Comparison of Univariate and Multivariate Gene Set Analysis in Acute Lymphoblastic Leukemia

Soheila, Khodakarim,Hamid, AlaviMajd,Farid, Zayeri,Mostafa, Rezaei-Tavirani,Nasrin, Dehghan-Nayeri,Syyed-Mohammad, Tabatabaee,Vahide, Tajalli Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.3

Background: Gene set analysis (GSA) incorporates biological with statistical knowledge to identify gene sets which are differentially expressed that between two or more phenotypes. Materials and Methods: In this paper gene sets differentially expressed between acute lymphoblastic leukaemia (ALL) with BCR-ABL and those with no observed cytogenetic abnormalities were determined by GSA methods. The BCR-ABL is an abnormal gene found in some people with ALL. Results: The results of two GSAs showed that the Category test identified 30 gene sets differentially expressed between two phenotypes, while the Hotelling's $T^2$ could discover just 19 gene sets. On the other hand, assessment of common genes among significant gene sets showed that there were high agreement between the results of GSA and the findings of biologists. In addition, the performance of these methods was compared by simulated and ALL data. Conclusions: The results on simulated data indicated decrease in the type I error rate and increase the power in multivariate (Hotelling's $T^2$) test as increasing the correlation between gene pairs in contrast to the univariate (Category) test.

Micropropagation of Ginkgo biloba by Using Nodal Buds of Juvenile Plants

Soheila Koorepaz,Hossein Arouiee,AbdolReza Bagheri,Reza Vessal 한국원예학회 2006 한국원예학회 기타간행물 Vol.- No.-

Cranberry and Sumac Extracts Exhibit Antibacterial and Anti-Adhesive Effects Against Streptococcus pyogenes

Soheila Abachi,Sabrina Mace,Song Lee,H.P. Vasantha Rupasinghe 한국식품영양과학회 2022 Journal of medicinal food Vol.25 No.4

Group A Streptococci (GAS) or Streptococcus pyogenes is responsible for acute bacterial pharyngitis in children as well as adults. Streptococcal pharyngitis is initiated by successful attachment and colonization of the bacteria, followed by the establishment of the biofilm in various environments. In this study, we examined the antibacterial activities of in-house prepared aqueous and ethanolic extracts of 10 Atlantic Canada fruits in the context of minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), time–kill kinetics, and adhesion inhibition properties against S. pyogenes. Per our findings, MIC and MBC for all the tested extracts ranged from 0.25 to 8 mg/mL and from 4 to 64 mg/mL, respectively. Accordingly, at 1⁄2 × MBC, cranberry and sumac extracts also lowered the attachment of GAS to the uncoated and fibronectin-coated substratum. Particularly, cranberry and sumac aqueous extracts were more effective against the adhesion of S. pyogenes ATCC 19615 to the fibronectin-coated surface than a clinical strain. In conclusion, ethanolic and aqueous extracts of cranberry and sumac could potentially be incorporated into natural health products designed for the amelioration of strep throat, yet a detailed understanding of its mode of action (e.g., biofilm inhibition and eradication) could pave its path to the field of antibacterial natural health product discovery, design, and development.

Form-finding of lifting self-forming GFRP elastic gridshells based on machine learning interpretability methods

Soheila Kookalani,Sandy Nyunn,Sheng Xiang 국제구조공학회 2022 Structural Engineering and Mechanics, An Int'l Jou Vol.84 No.5

Glass fiber reinforced polymer (GFRP) elastic gridshells consist of long continuous GFRP tubes that form elastic deformations. In this paper, a method for the form-finding of gridshell structures is presented based on the interpretable machine learning (ML) approaches. A comparative study is conducted on several ML algorithms, including support vector regression (SVR), K-nearest neighbors (KNN), decision tree (DT), random forest (RF), AdaBoost, XGBoost, category boosting (CatBoost), and light gradient boosting machine (LightGBM). A numerical example is presented using a standard double-hump gridshell considering two characteristics of deformation as objective functions. The combination of the grid search approach and k-fold cross-validation (CV) is implemented for fine-tuning the parameters of ML models. The results of the comparative study indicate that the LightGBM model presents the highest prediction accuracy. Finally, interpretable ML approaches, including Shapely additive explanations (SHAP), partial dependence plot (PDP), and accumulated local effects (ALE), are applied to explain the predictions of the ML model since it is essential to understand the effect of various values of input parameters on objective functions. As a result of interpretability approaches, an optimum gridshell structure is obtained and new opportunities are verified for form-finding investigation of GFRP elastic gridshells during lifting construction.

Feature Selection in Spectral Clustering

Soheila Ashkezari Toussi,Hadi Sadoghi Yazdi 보안공학연구지원센터(IJSIP) 2011 International Journal of Signal Processing, Image Vol.4 No.3

The Relationship Between Serum 25 Hydroxy Vitamin D Levels and Asthma in Children

Soheila Alyasin,Tooba Momen,Sara Kashef,Abbass Alipour,Reza Amin 대한천식알레르기학회 2011 Allergy, Asthma & Immunology Research Vol.3 No.4

Purpose: Asthma and other allergic disorders have increased over the past decades in nearly all nations. Many studies have suggested the role of vitamin D deficiency in both T-helper1 and T-helper2 diseases; however, the association between vitamin D, allergy, and asthma remains uncertain. In this study, the associations of 25-hydroxy vitamin D3 levels with asthma and with the severity of asthma were evaluated. Methods: This cross-sectional study was conducted on 50 asthmatic children and 50 healthy controls aged 6–18 years. Serum 25-hydroxy vitamin D3 levels were determined and compared between the two groups. The relationship between serum vitamin D levels and pulmonary function test outcomes and eosinophil counts were examined in asthmatic patients. Results: Univariate analysis of the relationship between asthma and vitamin D showed that decreased vitamin D levels were associated with significantly increased odds of asthmatic state (P=0.002). In a multivariate analysis after adjustment for age, body mass index, and sex, the relationship between vitamin D and asthma increased. In asthmatic patients, 25-hydroxy vitamin D levels had direct and significant correlations with both predicted FEV1 (R2=0.318; P=0.024) and FEV1/FVC (R2=0.315; P=0.026). There were no associations between vitamin D level and eosinophil counts, duration of disease, and the number of hospitalization or unscheduled visits in the previous year (P>0.05). Conclusions: These results showed that serum 25-hydroxy vitamin D levels were inversely associated with asthma, and there was a direct and significant relationship between vitamin D levels and pulmonary function test outcomes in asthmatic children. An interventional study in asthmatic patients with low serum vitamin D concentration may establish a causal relationship between asthma and vitamin D.

Single-Chain Conformational Characteristics of Comb-Like Polyelectrolytes: Molecular Dynamics Simulation Study

Soheila Emamyari,Hossein Fazli 한국고분자학회 2019 Macromolecular Research Vol.27 No.1

The single-chain conformation of a model comb polyelectrolyte, in which the electric charges are located on the last monomer of side chains, has been studied using molecular dynamics simulations. The model chain has a hydrophobic backbone and hydrophilic side chains. The influence of parameters such as the length of backbone and side chains, the grafting density of side chains, flexibility of the chain and different strengths of backbone hydrophobicity have been investigated. At high grafting density of side chains, a transition from turn to pearl-necklace and finally to globular conformation is observed by increasing the hydrophobicity. Radius of gyration (R g) of the backbone depends linearly on the number of backbone monomers at low values of the backbone hydrophobicity, but at high values of the backbone hydrophobicity, because of the appearance of turn-like segments between successive globular sections in the pearl-necklace structure, the scaling exponent of R g versus N is larger. Also, the chain flexibility affects the backbone conformation significantly. The increase of the persistence length leads to the appearance of the folded and then the extended conformations. In addition to the statistical properties of the chains, the investigation of the relaxation of the chains conformation shows that, the backbone takes almost its final conformation in the early time steps of the simulation for all conditions. It means that the relaxation time of the chain is relatively short (fast relaxation).

Pleuropulmonary blastoma is a rare malignancy in young adult and childhood

Soheila Zareifar,Mehran Karimi,Mandana Tasbihi,Babak Abdolkarimi,Bita Geramizadeh 대한종양외과학회 2015 Korean Journal of Clinical Oncology Vol.11 No.1

Identification of Gastrointestinal Digestion Stable Antihypertensive Fish Peptides from Atlantic Mackerel (Scomber scombrus)

Soheila Abachi Hokmabadinazhad,Jacinthe Thibodeau,Ismail Fliss,Andre´ Marette,Laurent Bazinet,Lucie Beaulieu 한국식품영양과학회 2022 Journal of medicinal food Vol.25 No.10

High blood pressure has been recognized as one of the main risk factors of cardiometabolic syndrome by health organizations. Hypertension is medicated by various classes of synthetic drugs; however, adverse effects have repeatedly been reported. Moreover, natural alternatives such as fish peptides have been effective in the treatment and prevention of hypertension. The aim of our study was to fractionate and identify antihypertensive peptides. Fractions were produced using different techniques of solid-phase extraction (SPE), pressure-driven ultrafiltration (UF), and electro04dialysis with UF membrane. According to our results, the hydrophobic fraction of SPE (IC50 5 μg) was the most potent anti-angiotensin converting enzyme (ACE) product. Findings of the study suggest that the separation technique plays an important role in the isolation efficiency of antihypertensive biopeptides. Importantly, the hydrophobic fraction's activity was retained through a static model of an in vitro gastrointestinal digestion system. In conclusion, polarity regardless of charge and size was the most important factor for anti-ACE activity of an Atlantic mackerel biopeptide. In addition, the presence of leucine at either of the extremities (C- or N-terminal) and/or leucine-rich motifs could well explain the hypotensive effect of our active fraction.

Spermine Modified PNIPAAm Nano-Hydrogel Serving as Thermo-Responsive System for Delivery of Cisplatin

Soheila Ghasemi,Marzieh Owrang,Farzad Javaheri,Fatemeh Farjadian 한국고분자학회 2022 Macromolecular Research Vol.30 No.5

Poly(N-isopropylacrylamide) (PNIPAAm) hydrogel as a temperatureresponsive polymer was prepared through controlled process using reversible addition fragmentation chain transfer (RAFT) polymerization. The hydrogel was then amino modified using a biocompatible polyamine i.e. spermine and next the antitumor cisplatin drug was conjugated to the modified hydrogel via pH-sensitive spermine linkage. This system had a pH dependency and temperature sensitivity at lower critical solution temperature (LCST). Cisplatin potentially is liberated from the carrier in the acidic environment. However, the release of cisplatin from this polymeric system is increased considerably around the transition temperature of the polymer. The drug release manner of the prepared hydrogel was determined at two pH values (5.5 and 7.4) and three temperatures (37, 40 and 42℃) at different time intervals. The in vitro toxicity assessment was conducted on MCF-7 cell line which showed the system efficiency in killing breast cancer cells.