Publications by authors named "Fatemeh Molaei"

12 Publications

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Molecular dynamics simulation of edge crack propagation in single crystalline alpha quartz.

Authors:
Fatemeh Molaei

J Mol Graph Model 2021 Nov 21;111:108085. Epub 2021 Nov 21.

Dept. Mining and Geological Engineering, University of Arizona, Tucson, AZ, USA; Geotechnical Engineer at Stantec, Chandler, AZ, USA. Electronic address:

Edge crack propagation of single-crystalline alpha quartz under mode I loading condition was investigated using a molecular dynamics simulation. Five different crack lengths are used to analyze the effects of crack length on each sample's crack growth behavior. The effect of crack length was studied in terms of the material's stress-strain curve, strain energy, fracture toughness, atomic analysis of crack propagation, and crack opening deformation. The results revealed that during tensile loading, the pre-cracked crystalline quartz samples are fractured in a brittle approach. The fracture stress in the pre-cracked sample (40 Å length) is dropped about 70% compared to pristine quartz. Moreover, the effect of loading velocity on the mechanical properties is investigated. According to the findings, maximum stress rises by enhancing the loading velocity, and fracture toughness improves. The fracture surface energy of the single crystalline alpha quartz is calculated, and based on the results, there is a good agreement with experimental data.
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http://dx.doi.org/10.1016/j.jmgm.2021.108085DOI Listing
November 2021

An insight into thermal properties of BC-graphene hetero-nanosheets: a molecular dynamics study.

Sci Rep 2021 Nov 29;11(1):23064. Epub 2021 Nov 29.

Department of Polymer Technology, Faculty of Chemistry, Gdańsk University of Technology, G. Narutowicza 11/12, 80-233, Gdańsk, Poland.

Simulation of thermal properties of graphene hetero-nanosheets is a key step in understanding their performance in nano-electronics where thermal loads and shocks are highly likely. Herein we combine graphene and boron-carbide nanosheets (BC3N) heterogeneous structures to obtain BC3N-graphene hetero-nanosheet (BC3GrHs) as a model semiconductor with tunable properties. Poor thermal properties of such heterostructures would curb their long-term practice. BCGrHs may be imperfect with grain boundaries comprising non-hexagonal rings, heptagons, and pentagons as topological defects. Therefore, a realistic picture of the thermal properties of BCGrHs necessitates consideration of grain boundaries of heptagon-pentagon defect pairs. Herein thermal properties of BCGrHs with various defects were evaluated applying molecular dynamic (MD) simulation. First, temperature profiles along BCGrHs interface with symmetric and asymmetric pentagon-heptagon pairs at 300 K, ΔT = 40 K, and zero strain were compared. Next, the effect of temperature, strain, and temperature gradient (ΔT) on Kaptiza resistance (interfacial thermal resistance at the grain boundary) was visualized. It was found that Kapitza resistance increases upon an increase of defect density in the grain boundary. Besides, among symmetric grain boundaries, 5-7-6-6 and 5-7-5-7 defect pairs showed the lowest (2 × 10 m K W) and highest (4.9 × 10 m K W) values of Kapitza resistance, respectively. Regarding parameters affecting Kapitza resistance, increased temperature and strain caused the rise and drop in Kaptiza thermal resistance, respectively. However, lengthier nanosheets had lower Kapitza thermal resistance. Moreover, changes in temperature gradient had a negligible effect on the Kapitza resistance.
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http://dx.doi.org/10.1038/s41598-021-02576-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8630025PMC
November 2021

Elucidated tumorigenic role of MAML1 and TWIST1 in gastric cancer is associated with Helicobacter pylori infection.

Microb Pathog 2021 Nov 21:105304. Epub 2021 Nov 21.

Medical Genetics Research Center, Faculty of Medical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran. Electronic address:

Background: Epithelial-mesenchymal transition (EMT) has a fundamental role in tumor initiation, progression, and metastasis. Helicobacter pylori (HP) induces EMT and thus causes gastric cancer (GC) by deregulating multiple signaling pathways involved in EMT. TWIST1 and MAML1 have been confirmed to be critical inducers of EMT via diverse signaling pathways such as Notch signaling. This study aimed to investigate for the first time possible associations between TWIST1/MAML1 mRNA expression levels, HP infection, and clinicopathological characteristics in GC patients.

Method: TWIST1 and MAML1 mRNA expression levels were evaluated in tumoral and adjacent normal tissues in 73 GC patients using the quantitative reverse transcription PCR (RT-qPCR) method. PCR technique was also applied to examine the infection with HP in GC samples.

Results: Upregulation of TWIST1 and MAML1 expression was observed in 35 (48%) and 34 (46.6%) of 73 tumor samples, respectively. Co-overexpression of these genes was found in 26 of 73 (35.6%) tumor samples; meanwhile, there was a significant positive correlation between MAML1 and TWIST1 mRNA expression levels (P < 0.001). MAML1 overexpression exhibited meaningful associations with advanced tumor stages (P = 0.006) and nodal metastases (P ˂ 0.001). 34 of 73 (46.6%) tumors tested positive for HP, and meanwhile, MAML1 expression was positively related with T (P = 0.05) and grade (P = 0.0001) in these HP-positive samples. Increased TWIST1 expression was correlated with patient sex (P = 0.035) and advanced tumor grade (P = 0.017) in HP-infected tumors. Furthermore, TWIST1 and MAML1 expression levels were inversely linked with histologic grade in HP-negative tumor samples (P = 0.021 and P = 0.048, respectively).

Conclusion: We propose TWIST1 and MAML1 as potential biomarkers of advanced-stage GC that determine the characteristics and aggressiveness of the disease. Based on accumulating evidence and our findings, they can be introduced as promising therapeutic targets to modify functional abnormalities in cells that promote GC progression. Moreover, HP may enhance GC growth and metastasis by disrupting TWIS1/MAML1 expression patterns and related pathways.
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http://dx.doi.org/10.1016/j.micpath.2021.105304DOI Listing
November 2021

Thermal conductivity of random polycrystalline BC nanosheets: A step towards realistic simulation of 2D structures.

J Mol Graph Model 2021 09 25;107:107977. Epub 2021 Jun 25.

Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran.

Boron carbide nanosheets (BCNSs) are semiconductors possessing non-zero bandgap. Nevertheless, there is no estimation of their thermal conductivity for practical circumstances, mainly because of difficulties in simulation of random polycrystalline structures. In the real physics world, BCNS with perfect monocrystalline is rare, for the nature produces structures with disordered grain regions. Therefore, it is of crucial importance to capture a more realistic picture of thermal conductivity of these nanosheets. Polycrystalline BCNS (PCBCNSs are herein simulated by Molecular Dynamics simulation to take their thermal conductivity fingerprint applying ΔT of 40 K. A series of PCBCNSs were evaluated for thermal conductivity varying the number of grains (3, 5, and 10). The effect of grain rotation was also modeled in terms of Kapitza thermal resistance per grain, varying the rotation angle (θ/2 = 14.5, 16, 19, and 25°). Overall, a non-linear temperature variation was observed for PCBCNS, particularly by increasing grain number, possibly because of more phonon scattering (shorter phonon relaxation time) arising from more structural defects. By contrast, the heat current passing across the slab decreased. The thermal conductivity of nanosheet dwindled from 149 W m K for monocrystalline BCNS to the values of 129.67, 121.32, 115.04, and 102.78 W m K for PCBCNSs having 2, 3, 5, and 10 grains, respectively. The increase of the grain̛s rotation angle (randomness) from 14.5° to 16°, 19° and 25° led to a rise in Kapitza thermal resistance from 2⨯10 m K·W to the values of 2.3⨯ 10, 2.9⨯10, and 4.7⨯ 10 m K·W, respectively. Thus, natural 2D structure would facilitate phonon scattering rate at the grain boundaries, which limits heat transfer across polycrystalline nanosheets.
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http://dx.doi.org/10.1016/j.jmgm.2021.107977DOI Listing
September 2021

Hypersonic impact properties of pristine and hybrid single and multi-layer CN and BC nanosheets.

Sci Rep 2021 Apr 12;11(1):7972. Epub 2021 Apr 12.

Mining and Geological Engineering Department, The University of Arizona, Arizona, USA.

Carbon, nitrogen, and boron nanostructures are promising ballistic protection materials due to their low density and excellent mechanical properties. In this study, the ballistic properties of C3N and BC3 nanosheets against hypersonic bullets with Mach numbers greater than 6 were studied. The critical perforation conditions, and thus, the intrinsic impact strength of these 2D materials were determined by simulating ballistic curves of C3N and BC3 monolayers. Furthermore, the energy absorption scaling law with different numbers of layers and interlayer spacing was investigated, for homogeneous or hybrid configurations (alternated stacking of C3N and the BC3). Besides, we created a hybrid sheet using van der Waals bonds between two adjacent sheets based on the hypervelocity impacts of fullerene (C60) molecules utilizing molecular dynamics simulation. As a result, since the higher bond energy between N-C compared to B-C, it was shown that C3N nanosheets have higher absorption energy than BC3. In contrast, in lower impact speeds and before penetration, single-layer sheets exhibited almost similar behavior. Our findings also reveal that in hybrid structures, the C3N layers will improve the ballistic properties of BC3. The energy absorption values with a variable number of layers and variable interlayer distance (X = 3.4 Å and 4X = 13.6 Å) are investigated, for homogeneous or hybrid configurations. These results provide a fundamental understanding of ultra-light multilayered armors' design using nanocomposites based on advanced 2D materials. The results can also be used to select and make 2D membranes and allotropes for DNA sequencing and filtration.
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http://dx.doi.org/10.1038/s41598-021-86537-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8041847PMC
April 2021

Design and synthesis of novel phe-phe hydroxyethylene derivatives as potential coronavirus main protease inhibitors.

J Biomol Struct Dyn 2021 Mar 30:1-9. Epub 2021 Mar 30.

Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran.

In response to the current pandemic caused by the novel SARS-CoV-2, we design new compounds based on Lopinavir structure as an FDA-approved antiviral agent which is currently under more evaluation in clinical trials for COVID-19 patients. This is the first example of the preparation of Lopinavir isosteres from the main core of Lopinavir conducted to various heterocyclic fragments. It is proposed that main protease inhibitors play an important role in the cycle life of coronavirus. Thus, the protease inhibition effect of synthesized compounds was studied by molecular docking method. All of these 10 molecules, showing a good docking score compared. Molecular dynamics (MD) simulations also confirmed the stability of the best-designed compound in Mpro active site.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1905549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8022343PMC
March 2021

Approaches for the integration of big data in translational medicine: single-cell and computational methods.

Ann N Y Acad Sci 2021 06 6;1493(1):3-28. Epub 2021 Jan 6.

Laser Research Centre, Faculty of Health Science, University of Johannesburg, South Africa.

Translational medicine describes a bench-to-bedside approach that eventually converts findings from basic scientific studies into real-world clinical research. It encompasses new treatments, advanced equipment, medical procedures, preventive and diagnostic approaches creating a bridge between basic studies and clinical research. Despite considerable investment in basic science, improvements in technology, and increased knowledge of the biology of human disease, translation of laboratory findings into substantial therapeutic progress has been slower than expected, and the return on investment has been limited in terms of clinical efficacy. In this review, we provide a fresh perspective on some experimental and computational approaches for translational medicine. We cover the analysis, visualization, and modeling of high-dimensional data, with a focus on single-cell technologies, sequence, and structure analysis. Current challenges, limitations, and future directions, with examples from cancer and fibrotic disease, will be discussed.
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http://dx.doi.org/10.1111/nyas.14544DOI Listing
June 2021

Long noncoding RNAs and exosomal lncRNAs: classification, and mechanisms in breast cancer metastasis and drug resistance.

Oncogene 2020 01 10;39(5):953-974. Epub 2019 Oct 10.

Department of Biochemistry and Molecular Biology, LSUHSC, School of Medicine, New Orleans, LA, USA.

Breast cancer is the most common cancer, and the second cause of cancer-related deaths (after lung cancer) among women. Developing tumor metastasis and invasion is the most important cause of death in breast cancer patients. Several key factors participate in breast cancer metastasis including long noncoding RNAs (lncRNAs). lncRNAs are a category of cellular RNAs that are longer than 200 nucleotides in length. Accumulating evidence suggests that lncRNAs have the potential to be promising diagnostic, prognostic biomarkers and therapeutic targets in breast cancer. Understanding the role of lncRNAs and their mechanisms of functions might help to further discovery of breast cancer biological characteristics. In this review, we discuss physiological functions, epigenetic regulation, transcriptional regulation of lncRNAs, and their important role in tumor progression and metastasis. Some lncRNAs function as oncogenes and some function as tumor suppressors. Interestingly, recent reports depict that hypomethylation of promoters of lncRNAs play a pivotal role in cancer progression, suggesting the importance of epigenetic regulation. Furthermore, we discuss the role of lncRNAs in exosomes and their function in drug resistance, and therapeutic importance of exosomal lncRNAs in cancer biology. In summary, lncRNAs have a great potential to consider them as novel prognostic biomarkers as well as new therapeutic targets in breast cancer.
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http://dx.doi.org/10.1038/s41388-019-1040-yDOI Listing
January 2020

In silico evidence of high frequency of miRNA-related SNPs in Esophageal Squamous Cell Carcinoma.

J Cell Physiol 2020 02 25;235(2):966-978. Epub 2019 Jul 25.

Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran.

Esophageal squamous cell carcinoma (ESCC) is the dominant histological type of esophageal cancer significantly reported in developing nations. There is an increasing evidence suggesting that single nucleotide polymorphisms (SNPs) in the untranslated regions of genes (3'-UTRs) targeted by microRNAs (miRNAs) can change the target gene's expression and thereby affect the individual's cancer risk. Thus, in support of the role of SNPs occurring in miRNA target sites (miR-TS-SNPs) in the cancer, we analyzed the next generation sequencing data of 10 ESCC patients. In each patient, about 3,000 SNPs in 3'-UTRs were obtained in their whole-exome sequencing profiles. We applied two separate methods, manual and computational in silico approaches, to predict the miR-TS-SNPs with more effects on the miRNA-target interactions. dbSNP, 1000G, ExAC, Iranome, miRandb, miRCancer, TargetScan, Human, miRNASNP2 and miRBase databases were used for positive selection of miR-TS-SNPs and DIANA-miRPath v3.0 for pathway analysis. We identified six rare germline miR-TS-SNPs and two other ones with unknown miR-TS-SNPs. We interestingly observed all of these variants in only one patient, which can be evidence of the relationship between miR-TS-SNPs and cancer incidence. The study of cancer genetics including miR-TS-SNPs reveals miRNAs and their related pathways, which will be greatly useful in cancer research from noninvasive biomarkers to new treatments.
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http://dx.doi.org/10.1002/jcp.29012DOI Listing
February 2020

Mutation Screening of KCNQ1 and KCNE1 Genes in Iranian Patients With Jervell and Lange-Nielsen Syndrome.

Fetal Pediatr Pathol 2019 Aug 3;38(4):273-281. Epub 2019 Apr 3.

d Human Genetic Division, Immunology Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences , Mashhad , Iran.

: Jervell and Lange-Nielsen syndrome (JLNS) is an autosomal recessive genetic disease with deafness and QT prolongation. Mutations in KCNQ1 and KCNE1 genes are a cause of JLNS. Our objective was to perform mutational analysis of the KCNQ1 and KCNE1 genes to determine the frequency of mutations in the Iranian population. : Fourteen patients and their families were investigated. Mutational screening of the KCNQ1 and KCNE1 genes was performed by a polymerase chain reaction (PCR) followed by direct Sanger sequencing. : We identified two frameshift mutations in the KCNQ1 gene, including a novel mutation, c.1356 1356delG, and a known mutation, c.1534_1534delG. A common single nucleotide polymorphism (SNP), c.112G > A, was also found in KCNE1 in seven probands. A novel mutation in the KCNQ1 gene is described. There may be less frequency of mutations in the KCNQ1 and of KCNE1 genes in Iranian JLNS patients compared with other populations.
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http://dx.doi.org/10.1080/15513815.2019.1585500DOI Listing
August 2019

Exosomes: composition, biogenesis, and mechanisms in cancer metastasis and drug resistance.

Mol Cancer 2019 04 2;18(1):75. Epub 2019 Apr 2.

Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, USA.

Tumor-derived exosomes (TDEs) participate in formation and progression of different cancer processes, including tumor microenvironment (TME) remodeling, angiogenesis, invasion, metastasis and drug-resistance. Exosomes initiate or suppress various signaling pathways in the recipient cells via transmitting heterogeneous cargoes. In this review we discuss exosome biogenesis, exosome mediated metastasis and chemoresistance. Furthermore, tumor derived exosomes role in tumor microenvironment remodeling, and angiogenesis is reviewed. Also, exosome induction of epithelial mesenchymal transition (EMT) is highlighted. More importantly, we discuss extensively how exosomes regulate drug resistance in several cancers. Thus, understanding exosome biogenesis, their contents and the molecular mechanisms and signaling pathways that are responsible for metastasis and drug-resistance mediated by TDEs may help to devise novel therapeutic approaches for cancer progression particularly to overcome therapy-resistance and preventing metastasis as major factors of cancer mortality.
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http://dx.doi.org/10.1186/s12943-019-0991-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444571PMC
April 2019

Molecular Signaling in Tumorigenesis of Gastric Cancer

Iran Biomed J 2018 07 30;22(4):217-30. Epub 2018 Apr 30.

Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.

Gastric cancer (GC) is regarded as the fifth most common cancer and the third cause of cancer-related deaths worldwide. Mechanism of GC pathogenesis is still unclear and relies on multiple factors, including environmental and genetic characteristics. One of the most important environmental factors of GC occurrence is infection with Helicobacter pylori that is classified as class one carcinogens. Dysregulation of several genes and pathways play an essential role during gastric carcinogenesis. Dysregulation of developmental pathways such as Wnt/β-catenin signaling, Hedgehog signaling, Hippo pathway, Notch signaling, nuclear factor-kB, and epidermal growth factor receptor have been found in GC. Epithelial-mesenchymal transition, as an important process during embryogenesis and tumorigenesis, is supposed to play a role in initiation, invasion, metastasis, and progression of GC. Although surgery is the main therapeutic modality of the disease, the understanding of biological processes of cell signaling pathways may help to develop new therapeutic targets for GC.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5949124PMC
http://dx.doi.org/10.22034/ibj.22.4.217DOI Listing
July 2018
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