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Öğe 'All In One' SARS-CoV-2 variant recognition platform: Machine learning-enabled point of care diagnostics(Elsevier Ltd, 2022) Beduk D.; Ilton de Oliveira Filho J.; Beduk T.; Harmanci D.; Zihnioglu F.; Cicek C.; Sertoz R.Point of care (PoC) devices are highly demanding to control current pandemic, originated from severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). Though nucleic acid-based methods such as RT-PCR are widely available, they require sample preparation and long processing time. PoC diagnostic devices provide relatively faster and stable results. However they require further investigation to provide high accuracy and be adaptable for the new variants. In this study, laser-scribed graphene (LSG) sensors are coupled with gold nanoparticles (AuNPs) as stable promising biosensing platforms. Angiotensin Converting Enzyme 2 (ACE2), an enzymatic receptor, is chosen to be the biorecognition unit due to its high binding affinity towards spike proteins as a key-lock model. The sensor was integrated to a homemade and portable potentistat device, wirelessly connected to a smartphone having a customized application for easy operation. LODs of 5.14 and 2.09 ng/mL was achieved for S1 and S2 protein in the linear range of 1.0–200 ng/mL, respectively. Clinical study has been conducted with nasopharyngeal swabs from 63 patients having alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2) variants, patients without mutation and negative patients. A machine learning model was developed with accuracy of 99.37% for the identification of the SARS-Cov-2 variants under 1 min. With the increasing need for rapid and improved disease diagnosis and monitoring, the PoC platform proved its potential for real time monitoring by providing accurate and fast variant identification without any expertise and pre sample preparation, which is exactly what societies need in this time of pandemic. © 2022Öğe Clinical outcome of pcr-negative covid-19 patients: A retrospective study(AVES, 2021) Sayıner A.; Sezai Tasbakan M.; Ergan B.; Kılınç O.; Sayıner A.; Sertoz R.; Ozuygur S.OBJECTIVE: To evaluate the clinical features and outcomes of patients who were admitted with a diagnosis of coronavirus disease 2019 (COVID-19) but who were not confirmed with polymerase chain reaction (PCR) positivity. MATERIAL AND METHODS: This is a retrospective analysis of all patients admitted to two tertiary care centers between March 15 and May 15, 2020, with a diagnosis of COVID-19. From a common database prepared for COVID-19, we retrieved the relevant data and compared the clinical findings and outcomes of PCR-positive patients with those of PCR-negative cases who had been diagnosed on the basis of typical clinical and radiographic findings. RESULTS: A total of 349 patients were included in the analysis, of which 126 (36.1%) were PCR-negative. PCR-negative patients were younger (54.6 ± 20.8 vs. 60.8 ± 18.9 years, P = .009) but were similar to PCR-positive patients in terms of demographics, comorbidities, and presenting symptoms. They had higher lymphocyte counts (1519 ± 868 vs. 1331 ± 737/mm3, P = .02) and less frequently presented with bilateral radiographic findings (68.3% vs. 79.4%, P = .046) than PCR-positive patients. Besides, they had less severe disease and better clinical outcomes regarding admission to the intensive care unit (9.6% vs. 20.6%, P = .023), oxygen therapy (21.4% vs. 43.5%, P < .001), ventilatory support (3.2% vs. 11.2%, P = .03) and length of hospital stay (5.0 ± 5.0 vs. 9.7 ± 5.9 days, P < .001). CONCLUSION: This study confirms that about one-third of the COVID-19 patients are PCR-negative and diagnosed based on clinicaand radiographic findings. These patients have a more favorable clinical course, shorter hospital stays, and are less frequently admitteto the intensive care unit. © 2021 by Turkish Thoracic Society.Öğe Cord formation in MB/BacT medium is a reliable criterion for presumptive identification of Mycobacterium tuberculosis complex in laboratories with high prevalence of M. tuberculosis(1999) Zuhre Badak F.; Goksel S.; Sertoz R.; Guzelant A.; Kizirgil A.; Bilgic A.We evaluated cord formation in MB/BacT broth as a rapid method for presumptive identification of the Mycobacterium tuberculosis complex. Kinyoun acid-fast-stained smears from 370 positive MB/BacT bottles were examined for the presence of serpentine cording. The smears were examined independently by two observers. Observer 1 (the supervisor of the mycobacteriology laboratory) examined all of the smears while observer 2 (a clinical microbiologist not familiar with acid-fast bacillus [AFB] microscopy) examined 148 randomly chosen smears that were read by observer 1 without knowledge of which smear was which. The sensitivity, specificity, and positive and negative predictive values of cording for the presumptive identification of M. tuberculosis read by observer 1 were 88.2, 97.4, 99.2, and 69.7%, respectively. These values were reported at 90.6, 52.3, 82.8, and 69.7%, respectively, by observer 2. Our laboratory prevalence of M. tuberculosis among positive cultures was 78% during the time this study was conducted. At the time of positive signal of the MB/BacT bottles, the broth of the bottles had sufficient cell mass to allow for observation of the presence or absence of serpentine cording. The presence of cords in MB/BacT broth is a reliable criterion for rapid, predictive identification of the M. tuberculosis complex for laboratories with a high proportion of the M. tuberculosis complex when the smears are examined by a microbiologist who has experience with AFB staining.Öğe Evaluation of viral etiology in central nervous system infections from a university hospital point of view in izmir based on seven years data [Santral Sinir Sistemi Enfeksiyonlarinda Viral Etiyolojinin izmir'de Bir Üniversite Hastanesinin Yedi Yillik Verileri Üzerinden Degerlendirilmesi](Ankara Microbiology Society, 2017) Zeytinoglu A.; Erensoy S.; Sertoz R.; Altuglu I.; Çiçek C.; Kayin M.; Şirin H.; Taner S.The serious diseases of the central nervous system (CNS); encephalitis and meningitis, have high mortality and morbidity rate especially not diagnosed and treated in time. Nucleic acid testing (NAT) is the tool of choice for viral diagnosis in CNS infections. In this study, viral etiological agents found in cerebrospinal fluid (CSF) samples sent to our university hospital virology laboratory for laboratory diagnosis of CNS infections were retrospectively evaluated and results were compared with other reports from our country. Viral etiological agents found in cerebrospinal fluid (CSF) samples sent to Ege University Faculty of Medicine Department of Medical Microbiology Virology Laboratories for laboratory diagnosis of CNS infection between 01.01.2009-31.12.2015 were evaluated retrospectively. A total of 3778 CSF tests were performed for cell culture of enterovirus (EV) in 487 samples and 3291 tests for nucleic acid testing (NAT) by real time polymerase chain reaction (PCR) in herpes simplex virus 1 (HSV1), herpes simplex virus 2 (HSV2), varicella zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), human herpes virus 6 (HHV6) and EV. VZV and EV NAPs were performed during the last one and five years period, respectively. NAT positive results for HSV1, HSV2, CMV, EBV, VZV, HHV6 and EV were 1.80% (24/1333), 0.08% (1/1333), 3.28% (19/580), 4.35% (22/506), 0.46% (1/216), 1.05% (5/478) and 3.37% (6/178), respectively. EV was isolated in 30 (6.20%) of 487 CSF samples by viral culture. Positive samples were mainly from pediatric, neurology and infectious diseases clinics as expected. The number of higher positive results were found in samples sentin December (35.3%), July (12.9%) and November (10.6%). Overall 80% of positive samples belonged to patients over 18 years old. When the results of other studies reported from Turkey are examined, although the positivity rates are generally similar, it is seen that the rates specific to certain factors are higher in selected smaller patient groups like HSV1 and EV. Rapid nucleic acid tests like multiplex PCR and microarray will provide more practical and effective laboratory diagnosis approach in CNS infections, since many more microorganisms may be causative agents.Öğe Follow-up of chronic HBV infected patients planned chemotherapy due to solid organ malignancy [Solit organ malignitesi nedeniyle kemoterapi planlanan kronik hepatit B enfeksiyonlu hastalarin takibi](UHOD - Uluslararasi Hematoloji Onkoloji Dergisi, 2017) Erdem H.A.; Pullukcu H.; Tasbakan M.; Sipahi O.R.; Ulusoy S.; Sertoz R.; Uslu R.; Yamazhan T.The aim of this study was to screen the patients with solid organ malignancy for HBV (Hepatitis B virus) infection before the start of chemotherapy and follow up in the oncology department of our setting. All cases admitted to oncology department for chemotherapy were screened prospectively for HBV infection and reactivation between March 2013-September 2014. A total of 225 patients were included in the study and divided into 3 groups; Group I: having recovered past HBV infection: 43 patients (19.1%), Group II: isolated Anti-HBcAg total positive: 20 patients (8.9%) and Group III: chronic HBV infection with 10 patients (4.4%). HBV reactivation developed in one (5.9%) of 17 patients in group II, and two (28.6%) of seven patients in group III while under lamivudine prophylaxis. Neither hepatitis flare by HBV reactivation nor HBV-related death were observed in our study. In the moderate endemicity areas like Turkey for HBV infection, all patients must be screened for HBV before starting of chemotherapy. © 2017, UHOD - Uluslararasi Hematoloji Onkoloji Dergisi. All rights reserved.Öğe The relationship between HBV-DNA level and histology in patients with naive chronic HBV infection(2010) Vardar R.; Gunsar F.; Sertoz R.; Ozacar T.; Nart D.; Barbet F.Y.; Karasu Z.; Ersoz G.; Akarca U.S.Background: In patients with chronic hepatitis B (CHB) infection, precise definition of the hepatic fibrosis stage is the most important parameter to assess the risk of disease progression. Correlation between the prognosis of the CHB and the level of hepatitis-B virus DNA (HBV-DNA) is well considered in recent years. Aims: The aim of this study is to investigate the relationship between serum HBV-DNA level and histology of the liver. We also wanted to determine a threshold level of HBV-DNA for differentiation of low and high risk patients for progression. Methods: Two-hundred-fifty-nine patients with serum HBV-DNA level >2000 copies/mL, determined by polymerase chain reaction (PCR), and biopsy proven naïve CHB infection were evaluated. Liver biopsies were evaluated histopathologically according to the Ishak scoring system. Laboratory values such as aspartate aminotransferase (AST), alanine aminotransferase ratio (ALT) were tested every 3 months and the highest value of each patient was evaluated. Results: Mean age was 40±11 and 60% (155/259) of the patients were male. Mean laboratory values were as follows: AST: 52±46 U/L, ALT: 93±133 U/L, PLT: 224±60 103/l HBV DNA: 5.9±1.5 log copies/mL. In histological evaluation, mean inflammatory score was 4.34±2.72 and fibrosis score was 1.38±1.46. The fibrosis score was 0 or 1 in 63.3% (164/259) of the patients. The relationship between HBV-DNA level and histologic grade/stage was investigated and 15.000 copies/mL HBV DNA level was found as the threshold level to describe the activity of the disease. Fibrosis score was <2 and/or grade ?5 in the patients who have HBV-DNA value below that level. Conclusion: In patients who have serum HBV-DNA level ?15000/copies/mL, histological activity was almost always low, and it seems that these patients do not need a liver biopsy regardless of hepatitis-B-e antigen (HBeAg) status. © H.G.E. Update Medical Publishing S.A.
