Nanogap based label-free impedimetric biosensors

Ankara : The Department of Electrical and Electronics Engineering and the Graduate School of Engineering and Science of Bilkent Univ., 2012.Thesis (Master's) -- Bilkent University, 2012.Includes bibliographical refences.Despite lots of research going on to find a hope, cancer is still a major cause of death in today‘s world. It has been reported that cancer has some biomarkers in human body and detecting these biomarkers timely can pave the way for early detection and successful treatments. Point-of-care biosensors are highly promising for this mission. If these biosensors can achieve sensitivity and reliability with a low-cost and simple platform, they can address a large mass of people who are at the early stages of cancer without any clear symptoms yet. For this purpose, various biosensing mechanisms can be used to convert the signal coming from the recognition elements on the biosensor surface to the digital domain for signal processing. One of these mechanisms, impedimetric (impedance based) sensing is a very appealing electrical biosensing method since this method can offer label-free, low-cost, low-power requirement, miniaturizable, and chip-integrable detection platforms. However, impedimetric sensing in liquid medium is problematic, since during the electrical measurements, ion-based undesired layers (electrical double layers) are formed over the electrodes in the target liquid. Unfortunately, these layers act like a shield against the applied electric field to the liquid and can prevent the detection of the target biomarkers. In this thesis, a nanogap based label-free biosensor structure is designed and using this design impedimetric sensing in liquid medium is demonstrated at low frequencies (1 kHz – 100 kHz). Low frequency platforms are quite amenable to low-cost applications like point-of-care biosensing. The designed structure utilizes nanometer scale electrode separation (nanogap). Theoretical calculations show that nanogap reduces the undesired effect of electrical double layer. Moreover, nanogap also helps in minimizing the volume of the required liquid for the measurement. Design, fabrication, surface functionalization and biotinylation stages of the biosensor are realized in a cleanroom environment and biomimetic materials laboratory. The fabricated biosensor is tested by introducing the target molecules (streptavidin) in a phosphate-buffered saline solution. A parameter analyzer with a capacitance-voltage unit and a probe station are used for the impedance measurements. With these biosensors, label-free detection of streptavidin is observed for 100 µg/mL, 10 µg/mL, 1 µg/mL, 100 ng/mL and 10 ng/mL concentrations. This is, to the best of our knowledge, the first demonstration of streptavidin detection in nanogap based label-free impedimetric biosensors. The above-mentioned concentrations show that these biosensors are promising for commercial applications. Sensitivity to the dielectric constant of the target medium is measured to be 132 pF per unit change in the dielectric constant at 10 kHz measurement frequency. Reliability tests are performed: stable and repeatable operation of the sensors are checked and verified. In conclusion, this proof-of-concept study shows that nanogap based biosensors would be a suitable and appealing choice for sensitive, reliable, simple, low-power and low-cost point-of care biosensing applications. Next step would be utilizing the platform presented in this work in detecting specific cancer biomarkers like PSA or CA125. Thereby, developed further and commercialized, nanogap based label-free impedimetric biosensors can act in the battle of human being against cancer in the future.Hanoğlu, OğuzM.S

Ulcerative Colitis Mayo Endoscopic Scoring Classification with Active Learning and Generative Data Augmentation

Endoscopic imaging is commonly used to diagnose Ulcerative Colitis (UC) and classify its severity. It has been shown that deep learning based methods are effective in automated analysis of these images and can potentially be used to aid medical doctors. Unleashing the full potential of these methods depends on the availability of large amount of labeled images; however, obtaining and labeling these images are quite challenging. In this paper, we propose a active learning based generative augmentation method. The method involves generating a large number of synthetic samples by training using a small dataset consisting of real endoscopic images. The resulting data pool is narrowed down by using active learning methods to select the most informative samples, which are then used to train a classifier. We demonstrate the effectiveness of our method through experiments on a publicly available endoscopic image dataset. The results show that using synthesized samples in conjunction with active learning leads to improved classification performance compared to using only the original labeled examples and the baseline classification performance of 68.1% increases to 74.5% in terms of Quadratic Weighted Kappa (QWK) Score. Another observation is that, attaining equivalent performance using only real data necessitated three times higher number of images.Comment: 6 pages, 3 figures, to be published in IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 202

fNIRS‐based evaluation of the impact of SARS‐CoV‐2 infection central auditory processing

Abstract Objectives Coronavirus disease‐2019 due to SARS‐CoV‐2 infection has been associated with neurological and neuropsychiatric illnesses as well as auditory system problems. In this study, we aimed to evaluate the impact of SARS‐CoV‐2 infection on the central auditory system by assessing the hemodynamic activation changes using functional near‐infrared spectroscopy (fNIRS). Methods Three participants who had SARS‐CoV‐2 infection (study group) and four participants who had no SARS‐CoV‐2 infection (control group) were included in the study. During the auditory oddball task in which two different frequencies of tonal stimulation were presented at 80 dB HL, the participants were asked to pay attention to the rare tonal stimulation and mentally count these target stimuli throughout the task. During this task, oxygenated hemodynamic response functions were evaluated with fNIRS. Results Significantly increased oxygenated hemodynamic responses were observed in both groups during the task (p < .05), which was significantly higher in the study group (p < .05). Significantly more HbO activation was observed in the vmPFC, superior temporal gyrus, and medial temporal gyrus in the study group compared to controls (p < .05). Significantly higher hemodynamic activation was observed in the right hemisphere in both groups, which was significantly higher in the study group (p < .05). Conclusion SARS‐CoV‐2 infections may impact on central auditory processing or auditory attention due to changes in oxyhemoglobin levels in the frontal and temporal brain regions. It seems that SARS‐CoV‐2 infection is associated with an additional load on neural activity, and difficulties in focusing in auditory attention, following speech and hearing in noise as well as increased effort to perceive auditory cues

Erken evre Parkinson hastalığında olfaktör disfonksiyon ve epizodik verbal bellek arasındaki İlişki

WOS: 000348845400013PubMed ID: 28360659Introduction: Olfactory dysfunction is an early and common symptom in idiopathic Parkinson's disease (IPD). Recently, the relation between olfactory dysfunction and cognitive loss in IPD has been reported. In our study, we aimed to investigate the relation between olfactory dysfunction and cognitive impairments in early IPD related with this theory. Methods: In this study, we included 28 patients with stage 1 and stage 2 IPD according to the Hoehn-Yahr (H-Y) scale and 19 healthy participants. The University of Pennsylvania Smell Identification Test (UPSIT) was performed for evaluating olfactory function. For cognitive investigation in participants, the clock drawing test, Stroop test, verbal fluency test, Benton face recognition test (BFR), Benton line judgment orientation test (BLO), and Auditory Verbal Learning Test (AVLT) were performed. Results: We found significantly lower UPSIT scores in the patient group compared to controls (p=0.018). In the neuropsychological investigation, only Stroop test and BLOT test scores were significantly lower in the patient group compared to controls (p=0.003, p=0.002, respectively). We found a negative correlation between UPSIT scores and Stroop time (p=0.033) and Stroop error (p=0.037) and a positive correlation between UPSIT scores and SBST long-term memory scores (p=0.016) in patients. Conclusion: In our study, we found mild cognitive impairment related with visuospatial and executive functions in early-stage IPD compared to controls. But, in the patient group, we detected a different impairment pattern of memory and frontal functions that correlated with hyposmia. This different pattern might be indicating a subgroup of IPD characterized by low performance in episodic verbal memory, with accompanying olfactory dysfunction in the early stage.Giriş: Olfaktör disfonksiyon, İdyopatik Parkinson Hastalığının (IPH) erken ve sık görülen bir semptomudur. Son zamanlarda, olfaktör disfonksiyon ile kognitif kayıp arasında ilişki olduğu bildirilmiştir. Çalışmamızda, bu teori ile ilişkili olarak, erken evre IPH’da olfaktör disfonksiyon ve kognitif bozukluklar arasındaki ilişkiyi araştırmayı amaçladık. Yöntem: Bu çalışmaya, Hoehn- Yahr (H-Y) evrelemesine göre evre 1 ve evre 2 IPH tanısı almış 28 hasta ve 19 sağlıklı birey dahil ettik. Olfaktör fonksiyonu değerlendirmek için University of Pennsylvania Smell Identification Test (UPSIT) uygulandı. Hastalarda kognitif fonksiyonu değerlendirmek için, Saat çizme testi, Stroop testi, verbal akıcılık testi, Benton face recognition testi (BFR), Benton line judgement orientation test (BLO), Sözel bellek süreçleri testi (SBST) uygulandı. Bulgular: Kontroller ile mukayese edildiğinde hasta grubunda UPSIT skorlarını anlamlı olarak daha düşük bulduk (p=0.018). Nöropsikolojik değerlendirmede sadece Stroop testi ve BLOT testi kontroller ile mukayese edildiğinde hasta grubunda anlamlı olarak daha düşüktü (sırasıyla p=0,003, p=0,002). UPSIT skorları ile Stroop zamanı ve Stroop hata skorları arasında negatif korelasyon (p=0,037), UPSIT skorları ile SBST uzun süreli bellek skorları arasında pozitif korelasyon bulduk. Sonuç: Çalışmamızda, daha önceki çalışmalardaki gibi, erken evre IPH’da vizyospasyal ve yürütücü fonksiyonlarla ilişkili hafif kognitif bozukluk saptadık. Fakat hasta grubunda hiposmi ile korele şekilde bellek ve frontal fonksiyonlarda farklı bir bozulma paterni saptadık. Bu farklı patern, IPH’ın erken döneminde koku bozukluğu eşliğinde epizodik verbal bellekte performans düşüklüğü görülmesi şeklinde bir alt gruba işaret ediyor olabili

Does Ability to Identify Odors Differ Among Clinical Subtypes of Parkinson's Disease?

OBJECTIVE: Parkinson's disease (PD) is characterized by motor dysfunction, whereas it is also a non-motor disorder. Olfactory dysfunction (OD) is a non-motor symptom in PD. In this study, we aimed to investigate whether OD varies among subtypes of PD. METHODS: Patients comprised 28 patients with idiopathic PD (23 male and 5 female) with a mean age 64.96±7.49 years. The patients were divided into tremor-dominant type (TDT), akinetic-rigid type (ART) and mixed type (MT) by means of part III of Unified Parkinson Disease Rating Scale. Patients were asked whether they had a relative with tremor or PD. University of Pennsylvania Smell Identification Test-40 (UPSIT) was used for testing olfactory function. Patients with any factor may influence olfactory function were excluded. RESULTS: Fourteen patients were classified into TDT, 12 into ART, and 2 into MT. There were no significant differences in mean age, UPDRS part III, UPDRS total. The UPSIT scores were highest in MT group and lowest in ART group, but it did not show statistically difference. CONCLUSION: Our results do not prove the differencies of OD between subtypes of PD, but it makes a suspicion that ART patients might have poor ability to identify odor