Physical Sciences and Mathematics | Open Access Articles

Software Jimenae Allows Efficient Dynamic Simulations Of Boolean Networks, Centrality And System State Analysis, Martin Kaltdorf, Tim Breitenbach, Stefan Karl, Maximilian Fuchs, David Komla Kessie, Eric Psota, Martina Prelog, Edita Sarukhanyan, Regina Ebert, Franz Jakob, Gudrun Dandekar, Muhammad Naseem, Chunguang Liang, Thomas Dandekar

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The signal modelling framework JimenaE simulates dynamically Boolean networks. In contrast to SQUAD, there is systematic and not just heuristic calculation of all system states. These specific features are not present in CellNetAnalyzer and BoolNet. JimenaE is an expert extension of Jimena, with new optimized code, network conversion into different formats, rapid convergence both for system state calculation as well as for all three network centralities. It allows higher accuracy in determining network states and allows to dissect networks and identification of network control type and amount for each protein with high accuracy. Biological examples demonstrate this: (i) High plasticity …

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Deep Learning For Plant Bioinformatics: An Explainable Gradient-Based Approach For Disease Detection, Muhammad Shoaib, Babar Shah, Nasir Sayed, Farman Ali, Rafi Ullah, Irfan Hussain

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Emerging in the realm of bioinformatics, plant bioinformatics integrates computational and statistical methods to study plant genomes, transcriptomes, and proteomes. With the introduction of high-throughput sequencing technologies and other omics data, the demand for automated methods to analyze and interpret these data has increased. We propose a novel explainable gradient-based approach EG-CNN model for both omics data and hyperspectral images to predict the type of attack on plants in this study. We gathered gene expression, metabolite, and hyperspectral image data from plants afflicted with four prevalent diseases: powdery mildew, rust, leaf spot, and blight. Our proposed EG-CNN model employs a …

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An Advanced Deep Learning Models-Based Plant Disease Detection: A Review Of Recent Research, Muhammad Shoaib, Babar Shah, Shaker Ei-Sappagh, Akhtar Ali, Asad Ullah, Fayadh Alenezi, Tsanko Gechev, Tariq Hussain, Farman Ali

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Plants play a crucial role in supplying food globally. Various environmental factors lead to plant diseases which results in significant production losses. However, manual detection of plant diseases is a time-consuming and error-prone process. It can be an unreliable method of identifying and preventing the spread of plant diseases. Adopting advanced technologies such as Machine Learning (ML) and Deep Learning (DL) can help to overcome these challenges by enabling early identification of plant diseases. In this paper, the recent advancements in the use of ML and DL techniques for the identification of plant diseases are explored. The research focuses on …

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A Fog Computing Framework For Intrusion Detection Of Energy-Based Attacks On Uav-Assisted Smart Farming, Junaid Sajid, Kadhim Hayawi, Asad Waqar Malik, Zahid Anwar, Zouheir Trabelsi

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Precision agriculture and smart farming have received significant attention due to the advancements made in remote sensing technology to support agricultural efficiency. In large-scale agriculture, the role of unmanned aerial vehicles (UAVs) has increased in remote monitoring and collecting farm data at regular intervals. However, due to an open environment, UAVs can be hacked to malfunction and report false data. Due to limited battery life and flight times requiring frequent recharging, a compromised UAV wastes precious energy when performing unnecessary functions. Furthermore, it impacts other UAVs competing for charging times at the station, thus disrupting the entire data collection mechanism. …

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Towards A Novel Approach For Smart Agriculture Predictability, Rima Grati, Myriam Aloulou, Khouloud Boukadi

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No abstract provided.

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An Effective Deep Learning Approach For The Classification Of Bacteriosis In Peach Leave, Muneer Akbar, Mohib Ullah, Babar Shah, Rafi Ullah Khan, Tariq Hussain, Farman Ali, Fayadh Alenezi, Ikram Syed, Kyung Sup Kwak

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Bacteriosis is one of the most prevalent and deadly infections that affect peach crops globally. Timely detection of Bacteriosis disease is essential for lowering pesticide use and preventing crop loss. It takes time and effort to distinguish and detect Bacteriosis or a short hole in a peach leaf. In this paper, we proposed a novel LightWeight (WLNet) Convolutional Neural Network (CNN) model based on Visual Geometry Group (VGG-19) for detecting and classifying images into Bacteriosis and healthy images. Profound knowledge of the proposed model is utilized to detect Bacteriosis in peach leaf images. First, a dataset is developed which consists …

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Deep Learning-Based Segmentation And Classification Of Leaf Images For Detection Of Tomato Plant Disease, Muhammad Shoaib, Tariq Hussain, Babar Shah, Ihsan Ullah, Sayyed Mudassar Shah, Farman Ali, Sang Hyun Park

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Plants contribute significantly to the global food supply. Various Plant diseases can result in production losses, which can be avoided by maintaining vigilance. However, manually monitoring plant diseases by agriculture experts and botanists is time-consuming, challenging and error-prone. To reduce the risk of disease severity, machine vision technology (i.e., artificial intelligence) can play a significant role. In the alternative method, the severity of the disease can be diminished through computer technologies and the cooperation of humans. These methods can also eliminate the disadvantages of manual observation. In this work, we proposed a solution to detect tomato plant disease using a …

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Utilization Of The Uae Date Palm Leaf Biochar In Carbon Dioxide Capture And Sequestration Processes, Imen Ben Salem, Maisa El Gamal, Manish Sharma, Suhaib Hameedi, Fares M. Howari

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This paper evaluates the potential use of date palm leaf biochar as a climate change solution through CO2 capture and sequestration. The pyrolysis of date palm leaf was performed at different temperatures 300°, 400°, 500°, and 600 °C. The physicochemical characteristics of the synthesized biochar were examined using Scanning Electron Microscopy (SEM) with Energy Dispersive X-Ray Analysis (EDX), Fourier transforms infrared spectroscopy (FTIR), Thermogravimetric analysis (TGA), and X-ray diffraction analysis (XRD). Direct gas-solid interaction was carried out in an integrated Fluidized Bed Reactor (FBR), connected with a gas analyzer for maximum and effective mixing between the biochar and CO2. LabView …

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Post-Treatment Of Synthetic Polyphenolic 1,3,4 Oxadiazole Compound A3, Attenuated Ischemic Stroke-Induced Neuroinflammation And Neurodegeneration, Arooj Mohsin Alvi, Lina Tariq Al Kury, Muhammad Umar Ijaz, Fawad Ali Shah, Muhammad Tariq Khan, Ahmed Sadiq Sheikh, Humaira Nadeem, Arif Ullah Khan, Alam Zeb, Shupeng Li

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Ischemic stroke is categorized by either permanent or transient blood flow obstruction, impeding the distribution of oxygen and essential nutrients to the brain. In this study, we examined the neuroprotective effects of compound A3, a synthetic polyphenolic drug product, against ischemic brain injury by employing an animal model of permanent middle cerebral artery occlusion (p-MCAO). Ischemic stroke induced significant elevation in the levels of reactive oxygen species and, ultimately, provoked inflammatory cascade. Here, we demonstrated that A3 upregulated the endogenous antioxidant enzymes, such as glutathione s-transferase (GST), glutathione (GSH), and reversed the ischemic-stroke-induced nitric oxide (NO) and lipid peroxidation (LPO) …

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Benzimidazole Containing Acetamide Derivatives Attenuate Neuroinflammation And Oxidative Stress In Ethanol-Induced Neurodegeneration, Muhammad Imran, Lina Tariq Al Kury, Humaira Nadeem, Fawad Ali Shah, Muzaffar Abbas, Shagufta Naz, Arif Ullah Khan, Shupeng Li

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© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Oxidative stress-induced neuroinflammation is the prominent feature of neurodegenerative disorders, and is characterized by a gradual decline of structure and function of neurons. Many biochemical events emerge thanks to the result of this neurodegeneration, and ultimately provoke neuroinflammation, activation of microglia, and oxidative stress, leading to neuronal death. This cascade not only explains the complexity of events taking place across different stages, but also depicts the need for more effective therapeutic agents. The present study was designed to investigate the neuroprotective effects of newly synthesized benzimidazole containing acetamide derivatives, 3a (2-(4-methoxyanilino)-N-[1-(4-methylbenzene-1-sulfonyl)-1H-benzimidazol-2-yl] …

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Role Of Outer Membrane Permeability, Efflux Mechanism, And Carbapenemases In Carbapenem-Nonsusceptible Pseudomonas Aeruginosa From Dubai Hospitals: Results Of The First Cross-Sectional Survey, Carole Ayoub Moubareck, Dalal Hammoudi Halat, Charbel Akkawi, Anju Nabi, Mouza A. Alsharhan, Zulfa O. Aldeesi, Christabel C. Peters, Handan Celiloglu, Dolla Karam Sarkis

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© 2019 The Authors Objectives: Carbapenem resistance in Pseudomonas aeruginosa is growing and results from variable mechanisms. The objectives of the current study were to investigate mechanisms of carbapenem resistance and genetic relatedness of P. aeruginosa isolates recovered in Dubai hospitals. Methods: From June 2015 through June 2016, carbapenem-nonsusceptible P. aeruginosa were collected from 4 hospitals in Dubai, and subjected to antimicrobial susceptibility testing, molecular investigation of carbapenemases by PCR-sequencing, analysis of outer membrane porin OprD2 and multidrug efflux channel MexAB-OprM levels by qPCR, and fingerprinting by ERIC-PCR. Results: Out of 1969 P. aeruginosa isolated during the study period, 471 …

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Neuroprotective Effects Of Melatonin And Celecoxib Against Ethanol-Induced Neurodegeneration: A Computational And Pharmacological Approach, Lina T. Al Kury, Alam Zeb, Zain Ul Abidin, Nadeem Irshad, Imran Malik, Arooj Mohsin Alvi, Atif Ali Khan Khalil, Sareer Ahmad, Muhammad Faheem, Arif Ullah Khan, Fawad Ali Shah, Shupeng Li

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© 2019 Al Kury et al. This work is published and licensed by Dove Medical Press Limited. Purpose: Melatonin and celecoxib are antioxidants and anti-inflammatory agents that exert protective effects in different experimental models. In this study, the neuroprotective effects of melatonin and celecoxib were demonstrated against ethanol-induced neuronal injury by in silico, morphological, and biochemical approaches. Methods: For the in silico study, 3-D structures were constructed and docking analysis performed. For in vivo studies, rats were treated with ethanol, melatonin, and celecoxib. Brain samples were collected for biochemical and morphological analysis. Results: Homology modeling was performed to build 3-D …

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Deep Learning For Plant Bioinformatics: An Explainable Gradient-Based Approach For Disease Detection, Muhammad Shoaib, Babar Shah, Nasir Sayed, Farman Ali, Rafi Ullah, Irfan Hussain

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An Advanced Deep Learning Models-Based Plant Disease Detection: A Review Of Recent Research, Muhammad Shoaib, Babar Shah, Shaker Ei-Sappagh, Akhtar Ali, Asad Ullah, Fayadh Alenezi, Tsanko Gechev, Tariq Hussain, Farman Ali

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A Fog Computing Framework For Intrusion Detection Of Energy-Based Attacks On Uav-Assisted Smart Farming, Junaid Sajid, Kadhim Hayawi, Asad Waqar Malik, Zahid Anwar, Zouheir Trabelsi

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Towards A Novel Approach For Smart Agriculture Predictability, Rima Grati, Myriam Aloulou, Khouloud Boukadi

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An Effective Deep Learning Approach For The Classification Of Bacteriosis In Peach Leave, Muneer Akbar, Mohib Ullah, Babar Shah, Rafi Ullah Khan, Tariq Hussain, Farman Ali, Fayadh Alenezi, Ikram Syed, Kyung Sup Kwak

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Deep Learning-Based Segmentation And Classification Of Leaf Images For Detection Of Tomato Plant Disease, Muhammad Shoaib, Tariq Hussain, Babar Shah, Ihsan Ullah, Sayyed Mudassar Shah, Farman Ali, Sang Hyun Park

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Utilization Of The Uae Date Palm Leaf Biochar In Carbon Dioxide Capture And Sequestration Processes, Imen Ben Salem, Maisa El Gamal, Manish Sharma, Suhaib Hameedi, Fares M. Howari

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Benzimidazole Containing Acetamide Derivatives Attenuate Neuroinflammation And Oxidative Stress In Ethanol-Induced Neurodegeneration, Muhammad Imran, Lina Tariq Al Kury, Humaira Nadeem, Fawad Ali Shah, Muzaffar Abbas, Shagufta Naz, Arif Ullah Khan, Shupeng Li

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