PubMed İndeksli Yayınlar Koleksiyonu

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Citation - WoS: 2
Citation - Scopus: 3
3d-Printed Actuator-Based Beam-Steering Approach for Improved Physical Layer Security in Visible Light Communication
(Optica Publishing Group, 2022) Erdem, Mehmet Can; Gurcuoglu, Oguz; Panayırcı, Erdal; Kurt, Gunes Karabulut; Ferhanoglu, Onur
In this study, we present the design, manufacture, and implementation of a 3D-printed lens scanner-based beam steering for use in visible light communication (VLC) applications. The 5 cm x 5 cm scanner is designed for low-cost 3D printing with fused deposition modeling using polylactic acid. Scanning is facilitated through electromagnetic actuation of the lens frame, carrying a conventional 25 mm lens, from two nearly orthogonal directions. The serpentine spring that connects the lens frame to the external frame is tailored to offer similar spring constants in the directions of actuation and has minimal (<1.5 mm) sag due to the mass of the lens. The manufactured actuator was integrated on a miniaturized VLC test bed (70 cm x 40 cm x 40 cm). Using the test bed, we characterized the applied voltage versus beam displacement behavior of the actuator in the lateral plane and demonstrated beam steering on amoving target with face-recognition feedback. The proposed scheme was targeted to offer an improved security measure in VLC through tracking the legitimate receiver (i.e., via face recognition) and uses the feedback to steer the focused light onto the targeted device. The joint use of focusing and steering features allows for the legitimate receiver to roam within the room while enjoying the improved secrecy due to the focused light. We calculate the secrecy capacity for the demonstrated approach, which compares favorably with a number of jamming, spatial modulation, and beam-forming counterparts. The presented actuator can be used with larger room dimensions, yet upscaling to larger illumination units will require the use of a lens having smaller focus to address a larger total steering angle. (C) 2022 Optica Publishing Group
Antibiyotikli kemik çimentosunun 0 ve 15. günlerde mekanik dayanımı: Surgical Simplex P kemik çimentosu ve teikoplanin ile biyomekanik çalışma
(Türk Ortopedi ve Travmatoloji Derneği, 2002) Göğüş, Abdullah; Akman, Şenol; Göksan, Bora S.; Bozdağ, Ergün
Amaç: Mekanik dayanım açısından 40 gr belirli bir kemik çimentosuna katılabilecek belirli bir antibiyotiğin maksimum dozu "0. gün" ve antibiyotik salınımı sonrası "15. gün" için araştırıldı. Çalışma planı: 40 g Surgical Simplex P kemik çimentosuna 0, 400, 800,1200,1600, 2000, 3200 ve 4000 mg teikoplanin katılarak sekiz deney grubu oluşturuldu. Kompresyon ve dört nokta eğme mekanik dayanım testleri için üçüncü kuşak sement hazırlama ve uygulama koşullarında örnekler elde edildi. Her bir konsantrasyon için "0. gün" ve "15. gün" için 10'ar örnek oluşturuldu. Örneklerin mekanik dayanım testleri ASTM ve ISO standartlarına göre "0. gün" ve 37∘ C su banyosunda antibiyotik salınımı sonrası "15. gün"de yapıldı. Değişik antibiyotik konsantrasyonları 0 mg kontrol grubu ile, ayrıca aynı antibiyotik konsantrasyonlarının 0. gün ve 15. gün mekanik test sonuçları karşılaştırıldı. Sonuçlar: Kompresyon testlerinde "0. gün" grubu içinde anlamlı farklılık bulunmadı; "15. gün" grubunda ise 800 mg'den itibaren anlamlı dayanım azalması saptandı. Her iki grupta tüm konsantrasyonlarda elde edilen mekanik dayanım değerleri ASTM alt limiti olan 70 MPa'nın üzerindeydi. Dört nokta eğme testinde "0. gün" grubunda 1200 mg'den itibaren, "15. gün" grubunda ise 400 mg'den itibaren anlamlı dayanım azalması saptandı. "15. gün" grubundan 4000 mg ISO'nun alt limiti olan 50 MPa'nın altında kalırken, 3200 ve 2000 mg gruplarında 50 MPa'ya çok yakın sonuçlar elde edildi. Çıkarımlar: Deney sonuçları, üçüncü kuşak çimento hazırlama ve uygulama koşullarında, 40 gr Surgical Simplex P kemik çimentosuna güvenle katılabilecek en yüksek teikoplanin dozunun 1600 mg olduğunu gösterdi.
Citation - WoS: 8
Citation - Scopus: 9
Apolipoprotein B Gene Variants Are Involved in the Determination of Blood Glucose and Lipid Levels in Patients With Non-Insulin Dependent Diabetes Mellitus
(Wiley, 2006) Duman, Belgin Süsleyici; Öztürk, Melek; Yilmazer, Selma; Çağatay, Penbe; Hatemi, Hüsrev
We have examined the frequency of the EcoRI XbaI and MspI RFLPs of the apolipoprotein B (apo 13) gene in I 10 type 2 diabetic patients and 9 1 healthy control subjects in order to ascertain whether variation in this gene may influence the development of non-insulin dependent diabetes mellitus (type 2 diabetes). Serum lipids including total-cholesterol (T-Chol) triacylglycerol (TAG) apolipoprotein E (apo E) apolipoprotein Al (apo Al) apolipoprotein B and lipoprotein (a) (Lp(a)) were analysed. Genomic DNA was extracted and the apo B polymorphic regions amplified by the polymerase chain reaction. Regions carrying EcoRI XbaI and MspI restriction sites present in the apo B gene were amplified and digested separately by the respective enzymes. No significant difference for genotypic frequencies was observed for the EcoRI XbaI and MspI restriction sites in type 2 diabetic patients as compared to controls. Type 2 diabetic patients and controls with EcoRI +/+ and XbaI +/+ genotypes had higher apo E levels. The MspI +/+ genotype is more frequent in the patient and control groups With elevated T-Chol. Furthermore the EcoRI -/- XbaI -/- and MspI +/+ genotypes were found to be significantly more frequent in type 2 diabetic patients with higher blood glucose levels. This study identifies the apo B gene polymorphisms in modulating plasma lipid/lipoprotein and glucose levels in patients with type 2 diabetes. Copyright 0 2005 John Wiley & Sons Ltd.
Citation - WoS: 1
The association of HLA-DRB1 alleles and MBL2 gene variant in pediatric acute lymphoblastic leukemia patients
(Elsevier, 2024) Oguz, Rustu; Ciftci, Hayriye Senturk; Gokce, Muge; Ogret, Yeliz; Karadeniz, Sedat; Pehlivan, Sacide; Ayd, Filiz
Introduction: Epidemio logic studies on pediatric acute lymphoblastic leukemias (ALL) have been conducted to evaluate the possible risk factors including genetic, infectious and environmental factors with the objective of idenfying the etiology. Mannose-binding lectin 2 (MBL2) plays an important role in first-line immune defense. HLA DRB1 alleles play a role in presentation of peptides to T cells and in activation of the adaptive immune response. Objective: In our study, we aimed to investigate both the MBL2 gene variant and HLA-DRB1 alleles in pediatric ALL patients. Materials: In this study, 86 high-risk ALL patients and 100 controls were included. Polymerase Chain Reaction (PCR)-Restriction Fragment Length Polymorphism (PCR-RFLP) and PCRsequence specific primer (SSP) methods were used for detection of polymorphism of the MBL2 and HLA-DRB1 alleles, respectively. Results: The frequency of the MBL2 AB genotype was lower in female ALL patients, compared to male ALL patients (p = 0.034). An association was found between the MBL2 BB genotype and DRB1*07 and among patients with the MBL2 BB genotype; those who also carried the DRB1*07 and *04 alleles were significantly higher than those without the DRB1*07 and *04 alleles. (p = 0.048, p = 0.022, respectively). Conclusion: This is the first study suggesting that the MBL2 BB genotype in association with the DRB1*07 or co-inheritance of the HLA-DRB1*04 and HLA DRB1*07 may have an impact on the etiopathogenesis of the disease. (c) 2023 Associa & ccedil;& atilde;o Brasileira de Hematologia, Hemoterapia e Terapia Celular. Published by Elsevier Espa & ntilde;a, S.L.U. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Attentional Modulation of Outlier Processing
(Springer, 2025) Gokce, Ahu; Yildirim, Bugay; Boduroglu, Aysecan
Ensemble perception enables the visual system to function effectively when the number of stimuli in the environment exceeds its capacity. Ensemble representations not only help the limited capacity of visual representations, but they also facilitate the detection and representation of items deviating from the group (i.e., the outlier). This study focuses on how attentional mechanisms modulate outlier processing. In three experiments, we presented participants with an ensemble that was formed by circle stimuli in varying sizes, and the outlier item was distinct in terms of its location. We measured outlier localization performance while manipulating attentional orienting via a spatial cueing paradigm. In Experiment 1, a valid, invalid, or neutral cue was presented before or after the display. Facilitation of outlier localization was most pronounced in the valid precue condition. Experiment 2 included a task to actively engage ensemble perception in addition to outlier localization, and cue validity effect was observed as in Experiment 1. Experiment 3A was carried to directly compare the top-down and bottom-up influences on outlier processing by presenting two spatial outliers-one target and another distractor outlier. The target outlier identity was previously determined and was identical across trials. In Experiment 3B, the target was in red, making it salient among the remaining items. In the invalid trials, where the distractor outlier was cued, responses were closer to the distractor item indicating that outlier processing is cue driven. These experiments overall demonstrate that automaticity of outlier processing can be overridden by cue-driven processes.
Citation - WoS: 4
Citation - Scopus: 4
Augmentation Mentoplasty Using a Custom-Design Wire Cage
(Lippincott Williams & Wilkins, 2003) Erol ,O.; Enacar, A.
Mentoplasty is often a complimentary procedure to rhinoplasty. At least 25% of all rhinoplasty patients may need a chin implant to balance facial features better. Augmentation mentoplasty using alloplastic implants such as silicone rubber or other materials provides a simple approach to the treatment of the hypoplastic chin. Although these types of implants are readily available in developed countries there are parts of the world where they are unavailable or quite expensive. The authors have developed a chin implant made of wire that is available throughout the world and is custom designed to the mentum of the patient after a cephalometric evaluation. This technique has been used in 125 patients along with rhinoplasty over the last 20 years at our institution. In an initial series of 8 patients the prosthesis became displaced and was removed in 2 patients. Since then a new radiographic technique has been developed to demonstrate the shape of the mentum before surgery and new bone formation after surgery. By using this special radiographic technique it was possible to detect four types of mentum before surgery and to construct a custom-design wire cage according to this shape. The prosthesis is constructed by an orthodontist according to the cephalometric measurements and shape of the mentum. By using the buccal approach a pocket is prepared subperiosteally and a wire cage is inserted. In the last 20 cases the wire cage was filled with diced cartilage wrapped with Surgicel. The results were esthetically satisfactory in most patients. After the shape of the wire prosthesis was modified to conform to the shape of the underlying bone better no displacement of the prosthesis has been experienced. In 3 patients it was necessary to remove the prosthesis when new tissue formation began to fill the prosthesis. These specimens were examined histologically and the regenerating tissue was found to be connective tissue with a thin layer of bone formation. Most patients could be followed up for only 3 to 12 years. In all patients the results have been consistent and the procedure has been safe.
Better Reflective Functioning in Mothers Linked To Longer Joint Attention With Infants
(Elsevier Ltd, 2026) Koç, N.; Ünlü, H.; Uzundag, B.A.
Joint attention is a foundational precursor to later developmental outcomes such as vocabulary, intelligence, and theory of mind. Previous research has shown that maternal sensitivity, depressive symptoms, and parent-child attachment security are associated with attention-sharing behaviors between mothers and their infants. The present study examined the relationship between mothers’ reflective functioning (the ability to recognize and interpret one’s own and one’s child’s mental states, as well as the behaviors motivated by those mental states) and joint attention. Data were collected from 72 infants aged 10–16 months and their mothers. Results indicated that mothers who reported greater difficulty in understanding and distinguishing between their own and their child's mental states (i.e., higher prementalization) tended to engage in joint attention episodes that were shorter and more frequent, and they were also more likely to terminate these interactions. In contrast, mothers expressing greater interest and curiosity about their infants’ mental states spent longer periods in joint attention, initiated these episodes less often, and were less inclined to terminate them. Additionally, mothers who felt more certain about their infants’ mental states were less likely to end joint attention episodes. After controlling for infant age and socioeconomic status, higher levels of interest and certainty continued to predict lower maternal termination, while prementalization was still linked to a higher number of joint attention episodes. These findings suggest that mothers’ perceptions of their infants’ mental states shape how they engage in shared attention during everyday play interactions. © 2025 Elsevier Inc.
Citation - WoS: 11
Citation - Scopus: 11
Cervical Radiculopathy Caused by Vertebral Artery Loop Formation - Multislice Computed Tomography Angiography Findings
(Lippincott Williams & Wilkins, 2005) Ganiyusufoğlu, A. Kursad; Kantarcı, Mecit; Şırvancı, Mustafa; Sildiroglu, Onur; Alparslan, L.
Vertebral artery tortuosity and loop formation are rare causes of cervical radiculopathy. The criterion standard for the detection of vertebral artery loop formation is digital subtraction angiography. Computed tomography (CT) and magnetic resonance imaging provide good accuracy in the evaluation of vertebral arteries. A case of vertebral artery loop formation is reported. The diagnosis was confirmed by 16-row multisection CT angiography findings of vertebral artery loop formation.
Citation - Scopus: 1
Cervical Spine Injuries in Children
(2004) Hamzaoglu, A.; Mirzanli, C.
Cervical spine injuries in children and adolescents are rare. Common mechanisms include motor vehicle accidents, sports injuries, fall from height, and gunshot injuries. Cervical spine injuries are classified by Allen and Ferguson according to the period they occur, as infantile, early juvenile, and late juvenile. Anatomically, two main types are defined as occipitoatlantal (upper cervical) and subaxial injuries. The purpose of this paper is to review cervical spine injuries in children and adolescents with respect to epidemiology, injury mechanisms, diagnosis, clinical and radiologic aspects, and treatment in the light of the current literature.
Citation - WoS: 3
Citation - Scopus: 5
Clinical Experience With Coronary Sinus Catheterization in Minimally Invasive Aortic Valve Surgery Under Transesophageal Echocardiography Guidance
(Kluwer Academic Publishers, 2002) Demirsoy, Ergun; Özbek, Uğur; Bayındır, Osman; Sönmez, Baris
We aimed to show conventional coronary sinus (CS) catheter could be used with transesophageal echocardiography (TEE) guidance through the limited surgical field in aortic valve surgery with 'J' sternotomy. This method was performed in 14 patients and completed successfully in 12. We believe that in minimally invasive aortic valve surgery the insertion of the conventional retrograde cardioplegia catheter to the CS with routine way may not be possible but application of TEE guidance is cost-effective and easily applicable method without significant complications.
Citation - WoS: 46
Citation - Scopus: 55
Comparison of Five Antimicrobial Regimens for the Treatment of Brucellar Spondylitis: a Prospective, Randomized Study
(E I F T Srl, 2003) Bayindir, Y; Sonmez, E; Aladag, A; Buyukberber, N
Brucellosis, a zoonosis with worldwide distribution, is a systemic infection and still an important public health problem in Turkey. The best antimicrobial combination and schedule for the treatment of brucellosis with spondylitis has not yet been clearly determined. In a prospective and randomized study, we compared the efficacy of five antimicrobial regimens for treatment of 102 patients with lumbar brucellar spondylitis. Patients were randomly assigned to receive antimicrobial combination therapy. Twenty patients received streptomycin 1 g/day intramuscularly for 15 days and tetracycline-HCl, 500 mg every 6 h orally for 45 days (ST), 21 patients received streptomycin 1 g/day i.m. for 15 days and doxycycline 100 mg every 12 h orally for 45 days (SD), 20 patients received doxycycline 100 mg every 12 h orally for 45 days and rifampicin 15 mg/kg per day in a single morning dose orally for 45 days (DR), 19 patients received ofloxacin, 200 mg every 12 h orally for 45 days and rifampicin 15 mg/kg per day in a single morning dose orally for 45 days (OR), and 22 patients received streptomycin 1 g/day i.m. for 15 days and doxycycline 100 mg every 12 h orally for 45 days plus rifampicin 15 mg/kg per day in a single morning dose orally for 45 days (SDR). Initial therapeutic failure occurred in 2 patients (10%) in the ST regimen group, 4 patients (19%) in the SD group, 3 patients (15%) in the DR group and 5 patients (26%) in the OR regimen. In addition, 2 patients (10%) in the DR group and 5 patients (26%) in the OR regimen relapsed during the follow-up period. There was no relapse in any patients in the ST, SD, and SDR groups. The response rates were 90% in the ST and 81% in the SD groups. In contrast, there was a maximum good response (100%) and no relapse in the SDR group. In conclusion, a combination of doxycycline, streptomycin, and rifampicin can be recommended as therapy for brucellar spondylitis and to reduce relapse rates.
Citation - WoS: 6
Citation - Scopus: 7
Comparison of the BBL-mycobacteria growth indicator tube method with culture in the diagnosis of tuberculosis and evaluation of the resistance patterns of isolated strains to four major drugs
(Karger, 2002) Kocazeybek, Bekir Sami
The BBL-mycobacteria growth indicator tube system (MGIT) is used for a rapid detection of the presence of mycobacteria. Our study aimed to compare MGIT with the Lowenstein-Jensen (LJ) reference method in clinical samples with suspected pulmonary and extrapulmonary tuberculosis and to evaluate the primary and secondary resistance patterns by determining the resistances of the isolated strains to four major anti mycobacteria I drugs. 648 clinical samples from different clinics with suspected pulmonary or extrapulmonary tuberculosis based on clinical radiological histopathological and immunological findings were included in the investigation. The samples were first stained with Ziehl-Neelsen (ZN) and then cultured in LJ medium according to the standard bacteriological procedure and in the MGIT as recommended by the manufacturer. Conventional biochemical tests and p-nitro-alpha-acethylamino-beta-hydroxypropiophene of the Bactec system were used to identify the isolated mycobacterial strains. The susceptibilities to streptomycin isoniazid rifampicin ethambutol were tested by the BBL-MGIT antibiotic susceptibility test and the resistances of the strains found to be resistant to any of the drugs were confirmed by the agar proportion method. Mycobacterium spp. were isolated in 61 (9.4%) out of 648 samples. Eventually 58 out of 61 strains were classified as Mycobacterium tuberculosis and the other 3 as Mycobacterium tuberculosis complex. 32 of these were ZN positive. The growth time was determined as 12.2 days by the MGIT method and 24.1 days by the LJ method (p < 0.001). 29 strains were ZN negative. Their growth time was 23 days by the MGIT method and 37 days by the LJ method (p < 0.001). Drug resistance was detected in 23 (37.7%) of 61 cases (of whom 39 were new and 22 were former patients)
Citation - WoS: 16
Corneal Ring Segments (intacs) for the Treatment of Asymmetrical Astigmatism of the Keratoconus. Follow-Up After 2 Years
(Masson Editeur, 2003) Tunç, Zeki; Deveci, Nuran; Sener, Bozkurt; Bahçecioğlu, Halil Ibrahim
Objective: To evaluate the use of corneal ring segments (INTACS) for the treatment of asymmetrical astigmatism in keratoconus. Material and methods: This prospective study involved nine eyes of seven patients who were operated on between December 1998 and June 2000. A case of keratoconus with opacified cornea was excluded from this study. The patients chosen were contact lens-intolerant. The surgical intervention was carried out under topical anesthesia. The INTACS (Addition Technology) corneal ring insert was inserted approximately 68% of the peripheral corneal depth and was centered to the cone of the cornea. Results: No intraoperative complications occurred. We noted a flattening of the central cornea and a decrease in irregular astigmatism for all patients. Mean preoperative uncorrected visual acuity was less than 1/10. Postoperatively two eyes had an uncorrected visual acuity of 10/10 seven eyes showed an improvement from an uncorrected visual acuity of 2/10 to 7/10. Conclusion: We have observed that the flattening effect of INTACS inserts on the soft corneal keratoconic tissue and on the high astigmatic tissue seems greater than that produced in normal cornea. Implantation of INTACS resulted in a significant reduction in asymmetrical astigmatism of the keratoconus.
Citation - Scopus: 17
Corneal Ring Segments (intacs) for the Treatment of Asymmetrical Astigmatism of the Keratoconus. Follow-Up After 2 Years;
(2003) Tunc,Z.; Deveci,N.; Sener,B.; Bahcecioglu,H.
Objective: To evaluate the use of corneal ring segments (INTACS) for the treatment of asymmetrical astigmatism in keratoconus. Material and methods: This prospective study involved nine eyes of seven patients who were operated on between December 1998 and June 2000. A case of keratoconus with opacified cornea was excluded from this study. The patients chosen were contact lens-intolerant. The surgical intervention was carried out under topical anesthesia. The INTACS (Addition Technology) corneal ring insert was inserted approximately 68% of the peripheral corneal depth and was centered to the cone of the cornea. Results: No intraoperative complications occurred. We noted a flattening of the central cornea and a decrease in irregular astigmatism for all patients. Mean preoperative uncorrected visual acuity was less than 1/10. Postoperatively two eyes had an uncorrected visual acuity of 10/10, seven eyes showed an improvement from an uncorrected visual acuity of 2/10 to 7/10. Conclusion: We have observed that the flattening effect of INTACS inserts on the soft corneal keratoconic tissue and on the high astigmatic tissue seems greater than that produced in normal cornea. Implantation of INTACS resulted in a significant reduction in asymmetrical astigmatism of the keratoconus.
Citation - WoS: 2
Citation - Scopus: 2
Correlated conformational dynamics of the human GluN1-GluN2A type N-methyl-D-aspartate (NMDA) receptor
(SPRINGER, 2021) Esşiz, Şebnem; Gencel, Melis; Aktolun, Muhammed; Demir, Ayhan; Carpenter, Timothy S.; Servili, Burak
N-Methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels found in the nerve cell membranes. As a result of overexcitation of NMDARs, neuronal death occurs and may lead to diseases such as epilepsy, stroke, Alzheimer's disease, and Parkinson's disease. In this study, human GluN1- GluN2A type NMDAR structure is modeled based on the X-ray structure of the Xenopus laevis template and missing loops are added by ab-initio loop modeling. The final structure is chosen according to two different model assessment scores. To be able to observe the structural changes upon ligand binding, glycine and glutamate molecules are docked into the corresponding binding sites of the receptor. Subsequently, molecular dynamics simulations of 1.3 mu s are performed for both apo and ligand-bound structures. Structural parameters, which have been considered to show functionally important changes in previous NMDAR studies, are monitored as conformational rulers to understand the dynamics of the conformational changes. Moreover, principal component analysis (PCA) is performed for the equilibrated part of the simulations. From these analyses, the differences in between apo and ligand-bound simulations can be summarized as the following: The girdle right at the beginning of the pore loop, which connects M2 and M3 helices of the ion channel, partially opens. Ligands act like an adhesive for the ligand-binding domain (LBD) by keeping the bi-lobed structure together and consequently this is reflected to the overall dynamics of the protein as an increased correlation of the LBD with especially the amino-terminal domain (ATD) of the protein.
Citation - WoS: 1
Citation - Scopus: 1
Covid-19 Modeling Based on Real Geographic and Population Data
(Tubitak Scientific & Technological Research Council Turkey, 2023) Baysazan, Emir; Berker, A. Nihat; Mandal, Hasan; Kaygusuz, Hakan
Background/aim: Intercity travel is one of the most important parameters for combating a pandemic. The ongoing COVID-19 pandemic has resulted in different computational studies involving intercity connections. In this study, the effects of intercity connections during an epidemic such as COVID-19 are evaluated using a new network model. Materials and methods: This model considers the actual geographic neighborhood and population density data. This new model is applied to actual Turkish data by means of provincial connections and populations. A Monte Carlo algorithm with a hybrid lattice model is applied to a lattice with 8802 data points. Results: Around Monte Carlo step 70, the number of active cases in Turkiye reaches up to 8.0% of the total population, which is followed by a second wave at around Monte Carlo step 100. The number of active cases vanishes around Monte Carlo step 160. Starting with Istanbul, the epidemic quickly expands between steps 60 and 100. Simulation results fit the actual mortality data in Turkiye. Conclusion: This model is quantitatively very efficient in modeling real-world COVID-19 epidemic data based on populations and geographical intercity connections, by means of estimating the number of deaths, disease spread, and epidemic termination.
Citation - WoS: 6
Citation - Scopus: 7
Cryogenic X-Ray Crystallographic Studies of Biomacromolecules at Turkish Light Source Turkish Delight
(Tubitak Scientific & Technological Research Council Turkey, 2023) Atalay, Necati; Akcan, Enver Kamil; Gul, Mehmet; Ayan, Esra; Destan, Ebru; Ertem, Fatma Betuel; Tokay, Nurettin
X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Turkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, Istanbul, Turkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis.
Citation - WoS: 15
Citation - Scopus: 17
Crystallographic Structure Versus Homology Model: a Case Study of Molecular Dynamics Simulation of Human and Zebrafish Histone Deacetylase 10
(Taylor & Francis, 2020) Uba, Abdullahi İbrahim; Yelekçi, Kemal
Histone deacetylase (HDAC) 10 has been implicated in the pathology of various cancers and neurodegenerative disorders, making the discovery of novel inhibitors of the isoform an important endeavor. However, the unavailability of crystallographic structure of human HDAC10 (hHDAC10) hinders structure-based drug design effort. Previously, we reported the homology modeled structure of human HDAC10 built using the crystallographic structure of Danio rerio (zebrafish) HDAC10 (zHDAC10) (Protein Data Bank (PDB) ID; 5TD7, released on 24 May 2017) as a template. Here, in continuation with our study, both hHDAC10 and zHDAC10, and their respective complexes with trichostatin A (TSA), quisinostat, and the native ligand (in 5TD7), 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol (PDB ID; FKS) were submitted to 100 ns-long unrestrained molecular dynamics (MD) simulations. Comparative analyses of the MD trajectories revealed that zHDAC10 and its complexes displayed higher stability than hHDAC10 and its corresponding complexes over time. Nonetheless, docking of active and inactive set molecules revealed that more reliable conformations of hHDAC10 could be obtained at an extended time period. This study may shed more light on the reliability of hHDAC10 modeled structure for use in selective inhibitor design.Communicated by Ramaswamy H. Sarma.
Citation - WoS: 25
Ct and Mr Characteristics of Hibernoma: Six Cases
(Elsevier Science Inc, 2008) Dursun, Memduh; Agayev, Ayaz; Bakir, Baris; Ozger, Harzem; Eralp, Levent; Şırvancı, Mustafa; Güven, Koray; Tunaci, Mehtap
Purpose: The purpose of this study was to describe the computed tomography (CT) and magnetic resonance (MR) imaging findings of hibernoma. Materials and methods: We retrospectively evaluated imaging findings of CT and MR examinations of six patients (three men and three woman aged 27-48 years) with histopathological diagnosis of hibernoma. Results: On CT examination the lesions were slightly hyperdense and on T1- and T2-weighted MR images they were isointense or slightly hypointense compared to the subcutaneous fat. All of these lesions showed contrast enhancement and one out of the six lesions had internal linear septations. Conclusion: Hibernoma has a wide spectrum of CT and MR imaging findings which should be considered in differential diagnosis especially with other lipomatous lesions. (C) 2008 Elsevier Inc. All rights reserved.
Citation - WoS: 5
Citation - Scopus: 5
Cultural Differences in Performance on Eriksen's Flanker Task
(Springer, 2020) Gutchess, Angela; Ksander, John; Millar, Peter R.; Arslan Uzundağ, Berna; Sekuler, Robert; Boduroğlu, Ayşecan
Eriksen's zoom model of attention implies a trade-off between the breadth and resolution of representations of information. Following this perspective, we used Eriksen's flanker task to investigate culture's influence on attentional allocation and attentional resolution. In Experiment1, the spatial distance of the flankers was varied to test whether people from Eastern cultures (here, Turks) experienced more interference than people from Western cultures (here, Americans) when flankers were further from the target. In Experiment2, the contrast of the flankers was varied. The pattern of results shows that congruency of the flankers (Experiment1) as well as the degree of contrast of the flankers compared with the target (Experiment2) interact with participants' cultural background to differentially influence accuracy or reaction times. In addition, we used evidence accumulation modeling to jointly consider measures of speed and accuracy. Results indicate that to make decisions in the Eriksen flanker task, Turks both accumulate evidence faster and require more evidence than Americans do. These cultural differences in visual attention and decision-making have implications for a wide variety of cognitive processes.

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