Browsing by Quartile "Q4"

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Open Access
25-hydroxyvitamin D levels are low but not associated with disease activity in chronic spontaneous urticaria and depression
(AEPress, 2020) Vurgun, Eren; Güntaş, Gürkan; Kocatürk Göncü, Özgür Emek; Memet, Bachar; Doctor; School of Medicine; Koç University Hospital; 217219; N/A
Aim: to evaluate vitamin D levels in patients with chronic spontaneous urticaria (CSU), depression and both of them, thus to fi nd out whether vitamin D may be a common causative factor of CSU and depression. Methods: thirty patients with CSU, 30 patients with depression, 30 patients with both CSU and depression and 30 healthy volunteers as control group were involved in the study. Serum 25-hydroxyvitamin D (25(OH) D) levels of these groups were measured and compared. Correlations between 25(OH)D levels and the activity of CSU and depression were analyzed. Results: healthy controls' 25(OH)D levels (17.2±8.8 ng/mL) were higher than patients with CSU (9.1±5.1 ng/mL), depression (8.9±6.1 ng/mL) and CSU with depression (7.7±4.7 ng/mL) (p<0.001, p<0.001 and p<0.001, respectively). There were no differences in 25(OH)D levels between CSU patients with and without depression, between depression patients and CSU patients with and without depression (p=0.43, p=0.82 and p=0.92, respectively). There were no correlations between 25(OH)D levels and the activity of CSU or depression (p=0.99 and p=0.76, respectively). Conclusion: Lower 25(OH)D levels in CSU and/or depression may appear as a secondary phenomenon, which means being result of these diseases rather than the cause (Tab. 1, Fig. 2, Ref. 41).
Open Access
3D engineered neural co-culture model and neurovascular effects of marine fungi-derived citreohybridonol
(American Institute of Physics (AIP) Publishing, 2022) Polat, İrem; Özkaya, Ferhat Can; El-Neketi, Mona; Ebrahim, Weaam; Şengül, Gülgün; Department of Mechanical Engineering; Sokullu, Emel; Sarabi, Misagh Rezapour; Taşoğlu, Savaş; Faculty Member; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); School of Medicine; Graduate School of Sciences and Engineering; College of Engineering; 163024; N/A; 291971
Marine-based biomolecules are emerging metabolites that have gained attention for developing novel biomaterials, drugs, and pharmaceutical in vitro platforms. Here, we developed a 3D engineered neural co-culture model via a 3D prototyped sliding frame-platform for multi-step UV lithography and investigated the neurovascular potential of citreohybridonol in neuroblastoma treatment. Citreohybridonol was isolated from a sponge-derived fungus Penicillium atrovenetum. The model was characterized by Fourier-transform infrared spectroscopy and scanning electron microscopy analysis. Human umbilical cord vein endothelial cells (HUVECs) and neuroblastoma (SH-SY5Y) cell lines were encapsulated in gelatin methacrylate (GelMA) with and without citreohybridonol. The effect of citreohybridonol on the proliferation capacity of cells was assessed via cell viability and immunostaining assays. GelMA and 3D culture characterization indicated that the cells were successfully encapsulated as axenic and mixed with/without citreohybridonol. The cytotoxic test confirmed that the 3D microenvironment was non-toxic for cultural experiments, and it showed the inhibitory effects of citreohybridonol on SH-SY5Y cells and induced the proliferation of HUVECs. Finally, immunohistochemical staining demonstrated that citreohybridonol suppressed SH-SY5Y cells and induced vascularization of HUVECs in mixed 3D cell culture.
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5-HT causes venodilatation to reduce blood pressure in the rat
(Karger, 2016) Seitz, Bridget M.; Krieger-Burke, Theresa; Darios, Emma S.; Thompson, Janice M.; Watts, Stephanie W.; N/A; Orer, Hakan S.; Faculty Member; School of Medicine; 53477
N/A
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A 3-year-old child with multi-drug resistant epilepsy responding to pharmacological and nonpharmacological treatments
(Taylor & Francis, 2022) Yıldırım, Canan; N/A; Coşkun, Yeşim; Doctor; N/A; Koç University Hospital; N/A
Introduction: Despite the development of new antiseizure drugs (ASDs), around one third of epilepsy patients become refractory to treatment or experience adverse events due to ASDs. Therefore, discovery of new ASDs and new therapy options are crucial to improve the quality of life. Herein, we report a 3-year-old child with multi-drug resistant epilepsy caused by perinatal asphyxia whose seizures were reduced by 90% after the introduction of ketogenic diet, vagal nerve stimulation (VNS) AspireSR (SR-seizure response) and oral cannabidiol.Case presentation: A 9-month-old female infant had a history of multidrug resistant epilepsy due to perinatal asphyxia. At admission, she was experiencing up to 20-25 seizures per day lasting for 2-3 minutes. In addition to antiseizure drugs (ASDs), she was put on ketogenic diet (KD), vagal nerve stimulation (VNS) aspire seizure response (AspireSR) was inserted and oral cannabidiol (CBD) was started sequentially. Using pharmacological and nonph armacological therapies, her seizures have been reduced by 90%.Conclusion: The concurrent use of pharmacological and nonpharmacological therapies may be beneficial to improve seizures in infants with multi- Furthermore, our patient is the youngest child inserted VNS AspireSR in Turkey.
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A 52-year-old man with progressive weakness and incontinence
(Sage, 2022) Danyeli, Ayca Ersen; Bozkurt, Subutay Berke; Uysal, Sanem Pinar; Akpek, Sergin; Kahyaoglu, Bulent; Peker, Selcuk; Altıntaş, Ayşe; Aygün, Murat Serhat; Akay, Olga Meltem; Üre, Ümit Barbaros; Ferhanoğlu, Ahmet Burhan; Faculty Member; Teaching Faculty; Faculty Member; Faculty Member; Faculty Member; School of Medicine; School of Medicine; School of Medicine; School of Medicine; School of Medicine; Koç University Hospital; 11611; 291692; 170966; N/A; 18320
Here we report a challenging case of a 52-year-old man presenting with subacute constipation, urinary retention, impotence, absent Achilles reflexes, and hypoesthesia in S2-S5 dermatomes. We review the clinical decision-making as the symptoms evolved and diagnostic testing changed over time. Once the diagnosis is settled, we discuss the sign and symptoms, additional diagnostic tools, treatment options and prognosis.
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A case of chordoma invading multiple neuroaxial bones: report of ten years follow up
(Turkish Neurosurgery Society, 2013) Aydın, Ahmet Levent; Sasani, Mehdi; Öktenoğlu, Bekir Tunç; Solaroğlu, İhsan; Özer, Ali Fahir; Faculty Member; Faculty Member; School of Medicine; School of Medicine; 102059; 1022
Aim: Chordoma is a rare, slow-growing primary malignant tumor of the axial skeleton, arising from the embryonic cells of primitive notochord. Chordomas may arise at different sites of the vertebral column simultaneously or more probably they may metastasise along the neural axis insidiously. Recurrence despite radical surgery and following adjuvant therapy is possible. MaterIal and Methods: A 46-year-old female patient presented weakness and numbness of the lower extremities. She was operated for clivus chordoma five years ago at another institute. Results: First the patient underwent surgery for resection of the tumor at the cervical region. a second surgery was performed to resect tumor on the foramen magnum and at the C1 level. Histologic examination of the removed vertebra confirmed the diagnosis of chordoma involving the vertebral body. Radiotherapy was administered after the second surgery. Follow-up neurological and radiological examinations revealed no abnormal neurological symptoms 2,5 years after second surgery. There were no distant organ metastases. ConclusIon: A patient with diagnosed chordoma of the spine must be investigated with MRI of other regions of the neuraxis to exclude second or even third source of chordoma metastases. In metastatic chordoma cases, radical or gross total resection should be performed for each lesion but if complete surgical resections are impossible, preoperative or postoperative radiation therapy should be planned to improve life expectancy. / AMAÇ: Kordoma, omurganın ender rastlanan, yavaş ilerleyen malign karakterli bir tümörüdür. Primitif notokordun embryo hücrelerinden köken alır. Omurganın farklı bölgelerinde, birbirinden bağımsız kordoma odakları eş zamanlı olarak gelişmeye başlayabilir. Fakat daha sıklıkla, birinci tümör odağından kaynaklanan metastatik kordoma lezyonları tüm nöral aks boyunca yayılabilir. Radikal cerrahiye ve ek onkolojik tedaviye rağmen rekürens sık görülür. YÖNTEM ve GEREÇLER: Bu sunumda tartışılan 46 yaşındaki kadın hasta, bacaklarında kuvvet ve his kaybı şikayetiyle kliniğimize başvurmuştur. Hasta, beş yıl önce, ayrı bir merkezde klivus kordoması tanısıyla opere edilmiştir. BULGULAR: Hasta öncelikle servikal bölgedeki tümör için opere edilmiştir. İkinci seansta foramen magnum ve C1 seviyesindeki tümör çıkarılmıştır. Patolojik inceleme sonucunda, omurga cismini tutan kordoma lezyonu tanısı konmuştur. İkinci cerrahi seansından sonra hasta radyoterapiye yönlendirilmiştir. Bu tedaviden ikibuçuk yıl sonra yapılan değerlendirmede, hastanın nörolojik muayenesinde progresyon gözlenmemiştir. SONUÇ: Omurganın herhangi bir lokalizasyonunda kordoma tanısı konulan bir hastada, tüm spinal bölge manyetik rezonans görüntüleme (MRG) tetkiki ile incelenmelidir. Bu hastalarda birden fazla kordoma odağına rastlanabilir. Birden fazla odak tespit edilmesi durumunda, her ayrı tümör odağı için rezeksiyon planlanmalıdır. Total rezeksiyonun mümkün olmaması durumunda, yaşam süresini uzatmak için operasyon öncesi ve sonrası dönemlerde radyoterapi uygulanmalıdır.
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A case of pathologic complete response after neoadjuvant triplet chemotherapy for locally advanced colon cancer with mismatch repair enzyme proficiency
(Via Medica, 2023) Kocak, Mehmet Zahid; Cakir, Murat; Kerimoglu, Ulku; Araz, Murat; Eryilmaz, Melek Karakurt; Artac, Mehmet; Yumuk, Perran Fulden; School of Medicine
Patients with potentially resectable colon cancer and expected to have negative margins should undergo resection rather than neoadjuvant chemotherapy. Recent studies have suggested that neoadjuvant immunotherapy may be an option for tumors with mismatch repair enzyme deficiency (dMMR), but standard treatment for locally advanced colon cancer with mismatch repair enzyme proficiency (pMMR) is still unclear. A 37-year-old male patient was diagnosed with clinical stage IIIC (T4b N1a M0) transverse colon cancer. Mismatch repair proteins were proficient. After 3 cycles of oxaliplatin (85 mg/m(2), day 1), irinotecan (150 mg/m2, IV, day 1), leucovorin (200 mg/m(2), IV, day 1), and 5-fluorouracil (3000 mg/m(2), 46 hours of continuous infusion initiating from day 1), there was a remarkable reduction in the tumoral mass on the abdominal computed tomography. A right hemicolectomy was performed. A pathologic complete response was obtained. Although there is no consensus on which patients are suitable for neoadjuvant therapy in pMMR locally advanced colon cancer, triplet chemotherapy may be a reasonable option in selected patients.
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A case with new-onset neuromyelitis optica spectrum disorder following COVID-19 mRNA BNT162b2 vaccination
(Lippincott Williams & Wilkins, 2022) Afşar, Nazire; N/A; N/A; N/A; Çalışkan, İlay; Buluş, Eser; Polat-Altıntaş, Sevgi; Master Student; Doctor; Researcher; N/A; N/A; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; School of Medicine; N/A; N/A; N/A; 150017
Introduction: In the midst of the coronavirus disease of 2019 pandemic, active immunization by effective vaccination gained utmost importance in terms of global health. The messenger RNA (mRNA) vaccines are novel strategies requiring clinical surveillance for adverse events. Case Report: We report a 43-year-old previously healthy female with an optic neuritis attack 24 hours following immunization with the second dose of coronavirus disease of 2019 mRNA BNT162b2 vaccine. A second transverse myelitis attack together with an elevated anti-AQP-4 antibody titer confirmed the diagnosis of neuromyelitis optica spectrum disorder. Conclusion: Our case identifies the BNT162b2 vaccine as a possible trigger for neuromyelitis optica spectrum disorder. This rare and potentially coincidental event has no implications for vaccine administration practices. However, further research is needed to elucidate the effects of mRNA vaccines on humoral and cell-mediated immunity.
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A challenge for peptide coarse graining: transferability of fragment-based models
(Wiley-V C H Verlag Gmbh, 2011) Villa, Alessandra; Peter, Christine; N/A; Department of Mechanical Engineering; Engin, Özge; Sayar, Mehmet; Master Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 109820
Peptides are highly promising building blocks for design and development of novel materials with potential application areas ranging from drug design to biotechnology. The necessity to understand the structural and thermodynamic properties of these complex materials has led to a dramatic increase in the development of computational techniques geared specifically towards peptide-based systems. Both all-atom (AA) and coarse-grained (CG) simulations of such materials have become extremely important, where the latter is an indispensable tool for reaching the time and length scales relevant to the experiments. Here, we review different approaches and discuss the challenges in the development of CG models for peptides. In particular, we concentrate on the transferability of fragment-based CG models. We analyze the transferability of a solvent-free CG model developed to model hydrophobic phenylalanine dipeptides (FF) in water. Here, we employ the same CG strategy-with non-bonded potentials based on peptide fragments-to two other hydrophobic dipeptides, valine-phenylalanine (VF) and isoleucine-phenylalanine (IF). In line with the previously developed model, the dipeptides are described by seven beads and the potentials developed for FF (bonded and non-bonded) are directly applied to describe the phenylalanine and backbone atoms, while new potentials are developed to account for the valine and isoleucine sidechains. By comparing AA and CG intra and intermolecular samplings, we show the ability of the CG model to reproduce the conformational behavior and thermodynamic association properties of the corresponding atomistic systems.
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A clinical comparison of home-based and hospital-based exercise programs following arthroscopic capsulolabral repair for anterior shoulder instability
(Human Kinetics Publ Inc, 2020) Atalar, Ata Can; Eren, Şule Meral; Uçak, Ayla; Çerezci, Önder; N/A; Eren, İlker; Canbulat, Nazan; Demirhan, Mehmet; Faculty Member; Faculty Member; Faculty Member; School of Medicine; School of Medicine; School of Medicine; Koc University Hospital; 168021; 58534; 9882
Context: Ideal rehabilitation method following arthroscopic capsulolabral repair surgery for anterior shoulder instability has not been proven yet. Although rapid or slow protocols were compared previously, home- or hospital-based protocols were not questioned before. Objective: The aim of this prospective unrandomized controlled clinical trial is to compare the clinical outcomes of home-based and hospital-based rehabilitation programs following arthroscopic Bankart repair. Design: Non-randomized controlled trial. Setting: Orthopedics and physical therapy units of a single institution. Patients: Fifty-four patients (49 males and 5 females) with an average age of 30.5 (9.1) years, who underwent arthroscopic capsulolabral repair and met the inclusion criteria, with at least 1-year follow-up were allocated into 2 groups: home-based (n = 33) and hospital-based (n = 21) groups. Interventions: Both groups received identical rehabilitation programs. Patients in the home-based group were called for follow-up every 3 weeks. Patients in the hospital-based group admitted for therapy every other day for a total of 6 to 8 weeks. Both groups were followed identically after the eighth week and the rehabilitation program continued for 6 months. Main Outcome Measures: Clinical outcomes were assessed using Disabilities of Arm Shoulder Hand, Constant, and Rowe scores. Mann-Whitney U test was used to compare the results in both groups. Wilcoxon test was used for determining the progress in each group. Results: Groups were age and gender matched (P= .61, P = .69). Average number of treatment sessions was 13.8 (7.3) for patients in the hospital-based group. Preoperative Disabilities of Ann Shoulder Hand (27.46 [11.81] vs 32.53 [16.42], P= .22), Constant (58.23 [14.23] vs 54.17 [10.46], P = .13), and Rowe (51.72 [15.36] vs 43.81 [19.16], P= .12) scores were similar between groups. Postoperative scores at sixth month were significantly improved in each group (P = .001, P = .001, and P = .001). No significant difference was observed between 2 groups regarding clinical scores in any time point. Conclusions: We have, therefore, concluded that a controlled home-based exercise program is as effective as hospital-based rehabilitation following arthroscopic capsulolabral repair for anterior shoulder instability.
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A comparative evaluation of segmental analysis of macular layers in patients with early glaucoma, ocular hypertension, and healthy eyes
(2020) Aksoy, F. E.; Altan, C.; Yılmaz, B. S.; Yılmaz, I; Tunç, U.; Kocamaz, M.; Paşaoğlu, I; N/A; Kesim, Cem; Doctor; Koç University Hospital; 387367
Purpose: To compare macular layer thicknesses between early glaucoma, ocular hypertension, and healthy eyes and to evaluate the accuracy of spectralis optical coherence tomography (OCT) segmentation software in discriminating early glaucoma from ocular hypertension and healthy eyes. Methods: OCT scans were performed using the standard macular and peripapillary retinal nerve fiber layer (pRNFL) protocols on the Spectralis-OCT. The following macular thickness parameters were compared in the inner and outer circles of the Early Treatment Diabetic Retinopathy Study: total macular thickness (MT), retinal nerve fiber layer (mRNFL), ganglion cell layer (mGCL), inner plexiform layer (mIPL), inner nuclear layer (mINL), outer plexiform layer (mOPL), outer nuclear layer (mONL) and ganglion cell complex (mGCC: sum of mRNFL, mGCL, and mIPL). Sectors and layers with the best area under the receiver operating characteristic curve (AUC) were determined and compared between groups. Results: Of a total of 200 eyes included in this study, 64 eyes had primary open angle glaucoma, 69 had ocular hypertension, and 67 were healthy. Peripapillary RNFL was significantly thinner in the early glaucoma group (P < 0.05). For the macular variables, there was a significant reduction in the MT, mGCC, mRNFL, mGCL, and mIPL thicknesses in the early glaucoma group; while there were no statistically significant differences between the ocular hypertension and control groups (P > 0.05). For distinguishing early glaucoma from normal eyes, AUCs for mGCC, mGCL, and mRNFL were similar to the pRNFL; and for early glaucoma and ocular hypertension, AUCs for mGCC, mGCL mRNF and mIPL were comparable to the pRNFL. Conclusion: Macular segmentation can assist in the early diagnosis of glaucoma as a complementary study to pRNFL analysis.
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A comparative study on thyroid function in alzheimer's disease: results from a Turkish multi-centre study
(Journal Neurological Sciences, 2015) Yılmaz, Gökhan; Erbayraktar, Zübeyde; Evlice, Ahmet; Genç, Metin; Aras, Sevgi; Avcı, Aslıhan; Yener, Görsev; Ulusu, Nuriye Nuray; Faculty Member; School of Medicine; 6807
Alzheimer's disease is a very severe degenerative disease that affects brain function. Neuronal loss, accumulation of extracellular amyloid beta containing plaques and accumulation of intracellular (tau) neurofibrillary tangles are the hallmarks of this disease. We aim to investigate serum thyroid function tests in Alzheimer's disease, in addition to other dementias, and geriatric Turkish patients. We evaluated patients from Ankara, Dokuz Eylul, Cukurova University Hospitals. 357 female and male geriatric subjects were enrolled. All the cases were selected from three different geographical regions irrespective of sex and socioeconomic status. In this study, we evaluated the results of thyroid functions in Alzheimer disease patients as well as in other dementias and geriatric patients. In patients from Ankara, Central Anatolia region, no significant difference between groups regarding the routine control of biochemical parameters was observed. However, thyroid function results revealed that hypothyroidism in Alzheimer's disease patients from Mediterranean region, Adana and Aegean region, Izmir is a recurrent medical condition and is often an embedded side of the normal aging process. We concluded that currently, routine thyroid functions tests should be a part of all geriatric patients for screening presymptomatic Alzheimer's disease. There might be an interplay between reduced thyroid function and Alzheimer's disease that could be exploited for diagnostic purposes.
Open Access
A comparison of glycemic parameters and their relationship with C-peptide and Proinsulin levels during partial remission and non-remission periods in children with type 1 diabetes mellitus-a cross-sectional study
(BioMed Central, 2021) Çakır, Esra Papatya; Yeşiltepe Mutlu, Rahime Gül; Çapacı, Merve; Can, Ecem; Gökçe, Tuğba; Bayrakçı, Gizem; Muradoğlu, Serra Küpçüoğlu; İncir, Said; Hatun, Şükrü; Faculty Member; Faculty Member; School of Medicine; Koç University Hospital; 153511; N/A; N/A; N/A; N/A; N/A; N/A; 153504
Background: currently, there is a lack of data relating to glycemic parameters and their relationship with C-peptide (CP) and proinsulin (PI) during the partial remission period (PRP) in type 1 diabetes mellitus (T1D). The aim of this study was to evaluate glycemic parameters in children with T1D who are in the PRP using intermittently scanned continuous glucose monitoring systems (isCGMS) and to investigate any relationships between CP and PI levels. Methods: the study included 21 children who were in the PRP and 31 children who were not. A cross-sectional, non-randomized study was performed. Demographic, clinical data were collected and 2 week- isCGMS data were retrieved. Results: the Serum CP showed a positive correlation with time-in-range in the PRP (p:0.03), however PI showed no correlations with glycemic parameters in both periods. The Serum CP and PI levels and the PI:CP ratio were significantly higher in the PRP group than in the non-PRP group. In the non-PRP group, the PI level was below 0.1 pmol/L (which is the detectable limit) in only 2 of the 17 cases as compared with none in the PRP group. Similarly, only 2 of the 17 children in the non-PRP group had CP levels of less than 0.2 nmol / L, although both had detectable PI levels. Overall time-in-range (3. 9-1.0 mmol/L) was significantly high in the PRP group. In contrast, the mean sensor glucose levels, time spent in hyperglycemia, and coefficient of variation levels (32.2vs 40.5%) were significantly lower in the PRP group. Conclusions: although the mean glucose and time in range during the PRP was better than that in the non-PRP group, the glycemic variability during this period was not as low as expected. While the CP levels showed an association with TIR during the PRP, there was no correlation between PI levels and glycemic parameters. Further studies are needed to determine if PI might prove to be a useful parameter in clinical follow-up.
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A computational biomechanical investigation of posterior dynamic instrumentation: combination of dynamic rod and hinged (dynamic) screw
(Asme, 2014) Kiapour, Ali; Goel, Vijay K.; N/A; N/A; Erbulut, Deniz Ufuk; Öktenoğlu, Bekir Tunç; Özer, Ali Fahir; Researcher; Faculty Member; School of Medicine, College of Engineering; School of Medicine; 37661; 220898; 1022
Currently, rigid fixation systems are the gold standard for degenerative disk disease treatment. Dynamic fixation systems have been proposed as alternatives for the treatment of a variety of spinal disorders. These systems address the main drawbacks of traditional rigid fixation systems, such as adjacent segment degeneration and instrumentation failure. Pedicle-screw-based dynamic stabilization (PDS) is one type of these alternative systems. The aim of this study was to simulate the biomechanical effect of a novel posterior dynamic stabilization system, which is comprised of dynamic (hinged) screws interconnected with a coiled, spring-based dynamic rod (DSDR), and compare it to semirigid (DSRR and RSRR) and rigid stabilization (RSRR) systems. A validated finite element (FE) model of L1-S1 was used to quantify the biomechanical parameters of the spine, such as range of motion, intradiskal pressure, stresses and facet loads after single-level instrumentation with different posterior stabilization systems. The results obtained from in vitro experimental intact and instrumented spines were used to validate the FE model, and the validated model was then used to compare the biomechanical effects of different fixation and stabilization constructs with intact under a hybrid loading protocol. The segmental motion at L4-L5 increased by 9.5% and 16.3% in flexion and left rotation, respectively, in DSDR with respect to the intact spine, whereas it was reduced by 6.4% and 10.9% in extension and left-bending loads, respectively. After instrumentation-induced intradiskal pressure at adjacent segments, L3-L4 and L5-S1 became less than the intact in dynamic rod constructs (DSDR and RSDR) except in the RSDR model in extension where the motion was higher than intact by 9.7% at L3-L4 and 11.3% at L5-S1. The facet loads were insignificant, not exceeding 12N in any of the instrumented cases in flexion. In extension, the facet load in DSDR case was similar to that in intact spine. The dynamic rod constructions (DSDR and RSDR) led to a lesser peak stress at screws compared with rigid rod constructions (DSRR and RSRR) in all loading cases. A dynamic construct consisting of a dynamic rod and a dynamic screw did protect the adjacent level from excessive motion.
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A critical analysis of low molecular weight heparin use during pregnancy in a tertiary referral centre
(Taylor & Francis, 2014) Kutuk, M. S.; Ozgun, M. T.; Uludag, S.; Dolanbay, M.; Tas, M.; Terzioğlu, Ayşecan; Faculty Member; School of Nursing; 177870
The aim of this study was to analyse low molecular weight heparin (LMWH) use during pregnancy in terms of patient evaluation, treatment indication and social and financial costs. This was a retrospective analysis of patients using LMWH in their pregnancies. A total of 147 women were included in the study. The most common indications were thrombophilia (55/147, 37.4%); recurrent pregnancy loss (RPL); (47/147, 32.0%) and previous single pregnancy loss (18/147, 12.2%). In the RPL group, 53.1% of patients were not evaluated with standard tests; 31.9% of women were incompletely evaluated and 15% were properly evaluated. Out of 104 women screened for thrombophilia, 32 (32/104, 30.8%) were tested during pregnancy. Despite published guidelines and increasing scientific evidence against their use in some indications, LMWHs are prescribed widely during pregnancy for a variety of indications. Public and healthcare providers' education to change this attitude should be implemented.
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A kernel-based multilayer perceptron framework to identify pathways related to cancer stages
(Springer International Publishing Ag, 2023) Mokhtaridoost, Milad; Department of Industrial Engineering; Soleimanpoor, Marzieh; Gönen, Mehmet; Department of Industrial Engineering; Graduate School of Sciences and Engineering; College of Engineering
Standard machine learning algorithms have limited knowledge extraction capability in discriminating cancer stages based on genomic characterizations, due to the strongly correlated nature of high-dimensional genomic data. Moreover, activation of pathways plays a crucial role in the growth and progression of cancer from early-stage to latestage. That is why we implemented a kernel-based neural network framework that integrates pathways and gene expression data using multiple kernels and discriminates early- and late-stages of cancers. Our goal is to identify the relevant molecular mechanisms of the biological processes which might be driving cancer progression. As the input of developed multilayer perceptron (MLP), we constructed kernel matrices on multiple views of expression profiles of primary tumors extracted from pathways. We used Hallmark and Pathway Interaction Database (PID) datasets to restrict the search area to interpretable solutions. We applied our algorithm to 12 cancer cohorts from the Cancer Genome Atlas (TCGA), including more than 5100 primary tumors. The results showed that our algorithm could extract meaningful and disease-specific mechanisms of cancers. We tested the predictive performance of our MLP algorithm and compared it against three existing classification algorithms, namely, random forests, support vector machines, and multiple kernel learning. Our MLP method obtained better or comparable predictive performance against these algorithms.
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A LES/PDF simulator on block-structured meshes
(Taylor & Francis Ltd, 2019) Pope, Stephen B.; N/A; Department of Mechanical Engineering; Türkeri, Hasret; Muradoğlu, Metin; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 46561
A block-structured mesh large-eddy simulation (LES)/probability density function (PDF) simulator is developed within the OpenFOAM framework for computational modelling of complex turbulent reacting flows. The LES/PDF solver is a hybrid solution methodology consisting of (i) a finite-volume (FV) method for solving the filtered mass and momentum equations (LES solver), and (ii) a Lagrangian particle-based Monte Carlo algorithm (PDF solver) for solving the modelled transport equation of the filtered joint PDF of compositions. Both the LES and the PDF methods are developed and combined to form a hybrid LES/PDF simulator entirely within the OpenFOAM framework. The in situ adaptive tabulation method [S.B. Pope, Computationally efficient implementation of combustion chemistry using in situ adaptive tabulation, Combust. Theory Model. 1 (1997), pp. 41-63; L. Lu, S.R. Lantz, Z. Ren, and B.S. Pope, Computationally efficient implementation of combustion chemistry in parallel PDF calculations, J. Comput. Phys. 228 (2009), pp. 5490-5525] is incorporated into the new LES/PDF solver for efficient computations of combustion chemistry with detailed reaction kinetics. The method is designed to utilise a block-structured mesh and can readily be extended to unstructured grids. The three-stage velocity interpolation method of Zhang and Haworth [A general mass consistency algorithm for hybrid particle/finite-volume PDF methods, J. Comput. Phys. 194 (2004), pp. 156-193] is adapted to interpolate the LES velocity field onto particle locations accurately and to enforce the consistency between LES and PDF fields at the numerical solution level. The hybrid algorithm is fully parallelised using the conventional domain decomposition approach. A detailed examination of the effects of each stage and the overall performance of the velocity interpolation algorithm is performed. Accurate coupling of the LES and PDF solvers is demonstrated using the one-way coupling methodology. Then the fully two-way coupled LES/PDF solver is successfully applied to simulate the Sandia Flame-D, and a turbulent non-swirling premixed flame and a turbulent swirling stratified flame from the Cambridge turbulent stratified flame series [M.S. Sweeney, S. Hochgreb, M.J. Dunn, and R.S. Barlow, The structure of turbulent stratified and premixed methane/air flames I: Non-swirling flows, Combust. Flame 159 (2012), pp. 2896-2911; M.S. Sweeney, S. Hochgreb, M.J. Dunn, and R.S. Barlow, The structure of turbulent stratified and premixed methane/air flames II: Swirling flows, Combust. Flame 159 (2012), pp. 2912-2929]. It is found that the LES/PDF method is very robust and the results are in good agreement with the experimental data for both flames.
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A metal nitride carbodiimide with a stuffed skutterudite-type structure: synthesis, crystal structure and ir spectra of (BA6N 5/6)2[NBN4][CN2]6
(Walter de Gruyter, 2007) Reckeweg, Olaf; Disalvo, Francis J.; Department of Chemistry; Somer, Mehmet Suat; Faculty Member; Department of Chemistry; College of Sciences; 178882
Coppery-red, transparent single crystals of (Ba6N 5/6)2[NbN4][CN2]6 [NbN4] [CN2]6 (Im3̄, no. 204, a = 1125.83(3) pm, Z = 2) are obtained by the reaction of Ba2N and ZnCN2 with the container walls of the arc-welded Nb ampoules at 1100 K. The title compound assumes a stuffed skutterudite-type structure in which edge-sharing (Ba6N5/6) octahedra form large voids which are occupied by either [NbN4] tetrahedra or by [N=C=N]2- units with symmetric C=N bond lengths of d = 121.8(6) pm but a bond angle deviating significantly from linearity (∠(N-C-N) = 175.3(9)°). The IR spectra corroborate this crystallographic result by the fact that all fundamental vibrations are visible in the IR spectrum [v1 = 1262 (symmetric stretching mode); v2 = 1957/2009 (antisymmetric stretching mode); v3 = 611/633/653 cm-1 (bending modes)], which is symmetry forbidden for [N=C=N]2- units having D∞h symmetry but expected for the C2v symmetry found in the title compound.
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A microstructure-sensitive model for simulating the impact response of a high-manganese austenitic steel
(Asme, 2016) N/A; N/A; Department of Mechanical Engineering; Mirzajanzadeh, Morad; Canadinç, Demircan; PhD Student; Faculty Member; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 23433
Microstructurally informed macroscopic impact response of a high-manganese austenitic steel was modeled through incorporation of the viscoplastic self-consistent (VPSC) crystal plasticity model into the ANSYS LS-DYNA nonlinear explicit finite-element (FE) frame. Voce hardening flow rule, capable of modeling plastic anisotropy in microstructures, was utilized in the VPSC crystal plasticity model to predict the micromechanical response of the material, which was calibrated based on experimentally measured quasi-static uniaxial tensile deformation response and initially measured textures. Specifically, hiring calibrated Voce parameters in VPSC, a modified material response was predicted employing local velocity gradient tensors obtained from the initial FE analyses as a new boundary condition for loading state. The updated micromechanical response of the material was then integrated into the macroscale material model by calibrating the Johnson-Cook (JC) constitutive relationship and the corresponding damage parameters. Consequently, we demonstrate the role of geometrically necessary multi-axial stress state for proper modeling of the impact response of polycrystalline metals and validate the presented approach by experimentally and numerically analyzing the deformation response of the Hadfield steel (HS) under impact loading.
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A mobile application for symptom management in patients with breast cancer
(Oncology Nursing Society, 2022) Seven M.; N/A; N/A; Department of Computer Engineering; N/A; Paşalak, Şeyma İnciser; Bağçivan, Gülcan; Özkasap, Öznur; Selçukbiricik, Fatih; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Computer Engineering; Graduate School of Health Sciences; School of Nursing; College of Engineering; School of Medicine; 125009; 261422; 113507; 202015
OBJECTIVES: To evaluate the effect of a symptom management mobile application on quality of life and symptom severity in women with breast cancer undergoing chemotherapy. SAMPLE & SETTING: This parallel randomized pilot study consisted of women with breast cancer admitted to oncology outpatient clinics between November 2019 and January 2021 in Turkey. METHODS & VARIABLES: Participants (N = 40) were randomly assigned to the intervention (n = 20) or control group (n = 20). The intervention group used the mobile application in conjunction with usual care. The control group received usual care. Participants were assessed during the first, third, and last chemotherapy cycles. Data were collected using the European Organisation for Research and Treatment of Cancer Quality-of-Life Questionnaire–Core 30 and the Edmonton Symptom Assessment System. RESULTS: During the study, the decrease in general health and physical functioning and the increase in the severity of depression/sadness in the intervention group were statistically lower than in the control group. IMPLICATIONS FOR NURSING: The use of a mobile application for symptom management may promote general well-being and physical function and may alleviate symptoms of depression/sadness in women with breast cancer undergoing chemotherapy. Further studies are needed to evaluate the application in clinical settings with larger groups.