MiRBase is the primary repository for published miRNA sequence and annotation data, and serves as the “go-to” place for miRNA research. However, the definition and annotation of miRNAs have been changed significantly across different versions of miRBase. The changes cause inconsistency in miRNA related data between different databases and articles published at different times. Several tools have been developed for different purposes of querying and converting the information of miRNAs between different miRBase versions, but none of them individually can provide the comprehensive information about miRNAs in miRBase and users will need to use a number of different tools in their analyses. We introduce miRBaseConverter, an R package integrating the latest miRBase version 22 available in Bioconductor to provide a suite of functions for converting and retrieving miRNA name (ID), accession, sequence, species, version and family information in different versions of miRBase. The package is implemented in R and available under the GPL-2 license from the Bioconductor website ( http://bioconductor.org/packages/miRBaseConverter/ ). A Shiny-based GUI suitable for non-R users is also available as a standalone application from the package and also as a web application at http://nugget.unisa.edu.au:3838/miRBaseConverter . miRBaseConverter has a built-in database for querying miRNA information in all species and for both pre-mature and mature miRNAs defined by miRBase. In addition, it is the first tool for batch querying the miRNA family information. The package aims to provide a comprehensive and easy-to-use tool for miRNA research community where researchers often utilize published miRNA data from different sources. The Bioconductor package miRBaseConverter and the Shiny-based web application are presented to provide a suite of functions for converting and retrieving miRNA name, accession, sequence, species, version and family information in different versions of miRBase. The package will serve a wide range of applications in miRNA research and could provide a full view of the miRNAs of interest.

The visible and near-infrared (Vis-NIR) reflectance spectroscopy was utilized for the rapid and nondestructive discrimination of edible oil adulteration. In total, 110 samples of sesame oil and rapeseed oil adulterated with soybean oil in different levels were produced to obtain the reflectance spectra of 350–2500 nm. A set of multivariant methods was applied to identify adulteration types and adulteration rates. In the qualitative analysis of adulteration type, the support vector machine (SVM) method yielded high overall accuracy with multiple spectra pretreatments. In the quantitative analysis of adulteration rate, the random forest (RF) combined with multivariate scattering correction (MSC) achieved the highest identification accuracy of adulteration rate with the full wavelengths of Vis-NIR spectra. The effective wavelengths of the Vis-NIR spectra were screened to improve the robustness of the multivariant methods. The analysis results suggested that the competitive adaptive reweighted sampling (CARS) was helpful for removing the redundant information from the spectral data and improving the prediction accuracy. The PLSR + MSC + CARS model achieved the best prediction performance in the two adulteration cases of sesame oil and rapeseed oil. The coefficient of determination ($R_{P_{cv}}^2$) and the root mean square error ($RMS{E}_{P_{cv}}$) of the prediction set were 0.99656 and 0.01832 in sesame oil adulterated with soybean oil, and the $R_{P_{cv}}^2$ and $RMS{E}_{P_{cv}}$ were 0.99675 and 0.01685 in rapeseed oil adulterated with soybean oil, respectively. The Vis-NIR reflectance spectroscopy with the assistance of multivariant analysis can effectively discriminate the different adulteration rates of edible oils.

The composition and content of fatty acids are critical indicators to identify the quality of edible oils. This study was undertaken to establish a rapid determination method for quality detection of edible oils based on quantitative analysis of palmitic acid, stearic acid, arachidic acid, and behenic acid. Seven kinds of oils were measured to obtain Vis-NIR spectra. Multivariate methods combined with pretreatment methods were adopted to establish quantitative analysis models for the four fatty acids. The model of support vector machine (SVM) with standard normal variate (SNV) pretreatment showed the best predictive performance for the four fatty acids. For the palmitic acid, the determination coefficient of prediction ($R_P^2$) was 0.9504 and the root mean square error of prediction ($RMS{E}_P$) was 0.8181. For the stearic acid, $R_P^2$ and $RMS{E}_P$ were 0.9636 and 0.2965. In the prediction of arachidic acid, $R_P^2$ and $RMS{E}_P$ were 0.9576 and 0.0577. In the prediction of behenic acid, the $R_P^2$ and $RMS{E}_P$ were 0.9521 and 0.1486. Furthermore, the effective wavelengths selected by successive projections algorithm (SPA) were useful for establishing simplified prediction models. The results demonstrate that Vis-NIR spectroscopy combined with multivariate methods can provide a rapid and accurate approach for fatty acids detection of edible oils.

The temperature effect is one of the critical factors to induce the resonance wavelength shift in fiber-optic surface plasmon resonance (SPR) sensors, which leads to the inaccuracy measurement of refractive index (RI) in practical applications. In this study, a novel dual-wavelength method is presented for fiber-optic SPR sensors to measure the changes of RI and temperature simultaneously in real time. A typical model of an SPR-based fiber optical sensor is constructed for theoretical analysis of temperature effect. Both the thermo-optic effect in the fiber core and phonon–electron scattering along with electron–electron scattering in the metal layer are studied systematically in the theoretical model. The linear and independent relationship, about the dependence of defined output signals on the RI and temperature, is validated by a theoretical calculation in specific dual wavelengths. A proof-of-concept experiment is conducted to demonstrate the capability of the presented dual-wavelength technique. The experimental results indicate that the presented dual-wavelength method is technically feasible and can be applied for practical application. Since the presented method only depends on the full advantages of the transfer spectrum data, it can be applied directly to the conventional single-channel fiber-optic SPR without any specific design structure of the sensor probe. The proposed method provides a new way to detect the RI under different thermal conditions and could lead to a better design for the fiber-optic SPR sensors.

Background: miRBase is the primary repository for published miRNA sequence and annotation data, and serves as the “go-to” place for miRNA research. However, the definition and annotation of miRNAs have been changed significantly across different versions of miRBase. The changes cause inconsistency in miRNA related data between different databases and articles published at different times. Several tools have been developed for different purposes of querying and converting the information of miRNAs between different miRBase versions, but none of them individually can provide the comprehensive information about miRNAs in miRBase and users will need to use a number of different tools in their analyses. Results: We introduce miRBaseConverter, an R package integrating the latest miRBase version 22 available in Bioconductor to provide a suite of functions for converting and retrieving miRNA name (ID), accession, sequence, species, version and family information in different versions of miRBase. The package is implemented in R and available under the GPL-2 license from the Bioconductor website ( http://bioconductor.org/packages/miRBaseConverter/ ). A Shiny-based GUI suitable for non-R users is also available as a standalone application from the package and also as a web application at http://nugget.unisa.edu.au:3838/miRBaseConverter . miRBaseConverter has a built-in database for querying miRNA information in all species and for both pre-mature and mature miRNAs defined by miRBase. In addition, it is the first tool for batch querying the miRNA family information. The package aims to provide a comprehensive and easy-to-use tool for miRNA research community where researchers often utilize published miRNA data from different sources. Conclusions: The Bioconductor package miRBaseConverter and the Shiny-based web application are presented to provide a suite of functions for converting and retrieving miRNA name, accession, sequence, species, version and family information in different versions of miRBase. The package will serve a wide range of applications in miRNA research and could provide a full view of the miRNAs of interest.

Fatty acid abundance is a key parameter for evaluating the quality of edible oils. This study developed a rapid and non-destructive method for predicting palmitic acid content in edible oils by combining visible-near-infrared (Vis-NIR) reflectance spectroscopy with deep learning models. A total of 1740 reflectance spectra in the range of 350–2500 nm were collected from 87 brands of edible oils, including peanut, soybean, corn, sunflower, rapeseed, sesame, and olive oils. Reference values of palmitic acid content were determined via gas chromatography–mass spectrometry (GC-MS). Two conventional machine learning models (SVR and KNN) and four deep learning models (1D-CNN, 1D-ResNet, 1D-Inception, and 1D-Inception-ResNet) were developed and compared using both full-spectrum data and CARS selected characteristic wavelengths. Among the full-spectrum models, the designed 1D-ResNet model achieved the best performance, with the determination coefficient of prediction ($R_p^2$) of 0.9027 and the root mean square error of prediction ($RMS{E}_p$) of 1.13 in the prediction dataset. The proposed 1D-Inception-ResNet model yielded the best prediction results based on the 91 selected informative wavelengths via competitive adaptive reweighted sampling (CARS), achieving an $R_p^2$ of 0.9825 and an $RMS{E}_p$ of 0.4804 in the prediction dataset. The experimental results indicated that Vis-NIR reflectance spectroscopy combined with informative wavelength selection and deep learning models provided an effective strategy for rapid prediction of palmitic acid content in edible oils.