Bayesian models and algorithms for protein beta-sheet prediction

Prediction of the three-dimensional structure greatly benefits from the information related to secondary structure, solvent accessibility, and non-local contacts that stabilize a protein's structure. Prediction of such components is vital to our understanding of the structure and function of a protein. In this paper, we address the problem of beta-sheet prediction. We introduce a Bayesian approach for proteins with six or less beta-strands, in which we model the conformational features in a probabilistic framework. To select the optimum architecture, we analyze the space of possible conformations by efficient heuristics. Furthermore, we employ an algorithm that finds the optimum pairwise alignment between beta-strands using dynamic programming. Allowing any number of gaps in an alignment enables us to model beta-bulges more effectively. Though our main focus is proteins with six or less beta-strands, we are also able to perform predictions for proteins with more than six beta-strands by combining the predictions of BetaPro with the gapped alignment algorithm. We evaluated the accuracy of our method and BetaPro. We performed a 10-fold cross validation experiment on the BetaSheet916 set and we obtained significant improvements in the prediction accuracy

Bayesian models and algorithms for protein beta-sheet prediction

Prediction of the three-dimensional structure greatly benefits from the information related to secondary structure, solvent accessibility, and non-local contacts that stabilize a protein's structure. Prediction of such components is vital to our understanding of the structure and function of a protein. In this paper, we address the problem of beta-sheet prediction. We introduce a Bayesian approach for proteins with six or less beta-strands, in which we model the conformational features in a probabilistic framework. To select the optimum architecture, we analyze the space of possible conformations by efficient heuristics. Furthermore, we employ an algorithm that finds the optimum pairwise alignment between beta-strands using dynamic programming. Allowing any number of gaps in an alignment enables us to model beta-bulges more effectively. Though our main focus is proteins with six or less beta-strands, we are also able to perform predictions for proteins with more than six beta-strands by combining the predictions of BetaPro with the gapped alignment algorithm. We evaluated the accuracy of our method and BetaPro. We performed a 10-fold cross validation experiment on the BetaSheet916 set and we obtained significant improvements in the prediction accuracy

CYBER SECURITY IN INDUSTRIAL CONTROL SYSTEMS (ICS): A SURVEY OF ROWHAMMER VULNERABILITY

Increasing dependence on Information and Communication Technologies (ICT) and especially on the Internet in Industrial Control Systems (ICS) has made these systems the primary target of cyber-attacks. As ICS are extensively used in Critical Infrastructures (CI), this makes CI more vulnerable to cyber-attacks and their protection becomes an important issue. On the other hand, cyberattacks can exploit not only software but also physics; that is, they can target the fundamental physical aspects of computation. The newly discovered RowHammer (RH) fault injection attack is a serious vulnerability targeting hardware on reliability and security of DRAM (Dynamic Random Access Memory). Studies on this vulnerability issue raise serious security concerns.  The purpose of this study was to overview the RH phenomenon in DRAMs and its possible security risks on ICSs and to discuss a few possible realistic RH attack scenarios for ICSs. The results of the study revealed that RH is a serious security threat to any computer-based system having DRAMs, and this also applies to ICS

An Analysis of Undergraduates’ Study Skills

AbstractThere is a growing need for the integration of various theoretical perspectives on academic achievement such as study skills. Study skills are approaches applied to learning that assist students to be successful in schools in a way of passing an exam or even obtaining good grades. The purpose of this study was to determine the effect of undergraduates’ study skills on academic achievement and significances in their study skills in terms of gender and department. The sample group of the study consists of 210 undergraduates studying in three different departments at School of Education. To determine their study skills, the data were collected using “Study Skills Scale” developed by Bay, Tugluk, and Gencdogan (2005). To determine the correlation between undergraduates’ study skills and academic achievement, the analysis of Pearson correlation was used. Also, to determine significant differences in undergraduates’ study skills regarding gender and departments, the analysis of independent samples of t-test and ANOVA were conducted. The results reveal that there is a positive correlation between study skills and academic achievement and also significant differences were found in undergraduates’ study skills in terms of gender and departments

Origin and Impact of Government Regulations

İnternet g&uuml;n&uuml;m&uuml;zde pek &ccedil;ok işlevinin yanında bilgi edinme s&uuml;re&ccedil;lerinde başvurulan &ouml;nemli bir kaynak konumundadır. Bu durum dini bilgi edinme pratikleri a&ccedil;ısından da ge&ccedil;erlidir. Bazı araştırma bulguları internetin dini bilgi arama/edinme s&uuml;re&ccedil;lerinde geleneksel bilgi kaynaklarıyla birlikte en &ccedil;ok başvurulan kaynaklar arasında olduğunu ortaya koymaktadır. Bu doğrultuda bu &ccedil;alışma &uuml;niversite &ouml;ğrencilerinin dini bilgi gereksinimlerini karşılama s&uuml;recinde kullandıkları bilgi edinme kaynakları ve bu kaynakların g&uuml;venilirliğiyle birlikte temelde onların internet &uuml;zerinden dini bilgi edinme s&uuml;re&ccedil;lerindeki eleştirel yeterliliklerine odaklanmaktadır. &Ouml;ğrencilerin dini bilgi arama/edinme s&uuml;re&ccedil;lerindeki eleştirel yeterliliklerini &ouml;l&ccedil;mek amacıyla, Eken ve Aydın (2018) tarafından geliştirilen, dini/enformasyonel i&ccedil;erikli internet sitelerinin değerlendirilmesine y&ouml;nelik kullanıcı merkezli kriterlerin baz alındığı &ccedil;alışma, Erciyes &Uuml;niversitesi İletişim Fak&uuml;ltesi &ouml;ğrencilerinden basit rastlantısal &ouml;rneklem tekniğiyle se&ccedil;ilen k&uuml;me &uuml;zerinde ger&ccedil;ekleştirilen ampirik bir araştırma niteliği taşımaktadır. &Ccedil;alışmadan elde edilen sonu&ccedil;lara g&ouml;re; internetin &uuml;niversite &ouml;ğrencileri i&ccedil;in en temel dini bilgi kaynaklarından biri olduğu; ancak bu yaygın kullanımın aksine &ouml;ğrencilerin internet ortamından elde edilen bilgilere yeterince g&uuml;venmediği ve anket formunda belirtilen kriterlere oranla alt-orta d&uuml;zeyde bir eleştirel yeterliliğe sahip olduğu ifade edilebilir. Bu sonu&ccedil; &uuml;niversite &ouml;ğrencileri i&ccedil;in eleştirel okuryazarlık becerisi kazandıracak eğitim s&uuml;re&ccedil;lerinin gerekliliğini ortaya koyması bakımından &ouml;nemlidirToday, the internet is an important resource which is used in information acquisition processes. This also applies to religious practice. Some research findings demonstrate that the internet is among the most frequently used sources in the process of religious information searching/acquiring with traditional sources of information. In this respect, this study focuses on the sources of information and the reliability of these sources in the process of meeting university students&#39; religious knowledge requirements and focuses on the critical competencies of these students in the process of acquiring religious knowledge on the internet. In order to measure the critical competencies of the students in the process of religious information searching, a study based on user-centered criteria for the evaluation of religious / informative websites, developed by Eken and Aydın (2018), is an empirical study conducted by the students of Erciyes University Faculty of Communication with a simple random sampling technique. According to the results obtained from the study; It can be stated that internet is one of the most basic sources for religious information for university students, but unlike this widespread use, students do not trust the information obtained from the Internet environment and have a moderate level of critical competency compared to the criteria specified in the survey form. This situation is important in terms of demonstrating the necessity of educational processes that will redound critical literacy skills for university students</p

Springback/Springforward Behaviour of DP Steels Used in the Automotive Industry

The springback/springforward behaviour in a V-die/punch of DP600 and DP780 steels used in the automotive industry was investigated. For this study, experiments were carried out by using different combinations of parameters, including material thickness, die/punch radius, bending angle and rolling direction and the resulting measurements showed that the DP780 steel consistently exhibited greater springback values than the DP600. Augmentation of the rolling direction at an angle from 0° to 90° and punch radius inhibited springback formation and hastened springforward, particularly for small bending angles. The springback angle decreased with increasing material thickness and curvature radius, and increased with the bending angle, particularly for the punch tip radius of 2 mm. Increasing the ratio of curvature radius to material thickness (rt−1) also caused the springback to decline. In addition, a new dimensionless parameter was developed and the critical value for calculating the transition from springback to springforward was determined

Effects of sulfasalazine on lipid peroxidation and histologic liver damage in a rat model of obstructive jaundice and obstructive jaundice with lipopolysaccharide-induced sepsis

AbstractBackground: Sulfasalazine, an inhibitor of cyclooxygenase, 5-lipoxygenase, and nuclear factor κB (NF-κB), has been found to alleviate oxidative damage, proinflammatory cytokine production, bile-duct proliferation, neutrophil infiltration, and fibrosis. Therefore, it may have a potential effect in attenuating lipid peroxidation and histologic liver damage in patients with biliary obstruction and biliary obstruction with sepsis.Objective: The aim of this study was to investigate the effect of sulfasalazine on lipid peroxidation and histologic liver damage due to obstructive jaundice (OJ) and to OJ with lipopolysaccharide (LPS)-induced sepsis in an experimental model.Methods: Male Wistar rats, weighing 150 to 220 g, were randomized into 6 groups: OJ; OJ + LPS; OJ + sulfasalazine; OJ + sulfasalazine + LPS (sulfasalazine administered before sepsis); OJ + LPS + sulfasalazine (sulfasalazine administered after sepsis); and sham. Liver malondialdehyde (MDA) and myeloperoxidase (MPO) activities were assessed to monitor lipid peroxidation and neutrophil infiltration in liver tissue. Histologic liver damage was evaluated with hematoxylin-eosin stained slides. Liver tissue NF-κB and caspase-3 expression were studied immunohistopathologically to evaluate lipid peroxidation, liver damage, and hepatocyte apoptosis.Results: Forty-eight rats were evenly randomized into 6 groups of 8. MDA (P = 0.001), MPO (P = 0.001), NF-κB (P = 0.003), caspase-3 expression (P = 0.002), and liver injury scores (P = 0.002) increased significantly in the OJ group compared with the sham group. Compared with the OJ group, MDA (P = 0.030) and MPO levels (P = 0.001), and liver injury scores (P = 0.033) were decreased significantly in the OJ + sulfasalazine group. In the OJ + sulfasalazine + LPS and OJ + LPS + sulfasalazine groups, MDA (P = 0.008 and P = 0.023, respectively) and MPO (both, P = 0.001) were significantly decreased; however, liver NF-κB, caspase-3 expression, and liver injury scores were not significantly different compared with the OJ + LPS group. There was no significant difference between the OJ + LPS + sulfasalazine and OJ + sulfasalazine + LPS groups in regard to all end points when comparing the effects of sulfasalazine administered before or after sepsis.Conclusions: Sulfasalazine was associated with decreased neutrophil accumulation and lipid peroxidation in these rats with OJ. Administration of sulfasalazine before or after LPS-induced sepsis was associated with a reduction in lipid peroxidation and neutrophil accumulation; however, it did not attenuate histologic liver damage. There was no difference between the findings when sulfasalazine was administered before or after sepsis in OJ

Differential evolution method for mobile robot optimal trajectory planning

Bu yayında &ouml;nerilen y&ouml;ntemle, mobil robotlarda, &ccedil;evreden gelen kısıtlamalar (engeller) ve robotun hız ve ivme gibi fiziksel kısıtlamaları dikkate alınarak, &ouml;nceden g&ouml;r&uuml;nebilirlik grafik metoduyla (VGM) planlanmış yol &uuml;zerinde zaman-optimal y&ouml;r&uuml;nge bulunmuştur. Y&ouml;r&uuml;ngeler, d&uuml;z kısımlardan (d&ouml;nme ivmesi as=0 ve d&ouml;nme hızı vs=0) ve eğri kısımlardan (&ouml;teleme ivmesi at=0 ve &ouml;teleme hızı vt= sabit ) oluşturulmuşlardır. Eğri kısımları oluşturmak i&ccedil;in sadece q&nbsp; (d&ouml;n&uuml;ş a&ccedil;ısı) ve vt (eğri kısım &ouml;teleme hızı) parametrelerinin bilinmesi yeterli olmaktadır. Olası t&uuml;m eğri kısımlar k&uuml;mesi (q&Icirc;(0,p]&deg; ve vt&nbsp;[0,40] in&ccedil;) i&ccedil;erisinden evrimsel bir global optimizasyon metodu olan diferansiyel evrim (DE) ile, engellerle &ccedil;akışmayan zaman-optimal ama&ccedil; &ouml;l&ccedil;&uuml;t&uuml;n&uuml; sağlayan y&ouml;r&uuml;ngenin se&ccedil;ilmesi ger&ccedil;eklenmiştir. Anahtar Kelimeler: Mobil robot, optimizasyon, y&ouml;r&uuml;nge planlama, diferansiyel evrim.A method is proposed to find the time optimal trajectory on predefined path of mobile robots, which is found by using visibility graph method. Constraints from environment (obstacles) and physical constraints (i.e. steering and translational accelerations/velocities) are taken into consideration in the method. The planned trajectories are composed of line segments (steering accaleration/deceleration as=0 and velocity vs0=0) and curve segments (translational acceleration/deceleration at=0 and velocity vt= vt0). The structures of the curves are determined by only two parameters: q, turn angles, these are produced by visibility graph method and vt, translational velocities on the curve segments, these are the elements of the parameter vector. A curves set is formed by all possible curves in parameters range qÎ(0,p]° and vt [0,40] inch. Then diferrential evolution (DE), that is an evolutionary optimizastion method is used to find time optimal trajectory from this set. The curve segments are formed in two ways: a) serial expansion of the robot?s equations (Mclauren series) and b) artificial neural networks (YSA). YSA model is used to form the curves instead of serial expansion of the robot?s equations. Thus, the optimization time is decreased to approximately 1/7. There is no need to a controller for tracking the planned trajectory. Keywords: Mobile robot, optimisation, trajectory planning, differential evolution