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The skin is the human body's largest organ and its cancer is considered among the most dangerous kinds of cancer. Various pathological variations in the human body can cause abnormal cell growth due to genetic disorders. These changes in human skin cells are very dangerous. Skin cancer slowly develops over further parts of the body and because of the high mortality rate of skin cancer, early diagnosis is essential. The visual checkup and the manual examination of the skin lesions are very tricky for the determination of skin cancer. Considering these concerns, numerous early recognition approaches have been proposed for skin cancer. With the fast progression in computer-aided diagnosis systems, a variety of deep learning, machine learning, and computer vision approaches were merged for the determination of medical samples and uncommon skin lesion samples. This research provides an extensive literature review of the methodologies, techniques, and approaches applied for the examination of skin lesions to date. This survey includes preprocessing, segmentation, feature extraction, selection, and classification approaches for skin cancer recognition. The results of these approaches are very impressive but still, some challenges occur in the analysis of skin lesions because of complex and rare features. Hence, the main objective is to examine the existing techniques utilized in the discovery of skin cancer by finding the obstacle that helps researchers contribute to future research. [ABSTRACT FROM AUTHOR]

The automated classification of brain tumors plays an important role in supporting radiologists in decision making. Recently, vision transformer (ViT)-based deep neural network architectures have gained attention in the computer vision research domain owing to the tremendous success of transformer models in natural language processing. Hence, in this study, the ability of an ensemble of standard ViT models for the diagnosis of brain tumors from T1-weighted (T1w) magnetic resonance imaging (MRI) is investigated. Pretrained and finetuned ViT models (B/16, B/32, L/16, and L/32) on ImageNet were adopted for the classification task. A brain tumor dataset from figshare, consisting of 3064 T1w contrast-enhanced (CE) MRI slices with meningiomas, gliomas, and pituitary tumors, was used for the cross-validation and testing of the ensemble ViT model's ability to perform a three-class classification task. The best individual model was L/32, with an overall test accuracy of 98.2% at 384 × 384 resolution. The ensemble of all four ViT models demonstrated an overall testing accuracy of 98.7% at the same resolution, outperforming individual model's ability at both resolutions and their ensembling at 224 × 224 resolution. In conclusion, an ensemble of ViT models could be deployed for the computer-aided diagnosis of brain tumors based on T1w CE MRI, leading to radiologist relief. [ABSTRACT FROM AUTHOR]

People suffering from epilepsy disorder are very much in need for precautionary measures. The only way to provide precaution to such people is to find some methods which help them to know in advance the occurrence of seizures. Using Electroencephalogram, the authors have worked on developing a forecasting method using simple LSTM with windowing technique. The window length was set to five time steps; step by step the length was increased by 1 time step. The number of correct predictions increased with the window length. When the length reached to 20 time steps, the model gave impressive results in predicting the future EEG value. Past 20 time steps are learnt by the neural network to forecast the future EEG in two stages; in univariate method, only one attribute is used as the basis to predict the future value. In multivariate method, 42 features were used to predict the future EEG. Multivariate is more powerful and provides the prediction which is almost equal to the actual target value. In case of univariate the accuracy achieved was about 70%, whereas in case of multivariate method it was 90%. [ABSTRACT FROM AUTHOR]

Hypertension is the main cause of blood pressure (BP), which further causes various cardiovascular diseases (CVDs). The recent COVID-19 pandemic raised the burden on the healthcare system and also limits the resources to these patients only. The treatment of chronic patients, especially those who suffer from CVD, has fallen behind, resulting in increased deaths from CVD around the world. Regular monitoring of BP is crucial to prevent CVDs as it can be controlled and diagnosed through constant monitoring. To find an effective and convenient procedure for the early diagnosis of CVDs, photoplethysmography (PPG) is recognized as a low-cost technology. Through PPG technology, various cardiovascular parameters, including blood pressure, heart rate, blood oxygen saturation, etc., are detected. Merging the healthcare domain with information technology (IT) is a demanding area to reduce the rehospitalization of CVD patients. In the proposed model, PPG signals from the Internet of things (IoT)-enabled wearable patient monitoring (WPM) devices are used to monitor the heart rate (HR), etc., of the patients remotely. This article investigates various machine learning techniques such as decision tree (DT), naïve Bayes (NB), and support vector machine (SVM) and the deep learning model one-dimensional convolutional neural network-long short-term memory (1D CNN-LSTM) to develop a system that assists physicians during continuous monitoring, which achieved an accuracy of 99.5% using PPG-BP data set. The proposed system provides cost-effective, efficient, and fully connected monitoring systems for cardiac patients. [ABSTRACT FROM AUTHOR]

Machine learning (ML) often provides applicable high-performance models to facilitate decision-makers in various fields. However, this high performance is achieved at the expense of the interpretability of these models, which has been criticized by practitioners and has become a significant hindrance in their application. Therefore, in highly sensitive decisions, black boxes of ML models are not recommended. We proposed a novel methodology that uses complex supervised ML models and transforms them into simple, interpretable, transparent statistical models. This methodology is like stacking ensemble ML in which the best ML models are used as a base learner to compute relative feature weights. The index of these weights is further used as a single covariate in the simple logistic regression model to estimate the likelihood of an event. We tested this methodology on the primary dataset related to cardiovascular diseases (CVDs), the leading cause of mortalities in recent times. Therefore, early risk assessment is an important dimension that can potentially reduce the burden of CVDs and their related mortality through accurate but interpretable risk prediction models. We developed an artificial neural network and support vector machines based on ML models and transformed them into a simple statistical model and heart risk scores. These simplified models were found transparent, reliable, valid, interpretable, and approximate in predictions. The findings of this study suggest that complex supervised ML models can be efficiently transformed into simple statistical models that can also be validated. [ABSTRACT FROM AUTHOR]

An introduction is presented in which the editor discusses several articles published within issue on DNA-centric modeling and practice for next-generation computing and communication systems.

Individual who have lost their lower limb because of amputation can use the prosthesis to restore daily living activities. The amputee intent recognition during locomotion modes can be used as source to control lower limb prosthesis. Due to continuous data recording from multiple sensors, the timely recognition of activities of daily living have become a challenging issue for traditional technology and conventional machine learning algorithms. This work hypothesize that parallel discriminant features can be learned from large amount of data generated by aggregating the neuromechanical signals from multiple subjects with parallel and distributed computing platform. Consequently, this paper apply three classifiers including support vector machine, decision tree and random forest on large data sets. The model performance is extensively evaluated in terms of different performance measurement parameters such as accuracy, efficiency, scalability and speedup in sequential and distributed environment. The experimental results show that the parallel approach achieved 3.9x computation speedup as compared to the sequential approach without affecting accuracy level. The parallel support vector machine algorithm demonstrated high speedup and scalability in comparison with random forest and decision tree algorithms. The outcome of this study could promote parallel based model for the unobtrusive recognition of lower limb locomotion modes and could promote the future design for the intelligent control of prostheses and exoskeleton. [ABSTRACT FROM AUTHOR]

It is increasingly clear that an extraordinarily diverse range of clinically important conditions—including infections, vaccinations, autoimmune diseases, transplants, transfusion reactions, aging, and cancers—leave telltale signatures in the millions of V(D)J-rearranged antibody and T cell receptor [TR per the Human Genome Organization (HUGO) nomenclature but more commonly known as TCR] genes collectively expressed by a person's B cells (antibodies) and T cells. We refer to these as the immunome. Because of its diversity and complexity, the immunome provides singular opportunities for advancing personalized medicine by serving as the substrate for a highly multiplexed, near-universal blood test. Here we discuss some of these opportunities, the current state of immunome-based diagnostics, and highlight some of the challenges involved. We conclude with a call to clinicians, researchers, and others to join efforts with the Adaptive Immune Receptor Repertoire Community (AIRR-C) to realize the diagnostic potential of the immunome. [ABSTRACT FROM AUTHOR]

Paralytic ileus (PI) is the pseudo-obstruction of the intestine secondary to intestinal muscle paralysis. Causes of PI include electrolyte imbalances, gastroenteritis (inflammation or infection of the stomach or intestines), overuse of medications, abdominal surgery, etc. Predicting mortality in PI patients hospitalized to ICU is crucial for assessing the severity of illness and adjudicating the value of treatment strategy and resource planning. We have developed a Statistically Robust Machine Learning based Mortality Prediction framework namely SRML-MortalityPredictor that could potentially help intensivists, surgeons, and other medical professionals to carefully plan treatment strategies for critically ill PI patients. We used MIMIC III v1.4, a publicly available ICU database to extract patients data (with age > 18 years old) admitted to the ICU with paralytic ileus (PI) as their primary illness. At phase 1, the SRML-MortalityPredictor framework uses univariate statistical analysis to filter out those risk factors which are not associated with the label of the data. Subsequently, it uses the risk survival statistical methods such as cox-regression and Kaplan–Meier survival analyses. The cox-regression analysis provides the hazard ratio about the potential PI risk factors that later used in conjunction with the Kaplan–Meier analysis to generate a rank order list (highest to lowest risk factors). At phase 2, we used several machine learning classification approaches such as linear discriminant analysis (LDA), Gaussian naive bayes (GNB), decision tree (DT) model, k-nearest neighbor (KNN), and support vector machine (SVM) to find the one with highest predictive power using the rank order features extracted at phase 1. We have evaluated the SRML-MortalityPredictor framework and recorded the accuracy, sensitivity, specificity, receiver operating characteristic (ROC) curves, and area under the curve (AUC) scores for each model. The SRML-MortalityPredictor framework with support vector machine (using RBF kernel) showed better performance and yielded an accuracy score: 81.30% and AUC score: 81.38% while predicting mortality in PI patients. We demonstrated a feasible framework for the mortality risk prediction in PI patients admitted to the ICU. The proposed framework could potentially be helpful for intensivists in clinical decision making. Further research is necessary to incorporate more risk factors associated with PI patients to ensure the adaptability of SRML-MortalityPredictor at the bedside. [ABSTRACT FROM AUTHOR]

Background: Modifiable risk factors are associated with cardiovascular mortality (CVM) which is a leading form of global mortality. However, diverse nature of urbanization and its objective measurement can modify their relationship. This study aims to investigate the moderating role of urbanization in the relationship of combined exposure (CE) of modifiable risk factors and CVM. Design and Methods: This is the first comprehensive study which considers different forms of urbanization to gauge its manifold impact. Therefore, in addition to existing original quantitative form and traditional two categories of urbanization, a new form consisted of four levels of urbanization was duly introduced. This study used data of 129 countries mainly retrieved from a WHO report, Non-Communicable Diseases Country Profile 2014. Factor scores obtained through confirmatory factor analysis were used to compute the CE. Age-income adjusted regression model for CVM was tested as a baseline with three bootstrap regression models developed for the three forms of urbanization. Results: Results revealed that the CE and CVM baseline relationship was significantly moderated through the original quantitative form of urbanization. Contrarily, the two traditional categories of urbanization could not capture the moderating impact. However, the four levels of urbanization were objectively estimated the urbanization impact and subsequently indicated that the CE was more alarming in causing the CVM in levels 2 and 3 urbanized countries, mainly from low-middle-income countries. Conclusion: This study concluded that the urbanization is a strong moderator and it could be gauged effectively through four levels whereas sufficiency of two traditional categories of urbanization is questionable. [ABSTRACT FROM AUTHOR]

Brain tumor detection depicts a tough job because of its shape, size and appearance variations. In this manuscript, a deep learning model is deployed to predict input slices as a tumor (unhealthy)/non-tumor (healthy). This manuscript employs a high pass filter image to prominent the inhomogeneities field effect of the MR slices and fused with the input slices. Moreover, the median filter is applied to the fused slices. The resultant slices quality is improved with smoothen and highlighted edges of the input slices. After that, based on these slices' intensity, a 4-connected seed growing algorithm is applied, where optimal threshold clusters the similar pixels from the input slices. The segmented slices are then supplied to the fine-tuned two layers proposed stacked sparse autoencoder (SSAE) model. The hyperparameters of the model are selected after extensive experiments. At the first layer, 200 hidden units and at the second layer 400 hidden units are utilized. The testing is performed on the softmax layer for the prediction of the images having tumors and no tumors. The suggested model is trained and checked on BRATS datasets i.e., 2012(challenge and synthetic), 2013, and 2013 Leaderboard, 2014, and 2015 datasets. The presented model is evaluated with a number of performance metrics which demonstrates the improved performance. [ABSTRACT FROM AUTHOR]

Increased interest in the immune system's involvement in pathophysiological phenomena coupled with decreased DNA sequencing costs have led to an explosion of antibody and T cell receptor sequencing data collectively termed "adaptive immune receptor repertoire sequencing" (AIRR-seq or Rep-Seq). The AIRR Community has been actively working to standardize protocols, metadata, formats, APIs, and other guidelines to promote open and reproducible studies of the immune repertoire. In this paper, we describe the work of the AIRR Community's Data Representation Working Group to develop standardized data representations for storing and sharing annotated antibody and T cell receptor data. Our file format emphasizes ease-of-use, accessibility, scalability to large data sets, and a commitment to open and transparent science. It is composed of a tab-delimited format with a specific schema. Several popular repertoire analysis tools and data repositories already utilize this AIRR-seq data format. We hope that others will follow suit in the interest of promoting interoperable standards. [ABSTRACT FROM AUTHOR]

The adaptation of high-throughput sequencing to the B cell receptor and T cell receptor has made it possible to characterize the adaptive immune receptor repertoire (AIRR) at unprecedented depth. These AIRR sequencing (AIRR-seq) studies offer tremendous potential to increase the understanding of adaptive immune responses in vaccinology, infectious disease, autoimmunity, and cancer. The increasingly wide application of AIRR-seq is leading to a critical mass of studies being deposited in the public domain, offering the possibility of novel scientific insights through secondary analyses and meta-analyses. However, effective sharing of these large-scale data remains a challenge. The AIRR community has proposed minimal information about adaptive immune receptor repertoire (MiAIRR), a standard for reporting AIRR-seq studies. The MiAIRR standard has been operationalized using the National Center for Biotechnology Information (NCBI) repositories. Submissions of AIRR-seq data to the NCBI repositories typically use a combination of web-based and flat-file templates and include only a minimal amount of terminology validation. As a result, AIRR-seq studies at the NCBI are often described using inconsistent terminologies, limiting scientists' ability to access, find, interoperate, and reuse the data sets. In order to improve metadata quality and ease submission of AIRR-seq studies to the NCBI, we have leveraged the software framework developed by the Center for Expanded Data Annotation and Retrieval (CEDAR), which develops technologies involving the use of data standards and ontologies to improve metadata quality. The resulting CEDAR-AIRR (CAIRR) pipeline enables data submitters to: (i) create web-based templates whose entries are controlled by ontology terms, (ii) generate and validate metadata, and (iii) submit the ontology-linked metadata and sequence files (FASTQ) to the NCBI BioProject, BioSample, and Sequence Read Archive databases. Overall, CAIRR provides a web-based metadata submission interface that supports compliance with the MiAIRR standard. This pipeline is available at http://cairr.miairr.org, and will facilitate the NCBI submission process and improve the metadata quality of AIRR-seq studies. [ABSTRACT FROM AUTHOR]

Manual identification of brain tumors is an error-prone and tedious process for radiologists; therefore, it is crucial to adopt an automated system. The binary classification process, such as malignant or benign is relatively trivial; whereas, the multimodal brain tumors classification (T1, T2, T1CE, and Flair) is a challenging task for radiologists. Here, we present an automated multimodal classification method using deep learning for brain tumor type classification. The proposed method consists of five core steps. In the first step, the linear contrast stretching is employed using edge-based histogram equalization and discrete cosine transform (DCT). In the second step, deep learning feature extraction is performed. By utilizing transfer learning, two pre-trained convolutional neural network (CNN) models, namely VGG16 and VGG19, were used for feature extraction. In the third step, a correntropy-based joint learning approach was implemented along with the extreme learning machine (ELM) for the selection of best features. In the fourth step, the partial least square (PLS)-based robust covariant features were fused in one matrix. The combined matrix was fed to ELM for final classification. The proposed method was validated on the BraTS datasets and an accuracy of 97.8%, 96.9%, 92.5% for BraTs2015, BraTs2017, and BraTs2018, respectively, was achieved. [ABSTRACT FROM AUTHOR]

The Adaptive Immune Receptor Repertoire (AIRR) Community is a research-driven group that is establishing a clear set of community-accepted data and metadata standards; standards-based reference implementation tools; and policies and practices for infrastructure to support the deposit, curation, storage, and use of high-throughput sequencing data from B-cell and T-cell receptor repertoires (AIRR-seq data). The AIRR Data Commons is a distributed system of data repositories that utilizes a common data model, a common query language, and common interoperability formats for storage, query, and downloading of AIRR-seq data. Here is described the principal technical standards for the AIRR Data Commons consisting of the AIRR Data Model for repertoires and rearrangements, the AIRR Data Commons (ADC) API for programmatic query of data repositories, a reference implementation for ADC API services, and tools for querying and validating data repositories that support the ADC API. AIRR-seq data repositories can become part of the AIRR Data Commons by implementing the data model and API. The AIRR Data Commons allows AIRR-seq data to be reused for novel analyses and empowers researchers to discover new biological insights about the adaptive immune system., (Copyright © 2020 Christley, Aguiar, Blanck, Breden, Bukhari, Busse, Jaglale, Harikrishnan, Laserson, Peters, Rocha, Schramm, Taylor, Vander Heiden, Zimonja, Watson, Corrie and Cowell.)

Systems biology involves the integration of multiple data types (across different data sources) to offer a more complete picture of the biological system being studied. While many existing biological databases are implemented using the traditional SQL (Structured Query Language) database technology, NoSQL database technologies have been explored as a more relationship-based, flexible and scalable method of data integration. In this paper, we describe how to use the Neo4J graph database to integrate a variety of types of data sets in the context of systems vaccinology. Specifically, we have converted into a common graph model diverse types of vaccine response measurement data from the NIH/NIAID ImmPort data repository, pathway data from Reactome, influenza virus strains from WHO, and taxonomic data from NCBI Taxon. While Neo4J provides a graph-based query language (Cypher) for data retrieval, we develop a web-based dashboard for users to easily browse and visualize data without the need to learn Cypher. In addition, we have prototyped a natural language query interface for users to interact with our system. In conclusion, we demonstrate the feasibility of using a graph-based database for storing and querying immunological data with complex biological relationships. Querying a graph database through such relationships has the potential to reveal novel relationships among heterogeneous biological data.