scholarly journals A framework for analysis of real-time nucleic acid amplification data using novel multidimensional standard curves

2018 ◽  
Author(s):  
Ahmad Moniri ◽  
Jesus Rodriguez-Manzano ◽  
Pantelis Georgiou
Keyword(s):  
Feature Space ◽  
Absolute Quantification ◽  
Clinical Diagnostics ◽  
Nucleic Acid Amplification ◽  
Multidimensional Space ◽  
Standard Curve ◽  
New Concepts ◽  
Mathematical Techniques ◽  
The Cost ◽  
Lambda Dna

ABSTRACTResearch into improving methods for absolute quantification of nucleic acids using standard curves has plateaued despite its positive, far-reaching impact on biomedical applications and clinical diagnostics. Currently, the mathematics involved in this mature area is restricted by the simplicity of conventional standard curves such as the gold standard cycle-threshold (Ct) method. Here, we propose a novel framework that expands current methods into multidimensional space and opens the door for more complex mathematical techniques, signal processing and machine learning to be implemented. The heart of this work revolves around two new concepts: the multidimensional standard curve and its home - the feature space. This work has been validated using phage lambda DNA and standard qPCR instruments. We show that the capabilities of standard curves can be extended in order to simultaneously: enhance absolute quantification, detect outliers and provide insights into the intersection between molecular biology and amplification data. This work and its vision aims to maximise the information extracted from amplification data using current instruments without increasing the cost or complexity of existing diagnostic settings.

scholarly journals Demonstration of an integrated nanophotonic chip-scale alkali vapor magnetometer using inverse design

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Yoel Sebbag ◽  
Eliran Talker ◽  
Alex Naiman ◽  
Yefim Barash ◽  
Uriel Levy
Keyword(s):  
Spatial Resolution ◽  
Near Field ◽  
Computer Assisted ◽  
Experimental Characterization ◽  
Optical Isolation ◽  
New Concepts ◽  
On Chip ◽  
The Cost ◽  
Micrometer Scale

AbstractRecently, there has been growing interest in the miniaturization and integration of atomic-based quantum technologies. In addition to the obvious advantages brought by such integration in facilitating mass production, reducing the footprint, and reducing the cost, the flexibility offered by on-chip integration enables the development of new concepts and capabilities. In particular, recent advanced techniques based on computer-assisted optimization algorithms enable the development of newly engineered photonic structures with unconventional functionalities. Taking this concept further, we hereby demonstrate the design, fabrication, and experimental characterization of an integrated nanophotonic-atomic chip magnetometer based on alkali vapor with a micrometer-scale spatial resolution and a magnetic sensitivity of 700 pT/√Hz. The presented platform paves the way for future applications using integrated photonic–atomic chips, including high-spatial-resolution magnetometry, near-field vectorial imaging, magnetically induced switching, and optical isolation.

scholarly journals Embedding Undersampling Rotation Forest for Imbalanced Problem

2018 ◽  
Vol 2018 ◽  
pp. 1-15 ◽  
Author(s):  
Huaping Guo ◽  
Xiaoyu Diao ◽  
Hongbing Liu
Keyword(s):  
Imbalanced Data ◽  
Feature Space ◽  
Original Data ◽  
Training Set ◽  
Data Set ◽  
Minority Class ◽  
Rotation Forest ◽  
Novel Method ◽  
Individual Classifier ◽  
The Cost

Rotation Forest is an ensemble learning approach achieving better performance comparing to Bagging and Boosting through building accurate and diverse classifiers using rotated feature space. However, like other conventional classifiers, Rotation Forest does not work well on the imbalanced data which are characterized as having much less examples of one class (minority class) than the other (majority class), and the cost of misclassifying minority class examples is often much more expensive than the contrary cases. This paper proposes a novel method called Embedding Undersampling Rotation Forest (EURF) to handle this problem (1) sampling subsets from the majority class and learning a projection matrix from each subset and (2) obtaining training sets by projecting re-undersampling subsets of the original data set to new spaces defined by the matrices and constructing an individual classifier from each training set. For the first method, undersampling is to force the rotation matrix to better capture the features of the minority class without harming the diversity between individual classifiers. With respect to the second method, the undersampling technique aims to improve the performance of individual classifiers on the minority class. The experimental results show that EURF achieves significantly better performance comparing to other state-of-the-art methods.

scholarly journals UJI AKTIVITAS EKSTRAK BUAS-BUAS (PREMNA SERRATIFOLIA LINN) SEBAGAI ANTI KOLESTEROL SECARA IN VITRO

2017 ◽  
Vol 5 (1) ◽  
Author(s):  
Dini Hadiarti
Keyword(s):  
Solvent Extraction ◽  
Side Effects ◽  
Herbal Medicine ◽  
Cholesterol Concentration ◽  
Standard Curve ◽  
Synthetic Drugs ◽  
Standard Solution ◽  
The Cost

ABSTRACTPremna Serratifolia Linn is believed to reduce cholesterol and as an alternative herbal medicine solution among the cost of medicine and the side effects caused by synthetic drugs. This study was conducted in several phases by using Premna Serratifolia Linn which was drained, mashed, and macerated using ethanol, choloform, and n-heksane. Extract obtained from evaporation, then whighed, and stored in a desiccators. Anti-cholesterol activity was tested test by using in vitro : began with determination of the maximum wavelength of the cholesterol standard solution with a UV-Vis spectrophotometer and continued by manufacturing the standard curve with the cholesterol concentration of 0.5; 0.75; 1; 1.25; and 1.5 mL and 1000 ppm cholesterol solution. Furthermore, maximum absorbance wavelength was measured in order to obtain the maximum wavelength of the cholesterol. The study reveled that the solvent extraction of ethanol produced the largest  rendement. The extract Premna Serratifolia Linn is functioned as an anti-cholesterol. In addition,  the absorbed reduction of 100 ppm cholesterol standard solution found in the addition of 0.5 mL choloform extract.Keywords: Anti-cholesterol, Premna Serratifolia Linn, In Vitro

scholarly journals Clinical diagnostic application of metagenomic next-generation sequencing in children with severe pneumonia

2019 ◽  
Author(s):  
Heping Wang ◽  
Zhiwei Lu ◽  
Yaomin Bao ◽  
Yonghong Yang ◽  
Ronald de Groot ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mycoplasma Pneumoniae ◽  
Severe Pneumonia ◽  
Clinical Diagnostics ◽  
Nucleic Acid Amplification ◽  
Direct Immunofluorescence ◽  
Specific Information ◽  
Next Generation ◽  
Blood Tests ◽  
Generation Sequencing

Abstract Background: Pneumonia is one of the most important causes of morbidity and mortality in children. Identification and characterization of pathogens that cause infections are crucial for accurate treatment and accelerated recovery of the patients. However, in most cases the causative agent cannot be identified partly due to the limited spectrum covered by current diagnostics based on nucleic acid amplification. Therefore, in this study we explored the application of metagenomic next-generation sequencing (mNGS) for the diagnosis of children with severe pneumonia. Methods: From April to July 2017, 32 children were hospitalized with severe pneumonia in Shenzhen Children’s Hospital. Blood tests were conducted immediately after hospitalization to assess infection, oropharygeal swabs were collected to identify common pathogens. After bronchoscopy, bronchoalveolar lavage fluids (BALFs) were collected for further pathogen identification using standardized laboratory and mNGS. Results: Blood tests were normal in 3 of the 32 children. In oropharygeal swabs from 5 patients Mycoplasma pneumoniae by qPCR, 27 cases showed negative results for common pathogens. In BALFs we detected 6 cases with Mycoplasma pneumoniae with qPCR, 9 patients with adenovirus by using a Direct Immunofluorescence Assay (DFA) and 4 patients with bacterial infections, as determined by culture, In 3 of the cases a co-infection was detected. In 15 cases no common pathogens were found in BALF samples, using the current diagnostics, while in all the 32 BALFS pathogens were identified using mNGS, including adenovirus, Mycoplasma pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, cytomegalovirus andbocavirus. Conclusions: mNGS can increase the sensitivity of detection of the causative pathogens in children with severe pneumonia. In addition, mNGS will give more strain specific information, will help to identify new pathogens and could potentially help to trace and control outbreaks. In this study we have shown that it is feasible to have the results within 24 hours, making the application of mNGS feasible for clinical diagnostics.

scholarly journals Prospect and Competence of Quantitative Methods via Real-time PCR in a Comparative Manner: An Experimental Review of Current Methods

2018 ◽  
Vol 11 (1) ◽  
pp. 1-11
Author(s):  
Hossein Mahboudi ◽  
Negin Mohammadizadeh Heidari ◽  
Zahra Irani Rashidabadi ◽  
Ali Houshmand Anbarestani ◽  
Soroush Karimi ◽  
...  
Keyword(s):  
Internal Control ◽  
Copy Number ◽  
Quantitative Methods ◽  
Absolute Quantification ◽  
Relative Quantification ◽  
Absolute Quantitation ◽  
Standard Curve ◽  
Qpcr Quantification ◽  
Comparative Manner

Background: There are numerous approaches dealing with relative and absolute quantitation. The methods differ in their efficiency assumption and applicability. Objective: Current methodologies and rations used in qPCR quantification were compared in an experimental study of transgenic copy number determination of a monoclonal antibody Daclizumab. Methods: With an inter and intra-methodical view, variations in relative and absolute quantification strategies were discretely extracted and compared to one another. Results: In relative quantification, six methods were studied and the ratios were computed relative to Glucagon as internal control. For Absolute quantification, the calculations were based on standard curve. Relative quantification considers the relative changes in expression levels while Absolute quantification relates the PCR signal to input copy number with a calibration curve. Conclusion: The observed unevenness of the ratios in Relative approach pointed mainly to the efficiency changes and its calculation formula. Whereas results in Absolute approach strategies showed homogeneity which indicates the consistency of the calculation method.

Should we still be testing for asymptomatic non-specific urethritis in departments of genitourinary medicine?

2005 ◽  
Vol 16 (4) ◽  
pp. 273-277 ◽  
Author(s):  
P J Horner
Keyword(s):  
Current Practice ◽  
Cost Effective ◽  
Review Article ◽  
Nucleic Acid Amplification ◽  
Sexually Transmitted ◽  
Non Invasive ◽  
Genitourinary Medicine ◽  
The Cost ◽  
Urine Specimens ◽  
Asymptomatic Men

It has recently been advocated that non-invasive testing with first-catch urine specimens using nucleic acid amplification techniques, to detect Chlamydia trachomatis and Neisseria gonorrhoeae, should replace routine microscopy on asymptomatic men. Although it is assumed that this strategy will be cost effective, the available evidence suggests that this will result in fewer sexually transmitted infections being averted than continuing the current practice of screening for urethritis and testing for both microorganisms in asymptomatic men. This review article summarizes the available evidence and argues that research is urgently needed in order to properly evaluate the cost-effectiveness of detecting urethritis in asymptomatic men.

scholarly journals Universal amplification-free molecular diagnostics by billion-fold hierarchical nanofluidic concentration

2019 ◽  
Vol 116 (33) ◽  
pp. 16240-16249 ◽  
Author(s):  
Wei Ouyang ◽  
Jongyoon Han
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Molecular Diagnostics ◽  
Troponin I ◽  
Direct Detection ◽  
Signal To Noise Ratio ◽  
Protein Detection ◽  
Clinical Diagnostics ◽  
Nucleic Acid Amplification ◽  
Enzyme Linked Immunosorbent Assay

Rapid and reliable detection of ultralow-abundance nucleic acids and proteins in complex biological media may greatly advance clinical diagnostics and biotechnology development. Currently, nucleic acid tests rely on enzymatic processes for target amplification (e.g., PCR), which have many inherent issues restricting their implementation in diagnostics. On the other hand, there exist no protein amplification techniques, greatly limiting the development of protein-based diagnosis. We report a universal biomolecule enrichment technique termed hierarchical nanofluidic molecular enrichment system (HOLMES) for amplification-free molecular diagnostics using massively paralleled and hierarchically cascaded nanofluidic concentrators. HOLMES achieves billion-fold enrichment of both nucleic acids and proteins within 30 min, which not only overcomes many inherent issues of nucleic acid amplification but also provides unprecedented enrichment performance for protein analysis. HOLMES features the ability to selectively enrich target biomolecules and simultaneously deplete nontargets directly in complex crude samples, thereby enormously enhancing the signal-to-noise ratio of detection. We demonstrate the direct detection of attomolar nucleic acids in urine and serum within 35 min and HIV p24 protein in serum within 60 min. The performance of HOLMES is comparable to that of nucleic acid amplification tests and near million-fold improvement over standard enzyme-linked immunosorbent assay (ELISA) for protein detection, being much simpler and faster in both applications. We additionally measured human cardiac troponin I protein in 9 human plasma samples, and showed excellent agreement with ELISA and detection below the limit of ELISA. HOLMES is in an unparalleled position to unleash the potential of protein-based diagnosis.

scholarly journals A Data Size Reduction Approach Applicable in Process Control System of Oil and Gas Plants

2020 ◽  
Vol 12 (2) ◽  
pp. 639
Author(s):  
Reza Abbasinejad ◽  
Farzad Hourfar ◽  
Chandra Mouli R Madhuranthakam ◽  
Ali Elkamel
Keyword(s):  
Oil And Gas ◽  
Process Control System ◽  
Monitoring Systems ◽  
Process Variables ◽  
Performance Quality ◽  
Mathematical Techniques ◽  
And Performance ◽  
The Cost ◽  
And Storage ◽  
Gas Plants

In oil and gas plants, the cost of devices applicable for supervising and controlling systems directly depends on the transmission and storage systems, which are related to the data size of process variables. In this paper, process variables frequency-domain and statistical analysis results have been studied to infer if there exists any possibility to reduce data size of the process variables without loss of any necessary information. Although automatic control is not applicable in a shutdown condition, for generalization of the obtained results, unscheduled shutdown data has also been analyzed and studied. The main goal of this paper is to develop an applicable algorithm for oil and gas plants to decrease the data size in controlling and monitoring systems, based on well-known and powerful mathematical techniques. The results show that it is possible to reduce the size of data dramatically (more than 99% for controlling, and more than 55% for monitoring purposes in comparison with existing methods), without loss of vital information and performance quality.

scholarly journals Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
Elizabeth Smith ◽  
Wei Zhen ◽  
Ryhana Manji ◽  
Deborah Schron ◽  
Scott Duong ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Severe Acute Respiratory Syndrome ◽  
Drug Administration ◽  
Clinical Performance ◽  
Absolute Quantification ◽  
Nucleic Acid Amplification ◽  
Clinical Correlation ◽  
Molecular Assays ◽  
Percent Agreement ◽  
Rna Transcript

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in December 2019 and has quickly become a worldwide pandemic. In response, many diagnostic manufacturers have developed molecular assays for SARS-CoV-2 under the Food and Drug Administration (FDA) Emergency Use Authorization (EUA) pathway. This study compared three of these assays, the Hologic Panther Fusion SARS-CoV-2 assay (Fusion), the Hologic Aptima SARS-CoV-2 assay (Aptima), and the BioFire Defense COVID-19 test (BioFire), to determine analytical and clinical performance as well as workflow. All three assays showed similar limits of detection (LODs) using inactivated virus, with 100% detection, ranging from 500 to 1,000 genome equivalents/ml, whereas use of a quantified RNA transcript standard showed the same trend but had values ranging from 62.5 to 125 copies/ml, confirming variability in absolute quantification of reference standards. The clinical correlation found that the Fusion and BioFire assays had a positive percent agreement (PPA) of 98.7%, followed by the Aptima assay at 94.7%, compared to the consensus result. All three assays exhibited 100% negative percent agreement (NPA). Analysis of discordant results revealed that all four samples missed by the Aptima assay had cycle threshold (Ct) values of >37 by the Fusion assay. In conclusion, while all three assays showed similar relative LODs, we showed differences in absolute LODs depending on which standard was employed. In addition, the Fusion and BioFire assays showed better clinical performance, while the Aptima assay showed a modest decrease in overall PPA. These findings should be kept in mind when making platform testing decisions.

scholarly journals Modeling Regulation of Economic Sustainability in Energy Systems with Diversified Resources

Sci ◽  
2020 ◽  
Vol 2 (1) ◽  
pp. 11
Author(s):  
Anatoly Alabugin ◽  
Sergei Aliukov
Keyword(s):  
Jump Process ◽  
Generalized Functions ◽  
Multidimensional Space ◽  
Economic Sustainability ◽  
New Methods ◽  
Control Functions ◽  
New Concepts ◽  
Methodological Approaches ◽  
Regulatory Models

The imperfection of theoretical and methodological approaches to regulate the jump process transition when combining differentiated energy resources is a pressing issue. The goal of this paper is to develop a theory and a method to regulate the integration-balancing processes of combining diversified resources. The concept of combining integration and balancing models has been substantiated by methods of transforming multidimensional space and approximating generalized functions that represent jump-like processes. Theoretical and operational-regulatory models of economic sustainability have been developed, substantiating new concepts, patterns, properties, dependencies and indicators of the dynamics of the processes of combination; the optimality conditions for the number of approximations of generalized functions, interpreting the effects of control functions of combining resources, are determined. New methods for solving problems have been developed: the organization of the energy technology complex of facilities for enhanced resource diversification and the Center for Sustainability, improving the quality of managing dynamic processes in terms of combining and diversifying resources.

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