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Publication Open Access Recommendations for clinical decision-making in children with type 1 diabetes and celiac disease: type 1 diabetes and celiac disease joint working group report(Galenos Yayınevi, 2022) Dalgıç, B.; Gökşen, D.; Aydoğdu, S.; Savaş, Erdeve Ş.; Kuloğu, Z.; Doğan, Y.; Aycan, Z.; Keser, A.; Beşer, Ö.F.; Özbek, M.N.; Bideci, A.; Ertem, D.; Evliyaoğlu, O.; Eliüz Tipici, B.; Gökçe, T.; Muradoğlu, S.; Koca, T.; Tütüncüler, F.; Baş, F.; Darendeliler, F.; Selimoğlu, M.A.; Hatun, Şükrü; Yeşiltepe Mutlu, Rahime Gül; Kızılkan, Nuray Uslu; Taşkın, Orhun Çığ; Faculty Member; Faculty Member; Faculty Member; School of Medicine; Koç University Hospital; 153504; 153511; 221274; 166686It is well-known that in children with type 1 diabetes (T1D), the frequency of Celiac disease (CD) is increased due to mechanisms which are not fully elucidated but include autoimmune injury as well as shared genetic predisposition. Although histopathologic examination is the gold standard for diagnosis, avoiding unnecessary endoscopy is crucial. Therefore, for both clinicians and patients’ families, the diagnosis of CD remains challenging. In light of this, a joint working group, the Type 1 Diabetes and Celiac Disease Joint Working Group, was convened, with the aim of reporting institutional data and reviewing current international guidelines, in order to provide a framework for clinicians. Several controversial issues were discussed: For CD screening in children with T1D, regardless of age, it is recommended to measure tissue transglutaminase-immunoglobulin A (tTG-IgA) and/or endomysial-IgA antibody due to their high sensitivity and specificity. However, the decision-making process based on tTG-IgA titer in children with T1D is still debated, since tTG-IgA titers may fluctuate in children with T1D. Moreover, seronegativity may occur spontaneously. The authors’ own data showed that most of the cases who have biopsy-proven CD had tTG-IgA levels 7-10 times above the upper limit. The decision for endoscopy based solely on tTG-IgA levels should be avoided, except in cases where tTG-IgA levels are seven times and above the upper limit. A closer collaboration should be built between divisions of pediatric endocrinology and gastroenterology in terms of screening, diagnosis and follow-up of children with T1D and suspicious CD.Publication Open Access Liver transplantation in hepatic myelopathy(Kare Yayıncılık, 2022) Acar, Sencan; Dinçkan, Ayhan; Akyıldız, Murat; Faculty Member; School of Medicine; 123080Hepatic myelopathy (HMy) is a rare neurological complication of liver cirrhosis that involves spastic paraplegia caused by lateral cord demyelination especially due to the accumulation of some metabolites such as ammonia and manganese. We report a young adult woman presenting with spasticity and paraparesis in extremities after intrahepatic portosystemic shunting (TIPS) application and underwent deceased liver transplantation (LT). A 39-year-old woman underwent deceased LT because of cryptogenic liver cirrhosis. She underwent a TIPS procedure 5 years ago. After that, hepatic encephalopathy and spasticity appeared. She was on the waiting list for 3 years. Neurological findings after LT significantly decreased, but did not return to normal. After the emergence of neurological findings, the earlier LT can provide improvement in neurological findings.Publication Open Access Early/fast VLF events produced by the quiescent heating of the lower ionosphere by thunderstorms(American Geophysical Union (AGU), 2017) Kabirzadeh, R.; Marshall, R. A.; Department of Electrical and Electronics Engineering; İnan, Umran Savaş; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 177880Large and easily distinguishable perturbations of the VLF transmitter signals due to interactions with thundercloud-driven ionospheric modifications have been observed and studied for about three decades. These events are called "early/fast VLF" or "early VLF" events due to their immediate detection (similar to 20 ms) after the causative lightning flash on the ground and the fast rise time of the perturbed signal. Despite many years of study, the physical mechanisms responsible for these perturbations are still under investigation. Modifications of the sustained heating level of the ionosphere due to a lightning flash has been previously proposed as the causative mechanism of early/fast VLF events. The perturbations predicted by this mechanism, however, have been much smaller than experimental observations of 0.2-1 dB or higher. In this study, by using an improved 3-D thundercloud electrostatic upward coupling model which uses a realistic geomagnetic field, we find that the sustained heating model can predict perturbations that are consistent with reported experimental observations. Modifications in the quiescent heating of the lower ionosphere by thundercloud fields by individual lightning flashes may thus account for some observations of early/fast VLF events. Large and easily distinguishable perturbations of the VLF transmitter signals due to interactions with thundercloud-driven ionospheric modifications have been observed and studied for about three decades. These events are called "early/fast VLF" or "early VLF" events due to their immediate detection (similar to 20 ms) after the causative lightning flash on the ground and the fast rise time of the perturbed signal. Despite many years of study, the physical mechanisms responsible for these perturbations are still under investigation. Modifications of the sustained heating level of the ionosphere due to a lightning flash has been previously proposed as the causative mechanism of early/fast VLF events. The perturbations predicted by this mechanism, however, have been much smaller than experimental observations of 0.2-1 dB or higher. In this study, by using an improved 3-D thundercloud electrostatic upward coupling model which uses a realistic geomagnetic field, we find that the sustained heating model can predict perturbations that are consistent with reported experimental observations. Modifications in the quiescent heating of the lower ionosphere by thundercloud fields by individual lightning flashes may thus account for some observations of early/fast VLF events.Publication Open Access Generation of transgene-free iPSC lines from three patients with Friedreich's ataxia (FRDA) carrying GAA triplet expansions in the first intron of FXN gene(Elsevier, 2021) Kelekçi, Simge; Uğurlu Çimen, Deniz; Demir, Ata Berk; Özçimen, Burcu; Yıldız, Abdullah Burak; Karakuş, Mehmet Batuhan; Börklü Yücel, Esra; Önder, Tamer Tevfik; PhD Student; Undergraduate Student; Other; Faculty Member; Graduate School of Health Sciences; School of Medicine; Koç University Hospital; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 42946Friedreich's ataxia (FRDA) is a rare neurodegenerative disorder which is caused by triplet repeat expansion (GAA) in the first intron of FXN gene. In this present study, we generated induced pluripotent stem cells (iPSC) lines from fibroblasts of three unrelated FRDA patients using integration-free episomal vectors. All iPSC lines express the pluripotency markers such as OCT4 and SSEA4, display normal karyotypes and can differentiate into all three germ layers via in vivo teratoma formation assay.Publication Open Access Irritable bowel syndrome demographics: a Middle Eastern multinational cross-sectional study(Iranian Association of Gastroenterology and Hepatology, 2022) Alavinejad, Pezhman; Ghanavati, Parvin Mousavi; Alboraie, Mohamed; Emara, Mohamed; Baghaee, Siamak; Daryani, Naser Ebrahimi; Farsi, Farnaz; Hajiani, Eskandar; Hashemi, Seyed Jalal; Lak, Elena; Taheri, Yasaman; Dangi, Abhijit; Baran, Bülent; Faculty Member; School of Medicine; Koç University Hospital; 167583Background: irritable bowel syndrome (IBS) is the most frequent functional gastrointestinal (GI) disorder. In this study, we aimed to evaluate the different aspects of IBS among Middle Eastern residents. Methods: during the study period, patients attending gastroenterology clinics of nine tertiary referral centers in four Middle Eastern couturiers (Iran, Egypt, Kuwait, and Turkey) were evaluated by Rome IV diagnostic criteria, and those who fulfilled the diagnostic criteria of IBS were asked to fill in a questionnaire covering different demographics and clinical aspects. Results: overall, during a 6-month period, 509 patients with IBS were included. 41.3% of the participants were male (210 patients), and 37.4% of them had academic education. 50% of the participants were Caucasian, and 34% were Arab, and originally, they were citizens of 18 countries. 77.4% of the participants were residents of subtropical areas, while 22.2% were living in temperate regions. The average age of the participants during the first presentation in subtropical and temperate areas were 38.4 ± 12.19 and 38.06 ± 12.18 years, respectively (P = 0.726). The most common subtypes of IBS in subtropical areas were unclassified (IBS-U, 44.4%), constipation dominant (IBS-C, 27.6%), mixed pattern (IBS-M, 21%), and diarrhea dominant (IBS-D, 6.8%) in descending order while in temperate areas the most common subtypes were IBS-U (43.3%), and IBS-D (22.1%), respectively (P < 0.001). Besides abdominal pain, the most common symptom of patients in each region was bloating (62.2% and 68.1%, respectively, P = 0.246). The rate of depression and anxiety were significantly higher among the residents of temperate areas in comparison with subtropical regions (41.6% vs. 16.5% and 80.5% vs. 58.4%, respectively, P < 0.001). Conclusion: although the average age of IBS presentation is the same in subtropical and temperate areas, it seems that in temperate areas, the rate of IBS-D is more prevalent than in subtropical regions. The rate of anxiety and depression are significantly higher among those who searched social media and the internet to get information about their problems.Publication Open Access A stochastic representation for mean curvature type geometric flows(Institute of Mathematical Statistics (IMS), 2003) Touzi, N.; Department of Mathematics; Soner, Halil Mete; Faculty Member; Department of Mathematics; College of Administrative Sciences and EconomicsA smooth solution {Gamma(t)}(tis an element of[0,T]) subset of R-d of a parabolic geometric flow is characterized as the reachability set of a stochastic target problem. In this control problem the controller tries to steer the state process into a given deterministic set T with probability one. The reachability set, V(t), for the target problem is the set of all initial data x from which the state process X-X(v)(t) is an element of T for some control process v. This representation is proved by studying the squared distance function to Gamma(t). For the codimension k mean curvature flow, the state process is dX(t) = root2P dW(t), where W(t) is a d-dimensional Brownian motion, and the control P is any projection matrix onto a (d - k)-dimensional plane. Smooth solutions of the inverse mean curvature flow and a discussion of non smooth solutions are also given.Publication Open Access What is the current role and what are the prospects of the robotic approach in liver surgery?(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Sijberden, J.P.; Hilal, M.A.; Bozkurt, Emre; Koç University HospitalRobotic liver surgery is being applied with increasing frequency. Comparable, and in specific settings superior, perioperative outcomes compared to laparoscopic liver surgery have been reported. In its current form, the most commonly mentioned advantage of robotic surgery is improved dexterity. Important obstacles to its wider implementation in daily clinical practice are the associated costs, technical difficulties, and a scarce amount of evidence. Robotic liver surgery will likely continue to evolve in parallel with technological developments that enhance the robots' abilities. In parallel with the historical development of minimally invasive surgery, the laparoscopic and robotic approaches are now frequently utilized to perform major abdominal surgical procedures. Nevertheless, the role of the robotic approach in liver surgery is still controversial, and a standardized, safe technique has not been defined yet. This review aims to summarize the currently available evidence and prospects of robotic liver surgery. Minimally invasive liver surgery has been extensively associated with benefits, in terms of less blood loss, and lower complication rates, including liver-specific complications such as clinically relevant bile leakage and post hepatectomy liver failure, when compared to open liver surgery. Furthermore, comparable R0 resection rates to open liver surgery have been reported, thus, demonstrating the safety and oncological efficiency of the minimally invasive approach. However, whether robotic liver surgery has merits over laparoscopic liver surgery is still a matter of debate. In the current literature, robotic liver surgery has mainly been associated with non-inferior outcomes compared to laparoscopy, although it is suggested that the robotic approach has a shorter learning curve, lower conversion rates, and less intraoperative blood loss. Robotic surgical systems offer a more realistic image with integrated 3D systems. In addition, the improved dexterity offered by robotic surgical systems can lead to improved intra and postoperative outcomes. In the future, integrated and improved haptic feedback mechanisms, artificial intelligence, and the introduction of more liver-specific dissectors will likely be implemented, further enhancing the robots' abilities.Publication Open Access Turk Cardiology Association completion report: COVID-19 pandemic and things to know about cardiovascular diseases (25 Mart 2020)(Turkish Society of Cardiology, 2020) Aktoz, Meryem; Altay, Hakan; Aslanger, Emre; Atalar, Enver; Baykan, Ahmet Oytun; Barçın, Cem; Barış, Nezihi; Boyacı, Asiye Ayça; Çavuşoğlu, Yüksel; Çelik, Ahmet; Cinier, Göksel; Değertekin, Muzaffer; Ertürk, Mehmet; Erol, M. Kemal; Görenek, Bülent; Gürsoy, Mustafa Ozan; Hunuk, Burak; Kahveci, Gökhan; Karabay, Can Yücel; Karaca, Ilgın; Kayıkcıoğlu, Meral; Keskin, Muhammed; Kılıç, Teoman; Kırma, Cevat; Kocabaş, Umut; Küçükoğlu, Serdar; Mutlu, Bülent; Nalbantgil, Sanem; Okuyan, Ertuğrul; Okyay, Kaan; Özen, Deniz Kaptan; Özgül, Sami; Özpelit, Ebru; Pirat, Bahar; Sert, Sena; Sinan, Ümit Yaşar; Şener, Yusuf Ziya; Tatlı, Ersan; Tekkesin, Ahmet İlker; Tutar, Eralp; Yıldırımtürk, Özlem; Aytekin, Vedat; Ural, Dilek; Ergönül, Önder; Faculty Member; Faculty Member; Faculty Member; School of Medicine; N/A; 1057; 110398In December 2019, in the city of Wuhan, in the Hubei province of China, treatment-resistant cases of pneumonia emerged and spread rapidly for reasons unknown. A new strain of coronavirus (severe acute respiratory syndrome coronavirus-2 [SARS-CoV-2]) was identified and caused the first pandemic of the 21st century. The virus was officially detected in our country on March 11, 2020, and the number of cases increased rapidly; the virus was isolated in 670 patients within 10 days. The rapid increase in the number of patients has required our physicians to learn to protect both the public and themselves when treating patients with this highly infectious disease. The group most affected by the outbreak and with the highest mortality rate is elderly patients with known cardiovascular disease. Therefore, it is necessary for cardiology specialists to take an active role in combating the epidemic. The aim of this article is to make a brief assessment of current information regarding the management of cardiovascular patients affected by COVID-19 and to provide practical suggestions to cardiology specialists about problems and questions they have frequently encountered. / Aralık 2019’da, Çin’in Hubei eyaletindeki Wuhan şehrinde, nedeni bilinmeyen, tedaviye dirençli pnömoni olguları ile ortaya çıkan ve devamında hızla yayılarak XXI. yüzyılın ilk pandemisine neden olan yeni koronavirüsün (severe acute respiratory syndrome koranavirüs-2 [SARS-CoV-2]) 11 Mart 2020 tarihinde ülkemizde de resmi olarak saptanmasının ardından olgu sayısı hızla artmış ve 10 gün içerisinde 670 hastada virüs izole edilmiştir. Hasta sayısındaki hızlı artış, hekimlerimizin bir yandan etkilenen hastalara müdahale ederken diğer yandan toplumu ve kendilerini korumayı öğrenmelerini gerektirmektedir. Salgından en çok etkilenen ve ölüm oranı en yüksek seyreden grup, bilinen kalp ve damar hastalıkları olan yaşlılardır. Bu nedenle, kardiyoloji uzmanlarının salgınla mücadelede aktif görev almaları kaçınılmazdır. Bu makale, COVID-19’dan etkilenen kalp-damar hastalarının yönetiminde güncel bilgilerin kısa bir değerlendirmesini yapmayı ve kardiyoloji uzmanlarına sık karşılaştıkları sorunlar ve sorular hakkında pratik öneriler sunmayı amaçlamaktadır.Publication Open Access Comparative spectroscopic investigation of Tm3+: tellurite glasses for 2-mu m lasing applications(Multidisciplinary Digital Publishing Institute (MDPI), 2018) Kurt, Adnan; Speghini, Adolfo; Bettinelli, Marco; Department of Electrical and Electronics Engineering; Department of Physics; Çankaya, Hüseyin; Görgülü, Adil Tolga; Sennaroğlu, Alphan; Researcher; Master Student; Faculty Member; Department of Electrical and Electronics Engineering; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; College of Sciences; N/A; N/A; 23851We performed a comparative spectroscopic analysis on three novel Tm3+: tellurite-based glasses with the following compositions Tm2O3: TeO2-ZnO (TeZnTm), Tm2O3: TeO2-Nb2O5 (TeNbTm), and Tm3+: TeO2-K2O-Nb2O5 (TeNbKTm), primarily for 2-mu m laser applications. Tellurite glasses were prepared at different doping concentrations in order to investigate the effect of Tm3+ ion concentration as well as host composition on the stimulated emission cross sections and the luminescence quantum efficiencies. By performing Judd-Ofelt analysis, we determined the average radiative lifetimes of the H-3(4) level to be 2.55 +/- 0.07 ms, 2.76 +/- 0.03 ms and 2.57 +/- 0.20 ms for the TeZnTm, TeNbTm and TeNbKTm samples, respectively. We clearly observed the effect of the cross-relaxation, which becomes significant at higher Tm2O3 concentrations, leading to the quenching of 1460-nm emission and enhancement of 1860-nm emission. Furthermore, with increasing Tm2O3 concentrations, we observed a decrease in the fluorescence lifetimes as a result of the onset of non-radiative decay. For the H-3(4) level, the highest obtained quantum efficiency was 32% for the samples with the lowest Tm2O3 ion concentration. For the 1860-nm emission band, the average emission cross section was determined to measure around 6.33 +/- 0.34 x 10(-21) cm(2), revealing the potential of thulium-doped tellurite gain media for 2-mu m laser applications in bulk and fiber configurations.Publication Open Access Pneumonia in HIV-infected patients(Aves, 2016) Önür, Seda Tural; Dalar, Levent; Yalçın, Arzu Didem; İliaz, Sinem; Doctor; Koç University Hospital; 168584Acquired immune deficiency syndrome (AIDS) is an immune system disease caused by the human immunodeficiency virus (HIV). The purpose of this review is to investigate the correlation between an immune system destroyed by HIV and the frequency of pneumonia. Observational studies show that respiratory diseases are among the most common infections observed in HIV-infected patients. In addition, pneumonia is the leading cause of morbidity and mortality in HIV-infected patients. According to articles in literature, in addition to antiretroviral therapy (ART) or highly active antiretroviral therapy (HAART), the use of prophylaxis provides favorable results for the treatment of pneumonia. Here we conduct a systematic literature review to determine the pathogenesis and causative agents of bacterial pneumonia, tuberculosis (TB), nontuberculous mycobacterial disease, fungal pneumonia, Pneumocystis pneumonia, viral pneumonia and parasitic infections and the prophylaxis in addition to ART and HAART for treatment. Pneumococcus-based polysaccharide vaccine is recommended to avoid some type of specific bacterial pneumonia.