Publications by authors named "Alireza Shams"

13 Publications

  • Page 1 of 1

vCOMBAT: a novel tool to create and visualize a computational model of bacterial antibiotic target-binding.

BMC Bioinformatics 2022 Jan 6;23(1):22. Epub 2022 Jan 6.

Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway.

Background: As antibiotic resistance creates a significant global health threat, we need not only to accelerate the development of novel antibiotics but also to develop better treatment strategies using existing drugs to improve their efficacy and prevent the selection of further resistance. We require new tools to rationally design dosing regimens from data collected in early phases of antibiotic and dosing development. Mathematical models such as mechanistic pharmacodynamic drug-target binding explain mechanistic details of how the given drug concentration affects its targeted bacteria. However, there are no available tools in the literature that allow non-quantitative scientists to develop computational models to simulate antibiotic-target binding and its effects on bacteria.

Results: In this work, we have devised an extension of a mechanistic binding-kinetic model to incorporate clinical drug concentration data. Based on the extended model, we develop a novel and interactive web-based tool that allows non-quantitative scientists to create and visualize their own computational models of bacterial antibiotic target-binding based on their considered drugs and bacteria. We also demonstrate how Rifampicin affects bacterial populations of Tuberculosis bacteria using our vCOMBAT tool.

Conclusions: The vCOMBAT online tool is publicly available at https://combat-bacteria.org/ .
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http://dx.doi.org/10.1186/s12859-021-04536-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8734216PMC
January 2022

Simultaneous determination of organophosphorus pesticides residues in vegetable, fruit juice, and milk samples with magnetic dispersive micro solid-phase extraction and chromatographic method; recruitment of simplex lattice mixture design for optimization of novel sorbent composites.

Anal Chim Acta 2021 Sep 28;1178:338802. Epub 2021 Jun 28.

Department of Chemistry, Payame Noor University, Tehran, Iran.

Dispersive micro solid-phase extraction procedure using a novel and selective sorbent prepared from four components was developed as a sample preparation strategy for extracting five organophosphorus pesticides, including fenitrothion, malathion, ethion, and chlorpyrifos, and diazinon in several vegetables, fruit juices, and cow's milk samples. Due to the high importance of the sorbent in the microextraction process, the percentages of sorbent components, including metal-organic framework (ZIF-67), chitosan, magnetic FeO nanoparticles, and silica nanoparticles, were optimized by a simplex lattice mixture design. After optimizing the sorbent composite, effective parameters on the extraction of organophosphorus pesticides were optimized using a definitive screening design and Box-Behnken design, respectively. A surfactant (Triton X100) as a dispersion agent with a low volume (10 μL) was utilized in the microextraction procedure to reduce the sorbent dispersion time and increase the sorbent dispersion efficiency. Under the optimal conditions, linearity for the determination of fenitrothion, malathion, ethion, chlorpyrifos, and diazinon was in the concentration ranges of 0.13-1100, 0.27-1000, 0.38-1000, 0.21-1200, and 0.11-1100 ng mL with a determination coefficient higher than 0.9906, respectively. The quantitation limits, detection limits, and relative standard deviations (n = 5) were lower than 0.38 ng mL, 0.11 ng mL, and 4.59% for the determination of organophosphorus pesticides. The method application for measuring OPPs on cucumber, carrot, tomato, apple juice, orange juice, and cow's milk indicated the presence of residual amounts of malathion in a cucumber sample, diazinon in a carrot sample, and chlorpyrifos in a tomato sample.
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http://dx.doi.org/10.1016/j.aca.2021.338802DOI Listing
September 2021

Facial nerve regeneration using silicone conduits filled with ammonia-functionalized graphene oxide and frankincense-embedded hydrogel.

Inflamm Regen 2021 Apr 26;41(1):13. Epub 2021 Apr 26.

Department of Anatomy, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.

Background: Silicone tube (ST) conduits have been accepted as a therapeutic alternative to direct nerve suturing in the treatment of nerve injuries; however, the search for optimal adjuncts to maximize the outcomes is still ongoing. Frankincense (Fr) and graphene oxide (GO) have both been cited as neuroregenerative compounds in the literature. This study assesses the efficacy of these materials using a ST conduit in a rat facial nerve motor neuron axotomy model, distal to the stylomastoid foramen.

Methods: Ammonia-functionalized graphene oxide (NH2-GO) and/or Fr extract were embedded in a collagen-chitosan hydrogel and were injected inside a ST. The ST was inserted in the gap between the axotomized nerve stumps. Return of function in eye closure, blinking reflex, and vibrissae movements were assessed and compared to control groups through 30 days following axotomy. To assess the histological properties of regenerated nerves, biopsies were harvested distal to the axotomy site and were visualized through light and fluorescence microscopy using LFB and anti-MBP marker, respectively.

Results: There was no significant difference in behavioral test results between groups. Histological analysis of the nerve sections revealed increased number of regenerating axons and mean axon diameter in NH2-GO group and decreased myelin surface area in Fr group. Using both NH2-GO and Fr resulted in increased number of regenerated axons and myelin thickness compared to the hydrogel group.

Conclusions: The findings suggest a synergistic effect of the substances above in axon regrowth, notably in myelin regeneration, where Fr supposedly decreases myelin synthesis.
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http://dx.doi.org/10.1186/s41232-021-00162-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8073952PMC
April 2021

Yes-associated protein-1 may serve as a diagnostic marker and therapeutic target for residual/recurrent hepatocellular carcinoma post-transarterial chemoembolization.

Liver Res 2020 Dec 8;4(4):212-217. Epub 2020 Nov 8.

Department of Pathology, Saint Louis University School of Medicine, Saint Louis, MO, USA.

Background And Aim: The transcriptional co-activator Yes-associated protein-1 (YAP1) has been implicated as an oncogene and is overexpressed in different kinds of human cancers, especially hepatocellular carcinoma (HCC). However, the role of YAP1 has not been reported in residual/recurrent HCC after transarterial chemoembolization (TACE). Our aim is to determine whether YAP1 is overexpressed in the residual/recurrent HCC after TACE.

Methods: A total of 105 tumor tissues from 71 patients including 30 cases of primary HCC without prior treatment, 35 cases of residual/recurrent HCC post TACE, and 6 cases of hepatoblastoma were included in the immunohistochemical study. YAP1 immunoreactivity was blindly scored as 0, 1+, 2+ or 3+ in density and percentages of positive cells.

Results: About 33.3% (10/30) of primary HCC without prior treatment showed 2+ of YAP1 immunoreactivity. While 82.8% (29/35) of residual/recurrent HCCs after TACE treatment displayed 2-3+ of YAP1 immunoreactivity, which was significantly higher compared to primary HCC without prior treatment ( = 0.0002). YAP1 immunoreactivity was moderately to strongly positive (2-3+) in 100% of the hepatoblastoma, particularly in the embryonal components (3+ in 100% cases).

Conclusions: YAP1 is significantly upregulated in the residual/recurrent HCCs post TACE treatment, suggesting that YAP1 may serve as a sensitive diagnostic marker and a treatment target for residual/recurrent HCC post TACE.
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http://dx.doi.org/10.1016/j.livres.2020.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7842263PMC
December 2020

Fabrication and characterisation of super-paramagnetic responsive PLGA-gelatine-magnetite scaffolds with the unidirectional porous structure: a physicochemical, mechanical, and evaluation.

IET Nanobiotechnol 2019 Oct;13(8):860-867

Tissues and Biomaterials Research Group (TBRG), Universal Scientific Education and Research Network (USERN), Tehran, Iran.

Architecture and composition of Scaffolds are influential factors in the regeneration of defects. Herein, synthesised iron oxide (magnetite) nanoparticles (MNPs) by co-precipitation technique were evenly distributed in polylactic-co-glycolic acid (PLGA)-gelatine Scaffolds. Hybrid structures were fabricated by freeze-casting method to the creation of a matrix with tunable pores. The synthesised MNPs were characterised by transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray diffraction spectroscopy, and vibrating sample magnetometer analysis. Scanning electron microscopy micrographs of porous Scaffolds confirmed the formation of unidirectional microstructure, so that pore size measurement indicated the orientation of pores in the direction of solvent solidification. The addition of MNPs to the PLGA-gelatine Scaffolds had no particular effect on the morphology of the pores, but reduced slightly pore size distribution. The MNPs contained constructs demonstrated increased mechanical strength, but a reduced absorption capacity and biodegradation ratio. Stability of the MNPs and lack of iron release was the point of strength in this investigation and were determined by atomic absorption spectroscopy. The evolution of rat bone marrow mesenchymal stem cells performance on the hybrid structure under a static magnetic field indicated the potential of super-paramagnetic constructs for further pre-clinical and clinical studies in the field of neural regeneration.
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http://dx.doi.org/10.1049/iet-nbt.2018.5305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8676357PMC
October 2019

Ultrasonic assisted magnetic dispersive solid phase microextraction for pre concentration of serotonin-norepinephrine reuptake inhibitor drugs.

Anal Biochem 2018 06 8;551:7-18. Epub 2018 May 8.

Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran.

A simple and sensitive ultrasonic assisted magnetic dispersive solid phase microextraction method (UAMDSPME) coupled with high performance liquid chromatography was developed to determine serotonin-norepinephrine reuptake inhibitor drugs including duloxetine (DUL), venlafaxine (VEN) and atomoxetine (ATO) in human urine, river water and well water samples. A novel and efficient SPME sorbent, magnetic p-Phenylenediamine functionalized reduced graphene oxide Quantum [email protected] Ni nanocomposites ([email protected] Ni), was prepared and applied for extraction of the analytes. Several effective parameters on the extraction efficiency of the analytes were investigated and optimized with experimental design approach. The performance of [email protected] Ni as the SPME sorbent for the extraction of DUL, VEN and ATO was then compared with magnetic graphene oxide ([email protected]) and magnetic reduced graphene oxide ([email protected] Ni). Under the optimized conditions for the [email protected] Ni sorbent, the intra-day relative standard deviations (RSDs, n = 5) and the limits of detections (LODs) were lower than 4.6% and 1.1 ngmL, respectively. Moreover, the good linear ranges were observed in wide concentration ranges with R-squared larger than 0.9878. Finally, the enrichment factors in the range of 137-183 and the recovery percentage in the range of 89.2-94.8% were obtained to determine the analytes in the real samples.
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http://dx.doi.org/10.1016/j.ab.2018.05.003DOI Listing
June 2018

68-Year Old Woman with Multiple Sclerosis, Cutaneous T-Cell Lymphoma and Seizures.

Brain Pathol 2018 05;28(3):439-440

Department of Pathology, Saint Louis University, Saint Louis, MO, USA.

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http://dx.doi.org/10.1111/bpa.12611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8028544PMC
May 2018

Magnetic ethylene diamine-functionalized graphene oxide as novel sorbent for removal of lead and cadmium ions from wastewater samples.

Environ Sci Pollut Res Int 2018 Feb 8;25(6):5655-5667. Epub 2017 Dec 8.

Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran.

In this paper, magnetic ethylene diamine-functionalized graphene oxide (MDFGO) as a novel sorbent was synthesized and applied for removal of Pb(II) and Cd(II) from real wastewater samples. The morphology and molecular structure of MDFGO were studied by different analytical methods. The effective parameters in adsorption efficiency of Pb(II) and Cd(II) were studied and optimized using experimental design. Under the optimal condition, the effective parameters including pH, sorbent dosage, shaking rate, and adsorption time were 6.2, 33.0 mg, 500 rpm, and 11 min, respectively. Mechanism of adsorption kinetic was investigated using the Lagergren pseudo-first-order, pseudo-second-order, and intraparticle diffusion models. It was found that adsorption of lead and cadmium ions in the MDFGO sorbent followed from pseudo-first-order and pseudo-second-order models, respectively. Thermodynamic parameters (ΔG°, ΔH°, and ΔS°) for the lead and cadmium ions uptake onto the MDFGO sorbent were calculated and indicated that the adsorption processes were spontaneous and endothermic in nature for both cations. In order to investigate the isotherm model for adsorption of Pb(II) and Cd(II), the experimental data were studied using the Langmuir, Freundlich, and Harkins-Jura isotherm models. The results fitted well with Freundlich model for both metal ions. The new sorbent (MDFGO) was applied to remove Pb(II) and Cd(II) from battery wastewater and electroplating wastewater. The removal percentage of Pb(II) and Cd(II) were 99.6±0.5 and 99.4±0.6, respectively, and demonstrated that the new sorbent was very suitable for removal of lead and cadmium ion from the real wastewater samples.
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http://dx.doi.org/10.1007/s11356-017-0929-7DOI Listing
February 2018

Comparison of Human Amniotic, Chorionic, and Umbilical Cord Multipotent Mesenchymal Stem Cells Regarding Their Capacity for Differentiation Toward Female Germ Cells.

Cell Reprogram 2017 02;19(1):44-53

2 Department of Anatomy, Faculty of Medicine, Tehran University of Medical Sciences , Tehran, Iran .

Placenta harbors a plentiful source of various cells with stem cells or stem-like cell properties, which can be used in therapeutic procedures and research. Mesenchymal stem cells (MSCs) have attracted much attention due to their specific differentiation potential and tolerogenic properties. MSCs have been isolated from different parts of placenta; however, in this study, we isolated MSCs from amnion and chorion membrane, as well as umbilical cord (Wharton's jelly [WJ]) and compared their capacity regarding differentiation toward female germ cells under influence of 10 ng/mL BMP4. All placenta samples were collected from delivering mothers by normal cesarean section and cells were isolated by different methods. Results showed that all isolated cells were mostly positive for the MSC markers CD73, CD166, and CD105, and minimally reacted with CD34 and CD45 (hematopoietic markers). After differentiation induction using third passage cultured cells, immunocytochemistry staining showed that cells were positive for germline cell-related genes Ssea4, Oct4, and Ddx4, and oocyte-related gene Gdf9. RT-qPCR results indicated that human chorion MSCs (hCMSCs) had a greater potential to be differentiated into female germline cells. Moreover, the results of this study indicate that human umbilical cord MSCs originated from either male or female umbilical cord have the same differentiation potential into female germline cells. We recommend that for presumptive application of MSCs for infertility treatment and research, hUMSCs are best candidates due to their higher differentiation potential, ease of proliferation and expansion, and low immunogenicity.
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http://dx.doi.org/10.1089/cell.2016.0035DOI Listing
February 2017

Focal Injection of Ethidium Bromide as a Simple Model to Study Cognitive Deficit and Its Improvement.

Basic Clin Neurosci 2016 Jan;7(1):63-72

Department of Physiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Introduction: Memory and cognitive impairments are some of devastating outcomes of Multiple Sclerosis (MS) plaques in hippocampus, the gray matter part of the brain. The present study aimed to evaluate the intrahippocampal injection of Ethidium Bromide (EB) as a simple and focal model to assess cognition and gray matter demyelination.

Methods: Thirty Wistar rats were divided into three groups: control group, which received saline, as solvent of EB, into the hippocampus; and two experimental groups, which received 3 μL of EB into the hippocampus, and then, were evaluated 7 and 28 days after EB injection (n=10 in each group), using a 5-day protocol of Morris Water Maze (MWM) task as well as Transmission Electron Microscopy (TEM) assay.

Results: Seven days after EB injection, the behavioral study revealed a significance increase in travelled distance for platform finding in the experimental group compared to the control group. In addition, the nucleus of oligodendrocyte showed the typical clumped chromatin, probably attributed to apoptosis, and the myelin sheaths of some axons were unwrapped and disintegrated. Twenty-eight days after EB injection, the traveled distance and the time spent in target quadrant significantly decreased and increased, respectively in experimental groups compared to the control group. Also, TEM micrographs revealed a thin layer of remyelination around the axons in 28 days lesion group.

Discussion: While intracerebral or intraventricular injection of EB is disseminated in different parts of the brain and can affect the other motor and sensory systems, this model is confined locally and facilitates behavioral study. Also, this project could show improvement of memory function subsequent to the physiological repair of the gray matter of the hippocampus.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892333PMC
January 2016

Disclination elastica model of loop collision and growth in confined nematic liquid crystals.

Soft Matter 2015 Jul;11(27):5455-64

Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada.

Theory and modeling are used to characterize disclination loop-loop interactions in nematic liquid crystals under capillary confinement with strong homeotropic anchoring. This defect process arises when a mesogen in the isotropic phase is quenched into the stable nematic state. The texture evolution starts with +1/2 disclination loops that merge into a single loop through a process that involves collision, pinching and relaxation. The process is characterized with a combined Rouse-Frank model that incorporates the tension and bending elasticity of disclinations and the rotational viscosity of nematics. The Frank model of disclinations follows the Euler elastica model, whose non-periodic solution, known as Poleni's curve, is shown to locally describe the loop-loop collision and to shed light on why loop-loop merging results in a disclination intersection angle of approximately 60°. Additional Poleni invariants demonstrate how tension and bending pinch the two loops into a single +1/2 disclination ring. The Rouse model of disclination relaxation yields a Cahn-Hilliard equation whose time constant combines the confinement, tension/bending stiffness ratio and disclination diffusivity. Based on predictions made using this three stage process, a practical procedure is proposed to find viscoelastic parameters from defect geometry and defect dynamics. These findings contribute to the evolving understanding of textural transformations in nematic liquid crystals under confinement using the disclination elastica methodology.
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http://dx.doi.org/10.1039/c5sm00708aDOI Listing
July 2015

Theoretical predictions of disclination loop growth for nematic liquid crystals under capillary confinement.

Phys Rev E Stat Nonlin Soft Matter Phys 2014 Oct 14;90(4):042501. Epub 2014 Oct 14.

Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada.

The combination of low elasticity modulus, anisotropy, and responsiveness to external fields drives the rich variety of experimentally observed pattern formation in nematic liquid crystals under capillary confinement. External fields of interest in technology and fundamental physics are flow fields, electromagnetic fields, and surface fields due to confinement. In this paper we present theoretical and simulation studies of the pattern formation of nematic liquid crystal disclination loops under capillary confinement including branching processes from a m=+1 disclination line to two m=+1/2 disclination curves that describe the postnucleation and growth regime of the textural transformation from radial to planar polar textures. The early postnucleation and growth of emerging disclination loops in cylindrical capillaries are characterized using analytical and computational methods based on the nematic elastica that takes into account line tension and line bending stiffness. Using subdiffusive growth and constant loop anisotropy, we found that the solution to the nematic elastica is a cusped elliptical geometry characterized by exponential curvature variations. The scaling laws that govern the loop growth reflect the tension to bending elasticity balance and reveal that the loop dilation rate depends on the curvature and normal velocity of the disclination. The line energy growth is accommodated by the decrease in branch-point curvature. These findings contribute to the evolving understanding of textural transformations in nematic liquid crystals under confinement using the nematic elastic methodology.
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http://dx.doi.org/10.1103/PhysRevE.90.042501DOI Listing
October 2014

Mechanisms and shape predictions of nematic disclination branching under conical confinement.

Soft Matter 2014 May 12;10(18):3245-58. Epub 2014 Mar 12.

Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada.

Liquid crystals (LCs) are self-organizing anisotropic viscoelastic soft materials that flow like viscous liquids and display anisotropies like crystals. When a nematic liquid crystal is confined to a capillary tube with strong anchoring conditions, disclination defects of higher (+1) and lower (+1/2) topological charges can coexist, connected through a defect branch point. The shape of the +1/2 disclination lines emanating from the branch point are functions of confinement and bulk elasticity. Previous work shows that nematic liquid crystals under cylindrical confinement display a radial (one +1 line)-to-planar polar (two +1/2 lines) defect texture transition through the nucleation and uniform motion of a disclination branch point. Here we present analysis, scaling and modeling based on a non-linear non-local nematic elastic equation that shows that a branch point also can be generated from disclinations in a liquid crystal confined to different conical geometries with homeotropic anchoring conditions. The cone aperture increases the bending stiffness but decreases the curvature of the disclination. These competing effects lead to a decrease in the total disclination curvature, increase in elastic energy and volume of the branching region. The results are summarized into power laws and integrated into a shape/energy diagram that reveals the effects of confinement and its gradient (cone angle) on disclination shape selection. These new findings are useful to assess the Frank elasticity of new nematic liquid crystals and to predict novel defect structures in complex confinement, including biological microfluidics and mesophase fiber spinning.
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http://dx.doi.org/10.1039/c3sm52634hDOI Listing
May 2014
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