scholarly journals Configurable Digital Virus Counter on Robust Universal DNA Chips

2020 ◽  
Author(s):  
Elif Seymour ◽  
Nese Lortlar Ünlü ◽  
Eric P. Carter ◽  
John H. Connor ◽  
M. Selim Ünlü
Keyword(s):  
Real Time ◽  
Dna Sequences ◽  
Ebola Virus ◽  
Rapid Test ◽  
Single Step ◽  
Genetically Engineered ◽  
Antibody Array ◽  
Antibody Immobilization ◽  
Chip Surface ◽  
Dna Conjugates

ABSTRACTHere, we demonstrate real-time multiplexed virus detection by applying DNA-directed antibody immobilization technique to a single-particle interferometric reflectance imaging sensor (SP-IRIS). In this technique, the biosensor chip surface spotted with different DNA sequences is converted to a multiplexed antibody array by flowing antibody-DNA conjugates and allowing specific DNA-DNA hybridization. The resulting antibody array is shown to detect three different recombinant Vesicular Stomatitis Viruses (rVSVs) genetically engineered to express surface glycoproteins of Ebola, Marburg, and Lassa viruses in real-time in a disposable microfluidic cartridge. We also show that this method can be modified to produce a single-step, homogeneous assay format by mixing the antibody-DNA conjugates with the virus sample in solution phase prior to flowing in the microfluidic cartridge, eliminating the antibody immobilization step. This homogenous approach achieved detection of the model Ebola virus, rVSV-EBOV, at a concentration of 100 PFU/ml in 1 hour. Finally, we demonstrate the feasibility of this homogeneous technique as a rapid test using a passive microfluidic cartridge. A concentration of 104 PFU/ml was detectable under 10 minutes for the rVSV-Ebola virus. Utilizing DNA microarrays for antibody-based diagnostics is an alternative approach to antibody microarrays and offers advantages such as configurable sensor surface, long-term storage ability, and decreased antibody use. We believe these properties will make SP-IRIS a versatile and robust platform for point-of-care diagnostics applications.

JOINT ESTIMATION OF THE TRANSMISSIBILITY AND SEVERITY OF EBOLA VIRUS DISEASE IN REAL TIME

2017 ◽  
Vol 25 (04) ◽  
pp. 587-603 ◽  
Author(s):  
YUSUKE ASAI ◽  
HIROSHI NISHIURA
Keyword(s):  
Real Time ◽  
Ebola Virus ◽  
Virus Disease ◽  
Critical Role ◽  
Estimation Method ◽  
Case Fatality ◽  
Ascertainment Bias ◽  
Joint Estimation ◽  
Ebola Virus Disease ◽  
Strong Impact

The effective reproduction number [Formula: see text], the average number of secondary cases that are generated by a single primary case at calendar time [Formula: see text], plays a critical role in interpreting the temporal transmission dynamics of an infectious disease epidemic, while the case fatality risk (CFR) is an indispensable measure of the severity of disease. In many instances, [Formula: see text] is estimated using the reported number of cases (i.e., the incidence data), but such report often does not arrive on time, and moreover, the rate of diagnosis could change as a function of time, especially if we handle diseases that involve substantial number of asymptomatic and mild infections and large outbreaks that go beyond the local capacity of reporting. In addition, CFR is well known to be prone to ascertainment bias, often erroneously overestimated. In this paper, we propose a joint estimation method of [Formula: see text] and CFR of Ebola virus disease (EVD), analyzing the early epidemic data of EVD from March to October 2014 and addressing the ascertainment bias in real time. To assess the reliability of the proposed method, coverage probabilities were computed. When ascertainment effort plays a role in interpreting the epidemiological dynamics, it is useful to analyze not only reported (confirmed or suspected) cases, but also the temporal distribution of deceased individuals to avoid any strong impact of time dependent changes in diagnosis and reporting.

Quantitative Detection of Species-Specific DNA in Feedstuffs and Fish Meals

2005 ◽  
Vol 68 (6) ◽  
pp. 1217-1221 ◽  
Author(s):  
PAVEL KRCMAR ◽  
EVA RENCOVA
Keyword(s):  
Mitochondrial Dna ◽  
Real Time ◽  
Dna Sequences ◽  
Real Time Pcr ◽  
Single Species ◽  
Absolute Quantification ◽  
Quantitative Detection ◽  
Vertebrate Species ◽  
Target Species ◽  
Species Specific

A sensitive and rapid method for the quantitative detection of bovine-, ovine-, swine-, and chicken-specific mitochondrial DNA sequences based on real-time PCR has been developed. The specificity of the primers and probes for real-time PCR has been tested using DNA samples of other vertebrate species that may also be present in rendered products. The quantitative detection was performed with dual-labeled probes (TaqMan) using absolute quantification with external standards of single species meat-and-bone meals. This method facilitates the detection of 0.01% of the target species–derived material in concentrate feed mixtures and fish meals.

scholarly journals DETEKSI CLOSTRIDIUM DIFFICILE TOKSIGENIK MENGGUNAKAN UJI CEPAT TOKSIN DAN REAL TIME POLYMERASE CHAIN REACTION (Toxigenic Clostridium Difficile Detection Using Toxin Rapid Test and Real Time Polymerase Chain Reaction)

2018 ◽  
Vol 22 (1) ◽  
pp. 22
Author(s):  
Ika Yasma Yanti ◽  
Dalima Ari Wahono Astrawinata
Keyword(s):  
Polymerase Chain Reaction ◽  
Clostridium Difficile ◽  
Antibiotic Therapy ◽  
Real Time ◽  
Real Time Pcr ◽  
Rapid Test ◽  
Chain Reaction ◽  
Chi Square ◽  
Polymerase Chain ◽  
Clostridium Difficile Associated Diarrhea

Toxigenic Clostridium difficile infection, causing a Pseudo Membrane Colitis (PMC) and Clostridium Difficile Associated Diarrhea(CDAD) has increased sharply. The largest risk factor is the use of antibiotics. The purpose of this study was to know how to determinethe prevalence and characteristics of subjects with Toxigenic Clostridium difficile and to assess the ability of the toxin rapid test comparedto real-time PCR. Ninety adult subjects with antibiotic therapy more than two (2) weeks were enrolled in this study. The results of toxinrapid test and real-time PCR were presented in a 2x2 table, statistical test used was Chi square. The prevalence of Toxigenic Clostridiumdifficile based on the toxin rapid test and by real-time PCR was 27.3% and 37.5%, respectively. There were significant differences betweenstool consistency and number of antibiotics used with the detection of Toxigenic Clostridium difficile. There was a relationship betweenthe duration of antibiotic therapy with the detection of Toxigenic Clostridium difficile using real-time PCR (p=0.010, RR=2.116). Thesensitivity, specificity, PPV, NPV, PLR and NLR rapid test against real-time PCR were 69.7%; 98.2%; 95.8%; 84.4%; 39.2 and 0.31,respectively. This study concluded that the prevalence of Clostridium difficile in RSCM was higher compared to that in Malaysia, Thailandand India; the subjects with antibiotic therapy for more than four (4) weeks had a double risk to have Toxigenic Clostridium difficilethan subjects with antibiotic therapy for less than that time (4 weeks). Thus, in this study, toxin rapid test could be used as a tool todetect Toxigenic Clostridium difficile.

scholarly journals Virus-Vectored Ebola Vaccines

Acta Naturae ◽  
2017 ◽  
Vol 9 (3) ◽  
pp. 4-11 ◽  
Author(s):  
I. V. Dolzhikova ◽  
E. A. Tokarskaya ◽  
A. S. Dzharullaeva ◽  
A. I. Tukhvatulin ◽  
D. V. Shcheblyakov ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Immune Response ◽  
West Africa ◽  
Protective Immunity ◽  
Viral Vectors ◽  
Ebola Virus ◽  
Virus Disease ◽  
Genetically Engineered ◽  
Preclinical Trials

The Ebola virus disease (EVD) is one of the most dangerous infections affecting humans and animals. The first EVD outbreaks occurred in 1976 in Sudan and Zaire. Since then, more than 20 outbreaks have occurred; the largest of which (2014-2016) evolved into an epidemic in West Africa and claimed the lives of more than 11,000 people. Although vaccination is the most effective way to prevent epidemics, there was no licensed vaccine for EVD at the beginning of the latest outbreak. The development of the first vaccines for EVD started in 1980 and has come a long technological way, from inactivated to genetically engineered vaccines based on recombinant viral vectors. This review focuses on virus-vectored Ebola vaccines that have demonstrated the greatest efficacy in preclinical trials and are currently under different phases of clinical trial. Particular attention is paid to the mechanisms of immune response development, which are important for protection from EVD, and the key vaccine parameters necessary for inducing long-term protective immunity against EVD.

EMBRYO MANIPULATION AND GENE TRANSFER IN LIVESTOCK

1985 ◽  
Vol 65 (3) ◽  
pp. 527-538 ◽  
Author(s):  
R. B. CHURCH ◽  
F. J. SCHAUFELE ◽  
K. MECKLING
Keyword(s):  
Gene Transfer ◽  
Genetic Engineering ◽  
Embryo Transfer ◽  
Dna Sequences ◽  
Recombinant Dna ◽  
Fusion Gene ◽  
Bovine Genome ◽  
Monozygotic Twins ◽  
Genetically Engineered ◽  
Livestock Species

In the past few years significant progress has been made in manipulation of reproduction and in development of genetic engineering techniques which can be applied to animal species. Artificial insemination and embryo transfer are now used widely in the livestock industry. The advent of non-surgical embryo collection and transfer, embryo freezing and splitting along with estrus synchronization has allowed the industry to move from the laboratory to the farm. Embryo manipulation now involves embryo splitting to produce monozygotic twins, in vitro fertilization, cross-species fertilization, embryo sexing, and chimeric production of tetraparental animals among others. Advances in recombinant DNA, plasmid construction and embryo manipulation technologies allow the production of genetically engineered animals. The application of recombinant DNA technology involves the isolation and manipulation of desired genes which have potential for significant changes in productivity in genetically engineered livestock. Recombinant DNA constructs involve the coupling of promoter, enhancer, regulatory and structural DNA sequences to form a "fusion gene" which can then be multiplied, purified, assayed and expressed in cell culture prior to being introduced into an animal genome. Such DNA gene constructs are readily available for many human and mouse genes. However, they are not readily available for livestock species because the detailed molecular biology has not yet been established in these species. Gene transfer offers a powerful new tool in animal research. Transfer of genes into the bovine genome has been accomplished. However, successful directed expression of these incorporated genes has not been achieved to date. New combinations of fusion genes may be an effective way of producing transgenic domestic animals which show controlled expression of the desired genes. Embryo manipulation and genetic engineering in livestock species is moving rapidly. The problems being addressed at present in numerous laboratories will result in enhanced livestock production in the not too distant future. Key words: Embryo transfer, embryo manipulation, transgenic livestock, genetic engineering, gene transfer, monozygotic twins

scholarly journals APPLICATION OF CHAOS GAME REPRESENTATION TO NONLINEAR TIME SERIES ANALYSIS

Fractals ◽  
2006 ◽  
Vol 14 (01) ◽  
pp. 27-35 ◽  
Author(s):  
TOMOYA SUZUKI ◽  
TOHRU IKEGUCHI ◽  
MASUO SUZUKI
Keyword(s):  
Time Series ◽  
Real Time ◽  
Dna Sequences ◽  
Surrogate Data ◽  
Nonlinear Time Series Analysis ◽  
Conditional Probabilities ◽  
Fractal Structures ◽  
Chaos Game Representation ◽  
Chaos Game ◽  
Game Representation

Iterative function systems are often used for investigating fractal structures. The method is also referred as Chaos Game Representation (CGR), and is applied for representing characteristic structures of DNA sequences visually. In this paper, we proposed an original way of plotting CGR to easily confirm the property of the temporal evaluation of a time series. We also showed existence of spurious characteristic structures of time series, if we carelessly applied the CGR to real time series. We revealed that the source of spurious identification came from non-uniformity of the frequency histograms of the time series, which is often the case of analyzing real time series. We also showed how to avoid such spurious identification by applying the method of surrogate data and introducing conditional probabilities of the time series.

Comparison of two rapid test kits with real time polymerase chain reaction for early diagnosis of dengue in Sri Lanka

2021 ◽  
pp. 1-9
Author(s):  
MHJD Ariyaratne ◽  
Peshala Gunasekara ◽  
Poornima Hasanthi Wajirasena ◽  
Dilini Malsha Rathnayake ◽  
Desha Dilani ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Sri Lanka ◽  
Early Diagnosis ◽  
Real Time ◽  
Rapid Test ◽  
Chain Reaction ◽  
Polymerase Chain

scholarly journals FPGA Implementation of a Single Step MFCV Estimator Based on EMG in Diabetic Neuropathy

2018 ◽  
Vol 2018 ◽  
pp. 1-10
Author(s):  
Daniela De Venuto ◽  
Giovanni Mezzina
Keyword(s):  
Diabetic Neuropathy ◽  
Real Time ◽  
Muscle Fibre ◽  
Diagnostic System ◽  
Correlation Method ◽  
Single Step ◽  
Velocity Estimation ◽  
In Vivo Test ◽  
Starting Point

This paper details the design and the hardware implementation of a real-time diagnostic system based on FPGA for the muscle fibre conduction velocity estimation (MFCV). The MFCV is considered as a principal monitoring index for diabetic neuropathy (DPN), as well as in muscle fatigue assessment, to evaluate the muscle fibre status. The FPGA platform evaluates the MFCV during dynamic contractions (e.g., gait), by exploiting a multichannel sensing system composed of 4 wireless surface EMG electrodes, placed in pair on each leg. Raw data are digitized and made binary to create two bitstreams for each monitored limb. Then, a comparison between the two-bit streamed EMGs extracted from the same leg is carried out. The comparison, which allows extracting the MFCV, exploits a computationally light version of the cross-correlation method. The overall architecture implemented and validated on an Altera Cyclone V FPGA is HPS-free and exploits 22.5% ALMs, 10,874 ALUTs, 9.81% registers, 3.36% block memory, and <2.7% of the total wires available on the platform. The choice of FPGA as computing system lies in the possibility to determine resource utilization, related timing constraints for a future real-time ASIC implementation in wearable applications. From the actual muscle contraction during gait (cyclical starting point of the computing), the system spends about 316 ms to acquire useful data and 47.5 ms (on average) to process the signal and provide the output, dynamically dissipating 28.6 mW. The accuracy of the tool evaluation has been evaluated proving the repeatability of the measurements by in vivo test. In this context, 1250 contractions from each subject involved in a protocolled 10-meter walk have been acquired (n=10 subjects evaluated). On average, the same MFCV estimation has been extracted on 1184/1250 contractions (standard deviation of 11 contractions), reaching an accuracy of 94.7%. These estimations fully match the physiological value range reported in literature.

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