Proteins carry out most of the work in the cell such as immunological recognition, DNA repair and replication, enzymatic activity, cell signaling by interacting with other proteins. Therefore, elucidation of the protein-protein interaction network will assist in understanding molecular mechanism of cellular activities. Recent advances in high-throughput experimental methods have provided a large amount of data that need to be sorted and interpreted to find biologically relevant interactions and pathways. In silico methods that can accurately predict properties of protein-protein interactions have gained increased interest. In this study, the network of sphingolipid (SL) signaling proteins was constructed using computational prediction methods to contribute to missing interactions among the components of sphingolipid protein-protein interaction (PPI) network. As a result of the studies by our group, the potential protein interactions between YER019W-YHL020C and YGR143W-YKL126W were identified. The new predictions proposed by this research can guide rational design of new experiments.
{"title":"Computational prediction of protein-protein interactions in sphingolipid signaling network","authors":"Yasemen Gungormez, Elif Ozkirimli Olmez, Kutlu Ozergin Ulgen","doi":"10.1109/BIYOMUT.2009.5130307","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2009.5130307","url":null,"abstract":"Proteins carry out most of the work in the cell such as immunological recognition, DNA repair and replication, enzymatic activity, cell signaling by interacting with other proteins. Therefore, elucidation of the protein-protein interaction network will assist in understanding molecular mechanism of cellular activities. Recent advances in high-throughput experimental methods have provided a large amount of data that need to be sorted and interpreted to find biologically relevant interactions and pathways. In silico methods that can accurately predict properties of protein-protein interactions have gained increased interest. In this study, the network of sphingolipid (SL) signaling proteins was constructed using computational prediction methods to contribute to missing interactions among the components of sphingolipid protein-protein interaction (PPI) network. As a result of the studies by our group, the potential protein interactions between YER019W-YHL020C and YGR143W-YKL126W were identified. The new predictions proposed by this research can guide rational design of new experiments.","PeriodicalId":119026,"journal":{"name":"2009 14th National Biomedical Engineering Meeting","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134401874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-05-20DOI: 10.1109/BIYOMUT.2009.5130274
Süleyman Sevinç
Chemotherapy is a well-established medical practice for treatment of various types of cancers. A chemotherapy programme is prepared by a specialist doctor. Preparation, scheduling and management of chemotherapy programmes, especially when many patients with competing requirements are involved, are complicated tasks. A chemotherapy programme involves a number of cycles, each cycle involving application of a number of cytotoxic agents to a patient intravenously over a specified length of time, e.g., 2 hours, on upto five consecutive days. Cycles are interleaved by intermission times during which patient's immune system is left to rest and recover. Intermission times are calculated based on clinical studies; chemotherapy agents and intermission times are selected by specialized doctors for individual patients to ensure maximum benefit to the patient being treated. Therefore, it is important that patient's chemotherapy plan is closely followed as prescribed by the expert. However, resource constraints on number of chemotherapy seats and health staff members available, conflicting schedules of many hundreds of patients and official holidays interfering with patients' schedules make it very difficult to plan for an optimal implementation of chemotherapy schedules as prepared by experts. In this article we examine issues involved in scheduling chemotherapy applications for multiple cancer patients under many constraints. We propose and simulate various approaches and calculate their performances.
{"title":"planCT : Chemotherapy scheduling system","authors":"Süleyman Sevinç","doi":"10.1109/BIYOMUT.2009.5130274","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2009.5130274","url":null,"abstract":"Chemotherapy is a well-established medical practice for treatment of various types of cancers. A chemotherapy programme is prepared by a specialist doctor. Preparation, scheduling and management of chemotherapy programmes, especially when many patients with competing requirements are involved, are complicated tasks. A chemotherapy programme involves a number of cycles, each cycle involving application of a number of cytotoxic agents to a patient intravenously over a specified length of time, e.g., 2 hours, on upto five consecutive days. Cycles are interleaved by intermission times during which patient's immune system is left to rest and recover. Intermission times are calculated based on clinical studies; chemotherapy agents and intermission times are selected by specialized doctors for individual patients to ensure maximum benefit to the patient being treated. Therefore, it is important that patient's chemotherapy plan is closely followed as prescribed by the expert. However, resource constraints on number of chemotherapy seats and health staff members available, conflicting schedules of many hundreds of patients and official holidays interfering with patients' schedules make it very difficult to plan for an optimal implementation of chemotherapy schedules as prepared by experts. In this article we examine issues involved in scheduling chemotherapy applications for multiple cancer patients under many constraints. We propose and simulate various approaches and calculate their performances.","PeriodicalId":119026,"journal":{"name":"2009 14th National Biomedical Engineering Meeting","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134450449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-05-20DOI: 10.1109/BIYOMUT.2009.5130370
Muge Ozker, Z. Bayraktaroglu, Itir Kasikci, Basri Erdogan, A. Akın, T. Demiralp
The aim of this experiment was to investigate the impact of steady-state visual stimulation on electrophysiology of the human brain. The study was performed on 6 subjects and the measurements were made by the non-invasive technique, EEG (Electroencephalography). The changes in the electrophysiological brain signals that had been obtained by EEG during visual stimulation were analyzed. The amount of changes in the recorded signals exhibited dependencies to the frequency of the applied visual stimulation. In this study, the frequency dependent electrophysiological response of the frontal cortex of the brain was analyzed and compared with the response of the occipital cortex. In both occipital and prefrontal cortexes, the highest EEG signal energy was observed at the 10–13 Hz stimulation band. Other than this frequency band, there were no similarities between the two regions in terms of local maximum and minimum signal energy values. On the other hand, when the EEG response to the whole stimulation frequency was considered, the correlation coefficient of the signal powers of both regions was found to be 0.84.
{"title":"Projection of the steady state visual evoked potentials on prefrontal cortex","authors":"Muge Ozker, Z. Bayraktaroglu, Itir Kasikci, Basri Erdogan, A. Akın, T. Demiralp","doi":"10.1109/BIYOMUT.2009.5130370","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2009.5130370","url":null,"abstract":"The aim of this experiment was to investigate the impact of steady-state visual stimulation on electrophysiology of the human brain. The study was performed on 6 subjects and the measurements were made by the non-invasive technique, EEG (Electroencephalography). The changes in the electrophysiological brain signals that had been obtained by EEG during visual stimulation were analyzed. The amount of changes in the recorded signals exhibited dependencies to the frequency of the applied visual stimulation. In this study, the frequency dependent electrophysiological response of the frontal cortex of the brain was analyzed and compared with the response of the occipital cortex. In both occipital and prefrontal cortexes, the highest EEG signal energy was observed at the 10–13 Hz stimulation band. Other than this frequency band, there were no similarities between the two regions in terms of local maximum and minimum signal energy values. On the other hand, when the EEG response to the whole stimulation frequency was considered, the correlation coefficient of the signal powers of both regions was found to be 0.84.","PeriodicalId":119026,"journal":{"name":"2009 14th National Biomedical Engineering Meeting","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132861344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-05-20DOI: 10.1109/BIYOMUT.2009.5130355
Cigdem Serdengecti, M. Engin, E. Z. Engin, Soner Balci
Biomedical signals taken from body surface by non-invasive methods include problems such as noise and mixing with other physiological signals. These problems also appear evidently during the extraction of fetal ECG's. Therefore, the fetal EKG signal is contaminated by maternal ECG signal and noise. In this study, the purpose is to determine the best algorithm for fetal ECG extraction by using two different Blind Source Separation based method. To determine the best algorithm, detection of fetal heart rate and signal-interface ration criterion were used.
{"title":"Extraction of fetal ECG from maternal ECG","authors":"Cigdem Serdengecti, M. Engin, E. Z. Engin, Soner Balci","doi":"10.1109/BIYOMUT.2009.5130355","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2009.5130355","url":null,"abstract":"Biomedical signals taken from body surface by non-invasive methods include problems such as noise and mixing with other physiological signals. These problems also appear evidently during the extraction of fetal ECG's. Therefore, the fetal EKG signal is contaminated by maternal ECG signal and noise. In this study, the purpose is to determine the best algorithm for fetal ECG extraction by using two different Blind Source Separation based method. To determine the best algorithm, detection of fetal heart rate and signal-interface ration criterion were used.","PeriodicalId":119026,"journal":{"name":"2009 14th National Biomedical Engineering Meeting","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122081373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-05-20DOI: 10.1109/BIYOMUT.2009.5130316
B. Dogan, I. Goker, M. Baslo, Hasan Erdal, Y. Ulgen
Scanning EMG is a method developed for examining the electro-physiological cross section and the size of the motor unit of a human muscle. Electrical specifications of the motor unit can be obtained as well as anatomical distribution of muscle fibers and pathological changes between different muscles can be examined by the help of this method. In this paper; an automation system which is designed for the execution of scanning EMG method, whether manually or automatically, and a user-interface are described. Parameters like step count and step size which are about the movement of an electrode, moved by a linear actuator, through muscle fibers can be defined as reference by user via designed interface. As a result, acquired signals are digitalized by data-acquisition card (DAQ) and saved as text file for the future signal process tasks.
{"title":"Interface design for automation of the scanning EMG method","authors":"B. Dogan, I. Goker, M. Baslo, Hasan Erdal, Y. Ulgen","doi":"10.1109/BIYOMUT.2009.5130316","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2009.5130316","url":null,"abstract":"Scanning EMG is a method developed for examining the electro-physiological cross section and the size of the motor unit of a human muscle. Electrical specifications of the motor unit can be obtained as well as anatomical distribution of muscle fibers and pathological changes between different muscles can be examined by the help of this method. In this paper; an automation system which is designed for the execution of scanning EMG method, whether manually or automatically, and a user-interface are described. Parameters like step count and step size which are about the movement of an electrode, moved by a linear actuator, through muscle fibers can be defined as reference by user via designed interface. As a result, acquired signals are digitalized by data-acquisition card (DAQ) and saved as text file for the future signal process tasks.","PeriodicalId":119026,"journal":{"name":"2009 14th National Biomedical Engineering Meeting","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127179615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-05-20DOI: 10.1109/BIYOMUT.2009.5130340
Duygu Altiok, E. Altiok, Oguz Bayraktar, Funda Tihminlioglu
trans-Resveratrol, (3,5,4′-trihydroxy-trans-stilbene), a phenolic compound present in some plant species, have been shown to posses antioxidative, anticarcinogenic and antitumour properties. However, under UV light, it turns into -cis form and looses its bioactivity.This study aims to increase the stability of trans-resveratrol by loading it into chitosan microspheres. Within this context, the trans-resveratrol loaded chitosan microspheres was produced by spray drying and then the resultant microspheres were characterized. The particle size and the surface morphology of resultant microspheres were investigated by scanning electron microscope (SEM) and the thermal properties were determined by thermogravimetry analyser(TGA). The stability of free and that of inside the microspheres was determined by high performance liquid chromatography (HPLC). It was found that the stability of trans-resveratrol incorporated into chitosan microspheres kept constant.
{"title":"Stability of trans-resveratrol incorporated in chitosan microspheres","authors":"Duygu Altiok, E. Altiok, Oguz Bayraktar, Funda Tihminlioglu","doi":"10.1109/BIYOMUT.2009.5130340","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2009.5130340","url":null,"abstract":"trans-Resveratrol, (3,5,4′-trihydroxy-trans-stilbene), a phenolic compound present in some plant species, have been shown to posses antioxidative, anticarcinogenic and antitumour properties. However, under UV light, it turns into -cis form and looses its bioactivity.This study aims to increase the stability of trans-resveratrol by loading it into chitosan microspheres. Within this context, the trans-resveratrol loaded chitosan microspheres was produced by spray drying and then the resultant microspheres were characterized. The particle size and the surface morphology of resultant microspheres were investigated by scanning electron microscope (SEM) and the thermal properties were determined by thermogravimetry analyser(TGA). The stability of free and that of inside the microspheres was determined by high performance liquid chromatography (HPLC). It was found that the stability of trans-resveratrol incorporated into chitosan microspheres kept constant.","PeriodicalId":119026,"journal":{"name":"2009 14th National Biomedical Engineering Meeting","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127605825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-05-20DOI: 10.1109/BIYOMUT.2009.5130255
Umit Aydin, Y. Serinağaoğlu
Geometric errors in inverse ECG are usually the errors occur in the mathematical model used for solution due to wrong interpretation of heart's position and size, conductivities of organs in the model and electrode positions. In this study the effects of geometric errors in inverse ECG problem for Kalman filter and Bayes-MAP methods are studied. Furthermore the method suggested by Kaipio et. al., which assumes that these geometric errors are additive noise and independent of the epicardial potentials, is implemented. With this method, the effects of geometric errors on Kalman filter and Bayes-MAP solutions are reduced at the cost of smoothing the wavefront.
{"title":"The effects of geometric errors on inverse ECG solutions using Kalman filter and Bayesian MAP estimation","authors":"Umit Aydin, Y. Serinağaoğlu","doi":"10.1109/BIYOMUT.2009.5130255","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2009.5130255","url":null,"abstract":"Geometric errors in inverse ECG are usually the errors occur in the mathematical model used for solution due to wrong interpretation of heart's position and size, conductivities of organs in the model and electrode positions. In this study the effects of geometric errors in inverse ECG problem for Kalman filter and Bayes-MAP methods are studied. Furthermore the method suggested by Kaipio et. al., which assumes that these geometric errors are additive noise and independent of the epicardial potentials, is implemented. With this method, the effects of geometric errors on Kalman filter and Bayes-MAP solutions are reduced at the cost of smoothing the wavefront.","PeriodicalId":119026,"journal":{"name":"2009 14th National Biomedical Engineering Meeting","volume":"44 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116877360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-05-20DOI: 10.1109/BIYOMUT.2009.5130282
A. Yardimci, K. Iijima, M. Sekine, T. Tamura
Correct postural balance effects will be felt in every movement and activity in daily life. In this study the ankle signal was evaluated for understanding body response to acceleration platform. The ankle front-back acceleration sensor data was analyzed using largest Lyapunov exponent. The results obtained from this work can be used to predict the response of elderly subjects and hemiplegics patients.
{"title":"Body response analysis using acceleration platform","authors":"A. Yardimci, K. Iijima, M. Sekine, T. Tamura","doi":"10.1109/BIYOMUT.2009.5130282","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2009.5130282","url":null,"abstract":"Correct postural balance effects will be felt in every movement and activity in daily life. In this study the ankle signal was evaluated for understanding body response to acceleration platform. The ankle front-back acceleration sensor data was analyzed using largest Lyapunov exponent. The results obtained from this work can be used to predict the response of elderly subjects and hemiplegics patients.","PeriodicalId":119026,"journal":{"name":"2009 14th National Biomedical Engineering Meeting","volume":"117 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121948674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-05-20DOI: 10.1109/BIYOMUT.2009.5130251
O. H. Colak, S. Bilgin, O. Polat
Heart rate variability is a important physiological data that presents information about sympathetic or parasympathetic domination in autonomic nervous system. Sympathovagal balance (SB) can be described as the power rate of low frequency/high frequency. In this study, we have investigated SB on ventricular tachyarrhythmia (VTA) patients and compared with normal data obtained from same patients. In VTA, min value and max value have been determined as 0.1236 and 11.0855. In normal data, SB min value is 0.3640 and SB max value is 6.5239.
{"title":"Analyze of sympathovagal balance on ventricular tachyarrhythmia patients using wavelet packet transform","authors":"O. H. Colak, S. Bilgin, O. Polat","doi":"10.1109/BIYOMUT.2009.5130251","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2009.5130251","url":null,"abstract":"Heart rate variability is a important physiological data that presents information about sympathetic or parasympathetic domination in autonomic nervous system. Sympathovagal balance (SB) can be described as the power rate of low frequency/high frequency. In this study, we have investigated SB on ventricular tachyarrhythmia (VTA) patients and compared with normal data obtained from same patients. In VTA, min value and max value have been determined as 0.1236 and 11.0855. In normal data, SB min value is 0.3640 and SB max value is 6.5239.","PeriodicalId":119026,"journal":{"name":"2009 14th National Biomedical Engineering Meeting","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123074465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-05-20DOI: 10.1109/BIYOMUT.2009.5130308
Ersin Tozduman, S. Albayrak
cDNA microarray image analysis has grown very important these days because of the growing field which it's part of: microarray expression analysis. In this work we propose a new cDNA microarray image analysis system. A cDNA microarray analysis system consists of three main parts which are Gridding, Segmentation and Information Extraction, respectively. In gridding stage we propose a new automated gridding technique which is based on mathematical morphology. For segmentation we propose two different algorithm which are based on K-Means clustering and Fuzzy C-Means clustering respectively. On the final stage, information extraction, our proposed system uses a classical approach which calculates background values locally. The proposed system has open parts in the way of developement and is still being worked on.
{"title":"cDNA microarray image analysis","authors":"Ersin Tozduman, S. Albayrak","doi":"10.1109/BIYOMUT.2009.5130308","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2009.5130308","url":null,"abstract":"cDNA microarray image analysis has grown very important these days because of the growing field which it's part of: microarray expression analysis. In this work we propose a new cDNA microarray image analysis system. A cDNA microarray analysis system consists of three main parts which are Gridding, Segmentation and Information Extraction, respectively. In gridding stage we propose a new automated gridding technique which is based on mathematical morphology. For segmentation we propose two different algorithm which are based on K-Means clustering and Fuzzy C-Means clustering respectively. On the final stage, information extraction, our proposed system uses a classical approach which calculates background values locally. The proposed system has open parts in the way of developement and is still being worked on.","PeriodicalId":119026,"journal":{"name":"2009 14th National Biomedical Engineering Meeting","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122885475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：