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Naeem A, Noureen N, Al-Naemi SK, Al-Emadi JA, Khan MJ. Computational design of anti-cancer peptides tailored to target specific tumor markers. BMC Chem 2024; 18:39. [PMID: 38388460 PMCID: PMC10882887 DOI: 10.1186/s13065-024-01143-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Anti-cancer peptides (ACPs) are short peptides known for their ability to inhibit tumor cell proliferation, migration, and the formation of tumor blood vessels. In this study, we designed ACPs to target receptors often overexpressed in cancer using a systematic in silico approach. Three target receptors (CXCR1, DcR3, and OPG) were selected for their significant roles in cancer pathogenesis and tumor cell proliferation. Our peptide design strategy involved identifying interacting residues (IR) of these receptors, with their natural ligands serving as a reference for designing peptides specific to each receptor. The natural ligands of these receptors, including IL8 for CXCR1, TL1A for DcR3, and RANKL for OPG, were identified from the literature. Using the identified interacting residues (IR), we generated a peptide library through simple permutation and predicted the structure of each peptide. All peptides were analyzed using the web-based prediction server for Anticancer peptides, AntiCP. Docking simulations were then conducted to analyze the binding efficiencies of peptides with their respective target receptors, using VEGA ZZ and Chimera for interaction analysis. Our analysis identified HPKFIKELR as the interacting residues (IR) of CXCR-IL8. For DcR3, we utilized three domains from TL1A (TDSYPEP, TKEDKTF, LGLAFTK) as templates, along with two regions (SIKIPSS and PDQDATYP) from RANKL, to generate a library of peptide analogs. Subsequently, peptides for each receptor were shortlisted based on their predicted anticancer properties as determined by AntiCP and were subjected to docking analysis. After docking, peptides that exhibited the least binding energy were further analyzed for their detailed interaction with their respective receptors. Among these, peptides C9 (HPKFELY) and C7 (HPKFEWL) for CXCR1, peptides D6 (ADSYPQP) and D18 (AFSYPFP) for DcR3, and peptides P19 (PDTYPQDP) and p16 (PDQDATYP) for OPG, demonstrated the highest affinity and stronger interactions compared to the other peptides. Although in silico predictions indicated a favorable binding affinity of the designed peptides with target receptors, further experimental validation is essential to confirm their binding affinity, stability and pharmacokinetic characteristics.
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Affiliation(s)
- Aisha Naeem
- QU Health, Qatar University, P.O. Box 2713, Doha, Qatar.
| | - Nighat Noureen
- Cancer Center and Department of Pediatrics, School of Medicine, Texas Tech University Health Sciences Center School of Medicine, Lubbock, TX, 79430, USA.
| | | | | | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
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Zafar A, Khan MJ, Abu J, Naeem A. Revolutionizing cancer care strategies: immunotherapy, gene therapy, and molecular targeted therapy. Mol Biol Rep 2024; 51:219. [PMID: 38281269 PMCID: PMC10822809 DOI: 10.1007/s11033-023-09096-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/04/2023] [Indexed: 01/30/2024]
Abstract
Despite the availability of technological advances in traditional anti-cancer therapies, there is a need for more precise and targeted cancer treatment strategies. The wide-ranging shortfalls of conventional anticancer therapies such as systematic toxicity, compromised life quality, and limited to severe side effects are major areas of concern of conventional cancer treatment approaches. Owing to the expansion of knowledge and technological advancements in the field of cancer biology, more innovative and safe anti-cancerous approaches such as immune therapy, gene therapy and targeted therapy are rapidly evolving with the aim to address the limitations of conventional therapies. The concept of immunotherapy began with the capability of coley toxins to stimulate toll-like receptors of immune cells to provoke an immune response against cancers. With an in-depth understating of the molecular mechanisms of carcinogenesis and their relationship to disease prognosis, molecular targeted therapy approaches, that inhibit or stimulate specific cancer-promoting or cancer-inhibitory molecules respectively, have offered promising outcomes. In this review, we evaluate the achievement and challenges of these technically advanced therapies with the aim of presenting the overall progress and perspective of each approach.
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Affiliation(s)
- Aasma Zafar
- Department of Biosciences, COMSATS University, Islamabad, 45550, Pakistan
| | | | - Junaid Abu
- Hazm Mebaireek General Hospital, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Aisha Naeem
- Qatar University Health, Qatar University, P.O. Box 2713, Doha, Qatar.
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Ali H, Gilani SO, Waris A, Shah UH, Khattak MAK, Khan MJ, Afzal N. Memorability-based multimedia analytics for robotic interestingness prediction system using trimmed Q-learning algorithm. Sci Rep 2023; 13:19799. [PMID: 37957144 PMCID: PMC10643645 DOI: 10.1038/s41598-023-44553-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/10/2023] [Indexed: 11/15/2023] Open
Abstract
Mobile robots are increasingly employed in today's environment. Perceiving the environment to perform a task plays a major role in the robots. The service robots are wisely employed in the fully (or) partially known user's environment. The exploration and exploitation of the unknown environment is a tedious task. This paper introduces a novel Trimmed Q-learning algorithm to predict interesting scenes via efficient memorability-oriented robotic behavioral scene activity training. The training process involves three stages: online learning and short-term and long-term learning modules. It is helpful for autonomous exploration and making wiser decisions about the environment. A simplified three-stage learning framework is introduced to train and predict interesting scenes using memorability. A proficient visual memory schema (VMS) is designed to tune the learning parameters. A role-based profile arrangement is made to explore the unknown environment for a long-term learning process. The online and short-term learning frameworks are designed using a novel Trimmed Q-learning algorithm. The underestimated bias in robotic actions must be minimized by introducing a refined set of practical candidate actions. Finally, the recalling ability of each learning module is estimated to predict the interesting scenes. Experiments conducted on public datasets, SubT, and SUN databases demonstrate the proposed technique's efficacy. The proposed framework has yielded better memorability scores in short-term and online learning at 72.84% and in long-term learning at 68.63%.
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Affiliation(s)
- Hasnain Ali
- School of Mechanical & Manufacturing Engineering, National University of Sciences and Technology, Robotics & AI, Islamabad, 44000, Pakistan.
| | - Syed Omer Gilani
- Department of Electrical, Computer, and Biomedical Engineering, Abu Dhabi University, Abu Dhabi, UAE
| | - Asim Waris
- School of Mechanical & Manufacturing Engineering, National University of Sciences and Technology, Biomedical Engineering & Sciences, Islamabad, 44000, Pakistan
| | - Umer Hameed Shah
- Department of Mechanical Engineering and Artificial Intelligence Research Center, College of Engineering and Information Technology, Ajman University, Ajman, UAE.
| | | | - Muhammad Jawad Khan
- School of Mechanical & Manufacturing Engineering, National University of Sciences and Technology, Robotics & AI, Islamabad, 44000, Pakistan
| | - Namra Afzal
- Department of Biomedical Engineering, University of Engineering and Technology, Lahore, 54000, Pakistan
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Dandare A, Khan MJ, Naeem A, Liaquat A. Clinical relevance of circulating non-coding RNAs in metabolic diseases: Emphasis on obesity, diabetes, cardiovascular diseases and metabolic syndrome. Genes Dis 2023; 10:2393-2413. [PMID: 37554181 PMCID: PMC10404886 DOI: 10.1016/j.gendis.2022.05.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/11/2022] [Indexed: 11/22/2022] Open
Abstract
Non-coding RNAs (ncRNAs) participate in the regulation of several cellular processes including transcription, RNA processing and genome rearrangement. The aberrant expression of ncRNAs is associated with several pathological conditions. In this review, we focused on recent information to elucidate the role of various regulatory ncRNAs i.e., micro RNAs (miRNAs), circular RNAs (circRNAs) and long-chain non-coding RNAs (lncRNAs), in metabolic diseases, e.g., obesity, diabetes mellitus (DM), cardiovascular diseases (CVD) and metabolic syndrome (MetS). The mechanisms by which ncRNAs participated in disease pathophysiology were also highlighted. miRNAs regulate the expression of genes at transcriptional and translational levels. circRNAs modulate the regulation of gene expression via miRNA sponging activity, interacting with RNA binding protein and polymerase II transcription regulation. lncRNAs regulate the expression of genes by acting as a protein decoy, miRNA sponging, miRNA host gene, binding to miRNA response elements (MRE) and the recruitment of transcriptional element or chromatin modifiers. We examined the role of ncRNAs in the disease pathogenesis and their potential role as molecular markers for diagnosis, prognosis and therapeutic targets. We showed the involvement of ncRNAs in the onset of obesity and its progression to MetS and CVD. miRNA-192, miRNA-122, and miRNA-221 were dysregulated in all these metabolic diseases. Other ncRNAs, implicated in at least three diseases include miRNA-15a, miRNA-26, miRNA-27a, miRNA-320, and miRNA-375. Dysregulation of ncRNAs increased the risk of development of DM and MetS and its progression to CVD in obese individuals. Hence, these molecules are potential targets to arrest or delay the progression of metabolic diseases.
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Affiliation(s)
- Abdullahi Dandare
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Department of Biochemistry, Usmanu Danfodiyo University, Sokoto 840104, Nigeria
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
| | - Aisha Naeem
- Ministry of Public Health, POB42, Doha, Qatar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Afrose Liaquat
- Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad 45550, Pakistan
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Anwar H, Khan SU, Ghaffar MM, Fayyaz M, Khan MJ, Weis C, Wehn N, Shafait F. The NWRD Dataset: An Open-Source Annotated Segmentation Dataset of Diseased Wheat Crop. Sensors (Basel) 2023; 23:6942. [PMID: 37571726 PMCID: PMC10422341 DOI: 10.3390/s23156942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023]
Abstract
Wheat stripe rust disease (WRD) is extremely detrimental to wheat crop health, and it severely affects the crop yield, increasing the risk of food insecurity. Manual inspection by trained personnel is carried out to inspect the disease spread and extent of damage to wheat fields. However, this is quite inefficient, time-consuming, and laborious, owing to the large area of wheat plantations. Artificial intelligence (AI) and deep learning (DL) offer efficient and accurate solutions to such real-world problems. By analyzing large amounts of data, AI algorithms can identify patterns that are difficult for humans to detect, enabling early disease detection and prevention. However, deep learning models are data-driven, and scarcity of data related to specific crop diseases is one major hindrance in developing models. To overcome this limitation, in this work, we introduce an annotated real-world semantic segmentation dataset named the NUST Wheat Rust Disease (NWRD) dataset. Multileaf images from wheat fields under various illumination conditions with complex backgrounds were collected, preprocessed, and manually annotated to construct a segmentation dataset specific to wheat stripe rust disease. Classification of WRD into different types and categories is a task that has been solved in the literature; however, semantic segmentation of wheat crops to identify the specific areas of plants and leaves affected by the disease remains a challenge. For this reason, in this work, we target semantic segmentation of WRD to estimate the extent of disease spread in wheat fields. Sections of fields where the disease is prevalent need to be segmented to ensure that the sick plants are quarantined and remedial actions are taken. This will consequently limit the use of harmful fungicides only on the targeted disease area instead of the majority of wheat fields, promoting environmentally friendly and sustainable farming solutions. Owing to the complexity of the proposed NWRD segmentation dataset, in our experiments, promising results were obtained using the UNet semantic segmentation model and the proposed adaptive patching with feedback (APF) technique, which produced a precision of 0.506, recall of 0.624, and F1 score of 0.557 for the rust class.
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Affiliation(s)
- Hirra Anwar
- School of Mechanical and Manufacturing Engineering, National University of Sciences & Technology, Islamabad 44000, Pakistan;
| | - Saad Ullah Khan
- School of Electrical Engineering and Computer Science, National University of Sciences & Technology, Islamabad 44000, Pakistan;
| | - Muhammad Mohsin Ghaffar
- Microelectronic Systems Design Research Group, University of Kaiserslautern-Landau, 67663 Kaiserslautern, Germany; (M.M.G.); (C.W.); (N.W.)
| | - Muhammad Fayyaz
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad 44000, Pakistan;
| | - Muhammad Jawad Khan
- School of Mechanical and Manufacturing Engineering, National University of Sciences & Technology, Islamabad 44000, Pakistan;
- Deep Learning Laboratory, National Center of Artificial Intelligence, Islamabad 44000, Pakistan
| | - Christian Weis
- Microelectronic Systems Design Research Group, University of Kaiserslautern-Landau, 67663 Kaiserslautern, Germany; (M.M.G.); (C.W.); (N.W.)
| | - Norbert Wehn
- Microelectronic Systems Design Research Group, University of Kaiserslautern-Landau, 67663 Kaiserslautern, Germany; (M.M.G.); (C.W.); (N.W.)
| | - Faisal Shafait
- School of Electrical Engineering and Computer Science, National University of Sciences & Technology, Islamabad 44000, Pakistan;
- Deep Learning Laboratory, National Center of Artificial Intelligence, Islamabad 44000, Pakistan
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Ejaz M, Usman SM, Amir S, Khan MJ. Holistic expression of miR-17-92 cluster in obesity, kidney diseases, cardiovascular diseases, and diabetes. Mol Biol Rep 2023; 50:6913-6925. [PMID: 37329480 DOI: 10.1007/s11033-023-08549-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/24/2023] [Indexed: 06/19/2023]
Abstract
miR-17-92 cluster encodes six micro RNAs (miRNAs) and plays a crucial role in the regulation of various cellular processes. Aberrant expression of this cluster may result in the onset of several diseases. Initially, the role of miR-17-92 cluster in tumorigenesis was discovered but recent research has also uncovered its role in other diseases. Members of the cluster may serve as potential biomarkers in the prognosis, diagnosis, and treatment of several diseases and their complications. In this article, we have reviewed the recent research carried out on the expression pattern of miR-17-92 cluster in non-communicable diseases i.e., obesity, cardiovascular diseases (CVD), kidney diseases (KD) and diabetes mellitus (DM). We examined miR-17-92 role in pathological processes and their potential importance as biomarkers. Each member of the cluster miR-17-92 was upregulated in obesity. miR-18a, miR-19b-3p, miR20a, and miR92a were significantly upregulated in CVD. An equal fraction of the cluster was dysregulated (upregulated and downregulated) in diabetes; however, miR-17-92 was downregulated in most studies on CKD.
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Affiliation(s)
- Maheen Ejaz
- Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shahzad Islamabad, Islamabad, 45550, Pakistan
| | - Syed Mohammad Usman
- Department of Biochemistry, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Saira Amir
- Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shahzad Islamabad, Islamabad, 45550, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shahzad Islamabad, Islamabad, 45550, Pakistan.
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Zafar A, Khan MJ, Naeem A. MDM2- an indispensable player in tumorigenesis. Mol Biol Rep 2023; 50:6871-6883. [PMID: 37314603 PMCID: PMC10374471 DOI: 10.1007/s11033-023-08512-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Murine double minute 2 (MDM2) is a well-recognized molecule for its oncogenic potential. Since its identification, various cancer-promoting roles of MDM2 such as growth stimulation, sustained angiogenesis, metabolic reprogramming, apoptosis evasion, metastasis, and immunosuppression have been established. Alterations in the expression levels of MDM2 occur in multiple types of cancers resulting in uncontrolled proliferation. The cellular processes are modulated by MDM2 through transcription, post-translational modifications, protein degradation, binding to cofactors, and subcellular localization. In this review, we discuss the precise role of deregulated MDM2 levels in modulating cellular functions to promote cancer growth. Moreover, we also briefly discuss the role of MDM2 in inducing resistance against anti-cancerous therapies thus limiting the benefits of cancerous treatment.
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Affiliation(s)
- Aasma Zafar
- Department of Biosciences, COMSATS University, Islamabad, 45550 Pakistan
| | | | - Aisha Naeem
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 20057 Washington, DC U.S
- Qatar University Health, Qatar University, P.O. Box 2713, Doha, Qatar
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Ashraf A, Liaquat A, Shabbir S, Bokhari SA, Tariq Z, Furrukh Z, Raja AA, Khan MJ. High level of lactate dehydrogenase and ischaemia-reperfusion injury regulate the multiple organ dysfunction in patients with COVID-19. Postgrad Med J 2023; 99:576-581. [PMID: 37319152 PMCID: PMC8960467 DOI: 10.1136/postgradmedj-2022-141573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/11/2022] [Indexed: 01/02/2023]
Abstract
BACKGROUND Multiple organ damage has been observed in patients with COVID-19, but the exact pathway is not known. Vital organs of the human body may get affected after replication of SARS-CoV-2, including the lungs, heart, kidneys, liver and brain. It triggers severe inflammation and impairs the function of two or more organ systems. Ischaemia-reperfusion (IR) injury is a phenomenon that can have disastrous effects on the human body. METHODS In this study, we analysed the laboratory data of 7052 hospitalised patients with COVID-19 including lactate dehydrogenase (LDH). A total of 66.4% patients were men and 33.6% were women, which indicated gender difference as a prominent factor to be considered. RESULTS Our data showed high levels of inflammation and elevated markers of tissue injury from multiple organs C reactive protein, white blood cell count, alanine transaminase, aspartate aminotransferase and LDH. The number of red blood cells, haemoglobin concentration and haematocrit were lower than normal which indicated a reduction in oxygen supply and anaemia. CONCLUSION On the basis of these results, we proposed a model linking IR injury to multiple organ damage by SARS-CoV-2. COVID-19 may cause a reduction in oxygen towards an organ, which leads to IR injury.
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Affiliation(s)
- Aleena Ashraf
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Afrose Liaquat
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Sana Shabbir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Zainab Tariq
- Shifa International Hospitals, Islamabad, Pakistan
| | | | - Afraz Ahmad Raja
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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Rafiq M, Liaquat A, Javed A, Ullah Shah S, Hussain R, Akram Z, Jawad Khan M. Association of leukocyte telomere attrition in coronary artery disease in Pakistani population: A case-control study with Metanalysis. Clin Chim Acta 2023:117416. [PMID: 37276942 DOI: 10.1016/j.cca.2023.117416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/14/2023] [Accepted: 05/31/2023] [Indexed: 06/07/2023]
Affiliation(s)
- Muhammad Rafiq
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad, Pakistan 45550; Department of Biosciences, COMSATS University Islamabad, Pakistan 45550.
| | - Afrose Liaquat
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad, Pakistan 45550
| | - Arham Javed
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad, Pakistan 45550; Department of Biosciences, COMSATS University Islamabad, Pakistan 45550.
| | - Saeed Ullah Shah
- Department of Cardiology, Shifa International Hospital, Shifa Tameer-E-Millat University, Islamabad Pakistan 45550.
| | - Rashid Hussain
- Department of Biosciences, Shifa Tameer-E-Millat University, Islamabad, Pakistan 45550.
| | - Zaineb Akram
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Punjab 46000, Pakistan.
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Nadeem H, Javed K, Nadeem Z, Khan MJ, Rubab S, Yon DK, Naqvi RA. Road Feature Detection for Advance Driver Assistance System Using Deep Learning. Sensors (Basel) 2023; 23:s23094466. [PMID: 37177670 PMCID: PMC10181670 DOI: 10.3390/s23094466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Hundreds of people are injured or killed in road accidents. These accidents are caused by several intrinsic and extrinsic factors, including the attentiveness of the driver towards the road and its associated features. These features include approaching vehicles, pedestrians, and static fixtures, such as road lanes and traffic signs. If a driver is made aware of these features in a timely manner, a huge chunk of these accidents can be avoided. This study proposes a computer vision-based solution for detecting and recognizing traffic types and signs to help drivers pave the door for self-driving cars. A real-world roadside dataset was collected under varying lighting and road conditions, and individual frames were annotated. Two deep learning models, YOLOv7 and Faster RCNN, were trained on this custom-collected dataset to detect the aforementioned road features. The models produced mean Average Precision (mAP) scores of 87.20% and 75.64%, respectively, along with class accuracies of over 98.80%; all of these were state-of-the-art. The proposed model provides an excellent benchmark to build on to help improve traffic situations and enable future technological advances, such as Advance Driver Assistance System (ADAS) and self-driving cars.
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Affiliation(s)
- Hamza Nadeem
- Engineering and Management Sciences, Balochistan University of Information Technology Engineering & Management Sciences, Quetta 87300, Pakistan
- School of Mechanical and Manufacturing Engineering, National University of Science and Technology, Islamabad 44000, Pakistan
| | - Kashif Javed
- School of Mechanical and Manufacturing Engineering, National University of Science and Technology, Islamabad 44000, Pakistan
| | - Zain Nadeem
- Engineering and Management Sciences, Balochistan University of Information Technology Engineering & Management Sciences, Quetta 87300, Pakistan
- School of Mechanical and Manufacturing Engineering, National University of Science and Technology, Islamabad 44000, Pakistan
| | - Muhammad Jawad Khan
- School of Mechanical and Manufacturing Engineering, National University of Science and Technology, Islamabad 44000, Pakistan
| | - Saddaf Rubab
- Department of Computer Engineering, College of Computing and Informatics, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Dong Keon Yon
- Center for Digital Health, Medical Science Research Institute, Kyung Hee University Medical Center, Kyung Hee University College of Medicine, Seoul 02447, Republic of Korea
| | - Rizwan Ali Naqvi
- Department of Unmanned Vehicle Engineering, Sejong University, Seoul 05006, Republic of Korea
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Salim HMU, Dandare A, Khalil F, Liaquat A, Khan MJ, Naeem A. Computational Analysis Reveals Distinctive Interaction of miRNAs with Target Genes in the Pathogenesis of Chronic Kidney Disease. Genes (Basel) 2023; 14:genes14040898. [PMID: 37107656 PMCID: PMC10137451 DOI: 10.3390/genes14040898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
The regulation of genes is crucial for maintaining a healthy intracellular environment, and any dysregulation of gene expression leads to several pathological complications. It is known that many diseases, including kidney diseases, are regulated by miRNAs. However, the data on the use of miRNAs as biomarkers for the diagnosis and treatment of chronic kidney disease (CKD) are not conclusive. The purpose of this study was to elucidate the potential of miRNAs as an efficient biomarker for the detection and treatment of CKD at its early stages. Gene expression profiling data were acquired from the Gene Expression Omnibus (GEO) and differentially expressed genes (DEGs) were identified. miRNAs directly associated with CKD were obtained from an extensive literature search. Network illustration of miRNAs and their projected target differentially expressed genes (tDEGs) was accomplished, followed by functional enrichment analysis. hsa-miR-1-3p, hsa-miR-206, hsa-miR-494 and hsa-miR-577 exhibited a strong association with CKD through the regulation of genes involved in signal transduction, cell proliferation, the regulation of transcription and apoptotic process. All these miRNAs have shown significant contributions to the inflammatory response and the processes which eventually lead to the pathogenesis of CKD. The in silico approach used in this research represents a comprehensive analysis of identified miRNAs and their target genes for the identification of molecular markers of disease processes. The outcomes of the study recommend further efforts for developing miRNA biomarkers set for the early diagnosis of CKD.
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Affiliation(s)
| | - Abdullahi Dandare
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Department of Biochemistry, Usmanu Danfodiyo University, Sokoto P.M.B. 2346, Nigeria
| | - Fareeha Khalil
- Shifa International Hospital, Shifa Tameer-E-Millat University, Islamabad 45550, Pakistan
| | - Afrose Liaquat
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad 45550, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
| | - Aisha Naeem
- Health Research Governance Department, Ministry of Public Health, Doha P.O. Box 42, Qatar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
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Rafiq M, Dandare A, Javed A, Liaquat A, Raja AA, Awan HM, Khan MJ, Naeem A. Competing Endogenous RNA Regulatory Networks of hsa_circ_0126672 in Pathophysiology of Coronary Heart Disease. Genes (Basel) 2023; 14:genes14030550. [PMID: 36980823 PMCID: PMC10047999 DOI: 10.3390/genes14030550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/08/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Coronary heart disease (CHD) is a global health concern, and its molecular origin is not fully elucidated. Dysregulation of ncRNAs has been linked to many metabolic and infectious diseases. This study aimed to explore the role of circRNAs in the pathogenesis of CHD and predicted a candidate circRNA that could be targeted for therapeutic approaches to the disease. circRNAs associated with CHD were identified and CHD gene expression profiles were obtained, and analyzed with GEO2R. In addition, differentially expressed miRNA target genes (miR-DEGs) were identified and subjected to functional enrichment analysis. Networks of circRNA/miRNA/mRNA and the miRNA/affected pathways were constructed. Furthermore, a miRNA/mRNA homology study was performed. We identified that hsa_circ_0126672 was strongly associated with the CHD pathology by competing for endogenous RNA (ceRNA) mechanisms. hsa_circ_0126672 characteristically sponges miR-145-5p, miR-186-5p, miR-548c-3p, miR-7-5p, miR-495-3p, miR-203a-3p, and miR-21. Up-regulation of has_circ_0126672 affected various CHD-related cellular functions, such as atherosclerosis, JAK/STAT, and Apelin signaling pathways. Our results also revealed a perfect and stable interaction for the hybrid of miR-145-5p with NOS1 and RPS6KB1. Finally, miR-145-5p had the highest degree of interaction with the validated small molecules. Henchashsa_circ_0126672 and target miRNAs, notably miR-145-5p, could be good candidates for the diagnosis and therapeutic approaches to CHD.
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Affiliation(s)
- Muhammad Rafiq
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad 45550, Pakistan
| | - Abdullahi Dandare
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Department of Biochemistry, Usmanu Danfodiyo University Sokoto, Sokoto P.M.B 2346, Nigeria
| | - Arham Javed
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad 45550, Pakistan
| | - Afrose Liaquat
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad 45550, Pakistan
| | - Afraz Ahmad Raja
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
| | - Hassaan Mehboob Awan
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Correspondence: (M.J.K.); (A.N.); Tel.: +92-519-049-6140 (M.J.K)
| | - Aisha Naeem
- Health Research Governance Department, Ministry of Public Health, Doha P.O. Box 42, Qatar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
- Correspondence: (M.J.K.); (A.N.); Tel.: +92-519-049-6140 (M.J.K)
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Rafeeq MM, Murad HAS, Najumuddin, Ullah S, Ahmed Z, Alam Q, Bilal M, Habib AH, Sain ZM, Khan MJ, Umair M. Case report: A novel de novo loss of function variant in the DNA-binding domain of TBX2 causes severe osteochondrodysplasia. Front Genet 2023; 13:1117500. [PMID: 36733940 PMCID: PMC9888409 DOI: 10.3389/fgene.2022.1117500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
Background: T-box family members are transcription factors characterized by highly conserved residues corresponding to the DNA-binding domain known as the T-box. TBX2 has been implicated in several developmental processes, such as coordinating cell fate, patterning, and morphogenesis of a wide range of tissues and organs, including lungs, limbs, heart, kidneys, craniofacial structures, and mammary glands. Methods: In the present study, we have clinically and genetically characterized a proband showing a severe form of chondrodysplasia with developmental delay. Whole-exome sequencing (WES), Sanger sequencing, and 3D protein modeling were performed in the present investigation. Results: Whole-exome sequencing revealed a novel nonsense variant (c.529A>T; p.Lys177*; NM_005994.4) in TBX2. 3D-TBX2 protein modeling revealed a substantial reduction of the mutated protein, which might lead to a loss of function (LOF) or nonsense-mediated decay (NMD). Conclusion: This study has not only expanded the mutation spectrum in the gene TBX2 but also facilitated the diagnosis and genetic counseling of related features in affected families.
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Affiliation(s)
- Misbahuddin M. Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hussam Aly Sayed Murad
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najumuddin
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, Pakistan
| | - Samee Ullah
- National Center for Bioinformatics (NCB), Islamabad, Pakistan
| | - Zaheer Ahmed
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Qamre Alam
- Molecular Genomics and Precision Medicine, ExpressMed Laboratories, Zinj, Bahrain
| | - Muhammad Bilal
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ziaullah M. Sain
- Department of Microbiology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan,Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia,*Correspondence: Muhammad Umair, ,
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14
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Ahmad Z, Liaqat R, Palander O, Bilal M, Zeb S, Ahmad F, Jawad Khan M, Umair M. Genetic overview of postaxial polydactyly: Updated classification. Clin Genet 2023; 103:3-15. [PMID: 36071556 DOI: 10.1111/cge.14224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 12/13/2022]
Abstract
Polydactyly or polydactylism, also known as a hyperdactyly, is a congenital limb defect with various morphologic phenotypes. Apart from physical and functional impairments, the presence of polydactyly is an indication of an underlying syndrome in the newborn. Usually, it follows as an autosomal dominant/recessive inheritance pattern with defects in the limb development's anteroposterior patterning. Although mutations in several genes have been associated with polydactyly; however, the exact underlying cause, pathways, and disease mechanisms are still unexplored, thus making it of multi-factorial origin. Polydactyly is divided into three subtypes; radial, ulnar, and central polydactyly. So far, 11 loci (PAPA1-PAPA11) and seven human genes have been reported to cause non-syndromic postaxial polydactyly in humans, including the ZNF141, GLI3, IQCE, GLI1, FAM92A1, KIAA0825, and DACH1. In this review, we discuss emerging evidences of clinical and molecular characterization of polydactyly types in term of the involvement of newly associated genes and loci for non-syndromic postaxial polydactyly, and how these might impact our understanding of the genetic mechanisms and molecular etiology involved in the cause of polydactyly.
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Affiliation(s)
- Zaheer Ahmad
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Romana Liaqat
- Institute of Chemical Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Oliva Palander
- Faculty of Medicine, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shah Zeb
- Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China.,College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, People's Republic of China
| | - Farooq Ahmad
- Department of Biochemistry, Women University Swabi, Swabi, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
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15
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Behrendsen LS, Menon PR, Khan MJ, Gregus A, Wirths O, Meyer T, Staab J. Evaluation of the putative lymphoma-associated point mutation D427H in the STAT3 transcription factor. BMC Mol Cell Biol 2022; 23:23. [PMID: 35752777 PMCID: PMC9233852 DOI: 10.1186/s12860-022-00422-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/23/2022] Open
Abstract
Background Signal transducer and activator of transcription 3 (STAT3) is an oncogenic transcription factor that promotes cell proliferation and immunomodulation in untransformed cells and maintains stemness of transformed cells, facilitating invasion and metastasis. Numerous point mutations in the STAT3 protein have been identified that drive malignancy in various tumor entities. The missense mutation D427H localized in the STAT3 DNA-binding domain has been previously reported in patients with NK/T cell lymphomas. To assess the biological activity of this missense mutation, we compared the STAT3-D427H mutant to wild-type (WT) protein as well as the known hyper-active mutant F174A. Results Although previously reported as an activating mutation, the STAT3-D427H mutant neither showed elevated cytokine-induced tyrosine phosphorylation nor altered nuclear accumulation, as compared to the WT protein. However, the D427H mutant displayed enhanced binding to STAT-specific DNA-binding sites but a reduced sequence specificity and dissociation rate from DNA, which was demonstrated by electrophoretic mobility shift assays. This observation is consistent with the phenotype of the homologous E421K mutation in the STAT1 protein, which also displayed enhanced binding to DNA but lacked a corresponding increase in transcriptional activity. Conclusions Based on our data, it is unlikely that the D427H missense mutation in the STAT3 protein possesses an oncogenic potential beyond the WT molecule. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-022-00422-9.
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16
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Arif W, Rana NF, Saleem I, Tanweer T, Khan MJ, Alshareef SA, Sheikh HM, Alaryani FS, AL-Kattan MO, Alatawi HA, Menaa F, Nadeem AY. Antibacterial Activity of Dental Composite with Ciprofloxacin Loaded Silver Nanoparticles. Molecules 2022; 27:7182. [PMID: 36364007 PMCID: PMC9658858 DOI: 10.3390/molecules27217182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 08/26/2023] Open
Abstract
Resin composites have been widely used in dental restoration. However, polymerization shrinkage and resultant bacterial microleakage are major limitations that may lead to secondary caries. To overcome this, a new type of antibacterial resin composite containing ciprofloxacin-loaded silver nanoparticles (CIP-AgNPs) were synthesized. The chemical reduction approach successfully produced CIP-AgNPs, as demonstrated by FTIR, zeta potential, scanning electron microscopy, and ultraviolet-visible (UV-vis) spectroscopy. CIP-AgNPs were added to resin composites and the antibacterial activity of the dental composite discs were realized against Enterococcus faecalis, Streptococcus mutans, and the Saliva microcosm. The biocompatibility of modified resin composites was assessed and mechanical testing of modified dental composites was also performed. The results indicated that the antibacterial activity and compressive strength of resin composites containing CIP-AgNPs were enhanced compared to the control group. They were also biocompatible when compared to resin composites containing AgNPs. In short, these results established strong ground application for CIP-AgNP-modified dental composite resins.
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Affiliation(s)
- Wafa Arif
- Department of Biomedical Engineering and Sciences, School of Mechanical & Manufacturing Engineering, National University of Sciences & Technology, Islamabad 44000, Pakistan
- Integrated Nanobiotechnology Laboratory, School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Nosheen Fatima Rana
- Department of Biomedical Engineering and Sciences, School of Mechanical & Manufacturing Engineering, National University of Sciences & Technology, Islamabad 44000, Pakistan
- Integrated Nanobiotechnology Laboratory, School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Iqra Saleem
- Department of Biomedical Engineering and Sciences, School of Mechanical & Manufacturing Engineering, National University of Sciences & Technology, Islamabad 44000, Pakistan
- Integrated Nanobiotechnology Laboratory, School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Tahreem Tanweer
- Department of Biomedical Engineering and Sciences, School of Mechanical & Manufacturing Engineering, National University of Sciences & Technology, Islamabad 44000, Pakistan
- Integrated Nanobiotechnology Laboratory, School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Muhammad Jawad Khan
- Department of Robotics & Artificial Intelligence, School of Mechanical & Manufacturing Engineering, National University of Science & Technology, Islamabad 44000, Pakistan
| | | | - Huda M. Sheikh
- Department of Biology, College of Science, University of Jeddah, Jeddah 21589, Saudi Arabia
| | - Fatima S. Alaryani
- Department of Biology, College of Science, University of Jeddah, Jeddah 21589, Saudi Arabia
| | - Manal Othman AL-Kattan
- Department of Biology, College of Science, University of Jeddah, Jeddah 21589, Saudi Arabia
| | - Hanan Ali Alatawi
- Department of Biological Sciences, University College of Haqel, Tabuk University, Tabuk 71491, Saudi Arabia
| | - Farid Menaa
- Internal Medicine and Nanomedicine, California Innovations Corporation, San Diego, CA 92037, USA
| | - Aroosa Younis Nadeem
- Department of Biomedical Engineering and Sciences, School of Mechanical & Manufacturing Engineering, National University of Sciences & Technology, Islamabad 44000, Pakistan
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Raja AA, Dandare A, Khan MJ, Khan MJ. Free Fatty Acid Overload Targets Mitochondria: Gene Expression Analysis of Palmitic Acid-Treated Endothelial Cells. Genes (Basel) 2022; 13:genes13101704. [PMID: 36292589 PMCID: PMC9601498 DOI: 10.3390/genes13101704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/30/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Lipotoxicity is known to cause cellular dysfunction and death in non-adipose tissue. A major cause of lipotoxicity is the accumulation of saturated free fatty acids (FFA). Palmitic acid (PA) is the most common saturated fatty acid found in the human body. Endothelial cells form the blood vessels and are the first non-adipose cells to encounter FFA in the bloodstream. FFA overload has a direct impact on metabolism, which is evident through the changes occurring in mitochondria. To study these changes, the PA-treated human coronary artery endothelial cell (HCAEC) dataset was obtained from the Gene Expression Omnibus (GEO), and it was analyzed to obtain differentially expressed genes (DEGs) from the nucleus and mitochondria. Functional and pathway enrichment analyses were performed on DEGs. Results showed that nuclear and mitochondrial DEGs were implicated in several processes, e.g., reactive oxygen species (ROS) production, mitochondrial fusion and fission, Ca2+ sequestering, membrane transport, the electron transport chain and the process of apoptosis. To better understand the role of FFA in endothelial cell damage, these DEGs can lead to future experiments based on these findings.
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Affiliation(s)
- Afraz Ahmad Raja
- Functional Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
| | - Abdullahi Dandare
- Functional Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Department of Biochemistry, Usmanu Danfodiyo University, Sokoto P.M.B. 2346, Nigeria
| | - Muhammad Jawad Khan
- Functional Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Correspondence: ; Tel.: +92-5190496140
| | - Muhammad Jadoon Khan
- Functional Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
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Mughal NE, Khan MJ, Khalil K, Javed K, Sajid H, Naseer N, Ghafoor U, Hong KS. EEG-fNIRS-based hybrid image construction and classification using CNN-LSTM. Front Neurorobot 2022; 16:873239. [PMID: 36119719 PMCID: PMC9472125 DOI: 10.3389/fnbot.2022.873239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
The constantly evolving human–machine interaction and advancement in sociotechnical systems have made it essential to analyze vital human factors such as mental workload, vigilance, fatigue, and stress by monitoring brain states for optimum performance and human safety. Similarly, brain signals have become paramount for rehabilitation and assistive purposes in fields such as brain–computer interface (BCI) and closed-loop neuromodulation for neurological disorders and motor disabilities. The complexity, non-stationary nature, and low signal-to-noise ratio of brain signals pose significant challenges for researchers to design robust and reliable BCI systems to accurately detect meaningful changes in brain states outside the laboratory environment. Different neuroimaging modalities are used in hybrid settings to enhance accuracy, increase control commands, and decrease the time required for brain activity detection. Functional near-infrared spectroscopy (fNIRS) and electroencephalography (EEG) measure the hemodynamic and electrical activity of the brain with a good spatial and temporal resolution, respectively. However, in hybrid settings, where both modalities enhance the output performance of BCI, their data compatibility due to the huge discrepancy between their sampling rate and the number of channels remains a challenge for real-time BCI applications. Traditional methods, such as downsampling and channel selection, result in important information loss while making both modalities compatible. In this study, we present a novel recurrence plot (RP)-based time-distributed convolutional neural network and long short-term memory (CNN-LSTM) algorithm for the integrated classification of fNIRS EEG for hybrid BCI applications. The acquired brain signals are first projected into a non-linear dimension with RPs and fed into the CNN to extract essential features without performing any downsampling. Then, LSTM is used to learn the chronological features and time-dependence relation to detect brain activity. The average accuracies achieved with the proposed model were 78.44% for fNIRS, 86.24% for EEG, and 88.41% for hybrid EEG-fNIRS BCI. Moreover, the maximum accuracies achieved were 85.9, 88.1, and 92.4%, respectively. The results confirm the viability of the RP-based deep-learning algorithm for successful BCI systems.
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Affiliation(s)
- Nabeeha Ehsan Mughal
- School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Jawad Khan
- School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
- National Center of Artificial Intelligence (NCAI) – NUST, Islamabad, Pakistan
| | - Khurram Khalil
- School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Kashif Javed
- School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Hasan Sajid
- School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
- National Center of Artificial Intelligence (NCAI) – NUST, Islamabad, Pakistan
| | - Noman Naseer
- Department of Mechatronics and Biomedical Engineering, Air University, Islamabad, Pakistan
| | - Usman Ghafoor
- School of Mechanical Engineering, Pusan National University, Busan, South Korea
| | - Keum-Shik Hong
- School of Mechanical Engineering, Pusan National University, Busan, South Korea
- *Correspondence: Keum-Shik Hong
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Dandare A, Rafiq M, Liaquat A, Khan MJ. Two hours method for RNA and DNA co-extraction from blood of coronary artery disease patients: Fast, simple and economical technique. Pak J Med Sci 2022; 38:1754-1759. [PMID: 36246703 PMCID: PMC9532648 DOI: 10.12669/pjms.38.7.5509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/30/2021] [Accepted: 06/28/2022] [Indexed: 11/27/2022] Open
Abstract
Objectives: Extraction of DNA and RNA is the first step in genomics and transcriptomics studies. Phenol-chloroform method for DNA extraction has been the widely used method. However, this method is relatively expensive and time-consuming. The objective of the present study was to validate a cost and time-effective protocol that will reduce the burden of molecular biology-based research and make a difference in laboratories with limited resources. Methods: A comparative study was conducted at Syed Qamer Alam Research Laboratory, Shifa College of Medicine; from February, 2021 to August, 2021. TRIzol™ method was used to extract RNA from blood samples of coronary artery disease patients and remnant was used to extract DNA. The quantity, purity and integrity of the extracted DNA by both methods (TRIzol and phenol-chloroform) was examined. PCR product amplification was performed with thrombomodulin (THBD) gene to validate the characteristic of the extracted DNA and its efficiency for downstream experiments. Results: The DNA yield in the TRIzol™ method was three-fold higher than phenol chloroform method. Both methods showed intact genomic DNA on the agarose gel, and extracted DNA was efficient for PCR amplification. Conclusion: The TRIzol™ method for RNA and DNA co-extraction is fast, simple and economical technique. So, it can be adopted for routine molecular biology analyses in limited resources setup.
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Affiliation(s)
- Abdullahi Dandare
- Abdullahi Dandare, Department of Biochemistry, Usmanu Danfodiyo University Sokoto, Nigeria. Department of Biosciences, COMSATS University Islamabad, 45550, Pakistan
| | - Muhammad Rafiq
- Muhammad Rafiq, Department of Biosciences, COMSATS University Islamabad, 45550, Pakistan, Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad, 45550, Pakistan
| | - Afrose Liaquat
- Afrose Liaquat, Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad, 45550, Pakistan
- Correspondence: Dr. Afrose Liaquat (MBBS, M.Phil, MHPE, PhD) Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad -45550, Pakistan.
| | - Muhammad Jawad Khan
- Muhammad Jawad Khan, Department of Biosciences, COMSATS University Islamabad, 45550, Pakistan
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Khan MJ, Rabia G, Dandare A, Awan HM, Raja AA. Abstract 1554: Functional analysis of human circular RNA_0001587 and its target miRNAs in oral cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Oral cancer is the sixth most aggressive malignancy around the world and accounts for 90% of head and neck lesions. It is the most prevalent type of cancer in South Asian countries and contributes to around 25% of all new cancer cases in the region. The involvement of non-coding circular RNAs (circRNAs) in various disease pathology has been reported. However, their role as diagnostic or therapeutic biomarkers is still unclear and needs to be further explored. This study was aimed to identify the role of hsa_circ_0001587 and competing endogenous RNA (ceRNA) mechanism in early diagnosis or as a therapeutic target for oral cancer. For this purpose, lists of circRNAs, miRNAs, and differentially expressed genes (DEGs) involved in oral squamous cell carcinoma (OSCC) were identified from the reported literature. Circinteractome was used to obtain target miRNAs that potentially bind to hsa_circ_0001587. Five miRNAs were selected for further in silico analysis on the basis of maximum target sites. Data were subjected to functional enrichment analysis, pathway analysis, and gene homology studies.Our results showed active participation of both hsa_circ_0001587 and its target miRNAs (miR-548c-3p, miR-520h, miR-1827, miR-607, and miR-579) in oral carcinogenesis via the regulation of genes including AKT, GADD45, PKA, PKC, and CASP8. Dysregulation of these genes disturbed the immune system, signaling pathways, cellular compartment activities, and molecular functions, indicating their role in tumor initiation and progression. Furthermore, it was predicted that hsa_circ_0001587 enhances the expression of genes for the RAS signaling pathway via its sponging effect on miR-548c-3p and miR-607. Noncoding RNAs including hsa_circ_0001587 and target miR-548c-3p and miR-607 play a critical role in the pathogenesis of OSCC. It is therefore suggested that hsa_circ_0001587 and its target miRNAs could be used as potential biomarkers for oral cancer.
Citation Format: Muhammad Jawad Khan, Ghulam Rabia, Abdullahi Dandare, Hassaan Mehboob Awan, Afraz Ahmad Raja. Functional analysis of human circular RNA_0001587 and its target miRNAs in oral cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1554.
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Affiliation(s)
| | - Ghulam Rabia
- 1COMSATS University Islamabad, Islamabad, Pakistan
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21
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Naeem A, Gupta N, Naeem U, Khan MJ, Elrayess MA, Cui W, Albanese C. A comparison of isolation and culture protocols for human amniotic mesenchymal stem cells. Cell Cycle 2022; 21:1543-1556. [PMID: 35412950 PMCID: PMC9291641 DOI: 10.1080/15384101.2022.2060641] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The successful translation of mesenchymal stem cells (MSCs) from bench to bedside is predicated upon their regenerative capabilities and immunomodulatory potential. Many challenges still exist in making MSCs a viable and cost-effective therapeutic option, due in part to the challenges of sourcing MSCs from adult tissues and inconsistencies in the characterization of MSCs. In many cases, adult MSC collection is an invasive procedure, and ethical concerns and age-related heterogeneity further complicate obtaining adult tissue derived MSCs at the scales needed for clinical applications. Alternative adult sources, such as post-partum associated tissues, offer distinct advantages to overcome these challenges. However, successful therapeutic applications rely on the efficient ex-vivo expansion of the stem cells while avoiding any culture-related phenotypic alterations, which requires optimized and standardized isolation, culture, and cell preservation methods. In this review, we have compared the isolation and culture methods for MSCs originating from the human amniotic membrane (hAMSCs) of the placenta to identify the elements that support the extended subculture potential of hAMSCs without compromising their immune-privileged, pluripotent regenerative potential.Abbreviations:AM: Human amniotic membrane; ASCs: Adipose tissue-derived stem cells; BM-MSCs: Bone marrow-mesenchymal stem cells; DMEM: Dulbecco's modified eagle medium; DT: Doubling time; EMEM: Eagle's modified essential medium; ESCM: Embryonic stem cell markers; ESCs: Embryonic stem cells; hAECs: Human amniotic epithelial cells; hAMSCs: Human amniotic mesenchymal stem cells; HLA: Human leukocyte antigen; HM: Hematopoietic markers; IM: Immunogenicity markers; MHC: Major histocompatibility complex; MSCs: Mesenchymal stem cells; MCSM: Mesenchymal cell surface markers; Nanog: NANOG homeobox; Oct: Octamer binding transcription factor 4; P: Passage; PM: Pluripotency markers; STRO-1: Stromal precursor antigen-1; SCP: Subculture potential; Sox-2: Sry-related HMG box gene 2; SSEA-4: Stage-specific embryonic antigen; TRA: Tumor rejection antigen.
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Affiliation(s)
- Aisha Naeem
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.,Health Research Governance Department, Ministry of Public Health, Qatar
| | - Nikita Gupta
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Usra Naeem
- Department of Health Professional Technology, University of Lahore, Pakistan
| | | | - Mohamed A Elrayess
- Omics, Biomedical Research Center, Qatar University, Doha, Qatar.,Research and Graduate Studies, College of Pharmacy, Qu Health, Qatar University, Doha, Qatar
| | - Wanxing Cui
- Cell Therapy Manufacturing Facility, MedStar Georgetown University Hospital, Washington, DC, USA
| | - Chris Albanese
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.,Department of Radiology, Georgetown University Medical Center, Washington, DC, USA.,Center for Translational Imaging, Georgetown University Medical Center, Washington, DC, USA
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Naeem A, Gupta N, Arzoo N, Naeem U, Khan MJ, Choudhry MU, Cui W, Albanese C. A Survey and Critical Evaluation of Isolation, Culture, and Cryopreservation Methods of Human Amniotic Epithelial Cells. Cell Cycle 2022; 21:655-673. [PMID: 35289707 PMCID: PMC8973348 DOI: 10.1080/15384101.2021.2020015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Human amniotic epithelial cells (hAECs), derived from an epithelial cell layer of the human amniotic membrane, possess embryonic stem-like properties and are known to maintain multilineage differentiation potential. Unfortunately, an inability to expand hAECs without significantly compromising their stem cell potency has precluded their widespread use for regenerative therapies. This article critically evaluates the methods used for isolation, expansion, and cryopreservation of hAECs. We assessed the impact of these methods on ex-vivo expansion and stem cell phenotype of hAECs. Moreover, the progress and challenges to optimize clinically suitable culture conditions for an efficient ex-vivo expansion and storage of these cells are highlighted. Additionally, we also reviewed the currently used hAECs isolation and characterization methods employed in clinical trials. Despite the developments made in the last decade, significant challenges still exist to overcome limitations of ex-vivo expansion and retention of stemness of hAECs in both xenogeneic and xenofree culture conditions. Therefore, optimization and standardization of culture conditions for robust ex-vivo maintenance of hAECs without affecting tissue regenerative properties is an absolute requirement for their successful therapeutic manipulation. This review may help the researchers to optimize the methods that support ex-vivo survival, proliferation, and self-renewal properties of the hAECs.Abbreviations: AM: Human amniotic membrane; CM-HBSS: Ca++ and Mg++ free HBSS; DMEM: Dulbecco's Modified Eagle Medium; DMEM-HG: DMEM-high glucose; EMEM: Eagle's Modified Essential Medium; EMT: Epithelial-to-mesenchymal transition; EpM: Epi-life complete media; ESC: Embryonic stem cells; ESCM: Epithelial cell surface markers; hAECs: Human amniotic epithelial cells; HLA: Human leukocyte antigen; IM: Immunogenicity markers; iPSC: Induced pluripotent stem cells; KOSR; KSR: Knockout serum replacement; KSI: Key success indicators; CHM: Cell heterogeneity markers; Nanog: NANOG homeobox; Oct-4: Octamer binding transcription factor 4; OR: Operation room; P: Passage; PM: Pluripotency markers; SCM: Stem cell markers for non-differentiated cells; Sox-2: Sry-related HMG box gene 2; SSEA-4: Stage-specific embryonic antigen; TRA: Tumor rejection antigen; UC: Ultra-culture; XF: Xenogeneic free.
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Affiliation(s)
- Aisha Naeem
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia, USA.,Health Research Governance Department, Ministry of Public Health, Qatar
| | - Nikita Gupta
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Natasha Arzoo
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Usra Naeem
- Department of Health Professional Technology, University of Lahore, Pakistan
| | | | - Muhammad Umer Choudhry
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Wanxing Cui
- Cell Therapy Manufacturing Facility, MedStar Georgetown University Hospital, Washington, District of Columbia, USA.,Department of Radiology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Chris Albanese
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia, USA.,Department of Radiology, Georgetown University Medical Center, Washington, District of Columbia, USA.,Department of Oncology, Center for Translational Imaging, Georgetown University Medical Center, Washington, District of Columbia, USA
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Ashraf A, Liaquat A, Shabbir S, Bokhari SA, Tariq Z, Furrukh Z, Raja AA, Khan MJ. High level of lactate dehydrogenase and ischaemia-reperfusion injury regulate the multiple organ dysfunction in patients with COVID-19. Postgrad Med J 2022:7130991. [PMID: 37076451 DOI: 10.1136/postmj/postgradmedj-2022-141573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/11/2022] [Indexed: 04/21/2023]
Abstract
BACKGROUND Multiple organ damage has been observed in patients with COVID-19, but the exact pathway is not known. Vital organs of the human body may get affected after replication of SARS-CoV-2, including the lungs, heart, kidneys, liver and brain. It triggers severe inflammation and impairs the function of two or more organ systems. Ischaemia-reperfusion (IR) injury is a phenomenon that can have disastrous effects on the human body. METHODS In this study, we analysed the laboratory data of 7052 hospitalised patients with COVID-19 including lactate dehydrogenase (LDH). A total of 66.4% patients were men and 33.6% were women, which indicated gender difference as a prominent factor to be considered. RESULTS Our data showed high levels of inflammation and elevated markers of tissue injury from multiple organs C reactive protein, white blood cell count, alanine transaminase, aspartate aminotransferase and LDH. The number of red blood cells, haemoglobin concentration and haematocrit were lower than normal which indicated a reduction in oxygen supply and anaemia. CONCLUSION On the basis of these results, we proposed a model linking IR injury to multiple organ damage by SARS-CoV-2. COVID-19 may cause a reduction in oxygen towards an organ, which leads to IR injury.
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Affiliation(s)
- Aleena Ashraf
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Afrose Liaquat
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Sana Shabbir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Zainab Tariq
- Shifa International Hospitals, Islamabad, Pakistan
| | | | - Afraz Ahmad Raja
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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24
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Khan MJ, Ganesan B, Fong KNK, Yip J, Forhadul Hoque M, Mahmudul Hasan SM, Zaman S, Hawlader MDH, Tong RKY. Factors predictive of Ponseti casting for treating clubfoot: analysis of Bayesian Poisson regression model. Eur Rev Med Pharmacol Sci 2022; 26:1868-1875. [PMID: 35363335 DOI: 10.26355/eurrev_202203_28332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
OBJECTIVE Clubfoot is a growing public health concern in Bangladesh, with the incidence of approximately 0.64 to 6.8 in every 1000 live births. For over a decade, Ponseti method has been considered a gold standard for treating the clubfoot. Despite few studies have been estimating the number of casts required to correct the clubfoot deformities by Ponseti method, the subject of interest has always remained. Therefore, this current study aimed to investigate the significant predictive factors for the number of casts required to correct congenital clubfoot. PATIENTS AND METHODS In this retrospective cohort study, we used Bayesian Poisson Regression Model to investigate the influencing factors that could predict how many casts are needed to correct the clubfoot. We included 69 patients with 99 affected feet, who completed their corrective phase of treatment in the Ponseti method. For this cohort study, we integrated only pre-tenotomy casting data with no age restrictions. We used Bayesian Poisson regression analysis technique to estimate the predictive factors. RESULTS In Bayesian Poisson model, age was the most influencing predictive factor (24.3%) for increasing the number of castings to correct the clubfoot deformity. The clubfoot offspring of the ≤1-year-old was positive, and the incidence rate increased significantly with the casting number. The number of Ponseti casts in male clubfoot children was 28% higher than in female, and this was marginally statistically significant. There was no marked change estimated in the pattern of clubfoot, foot involvement and Pirani score of the severity. CONCLUSIONS We concluded that the age factor may influence the number of casts required for the correction of clubfoot and specifically ≤ 1-year-old children are highly impacted. Treating clubfoot at an early age is suggested in this study to increase the success of clubfoot treatment and decrease the risk of relapse.
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Affiliation(s)
- M J Khan
- Department of Public Health, North South University, Dhaka, Bangladesh.
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Mehmood M, Khan MJ, Khan MJ, Akhtar N, Mughal F, Shah STA, Hyder MZ, Farrakh S, Sadiq I. Systematic analysis of HD-ZIP transcription factors in sesame genome and gene expression profiling of SiHD-ZIP class I entailing drought stress responses at early seedling stage. Mol Biol Rep 2022; 49:2059-2071. [PMID: 34993726 DOI: 10.1007/s11033-021-07024-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Sesame is an ancient oilseed crop, known for its high oil content and quality. Its sensitivity to drought at early seedling stage is one of the limiting factors affecting its world-wide growth and productivity. Among plant specific transcription factors, the association of HD-ZIPs with sesame drought responses at early seedling stage is not well-established yet and is very important to develop our molecular understanding on sesame drought tolerance. METHODS AND RESULTS In this study, total 61 sesame HD-ZIP proteins were identified, based on their protein sequence homology with Arabidopsis and protein domain(s) architecture prediction, followed by their phylogenetic, conserved domain(s) motifs and gene structure analyses to classify them into four classes (HD-ZIP Class I-IV). HD-ZIP Class I was also subdivided into four subgroups: α (SiHZ25, SiHZ43, SiHZ9 and SiHZ16), β1 (SiHZ10, SiHZ30, SiHZ32 and SiHZ26), β2 (SiHZ42 and SiHZ45) and γ (SiHZ17, SiHZ7 and SiHZ35) by a comparative phylogenetic analysis of sesame with Arabidopsis and maize. Afterwards, twenty-one days old sesame seedlings were exposed to drought stress by withholding water for 7 days (when soil moisture content reduced to ~16%) and gene expression of HD-ZIP Class I (13 members) was performed in well- watered (control) and drought stressed seedlings. The gene expression analysis showed that the expressions of SiHZ7 (6.8 fold) and SiHZ35 (2.6 fold) from γ subgroup were significantly high in drought seedlings. CONCLUSIONS This study is useful in demonstrating the role of SiHD-ZIP Class I in sesame drought responses at early seedling stage and to develop its novel drought tolerant varieties.
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Affiliation(s)
- Maryam Mehmood
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Muhammad Jadoon Khan
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Nadeem Akhtar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Fizza Mughal
- Illinois Informatics Institute, University of Illinois, Urbana-Champaign, USA
| | - Syed Tahir Abbas Shah
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | | | - Sumaira Farrakh
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan.
| | - Irfan Sadiq
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan.
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Hamid H, Naseer N, Nazeer H, Khan MJ, Khan RA, Shahbaz Khan U. Analyzing Classification Performance of fNIRS-BCI for Gait Rehabilitation Using Deep Neural Networks. Sensors (Basel) 2022; 22:s22051932. [PMID: 35271077 PMCID: PMC8914987 DOI: 10.3390/s22051932] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 05/11/2023]
Abstract
This research presents a brain-computer interface (BCI) framework for brain signal classification using deep learning (DL) and machine learning (ML) approaches on functional near-infrared spectroscopy (fNIRS) signals. fNIRS signals of motor execution for walking and rest tasks are acquired from the primary motor cortex in the brain's left hemisphere for nine subjects. DL algorithms, including convolutional neural networks (CNNs), long short-term memory (LSTM), and bidirectional LSTM (Bi-LSTM) are used to achieve average classification accuracies of 88.50%, 84.24%, and 85.13%, respectively. For comparison purposes, three conventional ML algorithms, support vector machine (SVM), k-nearest neighbor (k-NN), and linear discriminant analysis (LDA) are also used for classification, resulting in average classification accuracies of 73.91%, 74.24%, and 65.85%, respectively. This study successfully demonstrates that the enhanced performance of fNIRS-BCI can be achieved in terms of classification accuracy using DL approaches compared to conventional ML approaches. Furthermore, the control commands generated by these classifiers can be used to initiate and stop the gait cycle of the lower limb exoskeleton for gait rehabilitation.
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Affiliation(s)
- Huma Hamid
- Department of Mechatronics and Biomedical Engineering, Air University, Islamabad 44000, Pakistan; (H.H.); (H.N.)
| | - Noman Naseer
- Department of Mechatronics and Biomedical Engineering, Air University, Islamabad 44000, Pakistan; (H.H.); (H.N.)
- Correspondence:
| | - Hammad Nazeer
- Department of Mechatronics and Biomedical Engineering, Air University, Islamabad 44000, Pakistan; (H.H.); (H.N.)
| | - Muhammad Jawad Khan
- School of Mechanical and Manufacturing Engineering, National University of Science and Technology, Islamabad 44000, Pakistan;
| | - Rayyan Azam Khan
- Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada;
| | - Umar Shahbaz Khan
- Department of Mechatronics Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan;
- National Centre of Robotics and Automation (NCRA), Rawalpindi 46000, Pakistan
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Dandare A, Rafiq M, Liaquat A, Raja AA, Khan MJ. Identification of hsa_circ_0092576 regulatory network in the pathogenesis of coronary heart disease. Genes Dis 2022; 10:26-28. [PMID: 37013027 PMCID: PMC10066335 DOI: 10.1016/j.gendis.2021.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/15/2021] [Accepted: 12/26/2021] [Indexed: 10/19/2022] Open
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Qadir J, Riaz SK, Sahar NE, Aman D, Khan MJ, Malik MFA. Transcriptional elucidation of tumor necrosis factor-α-mediated nuclear factor-κB1 activation in breast cancer cohort of Pakistan. J Cancer Res Ther 2021; 16:1443-1448. [PMID: 33342810 DOI: 10.4103/jcrt.jcrt_484_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Initiation, promotion, progression, and metastasis of mammary tumors are mediated by dysregulation of multiple genes involved in various signaling pathways. Expressional variation of these molecules significantly influences cancer cell proliferation in breast cancer. Aims and Objectives In the current study, tumor necrosis factor-alpha (TNF-α) and its downstream effector nuclear factor kappa-B1 (NF-κB1) mean transcript levels were explored and associated with molecular subtypes in breast cancer cohort of Pakistan. Freshly excised tumors (n = 150) along with background tissues were collected for RNA isolation and cDNA synthesis. Materials and Methods Quantitative polymerase chain reaction was carried out for quantification of TNF-α, NF-κB1, and β-actin gene transcripts along with estrogen receptor, progesterone receptor, HER2, and Ki-67, followed by statistical analysis. Results For TNF-α and NF-κB1, 95% and 77% of the cohort was found to be positive, respectively. Both of these molecules were found to be significantly upregulated in tumors when compared against their respective controls (P < 0.0001). Association of TNF-α and NF-κB1 with late clinical stages, poorly differentiated tumors, increased tumor size, nodal involvement, and metastasis was observed to be statistically significant (P < 0.05). Strong positive correlation was established between TNF-α and NF-κB1(r = 0.465, P< 0.05). Moreover, mean transcript levels of TNF-α and NF-κB1 were significantly elevated in Luminal A and Luminal B subtypes of breast cancer patients, respectively. Conclusion Strong positive correlation between TNF-α and NF-κB1 proposed the putative role of these molecules as prognostic biomarkers in breast cancer.
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Affiliation(s)
- Javeria Qadir
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Syeda Kiran Riaz
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Namood-E Sahar
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Durkhshan Aman
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
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Shabbir S, Raza MH, Arshad M, Khan MJ. The interplay between the immune system and SARS-CoV-2 in COVID-19 patients. Arch Virol 2021; 166:2109-2117. [PMID: 33950288 PMCID: PMC8097254 DOI: 10.1007/s00705-021-05091-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/01/2021] [Indexed: 12/20/2022]
Abstract
Millions of people across the globe have been affected by coronavirus disease 2019 (COVID-19), which began in Wuhan, China, and is caused by SARS-CoV-2. COVID-19 has a variety of clinical characteristics and triggers immune responses required for the elimination of the viral agent. Currently, no effective treatment options are available for targeting SARS-CoV-2 infection. Repurposing of drugs such as chloroquine, thalidomide, and leflunomide alongside convalescent plasma is being employed as a therapeutic strategy. Clinical studies have shown that both asymptomatic and symptomatic patients can have an extremely active immune response that is largely attributable to immune system modulations. This includes cytokine storm syndrome (CSS), which affects the adaptive immune system, leading to exhaustion of natural killer (NK) cells and thrombocytopenia in some cases. This review examines the interaction of SARS-CoV-2 with the host immune system and the potential for the development of appropriate immunotherapy for the treatment of COVID-19.
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Affiliation(s)
- Sana Shabbir
- Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shahzad, Islamabad, 45550, Pakistan
| | - Muhammad Hassan Raza
- Department of Biological Sciences, International Islamic University Islamabad, Sri Nagar Highway, H10, Islamabad, 45550, Pakistan
| | - Muhammad Arshad
- Department of Biological Sciences, International Islamic University Islamabad, Sri Nagar Highway, H10, Islamabad, 45550, Pakistan.
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shahzad, Islamabad, 45550, Pakistan.
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Arif S, Khan MJ, Naseer N, Hong KS, Sajid H, Ayaz Y. Vector Phase Analysis Approach for Sleep Stage Classification: A Functional Near-Infrared Spectroscopy-Based Passive Brain-Computer Interface. Front Hum Neurosci 2021; 15:658444. [PMID: 33994983 PMCID: PMC8121150 DOI: 10.3389/fnhum.2021.658444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/09/2021] [Indexed: 11/13/2022] Open
Abstract
A passive brain-computer interface (BCI) based upon functional near-infrared spectroscopy (fNIRS) brain signals is used for earlier detection of human drowsiness during driving tasks. This BCI modality acquired hemodynamic signals of 13 healthy subjects from the right dorsolateral prefrontal cortex (DPFC) of the brain. Drowsiness activity is recorded using a continuous-wave fNIRS system and eight channels over the right DPFC. During the experiment, sleep-deprived subjects drove a vehicle in a driving simulator while their cerebral oxygen regulation (CORE) state was continuously measured. Vector phase analysis (VPA) was used as a classifier to detect drowsiness state along with sleep stage-based threshold criteria. Extensive training and testing with various feature sets and classifiers are done to justify the adaptation of threshold criteria for any subject without requiring recalibration. Three statistical features (mean oxyhemoglobin, signal peak, and the sum of peaks) along with six VPA features (trajectory slopes of VPA indices) were used. The average accuracies for the five classifiers are 90.9% for discriminant analysis, 92.5% for support vector machines, 92.3% for nearest neighbors, 92.4% for both decision trees, and ensembles over all subjects' data. Trajectory slopes of CORE vector magnitude and angle: m(|R|) and m(∠R) are the best-performing features, along with ensemble classifier with the highest accuracy of 95.3% and minimum computation time of 40 ms. The statistical significance of the results is validated with a p-value of less than 0.05. The proposed passive BCI scheme demonstrates a promising technique for online drowsiness detection using VPA along with sleep stage classification.
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Affiliation(s)
- Saad Arif
- School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Jawad Khan
- School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology, Islamabad, Pakistan.,National Center of Artificial Intelligence (NCAI), Islamabad, Pakistan
| | - Noman Naseer
- Department of Mechatronics Engineering, Air University, Islamabad, Pakistan
| | - Keum-Shik Hong
- School of Mechanical Engineering, Pusan National University, Busan, South Korea
| | - Hasan Sajid
- School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology, Islamabad, Pakistan.,National Center of Artificial Intelligence (NCAI), Islamabad, Pakistan
| | - Yasar Ayaz
- School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology, Islamabad, Pakistan.,National Center of Artificial Intelligence (NCAI), Islamabad, Pakistan
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Naeem M, Khan MJ, Yousf T. Eyeball Identification and Tracking using Digital Image Processing. 2021 International Conference on Artificial Intelligence and Mechatronics Systems (AIMS) 2021. [DOI: 10.1109/aims52415.2021.9466072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Tanveer MA, Khan MJ, Sajid H, Naseer N. Convolutional neural networks ensemble model for neonatal seizure detection. J Neurosci Methods 2021; 358:109197. [PMID: 33864835 DOI: 10.1016/j.jneumeth.2021.109197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Neonatal seizures are a common occurrence in clinical settings, requiring immediate attention and detection. Previous studies have proposed using manual feature extraction coupled with machine learning, or deep learning to classify between seizure and non-seizure states. NEW METHOD In this paper a deep learning based approach is used for neonatal seizure classification using electroencephalogram (EEG) signals. The architecture detects seizure activity in raw EEG signals as opposed to common state-of-art, where manual feature extraction with machine learning algorithms is used. The architecture is a two-dimensional (2D) convolutional neural network (CNN) to classify between seizure/non-seizure states. RESULTS The dataset used for this study is annotated by three experts and as such three separate models are trained on individual annotations, resulting in average accuracies (ACC) of 95.6 %, 94.8 % and 90.1 % respectively, and average area under the receiver operating characteristic curve (AUC) of 99.2 %, 98.4 % and 96.7 % respectively. The testing was done using 10-cross fold validation, so that the performance can be an accurate representation of the architectures classification capability in a clinical setting. After training/testing of the three individual models, a final ensemble model is made consisting of the three models. The ensemble model gives an average ACC and AUC of 96.3 % and 99.3 % respectively. COMPARISON WITH EXISTING METHODS This study outperforms previous studies, with increased ACC and AUC results coupled with use of small time windows (1 s) used for evaluation. CONCLUSION The proposed approach is promising for detecting seizure activity in unseen neonate data in a clinical setting.
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Affiliation(s)
- M Asjid Tanveer
- Intelligent Robotics Lab, National Center of Artificial Intelligence, National University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Jawad Khan
- Intelligent Robotics Lab, National Center of Artificial Intelligence, National University of Science and Technology, Islamabad, Pakistan; School of Mechanical and Manufacturing Engineering, National Center of Artificial Intelligence, National University of Science and Technology, Islamabad, Pakistan.
| | - Hasan Sajid
- Intelligent Robotics Lab, National Center of Artificial Intelligence, National University of Science and Technology, Islamabad, Pakistan; School of Mechanical and Manufacturing Engineering, National Center of Artificial Intelligence, National University of Science and Technology, Islamabad, Pakistan
| | - Noman Naseer
- Department of Mechatronics and Biomedical Engineering, Air University, Islamabad, Pakistan
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Javed OA, Khan MJ, Abbas Y, Pillai S, Hristova K, Chiang M, Mason W. P16 An audit of elderly patients with a femoral fracture: is the quality of care received by patients affected by where in the femur the fracture occurs? BJS Open 2021. [PMCID: PMC8153828 DOI: 10.1093/bjsopen/zrab032.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction
Elderly patients with femoral fractures are often frail and require a multidisciplinary approach to optimise medical care, rehabilitation and prevention of further injury. Previously, neck of femur fracture patients were the focus of such an approach, but NICE and BOAST guidelines emphasise extending this care to other elderly trauma patients.
Methods
A retrospective analysis of 43 patients over 60 years old at Gloucestershire Hospitals NHS Foundation Trust in 2019 with a femoral fracture other than a neck of femur fracture. BOAST guideline standards were surgery within 36 hours, orthogeriatric assessment within 72 hours, a documented ceiling of treatment, falls risk assessment, bone health review, nutritional assessment and physiotherapy review.
Results
Our study showed worse outcomes in all standards for patients with femoral shaft, distal femur and periprosthetic femur fractures compared to neck of femur fractures: surgery within 36 hours (63.9% vs. 66%); orthogeriatric assessment within 72 hours (32.6% vs. 91.9%); falls risk assessment (76.7% vs. 99.6%); bone health review (41.9% vs. 99.7%); nutritional assessment (55.8% vs. 99.6%); physiotherapy review (97.7% vs. 98.9%). The group also had worse outcomes for average length of stay (19 days vs. 14 days) and 30 day mortality (9.3% vs. 8.6%).
Discussion
Our study showed a discrepancy in care received by elderly patients with femoral fractures other than neck of femur. We will introduce a proforma for all femoral fractures, present our findings to orthogeriatric, bone health and physiotherapy teams to involve them in the care of such patients and re-audit following these recommendations.
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Affiliation(s)
- O A Javed
- Gloucestershire Hospitals NHS Foundation Trust
| | - M J Khan
- Gloucestershire Hospitals NHS Foundation Trust
| | - Y Abbas
- Gloucestershire Hospitals NHS Foundation Trust
| | - S Pillai
- Gloucestershire Hospitals NHS Foundation Trust
| | - K Hristova
- Gloucestershire Hospitals NHS Foundation Trust
| | - M Chiang
- Gloucestershire Hospitals NHS Foundation Trust
| | - W Mason
- Gloucestershire Hospitals NHS Foundation Trust
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Asgher U, Khan MJ, Asif Nizami MH, Khalil K, Ahmad R, Ayaz Y, Naseer N. Motor Training Using Mental Workload (MWL) With an Assistive Soft Exoskeleton System: A Functional Near-Infrared Spectroscopy (fNIRS) Study for Brain-Machine Interface (BMI). Front Neurorobot 2021; 15:605751. [PMID: 33815084 PMCID: PMC8012849 DOI: 10.3389/fnbot.2021.605751] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 02/05/2021] [Indexed: 11/24/2022] Open
Abstract
Mental workload is a neuroergonomic human factor, which is widely used in planning a system's safety and areas like brain-machine interface (BMI), neurofeedback, and assistive technologies. Robotic prosthetics methodologies are employed for assisting hemiplegic patients in performing routine activities. Assistive technologies' design and operation are required to have an easy interface with the brain with fewer protocols, in an attempt to optimize mobility and autonomy. The possible answer to these design questions may lie in neuroergonomics coupled with BMI systems. In this study, two human factors are addressed: designing a lightweight wearable robotic exoskeleton hand that is used to assist the potential stroke patients with an integrated portable brain interface using mental workload (MWL) signals acquired with portable functional near-infrared spectroscopy (fNIRS) system. The system may generate command signals for operating a wearable robotic exoskeleton hand using two-state MWL signals. The fNIRS system is used to record optical signals in the form of change in concentration of oxy and deoxygenated hemoglobin (HbO and HbR) from the pre-frontal cortex (PFC) region of the brain. Fifteen participants participated in this study and were given hand-grasping tasks. Two-state MWL signals acquired from the PFC region of the participant's brain are segregated using machine learning classifier-support vector machines (SVM) to utilize in operating a robotic exoskeleton hand. The maximum classification accuracy is 91.31%, using a combination of mean-slope features with an average information transfer rate (ITR) of 1.43. These results show the feasibility of a two-state MWL (fNIRS-based) robotic exoskeleton hand (BMI system) for hemiplegic patients assisting in the physical grasping tasks.
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Affiliation(s)
- Umer Asgher
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Jawad Khan
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Hamza Asif Nizami
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Florida State University College of Engineering, Florida A&M University, Tallahassee, FL, United States
| | - Khurram Khalil
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Riaz Ahmad
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Directorate of Quality Assurance and International Collaboration, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Yasar Ayaz
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- National Center of Artificial Intelligence (NCAI), National University of Sciences and Technology, Islamabad, Pakistan
| | - Noman Naseer
- Department of Mechatronics and Biomedical Engineering, Air University, Islamabad, Pakistan
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Nazeer H, Naseer N, Mehboob A, Khan MJ, Khan RA, Khan US, Ayaz Y. Enhancing Classification Performance of fNIRS-BCI by Identifying Cortically Active Channels Using the z-Score Method. Sensors (Basel) 2020; 20:s20236995. [PMID: 33297516 PMCID: PMC7730208 DOI: 10.3390/s20236995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 01/05/2023]
Abstract
A state-of-the-art brain–computer interface (BCI) system includes brain signal acquisition, noise removal, channel selection, feature extraction, classification, and an application interface. In functional near-infrared spectroscopy-based BCI (fNIRS-BCI) channel selection may enhance classification performance by identifying suitable brain regions that contain brain activity. In this study, the z-score method for channel selection is proposed to improve fNIRS-BCI performance. The proposed method uses cross-correlation to match the similarity between desired and recorded brain activity signals, followed by forming a vector of each channel’s correlation coefficients’ maximum values. After that, the z-score is calculated for each value of that vector. A channel is selected based on a positive z-score value. The proposed method is applied to an open-access dataset containing mental arithmetic (MA) and motor imagery (MI) tasks for twenty-nine subjects. The proposed method is compared with the conventional t-value method and with no channel selected, i.e., using all channels. The z-score method yielded significantly improved (p < 0.0167) classification accuracies of 87.2 ± 7.0%, 88.4 ± 6.2%, and 88.1 ± 6.9% for left motor imagery (LMI) vs. rest, right motor imagery (RMI) vs. rest, and mental arithmetic (MA) vs. rest, respectively. The proposed method is also validated on an open-access database of 17 subjects, containing right-hand finger tapping (RFT), left-hand finger tapping (LFT), and dominant side foot tapping (FT) tasks.The study shows an enhanced performance of the z-score method over the t-value method as an advancement in efforts to improve state-of-the-art fNIRS-BCI systems’ performance.
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Affiliation(s)
- Hammad Nazeer
- Department of Mechatronics Engineering, Air University, Islamabad 44000, Pakistan;
| | - Noman Naseer
- Department of Mechatronics Engineering, Air University, Islamabad 44000, Pakistan;
- Correspondence:
| | - Aakif Mehboob
- School of Mechanical and Manufacturing Engineering, National University of Science and Technology, Islamabad 44000, Pakistan; (A.M.); (M.J.K.); (Y.A.)
| | - Muhammad Jawad Khan
- School of Mechanical and Manufacturing Engineering, National University of Science and Technology, Islamabad 44000, Pakistan; (A.M.); (M.J.K.); (Y.A.)
- National Centre of Artificial Intelligence (NCAI), Islamabad 44000, Pakistan
| | - Rayyan Azam Khan
- Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK S7N5A9, Canada;
| | - Umar Shahbaz Khan
- Department of Mechatronics Engineering, National University of Sciences and Technology, H-12, Islamabad 44000, Pakistan;
- National Centre of Robotics and Automation (NCRA), Rawalpindi 46000, Pakistan
| | - Yasar Ayaz
- School of Mechanical and Manufacturing Engineering, National University of Science and Technology, Islamabad 44000, Pakistan; (A.M.); (M.J.K.); (Y.A.)
- National Centre of Artificial Intelligence (NCAI), Islamabad 44000, Pakistan
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Rafiq M, Liaquat A, Saeed N, Shamshad GU, Mumtaz S, Khan MJ. Gene expression of thrombomodulin, TNF-α and NF-KB in coronary artery disease patients of Pakistan. Mol Biol Rep 2020; 47:7575-7582. [PMID: 32930934 DOI: 10.1007/s11033-020-05824-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/07/2020] [Indexed: 11/28/2022]
Abstract
Thrombomodulin (THBD) is an endothelial surface glycoprotein receptor, having a pivotal role in maintaining laminar blood flow. It functions to protect endothelial integrity by exhibiting anti-coagulation and anti-inflammatory properties thereby playing a key role in cardiovascular disease (CVD) pathology. Cholesterol lowering drugs have shown to alter the anti-inflammatory effects of cytokines. Understanding the molecular aspects of THBD gene and its relation to inflammatory cytokines is important to identify new prognostic and therapeutic targets for the CVD treatments. The present study was conducted to measure the expression of THBD, TNF-α and NF-kB genes in coronary artery disease patients (CAD) in Pakistani population. Lipid profile and BMI was compared both on fifty CAD patients and fifty healthy individuals. Expression analysis for THBD, TNF-α and NF-kB was carried out using real time PCR. The effect of lipid lowering drugs on cardiometabolic risk variables especially gene expression was analyzed. Our results indicated that the difference in BMI was marginal; however LDL-cholesterol and triglycerides levels in CAD patients were significantly higher than healthy individuals. THBD gene was significantly up-regulated whereas TNF-α and NF-kB were significantly down regulated in CAD individuals. Further exploration revealed that these variations were accounted to the use of statins by the patients. The use of statins by CAD patients up-regulated the mRNA expression of THBD by down-regulation of inflammatory mediators. The enhanced expression of endothelial THBD in response to cholesterol lowering drugs establishes a novel pleiotropic target that can be of clinical significance in thromboembolic and inflammatory disorders.
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Affiliation(s)
- Muhammad Rafiq
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, 45550, Pakistan.,Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad, 45550, Pakistan
| | - Afrose Liaquat
- Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad, 45550, Pakistan.
| | - Nadia Saeed
- Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad, 45550, Pakistan
| | | | - Sana Mumtaz
- Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad, 45550, Pakistan.,Department of Psychosomatic Medicine and Psychotherapy, University Medical Center, 37075, Gottingen, Germany
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, 45550, Pakistan.
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Khan MJ, Zahra A, Rabia G, Ali SA, Sahar S, Bibi S, Fatmi MQ. Abstract 3700: Role of salivary miRNAs and their target genes in oral cancer patients as a potential diagnostic tool. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Oral squamous cell carcinoma (OSCC) is a major cancer type worldwide, ranked in among top ten cancers. However, in South Asia, OSCC is at third position in commonly occurring cancer. Pakistan is ranked at tenth level in world but second in South Asia in OSCC. High ratio of cancer suggests that it is a major reason of death around the globe and is mainly because of the late-stage diagnosis. Metastasis of OSCC depends on many environmental and genetic factors including different genes, proteins and non-coding RNAs i.e. miRNAs. In cancer cells, miRNAs express themselves differentially. This differential expression of miRNAs in cancer cells can be explored and is worth considering as a diagnostic biomarker. On account of these facts, this study was designed to aim at detection of miRNAs and their target genes in OSCC through functional and expression analysis. We already have reported a list of miRNAs and their differentially expressed target genes in OSCC along with their functional and network analysis, in an in silico study. To evaluate the role of miRNAs and their target genes in OSCC patients of Pakistan, we measured the expression of four miRNAs; miR-300, miR-27a-3p, miR-340-5p, miR-205-3p with their corresponding target genes; ALB, CDH1, CACNA1, ARID5B, CDKN1A, BCL2, ABL1 in saliva samples of patients (n=100) and healthy controls (n=100). Total RNA was extracted from saliva samples; cDNA was synthesized and real time quantitative PCR was used to measure the expression. Preliminary results showed that miRNAs were down regulated in saliva samples of patients as compared to healthy controls. Consequently, target genes of each miRNA were dysregulated in patients. miR-300 targets CDH-1 and ALB and there was a direct relationship of miR-300 with ALB. Both of them were down regulated in OSCC patients. We found a down regulation in the expression of miRNA-27a-3p and its target genes CACNA1I and ARID5B in the saliva samples of patients when compared with the healthy controls. This suggests that there is a direct relationship between the miRNA-27a-3p and its target genes CACNA1I and ARID5B. We identified that miRNA-340-5p targets BCL2 and CDKN1A genes; miR-340-5p was down regulated by targeting both genes and also down regulated their expression, which results in OSCC. miRNA-205-3p targets ABL1 gene and there is direct relationship between the two. Both of them were down regulated in OSCC patients and change in expression leads to OSCC. The change in expression pattern of miRNAs and their target genes suggests a potential diagnostic role of these miRNAs in early detection of OSCC by saliva samples at early stages.
Citation Format: Muhammad Jawad Khan, Andleeb Zahra, Ghulam Rabia, Syeda Aba Ali, Shanza Sahar, Sobia Bibi, M. Qaiser Fatmi. Role of salivary miRNAs and their target genes in oral cancer patients as a potential diagnostic tool [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3700.
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Affiliation(s)
| | | | - Ghulam Rabia
- COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Shanza Sahar
- COMSATS University Islamabad, Islamabad, Pakistan
| | - Sobia Bibi
- COMSATS University Islamabad, Islamabad, Pakistan
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Shabbir S, Hafeez A, Rafiq MA, Khan MJ. Estrogen shields women from COVID-19 complications by reducing ER stress. Med Hypotheses 2020; 143:110148. [PMID: 32759016 PMCID: PMC7390780 DOI: 10.1016/j.mehy.2020.110148] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/21/2020] [Accepted: 07/27/2020] [Indexed: 11/25/2022]
Abstract
Estrogen hormone acts as a potential key player in providing immunity against certain viral infection. It is found to be associated in providing immunity against acute lungs inflammation and influenza virus by modulating cytokines storm and mediating adaptive immune alterations respectively. Women are less affected by SARS-CoV-2 infection because of the possible influence of estrogen hormone as compared to men. We hypothesized that SARS-CoV-2 causes stress in endoplasmic reticulum (ER) which in turn aggravates the infection, estrogen hormone might play key role in decreasing ER stress by activating estrogen mediated signaling pathways, results in unfolded protein response (UPR). Estrogen governs degradation of phosphotidylinositol 4,5-bisphosphate (PIP2) into diacylglycerol (DAG) and inositol triphosphate (IP3) with the help of phospholipase C. IP3 start in-fluxing Ca+2 ions that helps in UPR activation. To support our hypothesis, we analyzed the data of 162,392 COVID-19 patients to determine the relation of this disease with gender. We observed that 26% of women and 74% of men were affected by SARS-CoV-2. It indicated that women are less affected because of the possible influence of estrogen hormone in women.
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Asgher U, Khalil K, Khan MJ, Ahmad R, Butt SI, Ayaz Y, Naseer N, Nazir S. Enhanced Accuracy for Multiclass Mental Workload Detection Using Long Short-Term Memory for Brain-Computer Interface. Front Neurosci 2020; 14:584. [PMID: 32655353 PMCID: PMC7324788 DOI: 10.3389/fnins.2020.00584] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 05/12/2020] [Indexed: 11/30/2022] Open
Abstract
Cognitive workload is one of the widely invoked human factors in the areas of human-machine interaction (HMI) and neuroergonomics. The precise assessment of cognitive and mental workload (MWL) is vital and requires accurate neuroimaging to monitor and evaluate the cognitive states of the brain. In this study, we have decoded four classes of MWL using long short-term memory (LSTM) with 89.31% average accuracy for brain-computer interface (BCI). The brain activity signals are acquired using functional near-infrared spectroscopy (fNIRS) from the prefrontal cortex (PFC) region of the brain. We performed a supervised MWL experimentation with four varying MWL levels on 15 participants (both male and female) and 10 trials of each MWL per participant. Real-time four-level MWL states are assessed using fNIRS system, and initial classification is performed using three strong machine learning (ML) techniques, support vector machine (SVM), k-nearest neighbor (k-NN), and artificial neural network (ANN) with obtained average accuracies of 54.33, 54.31, and 69.36%, respectively. In this study, novel deep learning (DL) frameworks are proposed, which utilizes convolutional neural network (CNN) and LSTM with 87.45 and 89.31% average accuracies, respectively, to solve high-dimensional four-level cognitive states classification problem. Statistical analysis, t-test, and one-way F-test (ANOVA) are also performed on accuracies obtained through ML and DL algorithms. Results show that the proposed DL (LSTM and CNN) algorithms significantly improve classification performance as compared with ML (SVM, ANN, and k-NN) algorithms.
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Affiliation(s)
- Umer Asgher
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Khurram Khalil
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Jawad Khan
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Riaz Ahmad
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Directorate of Quality Assurance and International Collaboration, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Shahid Ikramullah Butt
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Yasar Ayaz
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- National Center of Artificial Intelligence (NCAI) – NUST, Islamabad, Pakistan
| | - Noman Naseer
- Department of Mechatronics Engineering, Air University, Islamabad, Pakistan
| | - Salman Nazir
- Training and Assessment Research Group, Department of Maritime Operations, University of South-Eastern Norway, Kongsberg, Norway
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Muther T, Khan MJ, Chachar MH, Aziz H. A Study on designing appropriate hydraulic fracturing treatment with proper material selection and optimized fracture half-length in tight multilayered formation sequence. SN Appl Sci 2020. [DOI: 10.1007/s42452-020-2729-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Ullah A, Pirzada M, Jahan S, Ullah H, Razak S, Rauf N, Khan MJ, Mahboob SZ. Prenatal BPA and its analogs BPB, BPF, and BPS exposure and reproductive axis function in the male offspring of Sprague Dawley rats. Hum Exp Toxicol 2020; 38:1344-1365. [PMID: 31514588 DOI: 10.1177/0960327119862335] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Research in the past has indicated associated long-term and low levels of exposure of bisphenol A (BPA) in early life and neuroendocrine disorders, such as obesity, precocious puberty, diabetes, and hypertension. BPA and its analogs bisphenol B (BPB), bisphenol F (BPF), and bisphenol S (BPS) have been reported to have similar or even more toxic effect as compared to BPA. Exposure of rats to BPA and its analogs BPB, BPF, and BPS resulted in decreased sperm production, testosterone secretion, and histological changes in the reproductive tissues of male rats. In the present study, BPA, BPB, BPF, and BPS were administered in drinking water at concentrations of (5, 25, and 50 μg/L) from pregnancy day (PD) 1 to PD 21. Body weight (BW), hormonal concentrations, antioxidant enzymes, and histological changes were determined in the reproductive tissues. BPA and its analogs prenatal exposure to female rats induced significant statistical difference in the antioxidant enzymes, plasma testosterone, and estrogen concentrations in the male offspring when compared with the control. Histological parameters of both testis and epididymis revealed prominent changes in the reproductive tissues. The present study suggests that BPA and its analogs BPB, BPF, and BPS different concentrations led to marked alterations in the development of the male reproductive system.
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Affiliation(s)
- A Ullah
- Reproductive Physiology Laboratory, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - M Pirzada
- Reproductive Physiology Laboratory, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - S Jahan
- Reproductive Physiology Laboratory, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - H Ullah
- Reproductive Physiology Laboratory, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - S Razak
- Reproductive Physiology Laboratory, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - N Rauf
- Reproductive Physiology Laboratory, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - M J Khan
- Reproductive Physiology Laboratory, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - S Z Mahboob
- Reproductive Physiology Laboratory, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Shahzad W, Ayaz Y, Khan MJ, Naseer N, Khan M. Enhanced Performance for Multi-Forearm Movement Decoding Using Hybrid IMU-sEMG Interface. Front Neurorobot 2019; 13:43. [PMID: 31333441 PMCID: PMC6617522 DOI: 10.3389/fnbot.2019.00043] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 06/03/2019] [Indexed: 12/04/2022] Open
Abstract
Control of active prosthetic hands using surface electromyography (sEMG) signals is an active research area; despite the advances in sEMG pattern recognition and classification techniques, none of the commercially available prosthetic hands provide the user with an intuitive control. One of the major reasons for this disparity between academia and industry is the variation of sEMG signals in a dynamic environment as opposed to the controlled laboratory conditions. This research investigated the effects of sEMG signal variation on the performance of a hand motion classifier due to arm position variation and also explored the effect of static position and dynamic movement strategies for classifier training. A wearable system is used to measure the electrical activity of the muscles and the position of the forearm while performing six classes of hand motions. The system is made position aware (POS) using inertial measurement units (IMUs) for different arm movement gestures. The hand gestures are decoded under both static and dynamic forearm movements. Four time domain (TD) features are extracted from the sEMG signals along with IMU-based arm position information. The features are trained and tested using linear discriminant analysis (LDA) and support vector machine (SVM) for both TD and TD-POS features. The results for the SVM show a significant difference between the static and dynamic approaches, while the TD-POS features show enhanced classification performance in comparison to the TD-based classification. Results have shown the effectiveness of the dynamic training approach and sensor fusion techniques to improve the performance of existing stand-alone sEMG-based prosthetic control systems.
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Affiliation(s)
- Waseem Shahzad
- Department of Robotics and Intelligent Machine Engineering, School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Yasar Ayaz
- Department of Robotics and Intelligent Machine Engineering, School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan.,National Center of Artificial Intelligence, Islamabad, Pakistan
| | - Muhammad Jawad Khan
- Department of Robotics and Intelligent Machine Engineering, School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Noman Naseer
- Department of Mechatronics Engineering, Air University, Islamabad, Pakistan
| | - Mushtaq Khan
- Department of Robotics and Intelligent Machine Engineering, School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
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Zielen AC, Khan MJ, Pollock N, Jiang H, Ahmed J, Nazli R, Jabeen M, Yatsenko A, Rajkovic A. A novel homozygous frame-shift variant in the LHCGR gene is associated with primary ovarian insufficiency in a Pakistani family. Clin Genet 2018; 94:396-397. [PMID: 30016538 DOI: 10.1111/cge.13406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/07/2018] [Accepted: 06/12/2018] [Indexed: 11/29/2022]
Affiliation(s)
- A C Zielen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Women's Research Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - M J Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - N Pollock
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Women's Research Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - H Jiang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Women's Research Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - J Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - R Nazli
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - M Jabeen
- Khyber Medical University, Institute of Medical Sciences, Kohat, Pakistan
| | - A Yatsenko
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Women's Research Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - A Rajkovic
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Women's Research Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
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Khan MJ, Gerasimidis K, Edwards CA, Shaikh MG. Mechanisms of obesity in Prader-Willi syndrome. Pediatr Obes 2018; 13:3-13. [PMID: 27863129 DOI: 10.1111/ijpo.12177] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/12/2016] [Accepted: 07/18/2016] [Indexed: 11/27/2022]
Abstract
Obesity is the most common cause of metabolic complications and poor quality of life in Prader-Willi syndrome (PWS). Hyperphagia and obesity develop after an initial phase of poor feeding and failure to thrive. Several mechanisms for the aetiology of obesity in PWS are proposed, which include disruption in hypothalamic pathways of satiety control resulting in hyperphagia, aberration in hormones regulating food intake, reduced energy expenditure because of hypotonia and altered behaviour with features of autism spectrum disorder. Profound muscular hypotonia prevents PWS patients from becoming physically active, causing reduced muscle movements and hence reduced energy expenditure. In a quest for the aetiology of obesity, recent evidence has focused on several appetite-regulating hormones, growth hormone, thyroid hormones and plasma adipocytokines. However, despite advancement in understanding of the genetic basis of PWS, there are contradictory data on the role of satiety hormones in hyperphagia and data regarding dietary intake are limited. Mechanistic studies on the aetiology of obesity and its relationship with disease pathogenesis in PWS are required. . In this review, we focused on the available evidence regarding mechanisms of obesity and potential new areas that could be explored to help unravel obesity pathogenesis in PWS.
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Affiliation(s)
- M J Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan.,Human Nutrition, School of Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - K Gerasimidis
- Human Nutrition, School of Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - C A Edwards
- Human Nutrition, School of Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - M G Shaikh
- Department of Endocrinology, Royal Hospital for Children, Glasgow, UK
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Hong KS, Khan MJ. Hybrid Brain-Computer Interface Techniques for Improved Classification Accuracy and Increased Number of Commands: A Review. Front Neurorobot 2017; 11:35. [PMID: 28790910 PMCID: PMC5522881 DOI: 10.3389/fnbot.2017.00035] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/03/2017] [Indexed: 12/11/2022] Open
Abstract
In this article, non-invasive hybrid brain-computer interface (hBCI) technologies for improving classification accuracy and increasing the number of commands are reviewed. Hybridization combining more than two modalities is a new trend in brain imaging and prosthesis control. Electroencephalography (EEG), due to its easy use and fast temporal resolution, is most widely utilized in combination with other brain/non-brain signal acquisition modalities, for instance, functional near infrared spectroscopy (fNIRS), electromyography (EMG), electrooculography (EOG), and eye tracker. Three main purposes of hybridization are to increase the number of control commands, improve classification accuracy and reduce the signal detection time. Currently, such combinations of EEG + fNIRS and EEG + EOG are most commonly employed. Four principal components (i.e., hardware, paradigm, classifiers, and features) relevant to accuracy improvement are discussed. In the case of brain signals, motor imagination/movement tasks are combined with cognitive tasks to increase active brain-computer interface (BCI) accuracy. Active and reactive tasks sometimes are combined: motor imagination with steady-state evoked visual potentials (SSVEP) and motor imagination with P300. In the case of reactive tasks, SSVEP is most widely combined with P300 to increase the number of commands. Passive BCIs, however, are rare. After discussing the hardware and strategies involved in the development of hBCI, the second part examines the approaches used to increase the number of control commands and to enhance classification accuracy. The future prospects and the extension of hBCI in real-time applications for daily life scenarios are provided.
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Affiliation(s)
- Keum-Shik Hong
- School of Mechanical Engineering, Pusan National University, Busan, South Korea.,Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, South Korea
| | - Muhammad Jawad Khan
- School of Mechanical Engineering, Pusan National University, Busan, South Korea
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Agrawal A, Khan MJ, Graugnard DE, Vailati-Riboni M, Rodriguez-Zas SL, Osorio JS, Loor JJ. Prepartal Energy Intake Alters Blood Polymorphonuclear Leukocyte Transcriptome During the Peripartal Period in Holstein Cows. Bioinform Biol Insights 2017; 11:1177932217704667. [PMID: 28579762 PMCID: PMC5414586 DOI: 10.1177/1177932217704667] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/13/2017] [Indexed: 12/18/2022] Open
Abstract
In the dairy industry, cow health and farmer profits depend on the balance between diet (ie, nutrient composition, daily intake) and metabolism. This is especially true during the transition period, where dramatic physiological changes foster vulnerability to immunosuppression, negative energy balance, and clinical and subclinical disorders. Using an Agilent microarray platform, this study examined changes in the transcriptome of bovine polymorphonuclear leukocytes (PMNLs) due to prepartal dietary intake. Holstein cows were fed a high-straw, control-energy diet (CON; NEL = 1.34 Mcal/kg) or overfed a moderate-energy diet (OVE; NEL = 1.62 Mcal/kg) during the dry period. Blood for PMNL isolation and metabolite analysis was collected at −14 and +7 days relative to parturition. At an analysis of variance false discovery rate <0.05, energy intake (OVE vs CON) influenced 1806 genes. Dynamic Impact Approach bioinformatics analysis classified treatment effects on Kyoto Encyclopedia of Genes and Genomes pathways, including activated oxidative phosphorylation and biosynthesis of unsaturated fatty acids and inhibited RNA polymerase, proteasome, and toll-like receptor signaling pathway. This analysis indicates that processes critical for energy metabolism and cellular and immune function were affected with mixed results. However, overall interpretation of the transcriptome data agreed in part with literature documenting a potentially detrimental, chronic activation of PMNL in response to overfeeding. The widespread, transcriptome-level changes captured here confirm the importance of dietary energy adjustments around calving on the immune system.
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Affiliation(s)
- A Agrawal
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - M J Khan
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - D E Graugnard
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - M Vailati-Riboni
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - S L Rodriguez-Zas
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - J S Osorio
- Department of Dairy Science, South Dakota State University, Brookings, SD, USA
| | - J J Loor
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Abstract
In this paper, a hybrid electroencephalography–functional near-infrared spectroscopy (EEG–fNIRS) scheme to decode eight active brain commands from the frontal brain region for brain–computer interface is presented. A total of eight commands are decoded by fNIRS, as positioned on the prefrontal cortex, and by EEG, around the frontal, parietal, and visual cortices. Mental arithmetic, mental counting, mental rotation, and word formation tasks are decoded with fNIRS, in which the selected features for classification and command generation are the peak, minimum, and mean ΔHbO values within a 2-s moving window. In the case of EEG, two eyeblinks, three eyeblinks, and eye movement in the up/down and left/right directions are used for four-command generation. The features in this case are the number of peaks and the mean of the EEG signal during 1 s window. We tested the generated commands on a quadcopter in an open space. An average accuracy of 75.6% was achieved with fNIRS for four-command decoding and 86% with EEG for another four-command decoding. The testing results show the possibility of controlling a quadcopter online and in real-time using eight commands from the prefrontal and frontal cortices via the proposed hybrid EEG–fNIRS interface.
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Affiliation(s)
- Muhammad Jawad Khan
- School of Mechanical Engineering, Pusan National University , Busan , South Korea
| | - Keum-Shik Hong
- School of Mechanical Engineering, Pusan National University, Busan, South Korea; Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, South Korea
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Abstract
Cancer is a dreadful disease constituting abnormal growth and proliferation of malignant cells in the body. Next to lung cancer, breast cancer is the most common form of cancer affecting women. The apoptotic pathway regulators, B cell lymphoma family of protein, play a key role in various malignancies defining cancer and their constitutive expression plays an integral role in breast cancer chemotherapy. The research work discusses the identification and molecular cloning of a B cell lymphoma like gene from human breast cancer cell line. The open reading frame of the gene consisted of 965 nucleotides, encoding a protein of 380 amino acids with a predicted molecular weight of 42.5 kilodalton. The predicted physiochemical properties of the gene were as follows: Isoelectric point - 9.49, molecular formula - C1893H3004N534O548S16, total number of negatively charged residues, (Aspartate+Glutamate) - 26, total number of positively charged residues, (Arginine+Lysine)-39, instability index-42.08 (unstable protein) and grand average of hydropathicity is -0.202. Additionally, phobius prediction suggested non-cytoplasmic localization of the putative protein. The presence of secondary structure in the protein was determined by Memsat program. A 3 dimensional protein homology model was generated using threading based method of protein modeling for structural and functional annotation of the putative protein. Future prospects accounts for the biochemical characterization of the enzyme including in vitro assays on breast cancer cell line would establish the functional characteristics of the protein and its physiological mechanisms in breast cancer development and its therapeutic-target role in future.
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Affiliation(s)
- Pragya Tiwari
- Department of Metabolic and Structural Biology, Central Institute of Medicinal and Aromatic Plants, (CSIR-CIMAP), Lucknow-226 015, India
| | - M J Khan
- Department of Biochemistry, Aligarh Muslim University, Aligarh-202 002, India
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Khan MJ, Giasuddin ASM, Khalil MI. Risk Factors of Tendo-Achilles Injury in Football, Cricket and Badminton Players at Dhaka, Bangladesh. ACTA ACUST UNITED AC 2016; 41:19-23. [PMID: 27089630 DOI: 10.3329/bmrcb.v41i1.30228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Achilles tendon is the tendon connecting the heel with the calf muscles. Tendo-achilles injury (TAI) in players is common in games. The frequency of TAI is unknown and aetiology is controversial: The present descriptive cross-sectional study was done to determine the prevalence of TAI and associated factors contributing to it in football, cricket and badminton. From January to June 2012, male players (n = 131), age -17-35 years, were selected by purposive sampling technique from renowned sporting clubs at Dhaka, Bangladesh. TAI was diagnosed through structured questionnaire and interviewing the respondents. The analysis by Statistical Package for Social Sciences (SPSS) programme revealed that 11.5% players suffered from TAI, i.e. prevalence was 115 per 1000 respondents. Most injuries (70/131; 53.4%) occurred in the playground and (59/131; 45.3%) happened in practice field. Injuries among the players of third division were higher, i.e. about 36% (p = 0.000). TAI was significantly dependent on occupation (p = 0.046), BMI (p = 0.008), divisional status (p = 0.023), game type (p = 0.043), ground condition (p = 0.05) and injury severity (p = 0.000). The injured players referred for treatment to the physiotherapist was highest (9/15, i.e. 60%) followed by the physicians (5/15, i.e. 33%) (p = 0.000). The associations of TAI with various factors were discussed suggesting effective measures be taken and treatment, particularly physiotherapy, be given to injured players. However, there is a need of team work with sports medicine specialist also to enable the injured players to continue their professional games.
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