17 results on '"Aavani P"'
Search Results
2. Detecting Imprinting and Maternal Effects Using Monte Carlo Expectation Maximization Algorithm
- Author
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Aavani, Pooya, Trindade, Alexandre, and Zhang, Fangyuan
- Subjects
Statistics - Methodology - Abstract
Numerous statistical methods have been developed to explore genomic imprinting and maternal effects, which are causes of parent-of-origin patterns in complex human diseases. However, most of them either only model one of these two confounded epigenetic effects, or make strong yet unrealistic assumptions about the population to avoid over-parameterization. A recent partial likelihood method (LIME) can identify both epigenetic effects based on case-control family data without those assumptions. Theoretical and empirical studies have shown its validity and robustness. However, because LIME obtains parameter estimation by maximizing partial likelihood, it is interesting to compare its efficiency with full likelihood maximizer. To overcome the difficulty in over-parameterization when using full likelihood, in this study we propose a Monte Carlo Expectation Maximization (MCEM) method to detect imprinting and maternal effects jointly. Those unknown mating type probabilities, the nuisance parameters, can be considered as latent variables in EM algorithm. Monte Carlo samples are used to numerically approximate the expectation function that cannot be solved algebraically. Our simulation results show that though this MCEM algorithm takes longer computational time, and can give higher bias in some simulations compared to LIME, it can generally detect both epigenetic effects with higher power and smaller standard error which demonstrates that it can be a good complement of LIME method.
- Published
- 2023
3. Viral inactivation by light
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Sadraeian, Mohammad, Zhang, Le, Aavani, Farzaneh, Biazar, Esmaeil, and Jin, Dayong
- Published
- 2022
- Full Text
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4. A Family of Encodings for Translating Pseudo-Boolean Constraints into SAT
- Author
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Aavani, Amir
- Subjects
Computer Science - Logic in Computer Science ,Computer Science - Data Structures and Algorithms - Abstract
A Pseudo-Boolean (PB) constraint is a linear arithmetic constraint over Boolean variables. PB constraints are convenient and widely used in expressing NP-complete problems. We introduce a new, two step, method for transforming PB constraints to propositional CNF formulas. The first step involves re-writing each PB constraint as a conjunction of PB-Mod constraints. The advantage is that PB-Mod constraints are easier to transform to CNF. In the second step, we translate each PB-Mod constraints, obtained in the previous step, into CNF. The resulting CNF formulas are small, and unit propagation can derive facts that it cannot derive using in the CNF formulas obtained by other commonly-used transformations. We also characterize the constraints for which one can expect the SAT solvers to perform well on the produced CNF. We show that there are many constraints for which the proposed encoding has a good performance., Comment: Used as the reference for SAT-2013 submission
- Published
- 2011
5. Enhanced mechanical properties of in situ aluminium matrix composites reinforced by alumina nanoparticles
- Author
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Afkham, Yalda, Khosroshahi, Rasoul Azari, Rahimpour, Sajed, Aavani, Cassra, Brabazon, Dermot, and Mousavian, Reza Taherzadeh
- Published
- 2018
- Full Text
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6. Delivery Systems for Plasma-reactive Species and their Applications in the Field of Biomedicine
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Biazar, Esmaeil, Aavani, Farzaneh, Zeinali, Reza, Kheilnezhad, Bahareh, Taheri, Kiana, and Yahyaei, Zahra
- Abstract
Cold atmospheric plasma (CAP) is an ionized matter with potential applications in various medical fields, ranging from wound healing and disinfection to cancer treatment. CAP's clinical usefulness stems from its ability to act as an adjustable source of reactive oxygen and nitrogen species (RONS), which are known to function as pleiotropic signaling agents within cells. Plasma-activated species, such as RONS, have the potential to be consistently and precisely released by carriers, enabling their utilization in a wide array of biomedical applications. Furthermore, understanding the behavior of CAP in different environments, including water, salt solutions, culture medium, hydrogels, and nanoparticles, may lead to new opportunities for maximizing its therapeutic potential. This review article sought to provide a comprehensive and critical analysis of current biomaterial approaches for the targeted delivery of plasma-activated species in the hope to boost therapeutic response and clinical applicability.
- Published
- 2024
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7. Layer-by-Layer Deposition of Regenerated Silk Fibroin─An Approach to the Surface Coating of Biomedical Implant Materials
- Author
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Fuest, Sandra, Smeets, Ralf, Gosau, Martin, Aavani, Farzaneh, Knipfer, Christian, Grust, Audrey Laure Céline, Kopp, Alexander, Becerikli, Mustafa, Behr, Björn, and Matthies, Levi
- Abstract
Biomaterials and coating techniques unlock major benefits for advanced medical therapies. Here, we explored layer-by-layer (LbL) deposition of silk fibroin (SF) by dip coating to deploy homogeneous films on different materials (titanium, magnesium, and polymers) frequently used for orthopedic and other bone-related implants. Titanium and magnesium specimens underwent preceding plasma electrolytic oxidation (PEO) to increase hydrophilicity. This was determined as surface properties were visualized by scanning electron microscopy and contact angle measurements as well as Fourier transform infrared spectroscopy (FTIR) analysis. Finally, biological in vitro evaluations of hemocompatibility, THP-1 cell culture, and TNF-α assays were conducted. A more hydrophilic surface could be achieved using the PEO surface, and the contact angle for magnesium and titanium showed a reduction from 73 to 18° and from 58 to 17°, respectively. Coating with SF proved successful on all three surfaces, and coating thicknesses of up to 5.14 μm (±SD 0.22 μm) were achieved. Using FTIR analysis, it was shown that the insolubility of the material was achieved by post-treatment with water vapor annealing, although the random coil peak (1640–1649 cm–1) and the α-helix peak (at 1650 cm–1) were still evident. SF did not change hemocompatibility, regardless of the substrate, whereas the PEO-coated materials showed improved hemocompatibility. THP-1 cell culture showed that cells adhered excellently to all of the tested material surfaces. Interestingly, SF coatings induced a significantly higher amount of TNF-α for all materials, indicating an inflammatory response, which plays an important role in a variety of physiological processes, including osteogenesis. LbL coatings of SF are shown to be promising candidates to modulate the body’s immune response to implants manufactured from titanium, magnesium, and polymers. They may therefore facilitate future applications for bioactive implant coatings. However, further in vivo studies are needed to confirm the proposed effects on osteogenesis in a physiological environment.
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- 2023
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8. Maternal Immune Activation Produces Cerebellar Hyperplasia and Alterations in Motor and Social Behaviors in Male and Female Mice
- Author
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Aavani, Tooka, Rana, Shadna A., Hawkes, Richard, and Pittman, Quentin J.
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- 2015
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9. Do Titanium Dioxide Particles Stimulate Macrophages to Release Proinflammatory Cytokines and Increase the Risk for Peri-implantitis?
- Author
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Stolzer, Carolin, Müller, Matthias, Gosau, Martin, Henningsen, Anders, Fuest, Sandra, Aavani, Farzaneh, and Smeets, Ralf
- Abstract
Titanium dioxide (TiO 2) particles detached from titanium dental implants by tribocorrosion can be phagocytosed by macrophages, releasing various proinflammatory cytokines at the implant sites that may trigger peri-implantitis. The study objective was to measure the association between peri-implantitis and the presence of non-allergy-related proinflammatory cytokines associated with TiO 2 particles. The investigators implemented a retrospective cross-sectional study and enrolled a sample of 60 subjects from a dental practice. Subjects were excluded if the plaque index was grade 3 (Silness and Löe). The predictor variable was a positive or negative TiO 2 stimulation test, an in vitro macrophage proinflammatory response test. The outcome variable was peri-implantitis status defined as present or absent. Three groups were considered: control group with 20 patients without dental implants (group 1), 2 groups of patients with titanium dental implants, one without peri-implantitis (group 2), and the other with peri-implantitis (group 3) (n = 20 each). For patients with implants, depth of the gingival pockets of the implants were measured, and existing bleeding and suppuration were determined to assess peri-implantitis. Radiographs were taken if one or more factors applied to confirm the diagnosis of peri-implantitis. Further covariates were age, sex, duration of implant wear, and number of implants which were analyzed descriptively. Inferential analyses were undertaken using χ
2 test, Kruskal–Wallis-, Wilcoxon-two-sample tests, and logistic regressions. The sample was composed of 35 female and 25 male patients with a mean age of 54.2 years (standard deviation = 14.76). The overall TiO 2 stimulation test positivity frequency was 28.3% and were 30.0%, 5.0%, and 50.0% in the control, implants without peri-implantitis, and implants with peri-implantitis groups. No statistically significant differences could be seen in the frequencies of the TiO 2 stimulation test results between control group and combined groups 2 and 3 (P -value =.84). The risk for positive TiO 2 patients with a titanium implant of developing peri-implantitis was statistically significant and higher compared to negative TiO 2 patients (odds ratio, 19.0 with 95% confidence interval [2.12,170.38]; P -value<.01). The data in this study showed a statistically significant relationship between a positive TiO 2 stimulation test and peri-implantitis. Further studies with larger numbers of subjects are recommended to confirm this result. [ABSTRACT FROM AUTHOR]- Published
- 2023
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10. Compartmentation of the Cerebellar Cortex in the Naked Mole-Rat (Heterocephalus glaber)
- Author
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Marzban, Hassan, Hoy, Nathan, Aavani, Tooka, Sarko, Diana K., Catania, Kenneth C., and Hawkes, Richard
- Published
- 2011
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11. Antibacterial properties of functionalized silk fibroin and sericin membranes for wound healing applications in oral and maxillofacial surgery
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Schäfer, Sogand, Smeets, Ralf, Köpf, Marius, Drinic, Aleksander, Kopp, Alexander, Kröger, Nadja, Hartjen, Philip, Assaf, Alexandre Thomas, Aavani, Farzaneh, Beikler, Thomas, Peters, Ulrike, Fiedler, Imke, Busse, Björn, Stürmer, Ewa K., Vollkommer, Tobias, Gosau, Martin, and Fuest, Sandra
- Abstract
Oral wounds are among the most troublesome injuries which easily affect the patients' quality of life. To date, the development of functional antibacterial dressings for oral wound healing remains a challenge. In this regard, we investigated antibacterial silk protein-based membranes for the application as wound dressings in oral and maxillofacial surgery. The present study includes five variants of casted membranes, i.e., i) membranes-silver nanoparticles (CM-Ag), ii) membranes-gentamicin (CM-G), iii) membranes-control (without functionalization) (CM-C), iv) membranes-silk sericin control (CM-SSC), and v) membranes-silk fibroin/silk sericin (CM-SF/SS), and three variants of nonwovens, i.e., i) silver nanoparticles (NW-Ag), ii) gentamicin (NW-G), iii) control (without functionalization) (NW-C). The surface structure of the samples was visualized with scanning electron microscopy. In addition, antibacterial testing was accomplished using agar diffusion assay, colony forming unit (CFU) analysis, and qrt-PCR. Following antibacterial assays, biocompatibility was evaluated by cell proliferation assay (XTT), cytotoxicity assay (LDH), and live-dead assay on L929 mouse fibroblasts. Findings indicated significantly lower bacterial colony growth and DNA counts for CM-Ag with a reduction of bacterial counts by 3log levels (99.9% reduction) in CFU and qrt-PCR assay compared to untreated control membranes (CM-C and CM-SSC) and membranes functionalized with gentamicin (CM-G and NW-G) (p < 0.001). Similarly, NW-G yielded significantly lower DNA and colony growth counts compared to NW-Ag and NW-C (p < 0.001). In conclusion, CM-Ag represented 1log level better antibacterial activity compared to NW-G, whereas NW-G showed better cytocompatibility for L929 cells. As data suggest, these two membranes have the potential of application in the field of bacteria-free oral wound healing. However, provided that loading strategy and cytocompatibility are adjusted according to the antibacterial agents' characteristic and fabrication technique of the membranes.
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- 2022
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12. Inhibitory Effect of Codeine on Sucrase Activity
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Minai-Tehrani, Dariush, Minoui, Saeed, Sepehre, Marzie, Sharif-Khodai, Zohre, and Aavani, Tooka
- Abstract
Codeine is a common drug widely used in some countries as a pain reliever. The effect of codeine on yeast sucrase activity was studied in this report. Non-competitive inhibition was observed using double reciprocal plot. The Km of enzyme did not change in the presence of different concentrations of codeine (0.5- 1.5 mM) and was determined about 11.5 mM. The Vmax of enzyme was determined about 8.8 mM/min, and the Vmax decreased in the presence of codeine. The Ki of codeine was measured by using the reaction rate and the initial concentration of the inhibitor according to the Dixon plot. The Ki was found to be 0.42 mM and the IC50 of codeine was determined about 0.875 mM.
- Published
- 2009
13. Hamartoma-like lesions in the mouse retina: an animal model of Pten hamartoma tumour syndrome
- Author
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Tachibana, Nobuhiko, Touahri, Yacine, Dixit, Rajiv, David, Luke Ajay, Adnani, Lata, Cantrup, Robert, Aavani, Tooka, Wong, Rachel O., Logan, Cairine, Kurek, Kyle C., and Schuurmans, Carol
- Abstract
PTEN hamartoma tumour syndrome (PHTS) is a heterogeneous group of rare, autosomal dominant disorders associated with PTEN germline mutations. PHTS patients routinely develop hamartomas, which are benign tissue overgrowths comprised of disorganized ‘normal’ cells. Efforts to generate PHTS animal models have been largely unsuccessful due to the early lethality of homozygous germline mutations in Pten, together with the lack of hamartoma formation in most conditional mutants generated to date. We report herein a novel PHTS mouse model that reproducibly forms hamartoma-like lesions in the central retina by postnatal day 21. Specifically, we generated a Pten conditional knockout (cKO) using a retinal-specific Pax6::Cre driver that leads to a nearly complete deletion of Pten in the peripheral retina but produces a mosaic of ‘wild-type’ and Pten cKO cells centrally. Structural defects were only observed in the mosaic central retina, including in Müller glia and in the outer and inner limiting membranes, suggesting that defective mechanical integrity partly underlies the hamartoma-like pathology. Finally, we used this newly developed model to test whether rapamycin, an mTOR inhibitor that is currently the only PHTS therapy, can block hamartoma growth. When administered in the early postnatal period, prior to hamartoma formation, rapamycin reduces hamartoma size, but also induces new morphological abnormalities in the Pten cKO retinal periphery. In contrast, administration of rapamycin after hamartoma initiation fails to reduce lesion size. We have thus generated and used an animal model of retinal PHTS to show that, although current therapies can reduce hamartoma formation, they might also induce new retinal dysmorphologies. This article has an associated First Person interview with the first author of the paper.
- Published
- 2018
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14. The anxiogenic effects of Abeta (1- 40) and Abeta (1-42) in the dorsal raphe nucleus in male rats.
- Author
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Gholizadeh, Shervin, Aavani, Tooka, and Motamedi, Fereshteh
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- 2009
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15. When sexual selection in hosts benefits parasites.
- Author
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Aavani P and Rice SH
- Abstract
In host-parasite coevolution, the parasite is selected to increase its infectivity while host is selected to resist the parasite infection. It is widely held that parasite-mediated sexual selection can further amplify the selective pressure on the host to overcome parasite infection. In this paper we focus on certain types of parasites, those that can impair the activity of the host immune function to prevent signs of sickness. We show that the effect of sexual selection can actually reduce the selective pressure on the host immune response to adapt to the parasite infection. We design a simple mathematical model for a population of sexually reproducing organism in which individuals are choosy, preferring traits that are correlated negatively with immune system activity. We introduce to this population a parasite that can suppress activation of the host's immune response. Our results show that even though the host immune system is likely to ultimately evolve and adapt to the parasite infection, when sexual selection is part of this process, it can slow down this evolution on the host and give the parasite more time to get established., (© 2022 The Authors.)
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- 2022
- Full Text
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16. Re-positive PCR of SARS-CoV-2 in health care persons during COVID-19 pandemic.
- Author
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Alebouyeh M, Aavani P, Abdulrahman NA, Haleem AA, Karimi A, Armin S, Fallah F, Amirali A, Sadr S, Ghandchi G, Abdollahi N, Ghanaie RM, Tabatabaei SR, Fahimzad SA, Razmara R, Alzahrani KJ, Khanbabaee G, Vaghefi SS, Imanzadeh F, Eshghi P, and Azimi L
- Subjects
- Antibodies, Viral, Child, Delivery of Health Care, Humans, Pandemics prevention & control, Polymerase Chain Reaction, Reinfection, COVID-19 epidemiology, SARS-CoV-2
- Abstract
Reinfection rate with SARS-CoV-2 and degree of protection by the induced antibody after the first episode of the infection is not well known, so it makes a big dilemma for health care personnel (HCP) who work in the front line of combating SARS-CoV-2. In this study, we investigated the frequency of SARS-CoV-2 redetection among HCP after the initial onset of the infection in a children's hospital during one year. Out of 131 seropositive HCP, 13.7% of them were symptomatic and PCR positive during 74-360 days after first sampling. Analysis of demographic data of seropositive HCP showed a correlation between a higher number of family members, higher body mass index, and the existence of underlying diseases with SARS-CoV-2 redetection. In conclusion, reinfection is one of the important problems in the SARS-CoV-2 pandemic. Research on this topic can help us to find answers to questions for estimating the duration of human protection with produced immunity after the infection or vaccination.
- Published
- 2022
- Full Text
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17. Diagnostic and methodological evaluation of studies on the urinary shedding of SARS-CoV-2, compared to stool and serum: A systematic review and meta-analysis.
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Roshandel MR, Nateqi M, Lak R, Aavani P, Sari Motlagh R, F Shariat S, Aghaei Badr T, Sfakianos J, Kaplan SA, and Tewari AK
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- Adolescent, Adult, Aged, COVID-19, COVID-19 Testing, COVID-19 Vaccines, Child, Child, Preschool, Coronavirus Infections diagnosis, Coronavirus Infections mortality, Coronavirus Infections virology, Female, Humans, Incidence, Infant, Intensive Care Units, Male, Middle Aged, Pandemics, Patient Admission, Pneumonia, Viral mortality, Pneumonia, Viral virology, RNA, Viral genetics, Real-Time Polymerase Chain Reaction, SARS-CoV-2, Severity of Illness Index, Young Adult, Betacoronavirus genetics, Clinical Laboratory Techniques, Coronavirus Infections epidemiology, Feces virology, Pneumonia, Viral epidemiology, Urine virology, Viremia diagnosis, Virus Shedding
- Abstract
Investigating the infectivity of body fluid can be useful for preventative measures in the community and ensuring safety in the operating rooms and on the laboratory practices. We performed a literature search of clinical trials, cohorts, and case series using PubMed/MEDLINE, Google Scholar, and Cochrane library, and downloadable database of CDC. We excluded case reports and searched all-language articles for review and repeated until the final drafting. The search protocol was registered in the PROSPERO database. Thirty studies with urinary sampling for viral shedding were included. A total number of 1,271 patients were enrolled initially, among which 569 patients had undergone urinary testing. Nine studies observed urinary viral shedding in urine from 41 patients. The total incidence of urinary SARS-CoV-2 shedding was 8%, compared to 21.3% and 39.5 % for blood and stool, respectively. The summarized risk ratio (RR) estimates for urine positive rates compared to the pharyngeal rate was 0.08. The pertaining RR urine compared to blood and stool positive rates were 0.20 and 0.33, respectively. Our review concludes that not only the SARS-CoV-2 can be excreted in the urine in eight percent of patients but also its incidence may have associations with the severity of the systemic disease, ICU admission, and fatality rates. Moreover, the findings in our review suggest that a larger population size may reveal more positive urinary cases possibly by minimizing biases.
- Published
- 2020
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