36 results on '"Çakır U"'
Search Results
2. Effect of Obesity on Clinical Outcomes of Kidney Transplant Patients
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Erturk, T., Berber, I., and Cakir, U.
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- 2019
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3. Geographic Distribution of Multiple Arteries and Veins of 878 Kidney Donors From a Transplant Center in Turkey
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Cenal, U., Erturk, T., Karayagiz, A.H., Ozdemir, E., Polatkan, S.V., Cakir, U., and Berber, I.
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- 2019
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4. Transplantation of a Blue Kidney: A Case Report
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Nokay, E., Erturk, T., Karayagiz, A.H., Ozdemir, E., Baba, Z.F., Nokay, H.G., Cakır, U., and Berber, I.
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- 2019
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5. Role of Everolimus on Cardiac Functions in Kidney Transplant Recipients
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Cakir, U., Alis, G., Erturk, T., Karayagiz, A.H., Karabulut, U., and Berber, I.
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- 2017
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6. Evaluation of Bone Disease in Kidney Transplant Recipients
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Alis, G., Alis, M., Erturk, T., Karayagiz, A.H., Berber, I., and Cakir, U.
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- 2017
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7. Comparison of Two Different Laparoscopic Donor Nephrectomy With Vaginal Extraction Techniques—A Single-Center Experience
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Karayagiz, A.H., Erturk, T., Cakir, U., and Berber, I.
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- 2017
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8. Laparascopıc Donor Nephrectomy Is Safe for Extremely Old Donors and Provıdes a Good Outcome for Theır Recıpıents
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Cavdaroglu, O., Gurluler, E., Cakır, U., Gurkan, A., and Berber, I.
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- 2015
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9. Investigation of the effect of vitamin K1 prophylaxis on newborn screenings tests in newborns
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Caglayan Murat, Gonel Ataman, Tayman Cuneyt, Cakir Ufuk, Koyuncu Ismail, Temiz Ebru, and Sert Yasemin
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vitamin k1 ,heel blood ,hereditary disorders ,tandem ms ,interference ,newborn ,Biochemistry ,QD415-436 - Abstract
Background: Routine screening for hereditary disorders in newborns includes screening for treatable metabolic and endocrine disorders, such as biotidinase deficiency, galactosemia, maple syrup urine disease, hypothyroidism, and cystic fibrosis. Incorrect test results may be encountered due to the use of vitamin K1. To investigate the interference effect of vitamin K1 on neonatal screening tests and to raise awareness of erroneous measurements. Methods: Heel blood samples were taken from 25 newborns born in a neonatal intensive care unit. Dry blood C0, C2, C3, C4, C4DC, C5:1, C5OH, C5DC, C6, C6DC, C8, C8:1, C8DC, C10, C10:1, C10DC, C12, C14, C14:1, C14:2, C16, C16:1, C18, C18:1, C18:2, C18:OH, methylglutaryl, valine, leucine/isoleucine, methionine, phenylalanine, argininosuccinic acid, aspartate, alanine, arginine, citrulline, glycine, ornithine, and glutamate tests were studied using the tandem mass spectrometry (MS) method. The results of the heel blood samples obtained before and after the application of vitamin K1 (Phyto menadione) were compared. Results: In two studies conducted with in vitro and in vivo tests, C0, C2, C3, C4, C4DC, C5, C5OH, C6, C8, C10, C10:1, C14, C16, C16:1, C18, C18:1, methylglutaryl, phenylalanine, argininosuccinic acid, tyrosine, aspartate, arginine, citrulline, glycine, and glutamine were all significantly elevated (p < 0.05). Conclusions: Heel blood samples may yield false results due to vitamin K1 administration. In the case of doubtful results, a new sample should be taken and the measurement should be repeated.
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- 2023
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10. Geochemistry and origin of plagiogranites from the Eldivan Ophiolite, Çankırı (Central Anatolia, Turkey)
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Üner Tijen, Çakir Üner, Özdemir Yavuz, and Arat Irem
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Eldivan Ophiolite ,Early Jurassic ,plagiogranite ,fractional crystallization ,partial melting ,Geology ,QE1-996.5 - Abstract
The Eldivan Ophiolite, exposed around Ankara and Çankırı cities, is located at the central part of the Izmir-Ankara-Erzincan Suture Zone (IAESZ). It represents fragments of the Neotethyan Oceanic Lithosphere emplaced towards the south over the Gondwanian continent during the Albian time. It forms nearly complete series by including tectonites (harzburgites and rare dunites), cumulates (dunites, wherlites, pyroxenites, gabbro and plagiogranites) and sheeted dykes from bottom to top. Imbricated slices of volcanic-sedimentary series and discontinuous tectonic slices of ophiolitic metamorphic rocks are located at the base of tectonites. Plagiogranitic rocks of the Eldivan Ophiolite are mainly exposed at upper levels of cumulates. They are in the form of conformable layers within layered diorites and also dikes with variable thicknesses. Plagiogranites have granular texture and are mainly composed of quartz and plagioclases. The occurrences of chlorite and epidote revealed that these rocks underwent a low grade metamorphism. Eldivan plagiogranites have high SiO2 content (70-75 %) and low K2O content (0.5-1 %) and display flat patterns of REE with variable negative Eu anomalies. LREE/HREE ratio of these rocks varies between 0.2-0.99. All members of the Eldivan rocks have high LILE/HFSE ratios with depletion of Nb, Ti and P similar to subduction related tectonic settings. Geochemical modelling indicates that the Eldivan plagiogranites could have been generated by 50-90 % fractional crystallization and/or 5-25 % partial melting of a hydrous basaltic magma
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- 2014
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11. Report of a case of neonatal chylothorax that responded to long-term octreotide treatment, and review of the literature
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Çakır, U., Kahvecioğlu, D., Yıldız, D., Alan, S., OMER ERDEVE, Atasay, B., and Arsan, S.
12. Letter to the Editor,Ruh hekimliğinde türkçeninkullanimi: hekimler ve hastalaraçisindan ilaç isimlerinin durumu
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Yıldız, M., Boşgelmez, Ş, Çakır, U., Yazıcı, E., Yazıcı, A. B., Turgut, C., and Ay, Y. L.
13. Tolerability and first hints for potential efficacy of motor-cognitive training under inspiratory hypoxia in health and neuropsychiatric disorders: A translational viewpoint.
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Mennen SS, Franta M, Begemann M, Wilke JBH, Schröder R, Butt UJ, Cortés-Silva JA, Çakır U, Güra M, de Marées M, Gastaldi VD, Burtscher J, Schanz J, Bohn M, Burtscher M, Fischer A, Poustka L, Hammermann P, Stadler M, Lühder F, Singh M, Nave KA, Miskowiak KW, and Ehrenreich H
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Hypoxia is more and more perceived as pivotal physiological driving force, allowing cells in the brain and elsewhere to acclimate to lowered oxygen (O
2 ), and abridged metabolism. The mediating transcription program is induced by inspiratory hypoxia but also by intensive motor-cognitive tasks, provoking a relative decrease in O2 in relation to the acutely augmented requirement. We termed this fundamental, demand-dependent drop in O2 availability "functional hypoxia." Major players in the hypoxia response are hypoxia-inducible factors (HIFs) and associated prolyl-hydroxylases. HIFs are transcription factors, stabilized by low O2 accessibility, and control expression of a multitude of genes. Changes in oxygen, however, can also be sensed via other pathways, among them the thiol-oxidase (2-aminoethanethiol) dioxygenase. Considering the far-reaching biological response to hypoxia, hitherto mostly observed in rodents, we initiated a translational project, combining mild to moderate inspiratory with functional hypoxia. We had identified this combination earlier to benefit motor-cognitive attainment in mice. A total of 20 subjects were included: 13 healthy individuals and 7 patients with depression and/or autism spectrum disorder. Here, we show that motor-cognitive training under inspiratory hypoxia (12% O2 ) for 3.5 h daily over 3 weeks is optimally tolerated. We present first signals of beneficial effects on general well-being, cognitive performance, physical fitness and psychopathology. Erythropoietin in serum increases under hypoxia and flow cytometry analysis of blood reveals several immune cell types to be mildly modulated by hypoxia. To obtain reliable information regarding the "add-on" value of inspiratory on top of functional hypoxia, induced by motor-cognitive training, a single-blind study-with versus without inspiratory hypoxia-is essential and outlined here., Competing Interests: Conflict of Interest Statement The authors declare no conflict of interest.- Published
- 2024
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14. G protein-coupled estrogen receptor 1 and collagen XVII endodomain expression in human cutaneous melanomas: can they serve as prognostic factors?
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Çakır U, Balogh P, Ferenczik A, Brodszky V, Krenács T, Kárpáti S, Sárdy M, Holló P, and Fábián M
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- Humans, Female, Prognosis, Male, Middle Aged, Aged, Adult, Melanoma, Cutaneous Malignant, Aged, 80 and over, Melanoma pathology, Melanoma metabolism, Skin Neoplasms pathology, Skin Neoplasms metabolism, Receptors, G-Protein-Coupled metabolism, Receptors, G-Protein-Coupled genetics, Receptors, Estrogen metabolism, Biomarkers, Tumor metabolism, Collagen Type XVII, Non-Fibrillar Collagens metabolism, Non-Fibrillar Collagens genetics, Autoantigens metabolism
- Abstract
Melanoma incidence is increasing globally. Although novel therapies have improved the survival of primary melanoma patients over the past decade, the overall survival rate for metastatic melanoma remains low. In addition to traditional prognostic factors such as Breslow thickness, ulceration, and mitotic rate, novel genetic and molecular markers have been investigated. In our study, we analyzed the expression of G-protein coupled estrogen receptor 1 (GPER1) and the endodomain of collagen XVII (COL17) in relation to clinicopathological factors in primary cutaneous melanomas with known lymph node status in both sexes, using immunohistochemistry. We found, that GPER1 expression correlated with favorable clinicopathological factors, including lower Breslow thickness, lower mitotic rate and absence of ulceration. In contrast, COL17 expression was associated with poor prognostic features, such as higher tumor thickness, higher mitotic rate, presence of ulceration and presence of regression. Melanomas positive for both GPER1 and COL17 had significantly lower mean Breslow thickness and mitotic rate compared to cases positive for COL17 only. Our data indicate that GPER1 and COL17 proteins may be of potential prognostic value in primary cutaneous melanomas., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Çakır, Balogh, Ferenczik, Brodszky, Krenács, Kárpáti, Sárdy, Holló and Fábián.)
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- 2024
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15. Evaluation of beneficial effects of dexpanthenol on hypoxic-ischemic encephalopathy.
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Tayman C, Çakır U, Kurt A, Ertekin Ö, Taskin Turkmenoglu T, Çağlayan M, and Işık E
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- Animals, Rats, Apoptosis drug effects, Oxidative Stress drug effects, Animals, Newborn, Pantothenic Acid analogs & derivatives, Pantothenic Acid pharmacology, Hypoxia-Ischemia, Brain drug therapy, Hypoxia-Ischemia, Brain pathology
- Abstract
Hypoxic-ischemic encephalopathy (HIE) is a cause of serious morbidity and mortality in newborns. Dexpanthenol, which is metabolized into D-pantothenic acid, has antioxidant and other potentially therapeutic properties. We examined some effects of dexpanthenol on the brains of week-old rat pups with HIE induced by obstruction of the right carotid artery followed by keeping in 8% O
2 for 2 hours. Dexpanthenol (500 mg/kg) was administered intraperitoneally to 16 of 32 pups with HIE. Protein, DNA, and lipid oxidation degradation products were assayed and hippocampal and cortical cell apoptosis and neuronal cell numbers were evaluated in stained sections. Dexpanthenol application reduced oxidative stress and inflammation. TNF-α and IL-6 cytokine levels in HIE also decreased with dexpanthenol treatment. The numbers of caspase-3 positive cells in the dentate gyrus and CA1/CA2/CA3 regions of the hippocampus was lower, and apoptosis was decreased in the dexpanthenol-treated animals. These findings suggest possible clinical applications of dexpanthenol in human HIE.- Published
- 2024
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16. Serum ADAMTS-9 Level in Newborn Babies with Congenital Heart Disease.
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Becerir C, Tayman C, Kurt A, Çakır U, Koyuncu İ, Ceran B, Toprak K, and Kızılgün M
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- Humans, Infant, Newborn, Female, Male, Case-Control Studies, Gestational Age, ROC Curve, Heart Defects, Congenital blood, ADAMTS9 Protein blood, Biomarkers blood
- Abstract
Objective: A Disintegrin and Metalloproteinase with Thrombospondin-9 (ADAMTS-9), one of the ADAMTS enzymes, is expressed in all fetal tissues, unlike other ADAMTS enzymes, and is thus thought to play a role in fetal development. In this context, the objective of this study is to investigate the relationship between ADAMTS-9 activity and the development of congenital heart diseases (CHD) with a view to using ADAMTS-9 level as a biomarker for CHDs., Study Design: Newborns diagnosed with CHD and healthy newborns were included in the study as the CHD and control groups, respectively. Gestational age, maternal age, and mode of delivery information pertaining to the mothers and Apgar score and birthweight information pertaining to the newborns were recorded. Blood samples were taken from all newborns to determine their ADAMTS-9 levels in the first 24 hours of life., Results: Fifty-eight newborns with CHD and 46 healthy newborns were included in the study. Median ADAMTS-9 levels were 46.57 (interquartile range [IQR]: 33.31 [min: 26.92, max: 124.25]) and 23.36 (IQR: 5.48 [min: 11.7, max: 37.71]) ng/mL in the CHD and control groups, respectively. ADAMTS-9 levels in the CHD group were statistically significantly higher than in the control group ( p = 0.000). ADAMTS-9 levels of the CHD and control groups were analyzed by the receiver operating characteristics curve. The area under the curve value for ADAMTS-9 levels of >27.86 ng/mL as the cut-off value for predicting the development of CHD in newborns was 0.836 (95% confidence interval [CI]: 0.753-0.900, p = 0.0001). ADAMTS-9 levels of >27.86 ng/mL were determined to predict the development of CHD in newborns with a sensitivity of 77.78% (95% CI: 65.5-87.38) and a specificity of 84.78% (95% CI: 71.1-93.60)., Conclusion: In conclusion, it was found that the serum ADAMTS-9 levels were significantly higher in newborns with CHD than in healthy newborns. In parallel, ADAMTS-9 levels above a certain cut-off value were associated with CHD., Key Points: · ADAMTS-9 is expressed in fetal tissues.. · Its level increases in congenital heart diseases.. · It can be used as a biochemical marker in diagnosis.., Competing Interests: None declared., (Thieme. All rights reserved.)
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- 2024
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17. Targeting Melanoma-Associated Fibroblasts (MAFs) with Activated γδ (Vδ2) T Cells: An In Vitro Cytotoxicity Model.
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Hajdara A, Çakır U, Érsek B, Silló P, Széky B, Barna G, Faqi S, Gyöngy M, Kárpáti S, Németh K, and Mayer B
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- Humans, Zoledronic Acid pharmacology, Fibroblasts, Tumor Microenvironment, Melanoma, DiGeorge Syndrome, Cancer-Associated Fibroblasts
- Abstract
The tumor microenvironment (TME) has gained considerable scientific attention by playing a role in immunosuppression and tumorigenesis. Besides tumor cells, TME is composed of various other cell types, including cancer-associated fibroblasts (CAFs or MAFs when referring to melanoma-derived CAFs) and tumor-infiltrating lymphocytes (TILs), a subpopulation of which is labeled as γδ T cells. Since the current anti-cancer therapies using γδ T cells in various cancers have exhibited mixed treatment responses, to better understand the γδ T cell biology in melanoma, our research group aimed to investigate whether activated γδ T cells are capable of killing MAFs. To answer this question, we set up an in vitro platform using freshly isolated Vδ2-type γδ T cells and cultured MAFs that were biobanked from our melanoma patients. This study proved that the addition of zoledronic acid (1-2.5 µM) to the γδ T cells was necessary to drive MAFs into apoptosis. The MAF cytotoxicity of γδ T cells was further enhanced by using the stimulatory clone 20.1 of anti-BTN3A1 antibody but was reduced when anti-TCR γδ or anti-BTN2A1 antibodies were used. Since the administration of zoledronic acid is safe and tolerable in humans, our results provide further data for future clinical studies on the treatment of melanoma.
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- 2023
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18. Mosaic translation hypothesis: chimeric polypeptides produced via multiple ribosomal frameshifting as a basis for adaptability.
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Çakır U, Gabed N, Brunet M, Roucou X, and Kryvoruchko I
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- Base Sequence, Peptides genetics, Peptides metabolism, Ribosomes genetics, Ribosomes metabolism, Open Reading Frames genetics, Protein Biosynthesis genetics, Frameshifting, Ribosomal genetics, Proteome metabolism
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How many different proteins can be produced from a single spliced transcript? Genome annotation projects overlook the coding potential of reading frames other than that of the reference open reading frames (refORFs). Recently, alternative open reading frames (altORFs) and their translational products, alternative proteins, have been shown to carry out important functions in various organisms. AltORFs overlapping refORFs or other altORFs in a different reading frame may be involved in one fundamental mechanism so far overlooked. A few years ago, it was proposed that altORFs may act as building blocks for chimeric (mosaic) polypeptides, which are produced via multiple ribosomal frameshifting events from a single mature transcript. We adopt terminology from that earlier discussion and call this mechanism mosaic translation. This way of extracting and combining genetic information may significantly increase proteome diversity. Thus, we hypothesize that this mechanism may have contributed to the flexibility and adaptability of organisms to a variety of environmental conditions. Specialized ribosomes acting as sensors probably played a central role in this process. Importantly, mosaic translation may be the main source of protein diversity in genomes that lack alternative splicing. The idea of mosaic translation is a testable hypothesis, although its direct demonstration is challenging. Should mosaic translation occur, we would currently highly underestimate the complexity of translation mechanisms and thus the proteome., (© 2021 Federation of European Biochemical Societies.)
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- 2023
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19. Glucocorticoids in a Neonatal Hyperoxic Lung Injury Model: Pulmonary and Neurotoxic effects.
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Özer Bekmez B, Tayman C, Çakır U, Koyuncu İ, Büyüktiryaki M, Türkmenoğlu TT, and Çakır E
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- Animals, Humans, Infant, Newborn, Rats, Animals, Newborn, Antioxidants, Dexamethasone, Glucocorticoids therapeutic use, HSP70 Heat-Shock Proteins, Hydrocortisone, Lung, Methylprednisolone therapeutic use, Bronchopulmonary Dysplasia chemically induced, Bronchopulmonary Dysplasia drug therapy, Hyperoxia complications, Hyperoxia drug therapy, Lung Injury drug therapy, Neurotoxicity Syndromes
- Abstract
Background: We aimed to compare the effect of dexamethasone (Dex), hydrocortisone (Hc), and methylprednisolone (Mpz) at equivalent doses on somatic growth, lung healing, and neurotoxicity in a hyperoxic rat model. We hypothesized that Mpz and Hc would be superior to Dex with less neurotoxicity by exerting similar therapeutic efficacy on the injured lung., Methods: Neonatal rats were randomized to control, bronchopulmonary dysplasia (BPD), Dex, Hc, and Mpz groups. All drugs were administered daily following day 15 over 7 days. Histopathological and immunohistochemical analyses of the lung and brain were performed on day 22., Results: All types had much the same impact on lung repair. Oxidative markers in the lung were similar in the steroid groups. While nuclear factor erythroid 2-related factor and heat-shock protein 70 dropped following steroid treatment, no difference was noted in other biochemical markers in the brain between the study groups. Apoptotic activity and neuron loss in the parietal cortex and hippocampus were noted utmost in Dex, but alike in other BPD groups., Conclusions: Mpz does not appear to be superior to Dex or Hc in terms of pulmonary outcomes and oxidative damage in the brain, but safer than Dex regarding apoptotic neuron loss., Impact: This is the first study that compared the pulmonary efficacy and neurotoxic effects of Dex, Hc, and Mpz simultaneously in an established BPD model. This study adds to the literature on the importance of possible antioxidant and protective effects of glucocorticoid therapy in an oxidative stress-exposed brain. Mpz ended up with no more additional neuron loss or apoptosis risk by having interchangeable effects with others for the treatment of established BPD. Mpz and Hc seem safe as a rescue therapy in terms of adverse outcomes for established BPD in which lung and brain tissue is already impaired., (© 2021. The Author(s), under exclusive licence to the International Pediatric Research Foundation, Inc.)
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- 2022
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20. Mesenchymal-Stromal Cell-like Melanoma-Associated Fibroblasts Increase IL-10 Production by Macrophages in a Cyclooxygenase/Indoleamine 2,3-Dioxygenase-Dependent Manner.
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Çakır U, Hajdara A, Széky B, Mayer B, Kárpáti S, Mezey É, Silló P, Szakács G, Füredi A, Pós Z, Érsek B, Sárdy M, and Németh K
- Abstract
Melanoma-associated fibroblasts (MAFs) are integral parts of melanoma, providing a protective network for melanoma cells. The phenotypical and functional similarities between MAFs and mesenchymal stromal cells (MSCs) prompted us to investigate if, similarly to MSCs, MAFs are capable of modulating macrophage functions. Using immunohistochemistry, we showed that MAFs and macrophages are in intimate contact within the tumor stroma. We then demonstrated that MAFs indeed are potent inducers of IL-10 production in various macrophage types in vitro, and this process is greatly augmented by the presence of treatment-naïve and chemotherapy-treated melanoma cells. MAFs derived from thick melanomas appear to be more immunosuppressive than those cultured from thin melanomas. The IL-10 increasing effect is mediated, at least in part, by cyclooxygenase and indoleamine 2,3-dioxygenase. Our data indicate that MAF-induced IL-10 production in macrophages may contribute to melanoma aggressiveness, and targeting the cyclooxygenase and indoleamine 2,3-dioxygenase pathways may abolish MAF-macrophage interactions.
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- 2021
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21. The therapeutic effect of Apocynin against hyperoxy and Inflammation-Induced lung injury.
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Tayman C, Çakır U, Akduman H, Karabulut Ş, and Çağlayan M
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- Animals, Animals, Newborn, Female, Lung pathology, Lung Injury pathology, Pneumonia pathology, Pregnancy, Rats, Rats, Wistar, Acetophenones therapeutic use, Hyperoxia complications, Lung Injury drug therapy, Pneumonia drug therapy
- Abstract
Lung damage due to hyperoxia and inflammation are important causes of bronchopulmonary dysplasia (BPD). We aimed to investigate the beneficial effects of Apocynin (Apo) on rat pups exposed to hyperoxia and inflammation. Forty-eight rat pups were randomly divided into 3 groups as hyperoxia (95% O
2 ) + lipopolysaccharide (LPS), hyperoxia + LPS + Apo treated and control (21% O2 ). Rat pups in the Apo group received Apo at a daily dose of 40 mg/kg. Histopathological (Hematoxylin-Eosin, Masson trichrome), immunochemical (surfactant B and C protein staining) evaluations and biochemical studies incluiding, total antioxidant status (TAS), total oxidant status (TOS), OSI (oxidant stress index), AOPP (advanced protein degradation product), Lipid hydroperoxide (LPO), 8-OHdG, NADPH oxidase activity (NOX), superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), myeloperoxidase (MPO), tumor necrosis factor-alpha (TNF- α), interleukin-1 beta (IL-1β), IL-18, IL-6, caspase-1 and 3, nuclear factor erythroid 2-related factor 2 (NFR2), Nod-like receptor pyrin domain-containing 3 (NLRP3) activities were studied. After Apo treatment, AOPP, LPO, 8-OHdG, NOX, TOS, OSI levels decreased; SOD, CAT, GSH and TAS levels increased (P < 0.05). Apo reduced inflammatory cell infiltration and proinflammatory cytokines with reduction in NLRP3 inflammasome in addition to increased Nrf2 levels. Moreover, caspase-1 and 3 levels decreased with Apo (P < 0.05). Apo was found to provide preventive and therapeutic effects by reducing oxidant stress, blocking inflammation and increasing antioxidant status. Beyond anti-oxidative effects, Apo also have anti-inflammatory effects by suppressing NLRP3 inflammasome activation and inducing Nrf2 as well. Therefore, Apo might be a potential option in the treatment of BPD., (Copyright © 2021 Elsevier B.V. All rights reserved.)- Published
- 2021
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22. The Human Melanoma Proteome Atlas-Complementing the melanoma transcriptome.
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Betancourt LH, Gil J, Sanchez A, Doma V, Kuras M, Murillo JR, Velasquez E, Çakır U, Kim Y, Sugihara Y, Parada IP, Szeitz B, Appelqvist R, Wieslander E, Welinder C, de Almeida NP, Woldmar N, Marko-Varga M, Eriksson J, Pawłowski K, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Lindberg H, Oskolas H, Lee B, Berge E, Sjögren M, Eriksson C, Kim D, Kwon HJ, Knudsen B, Rezeli M, Malm J, Hong R, Horvath P, Szász AM, Tímár J, Kárpáti S, Horvatovich P, Miliotis T, Nishimura T, Kato H, Steinfelder E, Oppermann M, Miller K, Florindi F, Zhou Q, Domont GB, Pizzatti L, Nogueira FCS, Szadai L, Németh IB, Ekedahl H, Fenyö D, and Marko-Varga G
- Subjects
- Antineoplastic Agents therapeutic use, Blood Proteins metabolism, Cell Line, Chromatography, High Pressure Liquid, Databases, Factual, Humans, Melanoma drug therapy, Melanoma metabolism, Mutation, Protein Processing, Post-Translational genetics, Proto-Oncogene Proteins B-raf genetics, Proto-Oncogene Proteins B-raf metabolism, Tandem Mass Spectrometry, Melanoma pathology, Proteome metabolism, Proteomics methods, Transcriptome
- Abstract
The MM500 meta-study aims to establish a knowledge basis of the tumor proteome to serve as a complement to genome and transcriptome studies. Somatic mutations and their effect on the transcriptome have been extensively characterized in melanoma. However, the effects of these genetic changes on the proteomic landscape and the impact on cellular processes in melanoma remain poorly understood. In this study, the quantitative mass-spectrometry-based proteomic analysis is interfaced with pathological tumor characterization, and associated with clinical data. The melanoma proteome landscape, obtained by the analysis of 505 well-annotated melanoma tumor samples, is defined based on almost 16 000 proteins, including mutated proteoforms of driver genes. More than 50 million MS/MS spectra were analyzed, resulting in approximately 13,6 million peptide spectrum matches (PSMs). Altogether 13 176 protein-coding genes, represented by 366 172 peptides, in addition to 52 000 phosphorylation sites, and 4 400 acetylation sites were successfully annotated. This data covers 65% and 74% of the predicted and identified human proteome, respectively. A high degree of correlation (Pearson, up to 0.54) with the melanoma transcriptome of the TCGA repository, with an overlap of 12 751 gene products, was found. Mapping of the expressed proteins with quantitation, spatiotemporal localization, mutations, splice isoforms, and PTM variants was proven not to be predicted by genome sequencing alone. The melanoma tumor molecular map was complemented by analysis of blood protein expression, including data on proteins regulated after immunotherapy. By adding these key proteomic pillars, the MM500 study expands the knowledge on melanoma disease., (© 2021 The Authors. Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.)
- Published
- 2021
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23. The human melanoma proteome atlas-Defining the molecular pathology.
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Betancourt LH, Gil J, Kim Y, Doma V, Çakır U, Sanchez A, Murillo JR, Kuras M, Parada IP, Sugihara Y, Appelqvist R, Wieslander E, Welinder C, Velasquez E, de Almeida NP, Woldmar N, Marko-Varga M, Pawłowski K, Eriksson J, Szeitz B, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Lindberg H, Oskolas H, Lee B, Berge E, Sjögren M, Eriksson C, Kim D, Kwon HJ, Knudsen B, Rezeli M, Hong R, Horvatovich P, Miliotis T, Nishimura T, Kato H, Steinfelder E, Oppermann M, Miller K, Florindi F, Zhou Q, Domont GB, Pizzatti L, Nogueira FCS, Horvath P, Szadai L, Tímár J, Kárpáti S, Szász AM, Malm J, Fenyö D, Ekedahl H, Németh IB, and Marko-Varga G
- Subjects
- Adult, Aged, Aged, 80 and over, Cell Line, Tumor, Chromatography, High Pressure Liquid, Female, Humans, Male, Melanoma metabolism, Middle Aged, Skin Neoplasms metabolism, Tandem Mass Spectrometry, Young Adult, Melanoma, Cutaneous Malignant, Melanoma pathology, Proteome analysis, Proteomics methods, Skin Neoplasms pathology
- Abstract
The MM500 study is an initiative to map the protein levels in malignant melanoma tumor samples, focused on in-depth histopathology coupled to proteome characterization. The protein levels and localization were determined for a broad spectrum of diverse, surgically isolated melanoma tumors originating from multiple body locations. More than 15,500 proteoforms were identified by mass spectrometry, from which chromosomal and subcellular localization was annotated within both primary and metastatic melanoma. The data generated by global proteomic experiments covered 72% of the proteins identified in the recently reported high stringency blueprint of the human proteome. This study contributes to the NIH Cancer Moonshot initiative combining detailed histopathological presentation with the molecular characterization for 505 melanoma tumor samples, localized in 26 organs from 232 patients., (© 2021 The Authors. Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.)
- Published
- 2021
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24. Do Clothing Labels Play a Role for Weight Estimation in Pediatric Emergencies? A Prospective, Cross-Sectional Study.
- Author
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Karaca A, Akyol KC, Keşaplı M, Güngör F, Cengiz Çakır U, Janitzky A, and Güven R
- Subjects
- Body Weight, Child, Child, Preschool, Cross-Sectional Studies, Humans, Infant, Prospective Studies, Clothing, Emergencies
- Abstract
Introduction: The aim of this study was to investigate the usability of the age value listed on the labels on children's clothes in the age-based weight estimation method recommended by the Pediatric Advanced Life Support (PALS) guidelines., Material-Method: This prospective, cross-sectional study was organized in Antalya Training and Research Hospital Emergency Department. Children aged between 1-12 years were included in the study. The weight measurements of the children were obtained based on the age-related criteria on the labels of their clothes. The estimated values were compared with the real values of the cases measured on the scale., Results: One-thousand ninety-four cases were included, the mean age of cases in age-based measurements was 6.25 years, which was 6.5 years in label-based measurements. Average weights measured 25.75kg according to age-based measurements, 26.5kg according to label-based measurements, and 26.0kg on the scales, and showed no statistical difference (P <.0001). It was estimated that 741 (67.7%) of age-based measurements and 775 (70.8%) of label-based measurements were within (±)10% values within the normal measurement limits and no significant difference was measured., Conclusion: In the emergency department and prehospital setting, children with an unknown age and that need resuscitation and interventional procedures for stabilization, and have no time for weight estimation, checking the age on clothing label (ACL) instead of the actual age (AA) can be safely used for the age-dependent weight calculation formula recommended by the PALS guide.
- Published
- 2021
- Full Text
- View/download PDF
25. The effect of thyroid functions on osteopenia of prematurity in preterm infants.
- Author
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Çakır U and Tayman C
- Subjects
- Bone Diseases, Metabolic pathology, Female, Follow-Up Studies, Humans, Infant, Infant, Newborn, Infant, Premature, Diseases pathology, Male, Pregnancy, Prognosis, Retrospective Studies, Thyroid Function Tests, Bone Diseases, Metabolic etiology, Congenital Hypothyroidism complications, Infant, Premature, Infant, Premature, Diseases etiology, Infant, Very Low Birth Weight, Thyroid Gland physiopathology
- Abstract
Background It is known that thyroid hormones have effects on bone development. In particular, the effect of thyroid hormones on osteopenia of prematurity (OOP) has not been examined in preterm infants. Our study aimed to examine the relationship between OOP and congenital hypothyroidism (CH) in preterm infants. Methods Very low birth weight infants (VLBW, <1500 g) were included in the study. Thyroid-stimulating hormone (TSH) and free thyroxine (fT4) levels were measured on postnatal day 5. Serum calcium, phosphorus and alkaline phosphatase (ALP) levels were studied as standard screening parameters for OOP at postnatal week 4. Patients with serum ALP level >700 IU/L were included in the OOP group. We intended to figure out the relationship between OOP and CH in infants. Results In our study, OOP frequency was 14.9% among 543 VLBW infants. There was no statistically significant difference between groups with and without CH (21.7% and 14.8%, respectively) in terms of OOP (p=0.632). Gestational age (GA) was significantly lower in infants with diagnosed OOP (p<0.001, p<0.001, respectively). In addition, the prevalence rates of mothers with preeclampsia, small for gestational age (SGA), respiratory support requirement, late-onset neonatal sepsis (LOS), bronchopulmonary dysplasia (BPD) and full enteral feeding time were found to be higher in the OOP group (p<0.05). Conclusions We found that thyroid hormones had no effect on OOP in preterm infants. Therefore, future randomized controlled studies as well as long-term outcome studies are warranted on this topic.
- Published
- 2019
- Full Text
- View/download PDF
26. A promising, novel index in the diagnosis and follow-up of patent ductus arteriosus: Red cell distribution width-to-platelet ratio.
- Author
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Özer Bekmez B, Tayman C, Büyüktiryaki M, Çetinkaya AK, Çakır U, and Derme T
- Subjects
- Cohort Studies, Ductus Arteriosus, Patent diagnostic imaging, Ductus Arteriosus, Patent epidemiology, Echocardiography, Doppler, Erythrocyte Indices, Female, Gestational Age, Hematologic Tests, Humans, Infant, Infant, Premature, Diseases diagnostic imaging, Infant, Premature, Diseases epidemiology, Male, ROC Curve, Blood Platelets pathology, Ductus Arteriosus, Patent blood, Ductus Arteriosus, Patent diagnosis, Infant, Premature, Infant, Premature, Diseases blood
- Abstract
Background: The role of red cell distribution width-to-platelet ratio (RPR) has not previously been mentioned in reports on patent ductus arteriosus (PDA). Our objective was to evaluate whether RPR would have a role in the diagnosis and/or prediction of pharmacological closure of PDA., Methods: Preterm infants' gestational age ≤30 weeks and ≤1500 g who were given first ibuprofen treatment in the first week of life for hemodynamically significant PDA (hsPDA) were included in the study. The patients were matched for gestational age, birthweight, and sex. Patients were subdivided into two groups based on the response to medical treatment (open and closed PDA). Hemogram parameters were recorded before and after medical therapy. Groups were compared with regard to demographic and clinical characteristics and for three sequential hematological parameters. RPR was calculated. Patients with sepsis, anemia, perinatal asphyxia, and congenital/chromosomal anomaly were not included in the study., Results: A total of 112 infants had medically treated hsPDA. Of those, ductus closed in 70 neonates (closed PDA). A total of 96 infants constituted the control group. Mean gestational age and birthweight of the patients were 28.9 ± 2.4 weeks and 1207 ± 372 g. While RPR was significantly increased, PCT was lower in both hsPDA and open PDA groups (P < 0.05 and P < 0.05, respectively). In multivariate analysis, high RPR (OR 3.3, 95% CI 1.438-5.872, P < 0.05) and RDS (OR 2.9, 95% CI 1.903-4.811, P < 0.01) were detected as independent risk factors for hsPDA., Conclusion: Red cell distribution width-to-platelet ratio and PCT may be promising supportive tools for the diagnosis and prediction of pharmacotherapy success., (© 2018 Wiley Periodicals, Inc.)
- Published
- 2018
- Full Text
- View/download PDF
27. Ginger ( Zingiber officinale ) prevents severe damage to the lungs due to hyperoxia and inflammation
- Author
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Çifci A, Tayman C, Yakut Hİ, Halil H, Çakır E, Çakır U, and Aydemir S
- Subjects
- Animals, Animals, Newborn, Antioxidants metabolism, Apoptosis, Bronchopulmonary Dysplasia blood, Bronchopulmonary Dysplasia etiology, Chorioamnionitis, Disease Models, Animal, Female, Humans, Hyperoxia, Infant, Newborn, Inflammation blood, Inflammation chemically induced, Inflammation Mediators blood, Lung pathology, Lung Diseases drug therapy, Lung Diseases etiology, Malondialdehyde blood, Oxygen administration & dosage, Phytotherapy, Plant Extracts pharmacology, Plant Extracts therapeutic use, Pregnancy, Rats, Wistar, Bronchopulmonary Dysplasia drug therapy, Zingiber officinale, Infant, Premature, Inflammation complications, Lung drug effects, Oxidative Stress drug effects, Oxygen adverse effects
- Abstract
Background/aim: Hyperoxia- and inflammation-induced lung injury is an important cause of the development of bronchopulmonary dysplasia (BPD) in premature infants. We aimed to ascertain the beneficial effects of ginger ( Zingiber officinale ) on rat pups exposed to hyperoxia and inflammation., Materials and Methods: Thirty-six newborn Wistar rats were randomly divided into 3 groups as the hyperoxia (95% O 2 ) + lipopolysaccharide (LPS) group, the hyperoxia + LPS + ginger-treated group, and the control/no treatment group (21% O 2 ). Pups in the hyperoxia + LPS + ginger group were administered oral ginger at a dose of 1000 mg/kg daily during the study period. Histopathologic, immunochemical (SMA and lamellar body), and biochemical evaluations including total antioxidant status (TAS), total oxidant status (TOS), malondialdehyde (MDA), myeloperoxidase (MPO), tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β), interleukin-6 (IL-6), and caspase-3 activities were performed., Results: Better weight gain and survival rates were shown in the hyperoxia + LPS + ginger group (P < 0.05). In the histopathologic and immunochemical evaluation, severity of lung damage was significantly reduced in the hyperoxia + LPS + ginger group, as well as decreased apoptosis (ELISA for caspase-3) (P < 0.05). Tissue TAS levels were significantly protected, and TOS, MDA, and MPO levels were significantly lower in the hyperoxia + LPS + ginger group (P < 0.05). Tissue TNF-α, IL-1β, and IL-6 concentrations were significantly decreased in the ginger-treated group (P < 0.05)., Conclusion: Ginger efficiently reduced the lung damage and protected the lungs from severe damage due to hyperoxia and inflammation. Therefore, ginger may be an alternative option for the treatment of BPD.
- Published
- 2018
- Full Text
- View/download PDF
28. Influence of platelet count, platelet mass index, and platelet function on the spontaneous closure of ductus arteriosus in the prematurity.
- Author
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Kahvecioglu D, Erdeve O, Akduman H, Ucar T, Alan S, Çakır U, Yıldız D, Atasay B, Arsan S, and Atalay S
- Subjects
- Ductus Arteriosus, Patent diagnosis, Female, Humans, Infant, Newborn, Infant, Premature, Infant, Premature, Diseases diagnosis, Logistic Models, Male, Mean Platelet Volume, Platelet Count, Prognosis, Prospective Studies, Remission, Spontaneous, Blood Platelets physiology, Ductus Arteriosus, Patent blood, Infant, Premature, Diseases blood
- Abstract
Background: This study aims at evaluating the influence of platelet count, platelet mass index, and platelet function on the spontaneous closure of ductus arteriosus in prematurity., Methods: All preterm babies were divided into two groups, including Group 1 with "open PDA" and Group 2 with "closed PDA". The variables of platelet count, mean platelet volume, platelet mass index, and platelet function were analyzed and compared between two groups of patients to identify the factors that significantly influenced spontaneous closure of ductus arteriosus., Results: Twenty-four patients were in the "open PDA" group, whereas 36 patients were in the "closed PDA" group. Mean GA and BW were 27.6 ± 1.8 (23.1-30.4) and 28 ± 1.6 (23.4-30.6) weeks and 1009 ± 270 (585-1480) g and 1035 ± 298 (505-1500) g in "open PDA" and "closed PDA" groups, respectively (p > 0.05). The incidence of "Collagen-ADP > 130 s" was significantly higher in the "open PDA" group, and the levels of hemoglobin and hematocrit were significantly lower in the "open PDA" group (p < 0.05). Multivariate logistic regression analysis showed that respiratory distress syndrome (OR: 9, CI: 1.5-51.8) and collagen-ADP > 130 s (OR: 5.7 CI: 1.55-21.3) are two independent factors associated with ductal patency., Conclusion: This is the first study in the English literature providing evidence of the influence of platelet dysfunction on the spontaneous closure of ductus arteriosus in prematurity. Longer collagen-ADP duration is identified as a risk factor of ductal closure., (Copyright © 2017. Published by Elsevier B.V.)
- Published
- 2018
- Full Text
- View/download PDF
29. Urticaria and Angioedema Associated with Fluoxetine.
- Author
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Tuman TC, Tuman B, Polat M, and Çakır U
- Published
- 2017
- Full Text
- View/download PDF
30. Tardive Dyskinesia Associated with Bupropion.
- Author
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Tuman TC, Çakır U, Yıldırım O, and Camkurt MA
- Abstract
Present report describes a 46 year old male patient with a diagnosis of major depression who developed tardive dyskinesia during bupropion therapy. Our patient had no history of neuroleptic use and his laboratory and neurologic examinations were normal. He had no family history of neurologic diseases. Although bupropion induced dyskinesia has been previously reported in the literature, it is rare and our case is the first case regarding tardive dyskinesia.
- Published
- 2017
- Full Text
- View/download PDF
31. Transient tachypnea of the newborn: are there bedside clues for predicting the need of ventilation support?
- Author
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Kahvecioğlu D, Çakır U, Yıldız D, Alan S, Erdeve Ö, Atasay B, and Arsan S
- Subjects
- Female, Gestational Age, Humans, Infant, Newborn, Intensive Care Units, Neonatal, Male, Prospective Studies, Time Factors, Transient Tachypnea of the Newborn diagnosis, Oxygen Inhalation Therapy methods, Respiration, Artificial methods, Transient Tachypnea of the Newborn therapy
- Abstract
Decision making to transfer a late preterm or term neonate with the diagnosis of transient tachypnea of the newborn (TTN) to an intensive care unit for respiratory support is a challenge for caregivers in level one and two NICUs. The aim of this study was to identify "practical bedside clinical clues" that may help to predict the severity of disease and need for respiratory support in patients with the diagnosis of TTN. Newborns having the diagnosis of TTN were classified into two groups according to the intensity of the respiratory support. Infants receiving only supplemental oxygen and infants requiring nasal continuous positive airway pressure or mechanical ventilation constituted group 1 (mild) and group 2 (severe), respectively. Demographic, clinical and laboratory characteristics were compared between the two groups. Patients in group 2 had lower gestational age, higher Silverman and Richardson scores, longer mean duration of oxygen support and hospitalization. A positive correlation was found between subcostal and xiphoid retractions, asynchrony in chest-abdomen movements, arterial pH < 7.30, ratio of PaO < sub > 2 < /sub > / % inspired O < sub > 2 < /sub > < 1.2 and need of respiratory support (p < 0.05). We suggest that simple scores can help physicians to get a good sense of a given baby's likelihood of deterioration.
- Published
- 2016
- Full Text
- View/download PDF
32. Portal Vein Thrombosis of a Newborn with Corrected Total Anomalous Pulmonary Venous Return.
- Author
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Çakır U, Kahvecioğlu D, Alan S, Erdeve Ö, Atasay B, Uçar T, Arsan S, Çakmaklı H, Ertem M, and Atalay S
- Subjects
- Anticoagulants therapeutic use, Cardiopulmonary Bypass adverse effects, Heart-Lung Machine adverse effects, Heparin, Low-Molecular-Weight therapeutic use, Humans, Hypothermia, Induced adverse effects, Infant, Newborn, Male, Postoperative Complications diagnostic imaging, Postoperative Complications drug therapy, Ultrasonography, Doppler, Venous Thrombosis diagnostic imaging, Venous Thrombosis drug therapy, Portal Vein diagnostic imaging, Postoperative Complications etiology, Scimitar Syndrome surgery, Venous Thrombosis etiology
- Abstract
Total anomalous pulmonary venous return (TAPVR) is a rare and frequently isolated defect identified in 1% to 3% of all congenital heart diseases. To the best of our knowledge, portal vein thrombosis (PVT) associated with TAPVR has not been reported in the literature. We report a successfully managed PVT in a newborn with infracardiac-type TAPVR and review the literature. Anticoagulation therapies were used during the neonatal period to prevent thrombus progression. PVT should be kept in mind in TAPVR patients who have open heart repair with total correction. The treatment in each neonate should be individualized with consideration of the risk/benefit ratio.
- Published
- 2015
- Full Text
- View/download PDF
33. Increased neutrophil/lymphoctye ratio in patients with bipolar disorder: a preliminary study.
- Author
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Çakır U, Tuman TC, and Yıldırım O
- Subjects
- Adult, Blood Cell Count, Female, Humans, Male, Pilot Projects, Severity of Illness Index, Sex Factors, Bipolar Disorder blood, Lymphocytes, Neutrophils
- Abstract
Background: In this study, it has been aimed to investigate whether neutrophil-lymphocyte ratio (NLR) was higher in non-obese patients with bipolar disorder (BD) than in a healthy control group matched for age, sex, and body mass index, and also to determine if there was an interaction between NLR and severity of the bipolar disorder., Subjects and Methods: In this retrospective study, 103 non-obese patients with BD and 126 healthy control subjects were analyzed for complete blood count. The Young Mania Rating Scale (YMRS) was used to determine the severity of the disorder., Results: The NLR was higher in female patients than in female comparison subjects (3.2±2.2; versus 1.7±0.4) (p<0.001). Also, compared with the healthy male subjects, the male patients had significantly higher neutrophil/lymphocyte ratio (3.3±2.4; versus 2.0±0.7) (p<0.001). In the patients with bipolar disorder, NLR did not significantly correlate with severity (as measured with the YMRS) (r=0.052; p=0.204) and duration of the disorder (r=0.045; p=0.301)., Conclusions: Results of this study revealed that patients with bipolar disorder have statistically significant elevated NRL than healthy compares. According to this finding, elevated levels of NLR may be involved in inflammatory pathophysiology of bipolar disorder. Further studies are needed for a better understanding of the mechanism between elevation of NRL in patients with bipolar disorder.
- Published
- 2015
34. Report of a case of neonatal chylothorax that responded to long-term octreotide treatment, and review of the literature.
- Author
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Çakır U, Kahvecioğlu D, Yıldız D, Alan S, Erdeve Ö, Atasay B, and Arsan S
- Subjects
- Chylothorax complications, Chylothorax diagnosis, Chylothorax drug therapy, Drainage, Humans, Infant, Newborn, Male, Pleural Effusion, Prognosis, Chylothorax congenital, Gastrointestinal Agents therapeutic use, Octreotide therapeutic use
- Abstract
Chylothorax is a relatively uncommon condition defined as an abnormal collection of lymphatic fluid within the pleural space. Morbidity of congenital chylothorax (CC) is high, and prognosis is very poor if CC is associated with hydrops fetalis. Although the optimal treatment of CC has not been determined, conservative treatment and surgical intervention are employed. However, there is still little experience with the use of octreotide therapy for this condition, and optimal duration of the treatment for response evaluation is not known. We report a newborn with CC who presented with intrauterine bilateral pleural effusion and was resistant to conservative treatments. Octreotide (6 μg/kg/h) infusion was started on the 10th postnatal day due to ongoing pleural drainage. Although the patient improved rapidly with continuous administration of octreotide, we had to continue the drug for 151 days, even subcutaneously on outpatient follow-up. To the best of our knowledge, this patient is unique in receiving octreotide treatment for such a long time, with a successful outcome and a safe profile.
- Published
- 2015
35. [Letter to the Editor].
- Author
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Yıldız M, Boşgelmez Ş, Çakır U, Yazıcı E, Yazıcı AB, Turgut C, and Ay YL
- Subjects
- Humans, Psychiatry, Turkey, Mental Disorders
- Published
- 2013
36. Late neonatal hypocalcemic tetany as a manifestation of unrecognized maternal primary hyperparathyroidism.
- Author
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Çakır U, Alan S, Erdeve Ö, Atasay B, Şıklar Z, Berberoğlu M, and Arslan S
- Subjects
- Adult, Calcium blood, Diagnosis, Differential, Female, Humans, Hyperparathyroidism, Primary blood, Hypocalcemia blood, Hypocalcemia diagnosis, Infant, Newborn, Infant, Newborn, Diseases blood, Infant, Newborn, Diseases diagnosis, Male, Parathyroid Hormone blood, Pregnancy, Tetany, Time Factors, Hyperparathyroidism, Primary complications, Hypocalcemia etiology, Infant, Newborn, Diseases etiology, Pregnancy Complications
- Abstract
Maternal primary hyperparathyroidism causing hypercalcemia during pregnancy can suppress fetal and neonatal parathyroid hormone secretion. We report a newborn with transient hypoparathyroidism presented by hypocalcemic seizure and tetany on the 21st postnatal day in whom the final diagnosis was asymptomatic maternal primary hyperparathyroidism. Neonatal hypocalcemia usually occurs early in life in infants of maternal primary hyperparathyroidism, and although it is very rare, further investigation for unexplained late-onset hypocalcemia may reveal this diagnosis.
- Published
- 2013
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