PubMed İndeksli Yayınlar Koleksiyonu
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Article Citation Count: 5The acquisition and use of relative clauses in Turkish-learning children's conversational interactions: a cross-linguistic approach(Cambridge University Press, 2019) Uzundağ, Berna A.; Küntay, Aylin C.Using a cross-linguistic approach, we investigated Turkish-speaking children's acquisition and use of relative clauses (RCs) by examining longitudinal child-caregiver interactions and cross-sectional peer conversations. Longitudinal data were collected from 8 children between the ages of 8 and 36 months. Peer conversational corpus came from 78 children aged between 43 and 64 months. Children produced RCs later than in English (Diessel, 2004) and Mandarin (Chen & Shirai, 2015), and demonstrated increasing semantic and structural complexity with age. Despite the morphosyntactic difficulty of object RCs, and prior experimental findings showing a subject RC advantage, preschool-aged children produced object RCs, which were highly frequent in child-directed speech, as frequently as subject RCs. Object RCs in spontaneous speech were semantically less demanding (with pronominal subjects and inanimate head nouns) than the stimuli used in prior experiments. Results suggest that multiple factors such as input frequency and morphosyntactic and semantic difficulty affect the acquisition patterns.Article Citation Count: 1Across dimensions: Two- and three-dimensional phase transitions from the iterative renormalization-group theory of chains(2020) Keçoğlu, İbrahim; Berker, A. NihatSharp two- and three-dimensional phase transitional magnetization curves are obtained by an iterative renormalization-group coupling of Ising chains, which are solved exactly. The chains by themselves do not have a phase transition or nonzero magnetization, but the method reflects crossover from temperaturelike to fieldlike renormalization-group flows as the mechanism for the higher-dimensional phase transitions. The magnetization of each chain acts, via the interaction constant, as a magnetic field on its neighboring chains, thus entering its renormalization-group calculation. The method is highly flexible for wide application.Article Citation Count: 9Anterior instrumentation for adolescent idiopathic scoliosis(Springer Verlag, 2001) Göğüş, Abdullah; Talu, Ufuk; Akman, Sümeyra; Sar, Can; Hamzaoğlu, Azmi; Eralp, LeventThirty-two patients with adolescent idiopathic scoliosis underwent anterior fusion with rigid single rod (third generation instrumentation) and titanium mesh cages. The mean follow-up was 31 (24-45) months and the mean age was 14.9 years. There were 8 patients with King type I 10 with type II 6 with type III 4 with type IV and 4 with lumbar curves. Titanium mesh cages were used in all the lumbar procedures and at the cranial and caudal ends of the instrumented area in thoracic cases. All the patients were immobilized in an orthosis for 3-6 months postoperatively. Mean preoperative primary coronal Cobb angle of 56 degrees was improved to 8.6 degrees. Average correction rate was 84%. Sagittal balance was restored with a mean thoracic kyphosis of 28 degrees and a mean lumbar lordosis of 38 degrees. Spontaneous secondary curve decompensation did not occur and postoperative thoracolumbar junctional kyphosis was not seen. One case had to be revised due to proximal screw pull out and loss of correction.Article Citation Count: 7Antifungal screening and in silico mechanistic studies of an in-house azole library(2019) Sarı, Suat; Kart, Didem; Sabuncuoğlu, Suna; Doğan, İnci Selin; Özdemir, Zeynep; Bozbey, İrem; Gencel, Melis; Eşsiz, Şebnem; Reynisson, Jóhannes; Karakurt, Arzu; Saraç, Selma; Dalkara, SevimSystemic Candida infections pose a serious public health problem with high morbidity and mortality. C. albicans is the major pathogen identified in candidiasis; however, non-albicans Candida spp. with antifungal resistance are now more prevalent. Azoles are first-choice antifungal drugs for candidiasis; however, they are ineffective for certain infections caused by the resistant strains. Azoles block ergosterol synthesis by inhibiting fungal CYP51, which leads to disruption of fungal membrane permeability. In this study, we screened for antifungal activity of an in-house azole library of 65 compounds to identify hit matter followed by a molecular modeling study for their CYP51 inhibition mechanism. Antifungal susceptibility tests against standard Candida spp. including C. albicans revealed derivatives 12 and 13 as highly active. Furthermore, they showed potent antibiofilm activity as well as neglectable cytotoxicity in a mouse fibroblast assay. According to molecular docking studies, 12 and 13 have the necessary binding characteristics for effective inhibition of CYP51. Finally, molecular dynamics simulations of the C. albicans CYP51 (CACYP51) homology model's catalytic site complexed with 13 were stable demonstrating excellent binding.Article Citation Count: 20Apolipoprotein E polymorphism in Turkish subjects with Type 2 diabetes mellitus: Allele frequency and relation to serum lipid concentrations(EDITRICE KURTIS S R L, 2004) Duman, Belgin Süsleyici; Öztürk, Melek; Yilmazer, Selma; Hatemi, HüsrevThe role of apolipoprotein E (apoE) genotypes in modulating plasma lipid and apolipoprotein levels was studied in 112 patients with Type 2 diabetes mellitus (T2DM) and 94 healthy individuals. ApoE genotypes were identified by PCR amplification and subsequent restriction endonuclease digestion. The apoE allele and genotype frequencies were similar in both the diabetic and control subjects. The apoE allele frequencies were found to be 74.3 for e3 10.1 for e2 15.6 for e4 in the diabetic group and 68.1 for e3 13.2 for e2 and 18.7 for e4 in the control group. Sex-specific genotypic distribution of apoE polymorphism did not differ between the study groups. To elucidate the association of apoE with lipid abnormalities with respect to gender serum lipid and apolipoprotein levels were compared among apo e2 (e2/2 and e3/2) e3 (e3/3) and e4 (e4/3 and e4/4) groups of T2DM and control subjects. Apo e2 allele was found to be associated to triglycerides for both sexes and associated to glucose and BMI only in females. Subjects with e2 allele had higher levels of BMI glucose and triglyceride in comparison to e3 and e4. Our data suggest that genetic variation at the apoE locus in Turkish subjects is a genetic factor that influences lipid levels. Further studies attempting to correlate apoE polymorphism with lipid profile in a large number of individuals would be helpful in establishing the true significance of this polymorphism in the Turkish population. (C) 2004 Editrice Kurtis.Article Citation Count: 4Association of lipoprotein(a) concentration and apo(a) isoform size with restenosis after percutaneous transluminal coronary angioplasty(Springer Verlag, 2000) Sırıkcı, Onder; Aytekin, Vedat; Demiroglu, I. C. C.; Demiroğlu, Cemşid; Marcovina, S.M.Lp(a) is a unique class of lipoprotein particles that exhibits a considerable size heterogeneity resulting from the size polymorphism of apo(a) its unique protein component. An elevated level of Lp(a) in plasma has been proposed to be a risk factor for premature development of coronary artery disease. To evaluate the relationship between Lp(a) concentration and apo(a) isoform size with restenosis after percutaneous transluminal coronary angioplasty Lp(a) levels and apo(a) phenotypes were determined in 204 patients who underwent a successful coronary angioplasty procedure and stent implantation. The patients were followed with clinical examinations and exercise tests at 1 3 and 6 months and a control coronary angiography was performed after 6 months to evaluate restenosis. Lp(a) levels were determined with an ELISA that is insensitive to the size heterogeneity of Lp(a) and the apo(a) isoforms were determined by a high-resolution agarose gel electrophoresis method followed by immunoblotting with a specific monoclonal antibody. Of the 146 patients who underwent angiographic evaluation 57 (39%) had restenosis whereas 89 (61%) did not. Lp(a) levels and the distribution of the expressed apo(a) phenotypes were compared in these two groups of patients. Although the mean and median Lp(a) levels were higher in the restenosed group the difference was not statistically significant. However a significant difference in Lp(a) values was found in women (P=0.043) even though because of the small number of women in the study (n=35) no sound conclusions can be reached on the predictive role of Lp(a) in restenosis. There also was no difference in the distribution of apo(a) phenotypes between the two groups. Because of their wide distribution Lp(a) values and apo(a) isoforms do not seem to be a useful indicator of risk of restenosis after percutaneous transluminal coronary angioplasty in our study cohort.Article Citation Count: 77The association of the severity of obstructive sleep apnea with plasma leptin levels(Amer Medical Assoc., 2003) Öztürk, Levent; Ünal, Murat; Tamer, Lülüfer; Çelikoğlu, FiruzObjective: To examine whether circulating leptin levels correlate with the severity of disease in patients with obstructive sleep apnea. Design: Prospective nonrandomized study. Setting: Referral sleep laboratory for patients with sleep-disordered breathing and biochemistry laboratory. Patients: Thirty-two subjects (mean+/-SD age 47+/-12 years) who were referred for suspected sleep apnea underwent an overnight sleep study and fasting morning venous blood sampling. Patients were divided into 3 groups with respect to apnea-hypopnea index: (1) severe sleep apnea (n=8) apnea-hypopnea index greater than 20Article Citation Count: 54BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks(Oxford University Press, 2014) Erten, Cesim; Erten, CesimMotivation: Global many-to-many alignment of biological networks has been a central problem in comparative biological network studies. Given a set of biological interaction networks the informal goal is to group together related nodes. For the case of protein-protein interaction networks such groups are expected to form clusters of functionally orthologous proteins. Construction of such clusters for networks from different species may prove useful in determining evolutionary relationships in predicting the functions of proteins with unknown functions and in verifying those with estimated functions. Results: A central informal objective in constructing clusters of orthologous proteins is to guarantee that each cluster is composed of members with high homological similarity usually determined via sequence similarities and that the interactions of the proteins involved in the same cluster are conserved across the input networks. We provide a formal definition of the global many-to-many alignment of multiple protein-protein interaction networks that captures this informal objective. We show the computational intractability of the suggested definition. We provide a heuristic method based on backbone extraction and merge strategy (BEAMS) for the problem. We finally show through experiments based on biological significance tests that the proposed BEAMS algorithm performs better than the state-of-the-art approaches. Furthermore the computational burden of the BEAMS algorithm in terms of execution speed and memory requirements is more reasonable than the competing algorithms.Article Citation Count: 4Beyond sightseeing: How can tourism affect public/global health in modern society?(University of Edinburgh, 2022) Kozak, Metin; Kozak,M.; Jiang,Y.[No abstract available]Article Citation Count: 25Brow suspension, a minimally invasive technique in facial rejuvenation(2002) Erol, O. Onur; Sözer, S. Ozan; Velidedeoğlu, Hifzi V.People tend to prefer noninvasive or minimally invasive methods of facial rejuvenation, especially when it involves their face, which is the hallmark of a person's identity and impossible to hide. It is widely known that brow ptosis gives the face a "tired look" and also accentuates deformities of the upper eyelid. Most people who are interested in facial rejuvenation may not accept even a minor surgery, such as an endoscopic surgery. The senior author has developed a minimally invasive method of suspending the brow at a higher position. In this technique, there is neither surgical dissection nor a surgical incision except for four stab incisions and suture insertion, which is why we refer to it as a nonsurgical brow suspension. It is done under local anesthesia, and the brows are fixed in the position that they assume when the patient is supine. In the past 6 years, we performed 387 brow suspensions on 324 female and 63 male patients. The youngest patient was 19 years old, and the oldest was 74 years old. A retrospective chart review was done. These 387 cases were reviewed by comparison of preoperative and postoperative photographs. This approach was not only used for patients who were not interested in surgical rejuvenation but was also combined with lipofilling, laser resurfacing, and/or upper blepharoplasty. This technique is useful for correcting postsurgical brow asymmetry. We present this technique as an adjunct to the established techniques of facial rejuvenation. Despite the high patient acceptance and technical ease, it is not a replacement for the established techniques of facial rejuvenation.Article Citation Count: 14CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways(Oxford University Press, 2013) Erten, Cesim; Biyikoglu, Turker; Erten, CesimMotivation: Given a pair of metabolic pathways an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction drug design and overall may enhance our understanding of cellular metabolism. Results: We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database we demonstrate that when compared with a state-of-the-art alternative the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms.Article Citation Count: 3Clinical 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, BarisWe 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.Article Citation Count: 105Cognitive impairment in amyotrophic lateral sclerosis: evidence from neuropsychological investigation and event-related potentials(Elsevier Science Bv, 2002) Hanagasi, Hasmet A.; Gurvit, I. Hakan; Ermutlu, Numan; Kaptanoğlu, Gulustu; Karamürsel, Sacit; Idrisoğlu, Halil A.; Emre, Murat; Demiralp, TamerThe presence of subclinical cognitive impairment in patients with amyotrophic lateral sclerosis (ALS) is investigated using neuropsychological assessment and event-related potential recordings (ERP). An extensive battery of neuropsychological tests assessing the domains of attention memory language visuo-spatial and executive functions were administered to 20 non-demented patients with sporadic ALS and 13 age- and education-matched healthy control subjects. Mismatch negativity (MMN) P3b P3a (novelty P300) and contingent negative variation (CNV) were recorded. ALS patients were significantly impaired in tests of working memory sustained attention response inhibition naming verbal fluency and complex visuo-spatial processing. The memory impairment seemed to be secondary to deficits in forming learning strategies and retrieval. In ERP recordings P3a and P3b amplitudes of ALS patients were lower compared with the controls P3a latencies were significantly longer and mean CNV amplitudes were higher. These results indicate subclinical impairment of cognitive functions in patients with ALS. The pattern of cognitive impairment suggests the dysfunction of the frontal network. (C) 2002 Elsevier Science B.V. All rights reserved.Article Citation Count: 3Combined radiofrequency ablation and myxoma resection through a port access approach(Elsevier Science Inc, 2004) Güden, Mustafa; Akpınar, Belhhan; Ergenoğlu, Mehmet U.; Sağbaş, Ertan; Sanisoğlu, İlhan; Özbek, UğurMyxornas are common cardiac tumors that are traditionally managed by complete excision through a median sternotorny approach with the use of cardiopulmonary bypass. We discuss a patient with left atrial myxoma and chronic atrial fibrillation who underwent surgical excision and combined irrigated radiofrequency ablation for atrial fibrillation through a Port Access approach. Minimally invasive operations constitute an expanding field for the treatment of many cardiac diseases and may be an alternative for the treatment of this pathology because of less surgical trauma and cosmetic superiority. In this case both excision of the myxoma and radiofrequency ablation were feasible through this minimally invasive approach. The combination of direct and endoscopic views enabled both procedures to be performed safely and efficiently. (C) 2004 by The Society of Thoracic Surgeons.Article Citation Count: 35Comparison of three different combination therapies in the treatment of human brucellosis(ROYAL SOC MEDICINE PRESS LTD, 2005) Ersoy, Yasemin; Sönmez, Emine; Tevfik, Mehmet R.; But, Ayşe DinçThe efficacy and tolerability of three different combination treatment regimens in human brucellosis were compared in 118 uncomplicated patients enrolled in a prospective study between May 1997 and December 2002. Brucellosis was diagnosed using standard clinical and microbiological findings. Patients with central nervous system involvement spondylitis endocarditis or children under 16 years of age were excluded from the study. Patients were randomly assigned to receive 400 mg of ofloxacin plus 600 mg of rifampicin (OR n = 41)200 mg of doxycycline plus 600 mg of rifampicin (DR n = 45) or 1 g intramuscularly streptomycin (administered for three weeks) plus 200 mg doxycycline (DS n = 32) daily for 6 weeks. All patients were followed up at least 6 months after cessation of therapy. There was no statistical difference between the groups on relapse rates and clinical response to the treatment (P> 0.05). Five patients in OR (12.8%) six patients in DR (14.3%) and three patients in DS groups (9.7%) suffered relapse. The side-effects were seen in eight (19.5%) 21 (46.7%) and eight (25.0%) patients of OR DR and DS groups respectively. The use of combination therapy of ofloxacin plus rifampicin for 6 weeks was found to be as effective as DR and DS. The side-effects of therapy in OR and DS groups was less severe than in the DR group.Article Citation Count: 5Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics(Amer Chemical Soc, 2013) Eşsiz, Şebnem; Eşsiz, Şebnem; Wong, Sergio E.; Lau, Edmond Y.; Valdez, Carlos A.; Satcher, Joe H. Jr.; Aines, Roger D.; Lightstone, Felice C.Molecular dynamics simulations and quantum-mechanical calculations were performed to characterize a supra-molecular tris(imidazolyl) calix[6]arene Zn2+ aqua complex as a biomimetic model for the catalyzed hydration of carbon dioxide to bicarbonate H2O + CO2 -> H+ + HCO3-. On the basis of potential-of-mean-force (PMF) calculations stable conformations had distorted 3-fold symmetry and supported either one or zero encapsulated water molecules. The conformation with an encapsulated water molecule is calculated to be lower in free energy than the conformation with an empty cavity (Delta G = 1.2 kcal/mol) and is the calculated free-energy minimum in solution. CO2 molecule partitioning into the cavity is shown to be very facile proceeding with a barrier of 1.6 kcal/mol from a weak encounter complex which stabilizes the species by about 1.0 kcal/mol. The stabilization energy of CO2 is calculated to be larger than that of H2O (Delta Delta G = 1.4 kcal/mol) suggesting that the complex will preferentially encapsulate CO2 in solution. In contrast the PMF for a bicarbonate anion entering the cavity is calculated to be repulsive in all nonbonding regions of the cavity due to the diameter of the calix[6]arene walls. Geometry optimization of the Zn-bound hydroxide complex with an encapsulated CO2 molecule showed that multiple noncovalent interactions direct the reactants into optimal position for nucleophilic addition to occur. The calixarene complex is a structural mimic of the hydrophilic/hydrophobic divide in the enzyme providing a functional effect for CO2 addition in the catalytic cycle. The results show that Zn-binding calix[6]arene scaffolds can be potential synthetic biomimetics for CO2 hydration catalysis both in terms of preferentially encapsulating CO2 from solution and by spatially fixing the reactive species inside the cavity.Book Part Citation Count: 4Computational Chemistry and Molecular Modeling of Reversible MAO Inhibitors(Humana Press Inc., 2023) Yelekçi, Kemal; Erdem, S.S.Proper elucidation of drug-target interaction is one of the most significant steps at the early stages of the drug development research. Computer-aided drug design tools have substantial contribution to this stage. In this chapter, we specifically concentrate on the computational methods widely used to develop reversible inhibitors for monoamine oxidase (MAO) isozymes. In this context, current computational techniques in identifying the best drug candidates showing high potency are discussed. The protocols of structure-based drug design methodologies, namely, molecular docking, in silico screening, and molecular dynamics simulations, are presented. Employing case studies of safinamide binding to MAO B, we demonstrate how to use AutoDock 4.2.6 and NAMD software packages. © 2023, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.Article Citation Count: 16Corneal 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 IbrahimObjective: 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.Article Citation Count: 5Coronary bypass surgery in octogenarians(2001) Arbatli, H.; Unal, M.; Demirsoy, E.; Tansal, S.; Yagan, N.; Tükenmez, F.; Sener, D.OBJECTIVE: The age of the patients referred for coronary bypass surgery is getting older progressively. Early and late postoperative outcome of octogenarians were evaluated and compared with younger age group in this study. METHODS: Records of 55 patients aged 80 years or older (mean age 82.7 +/- 2.8) among 3834 patients, who had coronary bypass graft procedure, operated between 1995 and 2001 were reviewed retrospectively. RESULTS: There were 39 men (70.9%) and 16 women (29.1%). Three patients had aortic valve replacement, 1 had left ventricular aneurysm repair, 1 had carotid endarterectomy additionally. Atrial fibrillation (21.8%), renal dysfunction (16.4%), and prolonged ventilation (10.9%) were the prominent complications. The hospital mortality rate was 7.27% (4 patients). Kaplan Meier Survival Analysis estimated that at the end of 5 years 83.1 + 5.2% of patients were still alive. CONCLUSION: Coronary bypass operations can be performed in octogenarians with slightly increased but acceptable hospital mortality and longer hospital stay. Early intervention and individual modifications in cardiopulmonary bypass techniques may improve the results in this patient population.Article Citation Count: 44Crossover from Vibrational to Rotational Collectivity in Heavy Nuclei in the Shell-Model Monte Carlo Approach(Amer Physical Soc., 2013) Özen, Cem; Alhassid, Yoram; Nakada, HitoshiHeavy nuclei exhibit a crossover from vibrational to rotational collectivity as the number of neutrons or protons increases from shell closure towards midshell but the microscopic description of this crossover has been a major challenge. We apply the shell model Monte Carlo approach to families of even-even samarium and neodymium isotopes and identify a microscopic signature of the crossover from vibrational to rotational collectivity in the low-temperature behavior of < J(2)>(T) where J is the total spin and T is the temperature. This signature agrees well with its values extracted from experimental data. We also calculate the state densities of these nuclei and find them to be in very good agreement with experimental data. Finally we define a collective enhancement factor from the ratio of the total state density to the intrinsic state density as calculated in the finite-temperature Hartree-Fock-Bogoliubov approximation. The decay of this enhancement factor with excitation energy is found to correlate with the pairing and shape phase transitions in these nuclei. DOI: 10.1103/PhysRevLett.110.042502
