Inline biofilm monitoring based on near-infrared spectroscopy with ultracompact spectrometer technology

NIR news ◽  
2020 ◽  
Vol 31 (7-8) ◽  
pp. 9-13
Author(s):  
Robert Zimmerleiter ◽  
Elisabeth Leiss-Holzinger ◽  
Eva Maria Wagner ◽  
Kathrin Kober-Rychli ◽  
Martin Wagner ◽  
...  
Keyword(s):  
Near Infrared ◽  
Spectral Response ◽  
Principal Component ◽  
Cost Effective ◽  
Sensor Surface ◽  
Chain Reaction ◽  
Microelectromechanical System ◽  
Infrared Spectral ◽  
Infrared Measurement ◽  
Polymerase Chain

In this article, we demonstrate a promising inline near-infrared measurement scheme for 24/7 biofilm monitoring based on cost-effective microelectromechanical system-based spectrometer technology. The shown near-infrared spectral data, acquired at a beer-canning line during a representative time span of 10 days, are analyzed by means of principal component analysis and the performance of the monitoring system and its capability to identify biofilms on its sensor surface are investigated by comparing spectral response with results of offline polymerase chain reaction measurements of smear samples. Correlations between presence of a biofilm and its thickness with scores on PC1 and PC2, respectively, were observed.

scholarly journals Modern Methods for Assessing the Quality of Bee Honey and Botanical Origin Identification

Foods ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1028
Author(s):  
Anna Puścion-Jakubik ◽  
Maria Halina Borawska ◽  
Katarzyna Socha
Keyword(s):  
Near Infrared ◽  
Principal Component ◽  
Polyphenol Content ◽  
Chain Reaction ◽  
Dna Metabarcoding ◽  
Modern Methods ◽  
Quality Testing ◽  
Polymerase Chain ◽  
Origin Identification

This paper is a summary of the latest literature on methods for assessing quality of natural bee honey. The publication briefly characterizes methods recommended by the International Honey Commission, published in 2009, as well as newer methods published in the last 10 years. Modern methods of assessing honey quality focus mainly on analyzing markers of individual varieties and classifying them into varieties, using, among others, near infrared spectroscopy techniques (NIR), potentiometric tongue, electronic nose, nuclear magnetic resonance (NMR), zymography, polymerase chain reaction (PCR), DNA metabarcoding, and chemometric techniques including partial least squares (PLS), principal component analysis (PCA) and artificial neural networks (ANN). At the same time, effective techniques for analyzing adulteration, sugar, and water content, hydroxymethylfurfural (HMF), polyphenol content, and diastase activity are being sought. Modern techniques enable the results of honey quality testing to be obtained in a shorter time, using the principles of green chemistry, allowing, at the same time, for high precision and accuracy of determinations. These methods are constantly modified, so that the honey that is on sale is a product of high quality. Prospects for devising methods of honey quality assessment include the development of a fast and accurate alternative to the melissopalynological method as well as quick tests to detect adulteration.

Cost-Effectiveness of Nasopharyngeal Carcinoma Screening with Epstein-Barr Virus Polymerase Chain Reaction or Serology in High-Incidence Populations Worldwide

2020 ◽  
Author(s):  
Jacob A Miller ◽  
Quynh-Thu Le ◽  
Benjamin A Pinsky ◽  
Hannah Wang
Keyword(s):  
Cost Effectiveness ◽  
Epstein Barr Virus ◽  
Cost Effective ◽  
Chain Reaction ◽  
Men And Women ◽  
Barr Virus ◽  
Screening Strategies ◽  
High Incidence ◽  
Polymerase Chain ◽  
Epstein Barr

Abstract Background The incidence of endemic Epstein-Barr Virus (EBV)-associated nasopharyngeal carcinoma (NPC) varies considerably worldwide. In high-incidence regions, screening trials have been conducted. We estimated the mortality reduction and cost-effectiveness of EBV-based NPC screening in populations worldwide. Methods We identified 380 populations in 132 countries with incident NPC and developed a decision-analytic model to compare ten unique onetime screening strategies to no screening for men and women at age 50 years. Screening performance and the stage distribution of undiagnosed NPC were derived from a systematic review of prospective screening trials. Results Screening was cost-effective in up to 14.5% of populations, depending on the screening strategy. These populations were limited to East Asia, Southeast Asia, North Africa, or were Asian, Pacific Islander, or Inuit populations in North America. A combination of serology and nasopharyngeal polymerase chain reaction (PCR) was most cost-effective, but other combinations of serologic and/or plasma PCR screening were also cost-effective. The estimated reduction in NPC mortality was similar across screening strategies. For a hypothetical cohort of patients in China, 10-year survival improved from 71.0% (95%CI = 68.8%–73.0%) without screening to a median of 86.3% (range = 83.5%–88.2%) with screening. This corresponded to a median 10-year reduction in NPC mortality of 52.9% (range= 43.1%–59.3%). Screening interval impacted absolute mortality reduction and cost-effectiveness. Conclusions We observed decreased NPC mortality with EBV-based screening. Screening was cost-effective in many high-incidence populations and could be extended to men and women as early as age 40 years in select regions. These findings may be useful when choosing among local public health initiatives.

scholarly journals Development of a Genoserotyping Method for Salmonella Infantis Detection on the Basis of Pangenome Analysis

2020 ◽  
Vol 9 (1) ◽  
pp. 67
Author(s):  
Seung-Min Yang ◽  
Jiwon Baek ◽  
Eiseul Kim ◽  
Hyeon-Be Kim ◽  
Seyoung Ko ◽  
...  
Keyword(s):  
Public Health ◽  
Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Cost Effective ◽  
The Other ◽  
Gene Marker ◽  
Diagnostic Assay ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Substantial Economic Burden

In recent years, Salmonella Infantis has become a predominant serovariant in clinical and poultry isolates, thereby imposing a substantial economic burden on both public health and the livestock industry. With the aim of coping with the steep increase in serovar Infantis prevalence, a polymerase chain reaction (PCR)-based rapid and accurate diagnostic assay was developed in this study through pangenome profiling of 60 Salmonella serovars. A gene marker, SIN_02055, was identified, which is present in the S. Infantis genome but not in the pangenome of the other serovars. Primers specific to SIN_02055 were used to accurately detect serovar Infantis, and to successfully differentiate Infantis from the other 59 serovars in real-time PCR with a R2 of 0.999 and an efficiency of 95.76%. The developed method was applied to 54 Salmonella strains belonging to eight dominant serovars, and distinguished Infantis from the other seven serovars with an accuracy of 100%. The diagnostic primer set also did not show false positive amplification with 32 strains from eight non-Salmonella bacterial species. This cost-effective and rapid method can be considered an alternative to the classic serotyping using antisera.

Genetic diversity and phylogeny analysis of Azolla based on DNA amplification by arbitrary primers

Genome ◽  
1993 ◽  
Vol 36 (4) ◽  
pp. 686-693 ◽  
Author(s):  
Benoit Van Coppenolle ◽  
Iwao Watanabe ◽  
Charles Van Hove ◽  
Gerard Second ◽  
Ning Huang ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Polymerase Chain Reaction ◽  
Principal Component ◽  
Dna Amplification ◽  
Component Analysis ◽  
Genetic Distances ◽  
Group Method ◽  
Chain Reaction ◽  
Arbitrary Primers ◽  
Polymerase Chain

The polymerase chain reaction was used to amplify random sequences of DNA from 25 accessions of Azolla to evaluate the usefulness of this technique for identification and phylogenetic analysis of this aquatic fern. Accessions were selected to represent all known species within the genus Azolla and to encompass the worldwide distribution of the fern. Primers of 10 nucleotides with 70% G + C content were used to generate randomly amplified polymorphic DNA from the symbiotic Azolla–Anabaena complex. Twenty-two primers were used and each primer gave 4–10 bands of different molecular weights for each accession. Bands were scored as present or absent for each accession and variation among accessions was quantified using Nei's genetic distances. A dendrogram summarizing phenetic relationships among the 25 accessions was generated using the unweighted pair-group method with arithmetic mean. Principal component analysis was also used to evaluate genetic similarities. Three distinct groups were identified: group 1 contains five species, group 2 contains the pinnata species, and group 3 contains the nilotica species. The analysis demonstrates that the major groups of Azolla species can be easily distinguished from one an other and, in addition, that closely related accessions within species can be identified. We further found that using 10 primers, a phylogeny that is essentially the same as that derived from 22 primers can be constructed. Our results suggest that total DNA extracted from the Azolla–Anabaena symbionts is useful for classification and phylogenetic studies of Azolla.Key words: Azolla–Anabaena symbiosis, genetic distances, polymerase chain reaction, principal component analysis.

Determination of Wavelength Accuracy in the Near-Infrared Spectral Region Based on NIST's Infrared Transmission Wavelength Standard SRM 1921

2000 ◽  
Vol 54 (3) ◽  
pp. 450-455 ◽  
Author(s):  
Stephen R. Lowry ◽  
Jim Hyatt ◽  
William J. McCarthy
Keyword(s):  
Reference Material ◽  
Standard Reference Material ◽  
Spectral Region ◽  
Near Infrared ◽  
Cost Effective ◽  
Infrared Transmission ◽  
Internal Reference ◽  
Mid Infrared ◽  
Infrared Spectral Region ◽  
Infrared Spectral

A major concern with the use of near-infrared (NIR) spectroscopy in many QA/QC laboratories is the need for a simple reliable method of verifying the wavelength accuracy of the instrument. This requirement is particularly important in near-infrared spectroscopy because of the heavy reliance on sophisticated statistical vector analysis techniques to extract the desired information from the spectra. These techniques require precise alignment of the data points between the vectors corresponding to the standard and sample spectra. The National Institute of Standards and Technology (NIST) offers a Standard Reference Material (SRM 1921) for the verification and calibration of mid-infrared spectrometers in the transmittance mode. This standard consists of a 38 μm-thick film of polystyrene plastic. While SRM 1921 works well as a mid-infrared standard, a thicker sample is required for use as a routine standard in the near-infrared spectral region. The general acceptance and proven reliability of polystyrene as a standard reference material make it a very good candidate for a cost-effective NIR standard that could be offered as an internal reference for every instrument. In this paper we discuss a number of the parameters in a Fourier transform (FT)-NIR instrument that can affect wavelength accuracy. We also report a number of experiments designed to determine the effects of resolution, sample position, and optics on the wavelength accuracy of the system. In almost all cases the spectral reproducibility was better than one wavenumber of the values extrapolated from the NIST reference material. This finding suggests that a thicker sample of polystyrene plastic that has been validated with the SRM 1921 standard would make a cost-effective reference material for verifying wavelength accuracy in a medium-resolution FT-NIR spectrometer.

scholarly journals High-Resolution Melting-Based Quantitative Analysis of RASSF1 Methylation in Breast Cancer

Medicina ◽  
2013 ◽  
Vol 49 (2) ◽  
pp. 14 ◽  
Author(s):  
Kristina Stuopelytė ◽  
Kristina Daniūnaitė ◽  
Aida Laurinavičienė ◽  
Valerijus Ostapenko ◽  
Sonata Jarmalaitė
Keyword(s):  
Breast Cancer ◽  
Polymerase Chain Reaction ◽  
High Resolution ◽  
Quantitative Methods ◽  
High Resolution Melting ◽  
Cost Effective ◽  
Chain Reaction ◽  
Specific Polymerase Chain Reaction ◽  
Polymerase Chain ◽  
Breast Tissues

Background and Objective. Breast cancer is the leading cause of death from cancer among women worldwide. The aberrant promoter methylation of tumor suppressor genes is a typical epigenetic alteration for breast cancer and can be detected in early carcinogenesis. High-throughput and cost-effective methods are needed for the early and sensitive detection of epigenetic changes in clinical material. The main purpose of our study was to optimize a high-resolution melting (HRM) assay for the reliable and quantitative assessment of RASSF1 gene methylation, which is considered one of the earliest epigenetic alterations in breast cancer. Material and Methods. A total of 76 breast carcinomas and 10 noncancerous breast tissues were studied by means of HRM and compared with the results obtained by means of quantitative methylation-specific polymerase chain reaction (QMSP) and methylation-specific polymerase chain reaction (MSP). Results. Both quantitative methods, HRM and QMSP, showed a similar specificity and sensitivity for the detection of RASSF1 methylation in breast cancer (about 80% and 70%, respectively). In breast cancer, the mean methylation intensity of RASSF1 was 42.5% and 48.6% according to HRM and QMSP, respectively. Both methods detected low levels of methylation (less than 5%) in noncancerous breast tissues. In comparison with quantitative methods, MSP showed a lower sensitivity (70%), but a higher specificity (80%) for the detection of RASSF1 methylation in breast cancer. Conclusions. HRM is as a simple, cost-effective method for the reliable high-throughput quantification of DNA methylation in clinical material.

Use of near infrared spectroscopy and spectral databases to assess the quality of pharmaceutical products and aid characterization of unknown components

2019 ◽  
Vol 27 (5) ◽  
pp. 379-390
Author(s):  
Mazlina Mohd Said ◽  
Simon Gibbons ◽  
Anthony Moffat ◽  
Mire Zloh
Keyword(s):  
Principal Component Analysis ◽  
Infrared Spectroscopy ◽  
Near Infrared ◽  
Principal Component ◽  
Component Analysis ◽  
Score Plot ◽  
Principal Component Analysis Score ◽  
Infrared Spectral ◽  
Herbal Formulations ◽  
Spectral Database

This research was initiated as part of the fight against public health problems of rising counterfeit, substandard and poor quality medicines and herbal products. An effective screening strategy using a two-step combination approach of an incremental near infrared spectral database (step 1) followed by principal component analysis (step 2) was developed to overcome the limitations of current procedures for the identification of medicines by near infrared spectroscopy which rely on the direct comparison of the unknown spectra to spectra of reference samples or products. The near infrared spectral database consisted of almost 4000 spectra from different types of medicines acquired and stored in the database throughout the study. The spectra of the test samples (pharmaceutical and herbal formulations) were initially compared to the reference spectra of common medicines from the database using a correlation algorithm. Complementary similarity assessment of the spectra was conducted based on the observation of the principal component analysis score plot. The validation of the approach was achieved by the analysis of known counterfeit Viagra samples, as the spectra did not fully match with the spectra of samples from reliable sources and did not cluster together in the principal component analysis score plot. Pre-screening analysis of an herbal formulation (Pronoton) showed similarity with a product containing sildenafil citrate in the database. This finding supported by principal component analysis has indicated that the product was adulterated. The identification of a sildenafil analogue, hydroxythiohomosildenafil, was achieved by mass spectrometry and Nuclear Magnetic Resonance (NMR) analyses. This approach proved to be a suitable technique for quick, simple and cost-effective pre-screening of products for guiding the analysis of pharmaceutical and herbal formulations in the quest for the identification of potential adulterants.

Predictive Value and Cost-Effectiveness Analysis of a Rapid Polymerase Chain Reaction for Preoperative Detection of Nasal Carriage of Staphylococcus aureus

2003 ◽  
Vol 24 (5) ◽  
pp. 327-333 ◽  
Author(s):  
Nabin K. Shrestha ◽  
Kenneth M. Shermock ◽  
Steven M. Gordon ◽  
Marion J. Tuohy ◽  
Deborah A. Wilson ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Polymerase Chain Reaction ◽  
Cost Effectiveness ◽  
Cost Effective ◽  
Nasal Carriage ◽  
Initial Therapy ◽  
Cost Effectiveness Analysis ◽  
Chain Reaction ◽  
Effectiveness Analysis ◽  
Polymerase Chain

AbstractObjective:To determine the accuracy and cost-effectiveness of a polymerase chain reaction (PCR) for detecting nasal carriage of Staphylococcus aureus directly from clinical specimens.Cross-Sectional Study:This occurred in a tertiary-care hospital in Cleveland, Ohio, and included 239 consecutive patients who were scheduled for a cardiothoracic surgical procedure. Conventional cultures and a PCR for S. aureus from nasal swabs were used as measurements.Cost-Effectiveness Analysis:Data sources were market prices and Bureau of Labor Statistics. The time horizon was the maximum period for availability of culture results (3 days). Interventions included universal mupirocin therapy without testing; initial therapy, with termination if PCR negative (treat-PCR); initial therapy, with termination if culture negative (treat-culture); treat PCR-positive carriers (PCR-guided treatment); and treat culture-positive carriers (culture-guided treatment). The perspective was institutional and costs and the length of time to treatment were outcome measures.Results:Sixty-seven (28%) of the 239 swabs grew S. aureus. Rapid PCR was 97.0% sensitive and 97.1% specific for the detection of S. aureus. For populations with prevalences of nasal S. aureus carriage of up to 50%, the PCR assay had negative predictive values of greater than 97%. PCR-guided treatment had the lowest incremental cost-effectiveness ratio ($1.93 per additional day compared with the culture strategy). Among immediate treatment strategies, treat-PCR was most cost-effective. The universal therapy strategy cost $38.19 more per additional day gained with carrier identification compared with the PCR strategy.Conclusion:Rapid real-time PCR is an accurate, rapid, and cost-effective method for identifying S. aureus carriers for preoperative intervention.

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