Publications with Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Improving CO2 separation performance of MIL-53(Al) by incorporating 1-N-Butyl-3-methylimidazolium methyl sulfate(Wiley, 2019) Department of Chemical and Biological Engineering; N/A; Kulak, Harun; Polat, Hüsamettin Mert; Kavak, Safiyye; Keskin, Seda; Uzun, Alper; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; N/A; N/A; N/A; 40548; 599171-n-Butyl-3-methylimidazolium methyl sulfate is incorporated into MIL-53(Al). Detailed characterization is done by X-ray fluorescence, Brunauer-Emmett-Teller surface area, scanning electron microscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, and thermogravimetric analysis. Results show that ionic liquid (IL) interacts directly with the framework, significantly modifying the electronic environment of MIL-53(Al). Based on the volumetric gas adsorption measurements, CO2, CH4, and N-2 adsorption capacities decreased from 112.0, 46.4, and 19.6 cc (STP) g(MIL-53(Al))(-1) to 42.2, 13.0, and 4.3 cc (STP) g(MIL-53(Al))(-1) at 5 bar, respectively, upon IL incorporation. Data show that this postsynthesis modification leads to more than two and threefold increase in the ideal selectivity for CO2 over CH4 and N-2 separations, respectively, as compared with pristine MIL-53(Al). The isosteric heat of adsorption (Qst) values show that IL incorporation increases CO2 affinity and decreases CH4 and N-2 affinities. Cycling adsorption-desorption measurements show that the composite could be regenerated with almost no decrease in the CO2 adsorption capacity for six cycles and confirm the lack of any significant IL leaching. The results offer MIL-53(Al) as an excellent platform for the development of a new class of IL/MOF composites with exceptional performance for CO2 separation.Publication Open Access Mechanistic differences of activation of Rac1(P29S) and Rac1(A159V)(American Chemical Society (ACS), 2021) Jang, Hyunbum; Nussinov, Ruth; N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Şenyüz, Simge; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 26605; 8745Rac1 is a small GTPase that plays key roles in actin reorganization, cell motility, and cell survival/growth as well as in various cancer types and neurodegenerative diseases. Similar to other Ras superfamily GTPases, Rac1 switches between active GTP-bound and inactive GDP-bound states. Switch I and II regions open and close during GDP/GTP exchange. P29S and A159V (paralogous to K-Ras(A146)) mutations are the two most common somatic mutations of Rac1. Rac1(P2)(9S)( )is a known hotspot for melanoma, whereas Rac1(A159V) most commonly occurs in head and neck cancer. To investigate how these substitutions induce the Rac1 dynamics, we used atomistic molecular dynamics simulations on the wild-type Rac1 and two mutant systems (P29S and A159V) in the GTP bound state, and on the wild-type Rac1 and P29S mutated system in the GDP bound state. Here, we show that P29S and A159V mutations activate Rac1 with different mechanisms. In Rac1(P29S)-GTP, the substitution increases the flexibility of Switch I based on RMSF and dihedral angle calculations and leads to an open conformation. We propose that the open Switch I conformation is one of the underlying reasons for rapid GDP/GTP exchange of Rac1(P29S). On the other hand, in Rac1(A159V)-GTP, some of the contacts of the guanosine ring of GTP with Rac1 are temporarily lost, enabling the guanosine ring to move toward Switch I and subsequently close the switch. Rac1(A159V)-GTP adopts a Ras state 2 like conformation, where both switch regions are in closed conformation and Thr35 forms a hydrogen bond with the nucleotide.Publication Open Access Depression and Parkinson disease: prevalence, temporal relationship, and determinants(TÜBİTAK, 2017) Bora, Hatice Ayşe; Kuruoǧlu, Aslı Çepik; N/A; Eser, Hale Yapıcı; Faculty Member; School of Medicine; 134359Background/aim: Comorbidity of depression in Parkinson disease (PD) is a major factor that changes patients' quality of life. However, the neurobiological and sociodemographic risk factors for this comorbidity are not well studied. In this study, we aimed to define the prevalence, temporal relationship, and psychosocial and clinical determinants of depression comorbid with PD. Materials and methods: Fifty-five PD patients were evaluated with SCID, a data form that assessed sociodemographic and PD-related variables, UPDRS III, HAM-D, HAM-A, MMSE, and the Apathy Evaluation Scale.Results: Depression (lifetime: 45.5%, last month: 25.5%, before PD: 20%) was the most frequent psychiatric diagnosis. The major determinants of depression in the last month and depression before PD were early onset of PD and young age. Patients on pramipexole treatment were less likely to be diagnosed with depression in the last month. Other sociodemographic and PD-related variables were not significantly different for lifetime, last month, and pre-PD depression diagnosis compared to their counterparts. Conclusion: Depression is prevalent both before and after patient gets a PD diagnosis. Depression is not only the result of PD-related life changes but it is also a preceding factor that may decrease the age of PD onset.Publication Open Access Effects of antenatal magnesium exposure on intestinal blood flow and outcome in Preterm Neonates(Thieme Medical Publishers, 2015) İmamoğlu, Ebru Yalın; Ovalı, Fahri; Karatekin, Güner; N/A; Gürsoy, Tuğba; Faculty Member; School of Medicine; 214691Objective This study aims to investigate the effects of antenatal magnesium sulfate on intestinal blood flow in preterm neonates. Study Design In this prospective case-match study, 25 preterm neonates exposed to magnesium sulfate antenatally were included (study group). Overall, 25 gestational age-matched neonates who had no exposure to magnesium constituted the control group. Serial daily Doppler flow measurements of superior mesenteric artery (SMA) were performed. The time to reach full feeds, first meconium passage were assessed. Presence of feeding intolerance or necrotizing enterocolitis was recorded. Results Blood flow velocities of SMA were not different between the groups during the first five postnatal days. However, SMA blood flow showed an increasing trend in the control group unlike the study group (control group, p < 0.001; study group, p = 0.29). There was no significant difference between the two groups regarding the time to reach full feeds or first meconium passage and presence of feeding intolerance. No case of necrotizing enterocolitis was seen. Conclusion Antenatal magnesium does not significantly affect intestinal blood flow, but it seems to attenuate the increasing trend of the intestinal blood flow in the early postnatal days. However, this study failed to show any impact of this finding on clinical outcomes.Publication Open Access Modelling and analysis of the impact of correlated inter-event data on production control using Markovian arrival processes(Springer, 2019) Department of Business Administration; Department of Industrial Engineering; N/A; Tan, Barış; Dizbin, Nima Manafzadeh; Faculty Member; Department of Business Administration; Department of Industrial Engineering; College of Administrative Sciences and Economics; College of Engineering; Graduate School of Business; 28600; N/AEmpirical studies show that the inter-event times of a production system are correlated. However, most of the analytical studies for the analysis and control of production systems ignore correlation. In this study, we show that real-time data collected from a manufacturing system can be used to build a Markovian arrival processes (MAP) model that captures correlation in inter-event times. The obtained MAP model can then be used to control production in an effective way. We first present a comprehensive review on MAP modeling and MAP fitting methods applicable to manufacturing systems. Then we present results on the effectiveness of these fitting methods and discuss how the collected inter-event data can be used to represent the flow dynamics of a production system accurately. In order to study the impact of capturing the flow dynamics accurately on the performance of a production control system, we analyze a manufacturing system that is controlled by using a base-stock policy. We study the impact of correlation in inter-event times on the optimal base-stock level of the system numerically by employing the structural properties of the MAP. We show that ignoring correlated arrival or service process can lead to overestimation of the optimal base-stock level for negatively correlated processes, and underestimation for the positively correlated processes. We conclude that MAPs can be used to develop data-driven models and control manufacturing systems more effectively by using shop-floor inter-event data.Publication Open Access SARS-CoV-2 and influenza viruses: strategies to cope with coinfection and bioinformatics perspective(Wiley, 2022) Ghaznavi, H; Shirvaliloo, M.; Sargazi, S.; Mohammadghasemipour, Z.; Shams, Z.; Hesari, Z.; Shahraki, O.; Sheervalilou, R.; Shirvalilou S.; N/A; Nazarlou, Ziba; PhD Student; Graduate School of Sciences and EngineeringAlmost a century after the devastating pandemic of the Spanish flu, humankind is facing the relatively comparable global outbreak of COVID-19. COVID-19 is an infectious disease caused by SARS-CoV-2 with an unprecedented transmission pattern. In the face of the recent repercussions of COVID-19, many have argued that the clinical experience with influenza through the last century may have tremendous implications in the containment of this newly emerged viral disease. During the last 2 years, from the emergence of COVID-19, tremendous advances have been made in diagnosing and treating coinfections. Several approved vaccines are available now for the primary prevention of COVID-19 and specific treatments exist to alleviate symptoms. The present review article aims to discuss the pathophysiology, diagnosis, and treatment of SARS-CoV-2 and influenza A virus coinfection while delivering a bioinformatics-based insight into this subject matter.Publication Open Access Associations of fibroblast growth factor 23 and fetuin-a with coronary plaque burden and plaque composition in young adults(Elsevier, 2015) Akın, F.; Ömer, C.; Ayça, B.; İbrahim, A.; Diker, V.; Covic, A.; N/A; Kanbay, Mehmet; Faculty Member; School of Medicine; 110580The total burden of subclinical coronary artery disease (CAD) is significant among young adults. Serum fibroblast growth factor 23 (FGF-23) and fetuin-A are established predictors of morbidity and mortality because of cardiovascular disease. The objective of the study was to evaluate the relationship between subclinical CAD and serum FGF-23 and fetuin-A concentrations among a population of young adults. Methods A total of 241 subjects younger than 45 years who had undergone coronary computed tomographic angiography (CCTA) were included in the study. In 117 patients, the CCTA detected subclinical CAD; the rest of the patients had no CAD detected on CCTA. Results Serum FGF-23 and fetuin-A levels were significantly increased in the CAD patients as compared with the non-CAD patients (26.7 [interquartile range, 22.4-31.9] vs 15.7 [interquartile range, 13.2-18.1] pg/mL and 904.7 [interquartile range, 695.5-1021.6] vs 469.6 [331.4-660.5] mg/L, respectively; P <.001 for both). Furthermore, a positive correlation was identified between FGF-23 and fetuin-A levels and the total number of plaques (r = 0.21 and r = 0.28, respectively; P <.001 for both). In multivariate logistic regression analysis, age, smoking status, uric acid, FGF-23, and fetuin-A levels were found to be independently associated with the presence of CAD. Conclusions The presence of subclinical CAD is independently associated with FGF-23 and fetuin-A and could be used as novel risk markers of cardiovascular disease in the asymptomatic young adult population.Publication Open Access Predicting new iron garnet thin films with perpendicular magnetic anisotropy(Elsevier, 2020) N/A; Department of Electrical and Electronics Engineering; Zanjani, Saeedeh Mokarian; Onbaşlı, Mehmet Cengiz; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 258783Magnetic iron garnets are insulators with low Gilbert damping with many applications in spintronics. Many emerging spintronic applications require perpendicular magnetic anisotropy (PMA) although garnets have only a few PMA types (i.e. terbium and samarium garnet). More and stable PMA garnet options are needed for investigating new spintronic phenomena. In this study, we predict 20 new epitaxial magnetic iron garnet film/substrate pairs with stable PMA at room temperature. The effective anisotropy energies of 10 different garnet films that are lattice-matched to 5 different commercially available garnet substrates (total 50 film/substrate pairs) have been calculated using shape, magnetoelastic and magnetocrystalline anisotropy terms. Strain type, tensile or compressive depending on substrate choice, as well as the sign and the magnitude of the magnetostriction constants of garnets determine if a garnet film may possess PMA. We show the conditions in which Samarium, Gadolinium, Terbium, Holmium, Dysprosium and Thulium garnets may possess PMA on the investigated garnet substrate types. New PMA garnet films with tunable saturation moment and field may improve spin-orbit torque memory and compensated magnonic thin film devices.Publication Open Access A new method to determine reflex latency induced by high rate stimulation of the nervous system(Frontiers, 2014) Karacan, İlhan; Çakar, Halil İ.; Cidem, Muharrem; Kara, Sadık; N/A; Yılmaz, Gizem; Sebik, Oğuz; Türker, Kemal Sıtkı; PhD Student; Researcher; Faculty Member; School of Medicine; N/A; N/A; 6741High rate stimulations of the neuromuscular system, such as continuous whole body vibration, tonic vibration reflex and high frequency electrical stimulation, are used in the physiological research with an increasing interest. In these studies, the neuronal circuitries underlying the reflex responses remain unclear due to the problem of determining the exact reflex latencies. We present a novel 'cumulated average method" to determine the reflex latency during high rate stimulation of the nervous system which was proven to be significantly more accurate than the classical method. The classical method, cumulant density analysis, reveals the relationship between the two synchronously recorded signals as a function of the lag between the signals. The comparison of new method with the classical technique and their relative accuracy was tested using a computer simulation. In the simulated signals the EMG response latency was constructed to be exactly 40 ms. The new method accurately indicated the value of the simulated reflex latency (40 ms). However, the classical method showed that the lag time between the simulated triggers and the simulated signals was 49 ms. Simulation results illustrated that the cumulated average method is a reliable and more accurate method compared with the classical method. We therefore suggest that the new cumulated average method is able to determine the high rate stimulation induced reflex latencies more accurately than the classical method.Publication Open Access Conspicuity of peripheral zone prostate cancer on computed diffusion-weighted imaging: comparison of cDWI(1500), cDWI(2000), and cDWI(3000)(Hindawi, 2014) Acar, Ömer; Vural, Metin; Ertaş, Gökhan; Onay, Aslıhan; Sağlıcan, Yeşim; Zengingonul, Hale Pinar; Akpek, Sergin; N/A; N/A; Esen, Tarık; Akpek, Sergin; Faculty Member; School of Medicine; 50536; N/AIntroduction and Objective. Disadvantages associated with direct high b-value measurements may be avoided with use of computed diffusion-weighted imaging (cDWI). The purpose of this study is to assess the diagnostic performance of cDWI image sets calculated for high b-values of 1500, 2000, and 3000 s/mm(2). Materials and Methods. Twenty-eight patients who underwent multiparametric MRI of the prostate and radical prostatectomy consecutively were enrolled in this retrospective study. Using a software developed at our institute, cDWI 1500, cDWI 2000, and cDWI 3000 image sets were generated by fitting a monoexponential model. Index lesions on cDWI image sets were scored by two radiologists in consensus considering lesion conspicuity, suppression of background prostate tissue, distortion, image set preferability, and contrast ratio measurements were performed. Results. Lesion detection rates are the same for computed b-values of 2000 and 3000 s/ mm 2 and are better than b-values of 1500 s/ mm(2). Best lesion conspicuity and best background prostate tissue suppression are provided by cDWI(3000) image set. cDWI(2000) image set provides the best zonal anatomical delineation and less distortion and was chosen as the most preferred image set. Average contrast ratio measured on these image sets shows almost a linear relation with the b-values. Conclusion. cDWI 2000 image set with similar conspicuity and the same lesion detection rate, but better zonal anatomical delineation, and less distortion, was chosen as the preferable image set.