Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Background: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multidomain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. Methodology: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. Conclusions: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multidomain architecture.

Non-industrial private forest landowners’ choices of timber management strategies.

The factors affecting the non-industrial, private forest landowners' (hereafter referred to using the acronym NIPF) strategic decisions in management planning are studied. A genetic algorithm is used to induce a set of rules predicting potential cut of the landowners' choices of preferred timber management strategies. The rules are based on variables describing the characteristics of the landowners and their forest holdings. The predictive ability of a genetic algorithm is compared to linear regression analysis using identical data sets. The data are cross-validated seven times applying both genetic algorithm and regression analyses in order to examine the data-sensitivity and robustness of the generated models. The optimal rule set derived from genetic algorithm analyses included the following variables: mean initial volume, landowner's positive price expectations for the next eight years, landowner being classified as farmer, and preference for the recreational use of forest property. When tested with previously unseen test data, the optimal rule set resulted in a relative root mean square error of 0.40. In the regression analyses, the optimal regression equation consisted of the following variables: mean initial volume, proportion of forestry income, intention to cut extensively in future, and positive price expectations for the next two years. The R2 of the optimal regression equation was 0.34 and the relative root mean square error obtained from the test data was 0.38. In both models, mean initial volume and positive stumpage price expectations were entered as significant predictors of potential cut of preferred timber management strategy. When tested with the complete data set of 201 observations, both the optimal rule set and the optimal regression model achieved the same level of accuracy.

Non-linear Dynamic Analysis of a Piezoelectrically Actuated Flapping Wing

An energy method is used in order to derive the non-linear equations of motion of a smart flapping wing. Flapping wing is actuated from the root by a PZT unimorph in the piezofan configuration. Dynamic characteristics of the wing, having the same size as dragonfly Aeshna Multicolor, are analyzed using numerical simulations. It is shown that flapping angle variations of the smart flapping wing are similar to the actual dragonfly wing for a specific feasible voltage. An unsteady aerodynamic model based on modified strip theory is used to obtain the aerodynamic forces. It is found that the smart wing generates sufficient lift to support its own weight and carry a small payload. It is therefore a potential candidate for flapping wing of micro air vehicles.

Head-on infall of two compact objects: Third post-Newtonian energy flux

Head-on infall of two compact objects with arbitrary mass ratio is investigated using the multipolar post-Minkowskian approximation method. At the third post-Newtonian order the energy flux, in addition to the instantaneous contributions, also includes hereditary contributions consisting of the gravitational-wave tails, tails-of-tails, and the tail-squared terms. The results are given both for infall from infinity and also for infall from a finite distance. These analytical expressions should be useful for the comparison with the high accuracy numerical relativity results within the limit in which post-Newtonian approximations are valid.

Padé approach to potential transients: Part 1. Electron transfer without and with coupling to first-order homogeneous reactions at planar electrodes

Potential transients are obtained by using “Padé approximants” (an accurate approximation procedure valid globally — not just perturbatively) for all amplitudes of concentration polarization and current densities. This is done for several mechanistic schemes under constant current conditions. We invert the non-linear current-potential relationship in the form (using the Lagrange or the Ramanujan method) of power series appropriate to the two extremes, namely near reversible and near irreversible. Transforming both into the Pad́e expressions, we construct the potential-time profile by retaining whichever is the more accurate of the two. The effectiveness of this method is demonstrated through illustrations which include couplings of homogeneous chemical reactions to the electron-transfer step.

Cohésion modale et subordination : Le conditionnel et le jussif finnois au miroir de la valeur sémantique et discursive du subjonctif français

Modal cohesion and subordination. The Finnish conditional and jussive moods in comparison to the French subjunctive This study examines verb moods in subordinate clauses in French and Finnish. The first part of the analysis deals with the syntax and semantics of the French subjunctive, mood occurring mostly in subordinate positions. The second part investigates Finnish verb moods. Although subordinate positions in Finnish grammar have no special finite verb form, certain uses of Finnish verb moods have been compared to those of subjunctives and conjunctives in other languages. The present study focuses on the subordinate uses of the Finnish conditional and jussive (i.e. the third person singular and plural of the imperative mood). The third part of the analysis discusses the functions of subordinate moods in contexts beyond complex sentences. The data used for the analysis include 1834 complex sentences gathered from newspapers, online discussion groups and blog texts, as well as audio-recorded interviews and conversations. The data thus consist of both written and oral texts as well as standard and non-standard variants. The analysis shows that the French subjunctive codes theoretical modality. The subjunctive does not determine the temporal and modal meaning of the event, but displays the event as virtual. In a complex sentence, the main clause determines the temporal and modal space within which the event coded by the subjunctive clause is interpreted. The subjunctive explicitly indicates that the space constructed in the main clause extends its scope over the subordinate clause. The subjunctive can therefore serve as a means for creating modal cohesion in the discourse. The Finnish conditional shares the function of making explicit the modal link between the components of a complex construction with the French subjunctive, but the two moods differ in their semantics. The conditional codes future time and can therefore occur only in non-factual or counterfactual contexts, whereas the event expressed by French subjunctive clauses can also be interpreted as realized. Such is the case when, for instance, generic and habitual meaning is involved. The Finnish jussive mood is used in a relatively limited number of subordinate clause types, but in these contexts its modal meaning is strikingly close to that of the French subjunctive. The permissive meaning, typical of the jussive in main clause positions, is modified in complex sentences so that it entails inter-clausal relation, namely concession. Like the French subjunctive, the jussive codes theoretical modal meaning with no implication of the truth value of the proposition. Finally, the analysis shows that verb moods mark modal cohesion, not only on the syntagmatic level (namely in complexe sentences), but also on the paradigmatic axis of discourse in order to create semantic links over entire segments of talk. In this study, the subjunctive thus appears, not as an empty category without function, as it is sometimes described, but as an open form that conveys the temporal and modal meanings emerging from the context.

Carotid Surgery : A posse ad esse non valet consequentia

According to a large body of evidence, carotid endarterectomy (CEA) can prevent strokes, provided that appropriate inclusion criteria and high-quality perioperative treatment methods are utilised with low complication rates. From the patient s perspective, it is of paramount importance that the operation is as safe and effective as possible. From the community s point of view, it is important that CEA provision prevents as many strokes as possible. In order to define the stroke preventing potential of CEA in different communities, a comparison between eight European countries and Australia was performed including 53 077 carotid interventions. A more detailed evaluation was performed in Finland, the United Kingdom and Egypt. It could be estimated that many potentially preventable strokes occur due to insufficient diagnostics and CEA provision. The number of CEAs should be at least doubled in the Helsinki region. The theoretical power of CEA provision in stroke prevention varied significantly between the countries. Delay from symptom to surgery has been identified as one of the most important factors influencing the effectiveness of CEA. In 2008 only 11% of CEAs in Helsinki university central hospital (HUCH) were performed within the recommended14 days. Registered data of 673 CEAs in HUCH during 2000-2005 was analyzed. There was no systematic error that would have changed the outcome analysis. However it is important that registers are audited regularly and cross matching of different registries is possible. A previously unpublished method of combining medial mandibulotomy, neck incision and carotid artery interposition was carried out as a collaboration of maxillofacial, ear, nose and throat and vascular surgeons. Five patients were operated on with a technique that was feasible and possible to perform with little morbidity, but due to the significant risks involved, this technique should be reserved for carefully selected cases. In stroke prevention, organisational decisions seem far more important than details in interventional procedures when CEA is performed with low complication rates, as was the case in the present study. A TIA clinic approach with close co-operation between the on-call vascular surgeons, neurologists and radiologists should be available at all centres treating these patients. Patients should have a direct and fast admission to the hospital performing CEA.

Molecular profiling of indoor microbial communities in moisture damaged and non-damaged buildings

Epidemiological studies have shown an elevation in the incidence of asthma, allergic symptoms and respiratory infections among people living or working in buildings with moisture and mould problems. Microbial growth is suspected to have a key role, since the severity of microbial contamination and symptoms show a positive correlation, while the removal of contaminated materials relieves the symptoms. However, the cause-and-effect relationship has not been well established and knowledge of the causative agents is incomplete. The present consensus of indoor microbes relies on culture-based methods. Microbial cultivation and identification is known to provide qualitatively and quantitatively biased results, which is suspected to be one of the reasons behind the often inconsistent findings between objectively measured microbiological attributes and health. In the present study the indoor microbial communities were assessed using culture-independent, DNA based methods. Fungal and bacterial diversity was determined by amplifying and sequencing the nucITS- and16S-gene regions, correspondingly. In addition, the cell equivalent numbers of 69 mould species or groups were determined by quantitative PCR (qPCR). The results from molecular analyses were compared with results obtained using traditional plate cultivation for fungi. Using DNA-based tools, the indoor microbial diversity was found to be consistently higher and taxonomically wider than viable diversity. The dominant sequence types of fungi, and also of bacteria were mainly affiliated with well-known microbial species. However, in each building they were accompanied by various rare, uncultivable and unknown species. In both moisture-damaged and undamaged buildings the dominant fungal sequence phylotypes were affiliated with the classes Dothideomycetes (mould-like filamentous ascomycetes); Agaricomycetes (mushroom- and polypore-like filamentous basidiomycetes); Urediniomycetes (rust-like basidiomycetes); Tremellomycetes and the family Malasseziales (both yeast-like basidiomycetes). The most probable source for the majority of fungal types was the outdoor environment. In contrast, the dominant bacterial phylotypes in both damaged and undamaged buildings were affiliated with human-associated members within the phyla Actinobacteria and Firmicutes. Indications of elevated fungal diversity within potentially moisture-damage-associated fungal groups were recorded in two of the damaged buildings, while one of the buildings was characterized by an abundance of members of the Penicillium chrysogenum and P. commune species complexes. However, due to the small sample number and strong normal variation firm conclusions concerning the effect of moisture damage on the species diversity could not be made. The fungal communities in dust samples showed seasonal variation, which reflected the seasonal fluctuation of outdoor fungi. Seasonal variation of bacterial communities was less clear but to some extent attributable to the outdoor sources as well. The comparison of methods showed that clone library sequencing was a feasible method for describing the total microbial diversity, indicated a moderate quantitative correlation between sequencing and qPCR results and confirmed that culture based methods give both a qualitative and quantitative underestimate of microbial diversity in the indoor environment. However, certain important indoor fungi such as Penicillium spp. were clearly underrepresented in the sequence material, probably due to their physiological and genetic properties. Species specific qPCR was a more efficient and sensitive method for detecting and quantitating individual species than sequencing, but in order to exploit the full advantage of the method in building investigations more information is needed about the microbial species growing on damaged materials. In the present study, a new method was also developed for enhanced screening of the marker gene clone libraries. The suitability of the screening method to different kinds of microbial environments including biowaste compost material and indoor settled dusts was evaluated. The usability was found to be restricted to environments that support the growth and subsequent dominance of a small number microbial species, such as compost material.

Highly Efficient and Thermally Stable Second-Order Nonlinear Optical Chromophores and Electrooptic Polymers

Organic polymeric electro-optic (E-O) materials have attracted significant attention because of their potential use as fast and efficient components of integrated photonic devices (1,2). However, the practical application of these materials in optical devices is somewhat limited by the stringent material requirements imposed by the device design, fabrication processes and operating environments. Among the various material requirements, the most notable ones are large electro-optic coefficients (r(33)) and high thermal stability (3). The design of poled polymeric materials with high electro-optic activity (r(33)) involves the optimization of the percent incorporation of efficient (large beta mu) second order nonlinear optical (NLO) chromophores into the polymer matrices and the effective creation of poling-induced non-centrosymmetric structures. The factors that affect the material stability are a) the inherent thermal stability of the NLO chromophores, b) the chemical stability of the NLO chromophores during the polymer processing conditions, and c) the long-term dipolar alignment stability at high temperatures. Although considerable progress has been made in achieving these properties (4), organic polymeric materials suitable for practical E-O device applications are yet to be developed. This chapter highlights some of our approaches in the optimization of molecular and material nonlinear optical and thermal properties.

Nonsimilar mixed convection flow of a non-Newtonian fluid past a vertical wedge

The flow and heat transfer characteristics of a second-order fluid over a vertical wedge with buoyancy forces have been analysed. The coupled nonlinear partial differential equations governing the nonsimilar mixed convection flow have been solved numerically using Keller box method. The effects of the buoyancy parameter, viscoelastic parameter, mass transfer parameter, pressure gradient parameter, Prandtl number and viscous dissipation parameter on the skin friction and heat transfer have been examined in detail. Particular cases of the present results match exactly with those available in the literature.

Jointly Optimal MMSE design for non-redundant FIR precoding and equalization

We provide a filterbank precoding framework (FBP) for frequency selective channels using the minimum mean squared error (MMSE) criterion. The design obviates the need for introducing a guard interval between successive blocks, and hence can achieve the maximum possible bandwidth efficiency. This is especially useful in cases where the channel is of a high order. We treat both the presence and the absence of channel knowledge at the transmitter. In the former case, we obtain the jointly optimal precoder-equalizer pair of the specified order. In the latter case, we use a zero padding precoder, and obtain the MMSE equalizer. No restriction on the dimension or nature of the channel matrix is imposed. Simulation results indicate that the filterbank approach outperforms block based methods like OFDM and eigenmode precoding.

A new class of three dimensional D-pi-A trigonal cryptand derivatives for second-order nonlinear optics

Synthesis, crystal structures, linear and nonlinear optical properties of tris D-pi-A cryptand derivatives with C-3 symmetry are reported. Three fold symmetry inherent in the cryptand molecules has been utilized for designing these molecules. Molecular nonlinearities have been measured by hyper-Rayleigh scattering (HRS) experiments. Among the compounds studied, L-1 adopts non-centrosymmetric crystal structure. Compounds L-1, L-2, L-3 and L-4 show a measurable SHG powder signal. These molecules are more isotropic and have significantly higher melting points than the classical p-nitroaniline based dipolar NLO compounds, making them useful for further device applications. Besides, different acceptor groups can be attached to the cryptand molecules to modulate their NLO properties.

Non-Fermi-liquid theory for disordered metals near two dimensions

We consider the Finkelstein action describing a system of spin-polarized or spinless electrons in 2+2epsilon dimensions, in the presence of disorder as well as the Coulomb interactions. We extend the renormalization-group analysis of our previous work and evaluate the metal-insulator transition of the electron gas to second order in an epsilon expansion. We obtain the complete scaling behavior of physical observables like the conductivity and the specific heat with varying frequency, temperature, and/or electron density. We extend the results for the interacting electron gas in 2+2epsilon dimensions to include the quantum critical behavior of the plateau transitions in the quantum Hall regime. Although these transitions have a very different microscopic origin and are controlled by a topological term in the action (theta term), the quantum critical behavior is in many ways the same in both cases. We show that the two independent critical exponents of the quantum Hall plateau transitions, previously denoted as nu and p, control not only the scaling behavior of the conductances sigma(xx) and sigma(xy) at finite temperatures T, but also the non-Fermi-liquid behavior of the specific heat (c(v)proportional toT(p)). To extract the numerical values of nu and p it is necessary to extend the experiments on transport to include the specific heat of the electron gas.

Thermal Lipid Order−Disorder Transitions in Mixtures of Cationic Cholesteryl Lipid Analogues and Dipalmitoyl Phosphatidylcholine Membranes

Two types of cationic cholesteryl amphiphiles, one where the headgroup is attached to the steroid by an ester linkage and the second by an ether linkage, were synthesized. A third type of cholesteryl lipid bearing an oligoethylene glycol segment was also prepared. Each of these synthetic lipids generated vesicle-like aggregates with closed inner aqueous compartments from their aqueous suspensions. We examined their interaction with L-α-dipalmitoyl phosphatidylcholine (DPPC) membranes using fluorescence anisotropy, transmission electron microscopy (TEM), and differential scanning calorimetry (DSC). When included in membranes, the synthetic cholesteryl lipids were found to quench the chain motion of the acyl chains of DPPC. This suggests that these cationic cholesteryl derivatives act as filler molecules despite modification at the headgroup level from the molecular structure of natural cholesterol. Careful analyses of DSC and fluorescence anisotropy data suggest that the nature of perturbation induced by each of these cationic cholesterol derivatives is dependent on the details of their molecular structure and provides significant information on the nature of interaction of these derivatives with phospholipid molecules. In general, amphiphiles that support structured water at the interfacial region tend to rigidify the fluid phase more than others. Importantly, these cholesteryl amphiphiles behave less like cholesterol in that their incorporation in DPPC not only abolishes the phase transition but also depresses the phase transition temperature.

Numerical modeling of the contaminant Transport through stratified soil

The transport processes of the dissolved chemicals in stratified or layered soils have been studied for several decades. In case of the solute transport through stratified layers, interface condition plays an important role in determining appropriate transport parameters. First‐ type and third‐ type interface conditions are generally used in the literature. A first‐type interface condition will result in a continuous concentration profile across the interface at the expense of solute mass balance. On the other hand, a discontinuity in concentration develops when a third‐ type interface condition is used. To overcome this problem, a combined first‐ and third‐ type condition at the interface has been widely employed which yields second‐ type condition. This results in a similar break‐through curve irrespective of the layering order, which is non‐physical. In this work, an interface condition is proposed which satisfies the mass balance implicitly and brings the distinction between the breakthrough curves for different layering sequence corroborating with the experimental observations. This is in disagreement with the earlier work by H. M. Selim and co‐workers but, well agreement with the hypothetical result by Bosma and van der Zee; and Van der Zee.