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A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction

Genomics, Proteomics & Bioinformatics 2023年第6期21卷 1266-1285页

作者： Farzaneh esmaili Mahdi Pourmirzaei Shahin Ramazi Seyedehsamaneh Shojaeilangari Elham Yavari Department of Information Technology Tarbiat Modares UniversityTehran 14115-111Iran Department of Biophysics Faculty of Biological SciencesTarbiat Modares UniversityTehran 14115-111Iran Biomedical Engineering Group Department of Electrical Engineering and Information TechnologyIranian Research Organization for Science and Technology(IROST)Tehran 33535-111Iran

Post-translational modifications(PTMs)have key roles in extending the functional diversity of proteins and,as a result,regulating diverse cellular processes in prokaryotic and eukaryotic *** modification is a vital PTM that occurs in most proteins and plays a significant role in many biological *** in the phosphorylation process lead to multiple diseases,including neurological disorders and *** purpose of this review is to organize this body of knowledge associated with phosphorylation site(p-site)prediction to facilitate future research in this *** first,we comprehensively review all related databases and introduce all steps regarding dataset creation,data preprocessing,and method evaluation in p-site ***,we investigate p-site prediction methods,which are divided into two computational groups:algorithmic and machine learning(ML).Additionally,it is shown that there are basically two main approaches for p-site prediction by ML:conventional and end-to-end deep learning methods,both of which are given an ***,this review introduces the most important feature extraction techniques,which have mostly been used in p-site ***,we create three test sets from new proteins related to the released version of the database of protein post-translational modifications(dbPTM)in 2022 based on general and human *** online p-site prediction tools on newly added proteins introduced in the dbPTM 2022 release,distinct from those in the dbPTM 2019 release,reveals their *** other words,the actual performance of these online p-site prediction tools on unseen proteins is notably lower than the results reported in their respective research pape.

关键词： Phosphorylation Machinelearning Deep learning Post-translational modification Database

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Structure, formation, and decay of ■NN system by Faddeev-AGS calculations

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Chinese Physics C 2019年第6期43卷 21-31页

作者： S.Marri S.Z.Kalantari J.esmaili Department of Physics Isfahan University of TechnologyIsfahan 84156-83111Iran Department of Physics Faculty of Basic Sciences Shahrekord UniversityShahrekord115Iran

The Faddeev AGS equations for the coupled-channels ■NN-πΣN system with quantum numbers I=1/2 and S=0 are solved. Using separable potentials for the ■N-πΣ interaction, we calculate the transition probability for the(YK)I=0 + N→πΣN reaction. The possibility to observe the trace of the K-pp quasi-bound state in πΣN mass spectra was studied. Various types of chiral-based and phenomenological potentials are used to describe the ■N-πΣ interaction. Finally, we show that we can observe the signature of the K-pp quasi-bound state in the mass spectra, as well as the trace of branch points in the observables.

关键词： Faddeev method ■N interaction K^-pp system quasi-bound state

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Petrology, Geochemistry and Tectonomagmatic Setting of Neshveh Intrusion (NW Saveh)

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Open Journal of Geology 2014年第5期4卷 177-189页

作者： reza Keshavarzi Dariush esmaili Mehdi rezaei Kahkhaei Mir Ali Asghar Mokhtari reza Jabari Geology group Faculty of Science Islamic Azad University of Science and Research of Tehran Tehran Iran Geology Group Faculty of Science University of Zanjan Zanjan Iran School of Geology Faculty of Science University of Tehran Tehran Iran

Neshveh intrusion is located in the NW of Saveh City and is a part of Orumieh-Dokhtar magmatic arc. This intrusion consists of quartz monzodiorite, granodiorite and granite that have intruded into the Eocene volcano-sedimentary rocks. This intrusion is high-K calk-alkaline and metaluminous and is classified as I-type granitoids. Field investigations along with petrographic and geochemical studies indicate that all phases of Neshveh intrusion are derived from a common magma source as a result of mineral differentiation. Different phases of this intrusion have low Mg#, Ni, Cr, Co and V which are indicative for higher evolution of magma during the magma ascent and before complete crystallization. All phases of Neshveh granitoid are characterized by LREE-rich patterns with high LREE/HREE ratio and negative Eu anomalies. Similarity of the mentioned patterns suggests a comagmatic source for these rocks and demonstrates the role of magmatic differentiation in their evolution. There are negative anomalies in the Nb and Ti along with positive anomalies of Rb, Ba, K and Pb on the spider diagrams. These anomalies are indicative for a subduction setting for magma source of these rocks. Geochemical studies indicate that the Neshveh granitoid is formed in a volcanic arc and active continental margin. In this base, it is assumed that this intrusion is formed as a result of Neo-Tethys oceanic lithosphere subduction beneath the Central Iran zone which is replaced in the Orumieh-Dokhtar magmatic arc.

关键词： Petrology Geochemistry Intrusion Granitoid Neshveh Saveh

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Sound & Vibration 2019年第6期53卷 263-276页

作者： Jahede Tekeykhah Seyed Mohsen Hosseini Gholamali Jalali Jalil Alavi Abbas esmaili Sari Forestry Department Natural Resources and Marine Sciences FacultyTarbiat Modares UniversityNoorMazandaranIran Faculty of Natural Resources Tarbiat Modares UniversityNoorMazandaranIran Associate Professor of Forestry Department Tarbiat Modares UniversityNoorMazandaranIran Forestry Department Tarbiat Modares UniversityNoorMazandaranIran Department of Environmental Science Tarbiat Modares UniversityNoorMazandaranIran

Sound pollution is one of the most important urban problems which endangers mental and physical health of the *** study was aimed to assess the influence of different tree species,including Fraxinus rotundifolia,Robinia pseudoacacia,Platanus orientalis,Platycladus orientalis,and Pinus eldarica,in reducing noise pollution in the Abidar Forest Park.A further objective was to identify the contaminated areas of Sanandaj city and to propose suitable noise absorbent tree species in consistent *** each tree stands the noise measurements were performed during intervals at frequencies of 250,500 and 1000 Hz,besides an open area with the same *** regards to the second purpose,a total of 50 stations with residential,commercial,residentialcommercial,and green space applications were selected across the *** Continuous Sound Pressure Level(Leq)was determined in five replicates for 30 *** measurements were performed under stable weather conditions and low wind velocity at 17:00(traffic peak)in summer and *** of the Leq values were above the threshold noise *** highest noise reduction was recorded in summer(i.e.,green season);Platanus and Platycladus species demonstrated the highest and lowest noise absorption(31.43 dB and 22.28 dB,respectively).Furthermore,a meaningful difference was observed between Leq values of commercial,residential,commercial-residential,and green space urban applications,and the central parts of the city showed noticeable noise *** together,due to being exposed to higher than the acceptable threshold noise level,the residents of Sanandaj will be endangered to health problems in the near future;thus consideration should be given to the noise pollution sources.

关键词： Urban green space noise attenuation Abidar Forest Park

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Mineral Chemistry and Magmatic Differentiation Evidences in the Neshveh Intrusion (NW Saveh, Central Iran)

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Open Journal of Geology 2014年第6期4卷 262-288页

作者： reza Keshavarzi Dariush esmaili Mehdi rezaei Kahkhaei Mir Ali Asghar Mokhtari Mehdi Kordlou Geology group Faculty of Science Islamic Azad University of Science and Research of Tehran Tehran Iran Geology Group Faculty of Science University of Zanjan Zanjan Iran School of Geology Faculty of Science University of Tehran Tehran Iran School of Geosciences University of Shahrood Shahrood Iran

Neshveh intrusion which is located in the NW of Saveh City is a part of Sahand-Bazman magmatic arc within the Central Iranian zone. This intrusion consists of quartz-monzogabbro, quartz-monzodiorite, granodiorite and granite that have intruded into the Eocene volcano-sedimentary rocks. This intrusion is medium to high-K calc alkaline, metaluminous, and I-type granitoid. All phases of the Neshveh granitoid are characterized by LREE-rich patterns with high LREE/HREE ratio and negative Eu anomalies. Similarity of patterns suggests a comagmatic source for these rocks and demonstrates the role of magmatic differentiation in their evolution. Clinopyroxene classified as calcic type with varying from clinoenstatite-clinofferosillite to diopside and augite from quartz-monzogabbros to quartz-monzodiorite and granodiorite. Plagioclase composition varies from bytownite and labradorite in quartz-monzogabbros to andesine in quartz-monzodiorites and oligoclase in granodiorites and granites. Core of some plagioclases in granodiorites and granites shows the calcic composition which is labradorite and andesine in granodiorite and andesine in granites. Field investigations along with petrographic and geochemical studies indicate that all phases of the Neshveh intrusion derived from a common magma source as a result of mineral differentiation. Geochemical evidences show smooth differentiation trends in which most of major elements (except Al2O3, K2O and Na2O) are negatively correlated with SiO2?and K2O, Ba, Rb, Ce, Nb, and Zr are positively correlated with SiO2. Some elements such as Na2O, Sr, Eu and Y follow curves that reflect crystal fractionation of clinopyroxene, plagioc1ase and hornblende. Furthermore, large volumes of quartz-monzogabbros compared to granites, as well as the lack of mafic enclaves in more evolved rocks, are also indicative of crystal fractionation. Clinopyroxene fractionation was the main control in the evolution of the magmas up to 55 wt% SiO2. Hornblende took o

关键词： Mineral Chemistry Magmatic Differentiation Intrusion Granitoid Neshveh Saveh

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Different initial conditions in fuzzy Tumor model

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Journal of Biomedical Science and Engineering 2010年第10期3卷 1002-1006页

作者： Somayeh Saraf esmaili Ali Motie Nasrabadi 不详

One of the best ways for better understanding of biological experiments is mathematical modeling. Modeling cancer is one of the complicated biological modeling that has uncertainty. Therefore, fuzzy models have studied because of their application in achievement uncertainty in modeling. Overall, the main purpose of this modeling is creating a new view of complex phenomena. In this paper, fuzzy differential equation model consisting of tumor, the immune system and normal cells has been studied. Model derived from a classical model DePillis in 2003, which some parameters from a clinical point of view can be described in the region. In this model, by considering fuzzy parameters from clinical point of view, the three-dimensional fuzzy tumor cells in terms of time and membership function are pictured and region of uncertainties are determined. To access the uncertainty area we use fuzzy differential inclusion method that is one of the including methods of solving differential equations. Also, different initial conditions on the model are inserted and the results of them are analyzed because tumor has different treatment in different initial conditions. Results show that fuzzy models in the best way justify what happens in the reality.

关键词： Tumor Cells Mathematical Modeling Fuzzy Parameters Fuzzy Differential Equation

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Applying Surface-Based DNA Computing for Solving the Dominating Set Problem

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American Journal of Molecular Biology 2012年第3期2卷 286-290页

作者： Hassan Taghipour Mahdi rezaei Heydar Ali esmaili Department of pathology Tabriz University of medical sciences Tabriz Iran Department of Theoretical Physics and Astrophysics Tabriz University Tabriz 51664 Iran

The surface-based DNA computing is one of the methods of DNA computing which uses DNA strands immobilized on a solid surface. In this paper, we applied surface-based DNA computing for solving the dominating set problem. At first step, surface-based DNA solution space was constructed by using appropriate DNA strands. Then, by application of a DNA parallel algorithm, dominating set problem was resolved in polynomial time.

关键词： Parallel Computing Surface-Based DNA Computers Dominating Set Problem NP-Complete Problem

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Solving the independent set problem by sticker based DNA computers

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American Journal of Molecular Biology 2012年第2期2卷 153-158页

作者： Hassan Taghipour Ahad Taghipour Mahdi rezaei Heydar Ali esmaili Department of Computer Engineering Faculty of Engineering Isfahan University Isfahan Iran Department of Pathology Tabriz University of Medical Sciences Tabriz Iran Department of Theoretical Physics and Astrophysics Tabriz University Tabriz Iran

In this paper, the sticker based DNA computing was used for solving the independent set problem. At first, solution space was constructed by using appropriate DNA memory complexes. We defined a new operation called “divide” and applied it in construction of solution space. Then, by application of a sticker based parallel algorithm using biological operations, independent set problem was resolved in polynomial time.

关键词： Parallel Computing Sticker Based DNA Computers Independent Set Problem NP-Complete Problem

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Traffic crash accidents in Tehran, Iran： Its relation with circadian rhythm of sleepiness

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Chinese Journal of Traumatology 2015年第1期18卷 13-17页

作者： Khosro Sadeghniiat-Haghighi Zohreh Yazdi Mohsen Moradinia Omid Aminian Alireza esmaili Occupational Sleep Research Center Tehran University of Medical Sciences Tehran Iran Metabolic Disease Research Center Qazvin University of Medical Sdences Qazvin Iran Traffic Police University Tehran Iran

Purpose： Road traffic accidents are one of main problems in Iran. Multiple factors cause traffic accidents and the most important one is sleepiness. This factor, however, is given less attention in our country. Road traffic accidents relevant to sleepiness are studied. Methods： In this cross-sectional study, all road traffic accidents relevant to sleepiness, which were re- ported by police, were studied in Tehran province in 2009. Results： The risk of road traffic accidents due to sleepiness was increased by more than sevenfold （odds ratio = 7.33） in low alertness hours （0：00-6：00） compared to other time of day. The risk of road traffic accidents due to sleepiness was decreased by 0.15-fold （odds ratio - 0.15） in hours with maximum of alertness （18：00-22：00） of circadian rhythm compared to other time of day. Conclusion： The occurrence of road traffic accidents due to sleepiness has significant statistical relations with driving during lowest point of alertness of circadian rhythm.

关键词： Accidents, traffic Automobiles Circadian rhythm Iran

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Efficacy Analysis of an Experience on Development of the Combination Therapy Protocol for Endometriosis Management

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Open Journal of Obstetrics and Gynecology 2017年第1期7卷 31-40页

作者： Abo Taleb Saremi Ameneh Lahooti Eshkevari Katayoun esmaili Pour Arash Pooladi Sarem Fertility & Infertility Research Center (SAFIR) & Sarem Cell Research Center (SCRC) Sarem Women’s Hospital Tehran Iran Infertility Department Sarem Women’s Hospital Tehran Iran

Purpose: Endometriosis can be managed effectively by medication, surgery, or a combination of both. Numerous studies have been conducted on surgical and medication treatment options, but their results are still under discussion. Therefore, we performed a study to develop a combinational treatment for various stages of endometriosis. Methods: Over a 3-year period, 218 documented endometriosis patients were classified in 4 stages. After first laparoscopy (with electrocoagulation and adhesion removal for stages I to III), the patients were treated with GnRH analogs (Gonadotropin Releasing Hormone Agonist-375 mg of Decapeptyl) for 3, 6 & 6 months, respectively. The second and third laparoscopy procedures were performed after 3 and 6 months, with add-back therapy. The treatment was evaluated by direct observation based on laparoscopic view and the pain relief was measured by the VAS (Visual Analogue Scale) after the first step of medication for patients of stages I-III. Results: After 3 months, 70/76 patients (91.9%) with stage-I endometriosis showed complete recovery (six cases after 6 months) while 65/72 and 32/43 cases with stage-II and -III (90.3 and 74.4%), respectively, showed complete recovery after 6 months of treatment. The remaining patients had GnRH treatment for another 3 months, and all showed a complete recovery after 9 months. Furthermore, 12 of the patients with stage-IV symptoms were candidates for laparoscopy or laparotomy, and their treatment response rate was 55.6%. The pain relief was significant after the combinational treatment in patients with stages I-III (P = 0.0001). Conclusion: Our study showed efficacy of the developed protocol for the endometriosis management.

关键词： Endometriosis Combinational Therapy Management Protocol Development Efficacy

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