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Background Abstraction of critical data from unstructured radiologic reports using natural language processing (NLP) is a powerful tool to automate the detection of important clinical features and enhance research efforts. We present a set of NLP approaches to identify critical findings in patients with acute ischemic stroke from radiology reports of computed tomography (CT) and magnetic resonance imaging (MRI). Methods We trained machine learning classifiers to identify categorical outcomes of edema, midline shift (MLS), hemorrhagic transformation, and parenchymal hematoma, as well as rule-based systems (RBS) to identify intraventricular hemorrhage (IVH) and continuous MLS measurements within CT/MRI reports. Using a derivation cohort of 2289 reports from 550 individuals with acute middle cerebral artery territory ischemic strokes, we externally validated our models on reports from a separate institution as well as from patients with ischemic strokes in any vascular territory. Results In all data sets, a deep neural network with pretrained biomedical word embeddings (BioClinicalBERT) achieved the highest discrimination performance for binary prediction of edema (area under precision recall curve [AUPRC] > 0.94), MLS (AUPRC > 0.98), hemorrhagic conversion (AUPRC > 0.89), and parenchymal hematoma (AUPRC > 0.76). BioClinicalBERT outperformed lasso regression (p Conclusions Our study demonstrates robust performance and external validity of a core NLP tool kit for identifying both categorical and continuous outcomes of ischemic stroke from unstructured radiographic text data. Medically tailored NLP methods have multiple important big data applications, including scalable electronic phenotyping, augmentation of clinical risk prediction models, and facilitation of automatic alert systems in the hospital setting.

Background: The posterior wall of the nasopharynx is composed of loose connective tissue that includes many important anatomical structures. Various structures, such as the opening of the Eustachian tube (ET), the Rosenmuller fossa (RF), and the pharyngeal bursa (PB) are found here. Aim: To evaluate the nasopharynx posterior wall anatomic structures, including the Eustachian tube, Rosenmuller fossa, and pharyngeal bursa with cone-beam computed tomography. Materials and Methods: The depth, width, and length of the Eustachian tube, Rosenmuller fossa, and pharyngeal bursa were measured in 150 patients using axial-sagittal cone-beam computed tomography. The Eustachian tube and Rosenmuller fossa distance to the midsagittal plane, the coronal region passing through the posterior end of the nasal septum, the superior-inferior extremity of the recesses, and the nasal floor plane distance were measured. The relationship between Rosenmuller fossa types and other parameters were evaluated. Results: The incidence of right Rosenmuller fossa types 1, 2, and 3 were 16%, 18%, and 66%, respectively, and that of the left Rosenmuller fossa types 1, 2, and 3 were 16%, 19.3%, and 64.7%, respectively. The mean pharyngeal bursa width, length, and depth were 10.8, 5.7, and 4.0 mm, respectively; those of the Eustachian tube were 5.6, 7.1, and 7.3 m, respectively; those of the right Rosenmuller fossa were 4.0, 12.4, and 10.5 mm, respectively; and those of the left Rosenmuller fossa were 3.8, 12.5, and 10.9 mm, respectively. Conclusions: The posterior wall of the nasopharynx contains several important anatomical structures. Evaluation of these using cone-beam computed tomography has many clinical and radiological advantages. To understand and interpret the coincidental findings in CBCT, dental radiologists should have access to more detailed information concerning the anatomy of the nasopharynx.

Among the major pests of vegetables are Root-Knot Nematodes (Meloidogyne spp.) (RKNs), which cause loss of production due to galling and reduction in root development and shoot growth. Herein, the efficacy of plant extracts of Capsicum frutescens, Hyoscyamus niger, Melia azedarach, Xanthium strumarium and Achillea wilhelmsii were evaluated at 3 concentrations (3, 6, and 12%) against Meloidogyne javanica on pepper and eggplant. Experiments were carried in pots under greenhouse condition, using pepper cv. Charleston and eggplant cv. Kemer as assay plants that are commonly cultivated in Turkey. Approximately 3,000 eggs of M. javanica were used for hatching test and 1,000 J2 of M. javanica were used for mortality test. Approximately, 5 mL of plant extracts were added by a syringe into the soil. Each experiment was arranged in a Randomized Block Design (RBD) with 5 replications. The control (+) pots received water containing M. javanica and the control (-) pots received only water. At the end of the experiment, plants heights and weights were measured. According to the results, all plant extracts showed a different level of nematicidal activity at 3, 6, and 12% concentrations. The plant extracts of H. niger, and X. strumarium at 12% concentration were found more efficient than M. azedarach, C. frutescens and A. wilhelmsii extract on egg hatching, on both pepper and eggplant plants. J2s mortality experiments showed that 12% concentration of H. niger, M. azedarach and X. strumarium were more effective against M. javanica than the other treatments, on both pepper and eggplant plants. In general, there was no significant difference was found among nematode mortality and growth parameters (such as plant height, the fresh and dry weights of the above-ground parts of the plants, fresh and dry weights of roots of both pepper and eggplant plants). Accordingly, using H. niger and X. strumarium plant extracts can provide effective methods of M. javanica control. © 2018, Tarbiat Modares University. All rights reserved.

Objective: Children with Turner syndrome (TS) have a specific growth pattern that is quite different from that of healthy children. Many countries have population-specific growth charts for TS. Considering national and ethnic differences, we undertook this multicenter collaborative study to construct growth charts and reference values for height, weight and body mass index (BMI) from 3 years of age to adulthood for spontaneous growth of Turkish girls with TS. Methods: Cross-sectional height and weight data of 842 patients with TS, younger than 18 years of age and before starting any therapy, were evaluated. Results: The data were processed to calculate the 3rd, 10th, 25th, 50th, 75th, 90th and 97th percentile values for defined ages and to construct growth curves for height-for-age, weight-for-age and BMI-for-age of girls with TS. The growth pattern of TS girls in this series resembled the growth pattern of TS girls in other reports, but there were differences in height between our series and the others. Conclusion: This study provides disease-specific growth charts for Turkish girls with TS. These disease-specific national growth charts will serve to improve the evaluation of growth and its management with growth-promoting therapeutic agents in TS patients.

WOS: 000358899300006 The root-knot nematodes (Meloidogyne spp.) (RKNs) are one of the major pests of vegetables which cause yield losses due to galling and reduction in root development and shoot growth. Herein, effects of five different plants extracts; pepper, Capsicum frutescents (Cf); henbane, Hyoscyamus niger (bin); bead-tree, Melia azedarah (Ma); common cocklebur, Xanthium strumarium (Xs); and yarrow, Achillea wilhelmsii (Aw) on eggs and second stage juveniles (J2s) of the RKN (Meloidogyne javanica) were evaluated in vitro tests. All plant extracts showed different levels of anti-nematode's activity. Plant extract concentrations of 3, 6 and 12% for Hn, Xs and Ma caused 100% inhibition of egg hatching, followed by Cf and Aw. Ma and Xs were more effective for inducing mortality among J2s than the other tested extracts. Scientific and Technical Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [TUBITAK 111O784] The authors are grateful to Assoc. Prof. Dr. Z. Devran (Dept. of Plant Protection, Fac. of Agriculture, Antalya Univ., Antalya, Turkey) for supplying the root-knot nematode (M. javanica). Thanks also to the Plant Protection Central Research Institute, Ankara, Turkey for supplying the plant extracts. This study was supported by the Scientific and Technical Research Council of Turkey (TUBITAK 111O784).

WOS: 000358899300019 Potato (Solanum tuberosum L.) is one of the most important vegetable crops in Turkey as well in the world. Potato plants are attacked by a large number of insect pests such as aphids, beetles, leafhoppers and lepidopterous pests under both field and storage conditions. The Colorado potato beetle (CPB) [Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae)] and the potato tuber moth (PTM) [Phihorimaea operculella (Zeller) (Lepidoptera: Gelechiidae)] are the most destructive pests in potatoes grown areas. Many pesticides that used to control the potato pests are very toxic to environment and human. An alternative approach to the commercial pesticides is using biological agents like fungi. Purpureocillium lilacinum was described more than a century ago and is a commonly occurring fungus in soil. P. lilacinum (syn: Paecilomyces lilacinus) is the most widely tested fungus for the control of nematodes, aphids and insects. The fungus was determined in Turkey but its molecular identification has not been done yet. In this study, a Turkish isolate of P. lilacinum was identified by classical (morphologic and morphometric properties) and molecular methods. Also, the study concerned with the effect of different conidial concentrations of the fungal isolate on mortality rates of CPB and PTM at different temperatures. P. lilacinum was found to be most effective on the last larval instar of CPB and PTM (33.2 and 43.3% mortality, respectively) on 10th day of treatment with the fungal concentration of 108cfu ml(-1) at 25 degrees C. This fungus developed on all dead larvae and was highly susceptible at the tested temperatures, but its activity decreased at 15 degrees C. Findings of this study showed a potential of the fungus as a bioagent against the CPB and the PTM. Scientific and Technical Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [TUBITAK 111O784] A part of this study (preparation of P. lilacinum) was supported by the Scientific and Technical Research Council of Turkey (TUBITAK 111O784). Thanks are due to Drs. F.D. Erdogus and M. Alkan (Dept. of Entomology, Plant Protection Central Research Institute, Ankara-Turkey) for their assisstance throughout this study.

Objective: There are studies that conclude that Helicobacter pylon is transmitted through fecal oral and oral oral routes. In this study, we aimed to determine the source and mode of transmission of H. pylon in H. pylori infected patients by comparing H. pylori species isolated both from drinking water samples and gastric mucosa samples obtained by endoscopy from people who had dyspeptic symptoms and had been using these sampled water supplies as drinking water by biochemical and genotypic analysis. Material and Method: Twelve drinking water samples from different points and 37 gastric mucosa samples obtained by endoscopy from patients were collected. 109 bp length DNA segments from 16S rRNA location of H. pylon genome were amplified by nested PCR method from all water and human samples and the amplified genome were sequenced obtained from 7 of 12 water samples and 27 of 37 biopsy samples. The sequences were compared with the data from NIH by BLAST search program. Alignment has been performed by MEGA 4 alignment program between water and patient samples. Results: All the DNA sequences were detected to be related to the H. pylon genome with 92 to 98% similarity. With alignment, 85% to 100% matching were detected between patient and water supply samples of which all were already confirmed as H. pylori genome (92 to 98% similarity). Conclusion: These results suggest that contaminated and insufficiently disinfected drinking water supplies might be a reservoir for H. pylon which is a readily source for transmission to human in our region. Turkish Scientific Council (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [C-104-I-036] This research was supported by a grant from the Turkish Scientific Council (TUBITAK) (C-104-I-036).

In this study, two collections were evaluated: 64 varieties in the main collection of Malatya, while 12 varieties were investigated in Adana and Pozanti. Phenotypical and agronomical performances were combined. Characterisation was performed according to the descriptors of UPOV for shape in profile view, shape in frontal view, symmetry along the suture, dept of suture, dept of pedicel cavity, shape of tip, skin pubescence, ground colour, over colour, texture of flesh, adherence of stone to flesh, bitterness of kernel characters of 64 varieties in Malatya. The other characters such as fruit size, flesh juiciness, eating quality, fruit attractiveness, stone size and stone shape were done according to IPBGR descriptors in Malatya varieties. The characterisation of varieties in Pozanti and Adana were performed according to IPBGR apricot descriptor. In addition, self pollination studies were carried out, sensitivity to monilinia were evaluated and the presence of viruses (PPV, ACLSV, PNRSV) has been tested in important Turkish apricot varieties.

Using a vertical differentiation model of endogenous growth with stochastic R&D activity, we characterise the optimal patent lifetime a government would set in order to maximise economic growth. We show that a finite patent lifetime does exist and is unique provided that the expected rate of return from R&D is sufficiently large. Additionally, we analyse the impact of the level of competition in the R&D sector, the interest rate, the monopoly profit and the productivity parameter of research technology on this optimal patent lifetime.