Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions

In this project, several docking conditions, scoring functions and corresponding protein-aligned molecular field analysis (CoMFA) models were evaluated for a diverse set of neuraminidase (NA) inhibitors. To this end, a group of inhibitors were docked into the active site of NA. The docked structures were utilized to construct a corresponding protein-aligned CoMFA models by employing probe-based (H+, OH, CH3) energy grids and genetic partial least squares (G/PLS) statistical analysis. A total of 16 different docking configurations were evaluated, of which some succeeded in producing self-consistent and predictive CoMFA models. However, the best model coincided with docking the ionized ligands into the hydrated form of the binding site via PLP1 scoring function (r2LOO=0.735, r2PRESS against 24 test compounds=0.828). The highest-ranking CoMFA models were employed to probe NA-ligand interactions. Further validation by comparison with a co-crystallized ligand-NA crystallographic structure was performed. This combination of docking/scoring/CoMFA modeling provided interesting insights into the binding of different NA inhibitors.     

Online collaboration: Collaborative behavior patterns and factors affecting globally distributed team performance

Studying the collaborative behavior of online learning teams and how this behavior is related to communication mode and task type is a complex process. Research about small group learning suggests that a higher percentage of social interactions occur in synchronous rather than asynchronous mode, and that students spend more time in task-oriented interaction in asynchronous discussions than in synchronous mode. This study analyzed the collaborative interaction patterns of global software development learning teams composed of students from Turkey, US, and Panama. Data collected from students’ chat histories and forum discussions from three global software development projects were collected and compared. Both qualitative and quantitative analysis methods were used to determine the differences between a group’s communication patterns in asynchronous versus synchronous communication mode. K-means clustering with the Ward method was used to investigate the patterns of behaviors in distributed teams. The results show that communication patterns are related to communication mode, the nature of the task, and the experience level of the leader. The paper also includes recommendations for building effective online collaborative teams and describes future research possibilities.     

Some picture fuzzy Bonferroni mean operators with their application to multicriteria decision making

In this paper, we extend the Bonferroni mean (BM) operator with the picture fuzzy numbers (PFNs) to propose novel picture fuzzy aggregation operators and demonstrate their application to multicriteria decision making (MCDM). On the basis of the algebraic operational rules of PFNs and BM, we introduce some aggregation operators: the picture fuzzy Bonferroni mean, the picture fuzzy normalized weighted Bonferroni mean, and the picture fuzzy ordered weighted Bonferroni mean. Then, a new picture fuzzy MCDM method is proposed with the help of the proposed operators. Lastly, a practical application of proposed model is given to verify the developed model and related results of the proposed model is compared with the results of the existing models to indicate its applicability.     

Effective prediction and resource allocation method (EPRAM) in fog computing environment for smart healthcare system

Multimedia Tools and Applications - Recently, many concepts in technology has been changed. According to the digital transformation trends, Internet of Things (IoT) represents an interested...     

A hybrid discrete particle swarm optimization for vehicle routing problem with simultaneous pickup and delivery

Vehicle routing problem (VRP) is an important and well-known combinatorial optimization problem encountered in many transport logistics and distribution systems. The VRP has several variants depending on tasks performed and on some restrictions, such as time windows, multiple vehicles, backhauls, simultaneous delivery and pick-up, etc. In this paper, we consider vehicle routing problem with simultaneous pickup and delivery (VRPSPD). The VRPSPD deals with optimally integrating goods distribution and collection when there are no precedence restrictions on the order in which the operations must be performed. Since the VRPSPD is an NP-hard problem, we present a heuristic solution approach based on particle swarm optimization (PSO) in which a local search is performed by variable neighborhood descent algorithm (VND). Moreover, it implements an annealing-like strategy to preserve the swarm diversity. The effectiveness of the proposed PSO is investigated by an experiment conducted on benchmark problem instances available in the literature. The computational results indicate that the proposed algorithm competes with the heuristic approaches in the literature and improves several best known solutions.     

Smart structures and their applications on active vibration control: Studies in the Department of Aerospace Engineering, METU

This work presents the theoretical and experimental studies conducted in Aerospace Engineering Department of Middle East Technical University on smart structures with particular attention given to the structural modelling characteristics and active suppression of in-vacuo vibrations. The smart structures considered in these analyses are finite and flat aluminium cantilever beam-like (called as smart beam) and plate-like (called as smart fin) structures with surface bonded lead–zirconate–titanate patches. Finite element models of smart beam and smart fin are obtained. Then the experimental studies regarding open loop behaviour of the structures are performed by using strain gauges and laser displacement sensor to determine the system models. Further studies are carried out to obtain H _∞ and μ-synthesis controllers which are intended to be used in the suppression of free and forced vibrations of the smart structures. It is observed that satisfactory attenuation levels are achieved and robust performance of the systems in the presence of uncertainties is ensured. In that respect a comparative study involving H _∞ and sliding mode controls is also conducted. Recently, the studies involving aerodynamic loading are also gathering pace.     

Oil: Source rock correlations of Al Baraka oil field,Komombo basin,South Egypt: An implication from biomarkers characteristics

The objectives of this study are the correlation between the oil samples recovered from the Lower Cretaceous reservoirs and Lower and Upper Cretaceous source rocks. The investigated biomarkers of five oils indicated the oils were derived from mixed marine and terrigenous (lacustrine) organic matter and deposited under suboxic to anoxic conditions. These oils were also generated from source rocks of high thermal maturity at the peak oil window. So, based on the molecular indicators of organic source input,depositional environment and maturity parameters of oils and extracts, we can conclude that the oil recovered from Al Baraka oil field were derived from Lower Cretaceous source rocks especially KomOmbo (B) source rocks where it reached the oil window. Furthermore, we can indicate that the other lower Cretaceous formations as Abu Ballas Formation will have the opportunity to generate and expel oil at the deeper part of the basin as shown in the eastern part of the basin.     

Couscous, a traditional Turkish food product: production method and some applications for enrichment of nutritional value

Traditional Turkish couscous, a cereal‐based product, is made by covering bulgur with milk and flour. Traditionally Turkish couscous was produced from different flours (soyflour and oat flour) and eggs. The nutrient composition of traditional couscous was 90.6% dry matter, 11.27% protein, 2.58% fat, 71.80% carbohydrate, 42.25 mg sodium, 365.62 mg potassium, 2.73 mg iron and 48.30 mg calcium. The calorie content of traditional couscous is about 1487.41 kJ 100 g^?1. The addition of soy and oat flours increased protein content and Ca, K and Fe levels. Sensory properties were also affected. Panellists preferred traditional couscous and couscous with eggs or soyflour over couscous with oat flour.     

Bioavailability of Eight Brands of Ampicillin Capsules

An in vivo absorption study was performed in a crossover fashion on 6 healthy volunteers (4 males and 2 females) to compare the bioavailability of 8 brands of ampicillin capsules. Absorption was assessed by a urinary excretion method in which the drug was assayed chemically. Statistical analysis of the results was carried out to evaluate the significance of differences between brands and between subjects. Results of the analysis of variance indicated no significant differences between the tested brands of ampicillin capsules. However, significant differences between brand A and brand B were found on using the student t-test. A significant intersubject variation was also found between the volunteers participated in the present study.     

A novel technique for optical dense comb filters using sampled fiber Bragg gratings

The optical dense comb filters are indispensable components for dense wavelength multiplexing systems. In this paper, a novel and basic method is proposed to realize optical dense comb filters. The reflection spectrum of sampled fiber Bragg grating is analyzed after applying a phase shifting technique that varies the phase of the grating. The spectral densification and shifting effects of periodic phase shifts are investigated and it is shown that desired amount of channel multiplying can be provided by using appropriate value of densification factor. Moreover, a quantization technique is proposed in order to reduce the phase shifting series which complicated by the increase of densification factor.