A Comparative Study between Fixed-size Kernel Logistic Regression and Support Vector Machines Methods for beta-turns Prediction in Protein

Beta-turn is an important element of protein structure; it plays a significant role in protein configuration and function. There are several methods developed for prediction of beta-turns from protein sequences. The best methods are based on Neural Networks (NNs) or Support Vector Machines (SVMs). Although Kernel Logistic Regression (KLR) is a powerful classification technique that has been applied successfully in many classification problems, however it is often not found in beta-turns classification, mainly because it is computationally expensive. Fixed-Size Kernel Logistic Regression (FS-KLR) is a fast and accurate approximate implementation of KLR for large-scale data sets. It uses trust-region Newton’s method for large-scale Logistic Regression (LR) as a basis, to solve the approximate problem, and Nystrom method to approximate the features' matrix. In this paper we used FS-KLR for beta-turns prediction and the results obtained are compared to those obtained with SVM. Secondary structure information and Position Specific Scoring Matrices (PSSMs) are utilized as input features. The performance achieved using FS-KLR is found to be comparable to that of SVM method. FS-KLR has an advantage of yielding probabilistic outputs directly and its extension to the multi-class case is well-defined. In addition its evaluation time is less than that of SVM method. Beta-turn is an important element of protein structure; it plays a significant role in protein configuration and function. There are several methods developed for prediction of beta-turns from protein sequences. The best methods are based on Neural Networks (NNs) or Support Vector Machines (SVMs). Although Kernel Logistic Regression (KLR) is a powerful classification technique that has been applied successfully in many classification problems, however it is often not found in beta-turns classification, mainly because it is computationally expensive. Fixed-Size Kernel Logistic Regression (FS-KLR) is a fast and accurate approximate implementation of KLR for large-scale data sets. It uses trust-region Newton’s method for large-scale Logistic Regression (LR) as a basis, to solve the approximate problem, and Nystrom method to approximate the features' matrix. In this paper we used FS-KLR for beta-turns prediction and the results obtained are compared to those obtained with SVM. Secondary structure information and Position Specific Scoring Matrices (PSSMs) are utilized as input features. The performance achieved using FS-KLR is found to be comparable to that of SVM method. FS-KLR has an advantage of yielding probabilistic outputs directly and its extension to the multi-class case is well-defined. In addition its evaluation time is less than that of SVM method

Speech acts of thanking and thanking responses by Hijazi females

The speech act of thanking, in varied permutations and contexts, is probably one of the most common speech acts in the daily life of every culture. In the Hijazi dialect spoken in the western province of Saudi Arabia, thanking behavior has significant social value. This is why the failure to express or respond to gratitude expressions according to the social norms that are known among Hijazi speakers can affect the relationship between the interlocutors. In this study, I investigate the speech act of thanking and the strategies employed by Hijazi females in Saudi Arabia to express this. To explore these strategies, a corpus of naturally occurring thanking exchanges is analyzed. 400 exchanges were gathered based on an ethnographic approach that uses field observations to create a corpus. My investigation examined gratitude expressions produced by Hijazi females in three contexts: thanking for a favor, thanking for a meal, and thanking for a gift. To determine what strategies of expressing or responding to gratitude expression Hijazi female use, gratitude expressions and their responses were coded according to the model pioneered by Al-Zubaidi (2012). Results indicated that Hijazi females use various strategies in expressing and responding to thanking for a low imposition favor, such as, Thanking and Expressing Benediction. In expressing gratitude for a meal, Hijazi female speakers do not employ the wide variety of the thanking strategies posited in the literature. Rather, they prefer using Expressing Benediction to verbalize their thanking. On the other hand, thanking for a gift generally requires two turns. In the first turn, the beneficiary has to express her indebtedness. In response, the benefactor tries to minimize the debt. In the second turn, the beneficiaries express their willingness to offer repayment or just express thanking while the benefactor responds by acknowledging the thanking or by expressing blessings or prayers. Previous studies have investigated the speech act of thanking in certain Arabic dialects such as Jordanian, Iraqi and Egyptian Arabic. However, scholarly attention has yet to be paid to how thanking expressions are used and responded to in Saudi dialects. This study functions as a reference point for other researchers interested in the cross-cultural realization of the speech act of thanking. Also, since this paper focuses on Hijazi dialect at the western part of Saudi Arabia, researchers interested in the speech act of thanking in Saudi Arabic can use this study for comparison with other Saudi dialects.Thesis (M.A.)Department of EnglishObjectives, hypotheses and significance of the study -- Background : Saudi Arabia and the Hijazi dialect -- Review of literature -- Methodology -- Results and discussion

Nonlinear Numerical Modelling of Cable Elements in Bridges for Dynamic Analysis

Identifying cable force with vibration-based methods has become widely used in engineering practice due to simplicity of application. The string taut theory provides a simple definition of the relationship between natural frequencies and the tension force of a cable. However, this theory assumes a perfectly flexible non-sagging cable pinned at its ends. These assumptions do not reflect all cases, especially when the cable is short, under low tension forces or the supports are partially flexible. Extradosed bridges, which are distinguished from cable-stayed bridges by their low pylon height, have shorter cables. Therefore the application of the conventional string taut theory to identify cable forces on extradosed bridge cables might be inadequate to identify cable forces. In this work, numerical modelling of an extradosed bridge cable saddled on a circular deviator at pylon is conducted. The model is validated with the catenary analytical solution and its static and dynamic behaviours are studied. The effect of a saddle support is found to positively affect the cable stiffness by geometric means; longer saddle radius increases the cable stiffness by suppressing the deformations near the saddle. Further, accounting the effects of bending stiffness in the numerical model by using beam elements show considerable deviation from models with truss elements (i.e. zero bending stiffness). This deviation is manifested when comparing the static and dynamic properties. This motivates a more thorough study of bending stiffness effects on short cables. Bending stiffness effects are studied using two rods connected with several springs along their length. Under bending moments, the springs resist the rods' relative axial displacement by the springs' transverse component. This concept is used to identify bending stiffness values by utilizing the parallel axis theorem to quantify ratios of the second moment of area. These ratios are calculated based on the setup of the springs (e.g. number of springs per unit length, transverse stiffness, etc...). The numerical model based on this concept agrees well with the theoretical values computed using upper and lower bounds of the parallel axis theorem. The proposed concept of quantifying ratios of the second moment of area using springs as connection between cable rods is applied on an actual extradosed bridge geometry. The model is examined by comparison to the previously validated global numerical model. The two models showed good correlation under various changing parameters. This allowed further study of the effects of stick/slip behaviour between cable rods on an actual bridge geometry

Coupled heat and mass transfer in concrete exposed to fire

The first investigation of this study is concerned with the reasonableness of the assumptions related to diffusion of water vapour in concrete and with the development of a diffusivity equation for heated concrete. It has been demonstrated that diffusion of water vapour does occur in concrete at all temperatures and that the type of diffusion is concrete is Knudsen diffusion. Neglecting diffusion leads to underestimating the pressure. It results in a maximum pore pressure of less than 1 MPa. It has also been shown that the assumption that diffusion in concrete is molecular is unreasonable even when the tortuosity is considered. Molecular diffusivity leads to overestimating the pressure. It results in a maximum pore pressure of 2.7 MPa of which the vapour pressure is 1.5 MPa while the air pressure is 1.2 MPa. Also, the first diffusivity equation, appropriately named 'concrete diffusivity', has been developed specifically for concrete that determines the effective diffusivity of any gas in concrete at any temperature. In thick walls and columns exposed to fire, concrete diffusivity leads to a maximum pore pressures of 1.5 and 2.2 MPa (along diagonals), respectively, that are almost entirely due to water vapour pressure. Also, spalling is exacerbated, and thus higher pressures may occur, in thin heated sections, since there is less of a cool reservoir towards which vapour can migrate. Furthermore, the reduction of the cool reservoir is affected not only by the thickness, but also by the time of exposure to fire and by the type of exposure, i.e. whether the concrete member is exposed to fire from one or more sides. The second investigation is concerned with examining the effects of thickness and exposure time and type. It has been demonstrated that the build up of pore pressure is low in thick members, since there is a substantial cool zone towards which water vapour can migrate. Thus, if surface and/or explosive spalling occur on a thick member, then such spalling must be due to high thermal stresses, but corner spalling is likely to be pore pressure spalling. However, depending on the exposure time and type, the pore pressures can be more than twice those occurring in thick members and thought to be the maximum that can occur so far, and thus the enhanced propensity of pore pressure spalling occurring on thin sections heated on opposite sides has been conclusively demonstrated to be due to the lack of a cool zone towards which moisture can migrate. Expressions were developed for the determination of the maximum pore pressures that can occur in different concrete walls and columns exposed to fire and of the corresponding times of exposure

Dose-modified lenalidomide induces sustained hematological response in patients with intermediate to high risk myelodysplasia

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Synthesis and studies of pyrazolo[3,4-b]pyridin-4-one derivatives

A series of isolated/fused of pyrazole, isoxazolo, pyrimidine, pyrimidine thione, spiro thiazolodine and spiro β-lactam derivatives incorporating to 4-acetyl-5-imino-3-methyl-1-phenyl-2-pyrazoline have been synthesized by different methods. The structure of chemical reactions based on chemical and spectroscopic evidence. The detailed synthesis and spectroscopic data were reported

Successful Treatment with Thrombopoietin Receptor Agonist in Avoiding Splenectomy for Patients with Chronic Refractory Immune Thrombocytopenia

Background: Chronic immune thrombocytopenia (ITP) is a condition associated with significant morbidity; however the management options are often unsatisfactory with a portion of patients exhibiting a refractory-relapsing disease path despite various lines of treatment including splenectomy.  As a Thrombopoietin receptor agonist, eltrombopag (GlaxoSmithKline, Australia) provides a novel treatment option for patients with refractory disease.  We describe the outcomes of four patients with chronic ITP, who were treated with eltrombopag as a single agent.   Methods: Four Caucasian patients with chronic refractory ITP (2 males; 2 females) were enrolled in this study with a mean age of 48 years (range, 39–59). All patients were non-splenectomised and were refractory to several lines of treatment including steroids, intravenous immunogobulin, vincristine, and azathioprine, one patient has also received rituximab (a monoclonal antibody that binds the CD20 antigen expressed by B-lymphocytes). All patients were treated with oral eltrombopag (50-75 mg) for a median period of 12 months (range, 9-16).   Results: After a median follow up of 20 months (range, 11-34), platelet counts recovered to normal levels in two patients. One recovered a normal platelet count after 13 months, the other 34 months of completion of treatment with eltrombopag. No additional immune suppressive therapy was required. The other two patients also discontinued Eltromboapag at 27 and 11 months after achievement of satisfactory platelet counts above 30/nL without any bleeding complications. Other forms of immune therapy were also ceased in these two cases. None of the four patients required splenectomy.   Conclusion: The clinical outcomes in this small cohort of patients suggests that Eltrombapag may have a role to play in the long term control of chronic ITP with avoiding splenectomy and long term immunosuppressive therapy. The beneficial outcomes in our patients led to a sustained elevation in platelets with no adverse effects noted when used for relatively longer periods than previously reported.  It is worth noting that spontaneous remission does occur with ITP and is the most likely cause for the favourable outcome with eltrombopag therapy.  However, if Eltrombapag is able to reduce the need for splenectomy in patients with chronic ITP then a distinct quality of care outcome can be achieved by avoiding the recognised short- and long-term complications of splenectomy. Randomised controlled trials with long-term follow up are warranted

Synthesis and studies of pyrazolo[3,4-b]piperidin-4-one derivatives

A series of isolated/fused of pyrazole, isoxazolo, pyrimidine, pyrimidine thione, spiro thiazolodine and spiro β-lactam derivatives incorporating to 4-acetyl-5-amino-3-methyl-1-phenyl-2-pyrazoline have been synthesized by different methods of chemical reactions. The structure assignments of these compounds, based on chemical and spectroscopic evidence were deduced from their IR, 1H NMR, elemental analysis and mass spectrometry