Publications by authors named "Amir Farokh Payam"

6 Publications

  • Page 1 of 1

Clinical evaluation of SARS-CoV-2 lung HRCT and RT-PCR Techniques: Towards risk factor based diagnosis of infectious diseases.

Comput Struct Biotechnol J 2021 30;19:2699-2707. Epub 2021 Apr 30.

Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, United Kingdom.

This study uses image analysis techniques for comparative analysis of the lung HRCT features and RT-PCR of 325 suspected patients to COVID-19 pneumonia. Our findings propose more caution in the interpretation of RT-PCR data, promoting, instead, also the quantification of age and sex-based risk factors using HRCT images. Statistical analysis of our methodology reveals a direct relation between intensity, skewness and kurtosis of the radiological features and the gender of patients. Moreover, we investigate the effect of the age of patients on the appearance of COVID-19 pneumonia in the HRCT images. We have also applied our methodology to investigate the effect of time on the severity of COVID-19 pneumonia within the lungs. Subsequently, we find a strong relationship between image analysis and the informed medical diagnosis asserted by the radiologists. Additionally, our results also indicate increase in the severity of lung infection in the first and second week after the onset of the SARS-CoV-2 symptoms. Thereafter, a gradual decrease in the lung damage is observed during the third week. The proposed image analysis methodology can be used as a simple complementary tool for infectious disease diagnostics as demonstrated in this study with an example of SARS-CoV-2 to provide better understanding of the disease for drug and vaccine development.
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http://dx.doi.org/10.1016/j.csbj.2021.04.058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8084916PMC
April 2021

Opportunities and Challenges for Biosensors and Nanoscale Analytical Tools for Pandemics: COVID-19.

ACS Nano 2020 07 26;14(7):7783-7807. Epub 2020 Jun 26.

Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern Ireland, United Kingdom.

Biosensors and nanoscale analytical tools have shown huge growth in literature in the past 20 years, with a large number of reports on the topic of 'ultrasensitive', 'cost-effective', and 'early detection' tools with a potential of 'mass-production' cited on the web of science. Yet none of these tools are commercially available in the market or practically viable for mass production and use in pandemic diseases such as coronavirus disease 2019 (COVID-19). In this context, we review the technological challenges and opportunities of current bio/chemical sensors and analytical tools by critically analyzing the bottlenecks which have hindered the implementation of advanced sensing technologies in pandemic diseases. We also describe in brief COVID-19 by comparing it with other pandemic strains such as that of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) for the identification of features that enable biosensing. Moreover, we discuss visualization and characterization tools that can potentially be used not only for sensing applications but also to assist in speeding up the drug discovery and vaccine development process. Furthermore, we discuss the emerging monitoring mechanism, namely wastewater-based epidemiology, for early warning of the outbreak, focusing on sensors for rapid and on-site analysis of SARS-CoV2 in sewage. To conclude, we provide holistic insights into challenges associated with the quick translation of sensing technologies, policies, ethical issues, technology adoption, and an overall outlook of the role of the sensing technologies in pandemics.
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http://dx.doi.org/10.1021/acsnano.0c04421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319134PMC
July 2020

Sub-nanometer Resolution Imaging with Amplitude-modulation Atomic Force Microscopy in Liquid.

J Vis Exp 2016 12 20(118). Epub 2016 Dec 20.

Physics Department, Durham University;

Atomic force microscopy (AFM) has become a well-established technique for nanoscale imaging of samples in air and in liquid. Recent studies have shown that when operated in amplitude-modulation (tapping) mode, atomic or molecular-level resolution images can be achieved over a wide range of soft and hard samples in liquid. In these situations, small oscillation amplitudes (SAM-AFM) enhance the resolution by exploiting the solvated liquid at the surface of the sample. Although the technique has been successfully applied across fields as diverse as materials science, biology and biophysics and surface chemistry, obtaining high-resolution images in liquid can still remain challenging for novice users. This is partly due to the large number of variables to control and optimize such as the choice of cantilever, the sample preparation, and the correct manipulation of the imaging parameters. Here, we present a protocol for achieving high-resolution images of hard and soft samples in fluid using SAM-AFM on a commercial instrument. Our goal is to provide a step-by-step practical guide to achieving high-resolution images, including the cleaning and preparation of the apparatus and the sample, the choice of cantilever and optimization of the imaging parameters. For each step, we explain the scientific rationale behind our choices to facilitate the adaptation of the methodology to every user's specific system.
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http://dx.doi.org/10.3791/54924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5226432PMC
December 2016

Dynamic modeling and sensitivity analysis of dAFM in the transient and steady state motions.

Ultramicroscopy 2016 10 4;169:55-61. Epub 2016 Jul 4.

Nano Trading & Development Company, Tehran, Iran. Electronic address:

In this paper, based on the slow time varying function theory, dynamical equations for the amplitude and phase of the dynamic atomic force microscope are derived. Then, the sensitivity of the amplitude and phase to the dissipative and conservative parts of interaction force is investigated. The most advantage of this dynamical model is the ability to simulate and analysis the dynamics behavior of amplitude and phase of the AFM tip motion not only in the steady state but also in the transient regime. Using numerical analysis the transient and steady state behavior of amplitude and phase is studied and the sensitivity of amplitude and phase to the interaction force is analyzed.
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http://dx.doi.org/10.1016/j.ultramic.2016.05.011DOI Listing
October 2016

Effect of tip mass on frequency response and sensitivity of AFM cantilever in liquid.

Micron 2015 Mar 4;70:50-4. Epub 2014 Dec 4.

School of Electrical & Computer Engineering, University of Tehran, Tehran, Iran.

The effect of tip mass on the frequency response and sensitivity of atomic force microscope (AFM) cantilever in the liquid environment is investigated. For this purpose, using Euler-Bernoulli beam theory and considering tip mass and hydrodynamic functions in a liquid environment, an expression for the resonance frequencies of AFM cantilever in liquid is derived. Then, based on this expression, the effect of the surface contact stiffness on the flexural mode of a rectangular AFM cantilever in fluid is investigated and compared with the case where the AFM cantilever operates in the air. The results show that in contrast with an air environment, the tip mass has no significant impact on the resonance frequency and sensitivity of the AFM cantilever in the liquid. Hence, analysis of AFM behaviour in liquid environment by neglecting the tip mass is logical.
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http://dx.doi.org/10.1016/j.micron.2014.11.006DOI Listing
March 2015

Sensitivity of flexural vibration mode of the rectangular atomic force microscope micro cantilevers in liquid to the surface stiffness variations.

Ultramicroscopy 2013 Dec 12;135:84-8. Epub 2013 Jul 12.

Nano-electronics excellent centre of research, School of Electrical & Computer Engineering, University of Tehran, Iran. Electronic address:

In this paper, the resonance frequencies and modal sensitivity of flexural vibration modes of a rectangular atomic force microscope (AFM) cantilever immersed in a liquid to surface stiffness variations have been analyzed and a closed-form expression is derived. For this purpose, the Euler-Bernoulli beam theory is used to develop the AFM cantilever model in liquid. Then, an expression for the resonance frequencies of AFM cantilever in liquid is derived and the results of the derived expression are compared with the experimental measurements. Based on this expression, the effect of the surface contact stiffness on flexural mode of a rectangular AFM cantilever in a fluid is investigated and compared with the case that AFM cantilever operates in the air. The results show that in the low surface stiffness, the first mode is the most sensitive mode and the best image contrast is obtained by excitation this mode, but by increasing the sample surface stiffness the higher modes have better image contrast. In addition, comparison between modal sensitivities in air and liquid shows that the resonance frequency shifts in the air are greater than the shifts in the fluid, which means that for the similar surface stiffness the image contrast in air, is better than liquid.
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http://dx.doi.org/10.1016/j.ultramic.2013.07.006DOI Listing
December 2013