8,851 results on '"Farzan, M."'
Search Results
2. Correction: Tickner, Z.J.; Farzan, M. Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors. Pharmaceuticals 2021, 14, 554
- Author
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Zachary J. Tickner and Michael Farzan
- Subjects
RS1-441 ,n/a ,Pharmacy and materia medica ,Drug Discovery ,Medicine ,Pharmaceutical Science ,Molecular Medicine ,Correction - Abstract
Vectors developed from adeno-associated virus (AAV) are powerful tools for in vivo transgene delivery in both humans and animal models, and several AAV-delivered gene therapies are currently approved for clinical use. However, AAV-mediated gene therapy still faces several challenges, including limited vector packaging capacity and the need for a safe, effective method for controlling transgene expression during and after delivery. Riboswitches, RNA elements which control gene expression in response to ligand binding, are attractive candidates for regulating expression of AAV-delivered transgene therapeutics because of their small genomic footprints and non-immunogenicity compared to protein-based expression control systems. In addition, the ligand-sensing aptamer domains of many riboswitches can be exchanged in a modular fashion to allow regulation by a variety of small molecules, proteins, and oligonucleotides. Riboswitches have been used to regulate AAV-delivered transgene therapeutics in animal models, and recently developed screening and selection methods allow rapid isolation of riboswitches with novel ligands and improved performance in mammalian cells. This review discusses the advantages of riboswitches in the context of AAV-delivered gene therapy, the subsets of riboswitch mechanisms which have been shown to function in human cells and animal models, recent progress in riboswitch isolation and optimization, and several examples of AAV-delivered therapeutic systems which might be improved by riboswitch regulation.
- Published
- 2021
3. Enhancing human activity recognition for the elderly and individuals with disabilities through optimized Internet-of-Things and artificial intelligence integration with advanced neural networks
- Author
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R. Deeptha, K. Ramkumar, Sri Venkateswaran, Mohammad Mehedi Hassan, Md. Rafiul Hassan, Farzan M. Noori, and Md. Zia Uddin
- Subjects
human activity recognition ,Internet of Things ,artificial intelligence ,gated recurrent networks ,deep extreme feedforward neural networks ,artificial water drop optimization ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Elderly and individuals with disabilities can greatly benefit from human activity recognition (HAR) systems, which have recently advanced significantly due to the integration of the Internet of Things (IoT) and artificial intelligence (AI). The blending of IoT and AI methodologies into HAR systems has the potential to enable these populations to lead more autonomous and comfortable lives. HAR systems are equipped with various sensors, including motion capture sensors, microcontrollers, and transceivers, which supply data to assorted AI and machine learning (ML) algorithms for subsequent analyses. Despite the substantial advantages of this integration, current frameworks encounter significant challenges related to computational overhead, which arises from the complexity of AI and ML algorithms. This article introduces a novel ensemble of gated recurrent networks (GRN) and deep extreme feedforward neural networks (DEFNN), with hyperparameters optimized through the artificial water drop optimization (AWDO) algorithm. This framework leverages GRN for effective feature extraction, subsequently utilized by DEFNN for accurately classifying HAR data. Additionally, AWDO is employed within DEFNN to adjust hyperparameters, thereby mitigating computational overhead and enhancing detection efficiency. Extensive experiments were conducted to verify the proposed methodology using real-time datasets gathered from IoT testbeds, which employ NodeMCU units interfaced with Wi-Fi transceivers. The framework's efficiency was assessed using several metrics: accuracy at 99.5%, precision at 98%, recall at 97%, specificity at 98%, and F1-score of 98.2%. These results then were benchmarked against other contemporary deep learning (DL)-based HAR systems. The experimental outcomes indicate that our model achieves near-perfect accuracy, surpassing alternative learning-based HAR systems. Moreover, our model demonstrates reduced computational demands compared to preceding algorithms, suggesting that the proposed framework may offer superior efficacy and compatibility for deployment in HAR systems designed for elderly or individuals with disabilities.
- Published
- 2024
- Full Text
- View/download PDF
4. SwAV-driven diagnostics: new perspectives on grading diabetic retinopathy from retinal photography
- Author
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Md Nuho Ul Alam, Erfanul Hoque Bahadur, Abdul Kadar Muhammad Masum, Farzan M. Noori, and Md Zia Uddin
- Subjects
diabetic retinopathy ,contrasting clustering ,SwAV ,convolutional neural network ,ensemble learning ,transformer ,Mechanical engineering and machinery ,TJ1-1570 ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
Diabetic Retinopathy (DR) is a serious eye condition that occurs due to high blood sugar levels in patients with Diabetes Mellitus. If left untreated, DR can potentially result in blindness. Using automated neural network-based methods to grade DR shows potential for early detection. However, the uneven and non-quadrilateral forms of DR lesions provide difficulties for traditional Convolutional Neural Network (CNN)-based architectures. To address this challenge and explore a novel algorithm architecture, this work delves into the usage of contrasting cluster assignments in retinal fundus images with the Swapping Assignments between multiple Views (SwAV) algorithm for DR grading. An ablation study was made where SwAV outperformed other CNN and Transformer-based models, independently and in ensemble configurations with an accuracy of 87.00% despite having fewer parameters and layers. The proposed approach outperforms existing state-of-the-art models regarding classification metrics, complexity, and prediction time. The findings offer great potential for medical practitioners, allowing for more accurate diagnosis of DR and earlier treatments to avoid visual loss.
- Published
- 2024
- Full Text
- View/download PDF
5. Enhancing ECU identification security in CAN networks using distortion modeling and neural networks
- Author
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Azeem Hafeez, Hafiz Malik, Aun Irtaza, Md Zia Uddin, and Farzan M. Noori
- Subjects
intrusion detection system ,electronic control unit (ECU) ,controller area network (CAN) ,machine learning ,artificial neural network (ANN) ,digital-to-analog converter (DAC) ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
A novel technique for electronic control unit (ECU) identification is proposed in this study to address security vulnerabilities of the controller area network (CAN) protocol. The reliable ECU identification has the potential to prevent spoofing attacks launched over the CAN due to the lack of message authentication. In this regard, we model the ECU-specific random distortion caused by the imperfections in the digital-to-analog converter and semiconductor impurities in the transmitting ECU for fingerprinting. Afterward, a 4-layered artificial neural network (ANN) is trained on the feature set to identify the transmitting ECU and the corresponding ECU pin. The ECU-pin identification is also a novel contribution of this study and can be used to prevent voltage-based attacks. We have evaluated our method using ANNs over a dataset generated from 7 ECUs with 6 pins, each having 185 records, and 40 records for each pin. The performance evaluation against state-of-the-art methods revealed that the proposed method achieved 99.4% accuracy for ECU identification and 96.7% accuracy for pin identification, which signifies the reliability of the proposed approach.
- Published
- 2024
- Full Text
- View/download PDF
6. In vivo affinity maturation of the CD4 domains of an HIV-1-entry inhibitor.
- Author
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Pan A, Bailey CC, Ou T, Xu J, Aristotelous T, Liu X, Hu B, Crynen G, Skamangas N, Bronkema N, Tran MH, Mou H, Zhang X, Alpert MD, Yin Y, Farzan M, and He W
- Subjects
- Animals, Humans, Mice, B-Lymphocytes immunology, Protein Domains, Virus Internalization drug effects, HIV-1 immunology, CD4 Antigens metabolism
- Abstract
Human proteins repurposed as biologics for clinical use have been engineered through in vitro techniques that improve the affinity of the biologics for their ligands. However, the techniques do not select against properties, such as protease sensitivity or self-reactivity, that impair the biologics' clinical efficacy. Here we show that the B-cell receptors of primary murine B cells can be engineered to affinity mature in vivo the human CD4 domains of the HIV-1-entry inhibitor CD4 immunoadhesin (CD4-Ig). Specifically, we introduced genes encoding the CD4 domains 1 and 2 (D1D2) of a half-life-enhanced form of CD4-Ig (CD4-Ig-v0) into the heavy-chain loci of murine B cells and adoptively transferred these cells into wild-type mice. After immunization, the B cells proliferated, class switched, affinity matured and produced D1D2-presenting antibodies. Somatic hypermutations in the D1D2-encoding region of the engrafted cells improved the binding affinity of CD4-Ig-v0 for the HIV-1 envelope glycoprotein and the inhibitor's ability to neutralize a panel of HIV-1 isolates without impairing its pharmacokinetic properties. In vivo affinity maturation of non-antibody protein biologics may guide the development of more effective therapeutics., Competing Interests: Competing interests: A.P., W.H., T.O., Y.Y. and M.F. are inventors of a patent describing the in vivo affinity maturation of antibodies and biologics. C.C.B., M.D.A. and M.F. have equity stakes in Emmune, Inc., which developed CD4-Ig-v0. The other authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)
- Published
- 2024
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7. A biomimetic injectable chitosan/alginate hydrogel biocopmosites encapsulating selenium- folic acid nanoparticles for regeneration of spinal cord injury: An in vitro study.
- Author
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Farzan M, Soleimannejad M, Shariat S, Heidari Sureshjani M, Gholipour A, Ashrafi Dehkordi K, Alerasoul Dehkordi SMR, and Farzan M
- Subjects
- Animals, Biomimetic Materials chemistry, Biomimetic Materials pharmacology, Cell Proliferation drug effects, Spinal Cord Regeneration drug effects, Cell Survival drug effects, Rats, Chitosan chemistry, Alginates chemistry, Spinal Cord Injuries drug therapy, Hydrogels chemistry, Hydrogels pharmacology, Selenium chemistry, Selenium pharmacology, Folic Acid chemistry, Folic Acid pharmacology, Nanoparticles chemistry
- Abstract
Spinal cord injury (SCI) poses significant challenges to regenerative medicine due to its limited self-repair capabilities. In this study, we engineered a biomimetic injectable hydrogel using modified chitosan and alginate biopolymers encapsulating selenium-folic acid nanoparticles (Se-FA NPs) to facilitate SCI regeneration. The hydrogel exhibited a unique porous structure attributed to the incorporation of nanofiber fragments, enhancing its biocompatibility and bioactivity. Through a series of in vitro evaluations, including cell viability assays, proliferation studies, gene expression analysis, we assessed the hydrogel's cytocompatibility and its potential for supporting neural cell growth. Our results demonstrate the promising efficacy of the hydrogel in providing a conducive microenvironment for neural tissue regeneration. Moreover, the sustained release of Se-FA NPs from the hydrogel system offers neuroprotective, antioxidative, and anti-inflammatory benefits crucial for SCI therapy. Overall, our biomimetic hydrogel biocomposites hold great potential as a therapeutic strategy for promoting spinal cord regeneration, highlighting their significance in advancing the field of regenerative medicine., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)
- Published
- 2025
- Full Text
- View/download PDF
8. The emerging role of the microglia triggering receptor expressed on myeloid cells (TREM) 2 in multiple sclerosis.
- Author
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Farzan M, Saberi-Rounkian M, Asadi-Rizi A, Heidari Z, Farzan M, Fathi M, Aghaei A, Azadegan-Dehkordi F, and Bagheri N
- Subjects
- Humans, Animals, Myeloid Cells metabolism, Myeloid Cells immunology, Receptors, Immunologic metabolism, Multiple Sclerosis metabolism, Multiple Sclerosis pathology, Microglia metabolism, Membrane Glycoproteins metabolism
- Abstract
Background: The chronic inflammatory condition known as multiple sclerosis (MS) causes inflammation and demyelination in the central nervous system (CNS). The activation of multiple cell types, including the CNS's resident immune cells called microglia, is a component of the immunological response in MS. Recently, the triggering receptor expressed on myeloid cells (TREM) family has emerged as a crucial player in modulating microglial function and subsequent neuroinflammation. Understanding the role of TREM receptors in MS pathogenesis could provide insightful information on how to develop new therapeutic approaches., Main Body: The TREM family consists of several receptors, including TREM-1 and TREM-2, which can be expressed on both immune cells, such as myeloid cells and microglia, and non-immune cells. These receptors interact with their respective ligands and regulate signaling pathways, ultimately leading to the control of microglial activation and inflammatory reactions. TREM-2, in particular, has garnered significant interest because of its connection with MS and other neurodegenerative diseases. The activation of microglia through TREM receptors in MS is thought to influence the equilibrium between helpful and detrimental inflammatory responses. TREM receptors can promote the phagocytosis of myelin debris and remove apoptotic cells, thus contributing to tissue repair and regeneration. However, excessive or dysregulated activation of microglia mediated by TREM receptors can lead to the release of pro-inflammatory cytokines and neurotoxic factors, exacerbating neuroinflammation and neurodegeneration in MS., Conclusion: The emerging role of the TREM family in demyelinating diseases highlights the importance of microglia in disease pathogenesis. Understanding the mechanisms by which TREM receptors modulate microglial function can provide valuable insights into the development of targeted therapies for these disorders. By selectively targeting TREM receptors, it may be possible to harness their beneficial effects on tissue repair while dampening their detrimental pro-inflammatory responses. Further research is warranted to elucidate the precise signaling pathways and ligand interactions involved in TREM-mediated microglial activation, which could uncover novel therapeutic avenues for treating MS and other neuroinflammatory disorders., Competing Interests: Declaration of competing interest The authors declare that they have no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2025
- Full Text
- View/download PDF
9. Highlights from the Tenth International Workshop on HIV Persistence during Therapy, December 13-16, 2022, Miami, Florida-USA
- Author
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Archin, N., Bar, K.J., Burdo, T., Caskey, M., Chahroudi, A., Farzan, M., Ho, Y.-C., Jones, R.B., Kearney, Mary, Kuritzkes, D., Margolis, D., Martinez-Picado, J., Okoye, A., Salgado, M., and Stevenson, Mario
- Published
- 2023
- Full Text
- View/download PDF
10. Enhancing human activity recognition for the elderly and individuals with disabilities through optimized Internet-of-Things and artificial intelligence integration with advanced neural networks.
- Author
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Deeptha, R., Ramkumar, K., Venkateswaran, Sri, Hassan, Mohammad Mehedi, Hassan, Md. Rafiul, Noori, Farzan M., and Uddin, Md. Zia
- Subjects
ARTIFICIAL intelligence ,HUMAN activity recognition ,SYSTEMS design ,FEEDFORWARD neural networks ,DEEP learning ,MOTION capture (Human mechanics) - Abstract
Elderly and individuals with disabilities can greatly benefit from human activity recognition (HAR) systems, which have recently advanced significantly due to the integration of the Internet of Things (IoT) and artificial intelligence (AI). The blending of IoT and AI methodologies into HAR systems has the potential to enable these populations to lead more autonomous and comfortable lives. HAR systems are equipped with various sensors, including motion capture sensors, microcontrollers, and transceivers, which supply data to assorted AI and machine learning (ML) algorithms for subsequent analyses. Despite the substantial advantages of this integration, current frameworks encounter significant challenges related to computational overhead, which arises from the complexity of AI and ML algorithms. This article introduces a novel ensemble of gated recurrent networks (GRN) and deep extreme feedforward neural networks (DEFNN), with hyperparameters optimized through the artificial water drop optimization (AWDO) algorithm. This framework leverages GRN for effective feature extraction, subsequently utilized by DEFNN for accurately classifying HAR data. Additionally, AWDO is employed within DEFNN to adjust hyperparameters, thereby mitigating computational overhead and enhancing detection efficiency. Extensive experiments were conducted to verify the proposed methodology using real-time datasets gathered from IoT testbeds, which employ NodeMCU units interfaced with Wi-Fi transceivers. The framework's efficiency was assessed using several metrics: accuracy at 99.5%, precision at 98%, recall at 97%, specificity at 98%, and F1-score of 98.2%. These results then were benchmarked against other contemporary deep learning (DL)-based HAR systems. The experimental outcomes indicate that our model achieves near-perfect accuracy, surpassing alternative learning-based HAR systems. Moreover, our model demonstrates reduced computational demands compared to preceding algorithms, suggesting that the proposed framework may offer superior efficacy and compatibility for deployment in HAR systems designed for elderly or individuals with disabilities. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
11. Enhancing ECU identification security in CAN networks using distortion modeling and neural networks.
- Author
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Hafeez, Azeem, Malik, Hafiz, Irtaza, Aun, Uddin, Md Zia, and Noori, Farzan M.
- Published
- 2024
- Full Text
- View/download PDF
12. Semantic Temporal Object Search System Based on Heat Maps
- Author
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Mantelli, Mathias, Noori, Farzan M., Pittol, Diego, Maffei, Renan, Torresen, Jim, and Kolberg, Mariana
- Published
- 2022
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13. Enhancing the biological characteristics of aminolysis surface-modified 3D printed nanocomposite polycaprolactone/nanohydroxyapatite scaffold via gelatin biomacromolecule immobilization: An in vitro and in vivo study.
- Author
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Farnaghi M, Poursamar SA, Farzan M, Farzan M, Kouhi M, and Rafienia M
- Subjects
- Animals, Cell Survival drug effects, Cell Adhesion drug effects, Gelatin chemistry, Durapatite chemistry, Printing, Three-Dimensional, Tissue Scaffolds chemistry, Nanocomposites chemistry, Polyesters chemistry, Surface Properties, Tissue Engineering methods
- Abstract
The surface characteristics of scaffolds utilized in bone tissue engineering profoundly influence subsequent cellular response. This study investigated the efficacy of applying a gelatin coat to the surface of aminolysis surface-modified scaffolds fabricated through 3D printing with a polycaprolactone/hydroxyapatite nanocomposite, employing the hot-melt extrusion FDM technique. Initially, aminolysis surface modification using hexamethylenediamine enhanced surface hydrophilicity by introducing amine functional groups. Subsequently, gelatin solutions were applied to the scaffolds, and crosslinking with EDC/NHS was performed to increase coating strength. Contact angle measurements revealed a significantly increased surface hydrophilicity post-aminolysis. Aminolysis facilitated uniform gelatin coating formation and distribution. Subsequently, crosslinking enhanced coating durability. The addition of gelatin coating resulted in a notable 20 % increase in scaffold mechanical strength and more than 50 % rise in Young's modulus and exhibited enhancement of biodegradability and bioactivity. Gelatin coated scaffolds also demonstrated improved cell viability and adhesion and over two times higher expression of OPN and ALP genes, suggesting improved biological properties. In addition, in vivo bone formation studies verified the biological enhancement of scaffolds. Utilizing an immobilized crosslinked gelatin biomacromolecule coating effectively enhanced the biological characteristics of 3D printed scaffolds and their potential applications as bone tissue engineering scaffolds., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025. Published by Elsevier B.V.)
- Published
- 2025
- Full Text
- View/download PDF
14. A hybrid 3D-printed and electrospun bilayer pharmaceutical membrane based on polycaprolactone/chitosan/polyvinyl alcohol for wound healing applications.
- Author
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Mehdikhani M, Yilgör P, Poursamar SA, Etemadi N, Gokyer S, Navid S, Farzan M, Farzan M, Babaei M, and Rafienia M
- Subjects
- Animals, Rats, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, Bandages, Propolis chemistry, Propolis pharmacology, Nanofibers chemistry, Membranes, Artificial, Porosity, Tensile Strength, Fibroblasts drug effects, Cell Survival drug effects, Male, Humans, Chitosan chemistry, Polyvinyl Alcohol chemistry, Wound Healing drug effects, Polyesters chemistry, Printing, Three-Dimensional
- Abstract
Skin injuries resulting from physical trauma pose significant health risks, necessitating advanced wound care solutions. This investigation introduces an innovative bilayer wound dressing composed of 3D-printed propolis-coated polycaprolactone (PCL/PP) and an electrospun composite of polyvinyl alcohol, chitosan, polycaprolactone, and diltiazem (PVA/CTS/PCL/DTZ). SEM analysis revealed a bilayer structure with 89.23 ± 51.47 % porosity and uniformly distributed nanofibers. The scaffold tensile strength, with pore sizes of 100, 300, and 500 μm, was comparable to native skin. However, smaller pore sizes reduced water vapor transmission from 4211.59 ± 168.53 to 2358.49 ± 203.63 g/m
2 . The incorporation of DTZ lowered the contact angle to 35.23 ± 3.65°, while the addition of PCL reduced the degradation rate and modulated the release of DTZ by approximately 50 %. Moreover, lower pH increased the degradation rate and decreased swelling. The inclusion of propolis enhanced antibacterial activity, and 10 % DTZ promoted the viability, proliferation, and migration of fibroblasts and adipose-derived stem cells. However, increasing DTZ concentration to 12 % reduced cell viability. In vivo tests on rats demonstrated effective wound healing and anti-inflammatory properties of the bilayer samples. Regarding the aforementioned results, the PCL/PP-PVA/CTS/PCL/DTZ (10 % w/w) bilayer wound dressing is a promising candidate for wound healing applications., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)- Published
- 2024
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15. Molteno Tube Shunt with Pericardial Patch Graft
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Gorgani, Farzan M., Freedman, Jeffrey, Rosenberg, Eric D., editor, Nattis, Alanna S., editor, and Nattis, Richard J., editor
- Published
- 2021
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16. SwAV-driven diagnostics: new perspectives on grading diabetic retinopathy from retinal photography.
- Author
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Alam, Md Nuho Ul, Bahadur, Erfanul Hoque, Masum, Abdul Kadar Muhammad, Noori, Farzan M., Uddin, Md Zia, Huang, Ruisen, and Akhter, Jamila
- Subjects
ARTIFICIAL neural networks ,MACHINE learning ,PATTERN recognition systems ,ARTIFICIAL intelligence ,CONVOLUTIONAL neural networks ,DEEP learning - Abstract
Diabetic Retinopathy (DR) is a serious eye condition that occurs due to high blood sugar levels in patients with Diabetes Mellitus. If left untreated, DR can potentially result in blindness. Using automated neural network-based methods to grade DR shows potential for early detection. However, the uneven and non-quadrilateral forms of DR lesions provide difficulties for traditional Convolutional Neural Network (CNN)-based architectures. To address this challenge and explore a novel algorithm architecture, this work delves into the usage of contrasting cluster assignments in retinal fundus images with the Swapping Assignments between multiple Views (SwAV) algorithm for DR grading. An ablation study was made where SwAV outperformed other CNN and Transformer-based models, independently and in ensemble configurations with an accuracy of 87.00% despite having fewer parameters and layers. The proposed approach outperforms existing state-of-the-art models regarding classification metrics, complexity, and prediction time. The findings offer great potential for medical practitioners, allowing for more accurate diagnosis of DR and earlier treatments to avoid visual loss. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
17. In vivo evolution of env in SHIV-AD8 EO -infected rhesus macaques after AAV-vectored delivery of eCD4-Ig.
- Author
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O'Hagan D, Shandilya S, Hopkins LJ, Hahn PA, Fuchs SP, Martinez-Navio JM, Alpert MD, Gardner MR, Desrosiers RC, Gao G, Lifson JD, Farzan M, Ardeshir A, and Martins MA
- Subjects
- Animals, Mutation, Humans, HIV-1 genetics, Evolution, Molecular, env Gene Products, Human Immunodeficiency Virus genetics, Disease Models, Animal, Antibodies, Neutralizing immunology, Macaca mulatta, Simian Immunodeficiency Virus genetics, Genetic Vectors genetics, Genetic Vectors administration & dosage, Dependovirus genetics, Simian Acquired Immunodeficiency Syndrome virology
- Abstract
eCD4-immunoglobulin (Ig) is an HIV entry inhibitor that mimics the engagement of both CD4 and CCR5 with the HIV envelope (Env) protein, a property that imbues it with remarkable potency and breadth. However, env is exceptionally genetically malleable and can evolve to escape a wide variety of entry inhibitors. Here we document the evolution of partial eCD4-Ig resistance in SHIV-AD8
EO -infected rhesus macaques (RMs) treated with adeno-associated virus vectors encoding eCD4-Ig. In one RM, setpoint viremia plateaued at 1,000 vRNA copies/mL, despite concomitant serum concentrations of eCD4-Ig in the 60-110 μg/mL range, implying that the virus had gained partial eCD4-Ig resistance. Env mutations occurring prominently in this animal were cloned and further characterized. Three of these mutations (R315G, A436T, and G471E) were sufficient to confer substantial resistance to eCD4-Ig-mediated neutralization onto the parental Env, accompanied by a marked loss of viral fitness. This resistance was not driven by decreased CD4 affinity, subverted sulfopeptide mimicry, changes to co-receptor tropism, or by a gain of CD4 independence. Rather, our data argue that the Env evolving in this animal attained eCD4-Ig resistance by decreasing triggerability, stabilizing the triggered state, and changing the nature of its relationship to the host CD4., Competing Interests: Declaration of interests M.A.M., M.D.A., M.R.G., and M.F. have significant financial interests in Emmune, Inc., a company that is developing HIV immunotherapies based on the immunoadhesin eCD4-Ig, and each serve in a consulting capacity for the company. These potential conflicts of interest are being managed by the authors’ respective institutions. None of the other authors or their immediate family members have any conflicts of interest to declare., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2025
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18. Investigating the Safety of Fampridine in Patients with Different Stages of Multiple Sclerosis.
- Author
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Vaheb S, Farzan M, Afshari-Safavi A, Ebrahimi N, Shaygannejad V, and Mirmosayyeb O
- Abstract
Background: Fampridine is the only drug approved by the US Food and Drug Administration (FDA) for people with multiple sclerosis (MS) to improve their movement and has exhibited a clinically significant improvement in gait function in a subset of MS patients with Expanded Disability Status Scale (ESDSS) from 4 to 7. Nevertheless, this drug has been reported to possess some adverse effects (AEs) like seizure because of its pharmacological features. The aim of this study was to evaluate the incidence rate of post-medication side effects (SEs) of fampridine in MS patients., Methods: This prospective cohort study includes MS patients aged between 18 and 65 years, referred to the neurology clinic of Kashani Hospital from April 2022 to October 2022, all with administration of fampridine (10 mg tablet twice daily according to the product specifications). Safety in these patients was monitored through monthly SEs checklist questions during 6 months of screening. SPSS version 18 was used to analyze the data of this study., Results: From 319 participants screened at baseline, 254 patients with MS, including 127 relapsing-remitting multiple sclerosis (RRMS), 101 secondary progressive multiple sclerosis (SPMS), and 26 primary progressive multiple sclerosis (PPMS), were included in the study. The most observed AEs in SPMS and RRMS patients were dry mouth (13.9% vs. 15%) and insomnia (12.9% vs. 11%), respectively. Urinary tract infection (UTI) (11.5%) and stomachache (11.5%) were the most common SEs in PPMS patients. The most severe complication of the patients was back pain, while digestive complications were less severe. Also, insomnia and UTI were the patients' most persistent SEs., Conclusions: The drug seems to be safe and well tolerated, as the SEs were mild and transient and they were consistent with most of the previous studies focusing on this medication., Competing Interests: There are no conflicts of interest., (Copyright: © 2025 International Journal of Preventive Medicine.)
- Published
- 2025
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19. Towards adaptive technology in routine mental health care
- Author
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Yngve Lamo, Suresh K Mukhiya, Fazle Rabbi, Amin Aminifar, Svein I Lillehaug, Jim Tørresen, Minh H Pham, Ulysse Côtè-Allard, Farzan M Noori, Frode Guribye, Yavuz Inal, Eivind Flobakk, Jo D Wake, Sunniva Myklebost, Astri J Lundervold, Aasa Hammar, Emilie Nordby, Smiti Kahlon, Robin Kenter, Ragnhild JT Sekse, Kristine F Griffin, Petter Jakobsen, Ketil Joachim Ødegaard, Yngvar S Skar, and Tine Nordgreen
- Subjects
Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
This paper summarizes the information technology-related research findings after 5 years with the INTROducing Mental health through Adaptive Technology project. The aim was to improve mental healthcare by introducing new technologies for adaptive interventions in mental healthcare through interdisciplinary research and development. We focus on the challenges related to internet-delivered psychological treatments, emphasising artificial intelligence, human-computer interaction, and software engineering. We present the main research findings, the developed artefacts, and lessons learned from the project before outlining directions for future research. The main findings from this project are encapsulated in a reference architecture that is used for establishing an infrastructure for adaptive internet-delivered psychological treatment systems in clinical contexts. The infrastructure is developed by introducing an interdisciplinary design and development process inspired by domain-driven design, user-centred design, and the person based approach for intervention design. The process aligns the software development with the intervention design and illustrates their mutual dependencies. Finally, we present software artefacts produced within the project and discuss how they are related to the proposed reference architecture. Our results indicate that the proposed development process, the reference architecture and the produced software can be practical means of designing adaptive mental health care treatments in correspondence with the patients’ needs and preferences. In summary, we have created the initial version of an information technology infrastructure to support the development and deployment of Internet-delivered mental health interventions with inherent support for data sharing, data analysis, reusability of treatment content, and adaptation of intervention based on user needs and preferences.
- Published
- 2022
- Full Text
- View/download PDF
20. Pharmacological Activities and Molecular Mechanisms of Sinapic Acid in Neurological Disorders.
- Author
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Farzan M, Abedi B, Bhia I, Madanipour A, Farzan M, Bhia M, Aghaei A, Kheirollahi I, Motallebi M, Amini-Khoei H, and Ertas YN
- Subjects
- Humans, Animals, Nervous System Diseases drug therapy, Nervous System Diseases metabolism, Oxidative Stress drug effects, Antioxidants pharmacology, Coumaric Acids pharmacology, Neuroprotective Agents pharmacology
- Abstract
Sinapic acid (SA) is a phenylpropanoid derivative found in various natural sources that exhibits remarkable versatile properties, including antioxidant, anti-inflammatory, and metal-chelating capabilities, establishing itself as a promising candidate for the prevention and treatment of conditions affecting the central nervous system, such as Alzheimer's disease (AD), Parkinson's disease (PD), ischemic stroke, and other neurological disorders. These effects also include neuroprotection in epilepsy models, as evidenced by a reduction in seizure-like behavior, cell death in specific hippocampal regions, and lowered neuroinflammatory markers. In AD, SA treatment enhances memory, reverses cognitive deficits, and attenuates astrocyte activation. SA also has positive effects on cognition by improving memory and lowering oxidative stress. This is shown by lower levels of oxidative stress markers, higher levels of antioxidant enzyme activity, and better memory retention. Additionally, in ischemic stroke and PD models, SA provides microglial protection and exerts anti-inflammatory effects. This review emphasizes SA's multifaceted neuroprotective properties and its potential role in the prevention and treatment of various brain disorders. Despite the need for further research to fully understand its mechanisms of action and clinical applicability, SA stands out as a valuable bioactive compound in the ongoing quest to combat neurodegenerative diseases and enhance the quality of life for affected individuals.
- Published
- 2024
- Full Text
- View/download PDF
21. Ultra-Wideband Radar-Based Activity Recognition Using Deep Learning
- Author
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Farzan M. Noori, Md. Zia Uddin, and Jim Torresen
- Subjects
Human activity recognition ,LSTM ,LDA ,PCA ,XeThru UWB sensor ,Electrical engineering. Electronics. Nuclear engineering ,TK1-9971 - Abstract
With recent advances in the field of sensing, it has become possible to build better assistive technologies. This enables the strengthening of eldercare with regard to daily routines and the provision of personalised care to users. For instance, it is possible to detect a person’s behaviour based on wearable or ambient sensors; however, it is difficult for users to wear devices 24/7, as they would have to be recharged regularly because of their energy consumption. Similarly, although cameras have been widely used as ambient sensors, they carry the risk of breaching users’ privacy. This paper presents a novel sensing approach based on deep learning for human activity recognition using a non-wearable ultra-wideband (UWB) radar sensor. UWB sensors protect privacy better than RGB cameras because they do not collect visual data. In this study, UWB sensors were mounted on a mobile robot to monitor and observe subjects from a specific distance (namely, 1.5–2.0 m). Initially, data were collected in a lab environment for five different human activities. Subsequently, the data were used to train a model using the state-of-the-art deep learning approach, namely long short-term memory (LSTM). Conventional training approaches were also tested to validate the superiority of LSTM. As a UWB sensor collects many data points in a single frame, enhanced discriminant analysis was used to reduce the dimensions of the features through application of principal component analysis to the raw dataset, followed by linear discriminant analysis. The enhanced discriminant features were fed into the LSTMs. Finally, the trained model was tested using new inputs. The proposed LSTM-based activity recognition approach performed better than conventional approaches, with an accuracy of 99.6%. We applied 5-fold cross-validation to test our approach. We also validated our approach on publically available dataset. The proposed method can be applied in many prominent fields, including human–robot interaction for various practical applications, such as mobile robots for eldercare.
- Published
- 2021
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22. Neurotrophic corneal ulcer and iridocyclitis directly preceding Ramsay-Hunt Syndrome
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Farzan M. Gorgani, MS, DO. and Todd L. Beyer, DO, FAAO, FASOPRS.
- Subjects
Ramsay-Hunt ,Neurotrophic ,Zoster ,Facial palsy ,Keratitis ,Iridocyclitis ,Ophthalmology ,RE1-994 - Abstract
Purpose: To present to and inform the practitioner of an unusual presentation of Varicella zoster virus and Ramsay-Hunt Syndrome. Observations: A 69-year-old bedbound male with vascular dementia presented to the emergency room with a red right eye with associated tearing and mucus production. The patient could not express if he was in pain. The initial diagnosis from the emergency room was bacterial keratitis, confirmed with a positive pseudomonas culture. However, upon examination by the ophthalmologist it was noted that there was not only a large, infected epithelial defect, but also an intraocular pressure of 35 and a candy-cane hypopyon. The diagnosis of herpes neurotrophic keratitis and iridocyclitis was made and the patient was started on intravenous acyclovir along with the appropriate topical medications. A day later, it was noted that the patient developed a right sided facial palsy and vesicular lesions inside the right ear canal, as confirmed by otolaryngology. Conclusion and Importance: Ramsay-Hunt Syndrome is usually known to the ophthalmologist due to the exposure keratopathy caused by facial palsy. This case demonstrates varicella-zoster virus (VZV) neurotrophic keratitis preceding the development of facial palsy, which can further exacerbate an already neurotrophic cornea. The practitioner should be aware of these signs and symptoms and adjust their treatment with systemic acyclovir-prednisone.
- Published
- 2021
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23. Design and construction of a new ultraviolet sensor using CsI deposition in the ionization chamber
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Souri, R., Negarestani, A., Souri, S., Farzan, M., and Mahani, M.
- Published
- 2018
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24. An investigation of electronic and optical properties of InN nanosheet by first principle study
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Farzan, M., Elahi, S.M., Salehi, H., and Abolhassani, M.R.
- Published
- 2017
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- View/download PDF
25. First principles study of effects of vacancies on electronic, magnetic and optical properties of InN nanosheet
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Farzan, M., Elahi, S.M., Abolhassani, M.R., and Salehi, H.
- Published
- 2017
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26. Neuroprotective properties of Betulin, Betulinic acid, and Ursolic acid as triterpenoids derivatives: a comprehensive review of mechanistic studies.
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Farzan M, Farzan M, Shahrani M, Navabi SP, Vardanjani HR, Amini-Khoei H, and Shabani S
- Subjects
- Humans, Ursolic Acid, Pentacyclic Triterpenes, Betulinic Acid, Triterpenes therapeutic use, Triterpenes pharmacology, Neurodegenerative Diseases drug therapy
- Abstract
Cognitive deficits are the main outcome of neurological disorders whose occurrence has risen over the past three decades. Although there are some pharmacologic approaches approved for managing neurological disorders, it remains largely ineffective. Hence, exploring novel nature-based nutraceuticals is a pressing need to alleviate the results of neurodegenerative diseases, such as Alzheimer's disease (AD) and other neurodegenerative disorders. Some triterpenoids and their derivates can be considered potential therapeutics against neurological disorders due to their neuroprotective and cognitive-improving effects. Betulin (B), betulinic acid (BA), and ursolic acid (UA) are pentacyclic triterpenoid compounds with a variety of biological activities, including antioxidative, neuroprotective and anti-inflammatory properties. This review focuses on the therapeutic efficacy and probable molecular mechanisms of triterpenoids in damage prevention to neurons and restoring cognition in neurodegenerative diseases. Considering few studies on this concept, the precise mechanisms that mediate the effect of these compounds in neurodegenerative disorders have remained unknown. The findings can provide sufficient information about the advantages of these compounds against neurodegenerative diseases.
- Published
- 2024
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27. Simultaneous screening for selective SARS-CoV-2, Lassa, and Machupo virus entry inhibitors.
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Otsuka Y, Zhang L, Mou H, Shumate J, Kitzmiller CE, Scampavia L, Bannister TD, Farzan M, Choe H, and Spicer TP
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- Humans, COVID-19 virology, Drug Discovery methods, Drug Evaluation, Preclinical methods, COVID-19 Drug Treatment, Chlorocebus aethiops, Animals, SARS-CoV-2 drug effects, Antiviral Agents pharmacology, Virus Internalization drug effects, Lassa virus drug effects, High-Throughput Screening Assays methods
- Abstract
Emerging highly pathogenic viruses can pose profound impacts on global health, the economy, and society. To meet that challenge, the National Institute of Allergy and Infectious Diseases (NIAID) established nine Antiviral Drug Discovery (AViDD) centers for early-stage identification and validation of novel antiviral drug candidates against viruses with pandemic potential. As part of this initiative, we established paired entry assays that simultaneously screen for inhibitors specifically targeting SARS-CoV-2 (SARS2), Lassa virus (LASV) and Machupo virus (MACV) entry. To do so we employed a dual pseudotyped virus (PV) infection system allowing us to screen ∼650,000 compounds efficiently and cost-effectively. Adaptation of these paired assays into 1536 well-plate format for ultra-high throughput screening (uHTS) resulted in the largest screening ever conducted in our facility, with over 2.4 million wells completed. The paired infection system allowed us to detect two PV infections simultaneously: LASV + MACV, MACV + SARS2, and SARS2 + LASV. Each PV contains a different luciferase reporter gene which enabled us to measure the infection of each PV exclusively, albeit in the same well. Each PV was screened at least twice utilizing different reporters, which allowed us to select the inhibitors specific to a particular PV and to exclude those that hit off targets, including cellular components or the reporter proteins. All assays were robust with an average Z' value ranging from 0.5 to 0.8. The primary screening of ∼650,000 compounds resulted in 1812, 1506, and 2586 unique hits for LASV, MACV, and SARS2, respectively. The confirmation screening narrowed this list further to 60, 40, and 90 compounds that are unique to LASV, MACV, and SARS2, respectively. Of these compounds, 8, 35, and 50 compounds showed IC
50 value < 10 μM, some of which have much greater potency and excellent antiviral activity profiles specific to LASV, MACV, and SARS2, and none are cytotoxic. These selected compounds are currently being studied for their mechanism of action and to improve their specificity and potency through chemical modification., Competing Interests: Declaration of competing interest The are no conflicts of interest amongst any of the authors and the work pertained in this manuscript., (Copyright © 2024. Published by Elsevier Inc.)- Published
- 2024
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28. Fabrication and Evaluation of a Soy Protein Isolate/Collagen/Sodium Alginate Multifunctional Bilayered Wound Dressing: Release of Cinnamaldehyde, Artemisia absinthium, and Oxygen.
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Esmaeili J, Ghoraishizadeh S, Farzan M, Barati A, Salehi E, and Ai J
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- Animals, Rats, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, Anti-Bacterial Agents chemical synthesis, Escherichia coli drug effects, Materials Testing, Microbial Sensitivity Tests, Oxygen chemistry, Particle Size, Acrolein analogs & derivatives, Acrolein chemistry, Acrolein pharmacology, Alginates chemistry, Artemisia absinthium chemistry, Bandages, Biocompatible Materials chemistry, Biocompatible Materials pharmacology, Collagen chemistry, Soybean Proteins chemistry, Wound Healing drug effects
- Abstract
Chronic wounds, such as diabetic ulcers and pressure sores, pose significant challenges in modern healthcare due to their prolonged healing times and susceptibility to infections. This study aims to engineer a bilayered wound dressing (BLWD) composed of soy protein isolate/collagen with the ability to release Cinnamaldehyde, Artemisia absinthium (AA), and oxygen. Cinnamaldehyde, magnesium peroxide (MgO
2 ), and AA extract were encapsulated. Nanoparticles were evaluated using scanning electron microscopy (SEM), dynamic light scattering, and ZETA potential tests. Swelling, degradation, water vapor penetration, tensile, MTT, SEM, oxygen release, AA extract release, and antibacterial properties were performed. An in vivo study was carried out to assess the final wound dressing under Hematoxiline&Eosin and Masson trichrome staining analysis and compared to a commercial product. According to the results, the synthesized nanoparticles had an average diameter of about 20 nm with a zeta potential in the range of -20 to -30 mV. The layers had uniform and dense surfaces. The maximum swelling and degradation of the dressing was about 130 and 13% respectively. Generally, better mechanical properties were observed in BLWD than in the single-layer case. More than 90% biocompatibility for the wound dressing was reported. The BLWD could inhibit the growth of Gram-positive and Gram-negative microorganisms. Histopathological analysis showed an acceptable wound-healing property. To sum up, the engineered wound dressing can be a good candidate for more clinical trials.- Published
- 2024
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29. Neurological efficacy and safety of mesenchymal stem cells (MSCs) therapy in people with multiple sclerosis (pwMS): An updated systematic review and meta-analysis.
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Vaheb S, Afshin S, Ghoshouni H, Ghaffary EM, Farzan M, Shaygannejad V, Thapa S, Zabeti A, and Mirmosayyeb O
- Subjects
- Humans, Multiple Sclerosis, Relapsing-Remitting therapy, Multiple Sclerosis, Relapsing-Remitting diagnostic imaging, Outcome Assessment, Health Care, Mesenchymal Stem Cell Transplantation methods, Mesenchymal Stem Cell Transplantation adverse effects, Multiple Sclerosis therapy
- Abstract
Background: Current therapeutic strategies for multiple sclerosis (MS) aim to suppress the immune response and reduce relapse rates. As alternative treatments, mesenchymal stem cells (MSCs) are being explored. MSCs show promise in repairing nerve tissue and reducing autoimmune responses in people with MS (pwMS)., Objective: This review delves into the literature on the efficacy and safety of MSC therapy for pwMS., Methods: A comprehensive search strategy was employed to identify relevant articles from five databases until January 2024. The inclusion criteria encompassed interventional studies. Efficacy and safety data concerning MSC therapy in relapsing-remitting MS (RRMS), secondary progressive MS (SPMS), and primary progressive MS (PPMS) groups were extracted and analyzed., Results: A comprehensive analysis encompassing 30 studies revealed that individuals who underwent intrathecal (IT) protocol-based transplantation of MSCs experienced a noteworthy improvement in their expanded disability status scale (EDSS) compared to the placebo group. Weighted mean difference (WMD) was -0.28; 95 % CI -0.53 to -0.03, I
2 = 0 %, p-value = 0.028); however, the intravenous (IV) group did not show significant changes in EDSS scores. The annualized relapse rate (ARR) did not significantly decrease among pwMS (WMD = -0.34; 95 % CI -1.05 to 0.38, I2 = 98 %, p-value = 0.357). Favorable results were observed in magnetic resonance imaging (MRI), with only 19.11 % of pwMS showing contrast-enhanced lesions (CEL) in the short term and no long-term MRI activity. The most common complications in both short-term and long-term follow-ups were infection, back pain, and gastrointestinal symptoms., Conclusions: The study highlights the safety potential of MSC therapy for pwMS. While MRI-based neural regeneration shows significant treatment potential, the effectiveness of MSC therapy remains uncertain due to study limitations and ineffective outcome measures. Further research is needed to establish efficacy and optimize evaluation methods for MSC therapy on pwMS., Competing Interests: Declaration of competing interest The authors declare that they have no conflict of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)- Published
- 2024
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30. Classification of Individual Finger Movements from Right Hand Using fNIRS Signals
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Haroon Khan, Farzan M. Noori, Anis Yazidi, Md Zia Uddin, M. N. Afzal Khan, and Peyman Mirtaheri
- Subjects
functional near-infrared spectroscopy (fNIRS) ,finger-tapping ,classification ,motor cortex ,machine learning ,Chemical technology ,TP1-1185 - Abstract
Functional near-infrared spectroscopy (fNIRS) is a comparatively new noninvasive, portable, and easy-to-use brain imaging modality. However, complicated dexterous tasks such as individual finger-tapping, particularly using one hand, have been not investigated using fNIRS technology. Twenty-four healthy volunteers participated in the individual finger-tapping experiment. Data were acquired from the motor cortex using sixteen sources and sixteen detectors. In this preliminary study, we applied standard fNIRS data processing pipeline, i.e., optical densities conversation, signal processing, feature extraction, and classification algorithm implementation. Physiological and non-physiological noise is removed using 4th order band-pass Butter-worth and 3rd order Savitzky–Golay filters. Eight spatial statistical features were selected: signal-mean, peak, minimum, Skewness, Kurtosis, variance, median, and peak-to-peak form data of oxygenated haemoglobin changes. Sophisticated machine learning algorithms were applied, such as support vector machine (SVM), random forests (RF), decision trees (DT), AdaBoost, quadratic discriminant analysis (QDA), Artificial neural networks (ANN), k-nearest neighbors (kNN), and extreme gradient boosting (XGBoost). The average classification accuracies achieved were 0.75±0.04, 0.75±0.05, and 0.77±0.06 using k-nearest neighbors (kNN), Random forest (RF) and XGBoost, respectively. KNN, RF and XGBoost classifiers performed exceptionally well on such a high-class problem. The results need to be further investigated. In the future, a more in-depth analysis of the signal in both temporal and spatial domains will be conducted to investigate the underlying facts. The accuracies achieved are promising results and could open up a new research direction leading to enrichment of control commands generation for fNIRS-based brain-computer interface applications.
- Published
- 2021
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- View/download PDF
31. Severe rigid Scheuermann kyphosis in adult patients; correction with posterior-only approach
- Author
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Mirzashahi, B., Chehrassan, M., Arfa, A., and Farzan, M.
- Published
- 2018
- Full Text
- View/download PDF
32. An investigation of electronic and optical properties of TlN nanosheet and compare with TlN bulk (Wurtzite) by first principle
- Author
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Elahi, S.M., Farzan, M., Salehi, H., and Abolhasani, M.R.
- Published
- 2016
- Full Text
- View/download PDF
33. Immunoinformatics-based multi-epitope vaccine design for the re-emerging monkeypox virus.
- Author
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Farzan M, Farzan M, Mirzaei Y, Aiman S, Azadegan-Dehkordi F, and Bagheri N
- Subjects
- Humans, Male, Molecular Docking Simulation, Toll-Like Receptor 3, Homosexuality, Male, Epitopes, B-Lymphocyte, Escherichia coli, Toll-Like Receptor 4, Epitopes, T-Lymphocyte, Computational Biology methods, Vaccines, Subunit, Mpox, Monkeypox, Monkeypox virus, Sexual and Gender Minorities
- Abstract
Background: On May 7, 2022, WHO reported a new monkeypox case. By May 2023 over 80,000 cases had been reported worldwide outside previously endemic nations. (This primarily affected the men who have sex with men (MSM) community in rich nations). The present research aims to develop a multi-epitope vaccine for the monkeypox virus (MPXV) using structural and cell surface proteins., Methods: The first part of the research involved retrieving protein sequences. The Immune Epitope Database (IEDB) was then used to analyze the B and T lymphocyte epitopes. After analyzing the sensitizing properties, toxicity, antigenicity, and molecular binding, appropriate linkers were utilizedto connect selected epitopes to adjuvants, and the structure of the vaccine was formulated. Algorithms from the field of immunoinformatics predicted the secondary and tertiary structures of vaccines. The physical, chemical, and structural properties were refined and validated to achieve maximum stability. Molecular docking and molecular dynamic simulations were subsequently employed to assess the vaccine's efficacy. Afterward, the ability of the vaccine to interact with toll-like receptors 3 and 4 (TLR3 and TLR4) was evaluated. Finally, the optimized sequence was then introduced into the Escherichia coli (E. coli) PET30A + vector., Results: An immunoinformatics evaluation suggested that such a vaccine might be safe revealed that this vaccine is safe, hydrophilic, temperature- and condition-stable, and can stimulate innate immunity by binding to TLR3 and TLR4., Conclusion: Our findings suggest that the first step in MPXV pathogenesis is structural and cell surface epitopes. In this study, the most effective and promising epitopes were selected and designed throughprecision servers. Furthermore,through the utilization of multi-epitope structures and a combination of two established adjuvants, this research has the potential to be a landmarkin developing an antiviralvaccine against MPXV. However, additional in vitro and in vivo tests are required to confirm these results., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest., (Copyright © 2023 Elsevier B.V. All rights reserved.)
- Published
- 2023
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34. In vivo affinity maturation of mouse B cells reprogrammed to express human antibodies.
- Author
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Yin Y, Guo Y, Jiang Y, Quinlan B, Peng H, Crynen G, He W, Zhang L, Ou T, Bailey CC, and Farzan M
- Subjects
- Animals, Humans, Mice, Antibody Affinity immunology, CRISPR-Cas Systems genetics, COVID-19 Vaccines immunology, Antibodies, Viral immunology, Mice, Inbred C57BL, B-Lymphocytes immunology, HIV-1 immunology, SARS-CoV-2 immunology, HIV Antibodies immunology, Antibodies, Neutralizing immunology, COVID-19 immunology, COVID-19 virology
- Abstract
Mice adoptively transferred with mouse B cells edited via CRISPR to express human antibody variable chains could help evaluate candidate vaccines and develop better antibody therapies. However, current editing strategies disrupt the heavy-chain locus, resulting in inefficient somatic hypermutation without functional affinity maturation. Here we show that these key B-cell functions can be preserved by directly and simultaneously replacing recombined mouse heavy and kappa chains with those of human antibodies, using a single Cas12a-mediated cut at each locus and 5' homology arms complementary to distal V segments. Cells edited in this way to express the human immunodeficiency virus type 1 (HIV-1) broadly neutralizing antibody 10-1074 or VRC26.25-y robustly hypermutated and generated potent neutralizing plasma in vaccinated mice. The 10-1074 variants isolated from the mice neutralized a global panel of HIV-1 isolates more efficiently than wild-type 10-1074 while maintaining its low polyreactivity and long half-life. We also used the approach to improve the potency of anti-SARS-CoV-2 antibodies against recent Omicron strains. In vivo affinity maturation of B cells edited at their native loci may facilitate the development of broad, potent and bioavailable antibodies., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)
- Published
- 2024
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- View/download PDF
35. PP 2.16 – 00177 Development of a nonhuman primate model to study the immunological effects of feminizing hormone therapy in transgender women
- Author
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Hahn, P., primary, Alexander, E., additional, Weisgrau, K., additional, Rakasz, E., additional, Kurian, J., additional, Ou, T., additional, He, W., additional, Farzan, M., additional, and Martins, M., additional
- Published
- 2022
- Full Text
- View/download PDF
36. PP 8.2 – 00015 Retargeting cytomegalovirus-specific CD8+ cytotoxic T lymphocytes to kill HIV/SIV-infected cells via peptide-MHC Iantibody fusion proteins
- Author
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Rosen, B.C., primary, Ricciardi, M.J., additional, Louw, J.J., additional, Voigt, T.B., additional, Laurino, F.D., additional, Yrizarry-Medina, A., additional, Panayiotou, C., additional, Zhao, F., additional, Woolf, J., additional, Fuchs, S.P., additional, Martins, M.A., additional, Farzan, M., additional, Burton, D.R., additional, Sok, D., additional, Rakasz, E.G., additional, Desrosiers, R.C., additional, and Watkins, D.I., additional
- Published
- 2022
- Full Text
- View/download PDF
37. OP 6.8 – 00102 In vivo evolution of env in SHIV-AD8-infected rhesus macaques after AAV-eCD4-Ig therapy
- Author
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O'Hagan, D., primary, Shandilya, S., additional, Hahn, P., additional, Gardner, M., additional, Farzan, M., additional, and Ardeshir, A., additional
- Published
- 2022
- Full Text
- View/download PDF
38. Multilayer PVA/gelatin nanofibrous scaffolds incorporated with Tanacetum polycephalum essential oil and amoxicillin for skin tissue engineering application.
- Author
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Soleiman-Dehkordi E, Reisi-Vanani V, Hosseini S, Lorigooini Z, Zvareh VA, Farzan M, Khorasgani EM, Lozano K, and Abolhassanzadeh Z
- Subjects
- Mice, Animals, Amoxicillin pharmacology, Tissue Engineering, Gelatin chemistry, Anti-Bacterial Agents chemistry, Tissue Scaffolds chemistry, Polyvinyl Alcohol chemistry, Nanofibers chemistry, Oils, Volatile pharmacology
- Abstract
Wound infection is still an important challenge in healing of different types of skin injuries. This highlights the need for new and improved antibacterial agents with novel and different mechanisms of action. In this study, by electrospinning process Tanacetum polycephalum essential oil (EO), as a natural antibacterial and anti-inflammatory agent, along with Amoxicillin (AMX) as an antibiotic are incorporated into PVA/gelatin-based nanofiber mats individually and in combination to fabricate a novel wound dressing. Briefly, we fabricated PVA/gelatin loaded by Amoxicillin as first layer for direct contact with wound surface to protects the wound from exogenous bacteria, and then built a PVA/gelatin/Tanacetum polycephalum essential oil layer on the first layer to help cleanses the wound from infection and accelerates wound closure. Finally, PVA/gelatin layer as third layer fabricated on middle layer to guarantee desirable mechanical properties. For each layer, the electrospinning parameters were adjusted to form bead-free fibers. The morphology of fabricated nanofiber scaffolds was characterized by Fourier-transform infrared (FTIR) and scanning electron microscopy (SEM). Microscopic images demonstrated the smooth bead-free microstructures fabrication of every layer of nanofiber with a uniform fiber size of 126.888 to 136.833 nm. While, EO and AMX increased the diameter of nanofibers but there was no change in physical structure of nanofiber. The water contact angle test demonstrated hydrophilicity of nanofibers with 47.35°. Although EO and AMX had little effect on reducing hydrophilicity but nanofibers with contact angle between 51.4° until 65.4° are still hydrophilic. Multilayer nanofibers loaded by EO and AMX killed 99.99 % of both gram-negative and gram-positive bacteria in comparison with control and PVA/gelatin nanofiber. Also, in addition to confirming the non-toxicity of nanofibers, MTT results also showed the acceleration of cell proliferation. In vivo wound evaluation in mouse models showed that designed nanofibrous scaffolds could be an appropriate option for wound treatment due to their positive effect on angiogenesis, collagen deposition, granulation tissue formation, epithelialization, and wound closure., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)
- Published
- 2024
- Full Text
- View/download PDF
39. In vivo affinity maturation of the HIV-1 Env-binding domain of CD4.
- Author
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Pan A, Bailey CC, Ou T, Xu J, Liu X, Hu B, Crynen G, Skamangas N, Bronkema N, Tran M, Mu H, Zhang X, Yin Y, Alpert MD, He W, and Farzan M
- Abstract
Many human proteins have been repurposed as biologics for clinical use. These proteins have been engineered with in vitro techniques that improve affinity for their ligands. However, these approaches do not select against properties that impair efficacy such as protease sensitivity or self-reactivity. Here we engineer the B-cell receptor of primary murine B cells to express a human protein biologic without disrupting their ability to affinity mature. Specifically, CD4 domains 1 and 2 (D1D2) of a half-life enhanced-HIV-1 entry inhibitor CD4-Ig (CD4-Ig-v0) were introduced into the heavy-chain loci of murine B cells, which were then adoptively transferred to wild-type mice. After immunization, transferred B cells proliferated, class switched, affinity matured, and efficiently produced D1D2-presenting antibodies. Somatic hypermutations found in the D1D2-encoding region of engrafted B cells improved binding affinity of CD4-Ig-v0 for the HIV-1 envelope glycoprotein (Env) and the neutralization potency of CD4-Ig-v0 by more than ten-fold across a global panel of HIV-1 isolates, without impairing its pharmacokinetic properties. Thus, affinity maturation of non-antibody protein biologics in vivo can guide development of more effective therapeutics., Competing Interests: COMPETING INTEREST A.P., W.H., T.O., Y.Y. and M.F. are inventors of a pending patent describing the in vivo affinity maturation of antibodies and biologics. C.C.B., M.D.A., and M.F. have equity stakes in Emmune, Inc., which developed CD4-Ig-v0. The authors have no other competing interests.
- Published
- 2024
- Full Text
- View/download PDF
40. Predicting potential SARS-CoV-2 mutations of concern via full quantum mechanical modelling.
- Author
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Zaccaria M, Genovese L, Lawhorn BE, Dawson W, Joyal AS, Hu J, Autissier P, Nakajima T, Johnson WE, Fofana I, Farzan M, and Momeni B
- Subjects
- Humans, SARS-CoV-2, Mutation, Amino Acids, Protein Binding, Angiotensin-Converting Enzyme 2, COVID-19
- Abstract
Ab initio quantum mechanical models can characterize and predict intermolecular binding, but only recently have models including more than a few hundred atoms gained traction. Here, we simulate the electronic structure for approximately 13 000 atoms to predict and characterize binding of SARS-CoV-2 spike variants to the human ACE2 (hACE2) receptor using the quantum mechanics complexity reduction (QM-CR) approach. We compare four spike variants in our analysis: Wuhan, Omicron, and two Omicron-based variants. To assess binding, we mechanistically characterize the energetic contribution of each amino acid involved, and predict the effect of select single amino acid mutations. We validate our computational predictions experimentally by comparing the efficacy of spike variants binding to cells expressing hACE2. At the time we performed our simulations (December 2021), the mutation A484K which our model predicted to be highly beneficial to ACE2 binding had not been identified in epidemiological surveys; only recently (August 2023) has it appeared in variant BA.2.86. We argue that our computational model, QM-CR, can identify mutations critical for intermolecular interactions and inform the engineering of high-specificity interactors.
- Published
- 2024
- Full Text
- View/download PDF
41. Protective effects of vanillic acid on autistic-like behaviors in a rat model of maternal separation stress: Behavioral, electrophysiological, molecular and histopathological alterations.
- Author
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Farzan M, Farzan M, Amini-Khoei H, Shahrani M, Bijad E, Anjomshoa M, and Shabani S
- Subjects
- Rats, Animals, Antioxidants pharmacology, Antioxidants therapeutic use, Vanillic Acid pharmacology, Vanillic Acid therapeutic use, Maternal Deprivation, Nitrites, Disease Models, Animal, Autistic Disorder drug therapy, Autism Spectrum Disorder drug therapy
- Abstract
Compounds derived from herbs exhibit a range of biological properties, including anti-inflammatory, antioxidant, and neuroprotective properties. However, the exact mechanism of action of these compounds in various neurological disorders is not fully discovered yet. Herein, the present work detected the effect of Vanillic acid (VA), a widely-used flavoring agent derived from vanillin, on autistic-like behaviors to assess the probable underlying mechanisms that mediate behavioral, electrophysiological, molecular, and histopathological alterations in the rat model of maternal separation (MS) stress. Maternal separated rats were treated with VA (25, 50, and 100 mg/kg interperitoneally for 14 days). In addition, anxiety-like, autistic-like behaviors, and learning and memory impairment were evaluated using various behavioral tests. Hippocampus samples were assessed histopathologically by H&E staining. Levels of malondialdehyde (MDA) and antioxidant capacity (by the FRAP method), as well as nitrite levels, were measured in brain tissue. Moreover, gene expression of inflammatory markers (IL-1β, TLR-4, TNF-α, and NLRP3) was evaluated in the hippocampus. Electrophysiological alterations were also estimated in the hippocampus by long-term potentiation (LTP) assessments. Results showed that VA reversed the negative effects of MS on behavior. VA increased the diameter and decreased the percentage of dark neurons in the CA3 area. Accordingly, VA decreased MDA and nitrite levels and increased the antioxidant capacity in brain samples and decreased the expression of all inflammatory genes. VA treated rats showed significant improvements in all LTP parameters. This study provided evidence suggesting a possible role for VA in preventing autism spectrum disorder (ASD) by regulating immune signaling., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)
- Published
- 2023
- Full Text
- View/download PDF
42. Towards adaptive technology in routine mental health care.
- Author
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Lamo, Yngve, Mukhiya, Suresh K, Rabbi, Fazle, Aminifar, Amin, Lillehaug, Svein I, Tørresen, Jim, H Pham, Minh, Côtè-Allard, Ulysse, Noori, Farzan M, Guribye, Frode, Inal, Yavuz, Flobakk, Eivind, Wake, Jo D, Myklebost, Sunniva, Lundervold, Astri J, Hammar, Aasa, Nordby, Emilie, Kahlon, Smiti, Kenter, Robin, and Sekse, Ragnhild JT
- Published
- 2022
- Full Text
- View/download PDF
43. Carpal tunnel syndrome and contributing factors in 362 hospitalized patients
- Author
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Farzan M, Mazoochy H, Sobhani A, Shajirat Z, Zolfaghari R, and Espandar R
- Subjects
Carpal tunnel syndrome ,idiopathic ,occupation ,Medicine (General) ,R5-920 - Abstract
Background: Carpal tunnel syndrome is the most common focal neuropathy that results from pressure on a nerve. The goal of this study was to assess carpal tunnel syndrome and its associated factors such as occupation, sex, and accompanying complications in a teaching general hospital. Methods: This cross-sectional study investigated 362 patients with the diagnosis of carpal tunnel syndrome admitted in the orthopedic ward of Imam Khomeini Hospital affiliated to Tehran University of Medical Sciences in Tehran, Iran during 2000-2010. Results: The difference in the mean age of men and women was statistically significant (P
- Published
- 2012
44. Surgical Treatment Outcomes in Patients With Syndactyly in Imam Khomeini Hospital in Tehran, Iran During 1996-2011: A Breif Report
- Author
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Mazoochy H, Sobhani Eraghi A, Zeraati Z, Farzan M, and Espandar R
- Subjects
Hand Anomaly ,Surgical Treatment ,Syndactyly ,Medicine (General) ,R5-920 - Abstract
Background: Syndactyly is the most common congenital malformation of the hand, with an incidence of 1 in 2000-2500 live births. In this study we evaluated the surgical outcomes and complications of patients with syndactyly.Methods : The surgical outcomes and complications of 42 patients, 27 male and 15, female, undergoing surgery for syndactyly were evaluated. The study took place in Imam Khomeini Hospital, in Tehran, Iran during 1996 to 2011. Having had the inclusion criteria, the patients were assessed for function, cosmetic outcome, sensation and occurrence of complications. The patients were followed-up for at least 3 years.Results : The mean age of patients was 4.4 years. There was a positive familial history for the disease in 8 patients. 71.4%, 90.4% and 73.8% of the participants had good results regarding cosmetic outcome, sensation and function, respectively.Conclusion: The overall results of surgery for syndactyly in this study were interpreted as good in 78.5%, moderate in 12.5% and fair in 8.4% of the patients. This study confirmed better surgical outcomes in patients older than 18 months.
- Published
- 2011
45. An investigation of vacancy defects on electronic and magnetic properties of TlN nanosheet: By density function calculation
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Souri, R. and Farzan, M.
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- 2022
- Full Text
- View/download PDF
46. Frequency of upper extremity nerve entrapment syndromes in surgically operated patients: a ten-year study
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Farzan M, Espandar R, Fallah Y, and Farhoud AR
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Carpal tunnel syndrome ,cubital tunnel syndrome ,thoracic outlet syndrome ,nerve compression ,Medicine (General) ,R5-920 - Abstract
"n Normal 0 false false false EN-US X-NONE AR-SA MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Arial; mso-bidi-theme-font:minor-bidi;} Background: Nerve entrapment neuropathies are relatively frequent in the upper limb. Significant costs related to resultant disability and treatment, and also simultaneous occurrence of some of these syndromes can result in alteration in the treatment approach. The aim of this study was to evaluate the frequency of these syndromes, the rate of concurrence of carpal tunnel syndrome as the most prevalent syndrome with others, related risk factors, and accordance of clinical and electrophysiological findings."n"nMethods: In a retrospective study, data of the 170 affected patients to these syndromes operated during a period of 10 years in a referral center were searched using recorded documents. Information about patient's gender, age, occupation and associated co-morbidities, clinical and surgical findings and their accordance to the EMG-NCV findings, and also concurrence of these syndromes were assessed."n"nResults: Patients' range of age was 10-91 year (mean: 48.09 year) and 74.5% of them were female. In this study carpal tunnel and cubital tunnel syndrome were the most frequent (81.7% and 15.8% respectively). In 23.5% of patients with carpal tunnel syndrome, electrophysiological findings were negative but there was no false positive result. Concurrent carpal tunnel syndrome with other syndromes were found in three cases of cubital tunnel syndrome, two cases of thoracic outlet syndrome and one case of Guyon's canal syndrome."n"nConclusion: Constellation of symptoms, physical examination and electrophysiologic-al findings altogether should be considered for correct diagnosis of nerve entrapment syndromes in the upper extremity. Simultaneous entrapment in the other regions of the same nerve or other nerves in the same extremity is a probable condition
- Published
- 2009
47. Monitoring In-Home Emergency Situation and Preserve Privacy using Multi-modal Sensing and Deep Learning
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David Andreas Bordvik, Jie Hou, Farzan M. Noori, Md Zia Uddin, and Jim Torresen
- Abstract
Videos and images are commonly used in home monitoring systems. However, detecting emergencies in-home while preserving privacy is a challenging task concerning Human Activity Recognition (HAR). In recent years, HAR combined with deep learning has drawn much attention from the general public. Besides that, relying entirely on a single sensor modal-ity is not promising. In this paper, depth images and radar presence data were used to investigate if such sensor data can tackle the challenge of a system's ability to detect abnormal and normal situations while preserving privacy. The recurrence plots and wavelet transformations were used to make a two-dimensional representation of the presence radar data. Moreover, we fused data from both sensors using data-level, feature-level, and decision-level fusions. The decision-level fusion showed its superiority over the other two techniques. For the decision-level fusion, a combination of the depth images and presence data recurrence plots trained first on convolutional neural networks (CNN). The output was fed into support vector machines, which yielded the best accuracy of 99.98%.
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- 2022
48. Ulnar club hand surgical outcome: a 14 years study in Imam Khomeini hospital
- Author
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Espandar R., Bagher Darabpour M., and Farzan M.
- Subjects
Ulnar club hand ,ulnar deficiency ,anlage resection ,Medicine (General) ,R5-920 - Abstract
Background: Ulnar club hand (ulnar deficiency) is a rare congenital disorder of the upper extremity. In the Flatt series among 2758 congenital disorders of upper extremity only 28 cases of ulnar deficiency were reported. Due to its rarity and variations in presentation current data in the management of the deformity is very limited. Here we present our experience and results in comparing management of ulnar deficiency.Methods: We include all of the ulnar club hand patients (five boys and one girl with seven involved extremities) from 1993 to 2006. After recognizing the type of deformity the classic management approach was performed that was splinting in corrective position until six months of age and then anlage resection. Syndactyly release was done in appropriate age according to involved rays, other operations for restoration of apposition was done after 18 months of age. Two of our patients were neglected, the first one was a 12 years old boy without any ulnar deviation but with syndactyly of the remaining rays and the other was a 32 years old male with severe ulnar deviation and partial syndactyly who is a skillful worker. We determined the effect of anlage resection on ulnar deviation of the wrist and restoration of opposition and syndactyly release on function of the limb.Results: In short term follow up, anlage resection was effective in prevention and correction of ulnar deviation, however the deformity was partially recurred later. Surprisingly, the function of the limb was not significantly affected with the extent of the deformity. On the other hand, the operations used for opposition of the thumb like first metacarpal rotational osteotomies and tendon transfers for powerful opposition, were more effective in the hand and also limb function compared with anlage resection alone. Conclusions: Due to our observation of the neglected cases, the most important factor in the function of the hand is the function of the thumb, thus we believe that restoration of opposition and syndactyly release may be more effective than anlage resection on limb function in Ulnar Club Hand patients
- Published
- 2008
49. In vivo affinity maturation of murine B cells reprogrammed to express human antibodies.
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Yin Y, Guo Y, Jiang Y, Quinlan B, Peng H, Crynen G, He W, Zhang L, Ou T, Bailey CC, and Farzan M
- Abstract
CRISPR-edited murine B cells engineered to express human antibody variable chains proliferate, class switch, and secrete these antibodies in vaccinated mice. However, current strategies disrupt the heavy-chain locus, resulting in inefficient somatic hypermutation without functional affinity maturation. Here we show that recombined murine heavy- and kappa-variable genes can be directly and simultaneously overwritten, using Cas12a-mediated cuts at their 3'-most J segments and 5' homology arms complementary to distal V segments. Cells edited in this way to express the HIV-1 broadly neutralizing antibodies 10-1074 or VRC26.25-y robustly hypermutated and generated potent neutralizing plasma in vaccinated recipient mice. 10-1074 variants isolated from these mice bound and neutralized HIV-1 envelope glycoprotein more efficiently than wild-type 10-1074 while maintaining or improving its already low polyreactivity and long in vivo half-life. We further validated this approach by generating substantially broader and more potent variants of the anti-SARS-CoV-2 antibodies ZCB11 and S309. Thus, B cells edited at their native loci affinity mature, facilitating development of broad, potent, and bioavailable antibodies and expanding the potential applications of engineered B cells., Competing Interests: Competing interests Y.Y., W.H., T.O., and M.F. are inventors on a pending patent application describing methods for editing B cells. The other authors declare no competing interests.
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- 2023
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50. Effect of mRNA-LNP components of two globally-marketed COVID-19 vaccines on efficacy and stability.
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Zhang L, More KR, Ojha A, Jackson CB, Quinlan BD, Li H, He W, Farzan M, Pardi N, and Choe H
- Abstract
During the COVID-19 pandemic, Pfizer-BioNTech and Moderna successfully developed nucleoside-modified mRNA lipid nanoparticle (LNP) vaccines. SARS-CoV-2 spike protein expressed by those vaccines are identical in amino acid sequence, but several key components are distinct. Here, we compared the effect of ionizable lipids, untranslated regions (UTRs), and nucleotide composition of the two vaccines, focusing on mRNA delivery, antibody generation, and long-term stability. We found that the ionizable lipid, SM-102, in Moderna's vaccine performs better than ALC-0315 in Pfizer-BioNTech's vaccine for intramuscular delivery of mRNA and antibody production in mice and long-term stability at 4 °C. Moreover, Pfizer-BioNTech's 5' UTR and Moderna's 3' UTR outperform their counterparts in their contribution to transgene expression in mice. We further found that varying N1-methylpseudouridine content at the wobble position of mRNA has little effect on vaccine efficacy. These findings may contribute to the further improvement of nucleoside-modified mRNA-LNP vaccines and therapeutics., (© 2023. Springer Nature Limited.)
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- 2023
- Full Text
- View/download PDF
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