A model for the evaluation of domain based classification of GPCR

G-Protein Coupled Receptors (GPCR) are the largest family of membrane bound receptor and plays a vital role in various biological processes with their amenability to drug intervention. They are the spotlight for the pharmaceutical industry. Experimental methods are both time consuming and expensive so there is need to develop a computational approach for classification to expedite the drug discovery process. In the present study domain based classification model has been developed by employing and evaluating various machine learning approaches like Bagging, J48, Bayes net, and Naive Bayes. Various softwares are available for predicting domains. The result and accuracy of output for the same input varies for these software''s. Thus, there is dilemma in choosing any one of it. To address this problem, a simulation model has been developed using well known five softwares for domain prediction to explore the best predicted result with maximum accuracy. The classifier is developed for classification up to 3 levels for class A. An accuracy of 98.59% by Naïve Bayes for level I, 92.07% by J48 for level II and 82.14% by Bagging for level III has been achieved.     

A proposal for the structuring of water

In spite of much work, many of the properties of water remain puzzling. A fluctuating network of water molecules, with localised icosahedral symmetry, is proposed to exist derived from clusters containing, if complete, 280 fully hydrogen-bonded molecules. These are formed by the regular arrangement of identical units of 14 water molecules that can tessellate locally, by changing centres, in three-dimensions and interconvert between lower and higher density forms. The structure allows explanation of many of the anomalous properties of water including its temperature-density and pressure-viscosity behaviour, the radial distribution pattern, the presence of both pentamers and hexamers, the change in properties and 'two-state' model on supercooling and the solvation properties of ions, hydrophobic molecules, carbohydrates and macromolecules. The model described here offers a structure on to which large molecules can be mapped in order to offer insights into their interactions.     

Comparative evaluation of photoionization and flame ionization detectors for ethylene analysis

Abstract. This paper compares the use of photoionization and flame ionization detectors (PID and FID. respectively) for the analysis of ethylene in plant physiological studies. It is shown that PID has the capability to analyse ethylene levels in the order of 1 mm³ m⁻³. This represents an increase in sensitivity over FID of several-fold. Evidence is presented that this enhanced sensitivity allows for measurement of the rate of ethylene production from plants in continuous-flow systems by taking air samples directly from the air stream, thus eliminating the need for selective collection and concentration of ethylene.     

A comparative evaluation of sequence classification programs

Background

Here we present two new computer tools, PREMIM and EMIM, for the estimation of parental and child genetic effects, based on genotype data from a variety of different child-parent configurations. PREMIM allows the extraction of child-parent genotype data from standard-format pedigree data files, while EMIM uses the extracted genotype data to perform subsequent statistical analysis. The use of genotype data from the parents as well as from the child in question allows the estimation of complex genetic effects such as maternal genotype effects, maternal-foetal interactions and parent-of-origin (imprinting) effects. These effects are estimated by EMIM, incorporating chosen assumptions such as Hardy-Weinberg equilibrium or exchangeability of parental matings as required.

Results

In application to simulated data, we show that the inference provided by EMIM is essentially equivalent to that provided by alternative (competing) software packages such as MENDEL and LEM. However, PREMIM and EMIM (used in combination) considerably outperform MENDEL and LEM in terms of speed and ease of execution.

Conclusions

Together, EMIM and PREMIM provide easy-to-use command-line tools for the analysis of pedigree data, giving unbiased estimates of parental and child genotype relative risks.     

A proposal for revision of the quality factor

As a result of recent radiobiological research it has become evident that the RBE of neurons can at low absorbed doses reach values that are substantially higher than the values of the quality factor (Q) currently adopted for radiation protection. There is theoretical and observational evidence that such high RBE values are the rule rather than the exception and that they apply to at least one radiation effect on humans. New values as well as different formulations are proposed for the factor that is employed in radiation protection to weight absorbed doses for their biological effectiveness.     

A proposal for the mechanism of carbonic anhydrase action

A new catalytic mechanism is proposed for the hydration of CO₂ by the zinc metalloenzyme carbonic anhydrase. This mechanism identifies the group controlling catalytic activity as an active site histidine, in which the protonated imidazole ring coordinates to zinc, losing a proton. Geometric constraints on the histidine unit make the metal-ligand bond a strained and, therefore, labile one. In the hydration reaction, the metal-bound neutral histidine moiety serves as a proton acceptor for the transient ionization of metal-bound water. Zinc-bound hydroxide attacks the carbon of the substrate to generate metal-bound bicarbonate, and the system regenerates itself by losing the elements of carbonic acid.     

Bud banks and their role in vegetative regeneration – A literature review and proposal for simple classification and assessment

While sexual regeneration of plants after disturbance is relatively well understood, vegetative regeneration has attracted some attention only recently. Its role along environmental gradients and across biomes is poorly known and standard methods for assessment are not yet established. We review current knowledge about the role of bud banks in vegetative regeneration and the diversity of their modes of functioning. The similarities and differences between bud banks and seed banks are illustrated, focusing on dormancy, dispersability, seasonal dynamics, longevity and storage of carbohydrates. We try to formulate some principles that unify bud bank functioning across habitats and growth forms: (1) the bud banks consist of all buds which may be used for vegetative regeneration, including those formed adventitiously only after injury; (2) vertical distribution of buds reflects avoidance of disturbance; (3) seasonal changes in the bud bank make vegetative regeneration sensitive to timing of disturbance; and (4) ability to form adventitious buds provides a potential for vegetative regeneration from roots, stumps and leaves. Based on these principles, a simple classification of bud banks is presented similar to the classification of seed banks. Bud bank traits are considered in relation to severity, timing and frequency of disturbance. These include vertical distribution and seasonal fluctuations in the number of buds. Methods for quantitative assessment of bud numbers and resprouting capacity are reviewed, and a new approach based on indirect bud counts is proposed. The suggested concept of bud banks may be widely used in studies focusing on plant functional traits in relation to disturbance regimes at the levels of plant individuals, populations and communities. Its further development may incorporate adjustments for areas with non-seasonal climate and refinements for some growth forms, such as epiphytes.     

A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis

MOTIVATION: Cancer diagnosis is one of the most important emerging clinical applications of gene expression microarray technology. We are seeking to develop a computer system for powerful and reliable cancer diagnostic model creation based on microarray data. To keep a realistic perspective on clinical applications we focus on multicategory diagnosis. To equip the system with the optimum combination of classifier, gene selection and cross-validation methods, we performed a systematic and comprehensive evaluation of several major algorithms for multicategory classification, several gene selection methods, multiple ensemble classifier methods and two cross-validation designs using 11 datasets spanning 74 diagnostic categories and 41 cancer types and 12 normal tissue types. RESULTS: Multicategory support vector machines (MC-SVMs) are the most effective classifiers in performing accurate cancer diagnosis from gene expression data. The MC-SVM techniques by Crammer and Singer, Weston and Watkins and one-versus-rest were found to be the best methods in this domain. MC-SVMs outperform other popular machine learning algorithms, such as k-nearest neighbors, backpropagation and probabilistic neural networks, often to a remarkable degree. Gene selection techniques can significantly improve the classification performance of both MC-SVMs and other non-SVM learning algorithms. Ensemble classifiers do not generally improve performance of the best non-ensemble models. These results guided the construction of a software system GEMS (Gene Expression Model Selector) that automates high-quality model construction and enforces sound optimization and performance estimation procedures. This is the first such system to be informed by a rigorous comparative analysis of the available algorithms and datasets. AVAILABILITY: The software system GEMS is available for download from http://www.gems-system.org for non-commercial use. CONTACT: alexander.statnikov@vanderbilt.edu.     

A proposal for amendment of the diagnosis of the genusPichia hansen

Summary An amended diagnosis has been given for the genusPichia Hansen to allow inclusion of species characterized by a lack of pellicle formation, by the absence or a strongly reduced pseudomycelium or by a combination of both properties. The following species fit the amended diagnosis ofPichia: P haplophila Shifrine et Phaff,P. carsonii Phaff et Knapp,P. quercibus Phaff et Knapp andP. xylosa Phaff, Miller et Shifrine. Furthermore, it has been proposed to transferSaccharomyces pastori Guilliermond,Saccharomyces pini Holst andDebaryomyces vini Zimmermann to the amended genusPichia, where they fit well rather than occupying and exceptional position in their present genera.     

A wearable system for pre-impact fall detection

Unique features of body segment kinematics in falls and activities of daily living (ADL) are applied to make automatic detection of a fall in its descending phase, prior to impact, possible. Fall-related injuries can thus be prevented or reduced by deploying fall impact reduction systems, such as an inflatable airbag for hip protection, before the impact. In this application, the authors propose the following hypothesis: “Thigh segments normally do not exceed a certain threshold angle to the side and forward directions in ADL, whereas this abnormal behavior occurs during a fall activity”. Torso and thigh wearable inertial sensors (3D accelerometer and 2D gyroscope) are used and the whole system is based on a body area network (BAN) for the comfort of the wearer during a long term application. The hypothesis was validated in an experiment with 21 young healthy volunteers performing both normal ADL and fall activities. Results show that falls could be detected with an average lead-time of 700 ms before the impact occurs, with no false alarms (100% specificity), a sensitivity of 95.2%. This is the longest lead-time achieved so far in pre-impact fall detection.     

Selective pressure, putative recombination events and evolutionary relationships among members of the family Closteroviridae: A proposal for a new classification

Molecular evolution of viruses is driven by both positive selection and recombination. In an effort to determine putative recombination events in the entire genome of members of the family Closteroviridae comprising 54 accessions retrieved from the international databases, a detail study was carried out by using RDP algorithm version 3.31β. Only isolates of Citrus tristeza virus and Grapevine leafroll-associated virus 3 were potential recombinants. None of members of Crinivirus genus was possible recombinant, but in turn, they were under positive selection that might be correlated with vector and/or host interactions. In contrast, Citrus tristeza virus isolates were under purifying selection as well as one-third of isolates of Grapevine leafroll-associated virus 3. The evolutionary history of all members of the Closteroviridae showed that they split into three distinct clusters corresponding to the three genera constituting this family. Moreover, the inferred phylogeny reshuffled the existing classification actually adopted by the International Committee on Taxonomy of Viruses. In this regard, each genus should be constituted by two distinct subgroups.     

A proposal for modification of the Belgian biotic index method

Modifications to a standard biological water quality assessment method, used in Belgium since 1979, were studied.As a result, we recommend the following:- samples should be processed live- samples should not be washed through a series of sieves- systematic units represented by only one individual should be included in the calculation of the biotic index.Using this modification, the biotic index can be calculated more rapidly and shows a higher correlation with a chemical water quality assessment index.     

A proposal for the conservation of the family Cucurbitaceae in Mexico

The pantropical Cucurbitaceae is one of the most important families ofvascular plants. The family includes 118 genera and 825 species, and Mexicois one of its most important centers of diversity, with 34 genera and 141species and subspecific taxa, including 13 cultivated ones. Five genera and 70taxa are endemic to the country. Some Mexican and Latin American wild speciesare close relatives of important crops, and others are employed as food ormedicine. Accordingly, in countries like Mexico the conservation of members ofthis family should be a priority. In this paper a list of members ofCucurbitaceae occurring in Mexico and their distribution patterns at state levelare discussed. Using cluster strategies, the states were classified according totheir floristic similarities. Hotspots of total diversity and endemismsat state level are identified, in order to discuss their role in futureconservation strategies. Iterative methods applied by conservation biology todetermine the best places for conservation are used to identify hierarchicallythe most important states that merit to be considered in this goal. Resultsindicate that implementing conservation strategies in half of the states wouldallow the protection of all the diversity found in the country, especially theendemisms. The combination of the results provided by the different methods isalso discussed as a possibly more efficient way to propose conservationstrategies for important species of the family.     

A proposal for the role of ecto-enzymes and adenylates in traumatic shock

It is proposed that the biochemical mechanisms which lead to the pathology of irreversible traumatic shock are based on the vasodilatory action of adenylates and failure of ecto-enzymes to clear these substances from the vascular bed. Following massive injury, or another assault which produces significant cytolysis, cytoplasmic ATP is released into the circulation. Ecto-phosphoesterhydrolases on erythrocytes normally control plasma adenylate concentrations to be maintained below 10^?7 M. If a critical ATP (or ADP) concentration between 10^?5 and 10^?4 M is reached, erythrocytes become semi-permeable and themselves release additional ATP into the plasma compartment. When ecto-ATPase activity becomes insufficient in metabolizing plasma ATP at rates which are needed to compensate for the release of cytoplasmic ATP, the vasodilatory effects of adenylates will manifest themselves in a sustained manner. It is suggested that ecto-phosphoesterhydrolases on blood formed elements and endothelial cells serve a protective function. Circulatory shock ensues under conditions when these ecto-enzymes are rendered incompetent or when plasma adenylate concentrations exceed their catabolic capacity.