AMP-RNNpro: a two-stage approach for identification of antimicrobials using probabilistic features.

Antimicrobials are molecules that prevent the formation of microorganisms such as bacteria, viruses, fungi, and parasites. The necessity to detect antimicrobial peptides (AMPs) using machine learning and deep learning arises from the need for efficiency to accelerate the discovery of AMPs, and contribute to developing effective antimicrobial therapies, especially in the face of increasing antibiotic resistance. This study introduced AMP-RNNpro based on Recurrent Neural Network (RNN), an innovative model for detecting AMPs, which was designed with eight feature encoding methods that are selected according to four criteria: amino acid compositional, grouped amino acid compositional, autocorrelation, and pseudo-amino acid compositional to represent the protein sequences for efficient identification of AMPs. In our framework, two-stage predictions have been conducted. Initially, this study analyzed 33 models on these feature extractions. Then, we selected the best six models from these models using rigorous performance metrics. In the second stage, probabilistic features have been generated from the selected six models in each feature encoding and they are aggregated to be fed into our final meta-model called AMP-RNNpro. This study also introduced 20 features with SHAP, which are crucial in the drug development fields, where we discover AAC, ASDC, and CKSAAGP features are highly impactful for detection and drug discovery. Our proposed framework, AMP-RNNpro excels in the identification of novel Amps with 97.15% accuracy, 96.48% sensitivity, and 97.87% specificity. We built a user-friendly website for demonstrating the accurate prediction of AMPs based on the proposed approach which can be accessed at http://13.126.159.30/ .

Design and Analysis of Multi-Analyte Detection Based Biosensor in the Visible to Near-Infrared (VNIR) Region.

This manuscript introduces a highly sensitive dual-core photonic crystal fiber (PCF) based multi-analyte surface plasmon resonance (SPR) sensor, possessing the ability to detect multiple analytes at once. A chemically stable thin plasmonic substance of gold (Au) layer, holding a thickness of 30 nm, is employed to the outer portion of the stated design that manifests a negative real permittivity. Moreover, an ultra-thin film of aluminum oxide (Al2O3) , having a thickness of 10 nm, is inserted into the exterior of the gold film to calibrate the resonance wavelength as well as magnify the coupling strength. The performance of the sensor is rigorously explored employing the finite element method (FEM), where numerical investigation confirms that the intended sensor model exhibits a peak amplitude sensitivity (AS) of 2606 RIU-1 , as well as a highest wavelength sensitivity (WS) of 20,000 nm/RIU. The achieved outcomes affirm that the sensor design can be conceivably applied in numerous biological; as well as biochemical analyte refractive index (RI) detection to realize the relevant significant applications in the visible to near-infrared (VNIR) region of 0.5 to [Formula: see text].

A Novel Hybrid Approach for Classifying Osteosarcoma Using Deep Feature Extraction and Multilayer Perceptron.

Osteosarcoma is the most common type of bone cancer that tends to occur in teenagers and young adults. Due to crowded context, inter-class similarity, inter-class variation, and noise in H&E-stained (hematoxylin and eosin stain) histology tissue, pathologists frequently face difficulty in osteosarcoma tumor classification. In this paper, we introduced a hybrid framework for improving the efficiency of three types of osteosarcoma tumor (nontumor, necrosis, and viable tumor) classification by merging different types of CNN-based architectures with a multilayer perceptron (MLP) algorithm on the WSI (whole slide images) dataset. We performed various kinds of preprocessing on the WSI images. Then, five pre-trained CNN models were trained with multiple parameter settings to extract insightful features via transfer learning, where convolution combined with pooling was utilized as a feature extractor. For feature selection, a decision tree-based RFE was designed to recursively eliminate less significant features to improve the model generalization performance for accurate prediction. Here, a decision tree was used as an estimator to select the different features. Finally, a modified MLP classifier was employed to classify binary and multiclass types of osteosarcoma under the five-fold CV to assess the robustness of our proposed hybrid model. Moreover, the feature selection criteria were analyzed to select the optimal one based on their execution time and accuracy. The proposed model achieved an accuracy of 95.2% for multiclass classification and 99.4% for binary classification. Experimental findings indicate that our proposed model significantly outperforms existing methods; therefore, this model could be applicable to support doctors in osteosarcoma diagnosis in clinics. In addition, our proposed model is integrated into a web application using the FastAPI web framework to provide a real-time prediction.

PreOBP_ML: Machine Learning Algorithms for Prediction of Optical Biosensor Parameters.

To develop standard optical biosensors, the simulation procedure takes a lot of time. For reducing that enormous amount of time and effort, machine learning might be a better solution. Effective indices, core power, total power, and effective area are the most crucial parameters for evaluating optical sensors. In this study, several machine learning (ML) approaches have been applied to predict those parameters while considering the core radius, cladding radius, pitch, analyte, and wavelength as the input vectors. We have utilized least squares (LS), LASSO, Elastic-Net (ENet), and Bayesian ridge regression (BRR) to make a comparative discussion using a balanced dataset obtained with the COMSOL Multiphysics simulation tool. Furthermore, a more extensive analysis of sensitivity, power fraction, and confinement loss is also demonstrated using the predicted and simulated data. The suggested models were also examined in terms of R2-score, mean average error (MAE), and mean squared error (MSE), with all of the models having an R2-score of more than 0.99, and it was also shown that optical biosensors had a design error rate of less than 3%. This research might pave the way for machine learning-based optimization approaches to be used to improve optical biosensors.

Au-TiO2-Coated Spectroscopy-Based Human Teeth Disorder Detection Sensor: Design and Quantitative Analysis.

Human tooth functionality is the most important for the human body to become fit and healthy. Due to the disease attacks in human teeth, parts may lead to different fatal diseases. A spectroscopy-based photonic crystal fiber (PCF) sensor was simulated and numerically analyzed for the detection of dental disorders in the human body. In this sensor structure, SF11 is used as the base material, gold (Au) is used as the plasmonic material, and TiO2 is used within the gold and sensing analyte layer, and the sensing medium for the analysis of the teeth parts is the aqueous solution. The maximum optical parameter values for the human tooth parts enamel, dentine, and cementum in terms of wavelength sensitivity and confinement loss were obtained as 28,948.69 nm/RIU and 0.00015 dB/m for enamel, 33,684.99 nm/RIU and 0.00028 dB/m, and 38,396.56 nm/RIU and 0.00087 dB/m, respectively. The sensor is more precisely defined by these high responses. The PCF-based sensor for tooth disorder detection is a relatively recent development. Due to its design flexibility, robustness, and wide bandwidth, its application area has been spreading out. The offered sensor can be used in the biological sensing area to identify problems with human teeth.

High-precision multiclass classification of lung disease through customized MobileNetV2 from chest X-ray images.

In this study, multiple lung diseases are diagnosed with the help of the Neural Network algorithm. Specifically, Emphysema, Infiltration, Mass, Pleural Thickening, Pneumonia, Pneumothorax, Atelectasis, Edema, Effusion, Hernia, Cardiomegaly, Pulmonary Fibrosis, Nodule, and Consolidation, are studied from the ChestX-ray14 dataset. A proposed fine-tuned MobileLungNetV2 model is employed for analysis. Initially, pre-processing is done on the X-ray images from the dataset using CLAHE to increase image contrast. Additionally, a Gaussian Filter, to denoise images, and data augmentation methods are used. The pre-processed images are fed into several transfer learning models; such as InceptionV3, AlexNet, DenseNet121, VGG19, and MobileNetV2. Among these models, MobileNetV2 performed with the highest accuracy of 91.6% in overall classifying lesions on Chest X-ray Images. This model is then fine-tuned to optimise the MobileLungNetV2 model. On the pre-processed data, the fine-tuned model, MobileLungNetV2, achieves an extraordinary classification accuracy of 96.97%. Using a confusion matrix for all the classes, it is determined that the model has an overall high precision, recall, and specificity scores of 96.71%, 96.83% and 99.78% respectively. The study employs the Grad-cam output to determine the heatmap of disease detection. The proposed model shows promising results in classifying multiple lesions on Chest X-ray images.

Systematic approach to identify therapeutic targets and functional pathways for the cervical cancer.

BACKGROUND: In today's society, cancer has become a big concern. The most common cancers in women are breast cancer (BC), endometrial cancer (EC), ovarian cancer (OC), and cervical cancer (CC). CC is a type of cervix cancer that is the fourth most common cancer in women and the fourth major cause of death. RESULTS: This research uses a network approach to discover genetic connections, functional enrichment, pathways analysis, microRNAs transcription factors (miRNA-TF) co-regulatory network, gene-disease associations, and therapeutic targets for CC. Three datasets from the NCBI's GEO collection were considered for this investigation. Then, using a comparison approach between the datasets, 315 common DEGs were discovered. The PPI network was built using a variety of combinatorial statistical approaches and bioinformatics tools, and the PPI network was then utilized to identify hub genes and critical modules. CONCLUSION: Furthermore, we discovered that CC has specific similar links with the progression of different tumors using Gene Ontology terminology and pathway analysis. Transcription factors-gene linkages, gene-disease correlations, and the miRNA-TF co-regulatory network were revealed to have functional enrichments. We believe the candidate drugs identified in this study could be effective for advanced CC treatment.

Drug Repurposing and Systems Biology approaches of Enzastaurin can target potential biomarkers and critical pathways in Colorectal Cancer.

Colorectal cancer (CRC) is a severe health concern that results from a cocktail of genetic, epigenetic, and environmental abnormalities. Because it is the second most lethal malignancy in the world and the third-most common malignant tumor, but the treatment is unavailable. The goal of the current study was to use bioinformatics and systems biology techniques to determine the pharmacological mechanism underlying putative important genes and linked pathways in early-onset CRC. Computer-aided methods were used to uncover similar biological targets and signaling pathways associated with CRC, along with bioinformatics and network pharmacology techniques to assess the effects of enzastaurin on CRC. The KEGG and gene ontology (GO) pathway analysis revealed several significant pathways including in positive regulation of protein phosphorylation, negative regulation of the apoptotic process, nucleus, nucleoplasm, protein tyrosine kinase activity, PI3K-Akt signaling pathway, pathways in cancer, focal adhesion, HIF-1 signaling pathway, and Rap1 signaling pathway. Later, the hub protein module identified from the protein-protein interactions (PPIs) network, molecular docking and molecular dynamics simulation represented that enzastaurin showed strong binding interaction with two hub proteins including CASP3 (-8.6 kcal/mol), and MCL1 (-8.6 kcal/mol), which were strongly implicated in CRC management than other the five hub proteins. Moreover, the pharmacokinetic features of enzastaurin revealed that it is an effective therapeutic agent with minimal adverse effects. Enzastaurin may inhibit the potential biological targets that are thought to be responsible for the advancement of CRC and this study suggests a potential novel therapeutic target for CRC.

Terahertz Metasurface-Based Refractive Index Sensor for Amino Acid Detection: A Numerical Approach.

A graphene disk metasurface-inspired refractive index sensor (RIS) with a subwavelength structure is numerically investigated to enhance the functionality of flexible metasurface in the biosensor sector. The main aim behind the sensor development is to detect amino acids with high sensitivity. The results in form of transmittance and the electric field intensity are carried out to verify the sensor's performance. The optimal design of the proposed sensor is also obtained by varying several structural parameters such as glass-based substrate thickness, the inner radius of the graphene disk metasurface, and the angle of incidence. The proposed sensor is also wide-angle insensitive for the angle of incidence ranging from 0° to 60°. Furthermore, the sensor's attributes are analyzed based on numerous parameters with an achieved maximum sensitivity of 333.33 GHz/RIU, Figure of Merit (FOM) of 3.11 RIU-1, and Q-factor of 7.3 are achieved. As a result, these insights offered an enhanced direction for designing metasurface biosensors with a high Q-factor and FOM with high sensitivity for the detection of amino acids.

Federated Machine Learning for Detection of Skin Diseases and Enhancement of Internet of Medical Things (IoMT) Security.

Human skin disease, the most infectious dermatological ailment globally, is initially diagnosed by sight. Some clinical screening and dermoscopic analysis of skin biopsies and scrapings for accurate classification are medically compulsory. Classification of skin diseases using medical images is more challenging because of the complex formation and variant colors of the disease and data security concerns. Both the Convolution Neural Network (CNN) for classification and a federated learning approach for data privacy preservation show significant performance in the realm of medical imaging fields. In this paper, a custom image dataset was prepared with four classes of skin disease, a CNN model was suggested and compared with several benchmark CNN algorithms, and an experiment was carried out to ensure data privacy using a federated learning approach. An image augmentation strategy was followed to enlarge the dataset and make the model more general. The proposed model achieved a precision of 86%, 43%, and 60%, and a recall of 67%, 60%, and 60% for acne, eczema, and psoriasis. In the federated learning approach, after distributing the dataset among 1000, 1500, 2000, and 2500 clients, the model showed an average accuracy of 81.21%, 86.57%, 91.15%, and 94.15%. The CNN-based skin disease classification merged with the federated learning approach is a breathtaking concept to classify human skin diseases while ensuring data security.

Recent Advances in Biosensors for Detection of COVID-19 and Other Viruses.

This century has introduced very deadly, dangerous, and infectious diseases to humankind such as the influenza virus, Ebola virus, Zika virus, and the most infectious SARS-CoV-2 commonly known as COVID-19 and have caused epidemics and pandemics across the globe. For some of these diseases, proper medications, and vaccinations are missing and the early detection of these viruses will be critical to saving the patients. And even the vaccines are available for COVID-19, the new variants of COVID-19 such as Delta, and Omicron are spreading at large. The available virus detection techniques take a long time, are costly, and complex and some of them generates false negative or false positive that might cost patients their lives. The biosensor technique is one of the best qualified to address this difficult challenge. In this systematic review, we have summarized recent advancements in biosensor-based detection of these pandemic viruses including COVID-19. Biosensors are emerging as efficient and economical analytical diagnostic instruments for early-stage illness detection. They are highly suitable for applications related to healthcare, wearable electronics, safety, environment, military, and agriculture. We strongly believe that these insights will aid in the study and development of a new generation of adaptable virus biosensors for fellow researchers.

MLBioIGE: integration and interplay of machine learning and bioinformatics approach to identify the genetic effect of SARS-COV-2 on idiopathic pulmonary fibrosis patients.

SARS-CoV-2, the virus that causes COVID-19, is a current concern for people worldwide. The virus has recently spread worldwide and is out of control in several countries, putting the outbreak into a terrifying phase. Machine learning with transcriptome analysis has advanced in recent years. Its outstanding performance in several fields has emerged as a potential option to find out how SARS-CoV-2 is related to other diseases. Idiopathic pulmonary fibrosis (IPF) disease is caused by long-term lung injury, a risk factor for SARS-CoV-2. In this article, we used a variety of combinatorial statistical approaches, machine learning, and bioinformatics tools to investigate how the SARS-CoV-2 affects IPF patients' complexity. For this study, we employed two RNA-seq datasets. The unique contributions include common genes identification to identify shared pathways and drug targets, PPI network to identify hub-genes and basic modules, and the interaction of transcription factors (TFs) genes and TFs-miRNAs with common differentially expressed genes also placed on the datasets. Furthermore, we used gene ontology and molecular pathway analysis to do functional analysis and discovered that IPF patients have certain standard connections with the SARS-CoV-2 virus. A detailed investigation was carried out to recommend therapeutic compounds for IPF patients affected by the SARS-CoV-2 virus.

Discovering Common Pathophysiological Processes between COVID-19 and Cystic Fibrosis by Differential Gene Expression Pattern Analysis.

Coronaviruses are a family of viruses that infect mammals and birds. Coronaviruses cause infections of the respiratory system in humans, which can be minor or fatal. A comparative transcriptomic analysis has been performed to establish essential profiles of the gene expression of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) linked to cystic fibrosis (CF). Transcriptomic studies have been carried out in relation to SARS-CoV-2 since a number of people have been diagnosed with CF. The recognition of differentially expressed genes demonstrated 8 concordant genes shared between the SARS-CoV-2 and CF. Extensive gene ontology analysis and the discovery of pathway enrichment demonstrated SARS-CoV-2 response to CF. The gene ontological terms and pathway enrichment mechanisms derived from this research may affect the production of successful drugs, especially for the people with the following disorder. Identification of TF-miRNA association network reveals the interconnection between TF genes and miRNAs, which may be effective to reveal the other influenced disease that occurs for SARS-CoV-2 to CF. The enrichment of pathways reveals SARS-CoV-2-associated CF mostly engaged with the type of innate immune system, Toll-like receptor signaling pathway, pantothenate and CoA biosynthesis, allograft rejection, graft-versus-host disease, intestinal immune network for IgA production, mineral absorption, autoimmune thyroid disease, legionellosis, viral myocarditis, inflammatory bowel disease (IBD), etc. The drug compound identification demonstrates that the drug targets of IMIQUIMOD and raloxifene are the most significant with the significant hub DEGs.

Identification of Potential Key Genes and Molecular Mechanisms of Medulloblastoma Based on Integrated Bioinformatics Approach.

BACKGROUND: Medulloblastoma (MB) is the most occurring brain cancer that mostly happens in childhood age. This cancer starts in the cerebellum part of the brain. This study is designed to screen novel and significant biomarkers, which may perform as potential prognostic biomarkers and therapeutic targets in MB. METHODS: A total of 103 MB-related samples from three gene expression profiles of GSE22139, GSE37418, and GSE86574 were downloaded from the Gene Expression Omnibus (GEO). Applying the limma package, all three datasets were analyzed, and 1065 mutual DEGs were identified including 408 overexpressed and 657 underexpressed with the minimum cut-off criteria of ∣log fold change | >1 and P < 0.05. The Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and WikiPathways enrichment analyses were executed to discover the internal functions of the mutual DEGs. The outcomes of enrichment analysis showed that the common DEGs were significantly connected with MB progression and development. The Search Tool for Retrieval of Interacting Genes (STRING) database was used to construct the interaction network, and the network was displayed using the Cytoscape tool and applying connectivity and stress value methods of cytoHubba plugin 35 hub genes were identified from the whole network. RESULTS: Four key clusters were identified using the PEWCC 1.0 method. Additionally, the survival analysis of hub genes was brought out based on clinical information of 612 MB patients. This bioinformatics analysis may help to define the pathogenesis and originate new treatments for MB.

Machine learning-based statistical analysis for early stage detection of cervical cancer.

Cervical cancer (CC) is the most common type of cancer in women and remains a significant cause of mortality, particularly in less developed countries, although it can be effectively treated if detected at an early stage. This study aimed to find efficient machine-learning-based classifying models to detect early stage CC using clinical data. We obtained a Kaggle data repository CC dataset which contained four classes of attributes including biopsy, cytology, Hinselmann, and Schiller. This dataset was split into four categories based on these class attributes. Three feature transformation methods, including log, sine function, and Z-score were applied to these datasets. Several supervised machine learning algorithms were assessed for their performance in classification. A Random Tree (RT) algorithm provided the best classification accuracy for the biopsy (98.33%) and cytology (98.65%) data, whereas Random Forest (RF) and Instance-Based K-nearest neighbor (IBk) provided the best performance for Hinselmann (99.16%), and Schiller (98.58%) respectively. Among the feature transformation methods, logarithmic gave the best performance for biopsy datasets whereas sine function was superior for cytology. Both logarithmic and sine functions performed the best for the Hinselmann dataset, while Z-score was best for the Schiller dataset. Various Feature Selection Techniques (FST) methods were applied to the transformed datasets to identify and prioritize important risk factors. The outcomes of this study indicate that appropriate system design and tuning, machine learning methods and classification are able to detect CC accurately and efficiently in its early stages using clinical data.

Heart disease prediction using supervised machine learning algorithms: Performance analysis and comparison.

Machine learning and data mining-based approaches to prediction and detection of heart disease would be of great clinical utility, but are highly challenging to develop. In most countries there is a lack of cardiovascular expertise and a significant rate of incorrectly diagnosed cases which could be addressed by developing accurate and efficient early-stage heart disease prediction by analytical support of clinical decision-making with digital patient records. This study aimed to identify machine learning classifiers with the highest accuracy for such diagnostic purposes. Several supervised machine-learning algorithms were applied and compared for performance and accuracy in heart disease prediction. Feature importance scores for each feature were estimated for all applied algorithms except MLP and KNN. All the features were ranked based on the importance score to find those giving high heart disease predictions. This study found that using a heart disease dataset collected from Kaggle three-classification based on k-nearest neighbor (KNN), decision tree (DT) and random forests (RF) algorithms the RF method achieved 100% accuracy along with 100% sensitivity and specificity. Thus, we found that a relatively simple supervised machine learning algorithm can be used to make heart disease predictions with very high accuracy and excellent potential utility.

An empirical study on the effect of imbalanced data on bleeding detection in endoscopic video.

In biomedical applications including classification of endoscopic videos, class imbalance is a common problem arising from the significant difference between the prior probabilities of different classes. In this paper, we investigate the performance of different classifiers for varying training data distribution in case of bleeding detection problem through three experiments. In the first experiment, we analyze the classifier performance for different class distribution with a fixed sized training dataset. The experiment provides the indication of the required class distribution for optimum classification performance. In the second and third experiments, we investigate the effect of both training data size and class distribution on the classification performance. From our experiments, we found that a larger dataset with moderate class imbalance yields better classification performance compared to a small dataset with balanced distribution. Ensemble classifiers are more robust to the variation in training dataset compared to single classifier.

Unsupervised abnormality detection using saliency and Retinex based color enhancement.

An efficient and automated abnormality detection method can significantly reduce the burden of screening of the enormous visual information resulting from capsule endoscopic procedure. As a pre-processing stage, color enhancement could be useful to improve the image quality and the detection performance. Therefore, in this paper, we have proposed a two-stage automated abnormality detection algorithm. In the first stage, an adaptive color enhancement method based on Retinex theory is applied on the endoscopic images. In the second stage, an efficient salient region detection algorithm is applied to detect the clinically significant regions. The proposed algorithm is applied on a dataset containing images with diverse pathologies. The algorithm can successfully detect a significant percentage of the abnormal regions. From our experiment, it was evident that color enhancement method improves the performance of abnormality detection. The proposed algorithm can achieve a sensitivity of 97.33% and specificity of 79%, higher than state-of-the-art performance.

An accelerometer based system to measure myocardial performance index during stress testing.

Stress testing is used to measure the performance of the heart in an elevated stress state, in order to monitor or diagnose certain heart problems. Many measurements can be used to determine the performance of the heart, with the Tei index being the measurement of interest in this work. The Tei index has been used as a reliable method to evaluate systolic and diastolic performance, as it overcomes some limitations of the classical echocardiographic indices. It is calculated based on the time intervals derived from echocardiography. This paper presents an exploratory study, which uses an accelerometer to record mechanical events occurring in each cardiac cycle, also known as the seismocardiogram (SCG). From timing measurements corresponding to various events in the heart, a metric for myocardial performance is calculated based on the Tei index. The use of SCG in addition to ECG has the potential to provide further insights about the heart during stress testing, since the SCG quantifies mechanical actions of the heart.

Automated bleeding detection in capsule endoscopy videos using statistical features and region growing.

Wireless Capsule Endoscopy (WCE) is a technology in the field of endoscopic imaging which facilitates direct visualization of the entire small intestine. Many algorithms are being developed to automatically identify clinically important frames in WCE videos. This paper presents a supervised method for automated detection of bleeding regions present in WCE frames or images. The proposed method characterizes the image regions by using statistical features derived from the first order histogram probability of the three planes of RGB color space. Despite being inconsistent and tiresome, manual selection of regions has been a popular technique for creating training data in the studies of capsule endoscopic images. We propose a semi-automatic region-annotation algorithm for creating training data efficiently. All possible combinations of different features are exhaustively analyzed to find the optimum feature set with the best performance. During operation, regions from images are obtained by applying a segmentation method. Finally, a trained neural network recognizes the patterns of the data arising from bleeding and non-bleeding regions.