1
|
Marcinkevičs R, Reis Wolfertstetter P, Klimiene U, Chin-Cheong K, Paschke A, Zerres J, Denzinger M, Niederberger D, Wellmann S, Ozkan E, Knorr C, Vogt JE. Interpretable and intervenable ultrasonography-based machine learning models for pediatric appendicitis. Med Image Anal 2024; 91:103042. [PMID: 38000257 DOI: 10.1016/j.media.2023.103042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 11/10/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Appendicitis is among the most frequent reasons for pediatric abdominal surgeries. Previous decision support systems for appendicitis have focused on clinical, laboratory, scoring, and computed tomography data and have ignored abdominal ultrasound, despite its noninvasive nature and widespread availability. In this work, we present interpretable machine learning models for predicting the diagnosis, management and severity of suspected appendicitis using ultrasound images. Our approach utilizes concept bottleneck models (CBM) that facilitate interpretation and interaction with high-level concepts understandable to clinicians. Furthermore, we extend CBMs to prediction problems with multiple views and incomplete concept sets. Our models were trained on a dataset comprising 579 pediatric patients with 1709 ultrasound images accompanied by clinical and laboratory data. Results show that our proposed method enables clinicians to utilize a human-understandable and intervenable predictive model without compromising performance or requiring time-consuming image annotation when deployed. For predicting the diagnosis, the extended multiview CBM attained an AUROC of 0.80 and an AUPR of 0.92, performing comparably to similar black-box neural networks trained and tested on the same dataset.
Collapse
Affiliation(s)
- Ričards Marcinkevičs
- Department of Computer Science, ETH Zurich, Universitätstrasse 6, Zürich, 8092, Switzerland.
| | - Patricia Reis Wolfertstetter
- Department of Pediatric Surgery and Pediatric Orthopedics, Hospital St. Hedwig of the Order of St. John of God, University Children's Hospital Regensburg (KUNO), Steinmetzstrasse 1-3, Regensburg, 93049, Germany; Faculty of Medicine, University of Regensburg, Franz-Josef-Strauss-Allee 11, Regensburg, 93053, Germany.
| | - Ugne Klimiene
- Department of Computer Science, ETH Zurich, Universitätstrasse 6, Zürich, 8092, Switzerland
| | - Kieran Chin-Cheong
- Department of Computer Science, ETH Zurich, Universitätstrasse 6, Zürich, 8092, Switzerland
| | - Alyssia Paschke
- Faculty of Medicine, University of Regensburg, Franz-Josef-Strauss-Allee 11, Regensburg, 93053, Germany
| | - Julia Zerres
- Faculty of Medicine, University of Regensburg, Franz-Josef-Strauss-Allee 11, Regensburg, 93053, Germany
| | - Markus Denzinger
- Department of Pediatric Surgery and Pediatric Orthopedics, Hospital St. Hedwig of the Order of St. John of God, University Children's Hospital Regensburg (KUNO), Steinmetzstrasse 1-3, Regensburg, 93049, Germany; Faculty of Medicine, University of Regensburg, Franz-Josef-Strauss-Allee 11, Regensburg, 93053, Germany
| | - David Niederberger
- Department of Computer Science, ETH Zurich, Universitätstrasse 6, Zürich, 8092, Switzerland
| | - Sven Wellmann
- Faculty of Medicine, University of Regensburg, Franz-Josef-Strauss-Allee 11, Regensburg, 93053, Germany; Division of Neonatology, Hospital St. Hedwig of the Order of St. John of God, University Children's Hospital Regensburg (KUNO), Steinmetzstrasse 1-3, Regensburg, 93049, Germany
| | - Ece Ozkan
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar Street, Cambridge, 02139, USA
| | - Christian Knorr
- Department of Pediatric Surgery and Pediatric Orthopedics, Hospital St. Hedwig of the Order of St. John of God, University Children's Hospital Regensburg (KUNO), Steinmetzstrasse 1-3, Regensburg, 93049, Germany
| | - Julia E Vogt
- Department of Computer Science, ETH Zurich, Universitätstrasse 6, Zürich, 8092, Switzerland.
| |
Collapse
|
2
|
Ozkan E, Ozcelikay G, Gök Topak ED, Nemutlu E, Ozkan SA, Dizdar Ö, Aksoy S, Kır S. Molecularly imprinted electrochemical sensor for the selective and sensitive determination of octreotide in cancer patient plasma sample. Talanta 2023; 263:124679. [PMID: 37257237 DOI: 10.1016/j.talanta.2023.124679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/04/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023]
Abstract
In this study, a molecularly imprinted polymer film (P (ANI)@MIP) on the electrode surface was fabricated using aniline as a functional monomer and octreotide (OC) as a template molecule. The developed P (ANI)@MIP was electrochemically electropolymerized on a glassy carbon electrode (GCE) surface. Each step of MIP production was evaluated by viewing the [Fe (CN)6]3-/4- signal obtained using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The P (ANI)@MIP film layer was studied with a scanning electron microscope (SEM), Raman, and contact angle measurements. The parameters consisting of monomer, template ratio, cycle number, removal solution, removal time, and rebinding time were optimized to obtain the best electrochemical sensor. The developed method was validated in line with ICH guidelines. The linear range, LOD, and LOQ were found as 10-80 fM, 0.801 fM, and 2.670 fM, respectively. The selectivity of the method was tested with the response of somatostatin and lanreotide from the same growth hormone family by comparing the OC response. The developed P (ANI)@MIP/GCE sensor is the first reported method for electrochemical analysis of OC. The P (ANI)@MIP/GCE sensor exhibited high sensitivity and selectivity for OC. The novel MIP sensor was used to determine OC in cancer patient plasma samples. The concentration of OC in cancer patients varied between 8.98 ng/mL and 10.10 ng/mL.
Collapse
Affiliation(s)
- Ece Ozkan
- Ankara Medipol University, Faculty of Pharmacy, Analytical Chemistry Department, Ankara, 06790, Turkiye.
| | - Göksu Ozcelikay
- Ankara University, Faculty of Pharmacy, Analytical Chemistry Department, Ankara, 06560, Turkiye
| | - Elif Damla Gök Topak
- Hacettepe University, Faculty of Pharmacy, Analytical Chemistry Department, Ankara, 06100, Turkiye; Lokman Hekim University, Faculty of Pharmacy, Analytical Chemistry Department, Ankara, 06510, Turkiye
| | - Emirhan Nemutlu
- Hacettepe University, Faculty of Pharmacy, Analytical Chemistry Department, Ankara, 06100, Turkiye
| | - Sibel A Ozkan
- Ankara University, Faculty of Pharmacy, Analytical Chemistry Department, Ankara, 06560, Turkiye.
| | - Ömer Dizdar
- Hacettepe University, Cancer Institute, Medical Oncology Department, Ankara, 06100, Turkiye
| | - Sercan Aksoy
- Hacettepe University, Cancer Institute, Medical Oncology Department, Ankara, 06100, Turkiye
| | - Sedef Kır
- Hacettepe University, Faculty of Pharmacy, Analytical Chemistry Department, Ankara, 06100, Turkiye
| |
Collapse
|
3
|
Ozcelikay G, Kaya S, Ozkan E, Cetinkaya A, Nemutlu E, Kır S, Ozkan S. Sensor-based MIP technologies for targeted metabolomics analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2021.116487] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
4
|
Ozkan E, Bereket MC, Ozkan N. Knowledge and attitude regarding bisphosphonates and related osteonecrosis among Turkish dentist: A cross sectional study. Niger J Clin Pract 2021; 24:1485-1491. [PMID: 34657014 DOI: 10.4103/njcp.njcp_684_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background and Aims Bisphosphonates (BPs), the antiresorptive drugs, can cause osteonecrosis of the jaws. Having adequate knowledge about BPs and bisphosphonate-related osteonecrosis of the jaw (BRONJ) is very important to prevent complications. In this study, we aimed to determine the level of knowledge of dentists about BPs and BRONJ in Turkey and also aimed to share the results with health authorities to plan new education strategies. Materials and Methods A questionnaire consisting of 20 questions and two parts was used to determine the knowledge level, attitude, and training needs of the dentists. Answers to all questions were analyzed with descriptive statistics, and using Pearson Chi-square and Kruskal-Wallis tests. P values <0.05 were considered statistically significant. Results A total of 620 general and specialist dentists working in three different sectors and four different cities agreed to participate in the study. Statistically, more knowledge about BPs and BRONJ was observed in dentists who have less than 10 years of experience than those who have over 10 years, specialist dentists than general dentists, and those who working in university hospitals than in other sectors. In general, the rate of those who know BPs is 16.8%, the rate of those who know BRONJ is 20.2%. Conclusions Although the use of BPs increases day by day, the awareness of BPs and BRONJ among the dentists is insufficient. However, periodically organizing postgraduate training programs on this subject will increase the awareness and level of knowledge.
Collapse
Affiliation(s)
- E Ozkan
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Istanbul Medeniyet University, İstanbul, Turkey
| | - M C Bereket
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Ondokuz Mayıs University, Samsun, Turkey
| | - N Ozkan
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Ondokuz Mayıs University, Samsun, Turkey
| |
Collapse
|
5
|
Yalman D, Koylu M, Kayabasi C, Kamer S, Ozkan E, Yelken BO, Tayfur E, Celebi C, Bilge M, Susluer SY, Parlak C, Bilge M, Anacak Y, Gunduz C. Effect Of Tumor Treating Fields And Radiotherapy Combination On Brain Tumor And Normal Brain Cell Lines. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
6
|
Tas I, Yildirim A, Ozkan E, Ozyigitoglu G, Yavuz M, Turker A. Biological evaluation and phytochemical profiling of some lichen species. Acta Alimentaria 2019. [DOI: 10.1556/066.2019.48.4.7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- I. Tas
- Department of Biology, Faculty of Arts and Sciences, Bolu Abant Izzet Baysal University, 14280, Bolu. Turkey
- Korean Lichen Research Institute, Sunchon National University, Sunchon, Republic of Korea
| | - A.B. Yildirim
- Department of Field Crops, Faculty of Agriculture and Natural Sciences, Bolu Abant Izzet Baysal University, Bolu. Turkey
| | - E. Ozkan
- Department of Biology, Faculty of Arts and Sciences, Bolu Abant Izzet Baysal University, 14280, Bolu. Turkey
- Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Gwangju. Republic of Korea
| | - G.C. Ozyigitoglu
- Department of Biology, Faculty of Arts and Sciences, Marmara University, Istanbul. Turkey
| | - M.Z. Yavuz
- Department of Pharmacology, Faculty of Medicine, Bolu Abant Izzet Baysal University, Bolu. Turkey
| | - A.U. Turker
- Department of Biology, Faculty of Arts and Sciences, Bolu Abant Izzet Baysal University, 14280, Bolu. Turkey
| |
Collapse
|
7
|
Nemutlu E, Orgul G, Recber T, Aydin E, Ozkan E, Turgal M, Alikasifoglu M, Kir S, Beksac MS. Metabolic Infrastructure of Pregnant Women With Trisomy 21 Fetuses; Metabolomic Analysis. Z Geburtshilfe Neonatol 2019; 223:297-303. [PMID: 31132797 DOI: 10.1055/a-0877-7869] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We aimed to configure impaired/altered metabolomic profiles of pregnant women carrying Down syndrome (DS) fetuses. The study involved 21 and 32 pregnant women with DS and euploid fetuses, respectively, as determined by prenatal screening and diagnosis as part of an antenatal care program. Metabolomic analyses were carried out using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-qTOF-MS) methods. A total of 95 metabolites were identified. GC-MS analysis indicated that levels of 2-hydroxybutyric acid, benzoic acid, nonanoic acid, 3-hydroxybutyric acid, and 2-ketoisocaproic acid were increased in the DS group, where beta-alanine, threonic acid, oxalic acid, alpha-tocopherol, uracil, 2-piperidone, and creatinine were decreased. However, LC-qTOF-MS analysis showed that lipid-related metabolites were decreased in women carrying DS fetuses, whereas creatine, N4-phosphoagmatine, citrate, 2,5-dioxopentanoate, 2-furoate, pyruvate, and fructose levels were increased. Pathway analysis was also performed using metabolites whose levels were significantly altered (p<0.05) between the groups, and the findings indicated that the biosynthesis pathways of aminoacyl-tRNA and "valine-leucine-isoleucine", and metabolism pathways of "glycine-serine-threonine", nitrogen, "alanine-aspartate-glutamate", propanoate, glycerophospholipid, cysteine, methionine, and phenylalanine were significantly altered. Our findings indicate a special type of metabolic status/syndrome in pregnant women with Down syndrome fetuses. It could be speculated that altered metabolic status might influence both gametogenesis and embryogenesis. Down syndrome is a complex genetic disorder that is important to detect prenatally, but may also be prevented by taking necessary precautions prior to pregnancy.
Collapse
Affiliation(s)
- Emirhan Nemutlu
- Hacettepe University, Faculty of Pharmacy, Department of Analytical Chemistry, Ankara, Turkey
| | - Gokcen Orgul
- Hacettepe University Faculty of Medicine, Department of Obstetrics and Gynecology, Division of Perinatology, Ankara, Turkey
| | - Tuba Recber
- Hacettepe University, Faculty of Pharmacy, Department of Analytical Chemistry, Ankara, Turkey
| | - Emine Aydin
- Hacettepe University Faculty of Medicine, Department of Obstetrics and Gynecology, Division of Perinatology, Ankara, Turkey
| | - Ece Ozkan
- Hacettepe University, Faculty of Pharmacy, Department of Analytical Chemistry, Ankara, Turkey
| | - Mert Turgal
- Hacettepe University Faculty of Medicine, Department of Obstetrics and Gynecology, Division of Perinatology, Ankara, Turkey
| | - Mehmet Alikasifoglu
- Hacettepe University Faculty of Medicine, Department of Medical Genetics, Ankara, Turkey
| | - Sedef Kir
- Hacettepe University, Faculty of Pharmacy, Department of Analytical Chemistry, Ankara, Turkey
| | - Mehmet Sinan Beksac
- Hacettepe University Faculty of Medicine, Department of Obstetrics and Gynecology, Division of Perinatology, Ankara, Turkey
| |
Collapse
|
8
|
Sanabria SJ, Ozkan E, Rominger M, Goksel O. Spatial domain reconstruction for imaging speed-of-sound with pulse-echo ultrasound: simulation and in vivo study. Phys Med Biol 2018; 63:215015. [PMID: 30365398 DOI: 10.1088/1361-6560/aae2fb] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite many uses of ultrasound, some pathologies such as breast cancer still cannot reliably be diagnosed in either conventional B-mode ultrasound imaging nor with more recent ultrasound elastography methods. Speed-of-sound (SoS) is a quantitative imaging biomarker, which is sensitive to structural changes due to pathology, and hence could facilitate diagnosis. Full-angle ultrasound computed tomography (USCT) was proposed to obtain spatially-resolved SoS images, however, its water-bath setup involves practical limitations. To increase clinical utility and for widespread use, recently, a limited-angle Fourier-domain SoS reconstruction was proposed, however, it suffers from significant image reconstruction artifacts. In this work, we present a SoS reconstruction strategy, where the forward problem is formulated using differential time-of-flight measurements based on apparent displacements along different ultrasound wave propagation paths, and the inverse problem is solved in spatial-domain using a proposed total-variation scheme with spatially-varying anisotropic weighting to compensate for geometric bias from limited angle imaging setup. This is shown to be robust to missing displacement data and easily allow for incorporating any prior geometric information. In numerical simulations, SoS values in inclusions are accurately reconstructed with 90% accuracy up to a noise level of 50%. With respect to Fourier-domain reconstruction, our proposed method improved contrast ratio from 0.37 to 0.67 for even high noise levels such as 50%. Numerical full-wave simulation and our preliminary in vivo results illustrate the clinical applicability of our method in a breast cancer imaging setting. Our proposed method requires single-sided access to the tissue and can be implemented as an add-on to conventional ultrasound equipment, applicable to a range of transducers and applications.
Collapse
Affiliation(s)
- Sergio J Sanabria
- Computed-assisted Applications in Medicine Group, ETH Zurich, Zurich, Switzerland. Both first authors contributed equally
| | | | | | | |
Collapse
|
9
|
Kirbiyik F, Ozkan E. Approaches and knowledge of radiation oncologists to nutrition therapy: A questionnaire study. Clin Nutr 2018. [DOI: 10.1016/j.clnu.2018.06.1465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
10
|
Ozkan E, Vishnevsky V, Goksel O. Inverse Problem of Ultrasound Beamforming With Sparsity Constraints and Regularization. IEEE Trans Ultrason Ferroelectr Freq Control 2018; 65:356-365. [PMID: 28961111 DOI: 10.1109/tuffc.2017.2757880] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Ultrasound (US) beamforming is the process of reconstructing an image from acquired echo traces on several transducer elements. Typical beamforming approaches, such as delay-and-sum, perform simple projection operations, while techniques using statistical information also exist, e.g., adaptive, phase coherence, delay-multiply-and-sum, and sparse coding approaches. Inspired by the feasibility and success of inverse problem (IP) formulations in several image reconstruction problems, such as computed tomography, we herein devise an IP approach for US beamforming. We define a linear forward model for the synthesis of the beamformed image, and solve its IP thanks to several intuitive and physics-based constraints and regularization terms proposed. These reflect the prior knowledge about the spectra of carrier signal and spatial coherence of modulated signal. These constraints admit effective formulation through sparse representations. Our proposed method was evaluated for plane-wave imaging (PWI) that transmits unfocused waves, enabling high frame rates with large field of view at the expense of much lower image quality with conventional beamforming techniques. Results are evaluated in numerical simulations, as well as tissue-mimicking phantoms and in vivo data provided by PWI challenge in medical US. The best results achieved by our proposed techniques are 0.39-mm full-width at half-maximum for spatial resolution and 16.3-dB contrast-to-noise ratio, using a single plane-wave transmit.
Collapse
|
11
|
Bilir KA, Anli G, Ozkan E, Gunduz O, Ulugol A. Involvement of spinal cannabinoid receptors in the antipruritic effects of WIN 55,212-2, a cannabinoid receptor agonist. Clin Exp Dermatol 2018; 43:553-558. [DOI: 10.1111/ced.13398] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2017] [Indexed: 12/14/2022]
Affiliation(s)
- K. A. Bilir
- Department of Medical Pharmacology; Faculty of Medicine; Trakya University; Edirne Turkey
| | - G. Anli
- Department of Medical Pharmacology; Faculty of Medicine; Trakya University; Edirne Turkey
| | - E. Ozkan
- Department of Medical Pharmacology; Faculty of Medicine; Trakya University; Edirne Turkey
| | - O. Gunduz
- Department of Medical Pharmacology; Faculty of Medicine; Trakya University; Edirne Turkey
| | - A. Ulugol
- Department of Medical Pharmacology; Faculty of Medicine; Trakya University; Edirne Turkey
| |
Collapse
|
12
|
Ozkan E, Goksel O. Compliance boundary conditions for patient-specific deformation simulation using the finite element method. Biomed Phys Eng Express 2018. [DOI: 10.1088/2057-1976/aa918d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
13
|
Recber T, Ozkan E, Eren-Kocak E, Yılmaz M, Nemutlu E, Kır S. A Simple Extraction Procedure for HPLC Analysis of Fluoxetine in Rat Plasma Samples. CURR PHARM ANAL 2016. [DOI: 10.2174/1573412912666160422153616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
14
|
Soysal M, Ozkan E, Kok S, Occidente M, Tuna Y, Gurcan E, Matassino D. Genetic characterization of indigenous anatolian water buffalo breed using microsatellite dna markers. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2007.s2.409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
15
|
Soysal M, Tuna Y, Gurcan E, Ozkan E, Kok S, Castellano N, Cobanoglu O, Barone C. Anatolian water buffaloes husbandry in Turkey: preliminary results on somatic characterization. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2007.s2.1302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Ozkan E, Goksel O. Compliance boundary conditions for simulating deformations in a limited target region. Annu Int Conf IEEE Eng Med Biol Soc 2015; 2015:929-932. [PMID: 26736415 DOI: 10.1109/embc.2015.7318515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Patient-specific models in medical procedures are often limited to a relatively small region of interest due either to computational concerns or to the fact that only a part of anatomy could be observed in the input medical images. Thus, for deformable planning or training simulations, boundary conditions at the borders of such models are necessitated. Zero-displacement or -force constraints at outer boundaries are commonly used, with the assumption that the selected region is large enough to minimize effects on the deformable behavior inside the region of interest. This may, however, still result in errors and does require superfluous elements to extend models. In this work, a mixed boundary condition type, called compliance boundary condition, is proposed to constrain model boundaries. Different techniques to define and estimate these boundary constraints are studied with simulation experiments. Results are presented for palpation on 2D and 3D phantoms and needle insertion to a male pelvic anatomical model.
Collapse
|
17
|
Ozkan E. Positron emission tomography/computed tomography in locally advanced breast cancer. Exp Oncol 2013; 35:253-257. [PMID: 24382434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Locally advanced breast cancer (LABC) is a relatively small group of breast cancer, but is significant because it carries a higher risk of locoregional recurrence and distant metastasis. The accepted approach for these patients is neoadjuvant chemotherapy before surgery as determining the response to therapy in the early stages is of critical importance in respect of the approach taken to the disease. Positron emission tomography/computed tomography (PET/CT) using fluorine-18-fluorodeoxyglucose (18F-FDG) is currently used for staging, restaging and response monitoring in breast cancer. The areas of use of FDG PET/CT in LABC can be summarised as the evaluation of response to neoadjuvant chemotherapy in the early stage in particular, and the determination of unexpected areas of metastasis not detected by standard imaging techniques. There are current ongoing studies on promising new PET radiopharmaceuticals apart from FDG.
Collapse
Affiliation(s)
- E Ozkan
- Department of General Surgery, Ankara University Medical School, Ankara 06590, Turkey
| |
Collapse
|
18
|
Ozmen O, Seker I, Ertugrul O, Ozkan E, Tekin N. Prolactin receptor (<i>PRLR</i>) gene polymorphism in Chios, White Karaman and Awassi sheep breeds. Arch Anim Breed 2011. [DOI: 10.5194/aab-54-381-2011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The objective of the present study was to determine the polymorphism in the prolactine receptor (PRLR) gene in Chios, White Karaman and Awassi, which are native sheep breeds in Turkey. By means of PRLR gene sequence homology between sheep and humans, two primer pairs were designed for polymerase chain reaction (PCR) amplification within intron 1 and exon 10 of the PRLR gene in sheep. A total of 160 amplicons (99 for intron 1 and 61 for exon 10) were subjected to DNA sequence analysis. For intron 1, 6 different haplotypes were determined. For exon 10, 7 different haplotypes were obtained. Some variations determined for exon 10 (g.14A>T p.Q14L; g.160G>A p.D160N; g.166G>A p.E166K; g.167A>T p.E167V; g.176A>T p.H176L; g.206G>A p.S206N; g.208G>A p.G208R) led to changes in the amino acids, but no amino acid changes were determined in g.2A>T, g.81A>G, g.138A>G, g.186C>T, g.207T>C. It was noted in particular that White Karaman and Awassi were similar to each other in both PRLR exon 10 and intron 1 haplotypes, whereas the Chios breed had a different variation.
Collapse
|
19
|
Pariset L, Mariotti M, Nardone A, Soysal MI, Ozkan E, Williams JL, Dunner S, Leveziel H, Maróti-Agóts A, Bodò I, Valentini A. Relationships between Podolic cattle breeds assessed by single nucleotide polymorphisms (SNPs) genotyping. J Anim Breed Genet 2010; 127:481-8. [PMID: 21077972 DOI: 10.1111/j.1439-0388.2010.00868.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Italian Maremmana, Turkish Grey and Hungarian Grey breeds belong to the same Podolic group of cattle, have a similar conformation and recently experienced a similar demographic reduction. The aim of this study was to assess the relationship among the analysed Podolic breeds and to verify whether their genetic state reflects their history. To do so, approximately 100 single nucleotide polymorphisms (SNPs) were genotyped on individuals belonging to these breeds and compared to genotypes of individuals of two Italian beef breeds, Marchigiana and Piemontese, which underwent different selection and migration histories. Population genetic parameters such as allelic frequencies and heterozygosity values were assessed, genetic distances calculated and assignment test performed to evaluate the possibility of recent admixture between the populations. The data show that the physical similarity among the Podolic breeds examined, and particularly between Hungarian Grey and Maremmana cattle that experienced admixture in the recent past, is mainly morphological. The assignment of individuals from genotype data was achieved using Bayesian inference, confirming that the set of chosen SNPs is able to distinguish among the breeds and that the breeds are genetically distinct. Individuals of Turkish Grey breed were clearly assigned to their breed of origin for all clustering alternatives, showing that this breed can be differentiated from the others on the basis of the allelic frequencies. Remarkably, in the Turkish Grey there were differences observed between the population of Enez district, where in situ conservation studies are practised, and that of Bandirma district of Balikesir, where ex situ conservation studies are practised out of the original raising area. In conclusion, this study demonstrates that molecular data could be used to reveal an unbiased view of past events and provide the basis for a rational exploitation of livestock, suggesting appropriate cross-breeding plans based on genetic distance or breeding strategies that include the population structure.
Collapse
Affiliation(s)
- L Pariset
- Dipartimento di Produzioni Animali, Università degli Studi della Tuscia, Viterbo, Italy.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Jasinski J, Darr M, Ozkan E, Precheur R. Applying imidacloprid via a precision banding system to control striped cucumber beetle (Coleoptera: Chrysomelidae) in cucurbits. J Econ Entomol 2009; 102:2255-2264. [PMID: 20069855 DOI: 10.1603/029.102.0630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The striped cucumber beetle, Acalymma vittatum (F.) (Coleoptera: Chrysomelidae), is a key pest of cucurbit crops throughout its range. A novel precision band applicator was designed to inject a solid stream of imidacloprid solution in-furrow directly over the seed during planting to reduce beetle leaf feeding on pumpkin, zucchini, and cucumber crops. In 2004 and 2005, bioassays at the cotyledon through fifth leaf were conducted on striped cucumber beetles using seedling leaf tissue grown from seeds treated using both continuous and precision banded in-furrow imidacloprid solution applications. In 2004, 80% of bioassay trials had treatments with beetle mortality significantly higher than the check, whereas 70% of the bioassay trials showed no significant difference in mortality between continuous in-furrow and precision banded treatments. In 2005, 79% of bioassay trials had treatments with beetle mortality significantly higher than the check, whereas 100% of the bioassays showed no significant difference in beetle mortality between continuous in-furrow and precision banded treatments at the same insecticide rate. The environmental savings of precision banded treatments compared with continuous in-furrow treatment reduced imidacloprid up to 84.5% on a per hectare basis for all cucurbits tested in 2004 and 2005, translating into an economic savings up to $215/ha. In separate bioassay trials conducted in 2005 on pumpkin, where insecticide band length and injection volume were manipulated independently, several treatments had significantly higher beetle mortality than the check. There was a trend of increased beetle mortality in treatments using shorter band lengths combined with higher insecticide solution volumes.
Collapse
Affiliation(s)
- J Jasinski
- Integrated Pest Management Program, Ohio State University Extension, Urbana, OH 43078, USA.
| | | | | | | |
Collapse
|
21
|
Oztabak K, Ozkan E, Soysal I, Paya I, Ün C. Detection of prion gene promoter and intron1indelpolymorphisms in Anatolian water buffalo (Bubalus bubalis). J Anim Breed Genet 2009; 126:463-7. [DOI: 10.1111/j.1439-0388.2009.00821.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
22
|
Abstract
The genetic variation and relationships among six Turkish water buffalo populations, typical of different regions, were assessed using a set of 26 heterologous (bovine) microsatellite markers. Between seven and 17 different alleles were identified per microsatellite in a total of 254 alleles. The average number of alleles across all loci in all the analysed populations was found to be 12.57. The expected mean heterozygosity (H(e)) per population ranged between 0.5 and 0.58. Significant departures from Hardy-Weinberg equilibrium were observed for 44 locus-population combinations. Population differentiation was analysed by estimation of the F(st) index (values ranging from 0.053 to 0.123) among populations. A principal component analysis of variation revealed the Merzifon population to show the highest differentiation compared with the others. In addition, some individuals of the Danamandira population appeared clearly separated, while the Afyon, Coskun, Pazar and Thural populations represented a single cluster. The assignment of individuals to their source populations, performed using the Bayesian clustering approach implemented in the structure 2.2 software, supports a high differentiation of Merzifon and Danamandira populations. The results of this study are useful for the development of conservation strategies for the Turkish buffalo.
Collapse
Affiliation(s)
- M Gargani
- Department of Animal Production, University of Tuscia, Viterbo, Italy
| | | | | | | | | |
Collapse
|
23
|
Hazirolan T, Ozkan E, Erol M, Bluemke DA, Aytemir K, Oto A, Besim A. Myocardial delayed enhancement imaging: comparison of two-dimensional and three-dimensional inversion prepared fast gradient echo and steady state free precession sequences. JBR-BTR 2007; 90:124-7. [PMID: 17555074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We compared two-dimensional (2D) and three-dimensional (3D) inversion recovery prepared (IR) fast gradient echo (FGRE) and steady state free precession (SSFP) sequences used in myocardial delayed enhancement imaging. Twenty patients with a prior history of acute coronary syndrome were included in this study. Breath hold, ECG gated, segmented 2D and 3D IR_FGRE and SSFP sequences were acquired after intravenous administration of 0.15 mmol/kg gadodiamide-DTPA. Overall image quality, transmural extent of myocardial infarction, infarct volume, signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and signal intensity ratio (SIR) were calculated and compared for each technique. 3D IR trueFISP showed significantly higher mean values of SNR and CNR compared with 3D IR turboFLASH, 2D IR turboFLASH and 2D IR trueFISP (p < 0.04 and p < 0.001). 3D IR_FGRE showed the second highest SNR and CNR. 3D IR_SSFP and 3D IR_FGRE allowed the imaging of the whole heart within a single breath-hold which reduced the imaging time significantly compared to 2D IR_FGRE and 2D IR_SSFP. 3D IR_SSFP and 3D IR_FGRE offer higher SNR, CNR and rapid acquisiton compared to 2D IR_SSFP and 2D IR_FGRE with adequate image quality.
Collapse
Affiliation(s)
- T Hazirolan
- Department of Radiology, Hacettepe University Faculty of Medicine, Sihhiye, Ankara, Turkey
| | | | | | | | | | | | | |
Collapse
|
24
|
Akata F, Tatman-Otkun M, Ozkan E, Tansel O, Otkun M, Tugrul M. Prevalence of extended-spectrum beta-lactamases produced by nosocomial isolates of Enterobacteriaceae in Trakya University Hospital, Turkey. New Microbiol 2003; 26:257-62. [PMID: 12901421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The prevalence of extended-spectrum beta-lactamase (ESBL) production by 194 nosocomial isolates of Enterobacteriacea recovered from 1995 to 1999 was investigated. The ESBL production was determined by the double-disk synergy test and was confirmed by the E-test ESBL strip. Twenty-three isolates (21 Klebsiella pneumoniae, one Escherichia coli, one Providencia rettgeri) were found as ESBL-producers (11.8%). These isolates were also usually resistant to non-betalactam antibiotics. Most of them contained a beta-lactamase with a pI of 7.6. All the strains conjugally transferred their ESBLs to recipient E. coli. Contrary to others, ESBL-producing K. pneumoniae strains isolated in 1999 were resistant to ciprofloxacin, and had the identical plasmid profiles suggestive of an outbreak. Ciprofloxacin resistance in these strains could not be transferred. In conclusion, K. pneumoniae was the main ESBL-producing species among nosocomial isolates of Enterobacteriacae in our hospital.
Collapse
Affiliation(s)
- F Akata
- Department of Clinical Bacteriology and Infectious Diseases, Medical Faculty of Trakya University, 22030 Edirne, Turkey
| | | | | | | | | | | |
Collapse
|
25
|
Mueller DS, Dorrance AE, Derksen RC, Ozkan E, Kurle JE, Grau CR, Gaska JM, Hartman GL, Bradley CA, Pedersen WL. Efficacy of Fungicides on Sclerotinia sclerotiorum and Their Potential for Control of Sclerotinia Stem Rot on Soybean. Plant Dis 2002; 86:26-31. [PMID: 30822994 DOI: 10.1094/pdis.2002.86.1.26] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sclerotinia stem rot of soybean, caused by Sclerotinia sclerotiorum, is a major disease in the north central region of the United States. One approach to managing Sclerotinia stem rot on soybean is the use of fungicides. S. sclerotiorum was assayed for sensitivity to benomyl, tebuconazole, thiophanate methyl, and vinclozolin in pure cultures on agar medium, inoculated soybean seedlings, detached inoculated leaves, and in experimental field plots. To evaluate the inhibitory effect of four fungicides on growth of S. sclerotiorum in vitro, potato dextrose agar (PDA) was amended with the fungicides at six concentrations. Based on measurements of fungal radial growth, vinclozolin was the most effective in inhibiting S. sclerotiorum mycelial growth at 1.0 μg a.i./ml of PDA. Ranges of reduction of radial growth of 91 isolates of S. sclerotiorum on PDA amended with thiophanate methyl and vinclozolin were 18 to 93% and 93 to 99%, respectively, when compared with the nonamended agar control. Benomyl, thiophanate methyl, and vinclozolin applied to greenhouse-grown seedlings prevented S. sclerotiorum from expressing symptoms or signs on leaf tissue. Detached leaves sprayed with thiophanate methyl and then inoculated with mycelial plugs of S. sclerotiorum did not express symptoms or signs. Of 13 different environments in Illinois, Indiana, Ohio, and Wisconsin from 1995 through 2000, six had low Sclerotinia stem rot incidence (<1%), three environments had low to moderate Sclerotinia stem rot incidence (5 to 25%), and four environments had high Sclerotinia stem rot incidence (>25%). When disease incidence was high, no consistent control of Sclerotinia stem rot was observed with benomyl or thiophanate methyl using different application systems. However, under low disease incidence, spray systems that were able to penetrate the canopy reduced the incidence of Sclerotinia stem rot an average of 50%.
Collapse
Affiliation(s)
- D S Mueller
- Department of Crop Sciences, University of Illinois, Urbana 61801
| | | | | | - E Ozkan
- Department of Food Agriculture and Biological Engineering, Ohio State University, Wooster 44691
| | - J E Kurle
- Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | | | - J M Gaska
- Department of Agronomy, University of Wisconsin, Madison 53706
| | | | - C A Bradley
- Department of Crop Sciences, University of Illinois, Urbana 61801
| | - W L Pedersen
- Department of Crop Sciences, University of Illinois, Urbana 61801
| |
Collapse
|
26
|
Tang Z, Li B, Bharadwaj R, Zhu H, Ozkan E, Hakala K, Deisenhofer J, Yu H. APC2 Cullin protein and APC11 RING protein comprise the minimal ubiquitin ligase module of the anaphase-promoting complex. Mol Biol Cell 2001; 12:3839-51. [PMID: 11739784 PMCID: PMC60759 DOI: 10.1091/mbc.12.12.3839] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In mitosis, the anaphase-promoting complex (APC) regulates the onset of sister-chromatid separation and exit from mitosis by mediating the ubiquitination and degradation of the securin protein and mitotic cyclins. With the use of a baculoviral expression system, we have reconstituted the ubiquitin ligase activity of human APC. In combination with Ubc4 or UbcH10, a heterodimeric complex of APC2 and APC11 is sufficient to catalyze the ubiquitination of human securin and cyclin B1. However, the minimal APC2/11 ubiquitin ligase module does not possess substrate specificity, because it also ubiquitinates the destruction box deletion mutants of securin and cyclin B1. Both APC11 and UbcH10 bind to the C-terminal cullin homology domain of APC2, whereas Ubc4 interacts with APC11 directly. Zn(2+)-binding and mutagenesis experiments indicate that APC11 binds Zn(2+) at a 1:3 M ratio. Unlike the two Zn(2+) ions of the canonical RING-finger motif, the third Zn(2+) ion of APC11 is not essential for its ligase activity. Surprisingly, with Ubc4 as the E2 enzyme, Zn(2+) ions alone are sufficient to catalyze the ubiquitination of cyclin B1. Therefore, the Zn(2+) ions of the RING finger family of ubiquitin ligases may be directly involved in catalysis.
Collapse
Affiliation(s)
- Z Tang
- Departments of Pharmacology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Usher KC, Ozkan E, Gardner KH, Deisenhofer J. The plug domain of FepA, a TonB-dependent transport protein from Escherichia coli, binds its siderophore in the absence of the transmembrane barrel domain. Proc Natl Acad Sci U S A 2001; 98:10676-81. [PMID: 11526207 PMCID: PMC58525 DOI: 10.1073/pnas.181353398] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
FepA, an outer membrane iron siderophore transporter from Escherichia coli, is composed of a 22-stranded membrane-spanning beta barrel with a globular N-terminal "plug" domain of 148 residues that folds up inside the barrel and completely occludes the barrel's interior (1). We have overexpressed and purified this plug domain by itself and find that it behaves in vitro as a predominantly unfolded yet soluble protein, as determined by circular dichroism, thermal denaturation, and NMR studies. Despite its unfolded state, the isolated domain binds ferric enterobactin, the siderophore ligand of FepA, with an affinity of 5 microM, just 100-fold reduced from that of intact FepA. These findings argue against the hypothesis that the plug domain is pulled intact from the barrel during transport in vivo but may be consistent either with a model where the plug rearranges within the barrel to create a channel large enough to allow transport or with a model where the plug unfolds and comes out of the barrel.
Collapse
Affiliation(s)
- K C Usher
- Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | | | | | | |
Collapse
|
28
|
Affiliation(s)
- E Ozkan
- Department of Nuclear Medicine, Ankara University Medical Faculty, Ankara, Turkey
| | | | | | | | | |
Collapse
|
29
|
Otkun M, Erdem B, Akata F, Tatman-otkun M, Gerceker D, Yagci S, Ozkan E. Eur J Clin Microbiol Infect Dis 2001; 20:0206-0209. [DOI: 10.1007/s10096-001-8083-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
30
|
Otkun M, Erdem B, Akata F, Tatman-Otkun M, Gerceker D, Yagci S, Ozkan E. Antibiotic Resistance Patterns and Plasmid Profiles of Salmonella typhimurium Isolates in Turkey. Eur J Clin Microbiol Infect Dis 2001; 20:206-9. [PMID: 11347674 DOI: 10.1007/pl00011253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
To understand the resistance mechanisms present in 75 isolates of Salmonella typhimurium derived from clinical infections in Turkey, antimicrobial resistance patterns and associated plasmids were investigated. Among the 22 strains that produced extended-spectrum beta-lactamase (ESBL), 20 were resistant to aminoglycosides and 12 to trimethoprim-sulfamethoxazole. Strains that did not produce ESBL did not express aminoglycoside or trimethoprim-sulfamethoxazole resistance, although 27 of them were ampicillin resistant. None of the strains were resistant to imipenem or fluoroquinolones. Nineteen strains producing ESBL carried a plasmid of >100 MDa. Seven ESBL-producing strains conjugally transferred their ESBLs and trimethoprim-sulfamethoxazok resistance. No correlation was found between the resistance patterns and plasmids in non-ESBL-producing strains.
Collapse
Affiliation(s)
- M Otkun
- Department of Clinical Bacteriology and Infectious Diseases, Medical Faculty, Trakya University, Edirne, Turkey
| | | | | | | | | | | | | |
Collapse
|
31
|
Abstract
Summary.
The objective of this theoretical study is to delineate the characteristics of a well producing at a constant pressure in a naturally fractured reservoir. We consider flow to a well located at the center of a closed circular reservoir. New solutions not documented previously are presented. Five flow regimes are identified and information that can be extracted from each regime is documented. Methods to determine formation parameters and to predict well deliverability are discussed.
Introduction
This paper is a theoretical study of the performance of a well located in a fractured reservoir and produced at a constant pressure. As is well known, a fractured reservoir is usually considered to be a system in which the conducting properties of the rock are a result of the fracture system and the storage capacity of the reservoir is due to the matrix system. All mathematical models that describe the performance of fractured reservoirs assume that the well response is a combination of a rapid response that is a result of the fracture system and a slower induced response that reflects the contribution of the matrix system. The principal difference between the models suggested in the literature involves the interaction of the matrix system and the fracture system. Warren and Root and Odeh assume quasisteady- or pseudosteady-state flow in the matrix system, whereas Kazemi, deSwaan- O., Najurieta, and Kucuk and Sawyer assume unsteady-state flow in the matrix system. Mavor and Cinco-Ley and DaPrat et al. used the Warren and Root model to examine the response of a well flowing at a constant pressure. Their objective was to predict well deliverability when the reservoir parameters were determined independently. In this work, we assume that the fractured reservoir may be represented by the rectangular slabmodel idealization used in Refs. 3 and 4 (see Fig. 1). Our first objective is to discuss procedures whereby early-time rate data may be analyzed at a well to determine the properties of the fracture and the matrix systems. The second objective is to present methods to predict future performance or well deliverability.
In this work, we identify five possible flow regimes. Three of these flow regimes may exist if the well response is unaffected by boundary effects. Following the terminology of Ref. 9, we identify the flow regimes as Flow Regimes 1 through 3. Two other flow regimes may be evident after the outer boundary begins to dominate the well response. We refer to these flow regimes as Flow Regimes 4 and 5.
In the following, we delineate conditions under which Flow Regimes 1 through 5 will exist and discuss the information that can be extracted from each. In particular, we show that for specific values of reservoir properties, not all flow regimes will be evident. We also show that reservoir size determines the flow regime that will govern the well response during boundary-dominated flow.
Mathematical Model
We consider the flow of a slightly compressible fluid of constant viscosity in a cylindrical reservoir in which the outer boundary is closed. The well is located at the center of the cylinder and fluid is produced at a constant pressure. Initially, the pressure is uniform throughout the reservoir. Gravitational effects are assumed to be negligible. We consider a skin region and assume that it is "infinitesimally thin." The wellbore storage effect is not considered.
As already mentioned, we assume that the naturally fractured reservoir be described by the slab model suggested by Kazemi and deSwaan-O. (Fig. 1). Individually, the matrix system and the fracture system are assumed to be uniform, isotropic porous media. All production is by way of the fracture system, and flow from the matrix system to the fracture system is onedimensional (1D) (normal to the fracture system).
For modeling purposes, the mathematical problem may be formulated by examination of flow in only one of the repetitive elements shown in Fig. 1. The mathematical formulation is discussed in the Appendix. The solution in Laplace space (for infinite-acting and bounded systems) and the relevant asymptotic approximations are given in the Appendix. All results presented in this study were obtained by inversion of the rigorous analytic solution given in the Appendix numerically, and not from the asymptotic expansions. The asymptotic expansions are useful primarily in identifying the structure of the solutions.
SPEFE
P. 186^
Collapse
|
32
|
Büyüköztürk K, Korkut F, Meric M, Deligönül U, Ozkan E, Ozcan R. Prognostic significance of isolated left anterior hemiblock and left axis deviation in the course of acute myocardial infarction. Heart 1977; 39:1192-5. [PMID: 588375 PMCID: PMC483395 DOI: 10.1136/hrt.39.11.1192] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In 700 patients with acute myocardial infarction admitted to the intensive coronary care unit of our hospital, the incidence and significance of left anterior hemiblock and left axis deviation has been studied in the acute phase of disease. In 102 (14.6%) of the 700 patients, isolated left axis deviation (mean QRS axis-45 degrees) was found and 69 of them (9.9%) met the criteria of left anterior hemiblock. Of the 69 patients with left anterior hemiblock, 61 had acute anterior myocardial infarction, 5 had inferior infarction, and 3 had subendocardial infarction. The anterior hemiblock was transient in 5 patients, but persisted in 64. All patients with and without isolated left anterior hemiblock and left axis deviation were compared statistically with reference to mortality rate and the incidence of arrythmias; no significant difference was noted. However, in patients over the age of 65 and also in those with hypertension, the incidence of left axis deviation was significantly higher (P less than 0.05 and P less than 0.001, respectively). It was concluded that isolated left anterior hemiblock and left axis deviation occurring in the course of acute myocardial infarction no influence on the prognosis of acute myocardial infarction.
Collapse
|
33
|
|
34
|
|
35
|
Prinzmetal M, Ishikawa K, Nakashima M, Oishi H, Ozkan E, Wakayama J, Baines JM. Correlation between intracellular and surface electrograms in acute myocardial ischemia. J Electrocardiol 1968; 1:161-6. [PMID: 5710418 DOI: 10.1016/s0022-0736(68)80023-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
36
|
Prinzmetal M, Ishikawa K, Oishi H, Ozkan E, Wakayama J, Baines JM. Effects of quinidine on electrical behavior in cardiac muscle. J Pharmacol Exp Ther 1967; 157:659-64. [PMID: 6048022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
|
37
|
|
38
|
Ekmekçi A, Ozkan E, Ercan H, Prifti J. [Mechanism of atrial flutter in man]. Turk Tip Cemiy Mecm 1966; 32:263-6. [PMID: 5945907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
39
|
Dorken N, Ekmeçi A, Kuygu A, Ozkan E, Ozcan R. [Electrocardiographic changes in the course of mitral stenosis in relation with the dimensions of mitral valve, the degree of reflux and pulmonary hypertension]. Rev Med Moyen Orient 1965; 22:388-94. [PMID: 5216709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|