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    Developing Pretrained Language Models for Turkish Biomedical Domain
    (Ieee, 2022) Turkmen, Hazal; Dikenelli, Oguz; Eraslan, Cenk; Calli, Mehmet Cem; Ozbek, Suha Sureyya
    Pretrained language models elevated with in-domain corpora show impressive results in biomedicine and clinical NLP tasks in English. However, there is minimal work in low-resource languages. This work introduces the BioBERTurk family, three pretrained models in Turkish for biomedicine. To evaluate models, we also introduce a labeled dataset to classify radiology reports of CT exams. Our first model was initialized from BERTurk and pretrained with biomedical corpus. The second model again continues to pretrain the general BERT model with a corpus of Ph.D. theses on radiology to test the effect of the task-related text. The final model combines radiology and biomedicine corpora with the corpus of BERTurk and pretrained a BERT model from scratch. F-scores of our models in the radiology resort classification are 92.99, 92.75, and 89.49 respectively. As far as we know, this is the first model that evaluates the effect of small size in-domain corpus in pretraining from scratch.
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    MRI assessment of pituitary Iron accumulation by using pituitary-R2 in beta-thalassemia patients
    (Sage Publications Ltd, 2018) Bozdag, Mustafa; Bayraktaroglu, Selen; Aydinok, Yesim; Calli, Mehmet Cem
    Background: Patients with thalassemia major (TM) require repeated blood transfusions, which leads to accumulation of iron in a wide variety of tissues. Accumulation of iron in the pituitary gland can lead to irreversible hypogonadotropic hypogonadism (HH) in this group of patients. Purpose: To investigate the reliability of pituitary-R.2 as a marker to estimate the extent of pituitary iron load by comparing the pituitary magnetic resonance imaging (MRI) findings with hepatic iron load and serum ferritin levels. Material and Methods: A total of 38 beta-TM patients were classified into HH (group A, n = 18) and non-HH (group B, n = 17) groups. A third group, group C, consisted of 17 healthy participants. Each participant underwent 1.5-T MRI examinations. Pituitary gland heights (PGH), pituitary-R2 values, and liver-R2 values were measured by using multi-echo spin-echo sequences. Results: Pituitary-R2 values were significantly higher in group A compared with group B Rho < 0.05). A positive correlation was detected between the pituitary-R2 values and serum ferritin levels in TM patients Rho < 0. 01) A threshold value of 14.1 Hz for pituitary-R2 was found to give a high specificity and sensitivity in distinguishing the TM patients with HH from those with normal pituitary functions. PGH measurements were significantly lower in group A compared with group B Rho < 0.05). Conclusion: MRI-assessed pituitary-R2 seems to be a reliable marker for differentiating the TM patients with normal pituitary function from those with secondary hypogonadism due to iron toxicity.
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    MRI evaluation of progressive supranuclear palsy: differentiation from Parkinson's disease and multiple system atrophy
    (Taylor & Francis Ltd, 2019) Eraslan, Cenk; Acarer, Ahmet; Guneyli, Serkan; Akyuz, Esra; Aydin, Elcin; Colakoglu, Zafer; Kitis, Omer; Calli, Mehmet Cem
    Objectives: To evaluate the magnetic resonance imaging (MRI)-derived parameters in differentiation of patients with progressive supranuclear palsy (PSP) from patients with Parkinson's disease (PD), multiple system atrophy (MSA), and control subjects was aimed. Methods: Thirty-three patients [mean age, 65.21 +/- 4.75 years; PSP (n = 9), MSA (n = 8), PD (n = 6), and control subjects (n = 10)] who have undergone cranial MRI were included in this retrospective study. MRI-derived parameters including areas of midbrain and pons, midbrain area-to-pons area (M/P) ratio, widths of middle cerebellar peduncle (MCP) and superior cerebellar peduncle (SCP), MCP/SCP ratio, magnetic resonance parkinsonism index (MRPI), cerebral interpeduncular angle, and length of midbrain tegmentum were compared in patients with PSP, PD, MSA, and control subjects through the analysis of variance and Kruskal-Wallis tests with Bonferroni correction and Mann-Whitney U test. Results: The length of midbrain tegmentum, midbrain area, SCP, and M/P ratio were found to be lower, while cerebral interpeduncular angle and MRPI were higher in patients with PSP. Pons area, MCP width, and MCP/SCP ratio were found to be lower in patients with MSA. For PSP, cerebral interpeduncular angle has a sensitivity of 100% and specifity of 90%, and MRPI had a sensitivity of 88.9% and specifity of 100% for PSP. Discussion: Several MRI-derived parameters can be used in differentiation of patients with PSP from patients with PD, MSA and control subjects. The cerebral interpeduncular angle and MRPI, which demonstrated higher values in patients with PSP, were more significant for PSP than the other parameters.
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    MRI perfusion findings in acute cerebral infarction and perfusion parameters used in the evaluation penumbra
    (Yerkure Tanitim & Yayincilik Hizmetleri A S, 2016) Aydin, Elcin; Calli, Mehmet Cem; Uncu, Gulgun; Sirin, Hadiye
    Objective: In this trial, our objective is to emphasize the importance of the magnetic resonance perfusion in the early diagnosis and therapy of cerebral ischemia and to discuss the reliable perfusion maps for identifying peunumbra. Material and Methods: Participants of this trial have been selected among patients who applied to the Ege University Radiology Department with cerebrovascular event and had an acute infarct which was diagnosed by MR. Among 20 of these patients, dynamic suceptibilite contrast (DSC) imaging with 1.5 T MR Magnetom Vision, Siemens, Erlangen, Germany) was performed with standart head bandage. At contrast perfusion imaging a bolus of 0.1 mmol/kg Gadolinium was injected by a speed of 3ml/sec. Multishot echoplanar imaging (EPI) imaging was performed for determining the changes at T2* relaxation time. The DSC perfusion parametres and function maps were obtained and eveluated at the postprocessing stage. The precence of penumbra was diagnosed by comparing the perfusion maps with difusion images. Results: Seventy nine percent of the patients had a lesser degree of cerebral blood volume (CBV) and cerebral blood flow (CBF) at the infarcted area then contrary hemisphere but at 11% of the patients there was no difference with contrary hemisphere. Five percent of the patients had remarkable blood flow increase. This was thought to be cause of the important role of the brain's autoregulation function. There was an expected delay at 90% of the patients in contrast passing time and peak time. By comparing the diffusion with perfusion maps, the penumbra was diagnosed at 4 patients by mean transit time (MTT) and time to pic (TTP) maps, at 3 patients by CBF map and at 1 patient by CBV map. Conclusion: The early diagnosis and evaluation of acute ischemic stroke, improves the patients' quality of life. The perfusion MR has a pathfinder role in the diagnosis and therapy of acute infarct. Penumbra is a dynamic tissue and the treatment after the early identifying of the penumbra, defines the patients prognosis. The most reliable perfusion map for determining the penumbra is controversial and much more trials are need to be done about this subject. According to recent trials and our investigation, the penumbra area seems to be larger which is determined by using the TTP and MTT maps. This condition is due to the exaggerated appearance of the ischemic penumbra secondary to the benign oligemia with severe arterial occlusive changes. In the literature the most reliable maps are relative cerebral blood volume (rCBV) and relative cerebral blood flow (rCBF) maps for demonstrating the last infarct area and our findings are also in the same way.
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    Reflections of the sensory findings in the central nervous system in patients with neuropathic pain
    (Springer, 2022) Tanigor, Goksel; Hepguler, Simin; Koken, Idris; Calli, Mehmet Cem; Uyar, Meltem
    This study aimed to evaluate whether there was a difference in functional magnetic resonance imaging (fMRI) findings in patients who were found having hyperalgesia or hypoesthesia according to Quantitative Sensory Tests (QST). Forty participants were included in the study: 20 with neuropathic pain (NP) due to cervical disc pathology (NP group) and 20 healthy volunteers. After obtaining the socio-demographic and clinical data of the participants, the painDETECT questionnaire was administered, followed by QST analysis to show the presence of hypoesthesia and/or hyperalgesia, and fMRI examinations, which included sensory stimulation of both extremities. Sensory threshold tests were found to be higher in the NP group compared with the healthy volunteers, and the heat pain threshold was found to be lower in the tests showing pain thresholds in the intergroup analyses (p < 0.05). The changes described were found in both painful and non-painful limbs. In the hypoesthetic NP group, a lower somatosensory cortex activity was found in non-painful limbs compared with the healthy volunteers (p < 0.05). In the unilateral hyperalgesic NP group, a lower somatosensory cortex activity was found on the painful side, and if the hyperalgesia was widespread, lower blood oxygen-level-dependent activity was also found in the operculum and insular cortex (p < 0.05). The patients with different phenotypes of NP had different activities in the areas related to the processing of pain, and were more prominent in patients with widespread hyperalgesia. Studies with larger numbers of patients are required for a definite statement.