Clinical applications of spectroscopic techniques in conjunction with multivariate analysis in virus diagnosis

2021 ◽  
pp. 1-27
Author(s):  
Marfran C. D. Santos ◽  
João V. M. Mariz ◽  
Raissa V. O. Silva ◽  
Camilo L. M. Morais ◽  
Kássio M. G. Lima
Keyword(s):  
Multivariate Analysis ◽  
Near Infrared ◽  
Low Cost ◽  
Diagnostic Techniques ◽  
Clinical Samples ◽  
Spectroscopic Techniques ◽  
Global Pandemic ◽  
Molecular Fluorescence ◽  
Viral Diagnosis ◽  
Near Future

In view of the global pandemic that started in 2020, caused by COVID-19, the importance of the existence of fast, reliable, cheap diagnostic techniques capable of detecting the virus even in the first days of infection became evident. This review discusses studies involving the use of spectroscopic techniques in the detection of viruses in clinical samples. Techniques based on mid-infrared, near-infrared, Raman, and molecular fluorescence are explained and it was demonstrated how they can be used in conjunction with computational tools of multivariate analysis to build models capable of detecting viruses. Studies that used real clinical samples from 2011 to 2021 were analyzed. The results demonstrate the potential of the techniques in detecting viruses. Spectroscopic techniques, as well as chemometric techniques, were also explained. Viral diagnosis based on spectroscopy has interesting advantages compared to standard techniques such as: fast results, no need for reagents, non-destructiveness for the sample, no need for sample preparation, relatively low cost, among others. Several studies have corroborated the real possibility that, in the near future, we may have spectroscopic tools being successfully applied in viral diagnosis.

scholarly journals Detection of Microbial Agents in Oropharyngeal and Nasopharyngeal Samples of SARS-CoV-2 Patients

2021 ◽  
Vol 12 ◽  
Author(s):  
Tyler Seckar ◽  
Xiang Lin ◽  
Dipayan Bose ◽  
Zhi Wei ◽  
Joseph Rohrbaugh ◽  
...  
Keyword(s):  
Diagnostic Techniques ◽  
Clinical Samples ◽  
Respiratory Pathogens ◽  
The Novel ◽  
Respiratory Illnesses ◽  
Viral Genomes ◽  
Global Pandemic ◽  
Causative Agents ◽  
Novel Coronavirus ◽  
Microbial Agents

The novel coronavirus outbreak started in December 2019 and rapidly spread around the globe, leading to a global pandemic. Here we reported the association of microbial agents identified in oropharyngeal and nasopharyngeal samples from patients with SARS-CoV-2 infection, using a Pan-microarray based technology referred to as PathoChIP. To validate the efficiency of PathoChIP, reference viral genomes obtained from BEI resource and 25 SARS-CoV-2 positive clinical samples were tested. This technology successfully detected femtogram levels of SARS-CoV-2 viral RNA, which demonstrated greater sensitivity and specificity than conventional diagnostic techniques. Simultaneously, a broad range of other microorganisms, including other viruses, bacteria, fungi and parasites can be detected in those samples. We identified 7 viral, 12 bacterial and 6 fungal agents common across all clinical samples suggesting an associated microbial signature in individuals who are infected with SARS-CoV-2. This technology is robust and has a flexible detection methodology that can be employed to detect the presence of all human respiratory pathogens in different sample preparations with precision. It will be important for differentiating the causative agents of respiratory illnesses, including SARS-CoV-2.

scholarly journals Portable Spectroscopy

2018 ◽  
Vol 72 (12) ◽  
pp. 1701-1751 ◽  
Author(s):  
Richard A. Crocombe
Keyword(s):  
Near Infrared ◽  
Low Cost ◽  
Medical Diagnostics ◽  
Spectroscopic Techniques ◽  
The Public ◽  
Qualitative And Quantitative ◽  
Breakdown Spectroscopy ◽  
Crowdsourced Data ◽  
Laser Induced Breakdown ◽  
Consumer Devices

Until very recently, handheld spectrometers were the domain of major analytical and security instrument companies, with turnkey analyzers using spectroscopic techniques from X-ray fluorescence (XRF) for elemental analysis (metals), to Raman, mid-infrared, and near-infrared (NIR) for molecular analysis (mostly organics). However, the past few years have seen rapid changes in this landscape with the introduction of handheld laser-induced breakdown spectroscopy (LIBS), smartphone spectroscopy focusing on medical diagnostics for low-resource areas, commercial engines that a variety of companies can build up into products, hyphenated or dual technology instruments, low-cost visible-shortwave NIR instruments selling directly to the public, and, most recently, portable hyperspectral imaging instruments. Successful handheld instruments are designed to give answers to non-scientist operators; therefore, their developers have put extensive resources into reliable identification algorithms, spectroscopic libraries or databases, and qualitative and quantitative calibrations. As spectroscopic instruments become smaller and lower cost, “engines” have emerged, leading to the possibility of being incorporated in consumer devices and smart appliances, part of the Internet of Things (IOT). This review outlines the technologies used in portable spectroscopy, discusses their applications, both qualitative and quantitative, and how instrument developers and vendors have approached giving actionable answers to non-scientists. It outlines concerns on crowdsourced data, especially for heterogeneous samples, and finally looks towards the future in areas like IOT, emerging technologies for instruments, and portable hyphenated and hyperspectral instruments.

scholarly journals Excited-State Dynamics of Organic Dyes in Solar Cells

2020 ◽  
Author(s):  
Ahmed M. El-Zohry
Keyword(s):  
Solar Cells ◽  
Excited State ◽  
Solar Cell ◽  
Environmental Impact ◽  
Organic Dyes ◽  
Low Cost ◽  
Redox Couple ◽  
Spectroscopic Techniques ◽  
High Efficient ◽  
Near Future

Organic dyes are promising candidates for wide applications in solar cells, due to their controlled environmental impact, and low-cost. However, their performances in several solar cell architectures are not high enough to compete with the traditional semiconductor based solar cells. Therefore, several efforts should be gathered to improve the efficiency of these organic dyes. Herein, we discuss several deactivation processes recently found in several organic dyes using optical spectroscopic techniques. These processes are believed to be mostly detrimental for the performance of organic dyes in solar cells. These processes include deactivation phenomena such as isomerization, twisting, and chemical interactions with redox couple. Thus, based on similar studies, more optimized synthetic procedures for organic dyes could be implemented in the near future for high efficient solar cells based on organic dyes.

A Combined Acquisition and Analysis Protocol to Eliminate Spikes in near Infrared Spectra Measured with Germanium Detectors

1995 ◽  
Vol 3 (2) ◽  
pp. 63-71 ◽  
Author(s):  
Ueli Oetliker ◽  
Christian Reber
Keyword(s):  
Near Infrared ◽  
Low Cost ◽  
Inorganic Materials ◽  
Luminescence Spectra ◽  
Spectroscopic Techniques ◽  
Near Infrared Spectra ◽  
Order Of Magnitude ◽  
Nir Luminescence ◽  
Data Acquisition Process ◽  
Analysis Protocol

A new software-based method for eliminating voltage spikes in near infrared (NIR) spectra measured with germanium (Ge) detectors is described. The digitised signal from the detector is analysed statistically in order to reject spikes before the average signal at a given wavelength is calculated and stored. This analysis is an integral part of the data acquisition process and its properties and implementation are described in detail. The protocol is used to measure NIR luminescence spectra of inorganic materials and we show that acquisition times for spectra with equivalent signal-to-noise ratios are shorter by an order of magnitude than for conventional experiments. This low-cost methodology is easily adapted to other spectroscopic techniques involving Ge detectors.

scholarly journals Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone

2020 ◽  
Author(s):  
Parinaz Fozouni ◽  
Sungmin Son ◽  
María Díaz de León Derby ◽  
Gavin J Knott ◽  
Carley N Gray ◽  
...  
Keyword(s):  
Mobile Phone ◽  
Nasal Swab ◽  
Respiratory Virus ◽  
Direct Detection ◽  
Point Of Care ◽  
Low Cost ◽  
Clinical Samples ◽  
Dna Targeting ◽  
Global Pandemic ◽  
Rna And Dna

The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic and pre- symptomatic carriers of the virus. CRISPR-based diagnostics that utilize RNA and DNA-targeting enzymes can augment gold-standard PCR-based testing if they can be made rapid, portable and accurate. Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. The assay achieved ~100 copies/μL sensitivity in under 30 minutes and accurately detected a set of positive clinical samples in under 5 minutes. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity, and we directly quantified viral load using enzyme kinetics. Combined with mobile phone-based quantification, this assay can provide rapid, low-cost, point-of-care screening to aid in the control of SARS-CoV-2.

scholarly journals Highly sensitive and specific diagnosis of COVID-19 by reverse transcription multiple cross-displacement amplification-labelled nanoparticles biosensor

2020 ◽  
Vol 56 (6) ◽  
pp. 2002060 ◽  
Author(s):  
Shijun Li ◽  
Weijia Jiang ◽  
Junfei Huang ◽  
Ying Liu ◽  
Lijuan Ren ◽  
...  
Keyword(s):  
Reverse Transcription ◽  
Low Cost ◽  
Test Procedure ◽  
Diagnostic Techniques ◽  
Health Concern ◽  
Clinical Samples ◽  
Specific Diagnosis ◽  
Nucleoprotein Gene ◽  
Multiple Cross ◽  
Positive Results

BackgroundThe ongoing outbreak of the novel human coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (also known as 2019-nCoV) has become a global health concern. Rapid and easy-to-use diagnostic techniques are urgently needed to diagnose SARS-CoV-2 infection.MethodsWe devised a reverse transcription multiple cross-displacement amplification (RT-MCDA) coupled with a nanoparticle-based biosensor assay (RT-MCDA-BS) for rapid, sensitive and specific diagnosis of coronavirus disease 2019 (COVID-19). Two primer sets were designed to target the open reading frame 1a/b and nucleoprotein gene of SARS-CoV-2. A total of 183 clinical samples, including 65 patients with COVID-19 infection and 118 patients with other pathogen infections were used to testify the assay's feasibility. Diagnosis results were reported visually using the biosensor.FindingsThe assay designed was performed using a simple instrument which could maintain the reaction in a constant temperature at 64°C for only 35 min. The total COVID-19 RT-MCDA-BS test procedure could be finished within 1 h. The COVID-19 RT-MCDA-BS could detect down to five copies of target sequences. Among 65 clinical samples from the COVID-19 patients, 22 (33.8%) positive results were obtained from faeces, nasal, pharyngeal and anal swabs via COVID-19 RT-MCDA-BS assay, while real-time reverse transcription-PCR assay only detected 20 (30.7%) positive results in these samples. No positive results were obtained from clinical samples with non-COVID-19 infections.InterpretationCOVID-19 RT-MCDA-BS was a rapid, reliable, low-cost and easy-to-use assay, which could provide an attractive laboratory tool to diagnose COVID-19 in multiple clinical specimens, especially for field, clinic laboratories and primary care facilities in resource-poor settings.

scholarly journals Comparison of Spectroscopic Techniques Combined with Chemometrics for Cocaine Powder Analysis

2020 ◽  
Vol 44 (8) ◽  
pp. 851-860
Author(s):  
Joy Eliaerts ◽  
Natalie Meert ◽  
Pierre Dardenne ◽  
Vincent Baeten ◽  
Juan-Antonio Fernandez Pierna ◽  
...  
Keyword(s):  
Gas Chromatography ◽  
Near Infrared ◽  
Evaluation Criteria ◽  
Classification Model ◽  
Support Vector ◽  
Spectroscopic Techniques ◽  
Data Set ◽  
Promising Tool ◽  
Powder Analysis ◽  
Mir Spectra

Abstract Spectroscopic techniques combined with chemometrics are a promising tool for analysis of seized drug powders. In this study, the performance of three spectroscopic techniques [Mid-InfraRed (MIR), Raman and Near-InfraRed (NIR)] was compared. In total, 364 seized powders were analyzed and consisted of 276 cocaine powders (with concentrations ranging from 4 to 99 w%) and 88 powders without cocaine. A classification model (using Support Vector Machines [SVM] discriminant analysis) and a quantification model (using SVM regression) were constructed with each spectral dataset in order to discriminate cocaine powders from other powders and quantify cocaine in powders classified as cocaine positive. The performances of the models were compared with gas chromatography coupled with mass spectrometry (GC–MS) and gas chromatography with flame-ionization detection (GC–FID). Different evaluation criteria were used: number of false negatives (FNs), number of false positives (FPs), accuracy, root mean square error of cross-validation (RMSECV) and determination coefficients (R2). Ten colored powders were excluded from the classification data set due to fluorescence background observed in Raman spectra. For the classification, the best accuracy (99.7%) was obtained with MIR spectra. With Raman and NIR spectra, the accuracy was 99.5% and 98.9%, respectively. For the quantification, the best results were obtained with NIR spectra. The cocaine content was determined with a RMSECV of 3.79% and a R2 of 0.97. The performance of MIR and Raman to predict cocaine concentrations was lower than NIR, with RMSECV of 6.76% and 6.79%, respectively and both with a R2 of 0.90. The three spectroscopic techniques can be applied for both classification and quantification of cocaine, but some differences in performance were detected. The best classification was obtained with MIR spectra. For quantification, however, the RMSECV of MIR and Raman was twice as high in comparison with NIR. Spectroscopic techniques combined with chemometrics can reduce the workload for confirmation analysis (e.g., chromatography based) and therefore save time and resources.

scholarly journals Comparative Analysis of Digital Models of Objects of Cultural Heritage Obtained by the “3D SLS” and “SfM” Methods

2021 ◽  
Vol 11 (12) ◽  
pp. 5321
Author(s):  
Marcin Barszcz ◽  
Jerzy Montusiewicz ◽  
Magdalena Paśnikowska-Łukaszuk ◽  
Anna Sałamacha
Keyword(s):  
Cultural Heritage ◽  
Low Cost ◽  
Three Dimensional ◽  
3D Models ◽  
Silk Road ◽  
Digital Models ◽  
Global Pandemic ◽  
University Of Technology ◽  
Three Dimensional Models ◽  
3D Digitisation

In the era of the global pandemic caused by the COVID-19 virus, 3D digitisation of selected museum artefacts is becoming more and more frequent practice, but the vast majority is performed by specialised teams. The paper presents the results of comparative studies of 3D digital models of the same museum artefacts from the Silk Road area generated by two completely different technologies: Structure from Motion (SfM)—a method belonging to the so-called low-cost technologies—and by Structured-light 3D Scanning (3D SLS). Moreover, procedural differences in data acquisition and their processing to generate three-dimensional models are presented. Models built using a point cloud were created from data collected in the Afrasiyab museum in Samarkand (Uzbekistan) during “The 1st Scientific Expedition of the Lublin University of Technology to Central Asia” in 2017. Photos for creating 3D models in SfM technology were taken during a virtual expedition carried out under the “3D Digital Silk Road” program in 2021. The obtained results show that the quality of the 3D models generated with SfM differs from the models from the technology (3D SLS), but they may be placed in the galleries of the vitrual museum. The obtained models from SfM do not have information about their size, which means that they are not fully suitable for archiving purposes of cultural heritage, unlike the models from SLS.

scholarly journals Feasibility of Using VIS/NIR Spectroscopy and Multivariate Analysis for Pesticide Residue Detection in Tomatoes

Processes ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 196
Author(s):  
Araz Soltani Nazarloo ◽  
Vali Rasooli Sharabiani ◽  
Yousef Abbaspour Gilandeh ◽  
Ebrahim Taghinezhad ◽  
Mariusz Szymanek ◽  
...  
Keyword(s):  
Near Infrared ◽  
Cross Validation ◽  
Low Cost ◽  
Moving Average ◽  
Nir Spectroscopy ◽  
Control Treatment ◽  
Residue Detection ◽  
Non Destructive ◽  
Reflective Spectroscopy

The purpose of this work was to investigate the detection of the pesticide residual (profenofos) in tomatoes by using visible/near-infrared spectroscopy. Therefore, the experiments were performed on 180 tomato samples with different percentages of profenofos pesticide (higher and lower values than the maximum residual limit (MRL)) as compared to the control (no pesticide). VIS/near infrared (NIR) spectral data from pesticide solution and non-pesticide tomato samples (used as control treatment) impregnated with different concentrations of pesticide in the range of 400 to 1050 nm were recorded by a spectrometer. For classification of tomatoes with pesticide content at lower and higher levels of MRL as healthy and unhealthy samples, we used different spectral pre-processing methods with partial least squares discriminant analysis (PLS-DA) models. The Smoothing Moving Average pre-processing method with the standard error of cross validation (SECV) = 4.2767 was selected as the best model for this study. In addition, in the calibration and prediction sets, the percentages of total correctly classified samples were 90 and 91.66%, respectively. Therefore, it can be concluded that reflective spectroscopy (VIS/NIR) can be used as a non-destructive, low-cost, and rapid technique to control the health of tomatoes impregnated with profenofos pesticide.

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