Clustering 16S rRNA for OTU prediction: A similarity based method

To study the phylogeny and taxonomy of samples from complex environments Next-generation sequencing (NGS)-based 16S rRNA sequencing , which has been successfully used  jointly with the PCR amplification and NGS technology. First step for many downstream analyses is clustering 16S rRNA sequences into operational taxonomic units (OTUs). Heuristic clustering is one of the most widely employed approaches for generating OTUs in which one or more seed sequences to represent each cluster are selected. In this work we chose five random seeds for each cluster from a genes library, and  we present a novel distance measure to cluster bacteria in the sample. Artificially created sets of 16S rRNA genes selected from databases are successfully clustered with more than %98 accuracy, sensitivity, and specificity

Bor atıklarının Aerojel üretiminde değerlendirilmesi

06.03.2018 tarihli ve 30352 sayılı Resmi Gazetede yayımlanan “Yükseköğretim Kanunu İle Bazı Kanun Ve Kanun Hükmünde Kararnamelerde Değişiklik Yapılması Hakkında Kanun” ile 18.06.2018 tarihli “Lisansüstü Tezlerin Elektronik Ortamda Toplanması, Düzenlenmesi ve Erişime Açılmasına İlişkin Yönerge” gereğince tam metin erişime açılmıştır.Bu çalışmada, ETİ maden A.Ş.'den temin edilen sodyum içerikli boraks şlamı atığı hammadde olarak kullanılmıştır ve sol-jel üretim tekniğiyle borasilikat aerojellerin üretilmesi amaçlanmıştır. Yapılan çalışma ile bor atığının endüstriyel olarak aerojel üretiminde kullanılabilirliğinin arttırılması hedeflenmiştir. Kullanılan hammaddenin tane boyutunu değiştirmek ve kimyasal reaksiyonları hızlandırmak için başlangıç tozuna 0s, 1s ve 2s mekanik aktivasyon işlemi yapılmıştır. Böylece 0s, 1s, 2s aktive edilen boraks şlamı atığı sol-jel üretim tekniği kapsamında HCl asitle çözeltiye alınarak sol çözeltisi elde edilmiştir ve NaOH baz katalizörü ilavesiyle jelleşme meydana getirilmiştir. Jelleşme meydana geldikten sonra olgunlaşma aşamasına tabii tutulmuştur ve sonrasında çeşitli kimyasallar kullanılarak jel içindeki istenmeyen maddeler uzaklaştırılmış, jelin bağ yapısının dayanımının arttırılması sağlanmıştır. Isıtıcı kurutma ve dondurucu kurutucu kullanılarak aerojellerin kurutulması işlemi ile borasilikat aerojel tozları sentezlenmiştir. Sentezlenen aerojel tozları XRD, SEM, FESEM, EDS, FTIR, tane boyut analizi ve termal iletkenlik ölçümü analizi ile karakterize edilmiştir. Analizler sonucunda, borasilikat aerojel tozlarının yapısında yüksek miktarda gözeneklerin olduğu gözlenmiştir ve buna bağlı olarak düşük yoğunluğa, iyi derecede toz akışına, B-Si ve B-O bağlarına ve iyi termal iletkenlik katsayısı gibi özelliklere sahip katma değeri yüksek bir yalıtım malzemesi elde edilmiştir. Anahtar kelimeler: Borasilikat aerojel, sol-jel üretim tekniği, mekanik aktivasyonIn this study, the borax slime (slurry) waste supplied from ETİ maden A.Ş. containing sodium content was used as raw material and the aim was to produce borasilicate aerogels by left-gel production tecnique. The aim of this study is to increase the industrial usability of boron waste. In order to change the grain size of the raw material and accelerate chemical reactions 0h, 1h and 2h mechanical activation process was applied to the starting powder. Thus 0h, 1h, 2h activated borax slime waste within left-gel production technique the left-solution was obtained in solution with HCl acid and gelling was formed by the addition of NaOH base catalyst. After gelation occured, it was subjected to the maturation stage and then, by using various chemicals, unwanted materials was removed from the gel, as a result the strength of bond structure of the gel was increased. Borasilicate airgel powders were synthesized by using atmospheric drying and freezing dryer techniques. The synthesized aerogel powders were characterized by XRD, SEM, FESEM, EDS, FTIR, particle size analysis and thermal conductivity measurement analysis. As a result of the analyzes, it was observed that there was a high amount of pores in the structure of borasilicate airgel powders and consequently a high value-added insulating material with low density, good powder flow, B-Si and B-O bonds and good thermal conductivity coefficient is obtained. Keywords: Borasilicate aerogels, left-gel production technique, mechanical activatio

EVALUATION OF ADMINISTRATIVE EFFECTIVENESS LEVELS OF ACADEMICIANS: FACULTY OF SPORT SCIENCES AND SCHOOL OF PHYSICAL EDUCATION AND SPORTS EXAMPLE

Background/Objective: The purpose of this study is to examine the managerial effectiveness levels of the academicians who work in the sports science faculty and School of Physical Education and Sports.Methods: In the study, a descriptive scanning method aimed at revealing the current situation has been used. For the purposes of this study, the academicians population of Turkey in the research universities working in sports science and sports colleges with the faculty of physical education, from which a sample is chosen, which is determined by simple random sampling method, which consists of volunteer academicians (n=178) working at the faculties of sport sciences and school of physical education and sports of universities such as Erciyes, Selçuk, Ömer Halisdemir, Gaziantep, Dumlupınar, Uşak, Karamanoğlu Mehmet Bey, Fırat, Süleyman Demirel, Sakarya, Balıkesir, Gelişim, Esenyurt, Muğla Sıtkı Koçman ve Bingöl universities. A managerial efficacy scale developed by Murry (1993) and implemented in the Turkish version by İra and Şahin (2010) was used to measure managerial effectiveness. The obtained data was recorded with the package program "IBM SPSS 22". Kruskal Wallis analysis was applied as statistical process.Results: The level of managerial effectiveness of academicians is moderate and advanced, the level of managerial effectiveness is related to age, department, title and professional experience, and also there is a relation between the progress of age, title and professional experience of academicians and the development of managerial effectiveness. It can be assumed that this situation originated from the situations such as the maturity of academicians' knowledge and experience, efforts to improve their skills, the adoption of the management concept of modern life, self-evaluation and autonomy as well as being able to adapt to scientific, cultural and social changes. The development of managerial effectiveness perceptions and managerial skills of young academics can be supported by managerial development seminars. Determining the managerial perceptions of the faculty members who work in different faculties and higher schools may contribute to the updating of the managerial perspective.  Article visualizations

Privacy-preserving publishing of hierarchical data

Many applications today rely on storage and management of semi-structured information, for example, XML databases and document-oriented databases. These data often have to be shared with untrusted third parties, which makes individuals’ privacy a fundamental problem. In this article, we propose anonymization techniques for privacy-preserving publishing of hierarchical data. We show that the problem of anonymizing hierarchical data poses unique challenges that cannot be readily solved by existing mechanisms. We extend two standards for privacy protection in tabular data (k-anonymity and ℓ-diversity) and apply them to hierarchical data. We present utility-aware algorithms that enforce these definitions of privacy using generalizations and suppressions of data values. To evaluate our algorithms and their heuristics, we experiment on synthetic and real datasets obtained from two universities. Our experiments show that we significantly outperform related methods that provide comparable privacy guarantees

The comparison of bone mineral density in primary hyperparathyroidim, vitamin D induced secondary hyperparathyroidism, and patients with both condition: a single center experience

Background: To compare bone mineral densities via dual energy X-ray absorptiometry method (DXA) between various hyperparathyroidism (HPT) types such as primary, vitamin D induced secondary, and both conditions.Methods: Participants who were aged between 18-45 years and had elevated parathyroid hormone levels were included. After initial evaluations, patients were divided into 3 groups according to diagnoses: primary HPT (pHPT), vitamin D induced secondary HPT (sHPT), and combined (primary+secondary) one. In addition to the bone mineral density (BMD), demographic and laboratory datas were recorded.Results: Of 166 patients, 147 of the patients were female, 19 were male, and average age was 38.10±7.24 years. Significant difference was found in terms of age (p=0.03) between pHPT and sHPT. Blood calcium, PTH, 25-OH vitamin D, and daily urine calcium excretion levels were significantly higher and phosphorus levels were lower in the pHPT group compared to the sHPT and combined disease group. Both T and Z scores of the pHPT group were significantly lower than the sHPT group especially in the lumbar region. However, no significant difference was noted between pHPT and combined disease group with respect to T and Z scores in all regions.Conclusions: The results of this study indicate that pHPT has a significantly worse impact on skeletal mineral density particularly in the lumbar region than sHPT. The addition of vitamin D deficiency to the clinical picture seems to have no significant influence on BMD in pHPT. To confirm and clarify these findings, prospective studies with larger number of participants are needed

Graph-based modelling of query sets for differential privacy

Differential privacy has gained attention from the community as the mechanism for privacy protection. Significant effort has focused on its application to data analysis, where statistical queries are submitted in batch and answers to these queries are perturbed with noise. The magnitude of this noise depends on the privacy parameter " and the sensitivity of the query set. However, computing the sensitivity is known to be NP-hard. In this study, we propose a method that approximates the sensitivity of a query set. Our solution builds a query-region- intersection graph. We prove that computing the maximum clique size of this graph is equivalent to bounding the sensitivity from above. Our bounds, to the best of our knowledge, are the tightest known in the literature. Our solution currently supports a limited but expressive subset of SQL queries (i.e., range queries), and almost all popular aggregate functions directly (except AVERAGE). Experimental results show the efficiency of our approach: even for large query sets (e.g., more than 2K queries over 5 attributes), by utilizing a state-of-the-art solution for the maximum clique problem, we can approximate sensitivity in under a minute