1,773 results on '"Seker A"'
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2. Comparison of residual and dense neural network approaches for building extraction from high-resolution aerial images
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Batuhan Sariturk and Dursun Zafer Seker
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Atmospheric Science ,Geophysics ,Space and Planetary Science ,Aerospace Engineering ,General Earth and Planetary Sciences ,Astronomy and Astrophysics - Published
- 2023
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3. Comprehensive evaluation of Satellite-Based and reanalysis precipitation products over the Mediterranean region in Turkey
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Enes Hisam, Ali Danandeh Mehr, Ugur Alganci, and Dursun Zafer Seker
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Atmospheric Science ,Geophysics ,Space and Planetary Science ,Aerospace Engineering ,General Earth and Planetary Sciences ,Astronomy and Astrophysics - Published
- 2023
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4. Der Solinger Brandanschlag im Spiegel der Presse
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Derya Gür-Seker
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Derya Gür-Şeker analysiert in diesem Beitrag medien- und diskurslinguistisch die Medienberichterstattung über den Brandanschlag in Solingen 1993. Dabei werden in Anlehnung an die Ziele des Sammelbandes, Betroffenenperspektiven in den Fokus zu rücken, akteursspezifische Perspektiven eingenommen, die mediale Praktiken der Berichterstattung über die Betroffenen beleuchten. Hierfür werden ausgewählte Zeitungsberichte korpuslinguistisch, das heißt unter Einbezug von Häufigkeiten, mit Fokus auf Sprachgebrauch, Kontexte von Wörtern sowie betroffenenspezifischer Benennungspraktiken untersucht - insbesondere mit Blick auf die Familie Genç. Ziel ist es, Regelhaftigkeiten und Mechanismen der medialen Darstellung im Zeitverlauf zu bestimmen und linguistisch zu analysieren.
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- 2023
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5. Abstract P3-10-02: Cell cycle dysregulation in breast cancer: why the details matter
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Sinem Seker, Elena Oropeza, Sabrina Carrel, Aloran Mazumder, Nindo Punturi, Jonathan Lei, Meenakshi Anurag, Bora Lim, Matthew Bainbridge, and Svasti Haricharan
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Cancer Research ,Oncology - Abstract
Cell cycle dysregulation is a prerequisite for cancer formation. However, whether the type of cell cycle dysregulation event a cell incurs during transformation to malignancy influences the type of cancer that evolves or clinical outcome is unknown. In a comprehensive analysis of cell cycle dysregulation in breast cancer patient tumors, we associate mutations in each of four cell cycle checkpoint kinase genes, ATM, CHEK2, ATR and CHEK1, with known tumor characteristics and clinical outcome, and test these associations experimentally using transgenic mice, patient-derived xenografts and breast cancer cell line model systems. Results of this work demonstrate that dysregulation of specific cell cycle checkpoint kinases differently impacts the type of breast cancer that evolves in patients and in experimental model systems, and influences treatment responsiveness and disease progression. For instance, CHEK2 mutations associate preferentially with the incidence of metastatic, premenopausal estrogen receptor (ER)+/HER2- breast cancer in patient data (p=0.001) that is resistant to standard frontline therapy (HR=6.15, p=0.01). These associations appear causal when tested in an immune-competent genetically-engineered mouse model of Chk2 loss, in patient-derived xenograft, and in cell line experiments. On the other hand, ATR mutation by itself is not frequent in ER+/HER2- breast cancer, but co-incident mutation of ATR and TP53 is 2-fold enriched (p=0.002) and associates with metastatic progression (HR=2.01, p=0.007). Concordantly, ATR dysregulation induces metastatic phenotypes in ER+/HER- TP53 mutant, but not in TP53 wildtype, cell lines. Together, these results systematize the impact of individual cell cycle checkpoint kinases on the evolution of cancer subtypes, and on disease progression. Statement of Significance These findings reframe the paradigm of breast cancer classification through the lens of early cell cycle dysregulation events by demonstrating that cell cycle decisions during malignant transformation can direct the type of breast cancer that evolves, how it will respond to treatment, and whether it will metastasize. This work provides rationale for streamlined testing of checkpoint kinase dysregulation to improve precision diagnostics for cancer patients. Citation Format: Sinem Seker, Elena Oropeza, Sabrina Carrel, Aloran Mazumder, Nindo Punturi, Jonathan Lei, Meenakshi Anurag, Bora Lim, Matthew Bainbridge, Svasti Haricharan. Cell cycle dysregulation in breast cancer: why the details matter [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-10-02.
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- 2023
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6. Evaluation of shear bond strength of orthodontic adhesives with integrated primer: A comparative study
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Berza Sen Yilmaz, Zeynep Beyza Yildirim, Elif Dilara Seker, Furkan Ozden, and Gokmen Kurt
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Orthodontics - Abstract
Objectives: The study aimed to compare the shear bond strength (SBS) of three orthodontic adhesives with integrated primer, with those of self-etching and conventional bonding adhesives. Material and Methods: One hundred extracted premolars were randomly allocated to five groups. Brackets were bonded using three adhesives with integrated primer (GC Ortho Connect™, Biofix, and Orthocem). A group of brackets was bonded with the conventional bonding procedure (Transbond XT) and one group was bonded with a self-etching primer (Transbond™ Plus). All samples were subjected to thermal aging (5000 cycles: At 5°C and 55°C media). The compressive strength test was performed and the maximum load when the bracket detached was recorded. The amount of residual adhesive (ARI) remaining on the tooth surface was assessed visually. Results: Significantly higher SBS values were recorded with the conventional technique (14.01 ± 5.79 megapascals [MPa]), compared to other groups except for GC Ortho Connect™ (11.86 ± 3.83 MPa). There was no significant difference between the self-etching group and the groups containing integrated primer samples. However, one of the adhesives with integrated primer presented SBS values near-slightly below the limit considered clinically successful (7.65 ± 3.71 MPa). The ARI scores varied between adhesive groups; GC Ortho Connect™ and the self-etching primer samples showed statistically significantly higher scores compared to the three other groups. Conclusion: Clinically successful bonding values were achieved with two out of three different adhesives with integrated primer. One of the adhesives with integrated primer provided a similar SBS value to the tri-step conventional bonding procedure. ARI scores varied independently from SBS values.
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- 2023
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7. Comparative Analysis of Different CNN Models for Building Segmentation from Satellite and UAV Images
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Batuhan Sariturk, Damla Kumbasar, and Dursun Zafer Seker
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Computers in Earth Sciences - Abstract
Building segmentation has numerous application areas such as urban planning and disaster management. In this study, 12 CNN models (U-Net, FPN, and LinkNet using EfficientNet-B5 backbone, U-Net, SegNet, FCN, and six Residual U-Net models) were generated and used for building segmentation. Inria Aerial Image Labeling Data Set was used to train models, and three data sets (Inria Aerial Image Labeling Data Set, Massachusetts Buildings Data Set, and Syedra Archaeological Site Data Set) were used to evaluate trained models. On the Inria test set, Residual-2 U-Net has the highest F1 and Intersection over Union (IoU) scores with 0.824 and 0.722, respectively. On the Syedra test set, LinkNet-EfficientNet-B5 has F1 and IoU scores of 0.336 and 0.246. On the Massachusetts test set, Residual-4 U-Net has F1 and IoU scores of 0.394 and 0.259. It has been observed that, for all sets, at least two of the top three models used residual connections. Therefore, for this study, residual connections are more successful than conventional convolutional layers.
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- 2023
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8. Evaluation of the factors affecting opening-closing performance of wooden cabinet doors
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Emine Seda Erdinler, Sedanur Seker, Ender Hazır, and Kucuk Huseyin Koc
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Environmental Engineering ,Bioengineering ,Waste Management and Disposal - Abstract
This study determined the deflection performance of wooden cabinet doors during opening and closing by using different material types, opening-closing angle, and load force. The independent variables consisted of material type, opening-closing angle, and load force, and the dependent variable was determined as deflection value. Medium density fiberboard (MDF) and particleboard (PB), both melamine faced, were used as two different material types. Opening and closing angles and directions of forces were performed as directed in BS EN 16122 (2012) and TSE EN 9215 (2005) and the doors were loaded by forces of 300N, 375N and 450N. The factors affecting deflection value and the interaction between them were investigated by multivariate analysis of variance. The results showed that the material type, angle, load force, and the mean between the material type and load force was significant. As the loading force increased, the deflection value increased. As the moisture increased, the deflection value increased, and as the material density increased, deflection value decreased. The adequacy of models was evaluated by the R-square (R²) and Adjusted R-square (Adj-R2) values. The results for these values were 88.23% and 86.58%, respectively.
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- 2023
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9. Modeling the Effects of Oscillator Phase Noise and Synchronization on Multistatic SAR Tomography
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Eric Loria, Samuel Prager, Ilgin Seker, Razi Ahmed, Brian Hawkins, and Marco Lavalle
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General Earth and Planetary Sciences ,Electrical and Electronic Engineering - Published
- 2023
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10. Performance, Efficiency, and Target Setting for Bank Branches: Time Series With Automated Machine Learning
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Ilker Met, Ayfer Erkoc, and Sadi Evren Seker
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General Computer Science ,General Engineering ,General Materials Science ,Electrical and Electronic Engineering - Published
- 2023
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11. Analysis of the Causes of Newborn Priapism: A Retrospective Clinical Study
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Ekrem Guner, Fatih Akkas, Osman Ozdemir, Yusuf Arikan, Kamil Gokhan Seker, and Emre Sam
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General Medicine - Abstract
Priapism is a rare condition in the newborn. The aim of this study was to investigate the demographic, etiologic and clinical features of neonatal priapism. We retrospectively analysed the data of 11 patients diagnosed with neonatal priapism in the neonatal intensive care unit between 2000 and 2019. Priapism was defined as an erection in the neonatal period, lasting more than 4 hours. Etiological examinations revealed polycythemia in one (9.09%) patient, D-dimer elevation in three patients, and heterozygous methyltetrahydrofolate 667 gene mutations in one patient. Other patients were considered idiopathic. Detumescence was achieved in all 11 (100%) patients during the follow-up period. The median hospitalization duration was 6 (IQR [4, 8]; range, 2–9) days. The median follow-up duration was 38 (IQR [30, 42]; range, 13–94) months for patients followed-up in our hospital after discharge. Neonatal priapism is a rare condition. Successful treatment results can be achieved with conservative methods. Data acquired from our study showed that diseases with a tendency to hypercoagulation belong to the etiology by damaging penile microcirculation and make the response to conservative treatment more challenging.
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- 2023
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12. Self-Testing of Ketone Bodies, along with Glucose, Using Touch-Based Sweat Analysis
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Jong-Min Moon, Rafael Del Caño, Chochanon Moonla, Kittiya Sakdaphetsiri, Tamoghna Saha, Letícia Francine Mendes, Lu Yin, An-Yi Chang, Sumeyye Seker, and Joseph Wang
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Fluid Flow and Transfer Processes ,Process Chemistry and Technology ,Bioengineering ,Instrumentation - Abstract
β-Hydroxybutyrate (HB) is one of the main physiological ketone bodies that play key roles in human health and wellness. Besides their important role in diabetes ketoacidosis, ketone bodies are currently receiving tremendous attention for personal nutrition in connection to the growing popularity of oral ketone supplements. Accordingly, there are urgent needs for developing a rapid, simple, and low-cost device for frequent onsite measurements of β-hydroxybutyrate (HB), one of the main physiological ketone bodies. However, real-time profiling of dynamically changing HB concentrations is challenging and still limited to laboratory settings or to painful and invasive measurements (e.g., a commercial blood ketone meter). Herein, we address the critical need for pain-free frequent HB measurements in decentralized settings and report on a reliable noninvasive, simple, and rapid touch-based sweat HB testing and on its ability to track dynamic HB changes in secreted fingertip sweat, following the intake of commercial ketone supplements. The new touch-based HB detection method relies on an instantaneous collection of the fingertip sweat at rest on a porous poly(vinyl alcohol) (PVA) hydrogel that transports the sweat to a biocatalytic layer, composed of the β-hydroxybutyrate dehydrogenase (HBD) enzyme and its nicotinamide adenine dinucleotide (NAD
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- 2022
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13. Exact Basilar Artery Occlusion Location Indicates Stroke Etiology and Recanalization Success in Patients Eligible for Endovascular Stroke Treatment
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Matthias A. Mutke, Arne Potreck, Niclas Schmitt, Fatih Seker, Peter A. Ringleb, Simon Nagel, Markus A. Möhlenbruch, Martin Bendszus, Charlotte S. Weyland, and Jessica Jesser
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Radiology, Nuclear Medicine and imaging ,Neurology (clinical) - Abstract
Introduction Endovascular stroke treatment (EST) is commonly performed for acute basilar artery occlusion (BAO). We aimed to identify the role of the exact location of BAO in patients receiving EST regarding the stroke etiology, recanalization success and prediction of favorable clinical outcome. Methods Retrospective analysis of 191 consecutive patients treated for BAO with EST from 01/2013 until 06/2021 in a tertiary stroke center. Groups were defined according to exact location of BAO in I: proximal third, II: middle third, III: distal third and IV: tip of the basilar artery. Univariate and multivariate analyses were performed for BAO location comparing stroke etiology, recanalization result and favorable clinical outcome according to mRS 0–3 90 days after stroke onset. Results Occlusion sides types I–IV were evenly distributed (37, 36, 60 and 58 patients). Types I and II were more often associated with large artery atherosclerosis (50 vs. 10 patients, p p p p = 0.0076). The BAO site is not predicting favorable clinical outcome. Conclusion The exact basilar artery occlusion site in patients eligible for endovascular stroke treatment reflects the stroke etiology and is associated with differing recanalization success but does not predict favorable clinical outcome.
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- 2022
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14. Investigation of therapeutic and immunomodulatory activity of Bacopa saponin from Bacopa monnieri
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Govindan Pothiaraj, Murugan Manoranjani, Sasikumar Pitchaikani, Gowtham Kumar Seker, Konda Mani Saravanan, Mariappan Rajan, and Harshavardhan Shakila
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Plant Science - Published
- 2022
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15. Suriyeli Gençlerin Eğitim Sürecinde Kültürleşme Deneyimleri
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Betul Dilara Seker
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General Medicine - Abstract
Göç, günümüzde yaşanan çatışma ve karmaşalar nedeniyle devam etmektedir. Göç süreci, güvenli bir alana yeniden yerleşim ve kaynaklara erişim fırsatları sunmaktadır. Birey açısından bu konular belirsizlikler de taşımaktadır. Mülteciler/geçici sığınmacılar göç sürecini planlamadan ve zorunluluklar nedeniyle aniden hızla verilen kararlarla deneyimlerler. Mülteciler menşe ülkede, göç sürecinde ve yeni yerleşilen ülkede travmatik olaylara maruz kalarak çoklu kayıplar yaşarlar. Bu grup için Yeniden yerleşim, kültürleşme ve uyum süreci zorlu geçmektedir. Genellikle komşu ülkelere yerleşen mülteciler için coğrafik yakınlık nedeniyle kültürel farklılıklar fazla olmasa da sosyal ve kültürel açıdan farklı bir yere yerleşmek, fiziksel, psikolojik ve sosyal birtakım zorluklar bireylere ek yük getirebilir. Bu süreçte özellikle mülteci çocuklar ve gençler yaygın olarak savunmasız ve bağımlı olarak tanımlanmaktadır. Çocuklar ve gençler çalışma, eğitim gibi farklı nedenlerle baskın grupla etkileşim içine girerler. Aynı zamanda gençlik dönemi sosyal kimliğin geliştiği, kişilik oluşumunun dinamik olduğu bir süreçtir. Bu süreçte eğitim mülteci gençlerin uyumu ve psikolojik iyi oluşlarında önemli bir yere sahiptir. Mülteci gençler için eğitim hem yeni kültürle ilgili bilgi edinmelerine kaynaklık eder, hem de yeteneklerini geliştirmelerine aracılık eder. Mevcut politikalarla şekillendirilen eğitim sisteminin sonuçları bireysel olarak psikolojik iyi oluşu ve uyumu doğrudan etkilemektedir. Okullar, mülteci gençlere destek sağlamak için ideal alanlardır. Mülteci gençlerin eğitime katılımları ve okula başarılı uyumları, onların psikolojik iyi oluşlarını olumlu etkilemektedir. Bu nedenle baskın toplumla yaşanan kültürleşme, sosyal kimlik, ayrımcılık, uyum gibi kavramlara odaklanmak önemlidir. Gençlerin eğitim sistemindeki kültürleşme süreci uyumlarını etkilediği için bu kavramlar değerlendirilmiştir. Çalışmanın amacı Türkiye’de yaşayan mülteci gençlerin eğitim sürecinin kültürleşme, sosyal kimlik, kesişimsellik, ayrımcılık ve uyum gibi sosyal psikolojik kavramları bağlamında değerlendirilmesidir. Eğitim süreci mülteci gençler için yeni fırsatlar ve belirsizlikler barındırır. Eğitim fırsatları sadece başarılı bir uyum için değil, aynı zamanda psikolojik iyi oluş içinde bir zemin oluşturmaktadır. Sonuç olarak kültürleşme süreci ve bu süreçte karşılaşılan sorunlara karşı geliştirilen mekanizmaların öğrenilmesinin uzun vadede uyum politikalarının belirlenmesinde alana katkı sağlayacak işlevsel çıktılarının olacağı düşünülmektedir.
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- 2022
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16. Do antidiabetic drugs prevent the transformation of Acanthamoeba trophozoite into cyst form?
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Necati Ozpinar, Ulku Karaman, Hulya Ozpinar, and Seker Dag
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Infectious Diseases ,Public Health, Environmental and Occupational Health ,Parasitology ,General Medicine ,Microbiology - Published
- 2022
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17. DeepSym: Deep Symbol Generation and Rule Learning for Planning from Unsupervised Robot Interaction
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Alper Ahmetoglu, M. Yunus Seker, Justus Piater, Erhan Oztop, and Emre Ugur
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Artificial Intelligence - Abstract
Symbolic planning and reasoning are powerful tools for robots tackling complex tasks. However, the need to manually design the symbols restrict their applicability, especially for robots that are expected to act in open-ended environments. Therefore symbol formation and rule extraction should be considered part of robot learning, which, when done properly, will offer scalability, flexibility, and robustness. Towards this goal, we propose a novel general method that finds action-grounded, discrete object and effect categories and builds probabilistic rules over them for non-trivial action planning. Our robot interacts with objects using an initial action repertoire that is assumed to be acquired earlier and observes the effects it can create in the environment. To form action-grounded object, effect, and relational categories, we employ a binary bottleneck layer in a predictive, deep encoderdecoder network that takes the image of the scene and the action applied as input, and generates the resulting effects in the scene in pixel coordinates. After learning, the binary latent vector represents action-driven object categories based on the interaction experience of the robot. To distill the knowledge represented by the neural network into rules useful for symbolic reasoning, a decision tree is trained to reproduce its decoder function. Probabilistic rules are extracted from the decision paths of the tree and are represented in the Probabilistic Planning Domain Definition Language (PPDDL), allowing off-the-shelf planners to operate on the knowledge extracted from the sensorimotor experience of the robot. The deployment of the proposed approach for a simulated robotic manipulator enabled the discovery of discrete representations of object properties such as ‘rollable’ and ‘insertable’. In turn, the use of these representations as symbols allowed the generation of effective plans for achieving goals, such as building towers of the desired height, demonstrating the effectiveness of the approach for multi-step object manipulation. Finally, we demonstrate that the system is not only restricted to the robotics domain by assessing its applicability to the MNIST 8-puzzle domain in which learned symbols allow for the generation of plans that move the empty tile into any given position.
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- 2022
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18. Evaluating the changes in nasal airway volume and nasal airflow after surgically assisted rapid maxillary expansion
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Elifhan Alagoz, Tugba Unver, Elif Dilara Seker, Gokmen Kurt, Erol Senturk, Abdullah Ozdem, Dogan Dolanmaz, ÖZDEM, ABDULLAH, ŞENTÜRK, EROL, KURT, GÖKMEN, ŞEKER, Elif Dilara, ALAGÖZ, ELİFHAN, and DOLANMAZ, DOĞAN
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Adult ,Male ,Rhinometry, Acoustic ,Palatal Expansion Technique ,Adolescent ,Nose ,ALAGÖZ E., Unver T., ŞEKER E. D. , KURT G., ŞENTÜRK E., Ozdem A., DOLANMAZ D., -Evaluating the changes in nasal airway volume and nasal airflow after surgically assisted rapid maxillary expansion-, Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology, 2022 ,Rhinomanometry ,Pathology and Forensic Medicine ,Young Adult ,Quality of Life ,Humans ,Female ,Radiology, Nuclear Medicine and imaging ,Dentistry (miscellaneous) ,Surgery ,Nasal Obstruction ,Nasal Cavity ,Oral Surgery - Abstract
© 2022 Elsevier Inc.Objective: This study aims to compare the changes in the nasal airway volume and nasal airflow using acoustic rhinometry (AR), rhinomanometry (RMN), and dental volumetric tomography (DVT) after surgically assisted rapid maxillary expansion (SARME). Study Design: Our study consists of 13 adults, 3 male and 10 female patients, aged between 15 and 26, with completed skeletal development. In our study, DVT imaging was obtained twice, preoperation and 3 months after expansion. AR and RMN measurements were recorded, and Visual Analog Score (VAS) and Nasal Obstruction Symptom Evaluation (NOSE) Scale surveys were scored at preoperation and 3 months after expansion. Nasopharyngeal-oropharyngeal airway volume and areas were calculated using the Romexis 3.8.3.R (Planmeca, Helsinki, Finland) and Nemotec V2019 (Madrid, Spain) software programs. IBM SPSS Statistics 22 (SPSS IBM, Armonk, New York) was used for statistical analysis. Results: Comparing the preoperation and postexpansion measurements by both software programs revealed a statistically significant increase in the nasopharyngeal airway volume. No statistically significant change was observed in the oropharyngeal airway volume. Furthermore, we found a statistically significant increase in VAS but a significant decrease in NOSE. Conclusion: According to our findings, nasal airway volume increased after SARME, and although there was no significant change in nasal resistance, patients’ quality of life increased significantly.
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- 2022
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19. Potential therapeutic effects of ethyl pyruvate in an experimental rat appendicitis model
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Sefa Sag, Kaan Masrabaci, Yagmur Sonmez, Selenay Furat Recber, Esmanur Seker, Yusufhan Yazir, Levent Elemen, Karolin Yanar, and Seval Aydin
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medicine.medical_specialty ,medicine.drug_class ,medicine.medical_treatment ,Antibiotics ,Gastroenterology ,Internal medicine ,Antibiotic therapy ,medicine ,Animals ,Ethyl pyruvate ,Rats, Wistar ,Pyruvates ,Saline ,Interleukin-6 ,business.industry ,Ceftriaxone ,Therapeutic effect ,General Medicine ,Appendicitis ,medicine.disease ,Pathophysiology ,Rats ,Pediatrics, Perinatology and Child Health ,Surgery ,Saline Solution ,business ,medicine.drug - Abstract
Background Pathophysiology of appendicitis is associated with the underlying inflammatory processes. Ethyl pyruvate (EP) has potent antioxidant and anti-inflammatory properties. In this study, we aimed to investigate the effects of EP on the treatment of appendicitis and to examine whether adding EP to the antibiotic treatment could increases the effectiveness of the treatment in a rat appendicitis model. Method Thirty two Wistar rats, which had previously created appendicitis, were randomly divided into 4 groups: Group 1 (0.1 ml saline solution), Group 2 (15 mg/kg ceftriaxone), Group 3 (50 mg/kg EP), Group 4 (EP 50 mg/kg + ceftriaxone 15 mg/kg). In all groups, saline solution, ceftriaxone and EP were administered intraperitoneally and the same procedure was repeated twice a day for the following five days. On day 6, the rats underwent relaparotomy and then intraabdominal findings were recorded. Histopathological examination and interleukin-6 (IL-6) level were performed on appendiceal specimens. Results Intra-abdominal adhesion score was significantly lower in Group 4 than in Group 1. Total inflammation score was significantly lower in Group 2 than in Group 1 and was significantly lower in Group 4 than in Group 3 and 1. IL-6 level was significantly lower in Group 4 than in Group 3 and 1. Conclusion We found that adding EP to the antibiotic therapy increased the efficacy of the treatment in the rat appendicitis model. Further studies are required to apply our findings to the clinical setting.
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- 2022
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20. A Bibliometric Analysis of out of School Learning Environments: Science Mapping
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Fatih SEKER and Muhammed Dogukan BALCIN
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- 2022
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21. Combating Infectious Diseases with Synthetic Biology
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Anooshay Khan, Julian Ostaku, Ebru Aras, Urartu Ozgur Safak Seker, Khan, Anooshay, Ostaku, Julian, Aras, Ebru, and Safak Seker, Urartu Ozgur
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Engineered phage and bacteria ,SARS-CoV-2 ,Biomedical Engineering ,COVID-19 ,Therapeutics ,General Medicine ,Bacterial Physiological Phenomena ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Communicable Disease Control ,Infectious diseases ,Humans ,Bacteriophages ,Synthetic Biology ,Precision Medicine ,Diagnostics ,Pandemics ,Synthetic biology - Abstract
Over the past decades, there have been numerous outbreaks, including parasitic, fungal, bacterial, and viral infections, worldwide. The rate at which infectious diseases are emerging is disproportionate to the rate of development for new strategies that could combat them. Therefore, there is an increasing demand to develop novel, specific, sensitive, and effective methods for infectious disease diagnosis and treatment. Designed synthetic systems and devices are becoming powerful tools to treat human diseases. The advancement in synthetic biology offers efficient, accurate, and cost-effective platforms for detecting and preventing infectious diseases. Herein we focus on the latest state of living theranostics and its implications.
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- 2022
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22. Neutralizing antibody response and associated factors in Coronavirus-19 disease (COVID-19) up to one month
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Aliye Bastug, Hurrem Bodur, Urartu Ozgur Safak Seker, Nazlican Filazi, Omer Aydos, Ebru Sahin Kehribar, Ali Reza Hanifehnezhad, Sumeyye Kazancioglu, Recep Erdem Ahan, Volkan Aslan, Banu Cakir, Ahmet Sertcelik, Aykut Ozkul, Seker, Urartu Ozgur Safak, Kehribar, Ebru Sahin, Ahan, Recep Erdem, and Aslan, Volkan
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Humoral immunity ,IgM and IgG ,Antibody response ,Biochemistry (medical) ,Clinical Biochemistry ,COVID-19 ,Neutralizing antibodies ,Molecular Biology ,Biochemistry - Abstract
Background There is a knowledge gap about the characteristics of neutralizing antibody (NAb) response in patients who recovered COVID-19. In this study, it is aimed to elucidate the factors affecting the presence and titers of antibodies up to 30-days after onset. Material and methods A total of 129 laboratory-confirmed COVID-19 patients were enrolled. Clinical data were obtained retrospectively. SARS-CoV-2 specific NAb, IgM, and IgG antibody responses were analyzed. Results SARS-CoV-2 specific NAb, IgM and IgG, were detected at the time of hospital discharge in 60.5%, 30.2%, and 51.9% of the patients, respectively. The median time for obtaining serum samples for antibody tests after symptoms’ onset was 11 days. The median titer of neutralizing antibody (SN50) was significantly higher in severe patients (25 vs. 7.5, p=0.009). Of the 23 severe patients, 52.2% (n=12) had higher NAb titers (i.e., SN50≥1:25) when compared to that in non-severe patients (OR=2.89; 95%CI=1.15–7.28, p=0.021), yet, the potential effect of follow-up time on NAb status and titers could not be ruled out. Conclusions The presence of antibody response is not the only determinative factor for recovery. The presence and higher titers of NAb were detected more in severe patients than their non-severe counterparts. Survival analysis suggested that this difference could at least be partially explained by the length of follow-up through antibody testing (at discharge) after symptoms’ onset.
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- 2022
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23. Determination of erythrocyte Glutathione S-Transferase activity in individuals with gastric and colon cancer
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GÖKCE Kemal, DAG Seker, and ÖZPINAR Hülya
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General Medicine ,Colon cancer ,Gastric cancer ,Glutathione S-Transferase ,Biomarker - Abstract
Glutathione-S-Transferase (GST) in human cells has great importance in the detoxification mechanism of carcinogenic chemicals. Therefore, (GST) may be a useful tumor marker. This study examines whether GST activity in Gastric cancer (GC) and Colon Cancer (CC) is a helpful marker in diagnosing and monitoring the disease course. GST activity was investigated in patients with CC and GC and healthy individuals. Erythrocyte isolation was performed in 3 ml blood samples from volunteers aged 18-75 years. Hemoglobin amounts were determined from the standard graph drawn by monitoring the conversion of methemoglobin to cyanmethemoglobin in the presence of cyanide at 540 nm. Glutathione S-transferase activity was determined by measuring the amount of enzyme that catalyzes 1 µmol of S-(2,4-dinitrophenyl) glutathione formed per minute using 1-Chloro-2,4-Dinitrobenzene. The mean values of GST activities of patients with CC and GC, respectively; (1.28 ± 0.23 U/gHb; 1.20 ± 0.30 U/gHb), were significantly higher when compared to the mean values of healthy individuals with GST activity (0.59 ± 0.13 U/gHb) (p < 0.05). The GST activity of patients with colon cancer, measured as (1.56 ± 0.13 U/gHb) after chemotherapy, was significantly higher than before (1.09 ± 0.12 U/gHb) (p < 0.05). GST activity measured as (1.53± 0.24 U/gHb) after chemotherapy in gastric cancer patients was significantly higher when compared to the value measured before chemotherapy (0.97± 0.12 U/gHb) (p < 0.05). Our results show that the change in GST activity in CC and GC can be used as a biomarker to monitor the disease course and response to chemotherapy.
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- 2022
- Full Text
- View/download PDF
24. Fluoroscopy-free RIRS on the second session after ureteral stent placement
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Muammer Bozkurt and Kamil Gokhan Seker
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General Medicine - Abstract
Aim: Fluoroscopy is used in some stages of the conventional Retrograde Intrarenal Surgery (RIRS) procedure and is beneficial. On the other hand, radiation exposure is its most obvious disadvantage. As a subgroup, we aimed to show that fluoroscopy-free technique is safe and effective in patients who underwent RIRS after passive dilatation. Materials and methods: Between October 2018 and April 2020, 54 cases of second session RIRS of renal stones performed by a single surgeon were retrospectively evaluated. Patients’ demographic characteristics (age, gender), stone features (laterality, size, number, volume, and location), mean operative time, and, perioperative and postoperative complications, as well as the stone-free rate (SFR), were all retrospectively evaluated. The results were classified as stone free, clinical insignificant residual fragments (CIRF), and presence of residual stones. Complications were graded using the Clavien–Dindo classification system. We used a modified surgical technique. Results: All of complications were minor. There were no major complications (Clavien grade III–IV). The stone-free rate was 70.3% (38/54) on the first day after surgery and 83.3% (45/54) 1 month afterward, respectively. If we accept the absence of residual stone as success, we can say that it is about 91% successful in the first month. Conclusion: This technique has a high stone-free success rate and a low complication rate without the use of radiation. For surgeons experienced in endourology, we can say that the fluoroscopy-free technique is safe and effective in secondary-session RIRS cases which passive dilatation was performed by inserting a ureteral catheter before.
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- 2022
- Full Text
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25. Changing Bacterial Etiology and Antimicrobial Resistance Profiles as Prognostic Determinants of Diabetic Foot Infections: A Ten-Year Retrospective Cohort Study
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Serkan, Surme, Nese, Saltoglu, Ahmet Furkan, Kurt, Ridvan, Karaali, Ilker Inanc, Balkan, Semih, Baghaki, Bilge, Caglar, Meryem, Ozdemir, Aslı, Vatan, Eylem, Togluk-Yigitoglu, Beyhan, Budak, Berk, Arapi, Ali, Seker, Gunay, Can, Mustafa Sait, Gonen, and Oguz, Cetinkale
- Subjects
Acinetobacter baumannii ,Microbiology (medical) ,Bacteria ,Microbial Sensitivity Tests ,Prognosis ,Diabetic Foot ,Anti-Bacterial Agents ,Cohort Studies ,Infectious Diseases ,Carbapenems ,Drug Resistance, Multiple, Bacterial ,Reinfection ,Drug Resistance, Bacterial ,Pseudomonas aeruginosa ,Diabetes Mellitus ,Humans ,Surgery ,Retrospective Studies - Published
- 2022
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26. Characterization of laser-welded structures in glass using acoustic microscopy
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N. Seker, E. Benz, S. Schuhmacher, S. Ruck, M.-J. Kleefoot, H. Riegel, T. Djuric-Rissner, P. Hoffrogge, and P. Czurratis
- Subjects
Mechanics of Materials ,Metals and Alloys ,Condensed Matter Physics ,Electronic, Optical and Magnetic Materials - Abstract
Glass substrates are playing an increasingly important role in the production of microchips. This paper will demonstrate the potential of scanning acoustic microscopy (SAM) used for the characterization of laser-welded structures in thin glass slides. Structures within the volume of a glass sample can be imaged quickly and with high accuracy using this method. In particular, it should be noted that not only the depth information, but also the height profile of the structures can be obtained from ultrasonic cross-sectional images. Measurements only take a few minutes. While certain structures can be visualized in 3D using ultrasonic Time-of-Flight (ToF) measurements, current research is focusing on the 3D representation of more general structures based on the Synthetic Aperture Focusing Technique (SAFT).
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- 2022
- Full Text
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27. Performance analysis of modulation techniques in 5G communication system
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Muhammet Tahir Guneser, Ahmed Salahaldeenali Sahab, and Cihat Seker
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Computer Networks and Communications ,Electrical and Electronic Engineering - Published
- 2022
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28. Impact of serum sodium levels on Helicobacter pylori infection
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Muhammed Aydin, Tolga Yilmaz, Emrah Ozzengin, Ahmet Cumhur Dulger, Mustafa Yakarisik, Hasan Mucahit Ozbas, Demet Seker, Yaren Dirik, and Iskender Aksoy
- Abstract
Objective: Excessive salt consumption could play a role for developing gastric cancer as well as Helicobacter pylori (HP) infection. However, there is no report about the connection between serum sodium levels and HP infection. This study aimed to investigate the relationship between serum sodium disorders and HP infection. Material and Methods: In this single-center, retrospective, descriptive study, we evaluated the presence of HP infection by enzyme-linked immunosorbent assay (ELISA) among patient with serum sodium disturbances. Patients were divided into two groups as to their serum sodium levels (hypernatremia: Sodium level above 145 mmol/l, and hyponatremia: Sodium level below 135 mmol/l). Results: In total, 54 patients, half of them were hypernatremic (27), included in the study. At total, 15 (55.6%) patients tested positive for HP immunoglobulin G (Ig G) by ELISA method in hyponatremic patients, 17 (63%) patients tested positive for HP Ig G in hypernatremic patients. There was no difference between groups in terms of HP Ig G seropositivity (p=0.58). Other hand, 9 (33%) patients tested positive for HP Ig A among hyponatremic patients, 19 (70%) patients tested positive for HP Ig A in hypernatremic patients (p=0.029). Conclusion: According to our results, Hypernatremic patients have high risk for HP infection. Other hand, the presence of HP infection could be a driven-factor in the development of hypernatremia among elderly patients. Larger-scale studies are needed to reveal the relationship between hypernatremia and gastroenteritis.
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- 2022
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29. Prevalence of mecA and pvl genes in coagulase negative staphylococci isolated from bovine mastitis in smallholder dairy farms in Turkey
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Esra Seker, Erhan Ozenc, Oguz Kagan Turedi, and Muesser Yilmaz
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Animal Science and Zoology ,Bioengineering ,Biotechnology - Published
- 2022
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30. Performance evaluation of shallow and deep CNN architectures on building segmentation from high-resolution images
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Batuhan Sariturk, Dursun Zafer Seker, Ozan Ozturk, and Bulent Bayram
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General Earth and Planetary Sciences - Published
- 2022
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31. Automated LVO detection and collateral scoring on CTA using a 3D self-configuring object detection network: a multi-center study
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Omer Bagcilar, Deniz Alis, Ceren Alis, Mustafa Ege Seker, Mert Yergin, Ahmet Ustundag, Emil Hikmet, Alperen Tezcan, Gokhan Polat, Ahmet Tugrul Akkus, Fatih Alper, Murat Velioglu, Omer Yildiz, Hakan Hatem Selcuk, Ilkay Oksuz, Osman Kizilkilic, and Ercan Karaarslan
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Multidisciplinary - Abstract
The use of deep learning (DL) techniques for automated diagnosis of large vessel occlusion (LVO) and collateral scoring on computed tomography angiography (CTA) is gaining attention. In this study, a state-of-the-art self-configuring object detection network called nnDetection was used to detect LVO and assess collateralization on CTA scans using a multi-task 3D object detection approach. The model was trained on single-phase CTA scans of 2425 patients at five centers, and its performance was evaluated on an external test set of 345 patients from another center. Ground-truth labels for the presence of LVO and collateral scores were provided by three radiologists. The nnDetection model achieved a diagnostic accuracy of 98.26% (95% CI 96.25–99.36%) in identifying LVO, correctly classifying 339 out of 345 CTA scans in the external test set. The DL-based collateral scores had a kappa of 0.80, indicating good agreement with the consensus of the radiologists. These results demonstrate that the self-configuring 3D nnDetection model can accurately detect LVO on single-phase CTA scans and provide semi-quantitative collateral scores, offering a comprehensive approach for automated stroke diagnostics in patients with LVO.
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- 2023
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32. Match the Metatarsal Heads: A Case of All-Metatarsal Fractures After a Motorcycle Accident
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Nuri Ayoglu, Muhammed Yusuf Afacan, Mahmut Kursat Ozsahin, and Ali Seker
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General Engineering - Published
- 2023
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33. Review of: 'Online learning during the COVID-19 pandemic, lessons learned and what’s next?'
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Meral Seker
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- 2023
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34. Brief Review of Biological Effects of Electromagnetic Pollution(RF and 5G Waves) on Humans, Animals, and Vegetation
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Ozlem SIMSEK and S. Selim SEKER
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General Medicine - Abstract
All devices using electrical energy emit electromagnetic fields and radiation as a side effect while performing their normal functions. This causes thermal and non-thermal harmful effects on humans, plants, animals, and devices. The effect on humans is not much different from the effects on plants or animals since they are dielectric material and 70-80% of them all consist of water. Other than that, some damages such as cancer appear after 20-30 years medically. Health studies conducted on animals reveal that radiofrequency (RF) waves, as well as the millimeter waves used in the 5G system cause changes in the body, manifested in structural alteration, disturbance in various functions of the organism, including the nervous, cardiovascular, immune, blood and other systems. While microwaves used in 4G cause thermal effects, millimetric waves used in 5G cause non-thermal effects only due to low wave penetration. Based on evidence obtained from various studies carried out by the USA National Toxicology Program, the Italian Ramazzini study, and the EU Reflex study, a growing number of scientists say that electromagnetic (EM) waves are “human carcinogens”. As is known that all processes in the human body involve electromagnetic waves. Brain activity, heartbeat, cell division, and neuronal communication always use electrical energy. The activities of hormones and enzymes are regulated electrically. Millimeter waveused in the 5G system have a weak penetrating ability and are easily absorbed by humans, animals, and trees. Therefore, 5G base stations need to be installed approximately every 10 meters. This will result in millions of new base stations in addition to the present ones and increase electromagnetic pollution and health risks by leased by a factor of 100. This study will discuss the biological effects of EM Pollution on humans, animals, and vegetation.
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- 2023
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- View/download PDF
35. Intracranial Cancer Detection by Mobile Phone Electromagnetic Radiation
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S. Selim SEKER and Niyazi K. ULUAYDIN
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General Medicine - Abstract
Cancer is the topping cause of death only after ischemic heart disease in the world. Among cancers, brain tumors are generally one of the hardest to heal. And among the brain tumors, glioblastoma multiforme, which is a very aggressive intracranial cancer, has one of the highest mortality rates. These cancers are rather difficult to diagnose with the lack of manual diagnosis and very aggressive in their progression the disease, thus a later-stage diagnosis would not be much of a benefit. Therefore, medical doctors require advanced medical imaging techniques such as computed tomography and magnetic resonance imaging for intracranial tumors. The Covid-19 pandemic has caused a global lockdown and has put an enormous load on the medical system. Any similar pandemic would almost paralyze the medical system. In this study, the authors investigate the possibility of an early-stage detection of glioblastoma multiforme by use of mobile phone electromagnetic radiation. Since cancer tissue contains more blood vessels because of its intrinsic energy needs, external electromagnetic radiation would affect the cancer tissue faster than the normal tissue. The authors build the model by introducing a hypothetical ellipsoid cancer tissue into the IEEE phantom head SAR model. By applying two different levels of external electromagnetic exposure, the simulations seek to find a discriminatory temperature change, which can be detected externally.
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- 2023
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36. Cultured Vagal Afferent Neurons as Sensors for Intestinal Effector Molecules
- Author
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Girardi, Gregory, Zumpano, Danielle, Goshi, Noah, Raybould, Helen, and Seker, Erkin
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Central Nervous System ,Neurons ,gut-brain axis ,1.1 Normal biological development and functioning ,Neurosciences ,microbiome ,Vagus Nerve ,Afferent ,electrophysiology ,Analytical Chemistry ,primary vagal afferent neuron culture ,Underpinning research ,Neurological ,Biochemistry and Cell Biology ,Cholecystokinin ,gut–brain axis ,Digestive Diseases - Abstract
The gut-brain axis embodies the bi-directional communication between the gastrointestinal tract and the central nervous system (CNS), where vagal afferent neurons (VANs) serve as sensors for a variety of gut-derived signals. The gut is colonized by a large and diverse population of microorganisms that communicate via small (effector) molecules, which also act on the VAN terminals situated in the gut viscera and consequently influence many CNS processes. However, the convoluted in vivo environment makes it difficult to study the causative impact of the effector molecules on VAN activation or desensitization. Here, we report on a VAN culture and its proof-of-principle demonstration as a cell-based sensor to monitor the influence of gastrointestinal effector molecules on neuronal behavior. We initially compared the effect of surface coatings (poly-L-lysine vs. Matrigel) and culture media composition (serum vs. growth factor supplement) on neurite growth as a surrogate of VAN regeneration following tissue harvesting, where the Matrigel coating, but not the media composition, played a significant role in the increased neurite growth. We then used both live-cell calcium imaging and extracellular electrophysiological recordings to show that the VANs responded to classical effector molecules of endogenous and exogenous origin (cholecystokinin serotonin and capsaicin) in a complex fashion. We expect this study to enable platforms for screening various effector molecules and their influence on VAN activity, assessed by their information-rich electrophysiological fingerprints.
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- 2023
37. Coping with Administrative Workload: a Pilot Study in the Usefulness of a Workshop for Psychiatric Trainees
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Peter Deschamps, Asilay Seker, Marieke van der Schaaf, and Marie-Aude Piot
- Subjects
Psychiatry and Mental health ,General Medicine ,Education - Abstract
Objective Administrative workload may have detrimental effects on medical postgraduate trainee satisfaction, capacity, and quality of care. Best-practice guidelines to help trainees cope have yet to be developed. This study explores perceptions of factors that influence the experience or amount of administrative workload at the personal and workplace level and evaluates the usefulness of a workshop on coping with this workload. Methods A workshop was developed based on the Job Demands-Resources model, including a survey on perceptions of administrative workload; presentation on coping at personal (e.g., time management) and workplace (e.g., dealing with institutional rules) levels; personal plan of change during a group discussion; and reflective questionnaire after the session and again after 2 months. Perceptions of psychiatry trainee participants (N = 48) were collected. Results Trainees estimated they spent half their time on administration (average 50%, SD = 15%). They wanted to spend less time (average 23%, SD = 11%) on most administrative duties, except for health record keeping. Personal factors that trainees experienced as helpful to cope included time management and analytical skills. Perfectionism was perceived as impeding. Supportive job factors included helpful supervisors, competent administrative staff, trust in a team, allocated timeslots, and information technology support. High workload and cumbersome procedures were mentioned as impeding. On average, trainees rated the workshop quality and the likelihood of bringing change to their practice with a 7 out of 10. Conclusion Psychiatry trainees’ participation in a workshop on coping with administrative load during their training may be a worthwhile investment in the long term.
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- 2023
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- View/download PDF
38. Highly Potent Peptide Therapeutics To Prevent Protein Aggregation In Huntington’s Disease
- Author
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Anooshay Khan, Esra Yuca, Cemile Elif Özçelik, Ozge Begli, Oguzhan Oguz, Serkan Kasırga, and Urartu Ozgur Safak Seker
- Abstract
Huntington’s disease (HD) is a progressive, autosomal dominant neurodegenerative disorder resulting from a significant amplification of CAG repeats in exon 1 of the Huntingtin (Htt) gene. More than 36 CAG repeats result in the formation of mutant Htt (mHtt) protein. These amino-terminal mHtt fragments lead to the formation of misfolded proteins, which then form aggregates in relevant brain regions. Available treatments concentrate primarily on alleviating the disease’s symptoms. Therefore, therapies that can delay the progression of the disease are imperative to halt the course of the disease. Peptide-based drug therapies provide such a platform. Inhibitory peptides were screened against monomeric units of both wild type (Htt(Q25)) and mHtt fragments, including Htt(Q46)and Htt(Q103). It was accomplished by utilizing several display technologies. This study focuses on the in-vitro characterization of the screened peptides. Fibril kinetics was studied in real-time utilizing the Thioflavin T (ThT) assay. The impact of specific peptides on fibril formation was examined by observing the change in fluorescence signal. Atomic force microscopy was also used to study the influence of peptides on fibril formation. Three of the six chosen peptides (HHGANSLSLVSQD, HGLHSMHNKLTR, and WMFPSLKLLDYH) effectively inhibited aggregation. These experiments demonstrate that the chosen peptides suppress the formation of fibrils in mHtt proteins and can provide a therapeutic lead for further optimization and development.
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- 2023
- Full Text
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39. A Bacterial Living Therapeutics with Engineered Protein Secretion Circuits To Eliminate Breast Cancer Cells
- Author
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Gozeel Binte Shahid, Recep Erdem Ahan, Julian Ostaku, and Urartu Ozgur Safak Seker
- Abstract
Cancer therapy can be limited by potential side effects, and bacteria-based living cancer therapeutics have gained scientific interest in recent years. However, the full potential of bacteria as therapeutics has yet to be explored due to engineering challenges. n this study, we present a bacterial device designed to specifically target and eliminate breast cancer cells. We have engineeredEscherichia coli(E. coli) to secrete a Shiga toxin, HlyE, which is a pore-forming protein that binds to HER2 receptors on breast cancer cells. This binding is facilitated by a nanobody expressed on the bacteria’s surface via the Ag43 autotransporter protein system. Our findings demonstrate that the nanobody efficiently binds to HER2+ cells in vitro, and we have utilized the YebF secretion system to secrete HlyE and kill the target cancer cells. Overall, our results highlight the potential of our engineered bacteria as an innovative strategy for breast cancer treatment.
- Published
- 2023
- Full Text
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40. Pulmonary Hypertension Classification using Artificial Intelligence and Chest X-Ray:ATA AI STUDY-1
- Author
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Tarık Kıvrak, Burcu Yagmur, Hilal Erken, Derya Kocakaya, Turker Tuncer, Şengül Doğan, Orhan Yaman, Umit Yasar Sinan, Sena Sert Sekerci, Cagri Yayla, Ufuk Iyigun, Mehmet Kis, Ozkan Karaca, Emrah Yesil, Elif Ilkay Yuce Ersoy, Bahar Tekin Tak, Ahmet Oz, Mehmet Kaplan, Zeynep Ulutas, Gamze Yeter Aslan, Nihan Kahya Eren, Fatma Nihan Turhan Caglar, Hatice Solmaz, Ozge Ozden, Hakan Gunes, Umut Kocabas, Mustafa Yenercag, Omer Isık, Cem Yesilkaya, Ali Nail Kaya, Sefa Erdi Omur, Anil Sahin, Erdal In, Nurcan Kırıcı Berber, Cigdem Ileri Dogan, Fatih Poyraz, Emin Erdem Kaya, Ayca Gumusdag, Omer Kumet, Hakki Kaya, Remzi Sarikaya, Seda Turkan Tan, Hidayet Ozan Arabaci, Rengin Cetin Guvenc, Mehtap Yeni, Burcak Kılıckıran Avci, Dilek Cicek Yilmaz, Ahmet Celik, Berkay Ekici, Aycan Fahri Erkan, Veysel Ozgur Baris, Taner Seker, Ferit Böyük, Mehmet Mustafa Can, Hasan Gungor, Hakki Simsek, Bedrettin Yildizeli, Mehmet Ali Kobat, Mehmet Akbulut, Mehdi Zoghi, and Omer Kozan
- Abstract
An accurate diagnosis of pulmonary hypertension (PH) is crucial to ensure that patients receive timely treatment. One of the used imaging models to detect pulmonary hypertension is the X-ray. Therefore, a new automated PH-type classification model has been presented to depict the separation ability of deep learning for PH types. We retrospectively enrolled 6642 images of patients with PH and the control group. A new X-ray image dataset was collected from a multicentre in this work. A transfer learning-based image classification model has been presented in classifying PH types. Our proposed model was applied to the collected dataset, and this dataset contains six categories (five PH and a non-PH). The presented deep feature engineering (computer vision) model attained 86.14% accuracy on this dataset. According to the extracted ROC curve, the average area under the curve rate has been calculated at 0.945. Therefore, we believe that our proposed model can easily separate PH and non-PH X-ray images.
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- 2023
- Full Text
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41. Supplementary Data from Transcriptional Reprogramming Differentiates Active from Inactive ESR1 Fusions in Endocrine Therapy-Refractory Metastatic Breast Cancer
- Author
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Matthew J. Ellis, Charles E. Foulds, Dan R. Robinson, Adrian V. Lee, Shunqiang Li, Alana L. Welm, Michael T. Lewis, Nicholas Mitsiades, Lacey E. Dobrolecki, Harshavardhan Doddapaneni, Viktoriya Korchina, Jianhong Hu, Saif Rehman, Airi Han, Diana Fandino, Sinem Seker, Purba Singh, Beom-Jun Kim, Jonathan T. Lei, Meenakshi Anurag, and Xuxu Gou
- Abstract
It includes Supplementary Methods, Supplementary Figures, Supplementary Tables, and Supplementary References
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- 2023
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42. Data from Transcriptional Reprogramming Differentiates Active from Inactive ESR1 Fusions in Endocrine Therapy-Refractory Metastatic Breast Cancer
- Author
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Matthew J. Ellis, Charles E. Foulds, Dan R. Robinson, Adrian V. Lee, Shunqiang Li, Alana L. Welm, Michael T. Lewis, Nicholas Mitsiades, Lacey E. Dobrolecki, Harshavardhan Doddapaneni, Viktoriya Korchina, Jianhong Hu, Saif Rehman, Airi Han, Diana Fandino, Sinem Seker, Purba Singh, Beom-Jun Kim, Jonathan T. Lei, Meenakshi Anurag, and Xuxu Gou
- Abstract
Genomic analysis has recently identified multiple ESR1 gene translocations in estrogen receptor alpha–positive (ERα+) metastatic breast cancer (MBC) that encode chimeric proteins whereby the ESR1 ligand binding domain (LBD) is replaced by C-terminal sequences from many different gene partners. Here we functionally screened 15 ESR1 fusions and identified 10 that promoted estradiol-independent cell growth, motility, invasion, epithelial-to-mesenchymal transition, and resistance to fulvestrant. RNA sequencing identified a gene expression pattern specific to functionally active ESR1 gene fusions that was subsequently reduced to a diagnostic 24-gene signature. This signature was further examined in 20 ERα+ patient-derived xenografts and in 55 ERα+ MBC samples. The 24-gene signature successfully identified cases harboring ESR1 gene fusions and also accurately diagnosed the presence of activating ESR1 LBD point mutations. Therefore, the 24-gene signature represents an efficient approach to screening samples for the presence of diverse somatic ESR1 mutations and translocations that drive endocrine treatment failure in MBC.Significance:This study identifies a gene signature diagnostic for functional ESR1 fusions that drive poor outcome in advanced breast cancer, which could also help guide precision medicine approaches in patients harboring ESR1 mutations.
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- 2023
- Full Text
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43. Supplementary Tables from A Highly Potent TACC3 Inhibitor as a Novel Anticancer Drug Candidate
- Author
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Ozgur Sahin, Erden Banoglu, Burcu Caliskan, Aytekin Akyol, Aynur Isik, Urartu O.S. Seker, Elif Duman, Ozge Saatci, Deniz Lengerli, and Ozge Akbulut
- Abstract
Antibody list and primer sequences
- Published
- 2023
- Full Text
- View/download PDF
44. Data from A Highly Potent TACC3 Inhibitor as a Novel Anticancer Drug Candidate
- Author
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Ozgur Sahin, Erden Banoglu, Burcu Caliskan, Aytekin Akyol, Aynur Isik, Urartu O.S. Seker, Elif Duman, Ozge Saatci, Deniz Lengerli, and Ozge Akbulut
- Abstract
TACC3, a transforming acidic coiled-coil (TACC) family member, is frequently upregulated in a broad spectrum of cancers, including breast cancer. It plays critical roles in protecting microtubule stability and centrosome integrity that is often dysregulated in cancers; therefore, making TACC3 a highly attractive therapeutic target. Here, we identified a new TACC3-targeting chemotype, BO-264, through the screening of in-house compound collection. Direct interaction between BO-264 and TACC3 was validated by using several biochemical methods, including drug affinity responsive target stability, cellular thermal shift assay, and isothermal titration calorimetry. BO-264 demonstrated superior antiproliferative activity to the two currently reported TACC3 inhibitors, especially in aggressive breast cancer subtypes, basal and HER2+, via spindle assembly checkpoint–dependent mitotic arrest, DNA damage, and apoptosis, while the cytotoxicity against normal breast cells was negligible. Furthermore, BO-264 significantly decreased centrosomal TACC3 during both mitosis and interphase. BO-264 displayed potent antiproliferative activity (∼90% have less than 1 μmol/L GI50 value) in the NCI-60 cell line panel compromising of nine different cancer types. Noteworthy, BO-264 significantly inhibited the growth of cells harboring FGFR3–TACC3 fusion, an oncogenic driver in diverse malignancies. Importantly, its oral administration significantly impaired tumor growth in immunocompromised and immunocompetent breast and colon cancer mouse models, and increased survival without any major toxicity. Finally, TACC3 expression has been identified as strong independent prognostic factor in breast cancer and strongly prognostic in several different cancers. Overall, we identified a novel and highly potent TACC3 inhibitor as a novel potential anticancer agent, inducing spindle abnormalities and mitotic cell death.
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- 2023
- Full Text
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45. Der Solinger Brandanschlag Multiperspektivischer Rückblick, offene Fragen und Folgen bis in die Gegenwart
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Birgül Demirtas, Adelheid Schmitz, Çagri Kahveci, and Derya Gür-Seker
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- 2023
- Full Text
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46. Figure S2 from A Highly Potent TACC3 Inhibitor as a Novel Anticancer Drug Candidate
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Ozgur Sahin, Erden Banoglu, Burcu Caliskan, Aytekin Akyol, Aynur Isik, Urartu O.S. Seker, Elif Duman, Ozge Saatci, Deniz Lengerli, and Ozge Akbulut
- Abstract
TACC3 is an independent prognostic factor for breast cancer.
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- 2023
- Full Text
- View/download PDF
47. Autor*innenverzeichnis
- Author
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Birgül Demirtas, Adelheid Schmitz, Derya Gür-Seker, and Çagri Kahveci
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- 2023
- Full Text
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48. Inhalt
- Author
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Birgül Demirtas, Adelheid Schmitz, Derya Gür-Seker, and Çagri Kahveci
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- 2023
- Full Text
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49. Frontmatter
- Author
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Birgül Demirtas, Adelheid Schmitz, Derya Gür-Seker, and Çagri Kahveci
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- 2023
- Full Text
- View/download PDF
50. Figure S6 from A Highly Potent TACC3 Inhibitor as a Novel Anticancer Drug Candidate
- Author
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Ozgur Sahin, Erden Banoglu, Burcu Caliskan, Aytekin Akyol, Aynur Isik, Urartu O.S. Seker, Elif Duman, Ozge Saatci, Deniz Lengerli, and Ozge Akbulut
- Abstract
BO-264 impairs tumor growth better than SPL-B does at the same dose.
- Published
- 2023
- Full Text
- View/download PDF
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