Topic Review
Computer-Aided Drug Discovery for SMA
Spinal muscular atrophy (SMA), one of the leading inherited causes of child mortality, is a rare neuromuscular disease arising from loss-of-function mutations of the survival motor neuron 1 (SMN1) gene, which encodes the SMN protein. When lacking the SMN protein in neurons, patients suffer from muscle weakness and atrophy, and in the severe cases, respiratory failure and death. Several therapeutic approaches show promise with human testing and three medications have been approved by the U.S. Food and Drug Administration (FDA) to date. Despite the shown promise of these approved therapies, there are some crucial limitations, one of the most important being the cost. The FDA-approved drugs are high-priced and are shortlisted among the most expensive treatments in the world. The price is still far beyond affordable and may serve as a burden for patients. The blooming of the biomedical data and advancement of computational approaches have opened new possibilities for SMA therapeutic development. 
  • 153
  • 09 Oct 2021
Topic Review
Vancomycin with Muramyl Pentapeptide
Vancomycin and a native muramyl pentapeptide ended with D-alanine (MPP-D-Ala), and vancomycin and a modified muramyl pentapeptide ended with D-serine (MPP-D-Ser) form complexes in a very specific way. This complexes provide a basis for characterizing the type and stability of the connection. The type of experimentally measured and computer-simulated interactions opens the field for discussion on possible modifications to the structure of vancomycin or muramyl pentapeptide to obtain their desired characteristics.
  • 150
  • 07 Feb 2022
Topic Review
Deep Learning in Predicting Aging-Related Diseases
Aging refers to progressive physiological changes in a cell, an organ, or the whole body of an individual, over time. Aging-related diseases are highly prevalent and could impact an individual’s physical health. Recently, artificial intelligence (AI) methods have been used to predict aging-related diseases and issues, aiding clinical providers in decision-making based on patient’s medical records. Deep learning (DL), as one of the most recent generations of AI technologies, has embraced rapid progress in the early prediction and classification of aging-related issues.
  • 136
  • 29 Nov 2021
Topic Review
Disordered Proteins and Dynamic Interactions
Intrinsically disordered proteins (IDPs) or regions (IDRs), compared to the well-structural proteins, do not have stable tertiary structures under physiological conditions, and even remain dynamic in specific complexes and functional assemblies. It is now recognized that they are highly prevalent and play important roles in biology and human diseases due to the presence of many representative conformational states and potential dynamic interactions, which requires computer simulations for describing disordered protein ensembles and dynamic interactions involved in biological functions, diseases, and therapeutics.
  • 136
  • 27 Oct 2021
Topic Review
NNetEn Entropy
NNetEn is the first entropy measure that is based on artificial intelligence methods. The method modifies the structure of the LogNNet classification model so that the classification accuracy of the MNIST-10 digits dataset indicates the degree of complexity of a given time series. The calculation results of the proposed model are similar to those of existing methods, while the model structure is completely different and provides considerable advantages.
  • 134
  • 19 Apr 2022
Topic Review
Classification Algorithms for Unifloral Honeys
Unifloral honeys are highly demanded by honey consumers, especially in Europe. To ensure that a honey belongs to a very appreciated botanical class, the classical methodology is palynological analysis to identify and count pollen grains. Highly trained personnel are needed to perform this task, which complicates the characterization of honey botanical origins. Organoleptic assessment of honey by expert personnel helps to confirm such classification. In this study, the ability of different machine learning (ML) algorithms to correctly classify seven types of Spanish honeys of single botanical origins (rosemary, citrus, lavender, sunflower, eucalyptus, heather and forest honeydew) was investigated comparatively. The botanical origin of the samples was ascertained by pollen analysis complemented with organoleptic assessment. Physicochemical parameters such as electrical conductivity, pH, water content, carbohydrates and color of unifloral honeys were used to build the dataset. The following ML algorithms were tested: penalized discriminant analysis (PDA), shrinkage discriminant analysis (SDA), high-dimensional discriminant analysis (HDDA), nearest shrunken centroids (PAM), partial least squares (PLS), C5.0 tree, extremely randomized trees (ET), weighted k-nearest neighbors (KKNN), artificial neural networks (ANN), random forest (RF), support vector machine (SVM) with linear and radial kernels and extreme gradient boosting trees (XGBoost). The ML models were optimized by repeated 10-fold cross-validation primarily on the basis of log loss or accuracy metrics, and their performance was compared on a test set in order to select the best predicting model. Built models using PDA produced the best results in terms of overall accuracy on the test set. ANN, ET, RF and XGBoost models also provided good results, while SVM proved to be the worst. 
  • 127
  • 05 Jul 2021
Topic Review
Machine Learning-Based for Depressive Syndrome
The current polythetic and operational criteria for major depression inevitably contribute to the heterogeneity of depressive syndromes. The heterogeneity of depressive syndrome has been criticized using the concept of language game in Wittgensteinian philosophy. Moreover, “a symptom- or endophenotype-based approach, rather than a diagnosis-based approach, has been proposed” as the “next-generation treatment for mental disorders” by Thomas Insel. Understanding the heterogeneity renders promise for personalized medicine to treat cases of depressive syndrome, in terms of both defining symptom clusters and selecting antidepressants. Machine learning algorithms have emerged as a tool for personalized medicine by handling clinical big data that can be used as predictors for subtype classification and treatment outcome prediction. The large clinical cohort data from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D), Combining Medications to Enhance Depression Outcome (CO-MED), and the German Research Network on Depression (GRND) have recently began to be acknowledged as useful sources for machine learning-based depression research with regard to cost effectiveness and generalizability. In addition, noninvasive biological tools such as functional and resting state magnetic resonance imaging techniques are widely combined with machine learning methods to detect intrinsic endophenotypes of depression.
  • 109
  • 24 Sep 2021
Topic Review
Global Trends in Cancer Nanotechnology
This study presents a new way to investigate comprehensive trends in cancer nanotechnology research in different countries, institutions, and journals providing critical insights to prevention, diagnosis, and therapy. This paper applies the qualitative method of bibliometric analysis on cancer nanotechnology using the PubMed database during the years 2000-2021. Inspired by hybrid medical models and content-based and bibliometric features for machine learning models, our results show cancer nanotechnology studies have expanded exponentially since 2010. The highest production of articles in cancer nanotechnology is mainly from US institutions, with several countries notably the USA, China, UK, India, and Iran as concentrated focal points as centers of cancer nanotechnology research, especially in the last five years. The analysis shows the greatest overlap between nanotechnology and DNA, RNA, iron oxide or mesoporous silica, breast cancer, and cancer diagnosis and cancer treatment. Moreover, more than 50% of information related to the keywords, authors, institutions, journals, and countries are considerably investigated in the form of publications from the top 100 journals. This study has the potentials to provide past and current lines of research that can unmask comprehensive trends in cancer nanotechnology, key research topics, or pmost productive countries and authors in the field.
  • 108
  • 10 Sep 2021
Topic Review
Machine Learning for Process Monitoring
In the last few decades, hot-melt extrusion (HME) has emerged as a rapidly growing technology in the pharmaceutical industry, due to its various advantages over other fabrication routes for drug delivery systems. After the introduction of the ‘quality by design’ (QbD) approach by the Food and Drug Administration (FDA), many research studies have focused on implementing process analytical technology (PAT), including near-infrared (NIR), Raman, and UV–Vis, coupled with various machine learning algorithms, to monitor and control the HME process in real time. This review gives a comprehensive overview of the application of machine learning algorithms for HME processes, with a focus on pharmaceutical HME applications. The main current challenges in the application of machine learning algorithms for pharmaceutical processes are discussed, with potential future directions for the industry.
  • 107
  • 17 Sep 2021
Topic Review
Imaging Techniques for Cardiac Function
Cardiac imaging techniques include a variety of distinct applications with which we can visualize cardiac function non-invasively. Through different applications of physical entities such as sound waves, X-rays, magnetic fields, and nuclear energy, along with highly sophisticated computer hardware and software, it is now possible to reconstruct the dynamic aspect of cardiac function in many forms, from static images to high-definition videos and real-time three-dimensional projections.
  • 90
  • 19 Nov 2021
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