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https://www.readbyqxmd.com/read/28213308/simultaneous-estimation-of-detection-sensitivity-and-absolute-copy-number-from-digital-pcr-serial-dilution
#1
Xutao Deng, Brian S Custer, Michael P Busch, Sonia Bakkour, Tzong-Hae Lee
Digital polymerase chain reaction (dPCR) is a refinement of the conventional PCR approach to nucleic acid detection and absolute quantification. Digital PCR works by partitioning a sample of DNA or cDNA into many individual, parallel PCR reactions. Current quantification methods rely on the assumption that the PCR reactions are always able to detect single target molecules. When the assumption does not hold, the copy numbers will be severely underestimated. We developed a novel dPCR quantification method which determines whether the single copy assumption is violated or not by simultaneously estimating the assay sensitivity and the copy numbers using serial dilution data sets...
February 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28213086/comparison-of-protocols-for-the-analysis-of-type-1-porcine-reproductive-and-respiratory-syndrome-virus-by-rt-pcr-using-oral-fluids
#2
Elisa Gibert, Gerard Martín-Valls, Enric Mateu
The detection of porcine reproductive and respiratory syndrome virus (PRRSV) in oral fluids (OF) by quantitative real-time polymerase chain reaction (qRT-PCR) is gaining increasing popularity. However, the different steps leading to a result have not been extensively evaluated. The aim of the present study was to examine the effect on the performance of qRT-PCR with different sampling materials, conditions of storage of the OF, the need for centrifuging OF, as well as to compare RNA extraction methods and PCR mixes...
February 14, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28208248/development-of-a-sers-based-rapid-vertical-flow-assay-for-point-of-care-diagnostics
#3
O J R Clarke, B L Goodall, H P Hui, N Vats, C L Brosseau
Point-of-care (POC) diagnostic testing platforms are a growing sector of the healthcare industry as they offer the advantages of rapid provision of results, ease of use, reduced cost, and the ability to link patients to care. While many POC tests are based on chromatographic flow assay technology, this technology suffers from a lack of sensitivity along with limited capacity for multiplexing and quantitative analysis. Several recent reports have begun to investigate the feasibility of coupling chromatographic flow platforms to more advanced read-out technologies which in turn enable on-site acquisition, storage, and transmission of important healthcare metrics...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28204952/a-preliminary-report-of-indigenous-fungal-isolates-from-contaminated-municipal-solid-waste-site-in-india
#4
Abhishek Kumar Awasthi, Akhilesh Kumar Pandey, Jamaluddin Khan
Municipal solid waste (MSW) containing harmful substances is a major concern in waste management and can cause adverse effects on diversity of fungi in soil. The main objective was to evaluate the fungal diversity inhabiting in the soil nearby MSW disposal site. The fungal strains were isolated in potato dextrose agar (PDA), media at temperatures 28 ± 1 °C by using standard serial dilution pour plate method, and appeared fungal colonies identified based on morphological characteristics. The overall most fungal diversity was found in soil sample collected from S5, followed by S4, S3, S1, and least in S2 site...
February 15, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28199149/a-genetic-method-to-evaluate-the-prevalence-of-unique-dna-profiles-between-sequential-ground-beef-batches
#5
G Peters, B Cleveland, J Higgins, F Butler, C Meghen
The delineation of ground beef batches has implications for the management of product disposition policies in the event of Shiga toxin-producing Escherichia coli contamination. Analysis of individual contributor animal-specific DNA profiles can provide valuable empirical data for understanding the dynamics of ground meat production processes and can act as a surrogate for cross-contamination. A genetic method was developed for characterizing the source raw material flow and carryover between discrete batches of ground beef in a large-scale commercial beef grinding operation...
February 15, 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28194365/antibacterial-effect-of-urushiol-on-e-faecalis-as-a-root-canal-irrigant
#6
Sang-Wan Kim, Dong-Hoon Shin
OBJECTIVES: The purpose of this study was to compare the antibacterial activity of urushiol against Enterococcus faecalis (E. faecalis) to that of NaOCl. MATERIALS AND METHODS: The canals of thirty two single rooted human teeth were instrumented with Ni-Ti files (ProTaper Next X1, X2, X3, Dentsply). A pure culture of E. faecalis ATCC 19433 was prepared in sterile brain heart infusion (BHI) broth. The teeth were submerged in the suspension of E. faecalis and were incubated at 37℃ for 7 days to allow biofilm formation...
February 2017: Restorative Dentistry & Endodontics
https://www.readbyqxmd.com/read/28193164/proposed-phase-2-step-2-in-vitro-test-on-basis-of-en-14561-for-standardised-testing-of-the-wound-antiseptics-pvp-iodine-chlorhexidine-digluconate-polihexanide-and-octenidine-dihydrochloride
#7
Kathrin Schedler, Ojan Assadian, Uta Brautferger, Gerald Müller, Torsten Koburger, Simon Classen, Axel Kramer
BACKGROUND: Currently, there is no agreed standard for exploring the antimicrobial activity of wound antiseptics in a phase 2/ step 2 test protocol. In the present study, a standardised in-vitro test is proposed, which allows to test potential antiseptics in a more realistically simulation of conditions found in wounds as in a suspension test. Furthermore, factors potentially influencing test results such as type of materials used as test carrier or various compositions of organic soil challenge were investigated in detail...
February 13, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28192483/development-of-a-high-throughput-method-to-evaluate-serum-bactericidal-activity-using-bacterial-atp-measurement-as-survival-readout
#8
Francesca Necchi, Allan Saul, Simona Rondini
Serum Bactericidal Activity (SBA) assay is the method of choice to evaluate the complement-mediated functional activity of both infection- and vaccine-induced antibodies. To perform a typical SBA assay, serial dilutions of sera are incubated with target bacterial strains and complement. The conventional SBA assay is based on plating on agar the SBA reaction mix and counting the surviving bacterial colony forming units (CFU) at each serum dilution. Even with automated colony counting, it is labor-intensive, time-consuming and not amenable for large-scale studies...
2017: PloS One
https://www.readbyqxmd.com/read/28183170/physico-chemical-properties-of-late-incubation-egg-amniotic-fluid-and-a-potential-in-ovo-feed-supplement
#9
Apeh A Omede, Momenuzzaman M Bhuiyan, Fakrul A Islam, Paul A Iji
This study explored the physico-chemical properties of late-incubation egg amniotic fluid and a potential in ovo feed (IOF) supplement. Amniotic fluid was collected from broiler breeders (Ross 308, 51 weeks and Cobb 500, 35 weeks) on day 17 after incubation. A mixture of high-quality soy protein supplement - Hamlet Protein AviStart (HPA) was serially diluted in MilliQ water to obtain solutions ranging from 150 to 9.375 mg/ml. The mixtures were heat-treated (0, 30, 60 minutes) in a waterbath (80 oC) and then centrifuged to obtain supernatants...
January 26, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28181333/respiratory-motion-artifacts-during-arterial-phase-imaging-with-gadoxetic-acid-can-the-injection-protocol-minimize-this-drawback
#10
Stephan H Polanec, Hubert Bickel, Pascal A T Baltzer, Patrick Thurner, Florian Gittler, Jacqueline C Hodge, Mustafa R Bashir, Ahmed Ba-Ssalamah
PURPOSE: To determine which of three gadoxetic acid injection techniques best reduced the contrast-related arterial-phase motion artifacts. MATERIALS AND METHODS: This Institutional Review Board (IRB)-approved, retrospective study included a cohort of 78 consecutive patients who each had serial gadoxetic acid-enhanced 3.0T magnetic resonance imaging (MRI) of the liver (0.025 mmol/kg body weight) performed with at least two of three injection techniques: M1 test bolus, undiluted, power-injected 1 mL/s; M2 test bolus, diluted 50% with saline, power-injected 1 mL/s; M3 fixed delay, undiluted, manually injected...
February 9, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/28177537/rapid-sensitive-detection-of-bacteria-in-platelet-samples-with-fountain-flow-cytometry
#11
Paul Johnson, Mika Moriwaki, Joseph Johnson
BACKGROUND: There is a current need to develop a technique for bacterial screening of platelet donations that is more rapid, sensitive, and economical than alternatives. The objective of this research was to perform a pilot test of the viability of Fountain Flow Cytometry (FFC), for the rapid and sensitive detection of bacteria in platelet donations. METHODS: Platelet samples were inoculated with serial dilutions of five selected bacterial strains. Samples were then centrifuged, reconstituted in buffer, and stained with a live/dead bacterial stain cocktail...
February 8, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28166243/development-of-a-gexp-multiplex-pcr-assay-for-the-simultaneous-detection-and-differentiation-of-six-cattle-viruses
#12
Qing Fan, Zhixun Xie, Zhiqin Xie, Xianwen Deng, Liji Xie, Li Huang, Sisi Luo, Jiaoling Huang, Yanfang Zhang, Tingting Zeng, Sheng Wang, Jiabo Liu, Yaoshan Pang
Foot-and-mouth disease virus (FMDV), Bluetongue virus (BTV), Vesicular stomatitis Virus (VSV), Bovine viral diarrheal (BVDV), Bovine rotavirus (BRV), and Bovine herpesvirus 1 (IBRV) are common cattle infectious viruses that cause a great economic loss every year in many parts of the world. A rapid and high-throughput GenomeLab Gene Expression Profiler (GeXP) analyzer-based multiplex PCR assay was developed for the simultaneous detection and differentiation of these six cattle viruses. Six pairs of chimeric primers consisting of both the gene-specific primer and a universal primer were designed and used for amplification...
2017: PloS One
https://www.readbyqxmd.com/read/28163966/an-active-principle-of-nigella-sativa-l-thymoquinone-showing-significant-antimicrobial-activity-against-anaerobic-bacteria
#13
Mohammad Akram Randhawa, Awwad Khalaf Alenazy, Majed Gorayan Alrowaili, Jamith Basha
AIM/BACKGROUND: Thymoquinone (TQ) is the major active principle of Nigella sativa seed (black seed) and is known to control many fungi, bacteria, and some viruses. However, the activity of TQ against anaerobic bacteria is not well demonstrated. Anaerobic bacteria can cause severe infections, including diarrhea, aspiration pneumonia, and brain abscess, particularly in immunodeficient individuals. The present study aimed to investigate the in vitro antimicrobial activity of TQ against some anaerobic pathogens in comparison to metronidazole...
January 2017: Journal of Intercultural Ethnopharmacology
https://www.readbyqxmd.com/read/28157839/establishment-of-a-method-for-evaluating-endothelial-cell-injury-by-tnf-%C3%AE-in-vitro-for-clarifying-the-pathophysiology-of-virus-associated-acute-encephalopathy
#14
Kyohei Miyazaki, Koichi Hashimoto, Masatoki Sato, Masahiro Watanabe, Naoki Tomikawa, Shuto Kanno, Yukihiko Kawasaki, Nobuo Momoi, Mitsuaki Hosoya
BACKGROUND: Virus-associated acute encephalopathy (VAE) is a severe central nervous system complication caused by common viral infections in children. The pathophysiology of VAE is thought to be endothelial injury. This study was designed to establish an in vitro VAE model for evaluating endothelial injury caused by the proinflammatory cytokine TNF-α. METHODS: Transwell-grown human umbilical vein endothelial cells (HUVECs) monolayers were incubated with serially diluted TNF-α...
February 3, 2017: Pediatric Research
https://www.readbyqxmd.com/read/28153803/development-of-duplex-pcr-for-simultaneous-detection-of-theileria-spp-and-anaplasma-spp-in-sheep-and-goats
#15
Yanyan Cui, Yan Zhang, Fuchun Jian, Longxian Zhang, Rongjun Wang, Shuxuan Cao, Xiaoxing Wang, Yaqun Yan, Changshen Ning
Theileria spp. and Anaplasma spp., which are important tick-borne pathogens (TBPs), impact the health of humans and animals in tropical and subtropical areas. Theileria and Anaplasma co-infections are common in sheep and goats. Following alignment of the relevant DNA sequences, two primer sets were designed to specifically target the Theileria spp. 18S rRNA and Anaplasma spp. 16S rRNA gene sequences. Genomic DNA from the two genera was serially diluted tenfold for testing the sensitivities of detection of the primer sets...
January 30, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28152008/highly-sensitive-detection-of-a-her2-12-base-pair-duplicated-insertion-mutation-in-lung-cancer-using-the-eprobe-pcr-method
#16
Yoshiaki Takase, Kengo Usui, Kimihiro Shimizu, Yasumasa Kimura, Tatsuo Ichihara, Takahiro Ohkawa, Jun Atsumi, Yasuaki Enokida, Seshiru Nakazawa, Kai Obayashi, Yoichi Ohtaki, Toshiteru Nagashima, Yasumasa Mitani, Izumi Takeyoshi
Somatic mutation in human epidermal growth factor receptor-related 2 gene (HER2) is one of the driver mutations in lung cancer. HER2 mutations are found in about 2% of lung adenocarcinomas (ADCs). Previous reports have been based mainly on diagnostic screening by Sanger sequencing or next-generation sequencing (NGS); however, these methods are time-consuming and complicated. We developed a rapid, simple, sensitive mutation detection assay for detecting HER2 12 base pair-duplicated insertion mutation based on the Eprobe-mediated PCR method (Eprobe-PCR) and validated the sensitivity of this assay system for clinical diagnostics...
2017: PloS One
https://www.readbyqxmd.com/read/28138088/multi-center-evaluation-of-the-automated-immunohematology-instrument-the-ortho-vision-analyzer
#17
Agnes Aysola, Leslie Wheeler, Richard Brown, Rebecca Denham, Connie Colavecchia, Katerina Pavenski, Elizabeth Krok, Chelsea Hayes, Ellen Klapper
BACKGROUND: ORTHO VISION Analyzer (Vision), is an immunohematology instrument using ID-MT gel card technology with digital image processing. It has a continuous, random sample access with STAT priority processing. The efficiency and ease of operation of Vision was evaluated at 5 medical centers. METHODS: De-identified patient samples were tested on the ORTHO ProVue Analyzer (ProVue) and repeated on the Vision mimicking the daily workload pattern. Turnaround times (TAT) were collected and compared...
February 2017: Laboratory Medicine
https://www.readbyqxmd.com/read/28131737/in%C3%A2-vitro-activity-of-nitazoxanide-against-some-metronidazole-resistant-and-susceptible-trichomonas-vaginalis-isolates
#18
Aida A Abdel-Magied, Marwa M Hammouda, Alaa Mosbah, Abeer A El-Henawy
Trichomonas vaginalis cases refractory to metronidazole (MTZ) treatment had been reported. This study aimed to the assessment of in vitro metronidazole resistance among Trichomonas positive cases with treatment failure by determination of metronidazole minimal lethal concentration (MLC), and to the evaluation of the in vitro efficacy of nitazoxanide (NTZ) as compared to metronidazole (MTZ) in both resistant and susceptible isolates. Drug testing was carried out by an aerobic tube assay where suspension of Trichomonas trophozoites was exposed for 24 and 48 h to serial dilution of metronidazole and nitazoxanide...
January 25, 2017: Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy
https://www.readbyqxmd.com/read/28125707/digital-pcr-improves-mutation-analysis-in-pancreas-fine-needle-aspiration-biopsy-specimens
#19
Shonan Sho, Colin M Court, Stephen Kim, David R Braxton, Shuang Hou, V Raman Muthusamy, Rabindra R Watson, Alireza Sedarat, Hsian-Rong Tseng, James S Tomlinson
Applications of precision oncology strategies rely on accurate tumor genotyping from clinically available specimens. Fine needle aspirations (FNA) are frequently obtained in cancer management and often represent the only source of tumor tissues for patients with metastatic or locally advanced diseases. However, FNAs obtained from pancreas ductal adenocarcinoma (PDAC) are often limited in cellularity and/or tumor cell purity, precluding accurate tumor genotyping in many cases. Digital PCR (dPCR) is a technology with exceptional sensitivity and low DNA template requirement, characteristics that are necessary for analyzing PDAC FNA samples...
2017: PloS One
https://www.readbyqxmd.com/read/28124796/comparison-of-different-enzyme-linked-immunosorbent-assay-methods-for-avidity-determination-of-antiphospholipid-antibodies
#20
Lenka Fialová, Milada Petráčková, Oliver Kuchař
BACKGROUND: Avidity of antiphospholipid antibodies may be clinically useful as a valuable additional characteristic. The aim of this study was to compare several ELISA modifications with different chaotropic agents and calculation of avidity indices for the determination of anticardiolipin antibody (aCL) avidity. METHODS: We examined 28 serum samples with positive IgG aCL by adapted ELISA using various concentrations of urea and sodium chloride as chaotropic agents and different dilution of sera...
January 26, 2017: Journal of Clinical Laboratory Analysis
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