alperbulbul1/Variant_Prediction_Tool: Initial Release

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Olgu sunumu: 83 yaşındaki bir hastada primer varisella enfeksiyonu

İstanbul Bilim Üniversitesi, Tıp Fakültesi.Varisella enfeksiyonu Varicella zoster virus'un (VZV) etken olduğu, tüm dünyada yaygın olarak görülen çocukluk çağının bulaşıcı hastalıklarından biridir. Primer enfeksiyonu geçiren olguların %90'ı 10 yaşın altındadır. Hastalığın şiddeti yaşla birlikte artar. Yetişkinler, immunsuprese bireyler ve gebeler visseral tutulum ve komplikasyonlar açısından risk altındadır (1,2). Yoğun bakım ünitesinde izlenen ve kritik hastalıkları olanlar immunolojik olarak zayıf olma eğilimindedirler ve bu hastalarda çeşitli fırsatçı enfeksiyonlar sık görülür. Sistemik VZV enfeksiyonu bu grup hastalarda beklenen ve sık görülen fırsatçı enfeksiyonlardan biri değildir. Ancak enfeksiyonun akla getirilip tanının erken konulması ve gerekli tedavinin düzenlenmesi komplikasyon riskini azaltır (3). Burada birçok sistemik hastalığı bulunan 83 yaşındaki bir hastada gelişen sistemik VZV enfeksiyonu sunulmaktadır

Var3PPred: variant prediction based on 3-D structure and sequence analyses of protein-protein interactions on autoinflammatory diseases

We developed a pathogenicity classifier, named Var3PPred, for identifying pathogenic variants in genes associated with autoinflammatory disorders. Our comprehensive approach integrates protein-protein interaction analysis and 3D structural information. Initially, we collected a dataset of 702 missense disease-associated variants from 35 genes linked to systemic autoinflammatory diseases (SAIDs). This dataset, sourced from the Infevers database, served as the training and test sets. We used the SMOTE algorithm to balance the dataset comprising 130 benign and 572 pathogenic variations. Our approach included 3D docking analysis of protein-protein interactions, utilizing data from the STRING and Intact databases. We weighted ZDOCK and SPRINT values in accordance with HGPEC gene rank scores for robustness. Additionally, we integrated sequential and structural features, such as changes in folding free energies (ΔΔ G), accessible surface area, volume, per residue local distance difference test (pLDDT) scores, and position specific independent count (PSIC) scores. These features, calculated using PyRosetta and AF2 computed structures, provided insights into amino acid conservation at variant positions and the impact of variants on protein structure and stability. Through extensive hyperparameter tuning of six machine learning algorithms, we found the random forest classifier to be the most effective, yielding an AUROC of 99% on the test set. Var3PPred outperformed three other classifiers, SIFT, PolyPhen, and CADD, on an unseen test set of a SAID-related gene. This demonstrates its capacity for pathogenicity classification of SAID variations. The source code for Var3PPred and the predictions for all 420 missense variants of uncertain significance from the Infevers database are available on GitHub: (https://github.com/alperbulbul1/Var3PPred)

Turkey psoriasis treatment guide-2016

İstanbul Bilim Üniversitesi, Tıp Fakültesi.Psoriasis; kronik, tekrarlayıcı, etiyolojisi kesin olarak bilinmeyen, enflamatuvar, hiperproliferatif bir deri hastalığıdır. Deri tutulumu yanında sıklıkla eklem tutulumu ile seyretmekte ancak metabolik sendrom, kardiyovasküler hastalık, psikolojik/psikiyatrik bozukluklar, enflamatuvar barsak hastalığı gibi komorbiditelerin psoriasise eşlik etmesi, altta yatan enflamatuvar sürecin birçok organa zarar verdiğini göstermektedir. Bunun yanı sıra psoriasis, hastaların yaşam kalitelerini de önemli derecede etkilemektedir. Psoriasis hastalarında yaşam kalitesi, fiziksel psikolojik değerlendirmelerde kanser ve diyabet gibi diğer temel kronik hastalıklar kadar etkilenmektedir.Psoriasis is a common, chronic, recurrent, inflammatory disease of the skin with unknown etiology. In addition to skin involvement, joint involvement is often seen in psoriasis; however as comorbidities including metabolic syndrome, cardiovascular diseases, psychological/psychiatric disorders and inflammatory bowel disease accompany psoriasis, the inflammatory process underlying has been shown to damage several organs. It is also known that the risk of mortality is increased in patients with severe psoriasis. What’s more, psoriasis significantly affects the patients quality of life

Emerin expression in well differentiated epithelial lesions of thyroid: implications in papillary thyroid carcinoma diagnosis and predicting malignant behavior

İstanbul Bilim Üniversitesi, Tıp Fakültesi.Recently, it has been reported that identifying nuclear membrane irregularities with anti-emerin antibody is useful for papillary thyroid carcinoma diagnosis. However, literature regarding the significance of emerin immunohistochemistry in thyroid is limited. We evaluated the diagnostic accuracy of the well-established nuclear alterations, nuclear protrusions and recently described nuclear shapes (garlands and star-like shapes) with emerin immunohistochemistry and hematoxylin- eosin stain in thyroid lesions. We further evaluated the diagnostic accuracy measures of tissue microarrays evaluated with both stains, to detect whether emerin immunohistochemistry improves the diagnostic accuracy for papillary thyroid carcinoma

Patch Test Results to European Baseline Series in Turkey

Background Patch testing with the European Baseline Series (EBS) is an essential diagnostic tool for the assessment of allergic contact dermatitis. Objective The aims of the study were to describe the most common contact allergens identified with patch testing in Turkey and to establish the distribution of contact allergens among different regions in Turkey. Patients and Methods Twelve centers consisting of tertiary health care institutions were included in the study. A total of 1169 patients were patch tested with the EBS from 2015 to 2017. Results A total of 596 patients (51.0%) had 1 or more positive patch test reactions to the EBS. A total of 30.2% (n = 353) of those tested had clinical relevance. Contact sensitivity was more common in young patients. The most common 10 allergens were nickel sulfate (20.4%), followed by textile dye mix (8.6%), cobalt chloride (8.3%), potassium dichromate (8.0%), p-phenylenediamine base (4.5%), balsam of Peru (4.3%), methylchloroisothiazolinone/methylisothiazolinone (3.8%), thiuram mix (3.6%), fragrance mix I (3.0%), and methylisothiazolinone (2.9%). Conclusions This study provides a comprehensive profile of patch test results with the EBS in Turkey. An ongoing decrease in contact allergy to methylchloroisothiazolinone/methylisothiazolinone and methylisothiazolinone was observed. Textile dye mix and p-phenylenediamine are beginning to pose a new risk in Turkey

Patch Test Results to European Baseline Series in Turkey: A Prospective and Multicenter Study

Background Patch testing with the European Baseline Series (EBS) is an essential diagnostic tool for the assessment of allergic contact dermatitis. Objective The aims of the study were to describe the most common contact allergens identified with patch testing in Turkey and to establish the distribution of contact allergens among different regions in Turkey. Patients and Methods Twelve centers consisting of tertiary health care institutions were included in the study. A total of 1169 patients were patch tested with the EBS from 2015 to 2017. Results A total of 596 patients (51.0%) had 1 or more positive patch test reactions to the EBS. A total of 30.2% (n = 353) of those tested had clinical relevance. Contact sensitivity was more common in young patients. The most common 10 allergens were nickel sulfate (20.4%), followed by textile dye mix (8.6%), cobalt chloride (8.3%), potassium dichromate (8.0%), p-phenylenediamine base (4.5%), balsam of Peru (4.3%), methylchloroisothiazolinone/methylisothiazolinone (3.8%), thiuram mix (3.6%), fragrance mix I (3.0%), and methylisothiazolinone (2.9%). Conclusions This study provides a comprehensive profile of patch test results with the EBS in Turkey. An ongoing decrease in contact allergy to methylchloroisothiazolinone/methylisothiazolinone and methylisothiazolinone was observed. Textile dye mix and p-phenylenediamine are beginning to pose a new risk in Turkey