PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
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Article Citation - WoS: 2139Citation - Scopus: 2265The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions(Amer Assoc Advancement Science, 2007) Merchant, Sabeeha S.; Prochnik, Simon E.; Vallon, Olivier; Harris, Elizabeth H.; Karpowicz, Steven J.; Witman, George B.; Terry, Astrid; Allmer, JensChlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the similar to 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.Article Citation - WoS: 40Citation - Scopus: 46Animals as Mobile Biological Sensors for Forest Fire Detection(Mdpi, 2007) Sahin, Yasar GuneriThis paper proposes a mobile biological sensor system that can assist in early detection of forest fires one of the most dreaded natural disasters on the earth. The main idea presented in this paper is to utilize animals with sensors as Mobile Biological Sensors (MBS). The devices used in this system are animals which are native animals living in forests, sensors (thermo and radiation sensors with GPS features) that measure the temperature and transmit the location of the MBS, access points for wireless communication and a central computer system which classifies of animal actions. The system offers two different methods, firstly: access points continuously receive data about animals' location using GPS at certain time intervals and the gathered data is then classified and checked to see if there is a sudden movement (panic) of the animal groups: this method is called animal behavior classification (ABC). The second method can be defined as thermal detection (TD): the access points get the temperature values from the MBS devices and send the data to a central computer to check for instant changes in the temperatures. This system may be used for many purposes other than fire detection, namely animal tracking, poaching prevention and detecting instantaneous animal death.Article Citation - WoS: 22Citation - Scopus: 21Asymmetry of Visually Guided Sexual Behaviour in Adult Japanese Quail (coturnix Japonica)(Psychology Press, 2007) Gulbetekin, Evrim; Gunturkun, Onur; Dural, Seda; Çeti̇nkaya, HakanSexually active adult Japanese quail (Coturnix coturnix japonica) were trained to run across either it left- or a right-turning runway to obtain sexual access to a conspecific of the opposite sex. The birds tested with only their right eye in use showed significantly higher latencies to complete the runway task than the birds tested binocularly and those using the left eye. In all of the three experimental conditions, male birds were significantly faster than their female counterparts. Generally, these findings are compatible with previous evidence for lateralisation in sexually motivated behaviour in birds. However, unlike the previous findings that Suggested a loss of lateralisation in pattern discrimination in quail during adulthood, the present study shows that asymmetries in visually guided sexual behaviour persist in adult quail. Thus, our study implies that ontogenetic and lateralised changes within the visual system can be differently organised for different output pathways.Article Citation - WoS: 11Citation - Scopus: 13Vertex Separators for Partitioning a Graph(Mdpi, 2008) Evrendilek, CemFinite Element Method (FEM) is a well known technique extensively studied for spatial and temporal modeling of environmental processes, weather prediction computations, and intelligent signal processing for wireless sensors. The need for huge computational power arising in such applications to simulate physical phenomenon correctly mandates the use of massively parallel computers to distribute the workload evenly. In this study, a novel heuristic algorithm called Line Graph Bisection which partitions a graph via vertex separators so as to balance the workload amongst the processors and to minimize the communication overhead is proposed. The proposed algorithm is proved to be computationally feasible and makes cost-effective parallel implementations possible to speed up the solution process.Article Citation - WoS: 5Citation - Scopus: 7Detection of Hidden Hostile/Terrorist Groups in Harsh Territories by Using Animals as Mobile Biological Sensors(Mdpi, 2008) Sahin, Yasar Guneri; Ercan, TuncayTerrorism is the greatest threat to national security and cannot be defeated by conventional military force alone. In critical areas such as Iraq, Afghanistan and Turkey, regular forces cannot reach these hostile/terrorist groups, the instigators of terrorism. These groups have a clear understanding of the relative ineffectiveness of counter-guerrilla operations and rely on guerrilla warfare to avoid major combat as their primary means of continuing the conflict with the governmental structures. In Internal Security Operations, detection of terrorist and hostile groups in their hiding places such as caves, lairs, etc. can only be achieved by professionally trained people such as Special Forces or intelligence units with the necessary experience and tools suitable for collecting accurate information in these often harsh, rugged and mountainous countries. To assist these forces, commercial micro-sensors with wireless interfaces could be utilized to study and monitor a variety of phenomena and environments from a certain distance for military purposes. In order to locate hidden terrorist groups and enable more effective use of conventional military resources, this paper proposes an active remote sensing model implanted into animals capable of living in these environments. By using these mobile sensor devices, improving communications for data transfer from the source, and developing better ways to monitor and detect threats, terrorist ability to carry out attacks can be severely disrupted.Article Citation - WoS: 41Citation - Scopus: 46Leader-Member Exchange, Organizational Identification and the Mediating Role of Job Involvement for Nurses(Wiley, 2008) Katrinli, Alev; Atabay, Gulem; Gunay, Gonca; Güneri Çangarlı, BurcuAim. This paper is a report of a study to explore the relationship between leader-member exchange quality and organizational identification and the mediating role of job involvement in this relationship. Background. As a result of the fast-changing structures and increasing competition, healthcare organizations increasingly demand highly qualified nurses who also have positive work attitudes towards the job and the organization. Among these positive work attitudes, organizational identification affects nurses' job performance and, in turn, the quality of care and patient satisfaction. The quality of the relationship between nurse supervisors and nurses, which is examined in the leader-member exchange context, can be an important determinant for organizational identification. This relationship is also affected by nurses' job involvement. Method. The sample consisted of 148 nurses working in a private general hospital. Questionnaires, which included measures for organizational identification, level of leader-member exchange quality, job involvement and questions about the demographic characteristics of the sample, were distributed in 2007. The response rate was 87%. Results. A statistically significant and positive relationship was found between leader-member exchange quality and organizational identification. The results also reveal that job involvement mediates the positive effects of leader-member exchange quality on organizational identification. Conclusion. If nurse supervisors increase their awareness of the effects of their behaviours towards their nurses, they can increase the nurses' performance and achieve desired results through increasing job involvement and organizational identification.Article Citation - WoS: 6Citation - Scopus: 72db: a Proteomics Database for Storage, Analysis, Presentation, and Retrieval of Information From Mass Spectrometric Experiments(Biomed Central Ltd, 2008) Allmer, Jens; Kuhlgert, Sebastian; Hippler, MichaelBackground: The amount of information stemming from proteomics experiments involving (multi dimensional) separation techniques, mass spectrometric analysis, and computational analysis is ever-increasing. Data from such an experimental workflow needs to be captured, related and analyzed. Biological experiments within this scope produce heterogenic data ranging from pictures of one or two-dimensional protein maps and spectra recorded by tandem mass spectrometry to text-based identifications made by algorithms which analyze these spectra. Additionally, peptide and corresponding protein information needs to be displayed. Results: In order to handle the large amount of data from computational processing of mass spectrometric experiments, automatic import scripts are available and the necessity for manual input to the database has been minimized. Information is in a generic format which abstracts from specific software tools typically used in such an experimental workflow. The software is therefore capable of storing and cross analysing results from many algorithms. A novel feature and a focus of this database is to facilitate protein identification by using peptides identified from mass spectrometry and link this information directly to respective protein maps. Additionally, our application employs spectral counting for quantitative presentation of the data. All information can be linked to hot spots on images to place the results into an experimental context. A summary of identified proteins, containing all relevant information per hot spot, is automatically generated, usually upon either a change in the underlying protein models or due to newly imported identifications. The supporting information for this report can be accessed in multiple ways using the user interface provided by the application. Conclusion: We present a proteomics database which aims to greatly reduce evaluation time of results from mass spectrometric experiments and enhance result quality by allowing consistent data handling. Import functionality, automatic protein detection, and summary creation act together to facilitate data analysis. In addition, supporting information for these findings is readily accessible via the graphical user interface provided. The database schema and the implementation, which can easily be installed on virtually any server, can be downloaded in the form of a compressed file from our project webpage.Conference Object Citation - WoS: 17Citation - Scopus: 21Automated Patient-Specific Classification of Premature Ventricular Contractions(IEEE, 2008) İnce, Türker; Kiranyaz, Serkan; Gabbouj, MoncefIn this paper, we present an automated patient-specific electrocardiogram (ECG) beat classifier designed or accurate defection of premature ventricular contractions (PVCs). In the proposed feature extraction scheme, the principal component analysis (PCA) is applied to the dyadic wavelet transform (DWT) of the ECG signal to extract morphological ECG features, which are then combined with the temporal features to form a resultant efficient feature vector. For the classification scheme, we selected the feed-forward artificial neural networks (ANNs) optimally designed by the multi-dimensional particle swarm optimization (MD-PSO) technique, which evolves the structure and weights of the network specifically for each patient. Training data for the ANN classifier include both global (total of 150 representative beats randomly sampled from each class in selected training files) and local (the first 5 min of a patient's ECG recording) training patterns. Simulation results using 40 files in the MIT/BIH arrhythmia database achieved high average accuracy of 97% for differentiating normal, PVC, and other beats.Article Citation - Scopus: 21Automated Patient-Specific Classification of Premature Ventricular Contractions(2008) Ince, T.; Kiranyaz, S.; Gabbouj, M.In this paper, we present an automated patient-specific electrocardiogram (ECG) beat classifier designed for accurate detection of premature ventricular contractions (PVCs). In the proposed feature extraction scheme, the principal component analysis (PCA) is applied to the dyadic wavelet transform (DWT) of the ECG signal to extract morphological ECG features, which are then combined with the temporal features to form a resultant efficient feature vector. For the classification scheme, we selected the feed-forward artificial neural networks (ANNs) optimally designed by the multi-dimensional particle swarm optimization (MD-PSO) technique, which evolves the structure and weights of the network specifically for each patient. Training data for the ANN classifier include both global (total of 150 representative beats randomly sampled from each class in selected training files) and local (the first 5 min of a patient's ECG recording) training patterns. Simulation results using 40 files in the MIT/BIH arrhythmia database achieved high average accuracy of 97% for differentiating normal, PVC, and other beats.Article Citation - WoS: 8Citation - Scopus: 9Visual Asymmetries in Japanese Quail (coturnix Japonica) Retain a Lifelong Potential for Plasticity(Amer Psychological Assoc, 2009) Gulbetekin, Evrim; Gunturkun, Onur; Dural, Seda; Çeti̇nkaya, HakanAdult Japanese quail display left-eye/right-hemisphere dominance in visually guided sexual tracking. In 2 experiments, the authors set out to answer if this functional cerebral asymmetry is modifiable by posthatch monocular deprivation, In Experiment 1, the left or the right eye of 2-day old quail were closed for 70 days. Quail were run in a left- or a right-turning runway to obtain access to a conspecific of the opposite sex. The performance of both left and right eye systems was equal. In Experiment 2, the deprived eyes of the quail were opened and the previously open eyes were closed. They were tested with the same runways. Overall, running speed was very low, but the quail showed a left-eye/right-hemisphere superiority. Altogether, these experiments evince 3 insights into cerebral asymmetries in quail. First, posthatch asymmetries of visual input can alter lateralized behavior to an important extent. Second, cerebral asymmetries could involve an interhemispheric inhibition that can be modified by epigenetic factors. Third, even long-term visual deprivation does not abolish a previously established cerebral asymmetry.Article Citation - WoS: 190Citation - Scopus: 246Evolutionary Artificial Neural Networks by Multi-Dimensional Particle Swarm Optimization(Pergamon-Elsevier Science Ltd, 2009) Kiranyaz, Serkan; İnce, Türker; Yildirim, Alper; Gabbouj, MoncefIn this paper, we propose a novel technique for the automatic design of Artificial Neural Networks (ANNs) by evolving to the optimal network configuration(s) within an architecture space. It is entirely based on a multi-dimensional Particle Swarm Optimization (MD PSO) technique, which re-forms the native structure of swarm particles in such a way that they can make inter-dimensional passes with a dedicated dimensional PSO process. Therefore, in a multidimensional search space where the optimum dimension is unknown, swarm particles can seek both positional and dimensional optima. This eventually removes the necessity of setting a fixed dimension a priori, which is a common drawback for the family of swarm optimizers. With the proper encoding of the network configurations and parameters into particles, MID PSO can then seek the positional optimum in the error space and the dimensional optimum in the architecture space. The optimum dimension converged at the end of a MD PSO process corresponds to a unique ANN configuration where the network parameters (connections, weights and biases) can then be resolved from the positional optimum reached on that dimension. In addition to this, the proposed technique generates a ranked list of network configurations, from the best to the worst. This is indeed a crucial piece of information, indicating what potential configurations can be alternatives to the best one, and which configurations should not be used at all for a particular problem. In this study, the architecture space is defined over feed-forward, fully-connected ANNs so as to use the conventional techniques such as back-propagation and some other evolutionary methods in this field. The proposed technique is applied over the most challenging synthetic problems to test its optimality on evolving networks and over the benchmark problems to test its generalization capability as well as to make comparative evaluations with the several competing techniques. The experimental results show that the MD PSO evolves to optimum or near-optimum networks in general and has a superior generalization capability. Furthermore, the MID PSO naturally favors a low-dimension solution when it exhibits a competitive performance with a high dimension counterpart and such a native tendency eventually yields the evolution process to the compact network configurations in the architecture space rather than the complex ones, as long as the optimality prevails. (C) 2009 Elsevier Ltd. All rights reserved.Article Citation - WoS: 25Citation - Scopus: 24Exploring the Antecedents of Organizational Identification: the Role of Job Dimensions, Individual Characteristics and Job Involvement(Wiley, 2009) Katrinli, Alev; Atabay, Gulem; Gunay, Gonca; Güneri Çangarlı, BurcuAim This study aims to identify the antecedents of organizational identification such as job involvement and job dimensions in a health care setting. Background Organizational identification is an important work attitude that affects nurses' performance and job satisfaction. Hence, exploring antecedents of organizational identification in a health care setting is vital in understanding the role of organizational identification in nurse-and patient-related outcomes. Method A research model, which incorporates job design, individual characteristics, job involvement and organizational identification, was developed and tested. The research was conducted via a survey in a hospital setting in Turkey (n = 148). Results The results revealed that job involvement, which is the degree of importance of one's job to one's self-image, is related to organizational identification. Among job dimensions, task identity and autonomy explained a significant proportion of variance in job involvement. Conclusion Although job dimensions are not directly related to organizational identification, they have effects on job involvement, which is also an important construct. Implications for nursing management The results suggest that nurses' jobs should be designed with higher levels of task autonomy and task identity to increase their job involvement and in turn their organizational identification.Article Citation - WoS: 345Citation - Scopus: 446A Generic and Robust System for Automated Patient-Specific Classification of Ecg Signals(IEEE-Inst Electrical Electronics Engineers Inc, 2009) İnce, Türker; Kiranyaz, Serkan; Gabbouj, MoncefThis paper presents a generic and patient-specific classification system designed for robust and accurate detection of ECG heartbeat patterns. The proposed feature extraction process utilizes morphological wavelet transform features, which are projected onto a lower dimensional feature space using principal component analysis, and temporal features from the ECG data. For the pattern recognition unit, feedforward and fully connected artificial neural networks, which are optimally designed for each patient by the proposed multidimensional particle swarm optimization technique, are employed. By using relatively small common and patient-specific training data, the proposed classification system can adapt to significant interpatient variations in ECG patterns by training the optimal network structure, and thus, achieves higher accuracy over larger datasets. The classification experiments over a benchmark database demonstrate that the proposed system achieves such average accuracies and sensitivities better than most of the current state-of-the-art algorithms for detection of ventricular ectopic beats (VEBs) and supra-VEBs (SVEBs). Over the entire database, the average accuracy-sensitivity performances of the proposed system for VEB and SVEB detections are 98.3%-84.6% and 97.4%-63.5%, respectively. Finally, due to its parameter-invariant nature, the proposed system is highly generic, and thus, applicable to any ECG dataset.Article Citation - WoS: 32Citation - Scopus: 48Motives for Risk-Taking in Adolescence: a Cross-Cultural Study(Academic Press Ltd Elsevier Science Ltd, 2009) Kloep, M.; Gueney, N.; Cok, F.; Simsek, Oemer FarukMost research oil adolescent risk-taking has been conducted in Western societies, but it is as yet unknown whether motives to engage in risk behaviours show Cultural variety. This study sets out to investigate differences in perceived motives to engage in perceived risks in Turkish and Welsh samples of young people (N = 922) between 14 and 20 years of age. For this, a measurement scale to assess motives for risk-taking was constructed and validated cross-culturally. The scale was based oil Kloep and Hendry's [(1999). Challenges, risks and coping in adolescence. In D. Messer, & S. Millar (Eds.), Exploring developmental psychology (pp. 400 416). London: Arnold] theoretical framework and the results of a study by Guney and cok [(2006). Adolescent risk-taking: Calculated risks, Turkish experience. In Paper presented at the 10th Bi-annual conference of the European Association for Research on Adolescence, Antalya, Turkey]. Results show that different motives are associated with different risk behaviours, confirming Kloep and Hendry's expanded model. There were small, but significant, national differences, implying that motives to take risks-as opposed to actual risks taken could be similar across adolescent populations, independent of culture. (C) 2007 The Association for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.Article Citation - WoS: 8Citation - Scopus: 9Modeling of Polygalacturonase Enzyme Activity and Biomass Production by Aspergillus Sojae Atcc 20235(Springer Heidelberg, 2009) Tokatli, Figen; Tari, Canan; Ünlütürk, Mehmet Süleyman; Baysal, Nihan GogusAspergillus sojae, which is used in the making of koji, a characteristic Japanese food, is a potential candidate for the production of polygalacturonase (PG) enzyme, which of a major industrial significance. In this study, fermentation data of an A. sojae system were modeled by multiple linear regression (MLR) and artificial neural network (ANN) approaches to estimate PG activity and biomass. Nutrient concentrations, agitation speed, inoculum ratio and final pH of the fermentation medium were used as the inputs of the system. In addition to nutrient conditions, the final pH of the fermentation medium was also shown to be an effective parameter in the estimation of biomass concentration. The ANN parameters, such as number of hidden neurons, epochs and learning rate, were determined using a statistical approach. In the determination of network architecture, a cross-validation technique was used to test the ANN models. Goodness-of-fit of the regression and ANN models was measured by the R (2) of cross-validated data and squared error of prediction. The PG activity and biomass were modeled with a 5-2-1 and 5-9-1 network topology, respectively. The models predicted enzyme activity with an R (2) of 0.84 and biomass with an R (2) value of 0.83, whereas the regression models predicted enzyme activity with an R (2) of 0.84 and biomass with an R (2) of 0.69.Article Citation - WoS: 43Citation - Scopus: 58Early Forest Fire Detection Using Radio-Acoustic Sounding System(Mdpi, 2009) Sahin, Yasar Guneri; İnce, TürkerAutomated early fire detection systems have recently received a significant amount of attention due to their importance in protecting the global environment. Some emergent technologies such as ground-based, satellite-based remote sensing and distributed sensor networks systems have been used to detect forest fires in the early stages. In this study, a radio-acoustic sounding system with fine space and time resolution capabilities for continuous monitoring and early detection of forest fires is proposed. Simulations show that remote thermal mapping of a particular forest region by the proposed system could be a potential solution to the problem of early detection of forest fires.Article Citation - WoS: 47Citation - Scopus: 48Multiple Impacts of Epilepsy and Contributing Factors: Findings From an Ethnographic Study in Vietnam(Academic Press Inc Elsevier Science, 2009) Aydemir, Nuran; Dang Vu Trung; Snape, Dee; Baker, Gus A.; Jacoby, AnnWe investigated issues related to treatment, impact of epilepsy, attitudes toward epilepsy, and disclosure in Vietnam through in-depth interviews with people with epilepsy (PWE) and their family members. We found that although participants prefer Western to traditional treatment, they experience problems in accessing different kinds of antiepileptic drugs and higher-level treatment facilities and with respect to treatment expenses. The impact of epilepsy can be observed in a wide range of daily living activities which include working, education, marriage, and family formation. Although both families and society at large do not hold negative attitudes toward epilepsy, most PWE reported a sense of burden to others. Both PWE and family members generally prefer disclosing epilepsy rather than concealing it from others. Our findings strongly suggest a need in Vietnam for different types of antiepileptic drugs and epilepsy support information for PWE, family members, and the general public. (C) 2009 Elsevier Inc. All rights reserved.Article Citation - WoS: 8Citation - Scopus: 13Assistive Technologies for Visually Impaired Individuals in Turkey(R E S N A Press, 2010) Bengisu, MuratA phone survey was conducted with 80 visually impaired people in Turkey to understand what types of assistive products are used and to what extent. The perceived utility of selected products and reasons for nonuse were investigated. Descriptions of products that would be useful for the participants but may not be available on the market were also obtained. The three most used assistive products were found to be computer screen readers (46%), talking watches (26%), and screen readers for cellular phones (21%). Cellular phones with screen reading capability are the most desired assistive products among the visually impaired community, but their high cost is a major barrier. Most of the relevant technologies are available but some product development, such as adaptation to the Turkish language, is necessary. The three products most frequently requested are bus station/destination announcement systems, devices that warn the person about barriers, and devices that read printed documents and signs.Conference Object Citation - Scopus: 1Classification of Holter Registers by Dynamic Clustering Using Multi-Dimensional Particle Swarm Optimization(2010) Kiranyaz S.; İnce, Türker; Pulkkinen J.; Gabbouj M.In this paper, we address dynamic clustering in high dimensional data or feature spaces as an optimization problem where multi-dimensional particle swarm optimization (MD PSO) is used to find out the true number of clusters, while fractional global best formation (FGBF) is applied to avoid local optima. Based on these techniques we then present a novel and personalized long-term ECG classification system, which addresses the problem of labeling the beats within a long-term ECG signal, known as Holter register, recorded from an individual patient. Due to the massive amount of ECG beats in a Holter register, visual inspection is quite difficult and cumbersome, if not impossible. Therefore the proposed system helps professionals to quickly and accurately diagnose any latent heart disease by examining only the representative beats (the so called master key-beats) each of which is representing a cluster of homogeneous (similar) beats. We tested the system on a benchmark database where the beats of each Holter register have been manually labeled by cardiologists. The selection of the right master key-beats is the key factor for achieving a highly accurate classification and the proposed systematic approach produced results that were consistent with the manual labels with 99.5% average accuracy, which basically shows the efficiency of the system. © 2010 IEEE.Article Citation - WoS: 87Citation - Scopus: 99Modeling Inactivation Kinetics of Liquid Egg White Exposed To Uv-C Irradiation(Elsevier, 2010) Unluturk, Sevcan; Atilgan, Mehmet R.; Baysal, A. Handan; Unluturk, Mehmet S.The efficiency of UV-C irradiation as a non-thermal pasteurization process for liquid egg white (LEW) was investigated. LEW inoculated with Escherichia coli K-12 (ATCC 25253), pathogenic strain of Escherichia coli O157:H7 (NCTC12900) and Listeria innocua (NRRL B33314) were treated with UV light using a bench top collimated beam apparatus. Inoculated LEW samples were exposed to UV-C irradiation of known UV intensity of 1.314 mW/cm(2) and sample depth of 0.153 cm for 0, 3 5, 7, 10, 13, 17 and 20 min. The populations of E. coli K-12, E. coli 0157:H7 and L. innocua were reduced after 20 min of exposure by 0.896, 1.403 and 0.960 log CFU respectively. Additionally, the inactivation data obtained for each strain suspended in LEW was correlated by using Weibull (2 parameter), Log-Linear (1 parameter), Horn (2 parameter) and modified Chick Watson (2 parameter) models. The inactivation kinetics of E. coli K-12, E. coli 0157:H7 and L. innocua were best described by modified Chick Watson model with the smallest root mean squared error (RMSE) (R-2 >= 0.92). (C) 2010 Elsevier B.V. All rights reserved.

