secondly, the subglacial roughness, in part a function of the underlying geology across the region, imposes a strong influence on the continuity of the overlying deep internal layers, though whether it controls, or is a function of, ice flow, remains undetermined. We conclude that in the subglacially mountainous Ellsworth Subglacial Highlands sector, there is long-term stability in the spatial configuration of ice flow, but that elsewhere across Insitute and Möller Ice Streams, the ice-flow configuration is not stable.

Impact of continuous flow chemistry in the synthesis of natural products and active pharmaceutical ingredients.

PubMed

Souza, Juliana M DE; Galaverna, Renan; Souza, Aline A N DE; Brocksom, Timothy J; Pastre, Julio C; Souza, Rodrigo O M A DE; Oliveira, Kleber T DE

2018-01-01

We present a comprehensive review of the advent and impact of continuous flow chemistry with regard to the synthesis of natural products and drugs, important pharmaceutical products and definitely responsible for a revolution in modern healthcare. We detail the beginnings of modern drugs and the large scale batch mode of production, both chemical and microbiological. The introduction of modern continuous flow chemistry is then presented, both as a technological tool for enabling organic chemistry, and as a fundamental research endeavor. This part details the syntheses of bioactive natural products and commercial drugs.

Conjugated Polymers Via Direct Arylation Polymerization in Continuous Flow: Minimizing the Cost and Batch-to-Batch Variations for High-Throughput Energy Conversion.

PubMed

Gobalasingham, Nemal S; Carlé, Jon E; Krebs, Frederik C; Thompson, Barry C; Bundgaard, Eva; Helgesen, Martin

2017-11-01

Continuous flow methods are utilized in conjunction with direct arylation polymerization (DArP) for the scaled synthesis of the roll-to-roll compatible polymer, poly[(2,5-bis(2-hexyldecyloxy)phenylene)-alt-(4,7-di(thiophen-2-yl)-benzo[c][1,2,5]thiadiazole)] (PPDTBT). PPDTBT is based on simple, inexpensive, and scalable monomers using thienyl-flanked benzothiadiazole as the acceptor, which is the first β-unprotected substrate to be used in continuous flow via DArP, enabling critical evaluation of the suitability of this emerging synthetic method for minimizing defects and for the scaled synthesis of high-performance materials. To demonstrate the usefulness of the method, DArP-prepared PPDTBT via continuous flow synthesis is employed for the preparation of indium tin oxide (ITO)-free and flexible roll-coated solar cells to achieve a power conversion efficiency of 3.5% for 1 cm 2 devices, which is comparable to the performance of PPDTBT polymerized through Stille cross coupling. These efforts demonstrate the distinct advantages of the continuous flow protocol with DArP avoiding use of toxic tin chemicals, reducing the associated costs of polymer upscaling, and minimizing batch-to-batch variations for high-quality material. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enrichment of denitrifying methane-oxidizing microorganisms using up-flow continuous reactors and batch cultures.

PubMed

Hatamoto, Masashi; Kimura, Masafumi; Sato, Takafumi; Koizumi, Masato; Takahashi, Masanobu; Kawakami, Shuji; Araki, Nobuo; Yamaguchi, Takashi

2014-01-01

Denitrifying anaerobic methane oxidizing (DAMO) microorganisms were enriched from paddy field soils using continuous-flow and batch cultures fed with nitrate or nitrite as a sole electron acceptor. After several months of cultivation, the continuous-flow cultures using nitrite showed remarkable simultaneous methane oxidation and nitrite reduction and DAMO bacteria belonging to phylum NC10 were enriched. A maximum volumetric nitrite consumption rate of 70.4±3.4 mg-N·L(-1)·day(-1) was achieved with very short hydraulic retention time of 2.1 hour. In the culture, about 68% of total microbial cells were bacteria and no archaeal cells were detected by fluorescence in situ hybridization. In the nitrate-fed continuous-flow cultures, 58% of total microbial cells were bacteria while archaeal cells accounted for 7% of total cell numbers. Phylogenetic analysis of pmoA gene sequence showed that enriched DAMO bacteria in the continuous-flow cultivation had over 98% sequence similarity to DAMO bacteria in the inoculum. In contrast, for batch culture, the enriched pmoA gene sequences had 89-91% sequence similarity to DAMO bacteria in the inoculum. These results indicate that electron acceptor and cultivation method strongly affect the microbial community structures of DAMO consortia.

Multistep continuous-flow synthesis of (R)- and (S)-rolipram using heterogeneous catalysts

NASA Astrophysics Data System (ADS)

Tsubogo, Tetsu; Oyamada, Hidekazu; Kobayashi, Shū

2015-04-01

Chemical manufacturing is conducted using either batch systems or continuous-flow systems. Flow systems have several advantages over batch systems, particularly in terms of productivity, heat and mixing efficiency, safety, and reproducibility. However, for over half a century, pharmaceutical manufacturing has used batch systems because the synthesis of complex molecules such as drugs has been difficult to achieve with continuous-flow systems. Here we describe the continuous-flow synthesis of drugs using only columns packed with heterogeneous catalysts. Commercially available starting materials were successively passed through four columns containing achiral and chiral heterogeneous catalysts to produce (R)-rolipram, an anti-inflammatory drug and one of the family of γ-aminobutyric acid (GABA) derivatives. In addition, simply by replacing a column packed with a chiral heterogeneous catalyst with another column packed with the opposing enantiomer, we obtained antipole (S)-rolipram. Similarly, we also synthesized (R)-phenibut, another drug belonging to the GABA family. These flow systems are simple and stable with no leaching of metal catalysts. Our results demonstrate that multistep (eight steps in this case) chemical transformations for drug synthesis can proceed smoothly under flow conditions using only heterogeneous catalysts, without the isolation of any intermediates and without the separation of any catalysts, co-products, by-products, and excess reagents. We anticipate that such syntheses will be useful in pharmaceutical manufacturing.

Crystal and Particle Engineering Strategies for Improving Powder Compression and Flow Properties to Enable Continuous Tablet Manufacturing by Direct Compression.

PubMed

Chattoraj, Sayantan; Sun, Changquan Calvin

2018-04-01

Continuous manufacturing of tablets has many advantages, including batch size flexibility, demand-adaptive scale up or scale down, consistent product quality, small operational foot print, and increased manufacturing efficiency. Simplicity makes direct compression the most suitable process for continuous tablet manufacturing. However, deficiencies in powder flow and compression of active pharmaceutical ingredients (APIs) limit the range of drug loading that can routinely be considered for direct compression. For the widespread adoption of continuous direct compression, effective API engineering strategies to address power flow and compression problems are needed. Appropriate implementation of these strategies would facilitate the design of high-quality robust drug products, as stipulated by the Quality-by-Design framework. Here, several crystal and particle engineering strategies for improving powder flow and compression properties are summarized. The focus is on the underlying materials science, which is the foundation for effective API engineering to enable successful continuous manufacturing by the direct compression process. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Y-chromosomal testing of brown bears (Ursus arctos): Validation of a multiplex PCR-approach for nine STRs suitable for fecal and hair samples.

PubMed

Aarnes, Siv Grethe; Hagen, Snorre B; Andreassen, Rune; Schregel, Julia; Knappskog, Per M; Hailer, Frank; Stenhouse, Gordon; Janke, Axel; Eiken, Hans Geir

2015-11-01

High-resolution Y-chromosomal markers have been applied to humans and other primates to study population genetics, migration, social structures and reproduction. Y-linked markers allow the direct assessment of the genetic structure and gene flow of uniquely male inherited lineages and may also be useful for wildlife conservation and forensics, but have so far been available only for few wild species. Thus, we have developed two multiplex PCR reactions encompassing nine Y-STR markers identified from the brown bear (Ursus arctos) and tested them on hair, fecal and tissue samples. The multiplex PCR approach was optimized and analyzed for species specificity, sensitivity and stutter-peak ratios. The nine Y-STRs also showed specific STR-fragments for male black bears and male polar bears, while none of the nine markers produced any PCR products when using DNA from female bears or males from 12 other mammals. The multiplex PCR approach in two PCR reactions could be amplified with as low as 0.2 ng template input. Precision was high in DNA templates from hairs, fecal scats and tissues, with standard deviations less than 0.14 and median stutter ratios from 0.04 to 0.63. Among the eight di- and one tetra-nucleotide repeat markers, we detected simple repeat structures in seven of the nine markers with 9-25 repeat units. Allelic variation was found for eight of the nine Y-STRs, with 2-9 alleles for each marker and a total of 36 alleles among 453 male brown bears sampled mainly from Northern Europe. We conclude that the multiplex PCR approach with these nine Y-STRs would provide male bear Y-chromosomal specificity and evidence suited for samples from conservation and wildlife forensics. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Dynamic Transitions and Baroclinic Instability for 3D Continuously Stratified Boussinesq Flows

NASA Astrophysics Data System (ADS)

Şengül, Taylan; Wang, Shouhong

2018-02-01

The main objective of this article is to study the nonlinear stability and dynamic transitions of the basic (zonal) shear flows for the three-dimensional continuously stratified rotating Boussinesq model. The model equations are fundamental equations in geophysical fluid dynamics, and dynamics associated with their basic zonal shear flows play a crucial role in understanding many important geophysical fluid dynamical processes, such as the meridional overturning oceanic circulation and the geophysical baroclinic instability. In this paper, first we derive a threshold for the energy stability of the basic shear flow, and obtain a criterion for local nonlinear stability in terms of the critical horizontal wavenumbers and the system parameters such as the Froude number, the Rossby number, the Prandtl number and the strength of the shear flow. Next, we demonstrate that the system always undergoes a dynamic transition from the basic shear flow to either a spatiotemporal oscillatory pattern or circle of steady states, as the shear strength of the basic flow crosses a critical threshold. Also, we show that the dynamic transition can be either continuous or catastrophic, and is dictated by the sign of a transition number, fully characterizing the nonlinear interactions of different modes. Both the critical shear strength and the transition number are functions of the system parameters. A systematic numerical method is carried out to explore transition in different flow parameter regimes. In particular, our numerical investigations show the existence of a hypersurface which separates the parameter space into regions where the basic shear flow is stable and unstable. Numerical investigations also yield that the selection of horizontal wave indices is determined only by the aspect ratio of the box. We find that the system admits only critical eigenmodes with roll patterns aligned with the x-axis. Furthermore, numerically we encountered continuous transitions to multiple steady states, as well as continuous and catastrophic transitions to spatiotemporal oscillations.

[Economical benefit of continuous total intravenous anesthesia].

PubMed

Onaka, M; Yamamoto, H; Akatsuka, M; Mori, H

1999-05-01

Total intravenous anesthesia (TIVA) has been recommended in view of avoiding air pollution. However, intermittent administration of anesthetic agents has a large disadvantage of delayed emergence. We reported that continuous TIVA with propofol, ketamine, vecuronium and buprenorphine (PKBp) could bring rapid emergence. In this study, we calculated and compared the cost of anesthesia in the subjects who had undergone general anesthesia either with continuous PKBp or nitrous oxide-oxygen-sevoflurane. In group PKBp subjects, after induction with propofol, ketamine, vecuronium and buprenorphine, anesthesia was maintained with continuous intravenous administration of propofol corresponding to the patient's age using twice step down method; ketamine (240 micrograms.kg-1.h-1), vecuronium (80 micrograms.kg-1.h-1) and buprenorphine (0.4 microgram.kg-1.h-1). Group GOS subjects, after the same induction method, received nitrous oxide, sevoflurane and vecuronium. Moreover, the group GOS subjects were divided to two groups; the high flow GOS (N2O:O2:sevoflurane = 4 l:2 l:30 ml) and the low flow GOS (N2O:O2:sevoflurane = 2 l:1 l:15 ml). Continuous PKBp group showed lower cost than the high flow GOS group. The PKBp group showed lower cost than the low flow GOS group except in patients weighing more than 100 kg. Furthermore, we calculated the cost of continuous PKBp anesthesia in Japan, U.S.A. and U.K. The U.S.A. cost of PKBp was higher than the Japanese and the U.K., because the cost of ketamine in U.S.A. is higher than in the other countries. Continuous PKBp is more economical than the high flow GOS, and continuous PKBp in Japan is more economical than in U.S.A.

Heating and cooling system for an on-board gas adsorbent storage vessel

DOEpatents

Tamburello, David A.; Anton, Donald L.; Hardy, Bruce J.; Corgnale, Claudio

2017-06-20

In one aspect, a system for controlling the temperature within a gas adsorbent storage vessel of a vehicle may include an air conditioning system forming a continuous flow loop of heat exchange fluid that is cycled between a heated flow and a cooled flow. The system may also include at least one fluid by-pass line extending at least partially within the gas adsorbent storage vessel. The fluid by-pass line(s) may be configured to receive a by-pass flow including at least a portion of the heated flow or the cooled flow of the heat exchange fluid at one or more input locations and expel the by-pass flow back into the continuous flow loop at one or more output locations, wherein the by-pass flow is directed through the gas adsorbent storage vessel via the by-pass line(s) so as to adjust an internal temperature within the gas adsorbent storage vessel.

LONG-TERM MECHANICAL CIRCULATORY SUPPORT (DESTINATION THERAPY): ON TRACK TO COMPETE WITH HEART TRANSPLANTATIO?

PubMed Central

Kirklin, James K.; Naftel, David C.; Pagani, Francis D.; Kormos, Robert L.; Stevenson, Lynne; Miller, Marissa; Young, James B.

2012-01-01

Objective(s) Average two-year survival following cardiac transplantation is approximately 80%. The evolution and subsequent approval of larger pulsatile and, more recently, continuous flow mechanical circulatory support (MCS) technology for destination therapy (DT) offers the potential for triage of some patients awaiting cardiac transplantation to DT. Methods The National Heart, Lung and Blood Institute Interagency Registry for Mechanically Assisted Circulatory Support (INTERMACS) is a national multi-institutional study of chronic mechanical circulatory support. Between June 2006 and December 2011, 127 pulsatile and 1160 continuous flow pumps (24% of total primary LVADs) carried an initial strategy of DT therapy. Results By multivariable analysis, risk factors (p<0.05) for mortality following DT included older age, larger body mass index, history of cancer, history of cardiac surgery, INTERMACS level I (cardiogenic shock), dialysis, increased BUN, use of a pulsatile flow device and use of a RVAD. Among continuous flow LVAD patients who were not in cardiogenic shock, a particularly favorable survival was associated with no cancer, patients not in cardiogenic shock, and BUN < 50, resulting in one and two year survival of 88 and 80%. Conclusions 1) Evolution from pulsatile to continuous flow technology has dramatically improved one and two year survival; 2) Destination Therapy is not appropriate for patients with rapid hemodynamic deterioration; or severe right ventricular failure 4) Important subsets of continuous flow DT patients now enjoy survival which is competitive with heart transplantation out to about two years. PMID:22795459

APDS: the autonomous pathogen detection system.

PubMed

Hindson, Benjamin J; Makarewicz, Anthony J; Setlur, Ujwal S; Henderer, Bruce D; McBride, Mary T; Dzenitis, John M

2005-04-15

We have developed and tested a fully autonomous pathogen detection system (APDS) capable of continuously monitoring the environment for airborne biological threat agents. The system was developed to provide early warning to civilians in the event of a bioterrorism incident and can be used at high profile events for short-term, intensive monitoring or in major public buildings or transportation nodes for long-term monitoring. The APDS is completely automated, offering continuous aerosol sampling, in-line sample preparation fluidics, multiplexed detection and identification immunoassays, and nucleic acid-based polymerase chain reaction (PCR) amplification and detection. Highly multiplexed antibody-based and duplex nucleic acid-based assays are combined to reduce false positives to a very low level, lower reagent costs, and significantly expand the detection capabilities of this biosensor. This article provides an overview of the current design and operation of the APDS. Certain sub-components of the ADPS are described in detail, including the aerosol collector, the automated sample preparation module that performs multiplexed immunoassays with confirmatory PCR, and the data monitoring and communications system. Data obtained from an APDS that operated continuously for 7 days in a major U.S. transportation hub is reported.

A stroboscopic technique for using CCD cameras in flow visualization systems for continuous viewing and stop action photography

NASA Technical Reports Server (NTRS)

Franke, John M.; Rhodes, David B.; Jones, Stephen B.; Dismond, Harriet R.

1992-01-01

A technique for synchronizing a pulse light source to charge coupled device cameras is presented. The technique permits the use of pulse light sources for continuous as well as stop action flow visualization. The technique has eliminated the need to provide separate lighting systems at facilities requiring continuous and stop action viewing or photography.

Detection of Talaromyces marneffei from Fresh Tissue of an Inhalational Murine Pulmonary Model Using Nested PCR

PubMed Central

Liu, Yinghui; Huang, Xiaowen; Yi, Xiuwen; He, Ya; Mylonakis, Eleftherios; Xi, Liyan

2016-01-01

Penicilliosis marneffei, often consecutive to the aspiration of Talaromyces marneffei (Penicillium marneffei), continues to be one of the significant causes of morbidity and mortality in immunocompromised patients in endemic regions such as Southeast Asia. Improving the accuracy of diagnosing this disease would aid in reducing the mortality of associated infections. In this study, we developed a stable and reproducible murine pulmonary model that mimics human penicilliosis marneffei using a nebulizer to deliver Talaromyces marneffei (SUMS0152) conidia to the lungs of BALB/c nude mice housed in exposure chamber. Using this model, we further revealed that nested PCR was sensitive and specific for detecting Talaromyces marneffei in bronchoalveolar lavage fluid and fresh tissues. This inhalation model may provide a more representative analysis tool for studying the development of penicilliosis marneffei, in addition to revealing that nested PCR has a predictive value in reflecting pulmonary infection. PMID:26886887

Detection of dengue virus serotypes 1, 2 and 3 in selected regions of Kenya: 2011-2014.

PubMed

Konongoi, Limbaso; Ofula, Victor; Nyunja, Albert; Owaka, Samuel; Koka, Hellen; Makio, Albina; Koskei, Edith; Eyase, Fredrick; Langat, Daniel; Schoepp, Randal J; Rossi, Cynthia Ann; Njeru, Ian; Coldren, Rodney; Sang, Rosemary

2016-11-04

Dengue fever, a mosquito-borne disease, is associated with illness of varying severity in countries in the tropics and sub tropics. Dengue cases continue to be detected more frequently and its geographic range continues to expand. We report the largest documented laboratory confirmed circulation of dengue virus in parts of Kenya since 1982. From September 2011 to December 2014, 868 samples from febrile patients were received from hospitals in Nairobi, northern and coastal Kenya. The immunoglobulin M enzyme linked immunosorbent assay (IgM ELISA) was used to test for the presence of IgM antibodies against dengue, yellow fever, West Nile and Zika. Reverse transcription polymerase chain reaction (RT-PCR) utilizing flavivirus family, yellow fever, West Nile, consensus and sero type dengue primers were used to detect acute arbovirus infections and determine the infecting serotypes. Representative samples of PCR positive samples for each of the three dengue serotypes detected were sequenced to confirm circulation of the various dengue serotypes. Forty percent (345/868) of the samples tested positive for dengue by either IgM ELISA (14.6 %) or by RT-PCR (25.1 %). Three dengue serotypes 1-3 (DENV1-3) were detected by serotype specific RT-PCR and sequencing with their numbers varying from year to year and by region. The overall predominant serotype detected from 2011-2014 was DENV1 accounting for 44 % (96/218) of all the serotypes detected, followed by DENV2 accounting for 38.5 % (84/218) and then DENV3 which accounted for 17.4 % (38/218). Yellow fever, West Nile and Zika was not detected in any of the samples tested. From 2011-2014 serotypes 1, 2 and 3 were detected in the Northern and Coastal parts of Kenya. This confirmed the occurrence of cases and active circulation of dengue in parts of Kenya. These results have documented three circulating serotypes and highlight the need for the establishment of active dengue surveillance to continuously detect cases, circulating serotypes, and determine dengue fever disease burden in the country and region.

Metabolic engineering: the ultimate paradigm for continuous pharmaceutical manufacturing.

PubMed

Yadav, Vikramaditya G; Stephanopoulos, Gregory

2014-07-01

Research and development (R&D) expenditures by pharmaceutical companies doubled over the past decade, yet candidate attrition rates and development times rose markedly during this period. Understandably, companies have begun downsizing their pipelines and diverting investments away from R&D in favor of manufacturing. It is estimated that transitioning to continuous manufacturing could enable companies to compete for a share in emerging markets. Accordingly, the model for continuous manufacturing that has emerged commences with the conversion of late-stage intermediates into the active pharmaceutical ingredient (API) in a series of continuous flow reactors, followed by continuous solid processing to form finished tablets. The use of flow reactions for API synthesis will certainly generate purer products at higher yields in shorter times compared to equivalent batch reactions. However, transitioning from batch to flow configuration simply alleviates transport limitations within the reaction milieu. As the catalogue of reactions used in flow syntheses is a subset of batch-based chemistries, molecules such as natural products will continue to evade drug prospectors. Also, it is uncertain whether flow synthesis can deliver improvements in the atom and energy economies of API production at the scales that would achieve the levels of revenue growth targeted by companies. Instead, it is argued that implementing metabolic engineering for the production of oxidized scaffolds as gateway molecules for flow-based addition of electrophiles is a more effective and scalable strategy for accessing natural product chemical space. This new paradigm for manufacturing, with metabolic engineering as its engine, would also permit rapid optimization of production variables and allow facile scale-up from gram to ton scale to meet material requirements for clinical trials, thus recasting manufacturing as a tool for discovery. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of the cooling of continuous flow helium cryostats

NASA Astrophysics Data System (ADS)

Pust, L.

A mathematical model of the cooling of a continuous-flow cryostat which takes into account real values of the specific and latent heat of the cryogenic fluid and of the specific heat of the cryostat material is presented. The amount of liquid in the cooling fluid and four parasitic heat flows, caused by radiation and heat conduction in the construction materials and in the rest gas in the vacuum insulation, are also taken into account. The influence of different model parameters on performance, particularly in the non-stationary regime, is demonstrated by means of numerical solutions of the modelling equations. A quantitative criterion which assesses the properties of the planned cryostat, is formulated. The theoretical conclusions are compared with measurements performed on a continuous flow helium cryostat.

High-speed RNA microextraction technology using magnetic oligo-dT beads and lateral magnetophoresis.

PubMed

Lee, Hwanyong; Jung, Jinhee; Han, Song-I; Han, Ki-Ho

2010-10-21

This paper presents a high-speed RNA microextractor for the direct isolation of RNA from peripheral blood lysate using magnetic oligo-dT beads. The extraction is achieved through lateral magnetophoresis, generated by a ferromagnetic wire array inlaid on a glass substrate. This RNA microextractor separated more than 80% of magnetic beads with a flow rate up to 20 ml h(-1), and the overall extraction procedure was completed within 1 min. The absorbance ratio of RNA to protein (A(260)/A(280)) was >1.7, indicating that the extraction technology yielded nearly pure RNA. The feasibility of this technique was evaluated further for its applicability to reverse transcription polymerase chain reaction (RT-PCR) procedures by performing cDNA synthesis and PCR. The analysis verified that the RNA microextractor is a practical method for easy, rapid, and high-precision RT-PCR using minimal reagent volumes without requiring highly trained personnel. In addition, it can be readily incorporated into genetic analysis procedures for realizing automated on-chip genetic platforms in a micro format.

Detection of viable but non-culturable legionella in hospital water network following monochloramine disinfection.

PubMed

Casini, B; Baggiani, A; Totaro, M; Mansi, A; Costa, A L; Aquino, F; Miccoli, M; Valentini, P; Bruschi, F; Lopalco, P L; Privitera, G

2018-01-01

Prevention of legionellosis remains a critical issue in healthcare settings where monochloramine (MC) disinfection was recently introduced as an alternative to chlorine dioxide in controlling Legionella spp. contamination of the hospital water network. Continuous treatments with low MC doses in some instances have induced a viable but non-culturable state (VBNC) of Legionella spp. To investigate the occurrence of such dormant cells during a long period of continuous MC treatment. Between November 2010 and April 2015, 162 water and biofilm samples were collected and Legionella spp. isolated in accordance with standard procedures. In sampling sites where MC was <1.5mg/L, VBNC cells were investigated by ethidium monoazide bromide (EMA)-real-time polymerase chain reaction (qPCR) and 'resuscitation' test into Acanthamoeba polyphaga CCAP 1501/18. According to the Health Protection Agency protocol, free-living protozoa were researched in 60 five-litre water samples. In all, 136 out of 156 (87.2%) of the samples taken from sites previously positive for L. pneumophila ST269 were negative by culture, but only 47 (34.5%) negative by qPCR. Although no positive results were obtained by EMA-qPCR, four out of 22 samples associated with MC concentration of 1.3 ± 0.5mg/L showed VBNC legionella resuscitation. The presence of the amoeba A. polyphaga in the hospital water network was demonstrated. Our study is the first report evidencing the emergence of VNBC legionella during a long period of continuous MC treatment of a hospital water network, highlighting the importance of keeping an appropriate and uninterrupted MC dosage to ensure the control of legionella colonization in hospital water supplies. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

[EXPERIENCE OF STUDY AND POSSIBLE WAYS OF ELIMINATION OF FALSE POSITIVE AND FALSE NEGATIVE RESULTS DURING EXECUTION OF POLYMERASE CHAIN REACTION ON AN EXAMPLE OF JUNIN VIRUS RNA DETECTION].

PubMed

Sizikova, T E; Lebedev, V N; Pantyukhov, V B; Borisevich, S V; Merkulov, V A

2015-01-01

Experience of study and possible ways of elimination of false positive and false negative results during execution of polymerase chain reaction on an example of Junin virus RNA detection. MATERIALSS AND METHODS: Junin virus--causative agent of Argentine hemorrhagic fever (AHF) strain XJpR37/5787 was obtained from the State collection of pathogenicity group I causative agents of the 48th Central Research Institute. Reagent kit for detection of Junin virus RNA by RT-PCR was developed in the Institute and consists of 4 sets: for isolation of RNA, execution of reverse-transcription reaction, execution of PCR and electrophoretic detection of PCR products. RT-PCR was carried out by a standard technique. Continuous cell cultures of African green monkey Vero B, GMK-AH-1(D) were obtained from the museum of cell culture department of the Centre. An experimental study of the effect of various factors of impact on the sample under investigation ("thawing-freezing", presence of formaldehyde, heparin) on the obtaining of false negative results during Junin virus RNA detection by using RT-PCR was studied. Addition of 0.01% heparin to the samples was shown to completely inhibit PCR. Addition of 0.05% formaldehyde significantly reduces sensitivity of the method. A possibility of reduction of analysis timeframe from 15 to 5 days was shown during detection of the causative agent in samples with low concentration of the latter by growing the samples and subsequent analysis of the material obtained by using RT-PCR. During detection of causative agent by using RT-PCR false negative results could appear in the presence of formaldehyde and heparin in the sample. A possibility of elimination of false negative PCR results due to concentration of the causative agent in the sample under investigation at a level below sensitivity threshold was shown on the example of Junin virus RNA detection by using growing of the pathogen in appropriate accumulation system with subsequent analysis of the material obtained using PCR.

Restoration of Pulsatile Flow Reduces Sympathetic Nerve Activity Among Individuals With Continuous-Flow Left Ventricular Assist Devices.

PubMed

Cornwell, William K; Tarumi, Takashi; Stickford, Abigail; Lawley, Justin; Roberts, Monique; Parker, Rosemary; Fitzsimmons, Catherine; Kibe, Julius; Ayers, Colby; Markham, David; Drazner, Mark H; Fu, Qi; Levine, Benjamin D

2015-12-15

Current-generation left ventricular assist devices provide circulatory support that is minimally or entirely nonpulsatile and are associated with marked increases in muscle sympathetic nerve activity (MSNA), likely through a baroreceptor-mediated pathway. We sought to determine whether the restoration of pulsatile flow through modulations in pump speed would reduce MSNA through the arterial baroreceptor reflex. Ten men and 3 women (54 ± 14 years) with Heartmate II continuous-flow left ventricular assist devices underwent hemodynamic and sympathetic neural assessment. Beat-to-beat blood pressure, carotid ultrasonography at the level of the arterial baroreceptors, and MSNA via microneurography were continuously recorded to determine steady-state responses to step changes (200-400 revolutions per minute) in continuous-flow left ventricular assist device pump speed from a maximum of 10,480 ± 315 revolutions per minute to a minimum of 8500 ± 380 revolutions per minute. Reductions in pump speed led to increases in pulse pressure (high versus low speed: 17 ± 7 versus 26 ± 12 mm Hg; P<0.01), distension of the carotid artery, and carotid arterial wall tension (P<0.05 for all measures). In addition, MSNA was reduced (high versus low speed: 41 ± 15 versus 33 ± 16 bursts per minute; P<0.01) despite a reduction in mean arterial pressure and was inversely related to pulse pressure (P=0.037). Among subjects with continuous-flow left ventricular assist devices, the restoration of pulsatile flow through modulations in pump speed leads to increased distortion of the arterial baroreceptors with a subsequent decline in MSNA. Additional study is needed to determine whether reduction of MSNA in this setting leads to improved outcomes. © 2015 American Heart Association, Inc.

Microfluidic chemostat and turbidostat with flow rate, oxygen, and temperature control for dynamic continuous culture.

PubMed

Lee, Kevin S; Boccazzi, Paolo; Sinskey, Anthony J; Ram, Rajeev J

2011-05-21

This work reports on an instrument capable of supporting automated microscale continuous culture experiments. The instrument consists of a plastic-PDMS device capable of continuous flow without volume drift or evaporation. We apply direct computer controlled machining and chemical bonding fabrication for production of fluidic devices with a 1 mL working volume, high oxygen transfer rate (k(L)a≈0.025 s(-1)), fast mixing (2 s), accurate flow control (±18 nL), and closed loop control over temperature, cell density, dissolved oxygen, and pH. Integrated peristaltic pumps and valves provide control over input concentrations and allow the system to perform different types of cell culture on a single device, such as batch, chemostat, and turbidostat continuous cultures. Continuous cultures are demonstrated without contamination for 3 weeks in a single device and both steady state and dynamically controlled conditions are possible. © The Royal Society of Chemistry 2011

Smart catheter flow sensor for real-time continuous regional cerebral blood flow monitoring

NASA Astrophysics Data System (ADS)

Li, Chunyan; Wu, Pei-Ming; Hartings, Jed A.; Wu, Zhizhen; Ahn, Chong H.; LeDoux, David; Shutter, Lori A.; Narayan, Raj K.

2011-12-01

We present a smart catheter flow sensor for real-time, continuous, and quantitative measurement of regional cerebral blood flow using in situ temperature and thermal conductivity compensation. The flow sensor operates in a constant-temperature mode and employs a periodic heating and cooling technique. This approach ensures zero drift and provides highly reliable data with microelectromechanical system-based thin film sensors. The developed flow sensor has a sensitivity of 0.973 mV/ml/100 g/min in the range from 0 to 160 ml/100 g/min with a linear correlation coefficient of R2 = 0.9953. It achieves a resolution of 0.25 ml/100 g/min and an accuracy better than 5 ml/100 g/min.

Continuous flow hydrogenation of nitroarenes, azides and alkenes using maghemite-Pd nanocomposites

EPA Science Inventory

Maghemite-supported ultra-fine Pd (1-2 nm) nanoparticles, prepared by a simple co-precipitation method, find application in the catalytic continuous flow hydrogenation of nitroarenes, azides, and alkenes wherein they play an important role in reduction of various functional group...

Best Practices for Continuous Monitoring of Temperature and Flow in Wadeable Streams (Final Report)

EPA Science Inventory

This final report is a technical "best practices" document describing sensor deployment for and collection of continuous temperature and flow data at ungaged sites in wadeable streams. This document addresses questions related to equipment needs; configuration, placement, and ins...

[Quick Start-up and Sustaining of Shortcut Nitrification in Continuous Flow Reactor].

PubMed

Wu, Peng; Zhang Shi-ying; Song, Yin-ling; Xu, Yue-zhong; Shen, Yao-liang

2016-04-15

How to achieve fast and stable startup of shortcut nitrification has a very important practical value for treatment of low C/N ratio wastewater. Thus, the quick start-up and sustaining of shortcut nitrification were investigated in continuous flow reactor targeting at the current situation of urban wastewater treatment plant using a continuous flow process. The results showed that quick start-up of shortcut nitrification could be successfully achieved in a continuous flow reactor after 60 days' operation with intermittent aeration and controlling of three stages of stop/aeration time (15 min/45 min, 45 min/45 min and 30 min/30 min). The nitrification rates could reach 90% or 95% respectively, while influent ammonia concentrations were 50 or 100 mg · L⁻¹ with stop/aeration time of 30 min/30 min. In addition, intermittent aeration could inhibit the activity of nitrite oxidizing bacteria (NOB), while short hydraulic retention time (HRT) may wash out NOB. And a combined use of both measures was beneficial to sustain shortcut nitrification.

Continuous-flow separation of nanoparticles by electrostatic sieving at a micro-nanofluidic interface.

PubMed

Regtmeier, Jan; Käsewieter, Jörg; Everwand, Martina; Anselmetti, Dario

2011-05-01

Continuous-flow separation of nanoparticles (NPs) (15 and 39 nm) is demonstrated based on electrostatic sieving at a micro-nanofluidic interface. The interface is realized in a poly(dimethylsiloxane) device with a nanoslit of 525 nm laterally spanning the microfluidic channel (aspect ratio of 540:1). Within this nanoslit, the Debye layers overlap and generate an electrostatic sieve. This was exploited to selectively deflect and sort NPs with a sorting purity of up to 97%. Because of the continuous-flow operation, the sample is continuously fed into the device, immediately separated, and the parameters can be adapted in real time. For bioanalytical purposes, we also demonstrate the deflection of proteins (longest axis 6.8 nm). The continuous operation mode and the general applicability of this separation concept make this method a valuable addition to the current Lab-on-a-Chip devices for continuous sorting of NPs and macromolecules. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design and construction of a vertical hydroponic system with semi-continuous and continuous nutrient cycling

NASA Astrophysics Data System (ADS)

Siswanto, Dian; Widoretno, Wahyu

2017-11-01

Problems due to the increase in agricultural land use change can be solved by hydroponic system applications. Many hydroponic studies have been conducted in several countries while their applications in Indonesia requires modification and adjustment. This research was conducted to design and construct a hydroponic system with semi-continuous and continuous nutrition systems. The hydroponic system which was used adapts the ebb and flow system, and the nutrient film technique (NFT). This hydroponic system was made from polyvinyl chloride (PVC) pipes with a length of 197 cm, a diameter of 16 cm, and a slope of 4°. It was constructed from four PVC pipes. In semi-continuous irrigation treatment, nutrients flow four to six times for each of ten minutes depending on plant development and the estimated evapotranspiration occurring, while in a continuous nutrient system the nutrients are streamed for twenty-four hours without stopping at a maximum flow rate of 13.7 L per second.

[Effects of continuous cropping of vegetables on ammonia oxidizers community structure].

PubMed

Meng, De-Long; Yang, Yang; Wu, Yan-Zheng; Wu, Min-Na; Qin, Hong-Ling; Zhu, Yi-Jun; Wei, Wen-Xue

2012-04-01

Investigations were conducted on the effects of intensive application of chemical fertilizers in crop production on soil nitrifier communities and the relationship between nitrifier communities and soil nitrification ability. Two series of vegetable soils were selected from Huangxing, Changsha, reflecting continuous vegetable cropping with about 20 years and new vegetable field with only about 2 years vegetable growing history. In each series five independent topsoils (0-20 cm) were sampled and each soil was a mixture of 10 cores randomly taken in the same field. Terminal restriction fragment length polymorphism (T-RFLP) and quantity PCR (Q-PCR) were used to determine the composition and abundance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities. Results indicated that long-term and continuous vegetable cropping obviously changed the compositions of both AOB and AOA amoA gene, soil pH and Olsen-P content were the dominant factors affecting the composition of AOB amoA. In the vegetable soils, although the copy number of AOA amoA gene was about 5 times higher than AOB amoA gene, no significant correlation was detected between AOA amoA gene abundance and soil nitrification rate. It was not sure whether long-term and continuous vegetable cropping could shift the abundance of AOB and AOA, but it resulted in the enrichment of some dominant AOB species and increase of soil nitrification potential (PNF).

Malaria prevalence in asymptomatic and symptomatic children in Kiwangwa, Bagamoyo district, Tanzania.

PubMed

Sumari, Deborah; Mwingira, Felista; Selemani, Majige; Mugasa, Joseph; Mugittu, Kefas; Gwakisa, Paul

2017-05-25

Malaria prevalence continues to decline across sub-Saharan Africa as a result of various intervention strategies. However, the diseases still poses a public health concern in the region. While symptomatic malaria is recognized and treated, asymptomatic infections become increasingly important for interrupting transmission. A cross-sectional survey was conducted to assess malaria prevalence in symptomatic and asymptomatic children in Kiwangwa ward in Bagamoyo District in Tanzania. Four hundred school-aged children in Kiwanga ward were recruited in the study; 200 from Kiwangwa dispensary and 200 from nearby schools. Primary health parameters were examined and blood samples collected and examined for Plasmodium falciparum prevalence using rapid diagnostic test (RDT), light microscopy (LM) and reverse transcription quantitative PCR (RT-qPCR) targeting transcripts of A-type 18s rRNA of P. falciparum. Gametocytes were detected by LM and RT-qPCR targeting transcripts of gametocyte specific marker, Pfs25. Overall P. falciparum prevalence was 73.3, 40.8 and 36.3% by RT-qPCR, RDT and LM in the study area, respectively (P < 0.001). As expected symptomatic children had a significantly higher prevalence of 89, 67.5 and 64.5% by qPCR, RDT and LM, compared to 57.5, 14 and 8% in the asymptomatic group, respectively. However, gametocyte prevalence in asymptomatic individuals was higher by both LM (2%) and qPCR (14%) than in symptomatic individuals LM (0.5%) and qPCR (3%). A substantial difference in prevalence of symptomatic and asymptomatic infections observed in Kiwangwa ward underpins the use of molecular tools in malaria surveillance aiming at estimating prevalence and transmission. Notably, the higher gametocytaemia observed in asymptomatic children indicates the reservoir infections and points to the need for detection and treatment of both asymptomatic and symptomatic malaria.

Isolation of genes negatively or positively co-expressed with human recombination activating gene 1 (RAG1) by differential display PCR (DD RT-PCR).

PubMed

Verkoczy, L K; Berinstein, N L

1998-10-01

Differential display PCR (DD RT-PCR) has been extensively used for analysis of differential gene expression, but continues to be hampered by technical limitations that impair its effectiveness. In order to isolate novel genes co-expressing with human RAG1, we have developed an effective, multi-tiered screening/purification approach which effectively complements the standard DD RT-PCR methodology. In 'primary' screens, standard DD RT-PCR was used, detecting 22 reproducible differentially expressed amplicons between clonally related cell variants with differential constitutive expression of RAG mRNAs. 'Secondary' screens used differential display (DD) amplicons as probes in low and high stringency northern blotting. Eight of 22 independent DD amplicons detected nine independent differentially expressed transcripts. 'Tertiary' screens used reconfirmed amplicons as probes in northern analysis of multiple RAG-and RAG+sources. Reconfirmed DD amplicons detected six independent RAG co-expressing transcripts. All DD amplicons reconfirmed by northern blot were a heterogeneous mixture of cDNAs, necessitating further purification to isolate single cDNAs prior to subcloning and sequencing. To effectively select the appropriate cDNAs from DD amplicons, we excised and eluted the cDNA(s) directly from regions of prior northern blots in which differentially expressed transcripts were detected. Sequences of six purified cDNA clones specifically detecting RAG co-expressing transcripts included matches to portions of the human RAG2 and BSAP regions and to four novel partial cDNAs (three with homologies to human ESTs). Overall, our results also suggest that even when using clonally related variants from the same cell line in addition to all appropriate internal controls previously reported, further screening and purification steps are still required in order to efficiently and specifically isolate differentially expressed genes by DD RT-PCR.

Pressurized tundish for controlling a continuous flow of molten metal

DOEpatents

Lewis, Thomas W.; Hamill, Jr., Paul E.; Ozgu, Mustafa R.; Padfield, Ralph C.; Rego, Donovan N.; Brita, Guido P.

1990-01-01

A pressurized tundish for controlling a continous flow of molten metal characterized by having a pair of principal compartments, one being essentially unpressurized and receiving molten metal introduced thereto, and the other being adapted for maintaining a controlled gaseous pressure over the surface of the fluid metal therein, whereby, by controlling the pressure within the pressurized chamber, metal exiting from the tundish is made to flow continually and at a controlled rate.

An Experimental Study of Continuous Plasma Flows Driven by a Confined Arc in a Transverse Magnetic Field

NASA Technical Reports Server (NTRS)

Barger, R. L.; Brooks, J. D.; Beasley, W. D.

1961-01-01

A crossed-field, continuous-flow plasma accelerator has been built and operated. The highest measured velocity of the flow, which was driven by the interaction of the electric and magnetic fields, was about 500 meters per second. Some of the problems discussed are ion slip, stability and uniformity of the discharge, effect of the magnetic field on electron emission, use of preionization, and electrode contamination.

Estimation of the bacteriocin ColE7 conjugation-based "kill" - "anti-kill" antimicrobial system by real-time PCR, fluorescence staining and bioluminescence assays.

PubMed

Maslennikova, I L; Kuznetsova, M V; Toplak, N; Nekrasova, I V; Žgur Bertok, D; Starčič Erjavec, M

2018-05-07

The efficiency of the bacteriocin, colicin ColE7, bacterial conjugation-based "kill" - "anti-kill" antimicrobial system, was assessed using real-time PCR, flow cytometry and bioluminescence. The ColE7 antimicrobial system consists of the genetically modified Escherichia coli strain Nissle 1917 harbouring a conjugative plasmid (derivative of the F-plasmid) encoding the "kill" gene (ColE7 activity gene) and a chromosomally encoded "anti-kill" gene (ColE7 immunity gene). On the basis of traJ gene expression in the killer donor cells, our results showed that the efficiency of the here studied antimicrobial system against target E. coli was higher at 4 than at 24 h. Flow cytometry was used to indirectly estimate DNase activity of the antimicrobial system, as lysis of target E. coli cells in the conjugative mixture with the killer donor strain led to reduction in cell cytosol fluorescence. According to a lux assay, E. coli TG1 (pXen lux + Ap r ) with constitutive luminescence were killed already after 2 h of treatment. Target sensor E. coli C600 with DNA damage SOS-inducible luminescence showed significantly lower SOS induction 6 and 24 h following treatment with the killer donor strain. Our results thus showed that bioluminescent techniques are quick and suitable for estimation of the ColE7 bacterial conjugation-based antimicrobial system antibacterial activity. Bacterial antimicrobial resistance is worldwide rising and causing deaths of thousands of patients infected with multi-drug resistant bacterial strains. In addition, there is a lack of efficient alternative antimicrobial agents. The significance of our research is the use of a number of methods (real-time PCR, flow cytometry and bioluminescence-based technique) to assess the antibacterial activity of the bacteriocin, colicin ColE7, bacterial conjugation-based "kill" - "anti-kill" antimicrobial system. Bioluminescent techniques proved to be rapid and suitable for estimation of antibacterial activity of ColE7 bacterial conjugation-based antimicrobial system and possibly other related systems. © 2018 The Society for Applied Microbiology.

Diels–Alder reactions of myrcene using intensified continuous-flow reactors

PubMed Central

Álvarez-Diéguez, Miguel Á; Kohl, Thomas M; Tsanaktsidis, John

2017-01-01

This work describes the Diels–Alder reaction of the naturally occurring substituted butadiene, myrcene, with a range of different naturally occurring and synthetic dienophiles. The synthesis of the Diels–Alder adduct from myrcene and acrylic acid, containing surfactant properties, was scaled-up in a plate-type continuous-flow reactor with a volume of 105 mL to a throughput of 2.79 kg of the final product per day. This continuous-flow approach provides a facile alternative scale-up route to conventional batch processing, and it helps to intensify the synthesis protocol by applying higher reaction temperatures and shorter reaction times. PMID:28228853

Differentiation of isolated human umbilical cord mesenchymal stem cells into neural stem cells

PubMed Central

Chen, Song; Zhang, Wei; Wang, Ji-Ming; Duan, Hong-Tao; Kong, Jia-Hui; Wang, Yue-Xin; Dong, Meng; Bi, Xue; Song, Jian

2016-01-01

AIM To investigate whether umbilical cord human mesenchymal stem cell (UC-MSC) was able to differentiate into neural stem cell and neuron in vitro. METHODS The umbilical cords were obtained from pregnant women with their written consent and the approval of the Clinic Ethnics Committee. UC-MSC were isolated by adherent culture in the medium contains 20% fetal bovine serum (FBS), then they were maintained in the medium contain 10% FBS and induced to neural cells in neural differentiation medium. We investigated whether UC-MSC was able to differentiate into neural stem cell and neuron in vitro by using flow cytometry, reverse transcriptase-polymerase chain reaction (RT-PCR) and immunofluorescence (IF) analyzes. RESULTS A substantial number of UC-MSC was harvested using the tissue explants adherent method at about 2wk. Flow cytometric study revealed that these cells expressed common markers of MSCs, such as CD105 (SH2), CD73 (SH3) and CD90. After induction of differentiation of neural stem cells, the cells began to form clusters; RT-PCR and IF showed that the neuron specific enolase (NSE) and neurogenic differentiation 1-positive cells reached 87.3%±14.7% and 72.6%±11.8%, respectively. Cells showed neuronal cell differentiation after induced, including neuron-like protrusions, plump cell body, obviously and stronger refraction. RT-PCR and IF analysis showed that microtubule-associated protein 2 (MAP2) and nuclear factor-M-positive cells reached 43.1%±10.3% and 69.4%±19.5%, respectively. CONCLUSION Human umbilical cord derived MSCs can be cultured and proliferated in vitro and differentiate into neural stem cells, which may be a valuable source for cell therapy of neurodegenerative eye diseases. PMID:26949608

Development of Tat-Conjugated Dendrimer for Transdermal DNA Vaccine Delivery.

PubMed

Bahadoran, Azadeh; Moeini, Hassan; Bejo, Mohd Hair; Hussein, Mohd Zobir; Omar, Abdul Rahman

In order to enhance cellular uptake and to facilitate transdermal delivery of DNA vaccine, polyamidoamine (PAMAM) dendrimers conjugated with HIV transactivator of transcription (TAT) was developed. First, the plasmid DNA (pIRES-H5/GFP) nanoparticle was formulated using PAMAM dendrimer and TAT peptide and then characterized for surface charge, particle size, DNA encapsulation and protection of the pIRES-H5/GFP DNA plasmid to enzymatic digestion. Subsequently, the potency of the TAT-conjugated dendrimer for gene delivery was evaluated through in vitro transfection into Vero cells followed by gene expression analysis including western blotting, fluorescent microscopy and PCR. The effect of the TAT peptide on cellular uptake of DNA vaccine was studied by qRT-PCR and flow cytometry. Finally, the ability of TAT-conjugated PAMAM dendrimer for transdermal delivery of the DNA plasmid was assessed through artificial membranes followed by qRT-PCR and flow cytometry. TAT-conjugated PAMAM dendrimer showed the ability to form a compact and nanometre-sized polyplexes with the plasmid DNA, having the size range of 105 to 115 nm and a positive charge of +42 to +45 mV over the N/P ratio of 6:1(+/-).  In vitro transfection analysis into Vero cells confirms the high potency of TAT-conjugated PAMAM dendrimer to enhance the cellular uptake of DNA vaccine.  The permeability value assay through artificial membranes reveals that TAT-conjugated PAMAM has more capacity for transdermal delivery of the DNA compared to unmodified PAMAM dendrimer (P<0.05). The findings of this study suggest that TAT-conjugated PAMAM dendrimer is a promising non-viral vector for transdermal use.This article is open to POST-PUBLICATION REVIEW. Registered readers (see "For Readers") may comment by clicking on ABSTRACT on the issue's contents page.

A biosensor assay for the detection of Mycobacterium avium subsp. paratuberculosis in fecal samples

PubMed Central

Kumanan, Vijayarani; Nugen, Sam R.; Baeumner, Antje J.

2009-01-01

A simple, membrane-strip-based lateral-flow (LF) biosensor assay and a high-throughput microtiter plate assay have been combined with a reverse transcriptase polymerase chain reaction (RT-PCR) for the detection of a small number (ten) of viable Mycobacterium (M.) avium subsp. paratuberculosis (MAP) cells in fecal samples. The assays are based on the identification of the RNA of the IS900 element of MAP. For the assay, RNA was extracted from fecal samples spiked with a known quantity of (101 to 106) MAP cells and amplified using RT-PCR and identified by the LF biosensor and the microtiter plate assay. While the LF biosensor assay requires only 30 min of assay time, the overall process took 10 h for the detection of 10 viable cells. The assays are based on an oligonucleotide sandwich hybridization assay format and use either a membrane flow through system with an immobilized DNA probe that hybridizes with the target sequence or a microtiter plate well. Signal amplification is provided when the target sequence hybridizes to a second DNA probe that has been coupled to liposomes encapsulating the dye, sulforhodamine B. The dye in the liposomes provides a signal that can be read visually, quantified with a hand-held reflectometer, or with a fluorescence reader. Specificity analysis of the assays revealed no cross reactivity with other mycobacteria, such as M. avium complex, M. ulcerans, M. marium, M. kansasii, M. abscessus, M. asiaticum, M. phlei, M. fortuitum, M. scrofulaceum, M. intracellulare, M. smegmatis, and M. bovis. The overall assay for the detection of live MAP organisms is comparatively less expensive and quick, especially in comparison to standard MAP detection using a culture method requiring 6-8 weeks of incubation time, and is significantly less expensive than real-time PCR. PMID:19255522

An integrated, self-contained microfluidic cassette for isolation, amplification, and detection of nucleic acids

PubMed Central

Chen, Dafeng; Mauk, Michael; Qiu, Xianbo; Liu, Changchun; Kim, Jitae; Ramprasad, Sudhir; Ongagna, Serge; Abrams, William R.; Malamud, Daniel; Corstjens, Paul L. A. M.

2010-01-01

A self-contained, integrated, disposable, sample-to-answer, polycarbonate microfluidic cassette for nucleic acid—based detection of pathogens at the point of care was designed, constructed, and tested. The cassette comprises on-chip sample lysis, nucleic acid isolation, enzymatic amplification (polymerase chain reaction and, when needed, reverse transcription), amplicon labeling, and detection. On-chip pouches and valves facilitate fluid flow control. All the liquids and dry reagents needed for the various reactions are pre-stored in the cassette. The liquid reagents are stored in flexible pouches formed on the chip surface. Dry (RT-)PCR reagents are pre-stored in the thermal cycling, reaction chamber. The process operations include sample introduction; lysis of cells and viruses; solid-phase extraction, concentration, and purification of nucleic acids from the lysate; elution of the nucleic acids into a thermal cycling chamber and mixing with pre-stored (RT-)PCR dry reagents; thermal cycling; and detection. The PCR amplicons are labeled with digoxigenin and biotin and transmitted onto a lateral flow strip, where the target analytes bind to a test line consisting of immobilized avidin-D. The immobilized nucleic acids are labeled with up-converting phosphor (UCP) reporter particles. The operation of the cassette is automatically controlled by an analyzer that provides pouch and valve actuation with electrical motors and heating for the thermal cycling. The functionality of the device is demonstrated by detecting the presence of bacterial B.Cereus, viral armored RNA HIV, and HIV I virus in saliva samples. The cassette and actuator described here can be used to detect other diseases as well as the presence of bacterial and viral pathogens in the water supply and other fluids. PMID:20401537

An integrated, self-contained microfluidic cassette for isolation, amplification, and detection of nucleic acids.

PubMed

Chen, Dafeng; Mauk, Michael; Qiu, Xianbo; Liu, Changchun; Kim, Jitae; Ramprasad, Sudhir; Ongagna, Serge; Abrams, William R; Malamud, Daniel; Corstjens, Paul L A M; Bau, Haim H

2010-08-01

A self-contained, integrated, disposable, sample-to-answer, polycarbonate microfluidic cassette for nucleic acid-based detection of pathogens at the point of care was designed, constructed, and tested. The cassette comprises on-chip sample lysis, nucleic acid isolation, enzymatic amplification (polymerase chain reaction and, when needed, reverse transcription), amplicon labeling, and detection. On-chip pouches and valves facilitate fluid flow control. All the liquids and dry reagents needed for the various reactions are pre-stored in the cassette. The liquid reagents are stored in flexible pouches formed on the chip surface. Dry (RT-)PCR reagents are pre-stored in the thermal cycling, reaction chamber. The process operations include sample introduction; lysis of cells and viruses; solid-phase extraction, concentration, and purification of nucleic acids from the lysate; elution of the nucleic acids into a thermal cycling chamber and mixing with pre-stored (RT-)PCR dry reagents; thermal cycling; and detection. The PCR amplicons are labeled with digoxigenin and biotin and transmitted onto a lateral flow strip, where the target analytes bind to a test line consisting of immobilized avidin-D. The immobilized nucleic acids are labeled with up-converting phosphor (UCP) reporter particles. The operation of the cassette is automatically controlled by an analyzer that provides pouch and valve actuation with electrical motors and heating for the thermal cycling. The functionality of the device is demonstrated by detecting the presence of bacterial B.Cereus, viral armored RNA HIV, and HIV I virus in saliva samples. The cassette and actuator described here can be used to detect other diseases as well as the presence of bacterial and viral pathogens in the water supply and other fluids.

Tangential flow ultrafiltration for detection of white spot syndrome virus (WSSV) in shrimp pond water.

PubMed

Alavandi, S V; Ananda Bharathi, R; Satheesh Kumar, S; Dineshkumar, N; Saravanakumar, C; Joseph Sahaya Rajan, J

2015-06-15

Water represents the most important component in the white spot syndrome virus (WSSV) transmission pathway in aquaculture, yet there is very little information. Detection of viruses in water is a challenge, since their counts will often be too low to be detected by available methods such as polymerase chain reaction (PCR). In order to overcome this difficulty, viruses in water have to be concentrated from large volumes of water prior to detection. In this study, a total of 19 water samples from aquaculture ecosystem comprising 3 creeks, 10 shrimp culture ponds, 3 shrimp broodstock tanks and 2 larval rearing tanks of shrimp hatcheries and a sample from a hatchery effluent treatment tank were subjected to concentration of viruses by ultrafiltration (UF) using tangential flow filtration (TFF). Twenty to 100l of water from these sources was concentrated to a final volume of 100mL (200-1000 fold). The efficiency of recovery of WSSV by TFF ranged from 7.5 to 89.61%. WSSV could be successfully detected by PCR in the viral concentrates obtained from water samples of three shrimp culture ponds, one each of the shrimp broodstock tank, larval rearing tank, and the shrimp hatchery effluent treatment tank with WSSV copy numbers ranging from 6 to 157mL(-1) by quantitative real time PCR. The ultrafiltration virus concentration technique enables efficient detection of shrimp viral pathogens in water from aquaculture facilities. It could be used as an important tool to understand the efficacy of biosecurity protocols adopted in the aquaculture facility and to carry out epidemiological investigations of aquatic viral pathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

Immune modulation of CD4+CD25+ regulatory T cells by zoledronic acid.

PubMed

Liu, Hsien; Wang, Shih-Han; Chen, Shin-Cheh; Chen, Ching-Ying; Lo, Jo-Lin; Lin, Tsun-Mei

2016-11-25

CD4 + CD25 + regulatory T (Treg) cells suppress tumor immunity by inhibiting immune cells. Manipulation of Treg cells represents a new strategy for cancer treatment. Zoledronic acid (ZA), a nitrogen-containing bisphosphonate, inhibits the expression of receptor activator of nuclear factor kappa-B ligand (RANKL) on osteoblasts to inhibit osteoclastogenesis. In a mouse model of bisphosphonate-related osteonecrosis of the jaw, administration of ZA suppressed Treg-cell activity and activated inflammatory Th17 cells. However, the interaction between ZA and Treg cells remained unclear. This study investigated the immune modulation of Treg cells by ZA. Flow cytometry was used to analyze the phenotypic and immunosuppressive characteristics of Treg cells treated with ZA. Chemotactic migration was evaluated using transwell assays. Quantitative real-time PCR (qRT-PCR) was used to investigate the effect of ZA on the expression of suppressive molecules by Treg cells. Proliferation of isolated Treg cells in culture was inhibited by ZA, although ZA did not induce apoptosis. qRT-PCR and flow cytometry showed that ZA significantly downregulated the expression of CCR4, CTLA4, PD-1 and RANKL on Treg cells. Chemotactic migration and immunosuppressive functions were also significantly attenuated in Treg cells pretreated with ZA, and these effects were dose-dependent. Co-culture with Treg cells significantly increased the migration rate of breast cancer cells, while pretreatment of Treg cells with ZA attenuated this effect. Our findings demonstrated that ZA acted as an immune modulator by significantly inhibiting the expansion, migration, immunosuppressive function and pro-metastatic ability of Treg cells. Immunomodulation of Treg cells by ZA represents a new strategy for cancer therapy.

Specific capture and detection of Staphylococcus aureus with high-affinity modified aptamers to cell surface components

PubMed Central

Baumstummler, A; Lehmann, D; Janjic, N; Ochsner, UA

2014-01-01

Slow off-rate modified aptamer (SOMAmer) reagents were generated to several Staphylococcus aureus cell surface-associated proteins via SELEX with multiple modified DNA libraries using purified recombinant or native proteins. High-affinity binding agents with sub-nanomolar Kd's were obtained for staphylococcal protein A (SpA), clumping factors (ClfA, ClfB), fibronectin-binding proteins (FnbA, FnbB) and iron-regulated surface determinants (Isd). Further screening revealed several SOMAmers that specifically bound to Staph. aureus cells from all strains that were tested, but not to other staphylococci or other bacteria. SpA and ClfA SOMAmers proved useful for the selective capture and enrichment of Staph. aureus cells, as shown by culture and PCR, leading to improved limits of detection and efficient removal of PCR inhibitors. Detection of Staph. aureus cells was enhanced by several orders of magnitude when the bacterial cell surface was coated with SOMAmers followed by qPCR of the SOMAmers. Furthermore, fluorescence-labelled SpA SOMAmers demonstrated their utility as direct detection agents in flow cytometry. Significance and Impact of the Study Monitoring for microbial contamination of food, water, nonsterile products or the environment is typically based on culture, PCR or antibodies. Aptamers that bind with high specificity and affinity to well-conserved cell surface epitopes represent a promising novel type of reagents to detect bacterial cells without the need for culture or cell lysis, including for the capture and enrichment of bacteria present at low cell densities and for the direct detection via qPCR or fluorescent staining. PMID:24935714

Best Practices for Continuous Monitoring of Temperature and Flow in Wadeable Streams (External Review Draft)

EPA Science Inventory

This external review draft report is a technical "best practices" document describing sensor deployment for and data collection of continuous temperature and flow at ungaged sites in wadeable streams. This document addresses questions related to equipment needs; configuration, pl...

Circulation system for flowing uranium hexafluoride cavity reactor experiments

NASA Technical Reports Server (NTRS)

Jaminet, J. F.; Kendall, J. S.

1976-01-01

Research related to determining the feasibility of producing continuous power from fissile fuel in the gaseous state is presented. The development of three laboratory-scale flow systems for handling gaseous UF6 at temperatures up to 500 K, pressure up to approximately 40 atm, and continuous flow rates up to approximately 50g/s is presented. A UF6 handling system fabricated for static critical tests currently being conducted is described. The system was designed to supply UF6 to a double-walled aluminum core canister assembly at temperatures between 300 K and 400 K and pressure up to 4 atm. A second UF6 handling system designed to provide a circulating flow of up to 50g/s of gaseous UF6 in a closed-loop through a double-walled aluminum core canister with controlled temperature and pressure is described. Data from flow tests using UF6 and UF6/He mixtures with this system at flow rates up to approximately 12g/s and pressure up to 4 atm are presented. A third UF6 handling system fabricated to provide a continuous flow of UF6 at flow rates up to 5g/s and at pressures up to 40 atm for use in rf-heated, uranium plasma confinement experiments is described.

Inverse effects of Polyacrylamide (PAM) usage in furrow irrigation on advance time and deep percolation.

PubMed

Meral, Ramazan; Cemek, Bilal; Apan, Mehmet; Merdun, Hasan

2006-10-01

The positive effects of Polyacrylamide (PAM), which is used as a soil conditioner in furrow irrigation, on sediment transport, erosion, and infiltration have been investigated intensively in recent years. However, the effects of PAM have not been considered enough in irrigation system planning and design. As a result of increased infiltration because of PAM, advance time may be inversely affected and deep percolation increases. However, advance time in furrow irrigation is a crucial parameter in order to get high application efficiency. In this study, inverse effects of PAM were discussed, and as an alternative solution, the applicability of surge flow was investigated. PAM application significantly increased the advance time at the rates of 41.3-56.3% in the first irrigation. The application of surge flow with PAM removed this negative effect on advance time, where there was no statistically significant difference according to normal continuous flow (without PAM). PAM applications significantly increased the deep percolation, 80.3-117.1%. Surge flow with PAM had significantly positive effect on the deep percolation compared to continuous flow with PAM but not compared to normal continuous flow. These results suggested that irrigation planning should me made based on the new soil and flow conditions because of PAM usage, and surge flow can be a solution to these problems.

Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study

PubMed Central

Frank, Yulia A.; Kadnikov, Vitaly V.; Gavrilov, Sergey N.; Banks, David; Gerasimchuk, Anna L.; Podosokorskaya, Olga A.; Merkel, Alexander Y.; Chernyh, Nikolai A.; Mardanov, Andrey V.; Ravin, Nikolai V.; Karnachuk, Olga V.; Bonch-Osmolovskaya, Elizaveta A.

2016-01-01

The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50°C. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within 5 years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were Desulfovirgula thermocuniculi and Methanothermobacter spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured Firmicutes. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured Firmicutes, Chloroflexi, and Ignavibacteriae. A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained Hydrogenophilus thermoluteolus, which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO2, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles. PMID:28082967

Three-dimensional printed magnetophoretic system for the continuous flow separation of avian influenza H5N1 viruses.

PubMed

Wang, Yuhe; Li, Yanbin; Wang, Ronghui; Wang, Maohua; Lin, Jianhan

2017-04-01

As a result of the low concentration of avian influenza viruses in samples for routine screening, the separation and concentration of these viruses are vital for their sensitive detection. We present a novel three-dimensional printed magnetophoretic system for the continuous flow separation of the viruses using aptamer-modified magnetic nanoparticles, a magnetophoretic chip, a magnetic field, and a fluidic controller. The magnetic field was designed based on finite element magnetic simulation and developed using neodymium magnets with a maximum intensity of 0.65 T and a gradient of 32 T/m for dragging the nanoparticle-virus complexes. The magnetophoretic chip was designed by SOLIDWORKS and fabricated by a three-dimensional printer with a magnetophoretic channel for the continuous flow separation of the viruses using phosphate-buffered saline as carrier flow. The fluidic controller was developed using a microcontroller and peristaltic pumps to inject the carrier flow and the viruses. The trajectory of the virus-nanoparticle complexes was simulated using COMSOL for optimization of the carrier flow and the magnetic field, respectively. The results showed that the H5N1 viruses could be captured, separated, and concentrated using the proposed magnetophoretic system with the separation efficiency up to 88% in a continuous flow separation time of 2 min for a sample volume of 200 μL. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

STS-98 U.S. Lab Destiny is moved out of Atlantis' payload bay

NASA Technical Reports Server (NTRS)

2001-01-01

KENNEDY SPACE CENTER, Fla. -- Workers in the Payload Changeout Room check the U.S. Lab Destiny as its moves from Atlantis''' payload bay into the PCR. Destiny will remain in the PCR while Atlantis rolls back to the Vehicle Assembly Building to allow workers to conduct inspections, continuity checks and X-ray analysis on the 36 solid rocket booster cables located inside each booster'''s system tunnel. An extensive evaluation of NASA'''s SRB cable inventory revealed conductor damage in four (of about 200) cables on the shelf. Shuttle managers decided to prove the integrity of the system tunnel cables already on Atlantis.

Solar oxidation and removal of arsenic--Key parameters for continuous flow applications.

PubMed

Gill, L W; O'Farrell, C

2015-12-01

Solar oxidation to remove arsenic from water has previously been investigated as a batch process. This research has investigated the kinetic parameters for the design of a continuous flow solar reactor to remove arsenic from contaminated groundwater supplies. Continuous flow recirculated batch experiments were carried out under artificial UV light to investigate the effect of different parameters on arsenic removal efficiency. Inlet water arsenic concentrations of up to 1000 μg/L were reduced to below 10 μg/L requiring 12 mg/L iron after receiving 12 kJUV/L radiation. Citrate however was somewhat surprisingly found to promote a detrimental effect on the removal process in the continuous flow reactor studies which is contrary to results found in batch scale tests. The impact of other typical water groundwater quality parameters (phosphate and silica) on the process due to their competition with arsenic for photooxidation products revealed a much higher sensitivity to phosphate ions compared to silicate. Other results showed no benefit from the addition of TiO2 photocatalyst but enhanced arsenic removal at higher temperatures up to 40 °C. Overall, these results have indicated the kinetic envelope from which a continuous flow SORAS single pass system could be more confidently designed for a full-scale community groundwater application at a village level. Copyright © 2015 Elsevier Ltd. All rights reserved.

Feasibility of utilizing bioindicators for testing microbial inactivation in sweetpotato purees processed with a continuous-flow microwave system.

PubMed

Brinley, T A; Dock, C N; Truong, V-D; Coronel, P; Kumar, P; Simunovic, J; Sandeep, K P; Cartwright, G D; Swartzel, K R; Jaykus, L-A

2007-06-01

Continuous-flow microwave heating has potential in aseptic processing of various food products, including purees from sweetpotatoes and other vegetables. Establishing the feasibility of a new processing technology for achieving commercial sterility requires evaluating microbial inactivation. This study aimed to assess the feasibility of using commercially available plastic pouches of bioindicators containing spores of Geobacillius stearothermophilus ATCC 7953 and Bacillus subtilis ATCC 35021 for evaluating the degree of microbial inactivation achieved in vegetable purees processed in a continuous-flow microwave heating unit. Sweetpotato puree seeded with the bioindicators was subjected to 3 levels of processing based on the fastest particles: undertarget process (F(0) approximately 0.65), target process (F(0) approximately 2.8), and overtarget process (F(0) approximately 10.10). After initial experiments, we found it was necessary to engineer a setup with 2 removable tubes connected to the continuous-flow microwave system to facilitate the injection of indicators into the unit without interrupting the puree flow. Using this approach, 60% of the indicators injected into the system could be recovered postprocess. Spore survival after processing, as evaluated by use of growth indicator dyes and standard plating methods, verified inactivation of the spores in sweetpotato puree. The log reduction results for B. subtilis were equivalent to the predesigned degrees of sterilization (F(0)). This study presents the first report suggesting that bioindicators such as the flexible, food-grade plastic pouches can be used for microbial validation of commercial sterilization in aseptic processing of foods using a continuous-flow microwave system.

Transesophageal color Doppler evaluation of obstructive lesions using the new "Quasar" technology.

PubMed

Fan, P; Nanda, N C; Gatewood, R P; Cape, E G; Yoganathan, A P

1995-01-01

Due to the unavoidable problem of aliasing, color flow signals from high blood flow velocities cannot be measured directly by conventional color Doppler. A new technology termed Quantitative Un-Aliased Speed Algorithm Recognition (Quasar) has been developed to overcome this limitation. Employing this technology, we used transesophageal color Doppler echocardiography to investigate whether the velocities detected by the Quasar would correlate with those obtained by continuous-wave Doppler both in vitro and in vivo. In the in vitro study, a 5.0 MHz transesophageal transducer of a Kontron Sigma 44 color Doppler flow system was used. Fourteen different peak velocities calculated and recorded by color Doppler-guided continuous-wave Doppler were randomly selected. In the clinical study, intraoperative transesophageal echocardiography was performed using the same transducer 18 adults (13 aortic valve stenosis, 2 aortic and 2 mitral stenosis, 2 hypertrophic obstructive cardiomyopathy and 1 mitral valve stenosis). Following each continuous-wave Doppler measurement, the Quasar was activated, and a small Quasar marker was placed in the brightest area of the color flow jet to obtain the maximum mean velocity readout. The maximum mean velocities measured by Quasar closely correlated with maximum peak velocities obtained by color flow guided continuous-wave Doppler in both in vitro (0.53 to 1.65 m/s, r = 0.99) and in vivo studies (1.50 to 6.01 m/s, r = 0.97). We conclude that the new Quasar technology can accurately measure high blood flow velocities during transesophageal color Doppler echocardiography. This technique has the potential of obviating the need for continuous-wave Doppler.

40 CFR 1065.325 - Intake-flow calibration.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Section 1065.325 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calibrations and Verifications Flow-Related Measurements § 1065.325 Intake-flow calibration. (a) Calibrate intake-air flow meters upon initial installation. Follow the...

Mathematical Model for Collision-Coalescence Among Inclusions in the Bloom Continuous Caster with M-EMS

NASA Astrophysics Data System (ADS)

Lei, Hong; Jiang, Jimin; Yang, Bin; Zhao, Yan; Zhang, Hongwei; Wang, Weixian; Dong, Guiwen

2018-04-01

Mathematical simulation is an effective tool to analyze the fluid flow and the inclusion behavior in the bloom continuous caster with mold electromagnetic stirring (M-EMS). The mathematical model is applied to the modeling of magnetic field, flow field, and inclusion field. Due to the introduction of Archimedes force, the collision mechanism and inclusion's slipping velocity should be modified in the inclusion mass and population conservation model. Numerically predicted magnetic field, flow field, and the inclusion spatial distribution conform to the experimental results in the existing literature. Lorentz force plays an important role in the fluid flow, and Archimedes force plays an important role in the inclusion distribution in the continuous caster. Due to Brownian collision, Stokes collision, Archimedes collision, and turbulent collision, the coalescence among inclusions occurs in the bloom continuous caster with M-EMS. Among the four types of collisions, turbulent collision occurs most frequently, followed by Archimedes collision and Stokes collision. The frequency of Brownian collision is several orders of magnitudes smaller and is therefore negligible. The inclusion volume concentration, number density, and characteristic radius exhibit a U-shape in the continuous caster without M-EMS. However, with M-EMS, they exhibit an inverted U-shape.

Enhancing Zeolite Performance by Catalyst Shaping in a Mesoscale Continuous-Flow Diels-Alder Process.

PubMed

Seghers, Sofie; Lefevere, Jasper; Mullens, Steven; De Vylder, Anton; Thybaut, Joris W; Stevens, Christian V

2018-03-26

In contrast to most lab-scale batch procedures, a continuous-flow implementation requires a thorough consideration of the solid catalyst design. In a previous study, irregular zeolite pellets were applied in a miniaturized continuous-flow reactor for the Diels-Alder reaction in the construction of norbornene scaffolds. After having faced the challenges of continuous operation, the aim of this study is to exploit catalyst structuring. To this end, microspheres with high uniformity and various sphere diameters were synthesized according to the vibrational droplet coagulation method. The influence of the use of these novel zeolite shapes in a mesoscale continuous-flow Diels-Alder process of cyclopentadiene and methyl acrylate is discussed. An impressive enhancement of catalyst lifetime is demonstrated, as even after a doubled process time of 14 h, the microspheres still exceeded the conversion after 7 h when using zeolite pellets by 30 %. A dual reason is found for this beneficial impact of catalyst shaping. The significant improvement in catalyst longevity can be attributed to the interplay of the chemical composition and the porosity structure of the microspheres. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Continuous flow electrophoresis system experiments on shuttle flights STS-6 and STS-7

NASA Technical Reports Server (NTRS)

Snyder, Robert S.; Rhodes, Percy H.; Miller, Teresa Y.

1988-01-01

The development of a space continuous flow electrophoresis system (CFES) is discussed. The objectives of the experiment were: (1) to use a model sample material at a high concentration to evaluate the continuous flow electrophoresis process in the McDonnell Douglass CFES instrument and compare its separation resolution and sample throughput with related devices on Earth, and (2) to expand the basic knowledge of the limitations imposed by fluid flows and particle concentration effects on the electrophoresis process by careful design and evaluation of the space experiment. Hemoglobin and polysaccharide were selected as samples of concentration effects. The results from space show a large band spread of the high concentration of the single species of hemoglobin that was principally due to the mismatch of electrical conductivity between the sample and buffer.

Development of an open metadata schema for prospective clinical research (openPCR) in China.

PubMed

Xu, W; Guan, Z; Sun, J; Wang, Z; Geng, Y

2014-01-01

In China, deployment of electronic data capture (EDC) and clinical data management system (CDMS) for clinical research (CR) is in its very early stage, and about 90% of clinical studies collected and submitted clinical data manually. This work aims to build an open metadata schema for Prospective Clinical Research (openPCR) in China based on openEHR archetypes, in order to help Chinese researchers easily create specific data entry templates for registration, study design and clinical data collection. Singapore Framework for Dublin Core Application Profiles (DCAP) is used to develop openPCR and four steps such as defining the core functional requirements and deducing the core metadata items, developing archetype models, defining metadata terms and creating archetype records, and finally developing implementation syntax are followed. The core functional requirements are divided into three categories: requirements for research registration, requirements for trial design, and requirements for case report form (CRF). 74 metadata items are identified and their Chinese authority names are created. The minimum metadata set of openPCR includes 3 documents, 6 sections, 26 top level data groups, 32 lower data groups and 74 data elements. The top level container in openPCR is composed of public document, internal document and clinical document archetypes. A hierarchical structure of openPCR is established according to Data Structure of Electronic Health Record Architecture and Data Standard of China (Chinese EHR Standard). Metadata attributes are grouped into six parts: identification, definition, representation, relation, usage guides, and administration. OpenPCR is an open metadata schema based on research registration standards, standards of the Clinical Data Interchange Standards Consortium (CDISC) and Chinese healthcare related standards, and is to be publicly available throughout China. It considers future integration of EHR and CR by adopting data structure and data terms in Chinese EHR Standard. Archetypes in openPCR are modularity models and can be separated, recombined, and reused. The authors recommend that the method to develop openPCR can be referenced by other countries when designing metadata schema of clinical research. In the next steps, openPCR should be used in a number of CR projects to test its applicability and to continuously improve its coverage. Besides, metadata schema for research protocol can be developed to structurize and standardize protocol, and syntactical interoperability of openPCR with other related standards can be considered.

Uranium fate in wetland mesocosms: Effects of plants at two iron loadings with different pH values.

PubMed

Koster van Groos, Paul G; Kaplan, Daniel I; Chang, Hyun-Shik; Seaman, John C; Li, Dien; Peacock, Aaron D; Scheckel, Kirk G; Jaffé, Peter R

2016-11-01

Small-scale continuous flow wetland mesocosms (∼0.8 L) were used to evaluate how plant roots under different iron loadings affect uranium (U) mobility. When significant concentrations of ferrous iron (Fe) were present at circumneutral pH values, U concentrations in root exposed sediments were an order of magnitude greater than concentrations in root excluded sediments. Micro X-ray absorption near-edge structure (μ-XANES) spectroscopy indicated that U was associated with the plant roots primarily as U(VI) or U(V), with limited evidence of U(IV). Micro X-ray fluorescence (μ-XRF) of plant roots suggested that for high iron loading at circumneutral pH, U was co-located with Fe, perhaps co-precipitated with root Fe plaques, while for low iron loading at a pH of ∼4 the correlation between U and Fe was not significant, consistent with previous observations of U associated with organic matter. Quantitative PCR analyses indicated that the root exposed sediments also contained elevated numbers of Geobacter spp., which are likely associated with enhanced iron cycling, but may also reduce mobile U(VI) to less mobile U(IV) species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Colonization and Gut Flora Modulation of Lactobacillus kefiranofaciens ZW3 in the Intestinal Tract of Mice.

PubMed

Xing, Zhuqing; Tang, Wei; Yang, Ying; Geng, Weitao; Rehman, Rizwan Ur; Wang, Yanping

2018-06-01

This study evaluated the distribution and colonization of Lactobacillus kefiranofaciens ZW3 and determined its capacity to modulate the gut microbiota in an animal model. Based on (1) fluorescence imaging, (2) flow cytometry, and (3) qPCR, we found that ZW3 successfully adhered to mouse mucous tissue and colonized the mouse ileum. Gut microbiota profiling was performed using high-throughput sequencing. After continuous intubation with ZW3 for 1 week, the proportion of Lachnospiraceae, a family of butyric acid-producing bacteria, increased at day 7 (11.9% at day 0 versus 18.4% at day 7). In addition, Lactobacillaceae showed an increasing trend (4% at day 0 versus 13% at day 7) that was accompanied by an observable decline in the Rikenellaceae family (1.58% at day 7, 0.14% at day 14, and 0.75% at day 21) in the tested mouse. The results demonstrate that ZW3 could successfully adhere to and colonize the mouse gut throughout the course of the experiment. The profiling analysis of the gut microbiota also provided evidence supporting the function of ZW3 in improving the intestinal flora of mice.

Rapid quantification of proanthocyanidins (condensed tannins) with a continuous flow analyzer

Treesearch

James K. Nitao; Bruce A. Birr; Muraleedharan G. Nair; Daniel A. Herms; William J. Mattson

2001-01-01

Proanthocyanidins (condensed tannins) frequently need to be quantified in large numbers of samples in food, plant, and environmental studies. An automated colorimetric method to quantify proanthocyanidins with sulfuric acid (H2SO4) was therefore developed for use in a continuous flow analyzer. Assay conditions were...

76 FR 9984 - Airworthiness Directives; B/E Aerospace, Continuous Flow Passenger Oxygen Mask Assembly, Part...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-23

..., Continuous Flow Passenger Oxygen Mask Assembly, Part Numbers 174006-(), 174080-(), 174085-(), 174095... manufacturer and part number of the oxygen mask assemblies installed, an inspection to determine the manufacturing date and modification status if certain oxygen mask assemblies are installed, and corrective...

Performance of a continuous flow passenger oxygen mask at an altitude of 40,000 feet.

DOT National Transportation Integrated Search

1996-02-01

A redesigned continuous flow passenger oxygen mask was tested for its ability to deliver an adequate supply of oxygen at an altitude of 40,000 feet above sea level. Four male subjects participated in the study. Blood oxygen saturation (SaO2) baseline...

40 CFR Table 12 to Subpart G of... - Monitoring Requirements for Treatment Processes

Code of Federal Regulations, 2013 CFR

2013-07-01

... Appropriate methods as specified in § 63.143 and as approved by permitting authority. 2. Steam stripper (i... recorder. (ii) Wastewater feed mass flow rate; and Continuously Liquid flow meter installed at stripper... operating temperature Continuously (A) Liquid temperature monitoring device installed at stripper influent...

40 CFR Table 12 to Subpart G of... - Monitoring Requirements for Treatment Processes

Code of Federal Regulations, 2010 CFR

2010-07-01

... Appropriate methods as specified in § 63.143 and as approved by permitting authority. 2. Steam stripper (i... recorder. (ii) Wastewater feed mass flow rate; and Continuously Liquid flow meter installed at stripper... operating temperature Continuously (A) Liquid temperature monitoring device installed at stripper influent...

40 CFR Table 12 to Subpart G of... - Monitoring Requirements for Treatment Processes

Code of Federal Regulations, 2011 CFR

2011-07-01

... Appropriate methods as specified in § 63.143 and as approved by permitting authority. 2. Steam stripper (i... recorder. (ii) Wastewater feed mass flow rate; and Continuously Liquid flow meter installed at stripper... operating temperature Continuously (A) Liquid temperature monitoring device installed at stripper influent...

40 CFR Table 12 to Subpart G of... - Monitoring Requirements for Treatment Processes

Code of Federal Regulations, 2014 CFR

2014-07-01

... Appropriate methods as specified in § 63.143 and as approved by permitting authority. 2. Steam stripper (i... recorder. (ii) Wastewater feed mass flow rate; and Continuously Liquid flow meter installed at stripper... operating temperature Continuously (A) Liquid temperature monitoring device installed at stripper influent...

40 CFR Table 12 to Subpart G of... - Monitoring Requirements for Treatment Processes

Code of Federal Regulations, 2012 CFR

2012-07-01

... Appropriate methods as specified in § 63.143 and as approved by permitting authority. 2. Steam stripper (i... recorder. (ii) Wastewater feed mass flow rate; and Continuously Liquid flow meter installed at stripper... operating temperature Continuously (A) Liquid temperature monitoring device installed at stripper influent...

Effects Of Nutrient Source And Supply On Crude Oil Biodegradation In Continuous-Flow Beach Microcosms

EPA Science Inventory

Ammonium and nitrate were used as nitrogen sources to support microbial biodegradation of crude oil in continuous-flow beach microcosms to determine whether either nutrient was more effective in open systems, such as intertidal shorelines. No differences in the rate or the exten...

Continuous spin detonation of poorly detonable fuel-air mixtures in annular combustors

NASA Astrophysics Data System (ADS)

Bykovskii, F. A.; Zhdan, S. A.

2017-09-01

This paper reports on the results of experimental investigations of continuous spin detonation of three fuel-air mixtures (syngas-air, CH4/H2-air, and kerosene/H2-air in a flow-type annular cylindrical combustor 503 mm in diameter. The limits of existence of continuous detonation in terms of the specific flow rates of the mixtures (minimum values) are determined. It is found that all gas mixtures, including the least detonable methane-air mixture, with addition of hydrogen can be burned in the continuous spin detonation regime.

Thermally-actuated, phase change flow control for microfluidic systems.

PubMed

Chen, Zongyuan; Wang, Jing; Qian, Shizhi; Bau, Haim H

2005-11-01

An easy to implement, thermally-actuated, noninvasive method for flow control in microfluidic devices is described. This technique takes advantage of the phase change of the working liquid itself-the freezing and melting of a portion of a liquid slug-to noninvasively close and open flow passages (referred to as a phase change valve). The valve was designed for use in a miniature diagnostic system for detecting pathogens in oral fluids at the point of care. The paper describes the modeling, construction, and characteristics of the valve. The experimental results favorably agree with theoretical predictions. In addition, the paper demonstrates the use of the phase change valves for flow control, sample metering and distribution into multiple analysis paths, sealing of a polymerase chain reaction (PCR) chamber, and sample introduction into and withdrawal from a closed loop. The phase change valve is electronically addressable, does not require any moving parts, introduces only minimal dead volume, is leakage and contamination free, and is biocompatible.

The intracoelomic route: a new approach for in utero human cord blood stem cell transplantation.

PubMed

Noia, Giuseppe; Pierelli, Luca; Bonanno, Giuseppina; Monego, Giovanni; Perillo, Alessandro; Rutella, Sergio; Cavaliere, Anna Franca; Straface, Gianluca; Fortunato, Giuseppe; Cesari, Elena; Scambia, Giovanni; Terzano, Marinella; Iannace, Enrico; Zelano, Giovanni; Michetti, Fabrizio; Leone, Giuseppe; Mancuso, Salvatore

2004-01-01

The intracoelomic route for in utero hematopoietic stem cell transplantation has been evaluated in pre-immune fetal sheep and the engraftment characteristics defined. Twelve ovine fetuses (gestational ages: 40-45 days) received intracoelomic transplants of human CD3-depleted (50 x 10(6) per lamb) or CD34-selected (1-2 x 10(5) per lamb) cord blood hematopoietic stem cells. Engraftment was evaluated from cell suspension of the liver, spleen, bone marrow and thymus by flow cytometry, cloning assays and polymerase chain reaction (PCR) analysis for human beta(2)-microglobulin gene. The engraftment of liver samples was also evaluated by reverse transcriptase-polymerase chain reaction (RT-PCR), fluorescent in situ hybridization (FISH) and immunohistochemistry. Four fetuses (33%) aborted shortly after intracoelomic transplantation and were not evaluable for engraftment. Engraftment was detected in 4 fetuses obtained from cesarean delivery on day 70 after transplantation of CD3-depleted cord blood cells. The degree of engraftment in these 4 fetuses ranged from 6 to 22% in the different organs (as revealed by antigenic analysis of human CD45 with flow cytometry). Three fetuses obtained after cesarean section at 102 (No. 435184) and 105 (Nos 915293, 037568) days and 1 fetus delivered at term, which received CD34-selected cord blood cells, had human engraftment with 10, 32, 20 and 10% CD45+ cells in bone marrow, respectively. A further check of human chimerism was done at 1 year after birth of the fetus delivered at term and 7.6% of bone marrow chimerism was detected. In 6 out of 8 fetuses evaluable for human engraftment, chimerism was confirmed by PCR analysis for human beta(2)-microglobulin which also identified human cells in brain, spinal cord, heart, lung and skeletal muscle. On liver samples, FISH and RT-PCR confirmed the xenograft of human cells and the immunohistochemical analysis detected human markers of hematopoietic and hepatic lineage of differentiation. This preliminary study indicates that intracoelomic transplantation of human hematopoietic stem cells in fetal lambs is feasible and effective in terms of hematopoietic engraftment. Copyright 2004 S. Karger AG, Basel

Characterization of Chicken Splenic-Derived Dendritic Cells Following Vaccine and Very Virulent Strains of Infectious Bursal Disease Virus Infection.

PubMed

Yasmin, A R; Yeap, S K; Hair-Bejo, M; Omar, A R

2016-12-01

Studies have shown that infectious bursal disease virus (IBDV) infects lymphoid cells, mainly B cells and macrophages. This study was aimed to examine the involvement of chicken splenic-derived dendritic cells (ch-sDCs) in specific-pathogen-free chickens following inoculation with IBDV vaccine strain (D78) and a very virulent (vv) strain (UPM0081). Following IBDV infection, enriched activated ch-sDCs were collected by using the negative selection method and were examined based on morphology and immunophenotyping to confirm the isolation method for dendritic cells (DCs). The presence of IBDV on enriched activated ch-sDCs was analyzed based on the immunofluorescence antibody test (IFAT), flow cytometry, and quantitative real-time PCR (RT-qPCR) while the mRNAs of several cytokines were detected using RT-qPCR. The isolated ch-sDCs resembled typical DC morphologies found in mammals by having a veiled shape and they grew in clusters. Meanwhile, the expression of DC maturation markers, namely CD86 and MHCII, were increased at day 2 and day 3 following vvIBDV and vaccine strain inoculation, respectively, ranging from 10% to 40% compared to the control at 2.55% (P < 0.05). At day 3 postinfection, IBDV VP3 proteins colocalized with CD86 were readily detected via IFAT and flow cytometry in both vaccine and vvIBDV strains. In addition, enriched activated ch-sDCs were also detected as positive based on the VP4 gene by RT-qPCR; however, a higher viral load was detected on vvIBDV compared to the vaccine group. Infection with vaccine and vvIBDV strains induced the enriched activated ch-sDCs to produce proinflammatory cytokines and Th1-like cytokines from day 3 onward; however, the expressions were higher in the vvIBDV group (P < 0.05). These data collectively suggest that enriched activated ch-sDCs were permissive to IBDV infection and produced a strong inflammatory and Th1-like cytokine response following vvIBDV infection as compared to the vaccine strain.

Quantification of green fluorescent protein by in vivo imaging, PCR, and flow cytometry: comparison of transgenic strains and relevance for fetal cell microchimerism.

PubMed

Fujiki, Yutaka; Tao, Kai; Bianchi, Diana W; Giel-Moloney, Maryann; Leiter, Andrew B; Johnson, Kirby L

2008-02-01

Animal models are increasingly being used for the assessment of fetal cell microchimerism in maternal tissue. We wished to determine the optimal transgenic mouse strain and analytic technique to facilitate the detection of rare transgenic microchimeric fetal cells amongst a large number of maternal wild-type cells. We evaluated two strains of mice transgenic for the enhanced green fluorescent protein (EGFP): a commercially available, commonly used strain (C57BL/6-Tg(ACTB-EGFP)10sb/J) (CAG) and a newly created strain (ROSA26-EGFP) using three different techniques: in vivo and ex vivo fluorescent imaging (for whole body and dissected organs, respectively), PCR amplification of gfp, and flow cytometry (FCM). By fluorescent imaging, organs from CAG mice were 10-fold brighter than organs from ROSA26-EGFP mice (P < 0.0001). By PCR, more transgene from CAG mice was detected compared to ROSA26-EGFP mice (P = 0.04). By FCM, ROSA26-EGFP cell fluorescence was more uniform than CAG cells. A greater proportion of cells from ROSA26-EGFP organs were positive for EGFP than cells from CAG organs, but CAG mice had a greater proportion of cells with the brightest fluorescent intensity. Each transgenic strain possesses characteristics that make it useful under specific experimental circumstances. The CAG mouse model is preferable when experiments require brighter cells, whereas ROSA26-EGFP is more appropriate when uniform or ubiquitous expression is more important than brightness. Investigators must carefully select the transgenic strain most suited to the experimental design to obtain the most consistent and reproducible data. In vivo imaging allows for phenotypic evaluation of whole animals and intact organs; however, we did not evaluate its utility for the detection of rare, fetal microchimeric cells in the maternal organs. Finally, while PCR amplification of a paternally inherited transgene does allow for the quantitative determination of rare microchimeric cells, FCM allows for both quantitative and qualitative evaluations of fetal cells at very high sensitivity in a plethora of maternal organs. (c) 2008 International Society for Analytical Cytology

Development and validation of PCR-GLOBWB 2.0: a 5 arc min resolution global hydrology and water resources model

NASA Astrophysics Data System (ADS)

Sutanudjaja, Edwin H.; van Beek, Ludovicus P. H.; Wada, Yoshihide; Wisser, Dominik; de Graaf, Inge E. M.; Straatsma, Menno W.; Bierkens, Marc F. P.

2014-05-01

PCR-GLOBWB (PCRaster Global Water Balance) is a grid-based global hydrological model developed at the Department of Physical Geography, Utrecht University. For each grid cell, PCR-GLOBWB simulates moisture storage in vertically stacked soil layers, as well as the water exchange to the atmosphere and underlying groundwater reservoir. Exchange to the atmosphere comprises of precipitation, evaporation and transpiration, as well as snow accumulation and melt. All fluxes are all simulated by considering vegetation phenology and sub-grid variations in elevation, land cover and soil saturation. The model includes physically-based schemes for runoff-infiltration partitioning, interflow, groundwater recharge and baseflow, as well as river routing of discharge. Here we present and summarize the latest developments of PCR-GLOBWB. The new version of the model, PCR-GLOBWB 2.0, now runs at a spatial resolution of 5 arc min (about 10 km at the equator) and supersedes the previous generation of the model (30 arc min PCR-GLOBWB 1.0, van Beek et al., 2011). PCR-GLOBWB 2.0 consolidates all components that have been introduced since PCR-GLOWB 1.0 was first published (2011). Examples of these new components are: A comprehensive water demand and irrigation module (Wada et al., 2012). A dynamic attribution and return flow of water demand to surface water and groundwater resources (de Graaf et al., 2013). An advanced surface water routing scheme with wetland, lakes and floodplains of variable extent, thus simulating flooding and flood wave attenuation (Winsemius et al., 2013). An online scheme for dynamic withdrawal, allocation and consumptive use of groundwater and surface water resources, including a progressive introduction of reservoirs (Wada et al., 2013). Further development will include the inclusion of a dynamic reservoir operation/optimization scheme and a MODFLOW lateral groundwater flow module (Sutanudjaja et al., 2011; Sutanudjaja et al., 2014). Also, scripts used for deriving the parameterization from global data sources for the original model have been coupled with the model, resulting in a near-scalable model that facilitates its application for different domains and at varying resolutions. Results are very promising. When comparing simulated discharges to those observed by GRDC stations, the coefficient-of-determination is high. Human impacts, altering the seasonal and inter-annual variability of terrestrial water storage (TWS) signals, are well simulated by PCR-GLOBWB 2.0 and evident in the validation of simulated TWS with GRACE satellite observation (Tapley et al., 2004). Moreover, the simulation results of PCR-GLOBWB 2.0 compare well to several other remote sensing products, such as the soil moisture datasets of ERS/MetOp (Wagner et al., 1999) and AMSR-E (de Jeu and Owe, 2003), as well as the GLEAM evaporation product (Miralles et al., 2011). References: de Graaf et al., Advances in Water Resources (2013), http://dx.doi.org/10.1016/j.advwatres.2013.12.002 de Jeu and Owe, International Journal of Remote Sensing (2003), http://dx.doi.org/10.1080/0143116031000095934 Miralles et al., Hydrology and Earth System Sciences (2011), http://dx.doi.org/10.5194/hess-15-967-2011 Sutanudjaja et al., Hydrology and Earth System Sciences (2011), http://dx.doi.org/10.5194/hess-15-2913-2011 Sutanudjaja et al., Water Resources Research (2014), http://dx.doi.org/10.1002/2013WR013807 Tapley et al., Science (2004), http://dx.doi.org/10.1126/science.1099192 van Beek et al., Water Resources Research (2011), http://dx.doi.org/10.1029/2010WR009791 Wada et al., Water Resources Research (2012), http://dx.doi.org/10.1029/2011WR010562 Wada et al., Earth System Dynamics Discussion (2013), http://dx.doi.org/10.5194/esdd-4-355-2013 Wagner et al., Remote Sensing of Environment (1999), http://dx.doi.org/10.1016/S0034-4257(99)00036-X Winsemius et al., Hydrology and Earth System Sciences (2013), http://dx.doi.org/10.5194/hess-17-1871-2013

What assay is optimal for the diagnosis of measles virus infection? An evaluation of the performance of a measles virus real-time reverse transcriptase PCR using the Cepheid SmartCycler(®) and antigen detection by immunofluorescence.

PubMed

Chua, Kyra Y L; Thapa, Kiran; Yapa, Chaturangi M; Somerville, Lucy K; Chen, Sharon C-A; Dwyer, Dominic E; Sheppeard, Vicky; Kok, Jen

2015-09-01

Despite the World Health Organization (WHO)-reported elimination of measles in Australia, importation of cases especially in travellers from Asia continues in Sydney, Australia's largest city. Laboratory confirmation supports clinico-epidemiological evidence of measles virus infection, and is needed to establish elimination. To evaluate the performance of a random access real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay using the moderate complexity SmartCycler(®) platform, and measles antigen detection by immunofluorescence (IFA), for the detection of measles virus in patient samples. One hundred samples comprising nose and throat swabs, nasopharyngeal aspirates and urine, collected from patients with suspected measles were tested in parallel using IFA and nucleic acid testing using the SmartCycler(®) and LightCycler(®) RT-PCR platforms. The LightCycler(®) RT-PCR was used as the reference assay against which the SmartCycler(®) RT-PCR and IFA were compared. Using the LightCycler(®) RT-PCR, measles virus was detected in 35 clinical samples. There was 100% concordance between the results of the SmartCycler(®) and the LightCycler(®)-based RT-PCR. Measles genotypes detected included B3, D8, and D9. Testing urine in addition to NTS did not improve diagnostic yield. In contrast, the sensitivity and specificity of IFA compared to the reference LightCycler(®) RT-PCR was 34.3% and 96.7%, respectively. The performance of the SmartCycler(®) is comparable to the LightCycler(®) for the detection of measles virus. However, IFA had poor sensitivity and should not be used to confirm measles virus infection where nucleic acid testing is available. Copyright © 2015 Elsevier B.V. All rights reserved.

Identification of internal control genes for quantitative expression analysis by real-time PCR in bovine peripheral lymphocytes.

PubMed

Spalenza, Veronica; Girolami, Flavia; Bevilacqua, Claudia; Riondato, Fulvio; Rasero, Roberto; Nebbia, Carlo; Sacchi, Paola; Martin, Patrice

2011-09-01

Gene expression studies in blood cells, particularly lymphocytes, are useful for monitoring potential exposure to toxicants or environmental pollutants in humans and livestock species. Quantitative PCR is the method of choice for obtaining accurate quantification of mRNA transcripts although variations in the amount of starting material, enzymatic efficiency, and the presence of inhibitors can lead to evaluation errors. As a result, normalization of data is of crucial importance. The most common approach is the use of endogenous reference genes as an internal control, whose expression should ideally not vary among individuals and under different experimental conditions. The accurate selection of reference genes is therefore an important step in interpreting quantitative PCR studies. Since no systematic investigation in bovine lymphocytes has been performed, the aim of the present study was to assess the expression stability of seven candidate reference genes in circulating lymphocytes collected from 15 dairy cows. Following the characterization by flow cytometric analysis of the cell populations obtained from blood through a density gradient procedure, three popular softwares were used to evaluate the gene expression data. The results showed that two genes are sufficient for normalization of quantitative PCR studies in cattle lymphocytes and that YWAHZ, S24 and PPIA are the most stable genes. Copyright © 2010 Elsevier Ltd. All rights reserved.

Detection, quantitation and identification of enteroviruses from surface waters and sponge tissue from the Florida Keys using real-time RT-PCR

USGS Publications Warehouse

Donaldson, K.A.; Griffin, Dale W.; Paul, J.H.

2002-01-01

A method was developed for the quantitative detection of pathogenic human enteroviruses from surface waters in the Florida Keys using Taqman (R) one-step Reverse transcription (RT)-PCR with the Model 7700 ABI Prism (R) Sequence Detection System. Viruses were directly extracted from unconcentrated grab samples of seawater, from seawater concentrated by vortex flow filtration using a 100kD filter and from sponge tissue. Total RNA was extracted from the samples, purified and concentrated using spin-column chromatography. A 192-196 base pair portion of the 5??? untranscribed region was amplified from these extracts. Enterovirus concentrations were estimated using real-time RT-PCR technology. Nine of 15 sample sites or 60% were positive for the presence of pathogenic human enteroviruses. Considering only near-shore sites, 69% were positive with viral concentrations ranging from 9.3viruses/ml to 83viruses/g of sponge tissue (uncorrected for extraction efficiency). Certain amplicons were selected for cloning and sequencing for identification. Three strains of waterborne enteroviruses were identified as Coxsackievirus A9, Coxsackievirus A16, and Poliovirus Sabin type 1. Time and cost efficiency of this one-step real-time RT-PCR methodology makes this an ideal technique to detect, quantitate and identify pathogenic enteroviruses in recreational waters. Copyright ?? 2002 Elsevier Science Ltd.

Total heart replacement using dual intracorporeal continuous-flow pumps in a chronic bovine model: a feasibility study.

PubMed

Frazier, O H; Tuzun, Egemen; Cohn, William E; Conger, Jeffrey L; Kadipasaoglu, Kamuran A

2006-01-01

Continuous-flow pumps are small, simple, and respond physiologically to input variations, making them potentially ideal for total heart replacement. However, the physiological effects of complete pulseless flow during long-term circulatory support without a cardiac interface or with complete cardiac exclusion have not been well studied. We evaluated the feasibility of dual continuous-flow pumps as a total artificial heart (TAH) in a chronic bovine model. Both ventricles of a 6-month-old Corriente crossbred calf were excised and sewing rings attached to the reinforced atrioventricular junctions. The inlet portions of 2 Jarvik 2000 pumps were positioned through their respective sewing rings at the mid-atrial level and the pulseless atrial reservoir connected end-to-end to the pulmonary artery and aorta. Pulseless systemic and pulmonary circulations were thereby achieved. Volume status was controlled, and systemic and pulmonary resistance were managed pharmacologically to keep mean arterial pressures at 100+/-10 mmHg (systemic) and 20+/-5 mmHg (pulmonary) and both left and right atrial pressures at 15+/-5 mmHg. The left pump speed was maintained at 14,000 rpm and its output autoregulated in response to variations in right pump flow, systemic and pulmonary pressures, fluid status, and activity level. Hemodynamics, end-organ function, and neurohormonal status remained normal. These results suggest the feasibility of using dual continuous-flow pumps as a TAH.

Performance analysis of a continuous serpentine flow reactor for electrochemical oxidation of synthetic and real textile wastewater: Energy consumption, mass transfer coefficient and economic analysis.

PubMed

Pillai, Indu M Sasidharan; Gupta, Ashok K

2017-05-15

A continuous flow electrochemical reactor was developed, and its application was tested for the treatment of textile wastewater. A parallel plate configuration with serpentine flow was chosen for the continuous flow reactor. Uniparameter optimization was carried out for electrochemical oxidation of synthetic and real textile wastewater (collected from the inlet of the effluent treatment plant). Chemical Oxygen Demand (COD) removal efficiency of 90% was achieved for synthetic textile wastewater (initial COD - 780 mg L -1 ) at a flow rate of 500 mL h -1 (retention time of 6 h) and a current density of 1.15 mA cm -2 and the energy consumption for the degradation was 9.2 kWh (kg COD) -1 . The complete degradation of real textile wastewater (initial COD of 368 mg L -1 ) was obtained at a current density of 1.15 mA cm -2 , NaCl concentration of 1 g L -1 and retention time of 6 h. Energy consumption and mass transfer coefficient of the reactions were calculated. The continuous flow reactor performed better than batch reactor with reference to energy consumption and economy. The overall treatment cost for complete COD removal of real textile wastewater was 5.83 USD m -3 . Copyright © 2017 Elsevier Ltd. All rights reserved.

Method and apparatus for continuous electrophoresis

DOEpatents

Watson, Jack S.

1992-01-01

A method and apparatus for conducting continuous separation of substances by electrophoresis are disclosed. The process involves electrophoretic separation combined with couette flow in a thin volume defined by opposing surfaces. By alternating the polarity of the applied potential and producing reciprocating short rotations of at least one of the surfaces relative to the other, small increments of separation accumulate to cause substantial, useful segregation of electrophoretically separable components in a continuous flow system.

QUANTITATIVE MEASUREMENT OF HELICOBACTER PYLORI BY THE TAQMAN FLUOROGENIC PROBE SYSTEM

EPA Science Inventory

Culturing of H. pylori from environmental sources continues to be an obstacle in detecting and enumerating this organism. Successful methods of isolation and growth from water samples have not yet been developed. In this study a method involving real tme PCR product detection wit...

Evaluation of a watershed model for estimating daily flow using limited flow measurements

USDA-ARS?s Scientific Manuscript database

The Soil and Water Assessment Tool (SWAT) model was evaluated for estimation of continuous daily flow based on limited flow measurements in the Upper Oyster Creek (UOC) watershed. SWAT was calibrated against limited measured flow data and then validated. The Nash-Sutcliffe model Efficiency (NSE) and...

Noninvasive measurement of cerebrospinal fluid flow using an ultrasonic transit time flow sensor: a preliminary study.

PubMed

Pennell, Thomas; Yi, Juneyoung L; Kaufman, Bruce A; Krishnamurthy, Satish

2016-03-01

OBJECT Mechanical failure-which is the primary cause of CSF shunt malfunction-is not readily diagnosed, and the specific reasons for mechanical failure are not easily discerned. Prior attempts to measure CSF flow noninvasively have lacked the ability to either quantitatively or qualitatively obtain data. To address these needs, this preliminary study evaluates an ultrasonic transit time flow sensor in pediatric and adult patients with external ventricular drains (EVDs). One goal was to confirm the stated accuracy of the sensor in a clinical setting. A second goal was to observe the sensor's capability to record real-time continuous CSF flow. The final goal was to observe recordings during instances of flow blockage or lack of flow in order to determine the sensor's ability to identify these changes. METHODS A total of 5 pediatric and 11 adult patients who had received EVDs for the treatment of hydrocephalus were studied in a hospital setting. The primary EVD was connected to a secondary study EVD that contained a fluid-filled pressure transducer and an in-line transit time flow sensor. Comparisons were made between the weight of the drainage bag and the flow measured via the sensor in order to confirm its accuracy. Data from the pressure transducer and the flow sensor were recorded continuously at 100 Hz for a period of 24 hours by a data acquisition system, while the hourly CSF flow into the drip chamber was recorded manually. Changes in the patient's neurological status and their time points were noted. RESULTS The flow sensor demonstrated a proven accuracy of ± 15% or ± 2 ml/hr. The flow sensor allowed real-time continuous flow waveform data recordings. Dynamic analysis of CSF flow waveforms allowed the calculation of the pressure-volume index. Lastly, the sensor was able to diagnose a blocked catheter and distinguish between the blockage and lack of flow. CONCLUSIONS The Transonic flow sensor accurately measures CSF output within ± 15% or ± 2 ml/hr, diagnoses the blockage or lack of flow, and records real-time continuous flow data in patients with EVDs. Calculations of a wide variety of diagnostic parameters can be made from the waveform recordings, including resistance and compliance of the ventricular catheters and the compliance of the brain. The sensor's clinical applications may be of particular importance to the noninvasive diagnosis of shunt malfunctions with the development of an implantable device.

Low-flow characteristics for selected streams in Indiana

USGS Publications Warehouse

Fowler, Kathleen K.; Wilson, John T.

2015-01-01

The management and availability of Indiana’s water resources increase in importance every year. Specifically, information on low-flow characteristics of streams is essential to State water-management agencies. These agencies need low-flow information when working with issues related to irrigation, municipal and industrial water supplies, fish and wildlife protection, and the dilution of waste. Industrial, municipal, and other facilities must obtain National Pollutant Discharge Elimination System (NPDES) permits if their discharges go directly to surface waters. The Indiana Department of Environmental Management (IDEM) requires low-flow statistics in order to administer the NPDES permit program. Low-flow-frequency characteristics were computed for 272 continuous-record stations. The information includes low-flow-frequency analysis, flow-duration analysis, and harmonic mean for the continuous-record stations. For those stations affected by some form of regulation, low-flow frequency curves are based on the longest period of homogeneous record under current conditions. Low-flow-frequency values and harmonic mean flow (if sufficient data were available) were estimated for the 166 partial-record stations. Partial-record stations are ungaged sites where streamflow measurements were made at base flow.

Supported Ruthenium Catalysts for Sustainable Flow Chemistry

EPA Science Inventory

Continuous flow processes play a significant role in the process intensification of organic transformations, as is evident from the multitude of flow reactors that have been developed for various specific needs. These flow processes are deemed more sustainable due to the advantag...

40 CFR 1065.330 - Exhaust-flow calibration.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Section 1065.330 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calibrations and Verifications Flow-Related Measurements § 1065.330... ultrasonic flow meter for raw exhaust flow measurement, we recommend that you calibrate it as described in...

Cytological diagnostic of lymphadenitis tuberculosis by eosinophilic material

NASA Astrophysics Data System (ADS)

Delyuzar; Amir, Z.; Kusumawati, L.

2018-03-01

AFB sputum and chest X-ray are used to identify patients with pulmonary TB. For extrapulmonary TB, fine needle aspiration cytology is needed, even though occasionally found not atypical feature in the form of eosinophilic material with dark brown particles, suspected as TB. This research was to show that eosinophilic material with dark brown particles is accurate as new criteria for the cytological diagnosis of TB. By performing fine needle aspiration biopsy stained with Giemsa, if an eosinophilic material with dark brown particles was encountered, we continued with Ziehl-Neelsen AFB stain and confirmed with PCR. To assess accuracy, we used a diagnostic test to evaluate sensitivity and specificity of eosinophilic material with dark brown particles by using AFB and PCR as the gold standard. The sensitivity and specificity of cytological diagnosis in tuberculosis of eosinophilic material with dark brown particles were 93.65% and 70.99%, respectively if confirmed with AFB. On the other hand, if confirmed with PCR using Mycobacterium tuberculosis DNA, the sensitivity and specificity were 98.95% and 96.79%, respectively. In conclusion, eosinophilic masses with dark brown particles is accurate as new criteria of TB diagnostic cytology with high sensitivity and specificity confirmed with AFB and PCR test.

Unique clinical and imaging findings in a first ever documented PCR positive rabies survival patient: A case report.

PubMed

M, Netravathi; V, Udani; Rs, Mani; V, Gadad; M A, Ashwini; M, Bhat; S, Mehta; A, Chowdhary; P K, Pal; S N, Madhusudana; P, Satishchandra

2015-09-01

Rabies is fatal encephalitis which is a major public health problem in Asian and African countries. Till date, only 12 cases have been reported who have survived after rabies. In this communication we report a patient who is unique as the first documented long term rabies survivor with PCR positivity even after 4½ years of illness. Child sustained dog bite following which he received adequate prophylaxis. Within two weeks, child developed encephalopathy requiring evaluation. Child continues to have persistent myoclonic jerks, seizures, is dependent on all activities with severe neurological deficits. Nested reverse transcriptase PCR (RT-PCR) specific for rabies nucleoprotein gene in CSF and nuchal skin biopsy were positive for rabies viral RNA. The nuchal skin biopsy was also positive for rabies nucleoprotein antigen by fluorescent antibody test (FAT). We describe the clinical evolution and sequential MRI brain changes in this child. Despite the uniformly dismal prognosis of human rabies, these unusual reports of survival of rabies patients may provide an impetus to explore newer therapeutic strategies for this otherwise fatal disease. Copyright © 2015 Elsevier B.V. All rights reserved.

Elevated ground-level O(3) changes the diversity of anoxygenic purple phototrophic bacteria in paddy field.

PubMed

Feng, Youzhi; Lin, Xiangui; Yu, Yongchang; Zhu, Jianguo

2011-11-01

The knowledge of the impact of elevated ground-level O(3) below ground the agro-ecosystem is limited. A field experiment in China Ozone Free-Air Concentration Enrichment (FACE-O(3)) facility on a rice-wheat rotation system was carried out to investigate responses of anoxygenic phototrophic purple bacteria (AnPPB) to elevated ground-level O(3). AnPPB community structures and sizes in paddy soil were monitored by molecular approaches including PCR-DGGE and real-time quantitative PCR based upon the pufM gene on three typical rice growth stages. Repetitive sequence-based PCR (rep-PCR) in combination with culture-reliant method was conducted to reveal changes in genotypic diversity. Elevated ground-level O(3) statistically reduce AnPPB abundance and percentage in total bacterial community in flooded rice soil via decreasing their genotypic diversity and metabolic versatility. Concomitantly, their community composition changed after rice anthesis stage under elevated ground-level O(3). Our results from AnPPB potential responses imply that continuously elevated ground-level O(3) in the future would eventually harm the health of paddy ecosystem through negative effect on soil microorganisms.

Interleukin-12 in patients with cancer is synthesized by peripheral helper T lymphocytes.

PubMed

Michelin, Marcia A; Montes, Leticia; Nomelini, Rosekeila S; Abdalla, Douglas R; Aleixo, Andre A R; Murta, Eddie F C

2015-09-01

The production of cytokines by helper T lymphocytes is a critical event in the immune response, as alterations in the regulation of this process may result in an appropriate immune response, persistent infection or the development of autoimmune disease. Previously, this group has used flow cytometry to demonstrate the expression of interleukin-12 (IL-12) in peripheral blood CD4+ T lymphocytes from patients and mice with advanced cancer. The aim of the present study was to investigate whether CD4+ T lymphocytes from the peripheral blood (PB) of patients with cancer produce IL-12, using molecular approaches, flow cytometry and cellular imaging techniques. CD3+ and CD4+ cells, and cells producing IL-12, were isolated from the PB obtained from patients with cancer, using a cell sorting flow cytometry technique. The positivity of cells for CD3, CD4 and IL-12, which were identified by cell sorting, was visualized using immunofluorescent cellular imaging. Total RNA was extracted from the CD3+CD4+IL-12+ cells, obtained by cell sorting, for confirmation of the presence of IL-12 mRNA, using reverse transcription-polymerase chain reaction (RT-PCR). RT-PCR demonstrated the presence of IL-12 mRNA in all patients (n=14), in contrast to the control group, in whom IL-12 expression was not detected. Immunofluorescent analysis of CD4+ T lymphocytes showed positive intracytoplasmatic IL-12 staining. These results demonstrated that CD3+CD4+ T lymphocytes in the PB of patients with cancer have the capacity to synthesize and express IL-12.

Interleukin-12 in patients with cancer is synthesized by peripheral helper T lymphocytes

PubMed Central

MICHELIN, MARCIA A.; MONTES, LETICIA; NOMELINI, ROSEKEILA S.; ABDALLA, DOUGLAS R.; ALEIXO, ANDRE A. R.; MURTA, EDDIE F. C.

2015-01-01

The production of cytokines by helper T lymphocytes is a critical event in the immune response, as alterations in the regulation of this process may result in an appropriate immune response, persistent infection or the development of autoimmune disease. Previously, this group has used flow cytometry to demonstrate the expression of interleukin-12 (IL-12) in peripheral blood CD4+ T lymphocytes from patients and mice with advanced cancer. The aim of the present study was to investigate whether CD4+ T lymphocytes from the peripheral blood (PB) of patients with cancer produce IL-12, using molecular approaches, flow cytometry and cellular imaging techniques. CD3+ and CD4+ cells, and cells producing IL-12, were isolated from the PB obtained from patients with cancer, using a cell sorting flow cytometry technique. The positivity of cells for CD3, CD4 and IL-12, which were identified by cell sorting, was visualized using immunofluorescent cellular imaging. Total RNA was extracted from the CD3+CD4+IL-12+ cells, obtained by cell sorting, for confirmation of the presence of IL-12 mRNA, using reverse transcription-polymerase chain reaction (RT-PCR). RT-PCR demonstrated the presence of IL-12 mRNA in all patients (n=14), in contrast to the control group, in whom IL-12 expression was not detected. Immunofluorescent analysis of CD4+ T lymphocytes showed positive intracytoplasmatic IL-12 staining. These results demonstrated that CD3+CD4+ T lymphocytes in the PB of patients with cancer have the capacity to synthesize and express IL-12. PMID:26622702

Investigation of a lithium-halogen exchange flow process for the preparation of boronates by using a cryo-flow reactor.

PubMed

Newby, James A; Huck, Lena; Blaylock, D Wayne; Witt, Paul M; Ley, Steven V; Browne, Duncan L

2014-01-03

Conducting low-temperature organometallic reactions under continuous flow conditions offers the potential to more accurately control exotherms and thus provide more reproducible and scalable processes. Herein, progress towards this goal with regards to the lithium-halogen exchange/borylation reaction is reported. In addition to improving the scope of substrates available on a research scale, methods to improve reaction profiles and expedite purification of the products are also described. On moving to a continuous system, thermocouple measurements have been used to track exotherms and provide a level of safety for continuous processing of organometallic reagents. The use of an in-line continuous liquid-liquid separation device to circumvent labour intensive downstream off-line processing is also reported. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

System and method for continuous solids slurry depressurization

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

Leininger, Thomas Frederick; Steele, Raymond Douglas; Cordes, Stephen Michael

A system includes a first pump having a first outlet and a first inlet, and a controller. The first pump is configured to continuously receive a flow of a slurry into the first outlet at a first pressure and to continuously discharge the flow of the slurry from the first inlet at a second pressure less than the first pressure. The controller is configured to control a first speed of the first pump against the flow of the slurry based at least in part on the first pressure, wherein the first speed of the first pump is configured to resistmore » a backflow of the slurry from the first outlet to the first inlet.« less

Continuous-flow free acid monitoring method and system

DOEpatents

Strain, J.E.; Ross, H.H.

1980-01-11

A free acid monitoring method and apparatus is provided for continuously measuring the excess acid present in a process stream. The disclosed monitoring system and method is based on the relationship of the partial pressure ratio of water and acid in equilibrium with an acid solution at constant temperature. A portion of the process stream is pumped into and flows through the monitor under the influence of gravity and back to the process stream. A continuous flowing sample is vaporized at a constant temperature and the vapor is subsequently condensed. Conductivity measurements of the condensate produces a nonlinear response function from which the free acid molarity of the sample process stream is determined.

Continuous-flow free acid monitoring method and system

DOEpatents

Strain, James E.; Ross, Harley H.

1981-01-01

A free acid monitoring method and apparatus is provided for continuously measuring the excess acid present in a process stream. The disclosed monitoring system and method is based on the relationship of the partial pressure ratio of water and acid in equilibrium with an acid solution at constant temperature. A portion of the process stream is pumped into and flows through the monitor under the influence of gravity and back to the process stream. A continuous flowing sample is vaporized at a constant temperature and the vapor is subsequently condensed. Conductivity measurements of the condensate produces a nonlinear response function from which the free acid molarity of the sample process stream is determined.

Effects of hyperglycemia and effects of ketosis on cerebral perfusion, cerebral water distribution, and cerebral metabolism.

PubMed

Glaser, Nicole; Ngo, Catherine; Anderson, Steven; Yuen, Natalie; Trifu, Alexandra; O'Donnell, Martha

2012-07-01

Diabetic ketoacidosis (DKA) may cause brain injuries in children. The mechanisms responsible are difficult to elucidate because DKA involves multiple metabolic derangements. We aimed to determine the independent effects of hyperglycemia and ketosis on cerebral metabolism, blood flow, and water distribution. We used magnetic resonance spectroscopy to measure ratios of cerebral metabolites (ATP to inorganic phosphate [Pi], phosphocreatine [PCr] to Pi, N-acetyl aspartate [NAA] to creatine [Cr], and lactate to Cr) and diffusion-weighted imaging and perfusion-weighted imaging to assess cerebral water distribution (apparent diffusion coefficient [ADC] values) and cerebral blood flow (CBF) in three groups of juvenile rats (hyperglycemic, ketotic, and normal control). ATP-to-Pi ratio was reduced in both hyperglycemic and ketotic rats in comparison with controls. PCr-to-Pi ratio was reduced in the ketotic group, and there was a trend toward reduction in the hyperglycemic group. No significant differences were observed in NAA-to-Cr or lactate-to-Cr ratio. Cortical ADC was reduced in both groups (indicating brain cell swelling). Cortical CBF was also reduced in both groups. We conclude that both hyperglycemia and ketosis independently cause reductions in cerebral high-energy phosphates, CBF, and cortical ADC values. These effects may play a role in the pathophysiology of DKA-related brain injury.

Kaempferol impedes IL-32-induced monocyte-macrophage differentiation.

PubMed

Nam, Sun-Young; Jeong, Hyun-Ja; Kim, Hyung-Min

2017-08-25

Kaempferol possesses a wide range of therapeutic properties, including antioxidant, anti-inflammatory, and anticancer properties. The present study sought to evaluate the effects and possible pharmacological mechanisms of kaempferol on interleukin (IL)-32-induced monocyte-macrophage differentiation. In this study, we performed flow cytometry assay, immunocytochemical staining, quantitative real-time PCR, enzyme-linked immuno sorbent assay, caspase-1 assay, and Western blotting to observe the effects and underlying mechanisms of kaempferol using the human monocyte cell line THP-1. The flow cytometry, immunocytochemical staining, and real-time PCR results show that kaempferol attenuated IL-32-induced monocyte differentiation to product macrophage-like cells. Kaempferol decreased the production and mRNA expression of pro-inflammatory cytokines, in this case thymic stromal lymphopoietin (TSLP), IL-1β, tumor necrosis factor (TNF)-α, and IL-8. Furthermore, kaempferol inhibited the IL-32-induced activation of p38 and nuclear factor-κB in a dose-dependent manner in THP-1 cells. Kaempferol also ameliorated the lipopolysaccharide-induced production of the inflammatory mediators TSLP, IL-1β, TNF-α, IL-8, and nitric oxide of macrophage-like cells differentiated by IL-32. In brief, our findings may provide new mechanistic insights into the anti-inflammatory effects of kaempferol. Copyright © 2017 Elsevier B.V. All rights reserved.

Opening the medial tibiofemoral compartment by pie-crusting the superficial medial collateral ligament at its tibial insertion: a cadaver study.

PubMed

Roussignol, X; Gauthe, R; Rahali, S; Mandereau, C; Courage, O; Duparc, F

2015-09-01

Arthroscopic treatment of tears in the middle and posterior parts of the medial meniscus can be difficult when the medial tibiofemoral compartment is tight. Passage of the instruments may damage the cartilage. The primary objective of this cadaver study was to perform an arthroscopic evaluation of medial tibiofemoral compartment opening after pie-crusting release (PCR) of the superficial medial collateral ligament (sMCL) at its distal insertion on the tibia. The secondary objective was to describe the anatomic relationships at the site of PCR (saphenous nerve, medial saphenous vein). We studied 10 cadaver knees with no history of invasive procedures. The femur was held in a vise with the knee flexed at 45°, and the medial aspect of the knee was dissected. PCR of the sMCL was performed under arthroscopic vision, in the anteroposterior direction, at the distal tibial insertion of the sMCL, along the lower edge of the tibial insertion of the semi-tendinosus tendon. Continuous 300-N valgus stress was applied to the ankle. Opening of the medial tibiofemoral compartment was measured arthroscopically using graduated palpation hooks after sequential PCR of the sMCL. The compartment opened by 1mm after release of the anterior third, 2.3mm after release of the anterior two-thirds, and 3.9mm after subtotal release. A femoral fracture occurred in 1 case, after completion of all measurements. Both the saphenous nerve and the medial saphenous vein were located at a distance from the PCR site in all 10 knees. PCR of the sMCL is chiefly described as a ligament-balancing method during total knee arthroplasty. This procedure is usually performed at the joint line, where it opens the compartment by 4-6mm at the most, with some degree of unpredictability. PCR of the sMCL at its distal tibial insertion provides gradual opening of the compartment, to a maximum value similar to that obtained with PCR at the joint space. The lower edge of the semi-tendinosus tendon is a valuable landmark for PCR of the distal sMCL. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Non Lyapunov stability of a constant spatially developing 2-D gas flow

NASA Astrophysics Data System (ADS)

Balint, Agneta M.; Balint, Stefan; Tanasie, Loredana

2017-01-01

Different types of stabilities (global, local) and instabilities (global absolute, local convective) of the constant spatially developing 2-D gas flow are analyzed in a particular phase space of continuously differentiable functions, endowed with the usual algebraic operations and the topology generated by the uniform convergence on the plane. For this purpose the Euler equations linearized at the constant flow are used. The Lyapunov stability analysis was presented in [1] and this paper is a continuation of [1].

Methylation of 2-Naphthol Using Dimethyl Carbonate under Continuous-Flow Gas-Phase Conditions

ERIC Educational Resources Information Center

Tundo, Pietro; Rosamilia, Anthony E.; Arico, Fabio

2010-01-01

This experiment investigates the methylation of 2-naphthol with dimethyl carbonate. The volatility of the substrates, products, and co-products allows the reaction to be performed using a continuous-flow gas-phase setup at ambient pressure. The reaction uses catalytic quantities of base, achieves high conversion, produces little waste, and…

Anaerobic Biodegradation Of Methyl tert-Butyl Ether Under Iron-Reducing Conditions In Batch And Continuous-Flow Cultures

EPA Science Inventory

The feasibility of biodegradation of the fuel oxygenate methyl tert-butyl ether (MTBE) under iron-reducing conditions was explored in batch and continuous-flow systems. A porous pot completely-mixed reactor was seeded with diverse cultures and operated under iron-reducing...

Accuracy of delta 18O isotope ratio measurements on the same sample by continuous-flow isotope-ratio mass spectrometry

USDA-ARS?s Scientific Manuscript database

The doubly labeled water method is considered the reference method to measure energy expenditure. Conventional mass spectrometry requires a separate aliquot of the same sample to be prepared and analyzed separately. With continuous-flow isotope-ratio mass spectrometry, the same sample could be analy...

AEROSOL GROWTH IN A STEADY-STATE, CONTINUOUS FLOW CHAMBER: APPLICATION TO STUDIES OF SECONDARY AEROSOL FORMATION

EPA Science Inventory

An analytical solution for the steady-state aerosol size distribution achieved in a steady-state, continuous flow chamber is derived, where particle growth is occurring by gas-to-particle conversion and particle loss is occurring by deposition to the walls of the chamber. The s...

Separation of rat pituitary secretory granules by continuous flow electrophoresis

NASA Technical Reports Server (NTRS)

Hayes, Daniel; Exton, Carrie; Salada, Thomas; Shellenberger, Kathy; Waddle, Jenny; Hymer, W. C.

1990-01-01

The separation of growth hormone-containing cytoplasmic secretory granules from the rat pituitary gland by continuous flow electrophoresis is described. The results are consistent with the hypothesis that granule subpopulations can be separated due to differences in surface charge; these, in turn, may be related to the oligomeric state of the hormone.

Continuous flow synthesis of ZSM-5 zeolite on the order of seconds

PubMed Central

Liu, Zhendong; Okabe, Kotatsu; Anand, Chokkalingam; Yonezawa, Yasuo; Zhu, Jie; Yamada, Hiroki; Endo, Akira; Yanaba, Yutaka; Yoshikawa, Takeshi; Ohara, Koji; Okubo, Tatsuya; Wakihara, Toru

2016-01-01

The hydrothermal synthesis of zeolites carried out in batch reactors takes a time so long (typically, on the order of days) that the crystallization of zeolites has long been believed to be very slow in nature. We herein present a synthetic process for ZSM-5, an industrially important zeolite, on the order of seconds in a continuous flow reactor using pressurized hot water as a heating medium. Direct mixing of a well-tuned precursor (90 °C) with the pressurized water preheated to extremely high temperature (370 °C) in the millimeter-sized continuous flow reactor resulted in immediate heating to high temperatures (240–300 °C); consequently, the crystallization of ZSM-5 in a seed-free system proceeded to completion within tens of or even several seconds. These results indicate that the crystallization of zeolites can complete in a period on the order of seconds. The subtle design combining a continuous flow reactor with pressurized hot water can greatly facilitate the mass production of zeolites in the future. PMID:27911823

Rapid quantification of soilborne pathogen communities in wheat-based long-term field experiments

USDA-ARS?s Scientific Manuscript database

Traditional isolation and quantification of inoculum density is difficult for most soilborne pathogens. Quantitative PCR methods have been developed to rapidly identify and quantify many of these pathogens using a single DNA extract from soil. Rainfed experiments operated continuously for up to 84 y...

Investigation on hemolytic effect of poly(lactic co-glycolic) acid nanoparticles synthesized using continuous flow and batch processes

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

Libi, Sumit; Calenic, Bogdan; Astete, Carlos E.

Abstract With the increasing interest in polymeric nanoparticles for biomedical applications, there is a need for continuous flow methodologies that allow for the precise control of nanoparticle synthesis. Poly(lactide-co-glycolic) acid (PLGA) nanoparticles with diameters of 220–250 nm were synthesized using a lab-on-a-chip, exploiting the precise flow control offered by a millifluidic platform. The association and the effect of PLGA nanoparticles on red blood cells (RBCs) were compared for fluorescent PLGA nanoparticles made by this novel continuous flow process using a millifluidic chip and smaller PLGA nanoparticles made by a batch method. Results indicated that all PLGA nanoparticles studied, independent ofmore » the synthesis method and size, adhered to the surface of RBCs but had no significant hemolytic effect at concentrations lower than 10 mg/ml.« less

Apparatus and method for continuous production of materials

DOEpatents

Chang, Chih-hung; Jin, Hyungdae

2014-08-12

Embodiments of a continuous-flow injection reactor and a method for continuous material synthesis are disclosed. The reactor includes a mixing zone unit and a residence time unit removably coupled to the mixing zone unit. The mixing zone unit includes at least one top inlet, a side inlet, and a bottom outlet. An injection tube, or plurality of injection tubes, is inserted through the top inlet and extends past the side inlet while terminating above the bottom outlet. A first reactant solution flows in through the side inlet, and a second reactant solution flows in through the injection tube(s). With reference to nanoparticle synthesis, the reactant solutions combine in a mixing zone and form nucleated nanoparticles. The nucleated nanoparticles flow through the residence time unit. The residence time unit may be a single conduit, or it may include an outer housing and a plurality of inner tubes within the outer housing.

PCR detection of groundwater bacteria associated with colloidal transport

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

Cruz-Perez, P.; Stetzenbach, L.D.; Alvarez, A.J.

1996-02-29

Colloidal transport may increase the amount of contaminant material than that which could be transported by water flow alone. The role of colloids in groundwater contaminant transport is complicated and may involve many different processes, including sorption of elements onto colloidal particles, coagulation/dissolution, adsorption onto solid surfaces, filtration, and migration. Bacteria are known to concentrate minerals and influence the transport of compounds in aqueous environments and may also serve as organic colloids, thereby influencing subsurface transport of radionuclides and other contaminants. The initial phase of the project consisted of assembling a list of bacteria capable of sequestering or facilitating mineralmore » transport. The development and optimization of the PCR amplification assay for the detection of the organisms of interest, and the examination of regional groundwaters for those organisms, are presented for subsequent research.« less

Flow study in the cross sectional planes of a turbine scroll

NASA Technical Reports Server (NTRS)

Hamed, A.; Abdallah, S.; Tabakoff, W.

1977-01-01

A numerical study of the nonviscous flow characteristics in the cross-sectional planes of a radial inflow turbine scroll is presented. The velocity potential is used in the formulation to determine the flow velocity in these planes resulting from the continuous mass discharge. The effect of the through flow velocity is simulated by a continuous distribution of source/sink in the cross-section. A special iterative procedure is devised to handle the solution of the resulting Poisson's differential equation with Neumann boundary conditions in a domain with generally curved boundaries. The analysis is used to determine the effects of the radius of curvature, the location of the scroll section and its geometry on the flow characteristics in the turbine scroll.

Unjamming a granular hopper by vibration

NASA Astrophysics Data System (ADS)

Janda, A.; Maza, D.; Garcimartín, A.; Kolb, E.; Lanuza, J.; Clément, E.

2009-07-01

We present an experimental study of the outflow of a hopper continuously vibrated by a piezoelectric device. Outpouring of grains can be achieved for apertures much below the usual jamming limit observed for non-vibrated hoppers. Granular flow persists down to the physical limit of one grain diameter, a limit reached for a finite vibration amplitude. For the smaller orifices, we observe an intermittent regime characterized by alternated periods of flow and blockage. Vibrations do not significantly modify the flow rates both in the continuous and the intermittent regime. The analysis of the statistical features of the flowing regime shows that the flow time significantly increases with the vibration amplitude. However, at low vibration amplitude and small orifice sizes, the jamming time distribution displays an anomalous statistics.

River-induced flow dynamics in long-screen wells and impact on aqueous samples.

PubMed

Vermeul, Vince R; McKinley, James P; Newcomer, Darrell R; Mackley, Robert D; Zachara, J M

2011-01-01

Previously published field investigations and modeling studies have demonstrated the potential for sample bias associated with vertical wellbore flow in conventional monitoring wells constructed with long-screened intervals. This article builds on the existing body of literature by (1) demonstrating the utility of continuous (i.e., hourly measurements for ∼1 month) ambient wellbore flow monitoring and (2) presenting results from a field experiment where relatively large wellbore flows (up to 4 L/min) were induced by aquifer hydrodynamics associated with a fluctuating river boundary located approximately 250 m from the test well. The observed vertical wellbore flows were strongly correlated with fluctuations in river stage, alternating between upward and downward flow throughout the monitoring period in response to changes in river stage. Continuous monitoring of ambient wellbore flows using an electromagnetic borehole flowmeter allowed these effects to be evaluated in concert with continuously monitored river-stage elevations (hourly) and aqueous uranium concentrations (daily) in a long-screen well and an adjacent multilevel well cluster. This study demonstrates that when contaminant concentrations within the aquifer vary significantly over the depth interval interrogated, river-induced vertical wellbore flow can result in variations in measured concentration that nearly encompass the full range of variation in aquifer contaminant concentration with depth. Copyright © 2010 Battelle Memorial Institute. Journal compilation © 2010 National Ground Water Association.

14 CFR 25.1443 - Minimum mass flow of supplemental oxygen.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 14 Aeronautics and Space 1 2013-01-01 2013-01-01 false Minimum mass flow of supplemental oxygen... § 25.1443 Minimum mass flow of supplemental oxygen. (a) If continuous flow equipment is installed for use by flight crewmembers, the minimum mass flow of supplemental oxygen required for each crewmember...

14 CFR 25.1443 - Minimum mass flow of supplemental oxygen.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 14 Aeronautics and Space 1 2014-01-01 2014-01-01 false Minimum mass flow of supplemental oxygen... § 25.1443 Minimum mass flow of supplemental oxygen. (a) If continuous flow equipment is installed for use by flight crewmembers, the minimum mass flow of supplemental oxygen required for each crewmember...

14 CFR 25.1443 - Minimum mass flow of supplemental oxygen.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 14 Aeronautics and Space 1 2012-01-01 2012-01-01 false Minimum mass flow of supplemental oxygen... § 25.1443 Minimum mass flow of supplemental oxygen. (a) If continuous flow equipment is installed for use by flight crewmembers, the minimum mass flow of supplemental oxygen required for each crewmember...

14 CFR 25.1443 - Minimum mass flow of supplemental oxygen.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 14 Aeronautics and Space 1 2011-01-01 2011-01-01 false Minimum mass flow of supplemental oxygen... § 25.1443 Minimum mass flow of supplemental oxygen. (a) If continuous flow equipment is installed for use by flight crewmembers, the minimum mass flow of supplemental oxygen required for each crewmember...

A comparative parametric study of a catalytic plate methane reformer coated with segmented and continuous layers of combustion catalyst for hydrogen production

NASA Astrophysics Data System (ADS)

Mundhwa, Mayur; Parmar, Rajesh D.; Thurgood, Christopher P.

2017-03-01

A parametric comparison study is carried out between segmented and conventional continuous layer configurations of the coated combustion-catalyst to investigate their influence on the performance of methane steam reforming (MSR) for hydrogen production in a catalytic plate reactor (CPR). MSR is simulated on one side of a thin plate over a continuous layer of nickel-alumina catalyst by implementing an experimentally validated surface microkinetic model. Required thermal energy for the MSR reaction is supplied by simulating catalytic methane combustion (CMC) on the opposite side of the plate over segmented and continuous layer of a platinum-alumina catalyst by implementing power law rate model. The simulation results of both coating configurations of the combustion-catalyst are compared using the following parameters: (1) co-flow and counter-flow modes between CMC and MSR, (2) gas hourly space velocity and (3) reforming-catalyst thickness. The study explains why CPR designed with the segmented combustion-catalyst and co-flow mode shows superior performance not only in terms of high hydrogen production but also in terms of minimizing the maximum reactor plate temperature and thermal hot-spots. The study shows that the segmented coating requires 7% to 8% less combustion-side feed flow and 70% less combustion-catalyst to produce the required flow of hydrogen (29.80 mol/h) on the reforming-side to feed a 1 kW fuel-cell compared to the conventional continuous coating of the combustion-catalyst.

A Fully Magnetically Levitated Circulatory Pump for Advanced Heart Failure.

PubMed

Mehra, Mandeep R; Naka, Yoshifumi; Uriel, Nir; Goldstein, Daniel J; Cleveland, Joseph C; Colombo, Paolo C; Walsh, Mary N; Milano, Carmelo A; Patel, Chetan B; Jorde, Ulrich P; Pagani, Francis D; Aaronson, Keith D; Dean, David A; McCants, Kelly; Itoh, Akinobu; Ewald, Gregory A; Horstmanshof, Douglas; Long, James W; Salerno, Christopher

2017-02-02

Continuous-flow left ventricular assist systems increase the rate of survival among patients with advanced heart failure but are associated with the development of pump thrombosis. We investigated the effects of a new magnetically levitated centrifugal continuous-flow pump that was engineered to avert thrombosis. We randomly assigned patients with advanced heart failure to receive either the new centrifugal continuous-flow pump or a commercially available axial continuous-flow pump. Patients could be enrolled irrespective of the intended goal of pump support (bridge to transplantation or destination therapy). The primary end point was a composite of survival free of disabling stroke (with disabling stroke indicated by a modified Rankin score >3; scores range from 0 to 6, with higher scores indicating more severe disability) or survival free of reoperation to replace or remove the device at 6 months after implantation. The trial was powered for noninferiority testing of the primary end point (noninferiority margin, -10 percentage points). Of 294 patients, 152 were assigned to the centrifugal-flow pump group and 142 to the axial-flow pump group. In the intention-to-treat population, the primary end point occurred in 131 patients (86.2%) in the centrifugal-flow pump group and in 109 (76.8%) in the axial-flow pump group (absolute difference, 9.4 percentage points; 95% lower confidence boundary, -2.1 [P<0.001 for noninferiority]; hazard ratio, 0.55; 95% confidence interval [CI], 0.32 to 0.95 [two-tailed P=0.04 for superiority]). There were no significant between-group differences in the rates of death or disabling stroke, but reoperation for pump malfunction was less frequent in the centrifugal-flow pump group than in the axial-flow pump group (1 [0.7%] vs. 11 [7.7%]; hazard ratio, 0.08; 95% CI, 0.01 to 0.60; P=0.002). Suspected or confirmed pump thrombosis occurred in no patients in the centrifugal-flow pump group and in 14 patients (10.1%) in the axial-flow pump group. Among patients with advanced heart failure, implantation of a fully magnetically levitated centrifugal-flow pump was associated with better outcomes at 6 months than was implantation of an axial-flow pump, primarily because of the lower rate of reoperation for pump malfunction. (Funded by St. Jude Medical; MOMENTUM 3 ClinicalTrials.gov number, NCT02224755 .).

Bubble CPAP versus CPAP with variable flow in newborns with respiratory distress: a randomized controlled trial.

PubMed

Yagui, Ana Cristina Zanon; Vale, Luciana Assis Pires Andrade; Haddad, Luciana Branco; Prado, Cristiane; Rossi, Felipe Souza; Deutsch, Alice D Agostini; Rebello, Celso Moura

2011-01-01

To evaluate the efficacy and safety of nasal continuous positive airway pressure (NCPAP) using devices with variable flow or bubble continuous positive airway pressure (CPAP) regarding CPAP failure, presence of air leaks, total CPAP and oxygen time, and length of intensive care unit and hospital stay in neonates with moderate respiratory distress (RD) and birth weight (BW) ≥ 1,500 g. Forty newborns requiring NCPAP were randomized into two study groups: variable flow group (VF) and continuous flow group (CF). The study was conducted between October 2008 and April 2010. Demographic data, CPAP failure, presence of air leaks, and total CPAP and oxygen time were recorded. Categorical outcomes were tested using the chi-square test or the Fisher's exact test. Continuous variables were analyzed using the Mann-Whitney test. The level of significance was set at p < 0.05. There were no differences between the groups with regard to demographic data, CPAP failure (21.1 and 20.0% for VF and CF, respectively; p = 1.000), air leak syndrome (10.5 and 5.0%, respectively; p = 0.605), total CPAP time (median: 22.0 h, interquartile range [IQR]: 8.00-31.00 h and median: 22.0 h, IQR: 6.00-32.00 h, respectively; p = 0.822), and total oxygen time (median: 24.00 h, IQR: 7.00-85.00 h and median: 21.00 h, IQR: 9.50-66.75 h, respectively; p = 0.779). In newborns with BW ≥ 1,500 g and moderate RD, the use of continuous flow NCPAP showed the same benefits as the use of variable flow NCPAP.

Sensitive Detection of Norovirus Using Phage Nanoparticle Reporters in Lateral-Flow Assay

PubMed Central

Hagström, Anna E. V.; Garvey, Gavin; Paterson, Andrew S.; Dhamane, Sagar; Adhikari, Meena; Estes, Mary K.; Strych, Ulrich; Kourentzi, Katerina; Atmar, Robert L.; Willson, Richard C.

2015-01-01

Noroviruses are recognized worldwide as the principal cause of acute, non-bacterial gastroenteritis, resulting in 19-21 million cases of disease every year in the United States. Noroviruses have a very low infectious dose, a short incubation period, high resistance to traditional disinfection techniques and multiple modes of transmission, making early, point-of-care detection essential for controlling the spread of the disease. The traditional diagnostic tools, electron microscopy, RT-PCR and ELISA require sophisticated and expensive instrumentation, and are considered too laborious and slow to be useful during severe outbreaks. In this paper we describe the development of a new, rapid and sensitive lateral-flow assay using labeled phage particles for the detection of the prototypical norovirus GI.1 (Norwalk), with a limit of detection of 107 virus-like particles per mL, one hundred-fold lower than a conventional gold nanoparticle lateral-flow assay using the same antibody pair. PMID:25978622

Engineering controllable architecture in matrigel for 3D cell alignment.

PubMed

Jang, Jae Myung; Tran, Si-Hoai-Trung; Na, Sang Cheol; Jeon, Noo Li

2015-02-04

We report a microfluidic approach to impart alignment in ECM components in 3D hydrogels by continuously applying fluid flow across the bulk gel during the gelation process. The microfluidic device where each channel can be independently filled was tilted at 90° to generate continuous flow across the Matrigel as it gelled. The presence of flow helped that more than 70% of ECM components were oriented along the direction of flow, compared with randomly cross-linked Matrigel. Following the oriented ECM components, primary rat cortical neurons and mouse neural stem cells showed oriented outgrowth of neuronal processes within the 3D Matrigel matrix.

Fluid mechanics of continuous flow electrophoresis

NASA Technical Reports Server (NTRS)

Saville, D. A.; Ostrach, S.

1978-01-01

The following aspects of continuous flow electrophoresis were studied: (1) flow and temperature fields; (2) hydrodynamic stability; (3) separation efficiency, and (4) characteristics of wide gap chambers (the SPAR apparatus). Simplified mathematical models were developed so as to furnish a basis for understanding the phenomena and comparison of different chambers and operating conditions. Studies of the hydrodynamic stability disclosed that a wide gap chamber may be particularly sensitive to axial temperature variations which could be due to uneven heating or cooling. The mathematical model of the separation process includes effects due to the axial velocity, electro-osmotic cross flow and electrophoretic migration, all including the effects of temperature dependent properties.

An All-vanadium Continuous-flow Photoelectrochemical Cell for Extending State-of-charge in Solar Energy Storage.

PubMed

Wei, Zi; Shen, Yi; Liu, Dong; Liu, Fuqiang

2017-04-04

Greater levels of solar energy storage provide an effective solution to the inherent nature of intermittency, and can substantially improve reliability, availability, and quality of the renewable energy source. Here we demonstrated an all-vanadium (all-V) continuous-flow photoelectrochemical storage cell (PESC) to achieve efficient and high-capacity storage of solar energy, through improving both photocurrent and photocharging depth. It was discovered that forced convective flow of electrolytes greatly enhanced the photocurrent by 5 times comparing to that with stagnant electrolytes. Electrochemical impedance spectroscopy (EIS) study revealed a great reduction of charge transfer resistance with forced convective flow of electrolytes as a result of better mass transport at U-turns of the tortuous serpentine flow channel of the cell. Taking advantage of the improved photocurrent and diminished charge transfer resistance, the all-V continuous-flow PESC was capable of producing ~20% gain in state of charge (SOC) under AM1.5 illumination for ca. 1.7 hours without any external bias. This gain of SOC was surprisingly three times more than that with stagnant electrolytes during a 25-hour period of photocharge.

40 CFR 89.414 - Air flow measurement specifications.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 21 2013-07-01 2013-07-01 false Air flow measurement specifications. 89.414 Section 89.414 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Emission Test Procedures § 89.414 Air flow measurement specifications. (a) The air flow measurement method...

40 CFR 89.414 - Air flow measurement specifications.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 21 2012-07-01 2012-07-01 false Air flow measurement specifications. 89.414 Section 89.414 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Emission Test Procedures § 89.414 Air flow measurement specifications. (a) The air flow measurement method...

40 CFR 89.414 - Air flow measurement specifications.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Air flow measurement specifications. 89.414 Section 89.414 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Emission Test Procedures § 89.414 Air flow measurement specifications. (a) The air flow measurement method...

40 CFR 89.414 - Air flow measurement specifications.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 20 2011-07-01 2011-07-01 false Air flow measurement specifications. 89.414 Section 89.414 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Emission Test Procedures § 89.414 Air flow measurement specifications. (a) The air flow measurement method...

40 CFR 89.415 - Fuel flow measurement specifications.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Fuel flow measurement specifications. 89.415 Section 89.415 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Emission Test Procedures § 89.415 Fuel flow measurement specifications. The fuel flow rate measurement...

40 CFR 90.417 - Fuel flow measurement specifications.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Fuel flow measurement specifications. 90.417 Section 90.417 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Gaseous Exhaust Test Procedures § 90.417 Fuel flow measurement specifications. (a) Fuel flow measurement...

COMPRESSIBLE FLOW, ENTRAINMENT, AND MEGAPLUME

EPA Science Inventory

It is generally believed that low Mach number, i.e., low-velocity, flow may be assumed to be incompressible flow. Under steady-state conditions, an exact equation of continuity may then be used to show that such flow is non-divergent. However, a rigorous, compressible fluid-dynam...

Flow speed of the ablation vapors generated during laser drilling of CFRP with a continuous-wave laser beam

NASA Astrophysics Data System (ADS)

Faas, S.; Freitag, C.; Boley, S.; Berger, P.; Weber, R.; Graf, T.

2017-03-01

The hot plume of ablation products generated during the laser drilling process of carbon fiber reinforced plastics (CFRP) with a continuous-wave laser beam was analyzed by means of high-speed imaging. The formation of compression shocks was observed within the flow of the evaporated material, which is an indication of flow speeds well above the local speed of sound. The flow speed of the hot ablation products can be estimated by analyzing the position of these compression shocks. We investigated the temporal evolution of the flow speed during the drilling process and the influence of the average laser power on the flow speed. The flow speed increases with increasing average laser powers. The moment of drilling through the material changes the conditions for the drilling process and was confirmed to influence the flow speed of the ablated material. Compression shocks can also be observed during laser cutting of CFRP with a moving laser beam.

A Laminar Flow-Based Microfluidic Tesla Pump via Lithography Enabled 3D Printing.

PubMed

Habhab, Mohammed-Baker; Ismail, Tania; Lo, Joe Fujiou

2016-11-23

Tesla turbine and its applications in power generation and fluid flow were demonstrated by Nicholas Tesla in 1913. However, its real-world implementations were limited by the difficulty to maintain laminar flow between rotor disks, transient efficiencies during rotor acceleration, and the lack of other applications that fully utilize the continuous flow outputs. All of the aforementioned limits of Tesla turbines can be addressed by scaling to the microfluidic flow regime. Demonstrated here is a microscale Tesla pump designed and fabricated using a Digital Light Processing (DLP) based 3D printer with 43 µm lateral and 30 µm thickness resolutions. The miniaturized pump is characterized by low Reynolds number of 1000 and a flow rate of up to 12.6 mL/min at 1200 rpm, unloaded. It is capable of driving a mixer network to generate microfluidic gradient. The continuous, laminar flow from Tesla turbines is well-suited to the needs of flow-sensitive microfluidics, where the integrated pump will enable numerous compact lab-on-a-chip applications.

Integrating continuous stocks and flows into state-and-transition simulation models of landscape change

USGS Publications Warehouse

Daniel, Colin J.; Sleeter, Benjamin M.; Frid, Leonardo; Fortin, Marie-Josée

2018-01-01

State-and-transition simulation models (STSMs) provide a general framework for forecasting landscape dynamics, including projections of both vegetation and land-use/land-cover (LULC) change. The STSM method divides a landscape into spatially-referenced cells and then simulates the state of each cell forward in time, as a discrete-time stochastic process using a Monte Carlo approach, in response to any number of possible transitions. A current limitation of the STSM method, however, is that all of the state variables must be discrete.Here we present a new approach for extending a STSM, in order to account for continuous state variables, called a state-and-transition simulation model with stocks and flows (STSM-SF). The STSM-SF method allows for any number of continuous stocks to be defined for every spatial cell in the STSM, along with a suite of continuous flows specifying the rates at which stock levels change over time. The change in the level of each stock is then simulated forward in time, for each spatial cell, as a discrete-time stochastic process. The method differs from the traditional systems dynamics approach to stock-flow modelling in that the stocks and flows can be spatially-explicit, and the flows can be expressed as a function of the STSM states and transitions.We demonstrate the STSM-SF method by integrating a spatially-explicit carbon (C) budget model with a STSM of LULC change for the state of Hawai'i, USA. In this example, continuous stocks are pools of terrestrial C, while the flows are the possible fluxes of C between these pools. Importantly, several of these C fluxes are triggered by corresponding LULC transitions in the STSM. Model outputs include changes in the spatial and temporal distribution of C pools and fluxes across the landscape in response to projected future changes in LULC over the next 50 years.The new STSM-SF method allows both discrete and continuous state variables to be integrated into a STSM, including interactions between them. With the addition of stocks and flows, STSMs provide a conceptually simple yet powerful approach for characterizing uncertainties in projections of a wide range of questions regarding landscape change.

Continuous-flow cold therapy for outpatient anterior cruciate ligament reconstruction.

PubMed

Barber, F A; McGuire, D A; Click, S

1998-03-01

This prospective, randomized study evaluated continuous-flow cold therapy for postoperative pain in outpatient arthroscopic anterior cruciate ligament (ACL) reconstructions. In group 1, cold therapy was constant for 3 days then as needed in days 4 through 7. Group 2 had no cold therapy. Evaluations and diaries were kept at 1, 2, and 8 hours after surgery, and then daily. Pain was assessed using the VAS and Likert scales. There were 51 cold and 49 noncold patients included. Continuous passive movement (CPM) use averaged 54 hours for cold and 41 hours for noncold groups (P=.003). Prone hangs were done for 192 minutes in the cold group and 151 minutes in the noncold group. Motion at 1 week averaged 5/88 for the cold group and 5/79 the noncold group. The noncold group average visual analog scale (VAS) pain and Likert pain scores were always greater than the cold group. The noncold group average Vicodin use (Knoll, Mt. Olive, NJ) was always greater than the cold group use (P=.001). Continuous-flow cold therapy lowered VAS and Likert scores, reduced Vicodin use, increased prone hangs, CPM, and knee flexion. Continuous-flow cold therapy is safe and effective for outpatient ACL reconstruction reducing pain medication requirements.

Continuous monitoring of bacterial attachment

NASA Technical Reports Server (NTRS)

Koeing, D. W.; Mishra, S. K.; Pierson, D. L.

1994-01-01

A major concern with the Space Station Freedom (SSF) water supply system is the control of longterm microbial contamination and biofilm development in the water storage and distribution systems. These biofilms have the potential for harboring pathogens as well as microbial strains containing resistance factors that could negatively influence crew health. The proposed means for disinfecting the water system on SSF (iodine) may encourage the selection of resistant strains. In fact, biofilm bacteria were observed in water lines from the Space Shuttle Columbia (OV-102); therefore, an alternative remediation method is required to disinfect spacecraft water lines. A thorough understanding of colonization events and the physiological parameters that will influence bacteria adhesion is required. The limiting factor for development of this technology is the ability to continuously monitor adhesion events and the effects of biocides on sessile bacteria. Methods were developed to allow bacterial adhesion and subsequent biocidal treatment to be monitored continuously. This technique couples automated image analysis with a continuous flow of a bacterial suspension through an optical flow cell. A strain of Pseudomonas cepacia isolated from the water supply of the Space Shuttle Discovery (OV-103) during STS-39 was grown in a nitrogen-limited continuous culture. This culture was challenged continuously with iodine during growth, and the adhesion characteristics of this strain was measure with regard to flow rate. Various biocides (ozone, hypochlorite, and iodine) were added to the flow stream to evaluate how well each chemical removed the bacteria. After biocide treatment, a fresh bacterial suspension was introduced into the flow cell, and the attachment rate was evaluated on the previously treated surface. This secondary fouling was again treated with biocide to determine the efficacy of multiple batch chemical treatments in removing biofilm.