scholarly journals Bioinformatics Analysis on DNA Barcode Sequences for Species Identification: A Review

2019 ◽  
pp. 1-12 ◽  
Author(s):  
Huyen-Trang Vu ◽  
Ly Le
Keyword(s):  
Genetic Information ◽  
Bioinformatics Analysis ◽  
Low Cost ◽  
Dna Barcode ◽  
Large Data ◽  
Taxonomic Identification ◽  
Limited Information ◽  
Bioinformatics Analyses ◽  
Dna Library

Classification of organisms is the primary step in management of biodiversity, breeding, conservation and development of populations and distinguishing adulterant objects. There are many approaches in taxonomic identification, from morphological, PCR-based to sequence-based techniques. Molecular methods give more accurate results than morphological comparisons and are independent of plant stages. PCR-based methods are low-cost but their limited information gives less reproducibility and can only distinguish samples among determined groups. In contrast, in sequence-based methods each nucleotide site is considered as genetic information hence a sequence of nucleotide represents large data, which is highly specific and more stable than PCR bands. Establishment of worldwide DNA library for barcoding is essential. There were previous reviews on screenings and applications of barcodes in different taxa. In this review we discussed common bioinformatics analyses as well as some new improved techniques relying on barcoding approaches.

scholarly journals Quantification and Classification of Diclofenac Sodium Content in Dispersed Commercially Available Tablets by Attenuated Total Reflection Infrared Spectroscopy and Multivariate Data Analysis

2021 ◽  
Vol 14 (5) ◽  
pp. 440
Author(s):  
Eirini Siozou ◽  
Vasilios Sakkas ◽  
Nikolaos Kourkoumelis
Keyword(s):  
Infrared Spectroscopy ◽  
Low Cost ◽  
Diclofenac Sodium ◽  
Reference Method ◽  
Sodium Content ◽  
Attenuated Total Reflection ◽  
Accuracy And Precision ◽  
Significant Difference ◽  
Ft Ir

A new methodology, based on Fourier transform infrared spectroscopy equipped with an attenuated total reflectance accessory (ATR FT-IR), was developed for the determination of diclofenac sodium (DS) in dispersed commercially available tablets using chemometric tools such as partial least squares (PLS) coupled with discriminant analysis (PLS-DA). The results of PLS-DA depicted a perfect classification of the tablets into three different groups based on their DS concentrations, while the developed model with PLS had a sufficiently low root mean square error (RMSE) for the prediction of the samples’ concentration (~5%) and therefore can be practically used for any tablet with an unknown concentration of DS. Comparison with ultraviolet/visible (UV/Vis) spectrophotometry as the reference method revealed no significant difference between the two methods. The proposed methodology exhibited satisfactory results in terms of both accuracy and precision while being rapid, simple and of low cost.

Detection and Classification of Anomalies in Large Data Sets on the Basis of Information Granules

2021 ◽  
pp. 1-1
Author(s):  
Adam Kiersztyn ◽  
Pawe Karczmarek ◽  
Krystyna Kiersztyn ◽  
Witold Pedrycz
Keyword(s):  
Large Data ◽  
Large Data Sets ◽  
Data Sets ◽  
Information Granules

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.

scholarly journals FIWARE based low-cost wireless acoustic sensor network for monitoring and classification of urban soundscape

2021 ◽  
pp. 108199
Author(s):  
Pau Arce ◽  
David Salvo ◽  
Gema Piñero ◽  
Alberto Gonzalez
Keyword(s):  
Sensor Network ◽  
Low Cost ◽  
Acoustic Sensor

scholarly journals A Machine Vision Approach for Bioreactor Foam Sensing

2021 ◽  
pp. 247263032110088
Author(s):  
Jonas Austerjost ◽  
Robert Söldner ◽  
Christoffer Edlund ◽  
Johan Trygg ◽  
David Pollard ◽  
...  
Keyword(s):  
Machine Learning ◽  
Machine Vision ◽  
State Of The Art ◽  
Low Cost ◽  
High Accuracy ◽  
Consumer Electronics ◽  
Learning System ◽  
Automotive Applications ◽  
Fine Grained

Machine vision is a powerful technology that has become increasingly popular and accurate during the last decade due to rapid advances in the field of machine learning. The majority of machine vision applications are currently found in consumer electronics, automotive applications, and quality control, yet the potential for bioprocessing applications is tremendous. For instance, detecting and controlling foam emergence is important for all upstream bioprocesses, but the lack of robust foam sensing often leads to batch failures from foam-outs or overaddition of antifoam agents. Here, we report a new low-cost, flexible, and reliable foam sensor concept for bioreactor applications. The concept applies convolutional neural networks (CNNs), a state-of-the-art machine learning system for image processing. The implemented method shows high accuracy for both binary foam detection (foam/no foam) and fine-grained classification of foam levels.

scholarly journals Temperature distribution in a permafrost-affected rock ridge from conductivity and induced polarization tomography

2020 ◽  
Author(s):  
P-A Duvillard ◽  
F Magnin ◽  
A Revil ◽  
A Legay ◽  
L Ravanel ◽  
...  
Keyword(s):  
Electrical Conductivity ◽  
Temperature Distribution ◽  
Thermal State ◽  
Low Cost ◽  
Freezing Temperature ◽  
Induced Polarization ◽  
Rock Surface ◽  
European Alps ◽  
Limited Information ◽  
Polarization Tomography

Summary Knowledge of the thermal state of steep alpine rock faces is crucial to assess potential geohazards associated with the degradation of permafrost. Temperature measurements at the rock surface or in boreholes are however expensive, invasive, and provide spatially-limited information. Electrical conductivity and induced polarization tomography can detect permafrost. We test here a recently developed petrophysical model based on the use of an exponential freezing curve applied to both electrical conductivity and normalized chargeability to infer the distribution of temperature below the freezing temperature. We then apply this approach to obtain the temperature distribution from electrical conductivity and normalized chargeability field data obtained across a profile extending from the SE to NW faces of the lower Cosmiques ridge (Mont Blanc massif, Western European Alps, 3613 m a.s.l., France). The geophysical datasets were acquired both in 2016 and 2019. The results indicate that the only NW face of the rock ridge is frozen. To evaluate our results, we model the bedrock temperature across this rock ridge using CryoGRID2, a 1D MATLAB diffusive transient thermal model and surface temperature time series. The modelled temperature profile confirms the presence of permafrost in a way that is consistent with that obtained from the geophysical data. Our study offers a promising low-cost approach to monitor temperature distribution in Alpine rock walls and ridges in response to climate change.

scholarly journals Mask R-CNN Based C. Elegans Detection with a DIY Microscope

Biosensors ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 257
Author(s):  
Sebastian Fudickar ◽  
Eike Jannik Nustede ◽  
Eike Dreyer ◽  
Julia Bornhorst
Keyword(s):  
Cell Biology ◽  
High Throughput Screening ◽  
Low Cost ◽  
Image Acquisition ◽  
Rapid Development ◽  
Model Organism ◽  
Large Data ◽  
Data Set ◽  
C Elegans ◽  
Do It Yourself

Caenorhabditis elegans (C. elegans) is an important model organism for studying molecular genetics, developmental biology, neuroscience, and cell biology. Advantages of the model organism include its rapid development and aging, easy cultivation, and genetic tractability. C. elegans has been proven to be a well-suited model to study toxicity with identified toxic compounds closely matching those observed in mammals. For phenotypic screening, especially the worm number and the locomotion are of central importance. Traditional methods such as human counting or analyzing high-resolution microscope images are time-consuming and rather low throughput. The article explores the feasibility of low-cost, low-resolution do-it-yourself microscopes for image acquisition and automated evaluation by deep learning methods to reduce cost and allow high-throughput screening strategies. An image acquisition system is proposed within these constraints and used to create a large data-set of whole Petri dishes containing C. elegans. By utilizing the object detection framework Mask R-CNN, the nematodes are located, classified, and their contours predicted. The system has a precision of 0.96 and a recall of 0.956, resulting in an F1-Score of 0.958. Considering only correctly located C. elegans with an [email protected] IoU, the system achieved an average precision of 0.902 and a corresponding F1 Score of 0.906.

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