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1. A novel study to increase the classification parameters on automatic three-class COVID-19 classification from CT images, including cases from Turkey.

Author

Yaşar, Hüseyin, Ceylan, Murat, Cebeci, Hakan, Kılınçer, Abidin, Kanat, Fikret, and Koplay, Mustafa

Subjects
DEEP learning, CONVOLUTIONAL neural networks, AUTOMATIC classification, RECEIVER operating characteristic curves, COVID-19, COMPUTED tomography
Abstract

A computed tomography (CT) scan is an important radiological imaging method in diagnosing pneumonia caused by SARS-CoV-2. Within the scope of the study, three classes of automatic classification – COVID-19 pneumonia, healthy, and other pneumonia – were carried out. Using deep learning as a classifier, a total of 6,377 CT images were used, including 3,364 COVID-19 pneumonia, 1,766 healthy, and 1,247 other pneumonia images. A total of seven architectures, including the most recent convolutional neural network (CNN) architectures, MobileNetV2, ResNet-101, Xception, Inceptionv3, GoogLeNet, EfficientNetB0, and DenseNet201, were used in the study. The classification results were obtained using the CT images, and they were calculated using the feature images obtained by applying local binary patterns on the CT images. The results were then combined with the help of a pipeline algorithm. The results revealed that the best overall accuracy result obtained by using CNN architectures could be improved by 4.87% with a two-step pipeline algorithm. In addition, significant improvements were achieved in all other measurement parameters within the scope of the study. At the end of the study, the highest sensitivity, specificity, accuracy, F-1 score, and Area under the Receiver Operating Characteristic Curve (AUC) values obtained for the COVID-19 pneumonia class were 0.9004, 0.8901, 0.8956, 0.9010, and 0.9600, respectively. The highest overall accuracy value was 0.8332. The most important output of the work carried out is the demonstration that the results obtained with the most successful CNN architectures used in previous studies can be significantly improved thanks to pipeline algorithms. [ABSTRACT FROM AUTHOR]

Published
2024
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3. Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs

Author

Bastard, Paul, Vazquez, Sara, Liu, Jamin, Laurie, Matthew, Wang, Chung, Gervais, Adrian, Le Voyer, Tom, Bizien, Lucy, Zamecnik, Colin, Philippot, Quentin, Rosain, Jérémie, Catherinot, Emilie, Willmore, Andrew, Mitchell, Anthea, Bair, Rebecca, Garçon, Pierre, Kenney, Heather, Fekkar, Arnaud, Salagianni, Maria, Poulakou, Garyphallia, Siouti, Eleni, Sahanic, Sabina, Tancevski, Ivan, Weiss, Günter, Nagl, Laurenz, Manry, Jérémy, Duvlis, Sotirija, Arroyo-Sánchez, Daniel, Paz Artal, Estela, Rubio, Luis, Perani, Cristiano, Bezzi, Michela, Sottini, Alessandra, Quaresima, Virginia, Roussel, Lucie, Vinh, Donald, Reyes, Luis, Garzaro, Margaux, Hatipoglu, Nevin, Boutboul, David, Tandjaoui-Lambiotte, Yacine, Borghesi, Alessandro, Aliberti, Anna, Cassaniti, Irene, Venet, Fabienne, Monneret, Guillaume, Halwani, Rabih, Sharif-Askari, Narjes, Danielson, Jeffrey, Burrel, Sonia, Morbieu, Caroline, Stepanovskyy, Yurii, Bondarenko, Anastasia, Volokha, Alla, Boyarchuk, Oksana, Gagro, Alenka, Neuville, Mathilde, Neven, Bénédicte, Keles, Sevgi, Hernu, Romain, Bal, Antonin, Novelli, Antonio, Novelli, Giuseppe, Saker, Kahina, Ailioaie, Oana, Antolí, Arnau, Jeziorski, Eric, Rocamora-Blanch, Gemma, Teixeira, Carla, Delaunay, Clarisse, Lhuillier, Marine, Le Turnier, Paul, Zhang, Yu, Mahevas, Matthieu, Pan-Hammarström, Qiang, Abolhassani, Hassan, Bompoil, Thierry, Dorgham, Karim, Gorochov, Guy, Laouenan, Cédric, Rodríguez-Gallego, Carlos, Ng, Lisa, Renia, Laurent, Pujol, Aurora, Belot, Alexandre, Raffi, François, Allende, Luis, Martinez-Picado, Javier, Ozcelik, Tayfun, Imberti, Luisa, Notarangelo, Luigi, Troya, Jesus, Solanich, Xavier, Zhang, Shen-Ying, Puel, Anne, Wilson, Michael, Trouillet-Assant, Sophie, Abel, Laurent, Jouanguy, Emmanuelle, Ye, Chun, Cobat, Aurélie, Thompson, Leslie, Andreakos, Evangelos, Zhang, Qian, Anderson, Mark, Casanova, Jean-Laurent, Derisi, Joseph, Achille, Cristian, Aiuti, Alessandro, Al-Muhsen, Saleh, Al-Mulla, Fahd, Angelini, Micol, Arias, Andrés, Aytekin, Gokhan, Baldanti, Fausto, Feldman, Hagit, Bergami, Federica, Biggs, Catherine, Bogunovic, Dusan, Bolze, Alexandre, Bondarenko, Anastasiia, Bousfiha, Ahmed, Brodin, Petter, Bryceson, Yenan, Bustamante, Carlos, Butte, Manish, Casari, Giorgio, Christodoulou, John, Condino-Neto, Antonio, Constantinescu, Stefan, Conti, Francesca, Cooper, Megan, Dalgard, Clifton, Desai, Murkesh, Drolet, Beth, El Baghdadi, Jamila, Ergun, Recai, Ergun, Dilek, Espinosa-Padilla, Sara, Fellay, Jacques, Flores, Carlos, Franco, José, Froidure, Antoine, Ghirardello, Stefano, Gregersen, Peter, Grimbacher, Bodo, Haerynck, Filomeen, Hagin, David, Hammarström, Lennart, Heath, James, Henrickson, Sarah, Hsieh, Elena, Husebye, Eystein, Imai, Kohsuke, Itan, Yuval, Jarvis, Erich, Kanat, Fikret, Karamitros, Timokratis, Kisand, Kai, Kopcha, Vasyl, Korda, Mykhaylo, Ku, Cheng-Lung, Lau, Yu-Lung, Ling, Yun, Lucas, Carrie, Maniatis, Tom, Mansouri, Davood, Maródi, László, Meyts, Isabelle, Milner, Joshua, Mironska, Kristina, Mogensen, Trine, Mojoli, Francesco, Morandeira, Francisco, Morio, Tomohiro, O'Farrelly, Cliona, Okada, Satoshi, Okamoto, Keisuke, Pagani, Michele, Pape, Jean, de Diego, Rebeca, Perlin, David, Pesole, Graziano, Pession, Andrea, Piralla, Antonio, Planas, Anna, Prando, Carolina, Quintana-Murci, Lluis, Ramaswamy, Sathishkumar, Resnick, Igor, Rigo-Bonnin, Raúl, Sancho-Shimizu, Vanessa, Sediva, Anna, Seppänen, Mikko, Shahrooei, Mohammed, Shcherbina, Anna, Slaby, Ondrej, Snow, Andrew, Soler-Palacín, Pere, Spaan, András, Tangye, Stuart, Abou Tayoun, Ahmad, Tulek, Baykal, Turvey, Stuart, Uddin, K, Uddin, Mohammed, Clément, Bénédicte, Abe-Jones, Yumiko, Asthana, Saurabh, Bhide, Sharvari, Calfee, Carolyn, Carrillo, Sidney, Chak, Suzanna, Collins, Zachary, Erle, David, Fragiadakis, Gabriela, Ghale, Rajani, Hendrickson, Carolyn, Jauregui, Alejandra, Kangelaris, Kirsten, Krummel, Matthew, Langelier, Charles, Lea, Tasha, Lee, Deanna, Leligdowicz, Aleksandra, Leroux, Carolyn, Lota, Raphael, Matthay, Michael, Nguyen, Viet, Patel, Ravi, Pierce, Logan, Prasad, Priya, Rao, Arjun, Rashid, Ahmad, Rodriguez, Nicklaus, Samad, Bushra, Shaw, Cole, Sigman, Austin, Tang, Kevin, Altamirano, Luz, Ward, Alyssa, Woodruff, Prescott, Allavena, Clotilde, Andrejak, Claire, Angoulvant, François, Azoulay, Cecile, Bachelet, Delphine, Bartoli, Marie, Basmaci, Romain, Behilill, Sylvie, Beluze, Marine, Benech, Nicolas, Benkerrou, Dehbia, Bhavsar, Krishna, Bitker, Laurent, Bouadma, Lila, Bouscambert, Maude, Paz, Pauline, Cervantes-Gonzalez, Minerva, Chair, Anissa, Chirouze, Catherine, Coelho, Alexandra, Cordel, Hugues, Couffignal, Camille, Couffin-Cadiergues, Sandrine, D’ortenzio, Eric, de Montmollin, Etienne, Debard, Alexa, Debray, Marie-Pierre, Deplanque, Dominique, Descamps, Diane, Desvallée, Mathilde, Diallo, Alpha, Diehl, Jean-Luc, Diouf, Alphonsine, Dorival, Céline, Dubos, François, Duval, Xavier, Eloy, Philippine, Enouf, Vincent, Epaulard, Olivier, Esperou, Hélène, Esposito-Farese, Marina, Etienne, Manuel, Garot, Denis, Gault, Nathalie, Gaymard, Alexandre, Ghosn, Jade, Gigante, Tristan, Gilg, Morgane, Goehringer, François, Guedj, Jérémie, Hoctin, Alexandre, Hoffmann, Isabelle, Houas, Ikram, Hulot, Jean-Sébastien, Jaafoura, Salma, Kafif, Ouifiya, Kaguelidou, Florentia, Kali, Sabrina, Kerroumi, Younes, Khalil, Antoine, Khan, Coralie, Kimmoun, Antoine, Laine, Fabrice, Laouénan, Cédric, Laribi, Samira, Le, Minh, Le Bris, Cyril, Le Gac, Sylvie, Le Hingrat, Quentin, Le Mestre, Soizic, Le Nagard, Hervé, Lemaignen, Adrien, Lemee, Véronique, Lescure, François-Xavier, Letrou, Sophie, Levy, Yves, Lina, Bruno, Lingas, Guillaume, Lucet, Jean, Machado, Moïse, Malvy, Denis, Mambert, Marina, Manuel, Aldric, Mentré, France, Meziane, Amina, Mouquet, Hugo, Mullaert, Jimmy, Neant, Nadège, Nguyen, Duc, Noret, Marion, Papadopoulos, Aurélie, Paul, Christelle, Peiffer-Smadja, Nathan, Peigne, Vincent, Petrov-Sanchez, Ventzislava, Peytavin, Gilles, Pham, Huong, Picone, Olivier, Piquard, Valentine, Poissy, Julien, Puéchal, Oriane, Rosa-Calatrava, Manuel, Rossignol, Bénédicte, Rossignol, Patrick, Roy, Carine, Schneider, Marion, Su, Richa, Tardivon, Coralie, Tellier, Marie-Capucine, Téoulé, François, Terrier, Olivier, Timsit, Jean-François, Tual, Christelle, Tubiana, Sarah, van der Werf, Sylvie, Vanel, Noémie, Veislinger, Aurélie, Visseaux, Benoit, Wiedemann, Aurélie, Yazdanpanah, Yazdan, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Human genetics of infectious diseases : Mendelian predisposition (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Rockefeller University [New York], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Center for the Study of Primary Immunodeficiencies [Paris], Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Hôpital Foch [Suresnes], Grand Hôpital de l'Est Francilien (GHEF), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), 4th Department of Internal Medicine, ATTIKON University General Hospital, Innsbruck Medical University = Medizinische Universität Innsbruck (IMU), Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Goce Delchev University (UGD), Génétique Evolutive Humaine - Human Evolutionary Genetics, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)

Subjects
Basic medicine, Settore MED/03, [SDV]Life Sciences [q-bio], Immunology, COVID-19, Pneumònia, Pneumonia, General Medicine
Abstract

International audience; Life-threatening ‘breakthrough’ cases of critical COVID-19 are attributed to poor or waning antibody response to the SARS-CoV-2 vaccine in individuals already at risk. Pre-existing autoantibodies (auto-Abs) neutralizing type I IFNs underlie at least 15% of critical COVID-19 pneumonia cases in unvaccinated individuals; however, their contribution to hypoxemic breakthrough cases in vaccinated people remains unknown. Here, we studied a cohort of 48 individuals (age 20-86 years) who received 2 doses of an mRNA vaccine and developed a breakthrough infection with hypoxemic COVID-19 pneumonia 2 weeks to 4 months later. Antibody levels to the vaccine, neutralization of the virus, and auto-Abs to type I IFNs were measured in the plasma. Forty-two individuals had no known deficiency of B cell immunity and a normal antibody response to the vaccine. Among them, ten (24%) had auto-Abs neutralizing type I IFNs (aged 43-86 years). Eight of these ten patients had auto-Abs neutralizing both IFN-α2 and IFN-ω, while two neutralized IFN-ω only. No patient neutralized IFN-β. Seven neutralized 10 ng/mL of type I IFNs, and three 100 pg/mL only. Seven patients neutralized SARS-CoV-2 D614G and the Delta variant (B.1.617.2) efficiently, while one patient neutralized Delta slightly less efficiently. Two of the three patients neutralizing only 100 pg/mL of type I IFNs neutralized both D61G and Delta less efficiently. Despite two mRNA vaccine inoculations and the presence of circulating antibodies capable of neutralizing SARS-CoV-2, auto-Abs neutralizing type I IFNs may underlie a significant proportion of hypoxemic COVID-19 pneumonia cases, highlighting the importance of this particularly vulnerable population.

Published
2022

6. COVID-19 and Renal Artery Thrombosis: A Case Report

Author

Ergün, Recai, primary, Ergün, Dilek, additional, Shalabi, Hacer Sürer, additional, Shalabi, Mahmoud Yousef, additional, Kanat, Fikret, additional, Tulek, Baykal, additional, Yormaz, Burcu, additional, and Nayman, Alaaddin, additional

Published
2022
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7. Remdesivir treatment for patients with moderate to severe COVID-19

Author

HASANOĞLU, İMRAN, primary, GÜNER, HATİCE RAHMET, additional, ÇELİK, İLHAMİ, additional, KANAT, FİKRET, additional, BATIREL, AYŞE, additional, DİZMAN, GÜLÇİN TELLİ, additional, EREN, ESMA ERYILMAZ, additional, SEVGİ, DİLEK YILDIZ, additional, BOZKURT, İLKAY, additional, YAŞAR, KADRİYE KART, additional, ŞENOĞLU, SEVTAP, additional, KAZAK, ESRA, additional, KARAALİ, RIDVAN, additional, ÇELİKBAŞ, AYSEL KOCAGÜL, additional, and PULLUKÇU, HÜSNÜ, additional

Published
2022
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8. A Rare Cause of Hypoxemia: Hereditary Methemoglobinemia

Author

ERGÜN, Dilek, NARİN, Ecem, ERGÜN, Recai, KANAT, Fikret, and GÖKSEL, Büşra

Subjects
Health Care Sciences and Services, Sağlık Bilimleri ve Hizmetleri, Hereditary methemoglobinemia,CYB5R3 Gene Mutation,Hypoxemia,Dyspnea, Herediter Methemoglobinemi,CYB5R3 Gen Mutasyonu,Hipoksemi,Dispne,Siyanoz
Abstract

Herediter Methemoglobinemi hpokseminin nadir sebeplerinden biridir. CYB5R3 geninde oluşan mutasyonlar otozomal resesif herediter methemoglobinemiye neden olur. Çoğunlukla nefes darlığı, morarma, halsizlik gibi semptomlar görülebilir. Bazen erişkin yaşa kadar semptom vermeyebilir. Onsekiz yaşında ellerinde ve dudaklarında zaman zaman tekrarlayan morluk, nefes darlığı, çarpıntısı olan olgumuzun, oksijen satürasyonu (Sa02) %85 saptandı. Methemoglobin (Methb) düzeyi %20 (N;0-1.5) idi. Dispne ve siyanozu açıklayacak kardiyak ve pulmoner neden saptanmayan olguda satürasyonu düşüklüğü ve methb yüksekliği nedeniyle methemoglobinemi düşünülerek, yüksek doz ıntravenöz askorbik asit verildi. Satürasyonu yükselen ve methb düzeyi tedricen düşen hastanın takiplerinde genetik testler sonucunda CYB5R3 geni sekans analizi ile homozigot missense c.136C>T (p.R46W) mutasyonu saptandı. Hasta otozomal resesif herediter methemoglobinemi tip 1 olarak kabul edildi. Pulmoner ve kardiyovasküler nedenlerle açıklanamayan nefes darlığı, hipoksi, siyanoz birlikteliğinde nadir görülen herediter methemoglobineminin akla gelmesi gerektiğini vurgulamak için bu vakamızı sunuyoruz., Hereditary methemoglobinemia is one of the rare causes of hypoxemia. Mutations in the CYB5R3 gene cause autosomal recessive hereditary methemoglobinemia. Mostly, symptoms such as shortness of breath, bruise and and fatique occur. It may not display any symptoms until adult ages. Our case was at the age of 18 and had sometimes recurring bruise in hands and lips, shortness of breath, palpitations and oxygen saturation (SaO2) was 85%. Methemoglobin (Methb) level was %20 (N;0-1.5) No cardiac or pulmonary cause could be detected, which could account for dyspnea and cyanosis, and due to low saturation and high Methb. levels, metheglobinemia was considered and high dose IV ascorbic acid was administered. In follow up period, saturation increased and Methb. level gradually decreased and with genetic tests, homozygous missense c.136C> T (p.R46W) mutation was detected with CYB5R3 gene sequence analysis. Patient was diagnosed with autosomal recessive hereditary methemoglobinemia type 1. This case is presented ın order to emphasize that hereditary methemoglobinemia should be kept in mind when shortness of breath, hypoxia and cyanosis, occur together and can not be attributed to pulmonary and cardiovascular causes.

Published
2021

12. CAN DEEP LEARNING PREDICT LABORATORY VALUES IN COVID-19?

Author

DEMİR, NAZLIM AKTUĞ, primary, Ural, Onur, additional, Ural, Asli, additional, Sumer, Sua, additional, Kiratli, Hatice Esranur, additional, Demir, Lutfi Saltuk, additional, Uslu, Ediz, additional, Kanat, Fikret, additional, Arslan, Ugur, additional, Vatansev, Husamettin, additional, and Cebeci, Hakan, additional

Published
2021
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13. The Relationship between COVID-19 Severity and Bacillus Calmette-Guérin (BCG)/ Mycobacterium tuberculosis exposure history in healthcare workers: a multi-center study

Author

Torun, Serife, primary, Ozkaya, Sevket, additional, Şen, Nazan, additional, Kanat, Fikret, additional, Karaman, Irem, additional, Yosunkaya, Sebnem, additional, Sengoren Dikis, Ozlem, additional, Asan, Ali, additional, Aydogan Eroglu, Selma, additional, Semih Atal, Sefa, additional, Ayten, Omer, additional, Aksel, Nimet, additional, Ermiş, Hilal, additional, Özçelik, Neslihan, additional, Demirelli, Meryem, additional, Kara, Iskender, additional, Sümer, Sua, additional, Marakoğlu, Kamile, additional, Üzer, Fatih, additional, Uyar, Yasin, additional, Çiçek, Tuba, additional, E Ünsal, Zuhal, additional, Vatansev, Husamettin, additional, Botan Yildirim, Berna, additional, Kuruoğlu, Tuba, additional, Atilla, Aynur, additional, Ersoy, Yasemin, additional, Kandemir, Bahar, additional, Durduran, Yasemin, additional, Goksin​ Cihan, Fatma, additional, Demirbaş, Nur, additional, Yıldırım, Fatma, additional, Tatar, Dursun, additional, and Akcay, M Sule, additional

Published
2021
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14. Remdesivir treatment for patients with moderate to severe COVID-19

Author

Alp, Emine, Gül, Ahmet, Tabak, Fehmi, Erdinç, Şebnem, Ünal, Serhat, Çağatay, Arif Atahan, Pullukçu, Hüsnü, Çelikbaş, Aysel, Karaali, Ridvan, Kazak, Esra, Şenoğlu, Sevtap, Yaşar, Kadriye Kart, Bozkurt, Ilkay, Sevgi, Dilek Yildiz, Eren, Esma, Dizman, Gülçin Telli, Batirel, Ayşe, Kanat, Fikret, Çelik, Ilhami, Güner, Rahmet, and HASANOĞLU, İMRAN

Subjects
Adult, Treatment Outcome, treatment, SARS-CoV-2, COVID-19, Humans, remdesivir, General Medicine, antiviral, mortality, Pandemics, Antiviral Agents, COVID-19 Drug Treatment
Abstract

Background/aim: Remdesivir, which was first developed for the treatment of Ebola disease but failed to meet expectations, has become hope in the fight against the COVID-19 pandemic. This study aimed to evaluate risk factors for mortality and prognosis of adult moderate/severe COVID-19 patients treated with remdesivir, and safety and tolerability of 5 days of remdesivir treatment. Materials and methods: This multicenter prospective observational study was conducted in 14 centers in Turkey. Pregnancy or breastfeeding, multiorgan failure, or usage of vasopressors for septic shock, ALT>5 x the upper limit of the normal range, or eGRF, Health Institutes of Turkey [COVID-19-PMSRMD], Health Institutes of Turkey (Project ID: COVID-19-PMSRMD).

Published
2021

19. Impact of cognitive functions on the quality of spirometry performance in patients with COPD

Author

Atalay, Nart Bedin, Yıldırım, Gülfem, Süerdem, Mecit, Tülek, Baykal, Kanat, Fikret, Atalay, Nart Bedin, Yıldırım, Gülfem, Süerdem, Mecit, Tülek, Baykal, and Kanat, Fikret

Abstract

OBJECTIVE: We researched the relationship between the cognitive scores and the error codes which determine pulmonary function test (PFT) compliance accompanied by the phenotypic findings of chronic obstructive pulmonary disease (COPD) patients. MATERIALS AND METHODS: Patients in a stable condition with COPD, who were diagnosed with the criteria recommended in the international guidelines, were included in the study. PFTs were requested from all the patients during the regular outpatient admission. The following tests were applied to all the patients in a 30-min test session; COPD assessment test, modified British Medical Research Council and neurophysiological tests (Mini-Mental Test, Trail Making Test Part A and B, Clock Drawing Test, Straight and Backward Digit Span, Brown Peterson Task and Verbal Fluency Test). We analyzed the statistical relationship between data collected after cognitive tests and PFT quality data. RESULTS: The study was concluded with a total of 70 patients. When the PFT evaluations of the patients were examined, the percentage of patients who correctly fulfilled the repeatability criteria was found as 28%, who met the acceptability criteria as 57%, and who correctly fulfilled both criteria as 14%. The relationship between the results of patients, who fulfilled both repeatability and acceptability criteria correctly and incorrectly at the same time, with the backward digit span test results was found to be significant (P 0.05). It was found that the Mini-Mental Test was significantly better in those who performed all of the repeatability and acceptability criteria without errors than the other groups. When the PFT criteria of the patients were evaluated according to the cognitive test results, it was determined that the relationship between the Mini-Mental Test and the results of performing the repeatability and acceptability criteria together was found to be statistically significant (P 0.05). DISCUSSION AND CONCLUSION: Error codes that ident

Published
2020

20. Impact of cognitive functions on the quality of spirometry performance in patients with COPD

Author

Yıldırım, Gülfem, Tülek, Baykal, Kanat, Fikret, Süerdem, Mecit, Atalay, Nart Bedin, Yıldırım, Gülfem, Tülek, Baykal, Kanat, Fikret, Süerdem, Mecit, and Atalay, Nart Bedin

Abstract

OBJECTIVE: We researched the relationship between the cognitive scores and the error codes which determine pulmonary function test (PFT) compliance accompanied by the phenotypic findings of chronic obstructive pulmonary disease (COPD) patients. MATERIALS AND METHODS: Patients in a stable condition with COPD, who were diagnosed with the criteria recommended in the international guidelines, were included in the study. PFTs were requested from all the patients during the regular outpatient admission. The following tests were applied to all the patients in a 30-min test session; COPD assessment test, modified British Medical Research Council and neurophysiological tests (Mini-Mental Test, Trail Making Test Part A and B, Clock Drawing Test, Straight and Backward Digit Span, Brown Peterson Task and Verbal Fluency Test). We analyzed the statistical relationship between data collected after cognitive tests and PFT quality data. RESULTS: The study was concluded with a total of 70 patients. When the PFT evaluations of the patients were examined, the percentage of patients who correctly fulfilled the repeatability criteria was found as 28%, who met the acceptability criteria as 57%, and who correctly fulfilled both criteria as 14%. The relationship between the results of patients, who fulfilled both repeatability and acceptability criteria correctly and incorrectly at the same time, with the backward digit span test results was found to be significant (P 0.05). It was found that the Mini-Mental Test was significantly better in those who performed all of the repeatability and acceptability criteria without errors than the other groups. When the PFT criteria of the patients were evaluated according to the cognitive test results, it was determined that the relationship between the Mini-Mental Test and the results of performing the repeatability and acceptability criteria together was found to be statistically significant (P 0.05). DISCUSSION AND CONCLUSION: Error codes that ident

Published
2020

22. Evaluation of the relationship between perceived social support, coping strategies, anxiety, and depression symptoms among hospitalized COVID-19 patients

Author

Kandeğer, Ali, primary, Aydın, Memduha, additional, Altınbaş, Kürşat, additional, Cansız, Alparslan, additional, Tan, Özge, additional, Tomar Bozkurt, Hazan, additional, Eğilmez, Ümran, additional, Tekdemir, Rukiye, additional, Şen, Barış, additional, Aktuğ Demir, Nazlım, additional, Sümer, Şua, additional, Ural, Onur, additional, Yormaz, Burcu, additional, Ergün, Dilek, additional, Tülek, Baykal, additional, and Kanat, Fikret, additional

Published
2020
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30. Correlation of myeloid‐derived suppressor cells with C‐reactive protein, ferritin and lactate dehydrogenase levels in patients with severe COVID‐19.

Author

Emsen, Ayca, Sumer, Sua, Tulek, Baykal, Cizmecioglu, Hilal, Vatansev, Husamettin, Goktepe, Mevlut Hakan, Kanat, Fikret, Koksal, Yavuz, Arslan, Ugur, and Artac, Hasibe

Subjects
MYELOID-derived suppressor cells, LACTATE dehydrogenase, C-reactive protein, COVID-19, SARS-CoV-2
Abstract

The novel coronavirus disease 2019 (COVID‐19) remains a global health emergency, and understanding the interactions between the virus and host immune responses is crucial to preventing its lethal effects. The expansion of myeloid‐derived suppressor cells (MDSCs) in COVID‐19, thereby suppressing immune responses, has been described as responsible for the severity of the disease, but the correlation between MDSC subsets and COVID‐19 severity remains elusive. Therefore, we classified patients according to clinical and laboratory findings—aiming to investigate the relationship between MDSC subsets and laboratory findings such as high C‐reactive protein, ferritin and lactate dehydrogenase levels, which indicate the severity of the disease. Forty‐one patients with COVID‐19 (26 mild and 15 severe; mean age of 49.7 ± 15 years) and 26 healthy controls were included in this study. MDSCs were grouped into two major subsets—polymorphonuclear MDSCs (PMN‐MDSCs) and monocytic MDSCs—by flow cytometric immunophenotyping, and PMN‐MDSCs were defined as mature and immature, according to CD16 expressions, for the first time in COVID‐19. Total MDSCs, PMN‐MDSCs, mature PMN‐MDSCs and monocytic MDSCs were significantly higher in patients with COVID‐19 compared with the healthy controls (P <.05). Only PMN‐MDSCs and their immature PMN‐MDSC subsets were higher in the severe subgroup than in the mild subgroup. In addition, a significant correlation was found between C‐reactive protein, ferritin and lactate dehydrogenase levels and MDSCs in patients with COVID‐19. These findings suggest that MDSCs play a role in the pathogenesis of COVID‐19, while PMN‐MDSCs, especially immature PMN‐MDSCs, are associated with the severity of the disease. [ABSTRACT FROM AUTHOR]

Published
2022
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32. The effect of cognitive functions on the ability to learn how to use a Diskus device in patients with chronic obstructive pulmonary disease

Author

Atalay, Nart Bedin, Kanat, Fikret, Tülek, Baykal, Kurtipek, Ercan, Yıldırım, Gülfem, Süerdem, Mecit, Atalay, Nart Bedin, Kanat, Fikret, Tülek, Baykal, Kurtipek, Ercan, Yıldırım, Gülfem, and Süerdem, Mecit

Abstract

OBJECTIVE: Dry powder inhalers are a group of inhaled medications commonly used for the treatment of chronic obstructive pulmonary disease (COPD). Although they can be more easily administered than metered dose inhalers, there is a high rate of errors in device use. The present study aims to evaluate the relationship between the ability to learn how to use a Diskus device and cognitive functions in patients with COPD. MATERIALS AND METHODS: The study included 30 inhaler-naive patients who were newly diagnosed with COPD. During their first visit, patients were administered a broad array of standardized neuropsychological tests and given a training on inhaler use. During the second visit, patients were divided into two groups according to their performance in the use of Diskus device: effective and ineffective. RESULTS: Twenty-nine patients who completed the study showed a negative correlation between the cognitive test scores and Diskus training parameters. The number of errors and duration of training increased as the cognitive scores decreased. In Visit 2, a comparison between patients with ineffective and effective use of the Diskus device showed that cognitive function scores were higher in those with effective use. CONCLUSIONS: Evaluation of cognitive functions in COPD patients is important in establishing an effective inhalation treatment.

Published
2019

33. Cognitive function in chronic obstructive pulmonary disease: Relationship to global initiative for chronic obstructive lung disease 2011 categories

Author

Süerdem, Mecit, Kanat, Fikret, Yıldırım, Gülfem, Tülek, Baykal, Atalay, Nart Bedin, Süerdem, Mecit, Kanat, Fikret, Yıldırım, Gülfem, Tülek, Baykal, and Atalay, Nart Bedin

Abstract

Background and objective: Recently, comorbidities such as impaired cognitive function have been attracting more focus when considering the management of chronic obstructive pulmonary disease (COPD). Here we investigated the relationship between cognitive function and the categories given in the Global Initiative for Chronic Obstructive Lung Disease (GOLD) guidelines in 2011. Specifically, after controlling for non-COPD covariates, we assessed the clinical features that may be predictive of cognitive impairment in patients with COPD. Methods: We recruited 119 stable patients with mild to very severe COPD. We administered a broad array of standardized neuropsychological tests that assessed cognitive functions in the domains of attention, memory, psychomotor coordination and language. Results: Cognitive scores were significantly different between patients falling within GOLD 2011 categories. Scores were lower in patients with high future risk compared with low future risk. In parallel, there were significant differences in cognitive function between COPD patient subgroups when patients were grouped according to the forced expiratory volume in 1 s, exacerbation history and C-reactive protein levels. After controlling for non-COPD predictors, only exacerbation history remained a significant predictor of cognitive scores. Conclusions: The number of exacerbation events in a year may be used as a predictor of cognitive impairment in patients with COPD.

Published
2019

34. Cognitive function in chronic obstructive pulmonary disease: Relationship to global initiative for chronic obstructive lung disease 2011 categories

Author

Tülek, Baykal, Yıldırım, Gülfem, Kanat, Fikret, Süerdem, Mecit, Atalay, Nart Bedin, Tülek, Baykal, Yıldırım, Gülfem, Kanat, Fikret, Süerdem, Mecit, and Atalay, Nart Bedin

Abstract

Background and objective: Recently, comorbidities such as impaired cognitive function have been attracting more focus when considering the management of chronic obstructive pulmonary disease (COPD). Here we investigated the relationship between cognitive function and the categories given in the Global Initiative for Chronic Obstructive Lung Disease (GOLD) guidelines in 2011. Specifically, after controlling for non-COPD covariates, we assessed the clinical features that may be predictive of cognitive impairment in patients with COPD. Methods: We recruited 119 stable patients with mild to very severe COPD. We administered a broad array of standardized neuropsychological tests that assessed cognitive functions in the domains of attention, memory, psychomotor coordination and language. Results: Cognitive scores were significantly different between patients falling within GOLD 2011 categories. Scores were lower in patients with high future risk compared with low future risk. In parallel, there were significant differences in cognitive function between COPD patient subgroups when patients were grouped according to the forced expiratory volume in 1 s, exacerbation history and C-reactive protein levels. After controlling for non-COPD predictors, only exacerbation history remained a significant predictor of cognitive scores. Conclusions: The number of exacerbation events in a year may be used as a predictor of cognitive impairment in patients with COPD.

Published
2019

37. Evaluation of the relationship between perceived social support, coping strategies, anxiety, and depression symptoms among hospitalized COVID-19 patients.

Author

Kandeğer, Ali, Aydın, Memduha, Altınbaş, Kürşat, Cansız, Alparslan, Tan, Özge, Tomar Bozkurt, Hazan, Eğilmez, Ümran, Tekdemir, Rukiye, Şen, Barış, Aktuğ Demir, Nazlım, Sümer, Şua, Ural, Onur, Yormaz, Burcu, Ergün, Dilek, Tülek, Baykal, and Kanat, Fikret

Abstract

Objective: We aimed to evaluate the relationship between perceived social support, coping strategies, anxiety, and depression symptoms among hospitalized COVID-19 patients by comparing them with a matched control group in terms of age, gender, and education level. Method: The patient group (n = 84) and the healthy controls (HCs, n = 92) filled in the questionnaire including the socio-demographic form, Hospital Anxiety Depression Scale, Multidimensional Perceived Social Support Scale, and Brief Coping Orientation to Problems Experienced through the online survey link. Results: The COVID-19 patients had higher perceived social support and coping strategies scores than the HCs. However, anxiety and depression scores did not differ significantly between the two groups. In logistic regression analysis performed in COVID-19 patients, the presence of chest CT finding (OR = 4.31; 95% CI = 1.04–17.95) was a risk factor for anxiety and the use of adaptive coping strategies (OR = 0.86; 95% CI = 0.73–0.99) had a negative association with anxiety. In addition, the use of adaptive coping strategies (OR = 0.89; 95% CI = 0.79–0.98) and high perceived social support (OR = 0.97; 95% CI = 0.93– 0,99) had a negative association with depression symptoms. Conclusions: Longitudinal studies involving the return to normality phase of the COVID-19 pandemic are needed to investigate the effects of factors such as coping strategies and perceived social support that could increase the psychological adjustment and resilience of individuals on anxiety and depression. [ABSTRACT FROM AUTHOR]

Published
2021
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38. Flexible bronchoscopy may decrease respiratory muscle strength: premedicational midazolam in focus

Author

Tulek Baykal, Kanat Fikret, Tol Sule, and Suerdem Mecit

Subjects
Bronchoscopy, Midazolam, Respiratory muscle strength, Diseases of the respiratory system, RC705-779
Abstract

Abstract Background Flexible bronchoscopy (FB) is a procedure accepted to be safe in general, with low complication rates reported. On the other hand, it is known that patients with pre-existing respiratory failure have developed hypoventilation following FB. In this study the effects of FB on respiratory muscle strength were investigated by measuring maximum respiratory pressures. Methods One hundred and forty patients, aged between 25 and 90 years, who had undergone diagnostic bronchoscopy between February 2012 and May 2012, were recruited to the study. Pre- and post-procedure maximal inspiratory pressure (MIP) and maximal expiratory pressure (MEP) were measured. A correlation between the MIP and MEP changes and patient characteristics and FB variables were investigated. Results Significant decreases in both MIP and MEP values were observed following FB (p Conclusions It was determined that respiratory muscle weakness may arise post-procedure in patients who have undergone FB, and this is constitutively related to midazolam premedication. Respiratory muscle weakness might play a role in potential hypoventilation in critical patients who undergo FB.

Published
2012
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41. Development of Giant Substernal Thyroid After Thyroidectomy: A Case Report

Author

ÖNCEL, Murat, YILDIRIM, Gülfem, KANAT, Fikret, SUNAM, Güven Sadi, Selçuk Üniversitesi, Tıp Fakültesi, Cerrahi Tıp Bilimleri Bölümü, Öncel, Murat, Yıldırım, Gülfem, Kanat, Fikret, and Sunam, Güven Sadi

Subjects
lcsh:R5-920, Mediasten,Dev substernal tiroid, mediasten, dev substernal tiroid, giant substernal thyroid, Mediastinum,Giant Substernal thyroid, lcsh:Medicine (General), mediastinum, respiratory tract diseases, Cerrahi
Abstract

The origins of mediastinal masses could be traumatic, infectious, degenerative, or neoplastic origin. Occasionaly substernal goiters could grow into the mediastinum leading to giant mediastinal masses. We report a case of a 55-year-old female patient admitted to our clinic with major complaints of chronic cough and dyspnea. Mass that extended from the posterior mediastinum and multiple nodules in the left thyroid lobe were detected in thorax computed tomography which lead to operation . As in our case The development of a giant mediastinal mass in recurrent thyroid patients after thyroidectomy could occur rarely., Mediastinal kitleler, konjenital, travmatik,enfeksiyon, dejeneratif veya neoplazm kaynaklı olabilirler. Arasıra substernal guatrlar; mediastene doğru büyüyebilir ve mediastende dev kitleler oluşturabilirler. Bu yazıda sunulan olgu 55 yaşında bir kadın hasta, kronik öksürük ve dispne nedeniyle polikliniğimize başvurmuştur. Toraks BT de arka mediastene uzanım gösteren kitle ve sol tiroid lobunda multiple nodüller saptanmış, hasta opere edilmiştir. Olgumuzdaki gibi tiroidektomi sonrası nüks nodüllerle beraber dev mediastinal kitle gelişimi nadir olarak görülmektedir.

Published
2012

42. The Relationship between COVID-19 Severity and Bacillus Calmette-Guérin (BCG)/ Mycobacterium tuberculosisexposure history in healthcare workers: a multi-center study

Author

Torun, Serife, Ozkaya, Sevket, Şen, Nazan, Kanat, Fikret, Karaman, Irem, Yosunkaya, Sebnem, Sengoren Dikis, Ozlem, Asan, Ali, Aydogan Eroglu, Selma, Semih Atal, Sefa, Ayten, Omer, Aksel, Nimet, Ermiş, Hilal, Özçelik, Neslihan, Demirelli, Meryem, Kara, Iskender, Sümer, Sua, Marakoğlu, Kamile, Üzer, Fatih, Uyar, Yasin, Çiçek, Tuba, E Ünsal, Zuhal, Vatansev, Husamettin, Botan Yildirim, Berna, Kuruoğlu, Tuba, Atilla, Aynur, Ersoy, Yasemin, Kandemir, Bahar, Durduran, Yasemin, Goksin​ Cihan, Fatma, Demirbaş, Nur, Yıldırım, Fatma, Tatar, Dursun, and Akcay, M Sule

Abstract

ABSTRACTThe COVID-19 pandemic has brought countries’ health services into sharp focus. It was drawn to our group’s attention that healthcare workers (HCWs) had a lower mortality rate against higher COVID-19 incidence compared to the general population in Turkey. Since risk of exposure to tuberculosis bacillus among healthcare workers are higher than the population, we aimed to investigate if there is a relationship between BCG and Mycobacterium tuberculosisexposure history with COVID-19 severity in infected HCWs. This study was conducted with 465 infected HCWs from thirty-three hospitals to assess the relationship between COVID-19 severity (according to their hospitalization status and the presence of radiological pneumonia) and BCG and Mycobacterium tuberculosisexposure history. HCWs who required hospital admission had significantly higher rates of chronic diseases, radiological pneumonia, and longer working hours in the clinics. Higher rates of history of contact and care to tuberculosis patients, history of tuberculosis, and BCG vaccine were observed in hospitalized HCWs. HCWs who had radiological pneumonia had a significantly increased ratio of history of care to tuberculosis patients and a higher family history of tuberculosis. The findings from our study suggest that the lower mortality rate despite the more severe disease course seen in infected HCWs might be due to frequent exposure to tuberculosis bacillus and the mortality-reducing effects of the BCG vaccine.

Published
2021
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50. Cognitive function in chronic obstructive pulmonary disease: Relationship to global initiative for chronic obstructive lung disease 2011 categories

Author

Tulek, Baykal, Atalay, Nart Bedin, Yildirim, Gulfem, Kanat, Fikret, Suerdem, Mecit, TOBB ETU, Faculty of Science and Literature, Department of Psychology, TOBB ETÜ, Fen Edebiyat Fakültesi, Psikoloji Bölümü, and Atalay, Nart Bedin

Subjects
exacerbation, Mini Mental State Examination, cognitive function, respiratory tract diseases, chronic obstructive pulmonary disease
Abstract

Background and objective: Recently, comorbidities such as impaired cognitive function have been attracting more focus when considering the management of chronic obstructive pulmonary disease (COPD). Here we investigated the relationship between cognitive function and the categories given in the Global Initiative for Chronic Obstructive Lung Disease (GOLD) guidelines in 2011. Specifically, after controlling for non-COPD covariates, we assessed the clinical features that may be predictive of cognitive impairment in patients with COPD. Methods: We recruited 119 stable patients with mild to very severe COPD. We administered a broad array of standardized neuropsychological tests that assessed cognitive functions in the domains of attention, memory, psychomotor coordination and language. Results: Cognitive scores were significantly different between patients falling within GOLD 2011 categories. Scores were lower in patients with high future risk compared with low future risk. In parallel, there were significant differences in cognitive function between COPD patient subgroups when patients were grouped according to the forced expiratory volume in 1 s, exacerbation history and C-reactive protein levels. After controlling for non-COPD predictors, only exacerbation history remained a significant predictor of cognitive scores. Conclusions: The number of exacerbation events in a year may be used as a predictor of cognitive impairment in patients with COPD.

Published
2015

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