13 results on '"Mohammad Nabizadeh"'
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2. Life and death of colloidal bonds control the rate-dependent rheology of gels
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Mohammad Nabizadeh and Safa Jamali
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Science - Abstract
Understanding the origin of transient spatio-temporal response of colloidal gels is an essential aspect for their application. Nabizadeh and Jamali demonstrate the coupling between the lifetime of colloidal bonds and the rheology from computer simulations on steadily sheared model gels.
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- 2021
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3. Structure and Dynamics of Force Clusters and Networks in Shear Thickening Suspensions
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Mohammad Nabizadeh, Abhinendra Singh, and Safa Jamali
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General Physics and Astronomy - Abstract
Dense suspensions can exhibit shear thickening in response to large deformation. A consensus has emerged over the past few years on the formation of force networks, that span the entire system size, that lead to increased resistance to motion. Nonetheless, the characteristics of these networks are to a large extent poorly understood. Here, force networks formed in continuous and discontinuous shear thickening dense suspensions (CST and DST, respectively) are studied. We first show the evolution of the network formation and its topological heterogeneities as the applied stress increases. Subsequently, we identify force communities and coarse grain the suspension into a cluster network, and show that cluster-level dynamics are responsible for stark differences between the CST and DST behavior. Our results suggest that the force clusters formed in the DST regime are considerably more constrained in their motion, while CST clusters are loosely connected to their surrounding clusters.
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- 2022
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4. Nanopore signal deviations from pseudouridine modifications in RNA are sequence-specific: quantification requires dedicated synthetic controls
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Amr Makhamreh, Sepideh Tavakoli, Ali Fallahi, Xinqi Kang, Howard Gamper, Mohammad Nabizadehmashhadtoroghi, Miten Jain, Ya-Ming Hou, Sara H. Rouhanifard, and Meni Wanunu
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Medicine ,Science - Abstract
Abstract Chemical modifications to mRNA respond dynamically to environmental cues and are important modulators of gene expression. Nanopore direct RNA sequencing has been applied for assessing the presence of pseudouridine (ψ) modifications through basecalling errors and signal analysis. These approaches strongly depend on the sequence context around the modification, and the occupancies derived from these measurements are not quantitative. In this work, we combine direct RNA sequencing of synthetic RNAs bearing site-specific modifications and supervised machine learning models (ModQuant) to achieve near-analytical, site-specific ψ quantification. Our models demonstrate that the ionic current signal features important for accurate ψ classification are sequence dependent and encompass information extending beyond n + 2 and n − 2 nucleotides from the ψ site. This is contradictory to current models, which assume that accurate ψ classification can be achieved with signal information confined to the 5-nucleotide k-mer window (n + 2 and n − 2 nucleotides from the ψ site). We applied our models to quantitatively profile ψ occupancy in five mRNA sites in datasets from seven human cell lines, demonstrating conserved and variable sites. Our study motivates a wider pipeline that uses ground-truth RNA control sets with site-specific modifications for quantitative profiling of RNA modifications. The ModQuant pipeline and guide are freely available at https://github.com/wanunulab/ModQuant .
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- 2024
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5. Jamming Distance Dictates Colloidal Shear Thickening
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Safa Jamali, Alan R. Jacob, Lilian C. Hsiao, Mohammad Nabizadeh, and Shravan Pradeep
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Dilatant ,Materials science ,Rheometry ,Condensed matter physics ,Dissipative particle dynamics ,digestive, oral, and skin physiology ,General Physics and Astronomy ,FOS: Physical sciences ,Jamming ,02 engineering and technology ,Surface finish ,Condensed Matter - Soft Condensed Matter ,021001 nanoscience & nanotechnology ,01 natural sciences ,Condensed Matter::Soft Condensed Matter ,Colloid ,Shear (geology) ,0103 physical sciences ,Surface roughness ,Soft Condensed Matter (cond-mat.soft) ,010306 general physics ,0210 nano-technology - Abstract
We report experimental and computational observations of dynamic contact networks for colloidal suspensions undergoing shear thickening. The dense suspensions are comprised of sterically stabilized poly(methyl methacrylate) hard sphere colloids that are spherically symmetric and have varied surface roughness. Confocal rheometry and dissipative particle dynamics simulations show that the shear thickening strength scales exponentially with the scaled deficit contact number and the scaled jamming distance. Rough colloids, which experience additional tangential and rolling constraints, require an average of 1.5 - 2 fewer particle contacts as compared to smooth colloids, in order to generate the same shear thickening strength. This is because the surface roughness enhances geometric friction in a way that the rough colloids do not experience a large change in the free volume near the jamming point. In contrast, smooth colloids must undergo significant reduction in the free volume to support an equivalent shear stress. The available free volume for different colloid roughness is related to the deficiency from the maximum number of nearest neighbors at jamming under shear. Our results further suggest that the force per contact is different for particles with different morphologies.
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- 2020
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6. Carbonaceous sorbents alongside an optimized magnetic solid phase extraction (MSPE) towards enrichment of crude Paclitaxel extracts from callus cultures of Taxus baccata
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Alireza Mashouf, Mohammad Nabizadeh, Jaber Nasiri, Elaheh Motamedi, Mohammad Reza Fattahi Moghadam, Houshang Alizadeh, and Mohammad Reza Naghavi
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Clinical Biochemistry ,Oxide ,02 engineering and technology ,Carbon nanotube ,01 natural sciences ,Biochemistry ,Analytical Chemistry ,law.invention ,chemistry.chemical_compound ,law ,Solid phase extraction ,Graphite ,Response surface methodology ,Chromatography ,biology ,Graphene ,010401 analytical chemistry ,Cell Biology ,General Medicine ,021001 nanoscience & nanotechnology ,biology.organism_classification ,0104 chemical sciences ,chemistry ,Taxus ,Magnetic nanoparticles ,0210 nano-technology - Abstract
Here, a number of synthesized and commercial nano-sorbents including graphene (G), multi-wall carbon nanotube (MWCNT), graphene oxide (GO), reduced graphene oxide (rGO) and magnetic nanoparticles anchored on GO (Fe 3 O 4 NPs@GO) followed by graphite (Gt) powder were employed for paclitaxel pre-purification from callus culture-derived extract of Taxus baccata . Based on our preliminary work, rGO and Fe 3 O 4 NPs@GO exhibited the maximum potential, not only to remove impurities, but also to ameliorate taxol purity. According to the results of response surface methodology (RSM) developed for the superior nano-sorbent (i.e., Fe 3 O 4 NPs@GO), for both proposed quadratic polynomial models, statistically substantial relationships obtained between the actual and predicted values (p 3 O 4 NPs@GO nano-sorbent and RSM can be recommended as a simple, cost-effective and fast route for sorbent-assistant pre-purification investigations of paclitaxel.
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- 2017
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7. Characterization of the volatile oil compositions from Hypericum perforatum L. shoot cultures in different basal media
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Mohammad Reza Morshedloo, Mohammad Nabizadeh, Morteza Akramian, and Darab Yazdani
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Shoot culture ,lcsh:SB1-1110 ,In vitro culture ,lcsh:Agriculture (General) ,lcsh:Plant culture ,lcsh:S1-972 ,Essential oil ,Hypericum perforatum L - Abstract
St. John’s wort (Hypericum perforatum L.) is the most important species of the genus Hypericum and produces a wide range of chemical constituents including essential oil. Regarding advantages of in vitro culture techniques in production of desired metabolites, the present study was aimed to investigate volatile constituents of H. perforatum shoots cultured in different basal media. Shoot cultures were established by culturing six nodes of aseptic plants in three liquid media including MS (Murashige and Skoog), B5 (Gamborg B-5) and half-strength B5 containing 30 g L-1 sucrose and 0.5 mg L-1 BA (6-benzyladenine). According to the results, growth and profile of volatile constituents of cultured shoots were affected by the type of medium used and shoots cultured in the B5 medium exhibited the highest growth which was reached to 42.95 g flask-1. On the other hand, 44 components were totally identified by GC-FID and GC-MS analysis of essential oils of cultured shoots. Decane (27.7%), menthol (8.9%), methyl decanoate (4.6%) and β-elemene (4.6%) were the major volatile constituents of the shoots cultured in MS medium, while eudesma4(15),7-dien-1-β-ol (8.1-7.5%), thymol (7-7.2%) and 1,4-trans-1,7-trans-acorenone (5.2-5.5%) were found as the principal components of shoots cultured in B5 and half-strength B5 media.
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- 2017
8. Predicting vitamin E and C consumption intentions and behaviors among factory workers based on protection motivation theory
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Behzad Shahmoradi, Sahar Mohammad Nabizadeh, Parvaneh Taymoori, Mehra Shirazi, Mohammad Saleh Hazhir, and Daem Roshani
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Adult ,Male ,0301 basic medicine ,Vitamin ,Health Knowledge, Attitudes, Practice ,Coping (psychology) ,medicine.medical_treatment ,Health Behavior ,Ascorbic Acid ,Intention ,Structural equation modeling ,Developmental psychology ,Eating ,03 medical and health sciences ,chemistry.chemical_compound ,medicine ,Humans ,Vitamin E ,Vitamin C ,Consumption (economics) ,Motivation ,Protection motivation theory ,030109 nutrition & dietetics ,lcsh:Public aspects of medicine ,Construction Industry ,Public Health, Environmental and Occupational Health ,lcsh:RA1-1270 ,General Medicine ,Explained variation ,Self Efficacy ,chemistry ,Factory (object-oriented programming) ,Psychology ,Research Article - Abstract
Background Study of antioxidant vitamin consumption behavior, especially in high-risk groups with high exposure to toxic metals to reduce metal toxicity, is emphasized. This study aims to examine the structural relationships between knowledge, protection motivation theory constructs, and vitamin E and C consumption behavior among cement factory workers. Methods Protection motivation theory and food frequency questionnaires were completed by 420 factory workers. Data were subjected to structural equation modeling to examine associations between knowledge, protection motivation theory constructs, and vitamin E and C consumption behavior. Efficacy of current recommended models was also explored. Results Structural equation modeling showed high explained variance within the constructs of protection motivation theory for vitamin E and C consumption behavior and intention (56–76%). The overall fit of the structural models was acceptable for both vitamin E and C behavior. Knowledge, self-efficacy, response efficacy, and perceived vulnerability predicted intention, which in turn predicted vitamin consumption behavior. Significant relationships between knowledge and self-efficacy, response efficacy, perceived vulnerability, and perceived severity were also found, while self-efficacy and response efficacy showed significant relationships with vitamin E and C consumption behavior. Conclusions Considering that response efficacy, self-efficacy, and intention showed as strong predictors of vitamin E and C consumption behavior, specific attention should be paid to coping appraisals and intention when designing intervention plans. Additionally, establishing the predicting role of knowledge for protection motivation theory constructs and protective behaviors should be integrated into intervention programs.
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- 2018
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9. Educational Intervention Based on Protection Motivation Theory to Improve Vitamin E and C Consumption among Iranian Factory Workers
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Parvaneh Taymoori, Daem Roshani, Sahar Mohammad Nabizadeh, Mohammad Saleh Hazhir, and Mehra Shirazi
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Consumption (economics) ,vitamins intake ,Vitamin E ,medicine.medical_treatment ,lcsh:R ,Clinical Biochemistry ,nutrition education ,lcsh:Medicine ,General Medicine ,Protection motivation theory ,Environmental health ,Intervention (counseling) ,workers ,medicine ,Factory (object-oriented programming) ,Psychology - Abstract
Introduction: Various studies have suggested the protective role of antioxidant vitamins such as vitamin C and E against toxic injury and disease resulting from toxic metals. Thus, studying the antioxidant vitamins consumption behaviour, particularly in high-risk groups such as factory workers with high exposure to toxic metals is emphasised. Aim: This study examined the effects of educational interventions based on the Protection Motivation Theory (PMT) among cement factory workers after intervention and six months of follow-up. Materials and Methods: Cement factory workers were randomly assigned into three groups: indirect (n=70), face-to-face (n=70) and control (n=70). The content of face-to-face interventions included multimodal lectures with powerpoint presentations, discussion, questions and answers, individual counselling sessions, and educational pamphlets and booklets. The indirect group received recently designed educational content through pamphlets and booklets. Workers completed PMT questionnaire and Food Frequency Questionnaire (FFQ) at baseline, post-intervention, and at the six-month follow-up. Results: Results showed significant positive changes on all PMT constructs, knowledge, and vitamins E and C consumption in both intervention groups at immediate post-intervention and at six month follow-up. Knowledge and intention remained higher in face-to-face groups than in indirect group and higher maintenance was also observed in relation to vitamins and C consumption in the face-to-face group. Conclusion: Findings of this study indicated the PMT intervention, particularly face-to-face intervention, is sound and can be performed for other protective dietary behaviours, such as other antioxidants consumption.
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- 2018
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10. Animal models of stress-based depression
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Mohammad Nabizadeh
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Social defeat ,business.industry ,DNA methylation ,Hippocampus ,Medicine ,Learned helplessness ,Epigenetics ,business ,Prefrontal cortex ,Pathological ,Neuroscience ,Depression (differential diagnoses) - Abstract
Depression is one of the most common psychiatric disorders. Despite the prevalence and serious effects of depression, the pathological studies of depression are still preliminary. The main reason for this is limited access to valid animal models. Using animal models, the underlying molecular changes and causal relationship between environmental or genetic changes and depression can be studied, which provides a better insight into the pathology of depression. The role of stress as a key factor in the etiology of depression is emphasized. Because of the importance of stress in creating depression disorder in this study, animal models of stress - based depression have been investigated. Animal models of stress - based depression are:1- learned helplessness (LH) model 2- Models based on early-life stress 3- chronic mild stress (CMS) model 4- Social defeat stress model. Studies show that exposure to early life stress can continuously alter DNA methylation in the brain of adult mice or rodents. In this regard, we can mention the role of methylation of Nr3c1 gene in parts of the hippocampus of the brain, indicating that epigenetic changes may play a role in depressive like behavior. Also, an unpredictable chronic mild stress model in rodents shows that significantly reduced diffusion of astrocyte cell gap and abnormal ultrastructure gap junction in the prefrontal cortex (PFC) and low levels of adenosine triphosphate (ATP) in the mouse brain, are the cause of depressive like behavior.
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- 2019
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11. Modified AHP-based decision-making model toward accurate selection of eligible maintenance media for production of taxanes in Taxus baccata callus culture
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Jaber Nasiri, Mohammad Nabizadeh, Houshang Alizadeh, Alireza Mashouf, Mohammad Reza Naghavi, and Mohammad Reza Fattahi Moghadam
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biology ,Physiology ,business.industry ,Casamino acid ,Analytic hierarchy process ,Plant Science ,biology.organism_classification ,Biotechnology ,chemistry.chemical_compound ,Taxus ,chemistry ,Baccatin III ,Callus ,Production (economics) ,business ,Agronomy and Crop Science ,Selection (genetic algorithm) ,Explant culture ,Mathematics - Abstract
Attempts were made here to apply a modified analytic hierarchy process (AHP) approach based on refinement assay of dominated alternatives in monitoring the most reliable callus maintenance media (supplemented with l-glutamine and Casamino acid) of Taxus baccata callus cultures in terms of five criteria. Generally, regarding stem-derived calli, 6 out of 18 maintenance media were nominated as non-dominated alternatives, and following AHP ranking test Casamino acid-based media (i.e., A12, A15 and A19) were overall nominated as the premiere. Taking leaf-derived calli into account, only l-glutamine-based media in an ascending order of A8, A4, A6, A5, A9 and A3 were introduced as non-dominated alternatives. Such results connote that l-glutamine-based feeding appears to generate more significant results either for continuous calli growth or taxanes production. In contrast, regarding the second explant, stem, both amino acid supplies had fairly equal worth. Our findings, overall, demonstrate promising applications of the proposed AHP method regarding accurate selection of the best callus maintenance cultures of T. baccata for production of different taxanes including paclitaxel, Baccatin III and 10-deacetylbaccatin III. Similarly, this statistical approach could be also applicable for other crops, for instance, for accurate selection of the best callus cultures/media and consequently production improvement of a given plant secondary metabolite/product.
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- 2015
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12. Analysis of heavy metals concentration in water and sediment in the Hara biosphere reserve, southern Iran
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Sahar Mohammad Nabizadeh, Alireza Pourkhabbaz, Borhan Mansouri, and Mohsen Nowrouzi
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Analysis of Variance ,Geologic Sediments ,Southern Iran ,Health, Toxicology and Mutagenesis ,Public Health, Environmental and Occupational Health ,Sediment ,Biosphere ,Heavy metals ,Fresh Water ,Contamination ,Hydrogen-Ion Concentration ,Iran ,Toxicology ,Trees ,Environmental chemistry ,Metals, Heavy ,Environmental science ,Water Pollutants, Chemical - Abstract
This study determined the concentration of heavy metals (Al, Cr, Cu, and Zn) in water and sediments at nine sites in the Hara biosphere reserve of southern Iran during the summer and winter 2010. Determination of Al, Cr, Cu, and Zn in water was carried out by graphite furnace atomic absorption spectrometer (Shimadzu, AA 610s) and in sediment by flame atomic absorption spectrometer (Perkin Elmer, AA3030). Results showed that the heavy metal concentrations in the water samples decreased in the sequence of Zn > Al > Cu > Cr, while in sediment samples were Cr > Zn > Cu > Al. Data analysis indicated that with the exception of Al, there was a Pearson’s correlation coefficient between pH and Cu, Zn, and Cr at α = 0.01, 0.05, and 0.001 in sediment (in winter), respectively. There were also significant differences between heavy metals of Cr, Cu, and Zn during the two seasons ( p
- Published
- 2012
13. Non-Newtonian pulsatile blood flow through the stenosed arteries: comparison between the viscoelastic and elastic arterial wall in response to the alterations.
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Jannati S, Shahri MN, Jafarzadeh N, and Firouzi F
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- Humans, Constriction, Pathologic, Pulsatile Flow physiology, Viscosity, Arteries, Hemodynamics physiology
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In this study, we investigate the impact of aortic stenosis on the hemodynamics of pulsatile blood flow within a 3D aortic model. Employing a non-Newtonian Casson model with a hematocrit of 45%, our study introduces a preliminary hypothesis to simulate blood flow dynamics, incorporating both linear elastic and viscoelastic models to define the mechanical characteristics of the artery. Through simulations conducted with Ansys-Cfx (version 15), we utilize a 2-way fluid-structure interaction (FSI) approach, employing a Lagrangian-Eulerian formulation with second-order accuracy. We explore the influence of stenosis severity on variables including velocity profiles, pressure distribution, shear stress, wall displacement, and changes in the OSI parameter. Our investigation encompasses arteries with both elastic and viscoelastic walls. The key findings that arise from our results highlight the viscoelastic model's demonstration of reduced radial wall displacement when compared to the linear elastic model. Additionally, we observe that elevated arterial stenosis percentages lead to the elongation of vortex length, heightened wall shear stress, and increased slope of velocity profiles downstream of the stenosed region. Furthermore, bulky obstruction of viscoelastic arteries as opposed to elastic, resulted in a maximum 5 percent increase in velocity profile and a 29.6% decrease in radial displacement. The zenith of shear stress occurs concomitantly with the velocity's peak within the stenosed area. Viscoelastic arterial wall shear stress at the stenosis site escalates due to the rapid expansion of the stenosis. The viscoelastic wall, responding with a blend of viscous and elastic characteristics to applied stress, undergoes slight deformation in shape. Following stress reduction, the wall gradually reverts to its original form, thus alleviating some of the applied stress. In contrast, the elastic wall retains its altered shape due to stress preservation within the material. Additionally, we ascertain an augmentation in radial displacement corresponding with increased artery stenosis., (© 2023 IOP Publishing Ltd.)
- Published
- 2023
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