Integration of MALDI-TOF MS and machine learning to classify enterococci: A comparative analysis of supervised learning algorithms for species prediction.

This research focused on distinguishing distinct matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral signatures of three Enterococcus species. We evaluated and compared the predictive performance of four supervised machine learning algorithms, K-nearest neighbor (KNN), support vector machine (SVM), and random forest (RF), to accurately classify Enterococcus species. This study involved a comprehensive dataset of 410 strains, generating 1640 individual spectra through on-plate and off-plate protein extraction methods. Although the commercial database correctly identified 76.9% of the strains, machine learning classifiers demonstrated superior performance (accuracy 0.991). In the RF model, top informative peaks played a significant role in the classification. Whole-genome sequencing showed that the most informative peaks are biomarkers connected to proteins, which are essential for understanding bacterial classification and evolution. The integration of MALDI-TOF MS and machine learning provides a rapid and accurate method for identifying Enterococcus species, improving healthcare and food safety.

Classification of Latilactobacillus sakei subspecies based on MALDI-TOF MS protein profiles using machine learning models.

Latilactobacillus sakei is an important bacterial species used as a starter culture for fermented foods; however, two subspecies within this species exhibit different properties in the foods. Matrix-assisted laser desorption/ionization-time of flight mass spectrometer (MALDI-TOF MS) is the gold standard for microbial fingerprinting. However, the resolution power is down to the species level. This study was to combine MALDI-TOF mass spectra and machine learning to develop a new method to identify two L. sakei subspecies (L. sakei subsp. sakei and L. sakei subsp. carnosus) and non-L. sakei species. Totally, 227 strains were collected, with 908 spectra obtained via on- and off-plate protein extraction. Only 68.7% of strains were correctly identified at the subspecies level in the Biotyper database; however, a high level of performance was observed from the machine learning models. Partial least squares-discriminant analysis (PLS-DA), principal component analysis-K-nearest neighbor (PCA-KNN), and support vector machine (SVM) demonstrated 0.823, 0.914, and 0.903 accuracies, respectively, whereas the random forest (RF) achieved an accuracy of 0.954, with an area under the receiver operating characteristic (AUROC) curve of 0.99, outperforming the other algorithms in distinguishing the subspecies. The machine learning proved to be a promising technique for the rapid and high-resolution classification of L. sakei subspecies using MALDI-TOF MS. IMPORTANCE: Latilactobacillus sakei plays a significant role in the realm of food bacteria. One particular subspecies of L. sakei is employed as a protective agent during food fermentation, whereas another strain is responsible for food spoilage. Hence, it is crucial to precisely differentiate between the two subspecies of L. sakei. In this study, machine learning models based on protein mass peaks were developed for the first time to distinguish L. sakei subspecies. Furthermore, the efficacy of three commonly used machine learning algorithms for microbial classification was evaluated. Our results provide the foundation for future research on developing machine learning models for the classification of microbial species or subspecies. In addition, the developed model can be used in the food industry to monitor L. sakei subspecies in fermented foods in a time- and cost-effective method for food quality and safety.

Differentiation between Weissella cibaria and Weissella confusa Using Machine-Learning-Combined MALDI-TOF MS.

Although Weissella cibaria and W. confusa are essential food-fermenting bacteria, they are also opportunistic pathogens. Despite these species being commercially crucial, their taxonomy is still based on inaccurate identification methods. In this study, we present a novel approach for identifying two important Weissella species, W. cibaria and W. confusa, by combining matrix-assisted laser desorption/ionization and time-of-flight mass spectrometer (MALDI-TOF MS) data using machine-learning techniques. After on- and off-plate protein extraction, we observed that the BioTyper database misidentified or could not differentiate Weissella species. Although Weissella species exhibited very similar protein profiles, these species can be differentiated on the basis of the results of a statistical analysis. To classify W. cibaria, W. confusa, and non-target Weissella species, machine learning was used for 167 spectra, which led to the listing of potential species-specific mass-to-charge (m/z) loci. Machine-learning techniques including artificial neural networks, principal component analysis combined with the K-nearest neighbor, support vector machine (SVM), and random forest were used. The model that applied the Radial Basis Function kernel algorithm in SVM achieved classification accuracy of 1.0 for training and test sets. The combination of MALDI-TOF MS and machine learning can efficiently classify closely-related species, enabling accurate microbial identification.

Development of a classification model for Cynanchum wilfordii and Cynanchum auriculatum using convolutional neural network and local interpretable model-agnostic explanation technology.

Cynanchum wilfordii is a perennial tuberous root in the Asclepiadaceae family that has long been used medicinally. Although C. wilfordii is distinct in origin and content from Cynancum auriculatum, a genus of the same species, it is difficult for the public to recognize because the ripe fruit and root are remarkably similar. In this study, images were collected to categorize C. wilfordii and C. auriculatum, which were then processed and input into a deep-learning classification model to corroborate the results. By obtaining 200 photographs of each of the two cross sections of each medicinal material, approximately 800 images were employed, and approximately 3200 images were used to construct a deep-learning classification model via image augmentation. For the classification, the structures of Inception-ResNet and VGGnet-19 among convolutional neural network (CNN) models were used, with Inception-ResNet outperforming VGGnet-19 in terms of performance and learning speed. The validation set confirmed a strong classification performance of approximately 0.862. Furthermore, explanatory properties were added to the deep-learning model using local interpretable model-agnostic explanation (LIME), and the suitability of the LIME domain was assessed using cross-validation in both situations. Thus, artificial intelligence may be used as an auxiliary metric in the sensory evaluation of medicinal materials in future, owing to its explanatory ability.

Decision-tree-based ion-specific dosing algorithm for enhancing closed hydroponic efficiency and reducing carbon emissions.

The maintenance of ion balance in closed hydroponic solutions is essential to improve the crop quality and recycling efficiency of nutrient solutions. However, the absence of robust ion sensors for key ions such as P and Mg and the coupling of ions in fertilizer salts render it difficult to effectively manage ion-specific nutrient solutions. Although ion-specific dosing algorithms have been established, their effectiveness has been inadequately explored. In this study, a decision-tree-based dosing algorithm was developed to calculate the optimal volumes of individual nutrient stock solutions to be supplied for five major nutrient ions, i.e., NO3, K, Ca, P, and Mg, based on the concentrations of NO3, K, and Ca and remaining volume of the recycled nutrient solution. In the performance assessment based on five nutrient solution samples encompassing the typical concentration ranges for leafy vegetable cultivation, the ion-selective electrode array demonstrated feasible accuracies, with root mean square errors of 29.5, 10.1, and 6.1 mg·L-1 for NO3, K, and Ca, respectively. In a five-step replenishment test involving varying target concentrations and nutrient solution volumes, the system formulated nutrient solutions according to the specified targets, exhibiting average relative errors of 10.6 ± 8.0%, 7.9 ± 2.1%, 8.0 ± 11.0%, and 4.2 ± 3.7% for the Ca, K, and NO3 concentrations and volume of the nutrient solution, respectively. Furthermore, the decision tree method helped reduce the total fertilizer injections and carbon emissions by 12.8% and 20.6% in the stepwise test, respectively. The findings demonstrate that the decision-tree-based dosing algorithm not only enables more efficient reuse of nutrient solution compared to the existing simplex method but also confirms the potential for reducing carbon emissions, indicating the possibility of sustainable agricultural development.

Depth image conversion model based on CycleGAN for growing tomato truss identification.

BACKGROUND: On tomato plants, the flowering truss is a group or cluster of smaller stems where flowers and fruit develop, while the growing truss is the most extended part of the stem. Because the state of the growing truss reacts sensitively to the surrounding environment, it is essential to control its growth in the early stages. With the recent development of information and artificial intelligence technology in agriculture, a previous study developed a real-time acquisition and evaluation method for images using robots. Furthermore, we used image processing to locate the growing truss to extract growth information. Among the different vision algorithms, the CycleGAN algorithm was used to generate and transform unpaired images using generated learning images. In this study, we developed a robot-based system for simultaneously acquiring RGB and depth images of the growing truss of the tomato plant. RESULTS: The segmentation performance for approximately 35 samples was compared via false negative (FN) and false positive (FP) indicators. For the depth camera image, we obtained FN and FP values of 17.55 ± 3.01% and 17.76 ± 3.55%, respectively. For the CycleGAN algorithm, we obtained FN and FP values of 19.24 ± 1.45% and 18.24 ± 1.54%, respectively. When segmentation was performed via image processing through depth image and CycleGAN, the mean intersection over union (mIoU) was 63.56 ± 8.44% and 69.25 ± 4.42%, respectively, indicating that the CycleGAN algorithm can identify the desired growing truss of the tomato plant with high precision. CONCLUSIONS: The on-site possibility of the image extraction technique using CycleGAN was confirmed when the image scanning robot drove in a straight line through a tomato greenhouse. In the future, the proposed approach is expected to be used in vision technology to scan tomato growth indicators in greenhouses using an unmanned robot platform.

A Hyperspectral Data 3D Convolutional Neural Network Classification Model for Diagnosis of Gray Mold Disease in Strawberry Leaves.

Gray mold disease is one of the most frequently occurring diseases in strawberries. Given that it spreads rapidly, rapid countermeasures are necessary through the development of early diagnosis technology. In this study, hyperspectral images of strawberry leaves that were inoculated with gray mold fungus to cause disease were taken; these images were classified into healthy and infected areas as seen by the naked eye. The areas where the infection spread after time elapsed were classified as the asymptomatic class. Square regions of interest (ROIs) with a dimensionality of 16 × 16 × 150 were acquired as training data, including infected, asymptomatic, and healthy areas. Then, 2D and 3D data were used in the development of a convolutional neural network (CNN) classification model. An effective wavelength analysis was performed before the development of the CNN model. Further, the classification model that was developed with 2D training data showed a classification accuracy of 0.74, while the model that used 3D data acquired an accuracy of 0.84; this indicated that the 3D data produced slightly better performance. When performing classification between healthy and asymptomatic areas for developing early diagnosis technology, the two CNN models showed a classification accuracy of 0.73 with regards to the asymptomatic ones. To increase accuracy in classifying asymptomatic areas, a model was developed by smoothing the spectrum data and expanding the first and second derivatives; the results showed that it was possible to increase the asymptomatic classification accuracy to 0.77 and reduce the misclassification of asymptomatic areas as healthy areas. Based on these results, it is concluded that the proposed 3D CNN classification model can be used as an early diagnosis sensor of gray mold diseases since it produces immediate on-site analysis results of hyperspectral images of leaves.

Water Nitrate Remote Monitoring System with Self-Diagnostic Function for Ion-Selective Electrodes.

The detection of nitrate pollutants is a widely used strategy for protecting water sources. Although ion-selective electrodes (ISEs) have been considered for the determination of ion concentrations in water, the accuracy of ISE technology decreases owing to the signal drift and decreasing sensitivity over time. The objectives of the present study were: (1) to develop an online water monitoring system mainly consisting of an Arduino board-based Internet-of-Things (IoT) device and nitrate ISEs; and (2) to propose a self-diagnostic function for monitoring and reporting the condition of the ISEs. The developed system communicates with the cloud server by using the message queuing telemetry transport (MQTT) protocol and provides monitoring information through the developed cloud-based webpage. In addition, the online monitoring system provides information on the electrode status, which is determined based on a self-diagnostic index (SDI, with a range of 0-100) of the electrode drift and sensitivity. The diagnostic method for monitoring and reporting the electrode status was validated in a one-month-long laboratory test followed by a field test in a stream near an agricultural facility. Moreover, a self-diagnostic index (SDI) was applied in the final field experiments with an accuracy of 0.77.

Deep Learning-Based Cattle Vocal Classification Model and Real-Time Livestock Monitoring System with Noise Filtering.

The priority placed on animal welfare in the meat industry is increasing the importance of understanding livestock behavior. In this study, we developed a web-based monitoring and recording system based on artificial intelligence analysis for the classification of cattle sounds. The deep learning classification model of the system is a convolutional neural network (CNN) model that takes voice information converted to Mel-frequency cepstral coefficients (MFCCs) as input. The CNN model first achieved an accuracy of 91.38% in recognizing cattle sounds. Further, short-time Fourier transform-based noise filtering was applied to remove background noise, improving the classification model accuracy to 94.18%. Categorized cattle voices were then classified into four classes, and a total of 897 classification records were acquired for the classification model development. A final accuracy of 81.96% was obtained for the model. Our proposed web-based platform that provides information obtained from a total of 12 sound sensors provides cattle vocalization monitoring in real time, enabling farm owners to determine the status of their cattle.

Roles of the MPFC and insula in impression management under social observation.

People often engage in impression management by presenting themselves and others as socially desirable. However, specific behavioral manifestations and underlying neural mechanisms of impression management remain unknown. In this study, we investigated the neural mechanism of impression management during self- and friend-evaluation. Only participants assigned to the observation (OBS) group, not the control (CON) group, were informed that their responses would be monitored. They answered how well positive and negative trait adjectives described themselves or their friends. The behavioral results showed that the OBS group was more likely to reject negative traits for self-evaluation and to accept positive traits for friend-evaluation. An independent study revealed that demoting negative traits for oneself and promoting positive traits for a friend helps manage one's impression. In parallel with the behavioral results, in the OBS vs the CON group, the rostromedial prefrontal cortex (rmPFC) and anterior insula (AI) activity showed a greater increase as the negativity of negatively valenced adjectives increased during self-evaluation and also showed a greater increase as the positivity of positively valenced adjectives increased during friend-evaluation. The present study suggests that rmPFC and AI are critically involved in impression management, promoting socially desirable target evaluations under social observation.

Model Predictive Control via Output Feedback Neural Network for Improved Multi-Window Greenhouse Ventilation Control.

Maintaining environmental conditions for proper plant growth in greenhouses requires managing a variety of factors; ventilation is particularly important because inside temperatures can rise rapidly in warm climates. The structure of the window installed in a greenhouse is very diverse, and it is difficult to identify the characteristics that affect the temperature inside the greenhouse when multiple windows are driven, respectively. In this study, a new ventilation control logic using an output feedback neural-network (OFNN) prediction and optimization method was developed, and this approach was tested in multi-window greenhouses used for strawberry production. The developed prediction model used 15 inputs and achieved a highly accurate performance (R2 of 0.94). In addition, the method using an algorithm based on an OFNN was proposed for optimizing considered six window-opening behavior. Three case studies confirmed the optimization performance of OFNN in the nonlinear model and verified the performance through simulations. Finally, a control system based on this logic was used in a field experiment for six days by comparing two greenhouses driven by conventional control logic and the developed control logic; a comparison of the results showed RMSEs of 3.01 °C and 2.45 °C, respectively. It confirmed the improved control performance in comparison to a conventional ventilation control system.

Hybrid Signal-Processing Method Based on Neural Network for Prediction of NO3, K, Ca, and Mg Ions in Hydroponic Solutions Using an Array of Ion-Selective Electrodes.

In closed hydroponics, fast and continuous measurement of individual nutrient concentrations is necessary to improve water- and nutrient-use efficiencies and crop production. Ion-selective electrodes (ISEs) could be one of the most attractive tools for hydroponic applications. However, signal drifts over time and interferences from other ions present in hydroponic solutions make it difficult to use the ISEs in hydroponic solutions. In this study, hybrid signal processing combining a two-point normalization (TPN) method for the effective compensation of the drifts and a back propagation artificial neural network (ANN) algorithm for the interpretation of the interferences was developed. In addition, the ANN-based approach for the prediction of Mg concentration which had no feasible ISE was conducted by interpreting the signals from a sensor array consisting of electrical conductivity (EC) and ion-selective electrodes (NO3, K, and Ca). From the application test using 8 samples from real greenhouses, the hybrid method based on a combination of the TPN and ANN methods showed relatively low root mean square errors of 47.2, 13.2, and 18.9 mg∙L-1 with coefficients of variation (CVs) below 10% for NO3, K, and Ca, respectively, compared to those obtained by separate use of the two methods. Furthermore, the Mg prediction results with a root mean square error (RMSE) of 14.6 mg∙L-1 over the range of 10-60 mg∙L-1 showed potential as an approximate diagnostic tool to measure Mg in hydroponic solutions. These results demonstrate that the hybrid method can improve the accuracy and feasibility of ISEs in hydroponic applications.

Fusion of Spectroscopy and Cobalt Electrochemistry Data for Estimating Phosphate Concentration in Hydroponic Solution.

Phosphate is a key element affecting plant growth. Therefore, the accurate determination of phosphate concentration in hydroponic nutrient solutions is essential for providing a balanced set of nutrients to plants within a suitable range. This study aimed to develop a data fusion approach for determining phosphate concentrations in a paprika nutrient solution. As a conventional multivariate analysis approach using spectral data, partial least squares regression (PLSR) and principal components regression (PCR) models were developed using 56 samples for calibration and 24 samples for evaluation. The R2 values of estimation models using PCR and PLSR ranged from 0.44 to 0.64. Furthermore, an estimation model using raw electromotive force (EMF) data from cobalt electrodes gave R2 values of 0.58-0.71. To improve the model performance, a data fusion method was developed to estimate phosphate concentration using near infrared (NIR) spectral and cobalt electrochemical data. Raw EMF data from cobalt electrodes and principle component values from the spectral data were combined. Results of calibration and evaluation tests using an artificial neural network estimation model showed that R2 = 0.90 and 0.89 and root mean square error (RMSE) = 96.70 and 119.50 mg/L, respectively. These values are sufficiently high for application to measuring phosphate concentration in hydroponic solutions.

Social Observation Increases Functional Segregation between MPFC Subregions Predicting Prosocial Consumer Decisions.

Although it is now well documented that observation by others can be a powerful elicitor of prosocial behaviour, the underlying neural mechanism is yet to be explored. In the present fMRI study, we replicated the previously reported observer effect in ethical consumption, in that participants were more likely to purchase social products that are sold to support people in need than non-social products when being observed by others. fMRI data revealed that the anterior cingulate cortex (ACC) and the dorsomedial prefrontal cortex (dmPFC) encoded subject-specific value parameters of purchase decisions for social and non-social products, respectively, under social observation. The ACC showed strong functional coupling with the amygdala and the anterior insula when participants in the observation condition were making purchases of social versus non-social products. Finally, ventromedial prefrontal cortex (vmPFC) activity predicted faster reaction time and increased prosocial behavior during decisions to purchase social versus non-social products, regardless of social observation. The present findings suggest that subregions of the mPFC, namely the dmPFC, ACC, and vmPFC, are hierarchically organized to encode different levels of decision values from the value of context-sensitive reputation to that of internalized prosociality.

Spatial gradient in value representation along the medial prefrontal cortex reflects individual differences in prosociality.

Despite the importance of valuing another person's welfare for prosocial behavior, currently we have only a limited understanding of how these values are represented in the brain and, more importantly, how they give rise to individual variability in prosociality. In the present study, participants underwent functional magnetic resonance imaging while performing a prosocial learning task in which they could choose to benefit themselves and/or another person. Choice behavior indicated that participants valued the welfare of another person, although less so than they valued their own welfare. Neural data revealed a spatial gradient in activity within the medial prefrontal cortex (MPFC), such that ventral parts predominantly represented self-regarding values and dorsal parts predominantly represented other-regarding values. Importantly, compared with selfish individuals, prosocial individuals showed a more gradual transition from self-regarding to other-regarding value signals in the MPFC and stronger MPFC-striatum coupling when they made choices for another person rather than for themselves. The present study provides evidence of neural markers reflecting individual differences in human prosociality.

Dissociable neural processes underlying risky decisions for self versus other.

Previous neuroimaging studies on decision making have mainly focused on decisions on behalf of oneself. Considering that people often make decisions on behalf of others, it is intriguing that there is little neurobiological evidence on how decisions for others differ from those for oneself. The present study directly compared risky decisions for self with those for another person using functional magnetic resonance imaging (fMRI). Participants were asked to perform a gambling task on behalf of themselves (decision-for-self condition) or another person (decision-for-other condition) while in the scanner. Their task was to choose between a low-risk option (i.e., win or lose 10 points) and a high-risk option (i.e., win or lose 90 points) with variable levels of winning probability. Compared with choices regarding others, those regarding oneself were more risk-averse at lower winning probabilities and more risk-seeking at higher winning probabilities, perhaps due to stronger affective process during risky decisions for oneself compared with those for other. The brain-activation pattern changed according to the target, such that reward-related regions were more active in the decision-for-self condition than in the decision-for-other condition, whereas brain regions related to the theory of mind (ToM) showed greater activation in the decision-for-other condition than in the decision-for-self condition. Parametric modulation analysis using individual decision models revealed that activation of the amygdala and the dorsomedial prefrontal cortex (DMPFC) were associated with value computations for oneself and for another, respectively, during risky financial decisions. The results of the present study suggest that decisions for oneself and for other may recruit fundamentally distinct neural processes, which can be mainly characterized as dominant affective/impulsive and cognitive/regulatory processes, respectively.

Interactive responses of a thalamic neuron to formalin induced lasting pain in behaving mice.

Thalamocortical (TC) neurons are known to relay incoming sensory information to the cortex via firing in tonic or burst mode. However, it is still unclear how respective firing modes of a single thalamic relay neuron contribute to pain perception under consciousness. Some studies report that bursting could increase pain in hyperalgesic conditions while others suggest the contrary. However, since previous studies were done under either neuropathic pain conditions or often under anesthesia, the mechanism of thalamic pain modulation under awake conditions is not well understood. We therefore characterized the thalamic firing patterns of behaving mice in response to nociceptive pain induced by inflammation. Our results demonstrated that nociceptive pain responses were positively correlated with tonic firing and negatively correlated with burst firing of individual TC neurons. Furthermore, burst properties such as intra-burst-interval (IntraBI) also turned out to be reliably correlated with the changes of nociceptive pain responses. In addition, brain stimulation experiments revealed that only bursts with specific bursting patterns could significantly abolish behavioral nociceptive responses. The results indicate that specific patterns of bursting activity in thalamocortical relay neurons play a critical role in controlling long-lasting inflammatory pain in awake and behaving mice.