DeepSide: a deep learning approach for drug side effect prediction

Drug failures due to unforeseen adverse effects at clinical trials pose health risks for the participants and lead to substantial financial losses. Side effect prediction algorithms have the potential to guide the drug design process. LINCS L1000 dataset provides a vast resource of cell line gene expression data perturbed by different drugs and creates a knowledge base for context specific features. The state-of-the-art approach that aims at using context specific information relies on only the high-quality experiments in LINCS L1000 and discards a large portion of the experiments. Here, we aim to boost the prediction performance by utilizing this data to its full extent. We experiment with 5 deep learning architectures. We find that a multi-modal architecture produces the best predictive performance when drug chemical structure (CS), and drug-perturbed gene expression profiles (GEX) are used. We observe that the CS is more informative than the GEX. A convolutional neural network-based model that uses only SMILES string representation of drugs provides 13.0% macro-AUC and 3.1% micro-AUC improvements over the state-of-the-art. We also show that the model is able to predict side effect-drug pairs that are reported in the literature but was missing in the ground truth side effect dataset

[Demonstration of Cryptosporidium parvum in immune suppressed rats using nested PCR] [İmmun Sistemi Baskılanmış Sıçanlarda Cryptosporidium parvum'un Nested PZR Yöntemi ile Gösterilmesi]

PubMed ID: 24192616[No abstract available

Landmine associated injuries in children in Turkey

This study aims to examine trends of injuries due to landmines and unexploded ordnance (UXO) and to determine problems during and after the treatment of children and adolescent victims in Turkey. Data from the records of 23 children injured from landmines and UXO were analyzed from April 2001 to October 2008. Cases consist of 21 (91.3%) males and two (8.7%) females with a mean age of 12.8 years. Cause of injury was landmine explosion in 20 (87.0%) and UXO in three (13.0%) cases. Injuries in upper and lower extremities were determined in eight (34.8%) children. Hand amputation was the result in 10 (43.5%) children where in two cases a leg, in one case an eye, in one case a hand and arm, in two cases a hand and leg, in one case an eye and a leg and in three cases a hand and eye were lost. One case of death was recorded from UXO with an autopsy performed. Contaminated areas in our region should be cleared according to international contracts to prevent injuries in children, centers providing rehabilitation services should be established and policies regarding social support for child victims should be ascertained. (c) 2009 Published by Elsevier Ltd and Faculty of Forensic and Legal Medicine

Detection of Pneumocystis in the nasal swabs of immune-suppressed rats by use of PCR and microscopy.

PubMed ID: 23403744Detection of Pneumocystis jiroveci colonization in lungs or oral samples due to high sensitivity of PCR methods results in undue treatment of patients without any symptoms of Pneumocystis pneumonia. The aim of the present study is to demonstrate Pneumocystis carinii in rats, immune suppressed by oral and subcutaneous administration of dexamethasone. Blood, oral, nasal and eye swabs were collected prior to immune suppression and 2, 6, 12 weeks after administration of dexamethasone. Also, samples were collected from lung, heart, liver, kidney, diaphragm, brain, spleen, tongue, muscle, eye, intestine, and feces. Cysts and trophozoites were investigated in stained slides and MSG gene was detected by PCR. The results showed that weight loss is significantly higher in rats administered oral dexamethasone (P<0.05). Microscopy was positive only in lungs of rats orally administered dexamethasone. PCR was positive in lungs and oral swabs of rats prior to the administration of dexamethasone. After the administration of dexamethasone, the MSG gene was detected in oral swabs, lungs, spleen, kidney and (for the first time) in nasal swabs. PCR was positive in nasal swabs during the second and sixth weeks of oral and subcutaneous administration of dexamethasone, respectively. Presence of P. jiroveci in nasopharyngeal aspirate, oropharyngeal wash, oral swab, induced sputum or BAL, and absence in nasal swab in a patient without symptoms of PCP may support clinician's decision regarding colonization. Overall, detection of P. carinii in nasal swabs of rats by PCR demonstrated that nasal sampling can be used for the diagnosis of Pneumocystis pneumonia

Methyl palmitate attenuates lipopolysaccharide-induced acute lung injury in mice

Aim: The study is aimed to determine the beneficial effects of methyl palmitate (MP) which has antioxidant and anti-inflammatory effects demonstrated on murine model of acute lung injury induced by lipopolysaccharide (LPS)