222 research outputs found
Circular intensity differential scattering of light for biophotonics applications
No full textThis thesis demonstrate the application of a label-free, non-invasive biophysical method based on angle-resolved light scattering calculations to characterize different biological samples; virus particles, chromatin fiber, and hierarchical chiral polymers.
Chapter 1 provides an introduction on the foundation of electromagnetic theory, light scattering phenomenon, Mueller scattering matrix and its applications to characterize various samples based on numerical simulations and experimental measurements. A numerical method to calculate light scattering quantities, discrete dipole approximation (DDA) method is discussed. In this thesis we have performed the electromagnetic scattering calculations using the DDA method implemented as ADDA code.
Chapter 2 demonstrates the angle-resolved circularly polarized light scattering calculations to characterize virus model particles. A coronavirus particle is modeled as having a spherical shaped envelope with cylindrical spikes projected from the envelope surface, and the single-stranded RNA genome polymer has been mimicked with a toroidal helix. The influence of genome polymer packaged as a standard helix in the virion core is also demonstrated. We investigated four different electromagnetic models: (i) a nucleated sphere with spikes that is a coronavirus particle, (ii) a nucleated sphere with no spikes, (iii) a homogeneous sphere, and (iv) a respiratory fluid containing a virus particle. The angular pattern of scattered circularly polarized light, the circular intensity differential scattering of light (CIDS), served as a particle's signature. This scattering signature is found sensitive to the chiral parameters that reveal information about the particles. The effect of changes in the RNA polymer, changes in its packaging, number of turns, handedness, and size are demonstrated on the scattering calculations. Additionally, the extinction efficiency, the depolarization ratio, the total scattered intensity, and the effect of changes in the wavelength of incident light on these scattering quantities are investigated. This biophysical method can offer a label-free identification of virus particles and can help understand their interaction with light.
Chapter 3 focus on the the characterization of chromatin organization. Understanding the structural organization of chromatin is essential to comprehend the gene functions. The chromatin
organization changes in the cell cycle, and it conforms to various compaction levels. We investigated a chromatin solenoid model with nucleosomes shaped as cylindrical units arranged in a helical array. The solenoid with spherical-shaped nucleosomes was also modeled. The changes in chiral structural parameters of solenoid induced different compaction levels of chromatin fiber. We calculated the angle-resolved scattering of circularly polarized light to probe the changes in the organization of chromatin fiber in response to the changes in its chiral parameters. The electromagnetic scattering calculations were performed using discrete dipole approximation (DDA). In the chromatin structure,
nucleosomes have internal interactions that affect chromatin compaction. The merit of performing computations with DDA is that it takes into account the internal interactions. We demonstrated sensitivity of the scattering signal's angular behavior to the changes in these chiral parameters: pitch, radius, the handedness of solenoid, number of solenoid turns, the orientation of solenoid, the orientation of nucleosomes, number of nucleosomes, and shape of nucleosomes. These scattering calculations can potentially benefit applying a label-free polarized-light-based approach to characterize chromatin DNA and chiral polymers at the nanoscale level.
Chapter 4 demonstrates the differential scattering of circularly polarized light to characterize the macromolecular structures consisting of hierarchical chirality. We modeled the B-DNA structure composed of a double-helix and a base-pairs helical structure. The angle-resolved scattering of circularly polarized light calculated for the B-DNA shows the additive behavior of the scattering signal contributed from the two individual chirality levels of B-DNA structure, a double-helix and a base-pairs helix. This additive behavior of angle-resolved scattering signal has also been demonstrated for other macromolecular structures comprising different chirality levels; a biological cell is also mimicked as a nucleated sphere, a sphere with a helical nucleus in its core. The individual chiral features of a structure add up to the angle-resolved scattering signal of circularly polarized light produced by the parent structure. These electromagnetic wave scattering calculations can offer a label-free approach to characterize chiral macromolecular structures with hierarchical chirality
Multispectral Stokes/Mueller Detection Module for Multiphoton/Fluorescence Confocal Scanning Imaging Microscopy
No full textMueller-matrix microscopy as proved to be an important tool to extract the full optical properties of a sample, without labelling or a priori knowledge of the sample. It consists in studying the interaction between the polarized light and the medium, which can be summarized in a single 4x4 elements Mueller-matrix. In this way, this method gives access to physical parameters such as dichroism, birefringence and scattering, from the macro-to the microscopic scale. More particularly, it has been proven its efficiency for quantitative methods for materials science and biomedical diagnosis. Among these techniques, we have developed a versatile Stokes-vector/Mueller-matrix detection module, implemented in a commercial confocal fluorescence microscope. In our previous study, we have demonstrated its capability to image small animal (zebrafish) and biological fibers (collagen and muscle) at 808nm excitation/collection ..
Flood management, characterization and vulnerability analysis using an integrated RS-GIS and 2D hydrodynamic modelling approach: The case of Deg Nullah, Pakistan
No full textOne-dimensional (1D) hydraulic models have been extensively used to conduct flood simulations for investigating flood depth and extent maps. However, the 1D models cannot simulate many other flood characteristics, such as flood velocity, duration, arrival time and recession time when the flow is not restricted within the channel. These flood characteristics cannot be disregarded as they play an important role in developing flood mitigation and evacuation strategies. This study formulates a two-dimensional (2D) hydrodynamic model combined with remote sensing (RS) and geographic information system (GIS) approach to generate additional flood characteristic maps that cannot be produced with 1D models. The model was applied to a transboundary river of Deg Nullah in Pakistan to simulate an extreme flood event experience in 2014. The flood extent images from the moderate resolution imaging spectroradiometer (MODIS) and observed flood extents were used to evaluate the model performance. Moreover, an entropy distance-based approach was proposed to facilitate the integrated multivariate flood vulnerability classification. The simulated 2D flood modeling results showed a good agreement with the flood extents registered by MODIS and the observed ones. The northwest parts of Deg Nullah near Seowal, Dullam Kahalwan and Zafarwal were the most vulnerable areas due to high flood depths and prolonged flooding duration. Whereas high flood velocities, short flood arrival time, prolonged flood duration and recession times were observed in the upper reach of Deg Nullah thereby making it the most susceptible, critical and vulnerable region to flooding events.Higher Education Commission of Pakista
Challenges and Considerations in Assessing GERD: A Critical Review of a Study in Southern Punjab, Pakistan [Response to Letter]
No full textMuhammad Fawad Rasool,1 Rimsha Sarwar,1 Muhammad Subhan Arshad,1,2 Imran Imran,3 Hamid Saeed,4 Abdul Majeed,1 Muqarrab Akbar,5 Muhammad Omer Chaudhry,6 Anees Ur Rehman,1 Waseem Ashraf,3 Tanveer Ahmad,7 Waleed Badoghaish,8 Faleh Alqahtani9 1Department of Pharmacy Practice, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60800, Pakistan; 2Department of Pharmacy, Southern Punjab Institute of Health Sciences, Multan, 60000, Pakistan; 3Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60800, Pakistan; 4University College of Pharmacy, Allama Iqbal Campus, University of the Punjab, Lahore, 54000, Pakistan; 5Department of Political Science, Bahauddin Zakariya University, Multan, 60800, Pakistan; 6School of Economics, Bahauddin Zakariya University, Multan, 60800, Pakistan; 7Institute for Advanced Biosciences (Iab), CNRS UMR5309, INSERM U1209, Grenoble Alpes University, La Tronche, 38700, France; 8Department of Internal Medicine, College of Medicine, University of Tabuk, Tabuk, 71411, Saudi Arabia; 9Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi ArabiaCorrespondence: Muhammad Fawad Rasool; Faleh Alqahtani, Email [email protected]; [email protected]
Simulation, Fuzzy Analysis and Development of ZnO Nanostructure-based Piezoelectric MEMS Energy Harvester
No full textFuzzy logic-based control systems are widely used in various fields like home appliances, medical instruments, automobiles, textile machinery, agriculture equipment and aviation for process control and data analysis. Fuzzy logic technique has shown great potential to solve the complex problems of physical world due to similarity with human understanding. Its advancements have gained widespread attention in different research areas. In several cases, it is very suitable for electronic devices which need to be precisely self-powered. In this work, an ANSYS-based simulation, fuzzy analysis, development and testing of a microelectromechanical system (MEMS)-based energy harvester have been presented. Zinc oxide (ZnO) nano rods were synthesized on an anodic aluminum oxide (AAO) template to form the MEMS energy harvester and study the effect of energy generation by applying force. The power of 5.16 nano Watts has been obtained by taking the numerical value of voltage (Voc) and current (Isc) as 3.16 mV and 0.985 µA respectively using fuzzy logic tool. Experimental testing of the harvester shows that the range of Voc is 3⁻6.4 mV and Isc is 0.45⁻1.5 μA. The results depict that this device can be used for touch screens to generate energy that can be further utilized for charging smart devices
Folio
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Shaheer-Poetry-I Desire to Paint You. pp. 151; Uzma Azad-Poetry-Silent Wish. pp. 151; Uzma Azad-Poetry-Some Day. pp. 152; Amber M. Gill-Poetry-Patience. pp. 152; Ramla Zaheer-Poetry-Life Goes On. pp. 153; Awan, M. Shaheer-Poetry-Lost Angel. pp. 153; Jawad, M.-Poetry-The Foggy Trees. pp. 154; Sadia Riaz-Poetry-Tears and Laughter. pp. 154; Hafiz Ali Aziz Khokhar-Poetry-I Shine Now. pp. 155; Nauman Ahmad-Poetry-Life is Ephemeral. pp. 155; Ramla Zaheer-Poetry-To Time and Fate. pp. 156; Muhammad Adeel Ahmad-Poetry-Death of Beauty. pp. 156; Hafiz Ali Aziz-Poetry-What Should I do? pp. 157; Shaheryar Khan-Poetry-What May I Think? pp. 157; Azzam Saddique-Poetry-The Smith. pp. 158; Rao Ayyaz Ahmad-Poetry-Assignment Girls College. pp. 159; Zeeshan Zaighum-Poetry-Divorce. pp. 159; Folio [Urdu]. 146 p.Editorial Board (English). before the Editorial page; Kennedy Hall, Forman Christian College (1959-60). after page 30; Folio team with the President of Pakistan. after page 30; Offices. page 160; Visitors. after page 160; Convocation. after page 160; Sports. after page 160; Societies. after page 160; Drama. after page 160; Music. after page 160; College Life. after page 160; Alumni. after page 160; Sundaisay. after page 16
Interaction of Hepatitis C virus proteins with pattern recognition receptors
No full textAbstract Hepatitis C virus (HCV) is an important human pathogen that causes acute and chronic hepatitis, cirrhosis and hepatocellular carcinoma worldwide. This positive stranded RNA virus is extremely efficient in establishing persistent infection by escaping immune detection or hindering the host immune responses. Recent studies have discovered two important signaling pathways that activate the host innate immunity against viral infection. One of these pathways utilizes members of Toll-like receptor (TLR) family and the other uses the RNA helicase retinoic acid inducible gene I (RIG-I) as the receptors for intracellular viral double stranded RNA (dsRNA), and activation of transcription factors. In this review article, we summarize the interaction of HCV proteins with various host receptors/sensors through one of these two pathways or both, and how they exploit these interactions to escape from host defense mechanisms. For this purpose, we searched data from Pubmed and Google Scholar. We found that three HCV proteins; Core (C), non structural 3/4 A (NS3/4A) and non structural 5A (NS5A) have direct interactions with these two pathways. Core protein only in the monomeric form stimulates TLR2 pathway assisting the virus to evade from the innate immune system. NS3/4A disrupts TLR3 and RIG-1 signaling pathways by cleaving Toll/IL-1 receptor domain-containing adapter inducing IFN-beta (TRIF) and Cardif, the two important adapter proteins of these signaling cascades respectively, thus halting the defense against HCV. NS5A downmodulates the expressions of NKG2D on natural killer cells (NK cells) via TLR4 pathway and impairs the functional ability of these cells. TLRs and RIG-1 pathways have a central role in innate immunity and despite their opposing natures to HCV proteins, when exploited together, HCV as an ever developing virus against host immunity is able to accumulate these mechanisms for near unbeatable survival.</p
Micro Electromechanical Systems (MEMS) Based Microfluidic Devices for Biomedical Applications
No full textMicro Electromechanical Systems (MEMS) based microfluidic devices have gained popularity in biomedicine field over the last few years. In this paper, a comprehensive overview of microfluidic devices such as micropumps and microneedles has been presented for biomedical applications. The aim of this paper is to present the major features and issues related to micropumps and microneedles, e.g., working principles, actuation methods, fabrication techniques, construction, performance parameters, failure analysis, testing, safety issues, applications, commercialization issues and future prospects. Based on the actuation mechanisms, the micropumps are classified into two main types, i.e., mechanical and non-mechanical micropumps. Microneedles can be categorized according to their structure, fabrication process, material, overall shape, tip shape, size, array density and application. The presented literature review on micropumps and microneedles will provide comprehensive information for researchers working on design and development of microfluidic devices for biomedical applications
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