Predicting primary sequence-based protein-protein interactions using a Mercer series representation of nonlinear support vector machine

© 2022 The Authors. Published by IEEE. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://ieeexplore.ieee.org/document/9956991The prediction of protein-protein interactions (PPIs) is essential to understand the cellular processes from a medical perspective. Among the various machine learning techniques, kernel-based Support Vector Machine (SVM) has been commonly employed to discriminate between interacting and non-interacting protein pairs. The main drawback of employing the kernel-based SVM to datasets with many features, such as the primary sequence-based protein-protein dataset, is the significant increase in computational time of training stage. This increase in computational time is mainly due to the presence of the kernel in solving the quadratic optimisation problem (QOP) involved in nonlinear SVM. In order to fix this issue, we propose a novel and efficient computational algorithm by approximating the kernel-based SVM using a low-rank truncated Mercer series as well as desired. As a result, the QOP for the approximated kernel-based SVM will be very tractable in the sense that there is a significant reduction in computational time of training and validating stages. We illustrate the novelty of the proposed method by predicting the PPIs of “S. Cerevisiae” where the protein features extracted using the multiscale local descriptor (MLD), and then we compare the predictive performance of the proposed low-rank approximation with the existing methods. Finally, the new method results in significant reduction in computational time for predicting PPIs with almost as accuracy as kernel-based SVM.The authors extend their appreciation to the Deputyship for Research & Innovation, Ministry of Education in Saudi Arabia for funding this research work through the project number IF-2020-NBU-412.Published versio

Induced third-degree burn in rat: healing by Melilotus officinalis extract as medicinal plant

Introduction: burn wounds are common happenings which cause many people have irreversible defects and to be death around the world every year.  In this study, we evaluated the effects of Melilotus officinalis and Alpha ointment in the healing of burn wounds and compare their findings with silver sulfadiazine (SSD).Methods: Seventy-five male Sprague-Dawley rats were randomly divided into five groups, and similar burn ulcers were produced on the back of rats. The first group of rats received no treatment, base gel was used topically to group II, in groups III-V, Alpha, SSD and Melilotus officinalis preparations were applied, respectively. Wound healing, contraction and histopathological examination were evaluated at the end of 7, 14, and 21 days.Results: Alpha ointment was equally effective as Melilotus officinalis gel, while its efficacy was better compared to SSD for all parameters of wound healing on days 7, 14 and 21. Alpha and Melilotus officinalis preparations as less expensive medications which significantly improve the quality of wound healing and scar formation and also are more appropriate treatment choices than SSD.Conclusion: Alpha and Melilotus officinalis are recommended as alternative to SSD, especially in patients with low economical backgrounds or in those who show adverse reactions to SSD.</p

Characterization of greater middle eastern genetic variation for enhanced disease gene discovery

The Greater Middle East (GME) has been a central hub of human migration and population admixture. The tradition of consanguinity, variably practiced in the Persian Gulf region, North Africa, and Central Asia1-3, has resulted in an elevated burden of recessive disease4. Here we generated a whole-exome GME variome from 1,111 unrelated subjects. We detected substantial diversity and admixture in continental and subregional populations, corresponding to several ancient founder populations with little evidence of bottlenecks. Measured consanguinity rates were an order of magnitude above those in other sampled populations, and the GME population exhibited an increased burden of runs of homozygosity (ROHs) but showed no evidence for reduced burden of deleterious variation due to classically theorized ‘genetic purging’. Applying this database to unsolved recessive conditions in the GME population reduced the number of potential disease-causing variants by four- to sevenfold. These results show variegated genetic architecture in GME populations and support future human genetic discoveries in Mendelian and population genetics

Silent Paroxysmal Atrial Fibrillation Detection by Neural Networks Based on ECG Records

Atrial Fibrillation (AF) is one of the most common arrhythmias in the world and it is a life-threatening disorder which increases the risk of stroke with time. PAF is a special type of AF which is usually seen as temporarily AF that could last less than a week and terminated by itself. The disorder increases with age and is associated with cardiac morbidity. In this study, silent AF (SAF) detection is done by using different neural network schemes. At first step, features selection is done by utilizing Genetic algorithm. This step results in obtaining 8 HRV features. In the next step, obtained feature space is given to neural networks. The proposed approach provides good classification performance in detecting PAF events

Puerarin as potential treatment in diabetic retinopathy

Diabetic retinopathy (DR) is one of the most prevalent microvascular complications of diabetes, and the most leading cause of visual loss around the world. The lack of effective and approved treatment in DR is a major challenge for diabetic patients. Nowadays, natural compounds have got attention of the researchers for management of DR. Many evidences suggest that puerarin as a natural polyphenol exerts advantageous effects against DR. In the present review, we summarized the protective effects of puerarin against DR, and discussed the underlying mechanisms of these effects. Puerarin attenuates retinal neovascularization and neurodegeneration in diabetes mellitus, and the underlying mechanisms are related to antioxidant, anti-inflammatory, and antiapoptotic properties of the compound. In conclusion, puerarin might be a potential adjuvant agent for the prevention and treatment of DR. However, comprehensive studies are necessary to show its effectiveness and safety, particularly in human

Synthesis and structural evolution of vanadium carbide in nano scale during mechanical alloying

In this study, nano crystalline vanadium carbide was synthesized by mechanical alloying method. V2O5, C and Mg powders were placed in a planetary ball mill and sampled after different milling times. XRD and FESEM were used for characterization of synthesized powder. Studies showed that crystalline V8C7 has been synthesized by 24 h milling and subsequently heat treatment at 800 °C. It was concluded that the V8C7 crystallites were nano sized and the lattice parameter deviated slightly from the standard size. Furthermore, milling led to increase in strain and decrease of vanadium carbide particle size

An ethnobotanical survey on hormozgan province, Iran

Objective: The present study is based on an ethnobotanical research project conducted in Hormozgan province that is located in south of Iran, bordering waters of the Persian Gulf and Oman Sea. This survey was carried out in order to recover the ethnobotanical and ethnomedicinal knowledge of the residents of this province. They are using medicinal and functional plants for treating or preventing several diseases. Materials and Methods: Ethnobotanical data sheets were run with the native inhabitants and people of the province by arranging frequent field trips to different parts of the province and direct interviews with them especially those who were more familiar with the plants and their usage.Results: A total of 150 plant species belonging to 53 families were recorded for their ethnobotanical and ethnomedicinal uses among the people of province. The records were developed by scientific names, family names, local names, medicinal parts used, different ways of their application, and traditional uses of the plants. There was high compliance in the use of plants in painful disorders, gastrointestinal, and dermatological diseases.Conclusion: This study revealed that the people of Hormozgan province have a rich knowledge of natural resources. The use and consumption of medicinal plants are still important parts of their life. Rational use of native medicinal plants may benefit and improve their living standards and quality of life. The results of this study can be used as a basis for selecting herbs for further pharmacological, phytochemical, and pharmacognostical studies