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Interpretation, Stratification and Evidence for Sequence Variants Affecting mRNA Splicing in Complete Human Genome Sequences

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Genomics, Proteomics & Bioinformatics 2013年第2期11卷 77-85页

作者： Ben C.Shirley Eliseos J.Mucaki Tyson Whitehead Paul I.Costea pelin akan Peter K.Rogan Department of Computer Science Middlesex CollegeThe University of Western Ontario Department of Biochemistry Schulich School of Medicine and DentistryThe University of Western Ontario SHARCNET Royal Institute of Technology Science for Life Laboratory Cytognomix Inc.

Information theory-based methods have been shown to be sensitive and specific for pre- dicting and quantifying the effects of non-coding mutations in Mendelian diseases. We present the Shannon pipeline software for genome-scale mutation analysis and provide evidence that the soft- ware predicts variants affecting mRNA splicing. Individual information contents （in bits） of refer- ence and variant splice sites are compared and significant differences are annotated and prioritized. The software has been implemented for CLC-Bio Genomics platform. Annotation indicates the context of novel mutations as well as common and rare SNPs with splicing effects. Potential natural and cryptic mRNA splicing variants are identified, and null mutations are distinguished from leaky mutations. Mutations and rare SNPs were predicted in genomes of three cancer cell lines （U2OS, U251 and A431）, which were supported by expression analyses. After filtering, tractable numbers of potentially deleterious variants are predicted by the software, suitable for further laboratory investigation. In these cell lines, novel functional variants comprised 6-17 inactivating mutations, 1 5 leaky mutations and 6-13 cryptic splicing mutations. Predicted effects were validated by RNA-seq analysis of the three aforementioned cancer cell lines, and expression microarray analysis of SNPs in HapMap cell lines.

关键词： Mutation mRNA splicing Information theory Next-generation sequencing Genome interpretation

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Inflammatory responses in esophageal mucosa before and after laparoscopic antireflux surgery

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World Journal of Gastrointestinal Surgery 2024年第3期16卷 871-881页

作者： pelin Ergun Sezgi Kipcak Nur Selvi Gunel Eser Yildirim Sozmen Serhat Bor Department of Otolaryngology Medical College of WisconsinMilwaukeeWI 53226United States Division of Gastroenterology Ege UniversityFaculty of MedicineEge Reflux GroupIzmir 35100Turkiye Department of Medical Biology Ege UniversityFaculty of MedicineIzmir 35100Turkiye Department of Medical Biochemistry Ege UniversityFaculty of MedicineIzmir 35100Turkiye

BACKGROUND Currently,the primary treatment for gastroesophageal reflux is acid suppression with proton pump inhibitors,but they are not a cure,and some patients don’t respond well or refuse long-term ***,alternative therapies are needed to understand the disease and develop better *** anti-reflux surgery(LARS)can resolve symptoms of these patients and plays a significant role in evaluating esophageal healing after preventing harmful *** LARS improves typical gastroesophageal reflux symptoms in most patients,main-ly by reducing the exposure time to gastric contents in the ***-ration of the inflammatory response and a recovery response in the esophageal epithelium is expected following the cessation of the noxious *** To explore the role of inflammatory biomolecules in LARS and assess the time required for esophageal epithelial *** Of 22 patients with LARS(pre-and post/5.8±3.8 months after LARS)and 25 healthy controls(HCs)were *** subjects underwent 24-h multichannel intraluminal impedance-pH monitoring and upper gastrointestinal endoscopy,during which esophageal biopsy samples were collected using endoscopic *** molecules in esophageal biopsies were investigated by reverse transcription-polymerase chain reaction and multiplex-enzyme-linked immunosorbent *** Post-LARS samples showed significant increases in proinflammatory cytokines[interleukin(IL)-1β,interferon-γ,C-X-C chemokine ligand 2(CXCL2)],anti-inflammatory cytokines[CC chemokine ligand(CCL)11,CCL13,CCL17,CCL26,CCL1,CCL7,CCL8,CCL24,IL-4,IL-10],and homeostatic cytokines(CCL27,CCL20,CCL19,CCL23,C-CL25,CXCL12,migration inhibitory factor)compared to both HCs and pre-LARS ***17 and CCL21 levels were higher in pre-LARS than in HCs(P<0.05).The mRNA expression levels of AKT1,fibroblast growth factor 2,HRAS,and mitogen-activated protein kinase 4 were significantly decreased post-LARS vs pre-LARS.

关键词： Anti-reflux surgery Gastroesophageal reflux disease Cytokine Inflammatory response Esophagus

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An Ordinal Multi-Dimensional Classification(OMDC)for Predictive Maintenance

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Computer Systems Science & Engineering 2023年第2期44卷 1499-1516页

作者： pelin Yildirim Taser Izmir Bakircay University Department of Computer EngineeringIzmir35665Turkey

Predictive Maintenance is a type of condition-based maintenance that assesses the equipment's states and estimates its failure probability and when maintenance should be *** machine learning techniques have been frequently implemented in this area,the existing studies disregard to the nat-ural order between the target attribute values of the historical sensor ***,these methods cause losing the inherent order of the data that positively affects the prediction *** deal with this problem,a novel approach,named Ordinal Multi-dimensional Classiﬁcation(OMDC),is proposed for estimating the conditions of a hydraulic system's four components by taking into the natural order of class *** demonstrate the prediction ability of the proposed approach,eleven different multi-dimensional classiﬁcation algorithms(traditional Binary Relevance(BR),Classiﬁer Chain(CC),Bayesian Classiﬁer Chain(BCC),Monte Carlo Classiﬁer Chain(MCC),Probabilistic Classiﬁer Chain(PCC),Clas-siﬁer Dependency Network(CDN),Classiﬁer Trellis(CT),Classiﬁer Dependency Trellis(CDT),Label Powerset(LP),Pruned Sets(PS),and Random k-Labelsets(RAKEL))were implemented using the Ordinal Class Classiﬁer(OCC)***,seven different classiﬁcation algorithms(Multilayer Perceptron(MLP),Support Vector Machine(SVM),k-Nearest Neighbour(kNN),Decision Tree(C4.5),Bagging,Random Forest(RF),and Adaptive Boosting(AdaBoost))were chosen as base learners for the OCC *** experimental results present that the proposed OMDC approach using binary relevance multi-dimensional classiﬁcation methods predicts the conditions of a hydraulic system's multiple components with high ***,it is clearly seen from the results that the OMDC models that utilize ensemble-based classiﬁcation algorithms give more reliable prediction performances with an average Hamming score of 0.853 than the others that use traditional algorithms as base learners.

关键词： Machine learning multi-dimensional classiﬁcation ordinal classiﬁcation predictive maintenance

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Microplastics in municipal wastewater treatment plants: a case study of Denizli/Turkey

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环境科学与工程前沿(英文) 2023年第8期17卷 95-105页

作者： pelin Koyuncuoğlu Gülbin Erden Environmental Engineering Department Engineering FacultyPamukkale UniversityKınıklıCampusDenizli 20160Turkey

Plastic particles smaller than 5 mm are *** are among the significant pollutants that recently attracted *** quantities of microplastics enter the sewage system daily and reach wastewater treatment plants(WWTPs).As a result,WWTPs are potential microplastic ***,they create a pathway for microplastics to reach aquatic environments with treated wastewater *** on microplastic characterization in WWTPs have gained momentum in *** study investigates the abundance,size,shape,color,polymer type,and removal efficiencies of microplastics in a municipal wastewater treatment plant(WWTP)in Denizli/*** results showed that the dominant microplastic shape in wastewater samples was fibers(41.78%–60.77%)in the 100–500μm(58.57%–80.07%)size *** of the microplastics were transparent-white(32.86%–58.93%).The dominant polymer types were polyethylene(54.05%)and polyethylene vinyl acetate(37.84%)in raw ***,the microplastic removal efficiencies of the Denizli Central WWTP as a whole and for individual treatment units were *** the microplastic pollution removal efficiency of the Denizli Central WWTP was over 95%,the microplastic concentration discharged daily into the receiving environment was considerably high(1.28×1010 MP/d).Thus,Denizli Central WWTP effluents result in a high volume of emissions in terms of microplastic pollution with a significant daily discharge to theÇürüksu Stream.

关键词： Microplastics Wastewater treatment plant Removal efficiency Daily discharge

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A new hybrid approach to assessing soil quality using neutrosophic fuzzy-AHP and support vector machine algorithm in sub-humid ecosystem

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Journal of Mountain Science 2023年第11期20卷 3186-3202页

作者： ÖZKAN Barış DENGIZ Orhan ALABOZ pelin KAYA NursaçSerda Department of Industrial Engineering Faculty of EngineeringOndokuz Mayis UniversitySamsun 55200Türkiye Department of Soil Sciences and Plant Nutrition Faculty of AgricultureOndokuz Mayis UniversitySamsun 55200Türkiye Department of Soil Science and Plant Nutrition Faculty of AgricultureIsparta University of Applied SciencesIsparta32000Türkiye

Soil quality determination and estimation is an important issue not only for terrestrial ecosystems but also for sustainable management of *** this study,soil quality was determined by linear and nonlinear standard scoring function methods integrated with a neutrosophic fuzzy analytic hierarchy process in the micro *** addition,soil quality values were estimated using a support vector machine(SVM)in machine learning *** order to generate spatial distribution maps of soil quality indice values,different interpolation methods were evaluated to detect the most suitable semivariogram *** the soil quality index values obtained by the linear method were determined between 0.458-0.717,the soil quality index with the nonlinear method showed variability at the levels of *** was no statistical difference between the two methods,and they were determined to be *** the estimation of soil quality with SVM,the normalized root means square error(NRMSE)values obtained in the linear and nonlinear method estimation were determined as 0.057 and 0.047,*** spherical model of simple kriging was determined as the interpolation method with the lowest RMSE value in the actual and predicted values of the linear method while,in the nonlinear method,the lowest error in the distribution maps was determined with exponential of the simple kriging.

关键词： Soil quality Support vector machine Neutrosophic fuzzy Humid ecosystem

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A 3D in vitro co-culture model for evaluating biomaterial-mediated modulation of foreign-body responses

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Bio-Design and Manufacturing 2022年第3期5卷 465-480页

作者： Betul Cakmak pelin Saglam-Metiner Goze Beceren Yu S.Zhang Ozlem Yesil-Celiktas Department of Bioengineering Faculty of EngineeringEge University35100 IzmirTurkey Division of Engineering in Medicine Brigham and Women’s HospitalDepartment of MedicineHarvard Medical SchoolCambridgeMAUSA

The immune response after implantation of a biomaterial may shorten the functional life of the implant,depending on the degree of the *** this study,we used a polyacrylamide-alginate(PAAm-Alg)hydrogel,which has been previously characterized as a biocompatible material and shown to enhance regeneration of cartilage in vivo,along with a graphiteenhanced hydrogel(PAAm-Alg-G)as a non-biocompatible counterpart,to evaluate macrophage attachment and polarization to pro-or anti-inflammatory *** performance of each biomaterial in the presence of fibroblasts and chondrocytes was validated by an in vitro model which demonstrated modulation of the foreign-body response.A blend of 5%gelatin methacryloyl and 0.1%methacrylated hyaluronic acid was optimized to mimic the extracellular matrix(ECM)and support cell viability,proliferation,migration,and functionality at an initial concentration of 3.25×10^(5) cells/*** PAAm-Alg-G hydrogel localized in the simulated ECM showed cytotoxic and genotoxic effects for both fibroblasts and chondrocytes,while exhibiting a proliferative effect on macrophages with elevated immune *** M1/M2 ratio was 0.73 for PAAm-Alg hydrogel but 2.64 for PAAm-Alg-G,leading to significant M1 dominance(p0.05).The interleukin-6(IL-6)concentration secreted in the presence of PAAm-Alg hydrogel(4.58 pg/mL)significantly decreased(p<0.0001)on day 13,while the increase(p<0.0001)in interleukin-10(IL-10)concentration(120.73 pg/mL)confirmed the switch from a pro-inflammatory to an anti-inflammatory *** immune responses by developing a simplistic yet powerful three-dimensional in vitro model provides advantages in preparing for clinical use of biomaterials.

关键词： Biomaterial Macrophage polarization Genotoxicity Biocompatibility Immune response

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Numerical investigation of seismic performance of high modulus columns under earthquake loading

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Earthquake Engineering and Engineering Vibration 2019年第4期18卷 811-822页

作者： Selcuk Demir pelin Ozener Abant Izzet Baysal University Bolu 14030 Turkey Yildiz Technical University Istanbul 34210 Turkey

This paper presents the result of two-dimensional fi nite element modeling studies in order to investigate the seismic behavior of high modulus columns in liquefi able soil. Particular attention was paid to the shear stress reduction mechanism of the high modulus columns and the shear strain distribution between soil and columns during earthquake motion. Numerical analyses were performed using a nonlinear elasto-plastic model in Plaxis 2016. The reliability of the numerical simulations was verifi ed through the results of a centrifuge test model designed to investigate the contribution of high modulus columns in liquefaction mitigation. The capability of numerical simulations was assessed primarily through comparison of predicted acceleration-time histories, pore water pressures, and displacements with the measured counterparts. The results of the numerical analysis showed that the presence of the columns did not reduce seismic shear stresses in the soil when compared to the unimproved soil condition and pure shear behavior between soil and column did not develop as expected in the current design methodology.

关键词： liquefaction high modulus column soil improvement UBC3D-PLM

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Effects of Tungsten and Boron Contents on Crystallization Temperature and Microhardness of Tungsten Based Metallic Glasses

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Acta Metallurgica Sinica(English Letters) 2015年第6期28卷 733-738页

作者： pelin ztürk Aytekin Hitit Department of Materials Science and Engineering AfyonKocatepe University

Effects of tungsten and boron contents on the thermal properties and microhardness of W-Fe-B metallic glass system were studied. Thin foils, with thicknesses of 20 and 100 ktm, of the alloys were produced by piston and anvil method in an arc furnace. The structures of the foils were investigated by X-ray diffraction. Thermal stabilities of the alloys were examined by using differential scanning calorimetry. 20-μm- thick foils of all the alloys were determined to be fully amorphous, but crystalline phases were detected in the 100-μm-thick foils. It was found that crystallization temperatures of the alloys are between 1060 and 1177 K. Tungsten and boron content increases improve the crystallization temperature and microhardness of the alloys significantly, but deteriorate the glass forming ability of the alloys. It was also observed that for constant Fe content, increasing tungsten content to the level higher than that of boron content does not result in any further improvement in crystallization temperature, but improves glass forming ability significantly. The alloy containing highest total amount of tungsten and boron, W35Fe35B3o, has the highest crystallization temperature, 1177 K, and microhardness, 1634 HV.

关键词： Metallic glass Refractory metal Crystallization temperature Hardness

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Estimation of residual shear strength ratios of liquefied soil deposits from shear wave velocity

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Earthquake Engineering and Engineering Vibration 2012年第4期11卷 461-484页

作者： pelinzener Yildiz Technical University Davutpasa CampusDepartment of Civil Engineering

For sites susceptible to liquefaction induced lateral spreading during a probable earthquake, geotechnical engineers often need to know the undrained residual shear strength of the liquefied soil deposit to estimate lateral spreading displacements, and the forces acting on the piles from the liquefied soils in order to perform post liquefaction stability analyses. The most commonly used methods to estimate the undrained residual shear strength （Su~） of liquefied sand deposits are based on the correlations determined from liquefaction induced flow failures with SPT and CPT data. In this study, 44 lateral spread case histories are analyzed and a new relationship based on only lateral spread case histories is recommended, which estimates the residual shear strength ratio of the liquefiable soil layer from normalized shear wave velocity. The new proposed method is also utilized to estimate the residual lateral displacement of an example bridge problem in an area susceptible to lateral spreading in order to provide insight into how the proposed relationship can be used in geotechnical engineering practice.

关键词： liquefaction lateral spread undrained residual shear strength undrained residual shear strength ratio shearwave velocity

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Piezoelectric d_(15) shear response-based torsion actuation mechanism:an experimental benchmark and its 3D finite element simulation

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International Journal of Smart and Nano Materials 2010年第3期1卷 224-235页

作者： pelin Berik Ayech Benjeddou Institute of Technical Mechanics Johannes Kepler University of LinzLinzAustria Institut Supérieur de Mécanique de Paris(Supméca) ParisFrance

An experimental benchmark is proposed for piezoelectric,direct-torsion actuation using mono-morph piezoceramic d_(15)shear *** is reached by designing and assembling an adaptive plate having two identical composite faces sandwiching a core made of connected six oppositely polarized(OP)piezoceramic d15 shear patches along the *** electronic speckle pattern interferometry system was used to measure the static tip deflection of the adaptive sandwich composite plate that was mounted in a cantilever configuration and actuated in torsion by progressively applied voltages on the piezoceramic shear core electroded major ***,the effective rate of twist was post-processed and proposed as an evaluation criterion for smart composites under piezoelectric torsion *** verification of the experimental results,the proposed experimental benchmark was simulated using three-dimensional piezoelectric finite elements(FE)within ABAQUS®commercial *** comparison of the obtained experimental and simulation results showed reasonable agreement,but the slight nonlinear experimental response was not confirmed by the linear FE *** experimentally proved torsion actuation mechanism,produced by OP piezoceramic d15 shear patches,can be applied actively to prevent torsion in many applications,such as in wind turbines,helicopter blades,robot arms,flexible space structures,etc.

关键词： torsion actuation shear-mode piezoceramic benchmark experiment simulation

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