Aslı Suner

PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants

Transposable elements (TEs) are mobile DNA sequences that play roles in gene regulation, and have a potential to influence the expression of nearby genes by functioning as cis-regulatory sequences. However, bioinformatics tools facilitating analysis of the associations between TEs and nearby genes in plants are still lacking. We therefore reanalyzed the comprehensive annotation data of gene models and TEs of 11 plant species available in Ensembl Plants database, and built an up-to-date, unique tool called PlanTEnrichment, enabling enrichment analysis of TEs located within the upstream regions of a given gene list. PlanTEnrichment takes, for example, a group of differentially expressed genes under a particular biological condition as input and returns the list of TEs associated with those genes, along with their calculated enrichment scores and statistical significances. PlanTEnrichment is freely available at http://tools.ibg.deu.edu.tr/plantenrichment/ and is likely to substantially enhance our understanding of the role of TEs in diverse biological processes.

C-Reactive Protein and Platelet-Lymphocyte Ratio as Potential Tumor Markers in Low-Alpha-Fetoprotein Hepatocellular Carcinoma

The hepatocellular carcinoma (HCC) tumor marker alpha-fetoprotein (AFP) is only elevated in about half of the HCC patients, limiting its usefulness in following the effects of therapy or screening. New markers are needed. It has been previously noted that the inflammation markers C-reactive protein (CRP) and platelet-lymphocyte ratio (PLR) are prognostically important and may reflect HCC aggressiveness. We therefore examined these 2 markers in a low-AFP HCC cohort and found that for HCCs > 2 cm, both markers significantly rise with an increasing maximum tumor diameter (MTD). We calculated the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Youden index value for each marker, and their area-under-the-curve values for each MTD group. Patients were dichotomized into 2 groups based on the CRP and PLR from the receiver-operating characteristic curve analysis. In the logistic regression models of the 4 different MTD patient groups, CRP and PLR levels were statistically significant to estimate MTD in univariate logistic regression models of MTD groups > 2 cm. CRP and PLR were then combined, and the combination was statistically significant to estimate MTD groups of 3-, 4-, and 5-cm cutoffs. CRP and PLR thus have potential as tumor markers for low-AFP HCC patients, and possibly for screening.

Circulating Lipocalin-2 Levels Are Associated With Soluble Lectin-Like Oxidized Low-Density Lipoprotein Receptor-1 Levels In Type 2 Diabetic Patients

Purpose: Diabetes mellitus is associated with atherosclerotic and cardiovascular diseases. Our aim was to investigate the levels of lipocalin-2 (LCN-2) and soluble Lectin-like oxidized low-density lipoprotein receptor-1(sLOX-1) levels in both diabetics and prediabetic with comparison to non-diabetic subjects. We also examined the association of LCN-2 with sLOX-1 and albuminuria Methods: One hundred forty-two subjects with type 2 diabetes mellitus, 32 prediabetic subjects, 58 non-diabetic controls were consecutively enrolled in this study. LCN-2 and sLOX-1 levels were measured with ELISA assays. Results: LCN-2 levels didn’t show significant difference between diabetics, prediabetic and control groups (p = 0.864). sLOX-1 levels were significantly lower in diabetic group (2.53 ng/mL, median) compared with prediabetic (2.84 ng/mL, median; p = 0.041) and control groups (3.00 ng/mL, median; p = 0.001). Multiple linear regression analysis showed that urinary albumin excretion and sLOX1 were independently associated with LCN-2. When logistic regression analysis was performed LCN-2 was independent factor determining albuminuria (p = 0.021; OR, 1.001; (1.000-1.001) 95% CI). Conclusion: Our study provides the first clinical evidence demonstrating serum LCN-2 concentrations are independently associated with sLOX-1 levels which were found to be lower in type 2 diabetics unexpectedly. LCN-2 was also associated with albuminuria. Received: September 24,2018; Accepted: October 01,2018; Published: October 02,2018 *Corresponding author : Banu Sarer Yurekli, Ege University Faculty of Medicine, Department of Endocrinology, Ankara Street, Bornova, Izmir, Turkey, 35100,Tel: +90 5055250373;Fax: +902323247880;E-mail: bsareryurekli@yahoo.com

The role of mean platelet volume in the early detection of acute bronchiolitis: A prospective study: XXXX

Acute bronchiolitis might be associated with morbidity and mortality in infants. The aim of this study was to evaluate the role of mean platelet volume (MPV) in the prediction of acute bronchiolitis.

Evaluation of infectious diseases and clinical microbiology specialists’ preferences for hand hygiene: analysis using the multi-attribute utility theory and the analytic hierarchy process methods

BackgroundHand hygiene is one of the most effective attempts to control nosocomial infections, and it is an important measure to avoid the transmission of pathogens. However, the compliance of healthcare workers (HCWs) with hand washing is still poor worldwide. Herein, we aimed to determine the best hand hygiene preference of the infectious diseases and clinical microbiology (IDCM) specialists to prevent transmission of microorganisms from one patient to another.MethodsExpert opinions regarding the criteria that influence the best hand hygiene preference were collected through a questionnaire via face-to-face interviews. Afterwards, these opinions were examined with two widely used multi-criteria decision analysis (MCDA) methods, the Multi-Attribute Utility Theory (MAUT) and the Analytic Hierarchy Process (AHP).ResultsA total of 15 IDCM specialist opinions were collected from diverse private and public hospitals located in İzmir, Turkey. The mean age of the participants was 49.73 ± 8.46, and the mean experience year of the participants in their fields was 17.67 ± 11.98. The findings that we obtained through two distinct decision making methods, the MAUT and the AHP, suggest that alcohol-based antiseptic solution (ABAS) has the highest utility (0.86) and priority (0.69) among the experts’ choices.ConclusionIn conclusion, the MAUT and the AHP, decision models developed here indicate that rubbing the hands with ABAS is the most favorable choice for IDCM specialists to prevent nosocomial infection.

The evaluation of the sensitivity and specificity of wrist examination findings for predicting fractures

Background: The aim of this study was to evaluate the sensitivity and specificity of physical examination findings and functional tests in adult acute wrist trauma patients who presented to the emergency department (ED) and to create a reliable and practical clinical decision rule for determining the necessity of radiography in wrist trauma. Methods: This prospective observational study was conducted in a tertiary ED. Each patient was checked for 18 physical examination findings and functional tests. Patients with suspected fracture were enrolled consecutively. Antero‐posterior and lateral wrist views were performed for each patient. All radiographical studies were interpreted by an orthopedic surgeon. The prevalence, sensitivity and specificity, negative and positive predictive values of each finding were calculated. A modeling for predicting fractures was created using computer. Results: 207 patients were evaluated and 69 patients (33.3%) had fractures. The most common encounterd fracture site was distal radius (29.5%). The most sensitive examination finding was pain in dorsiflexion (95.7%) and the most specific finding was ecchymosis (97.8%). Wrist edema, deformity and pain aggravated by pronation were found to be strong predictors of fracture. The area under the receiver operating characteristic curve at internal validation for a prediction model based on these three predictors was 0.88 (95% CI: 0.83–0,93). The overall sensitivity and specificity of this model were 94% (95% CI: 85–98%) and 51% (95% CI 43–60%) respectively. According to the model created in this study, 34% of acute blunt wrist trauma patients do not require any X‐ray imaging. Conclusions: This triple modeling may be used as an effective decision rule for predicting all wrist fractures in the ED and in the disaster setting.

Effects of environmental factors and storage conditions on the performance of Olyset® Plus against sand flies in WHO cone bioassays.

BACKGROUND Leishmaniasis, visceral and cutaneous, is seen in Turkey and has both public and veterinary importance. So far, four Leishmania species and their vectors have been detected in Turkey. Vector control is essential in endemic areas and several personal protection methods are available including long-lasting insecticidal nets (LLINs). In this study, we aimed to measure the effects of usage and storage conditions on LLINs in a village-scale study. METHODS Olyset(®) Plus bed nets were set up in different climatic conditions (rain, exposed to sunlight and humidity) and collected after 6 months. The effectiveness of bed nets were tested by WHOs cone test method using wild-caught sand flies. RESULTS Bed nets, which were placed directly exposed to sunlight (A1, A2) showed lower (17.2%) knock down effect compared to bed nets placed indoors (A3, B1). Twenty-four hour mortality was 100% for the five study groups (A2, A3, B1, C1, C2) whereas group A1 was found to have a lower mortality rate (44.4%). CONCLUSION Bed nets need to avoid direct exposure to sunlight. When used and stored in appropriate conditions (cool, well-ventilated place away from sunlight) they can be used as an effective vector control tool in endemic areas.