Van der Waals Forces Between Plasmonic Nanoparticles

We propose a new approach to calculate van der Waals forces between nanoparticles where the van der Waals energy can be reduced to the energy of localized plasmons in nanoparticles. The general theory is applied to describe the interaction between two metallic nanoparticles and between a nanoparticle and a perfectly conducting plane. Our results could be used to prove experimentally the existence of new, recently predicted type of plasmon oscillation (Klimov and Guzatov, Phys Rev B 75:024303, 2007a; Klimov and Guzatov, Quantum Electron 37:209, 2007b) and to elaborate new control mechanisms for the adherence of nanoparticles between each other or onto surfaces.     

The relationship between the pleiotropic phenotypic effects of a mutation fixed by selection

A pleiotropic model of mutation is presented that allows for correlations between the effects of a new mutation and for the distribution of mutational effects to vary from being leptokurtic to normally distributed. Using this model I quantify how selection transforms the correlation between the effects of a new (random) mutation into the correlation between the effects of a mutation that is fixed by selection and contributes to an adaptation. Results suggest that under most conditions the correlation between the effects of a fixed mutation is less than the correlation between the effects of a new mutation. I also generalize previous results that quantified the expected size of a fixed mutation's effect on a character given an observed effect of that mutation on another character. In agreement with previous results, work here suggests that as the observed effect becomes large and beneficial the expected effect on another character approaches the expected effect of a new (random) mutation given the observed effect. Lastly, these theoretical results are related to recent empirical work that found beneficial mutations had a positive correlation in their pleiotropic effects.     

Characterization of an RNA receptor motif that recognizes a GCGA tetraloop

Tertiary interactions between a new RNA motif and RNA tetraloops were analyzed to determine whether this new motif shows preference for a GCGA tetraloop. In the structural context of a ligase ribozyme, this motif discriminated GCGA loop from 3 other tetraloops. The affinity between the GCGA loop and its receptor is strong enough to carry out the ribozyme activity.     

Literature Mining for the Discovery of Hidden Connections between Drugs,Genes and Diseases

The scientific literature represents a rich source for retrieval of knowledge on associations between biomedical concepts such as genes, diseases and cellular processes. A commonly used method to establish relationships between biomedical concepts from literature is co-occurrence. Apart from its use in knowledge retrieval, the co-occurrence method is also well-suited to discover new, hidden relationships between biomedical concepts following a simple ABC-principle, in which A and C have no direct relationship, but are connected via shared B-intermediates. In this paper we describe CoPub Discovery, a tool that mines the literature for new relationships between biomedical concepts. Statistical analysis using ROC curves showed that CoPub Discovery performed well over a wide range of settings and keyword thesauri. We subsequently used CoPub Discovery to search for new relationships between genes, drugs, pathways and diseases. Several of the newly found relationships were validated using independent literature sources. In addition, new predicted relationships between compounds and cell proliferation were validated and confirmed experimentally in an in vitro cell proliferation assay. The results show that CoPub Discovery is able to identify novel associations between genes, drugs, pathways and diseases that have a high probability of being biologically valid. This makes CoPub Discovery a useful tool to unravel the mechanisms behind disease, to find novel drug targets, or to find novel applications for existing drugs.     

Ocean annual phytoplankton carbon and new production,and annual export production estimated with empirical equations and CZCS data

Empirical equations are parameterized for use with chlorophyll a, derived from satellite ocean colour data, to calculate phytoplankton carbon production, phytoplankton new production, and export production. For environments in a high variance (HV) pigment statistical class, annual phytoplankton particulate organic carbon production (AIP) is linearly related to annual average in situ chlorophyll a within the near‐surface layer. Linear relations were also obtained between AIP and annual new nitrogen production, and between AIP and particulate organic carbon annually exported from the euphotic zone for environments in that class. We found no relation between AIP and C_SFC, or between the annual production variables, for oceanic environments characterized by low pigment variance (LV). Ratios of export production to AIP, called e, and new production to nitrogen annually used in phytoplankton production, called f, are widely used to express marine food web processes. The trends of these ratios with AIP differ between HV and LV environments. This is a result of differences in the coupling between nitrogen and carbon transfer in pelagic food webs, which contain different organism size classes in HV compared to LV environments. We applied the empirical equations to CZCS data to estimate global new and export production. The HV environments are responsible for about 40% of global ocean annual phytoplankton carbon production and 70% of global ocean annual new and export production.     

Evolutionary shifts between host oak sections and host-plant organs in Andricus gallwasps

Abstract.— Gall-inducing insects have especially intimate interactions with their host plants and generally show great specificity with regard to both the host-plant species and the organ (e.g. flower, leaf) galled. However, the relative roles of shifts between host species and between host-plant organs in the diversification of gall-inducers are uncertain. We employ a novel and general maximum-likelihood approach to show that shifts between host-plant organs occur at a significantly greater rate than shifts between host oak sections in European Andricus gallwasps. This suggests that speciation has more often been associated with gall location shifts than with colonization of new host-plant species, and implies that it may be easier for gall-inducers to colonize new plant organs than new plant species.
Andricus gallwasps have complex life cycles, with obligate alternation of sexual and parthenogenetic generations. Our phylogenetic analyses show that a life cycle with both generations galling white oaks (section Quercus ) is ancestral, with a single shift of the sexual generation onto black oaks (section Cerris ) to generate a clade with a novel host-alternating life cycle. This new life cycle provided the opportunity for further speciation, but may have also increased the risk of extinction of one or both generations by the demographic requirement for co-existence of both host-plant groups. In summary, it appears that Andricus gallwasp radiation may be a two-level process. Speciation events often involve shifts in gall location on the same host species. However, there are only so many ways to gall an oak, and rare shifts to new oak sections may contribute greatly to long-term diversification by opening up whole new adaptive zones.     

Combinational Reasoning of Quantitative Fuzzy Topological Relations for Simple Fuzzy Regions

In recent years, formalization and reasoning of topological relations have become a hot topic as a means to generate knowledge about the relations between spatial objects at the conceptual and geometrical levels. These mechanisms have been widely used in spatial data query, spatial data mining, evaluation of equivalence and similarity in a spatial scene, as well as for consistency assessment of the topological relations of multi-resolution spatial databases. The concept of computational fuzzy topological space is applied to simple fuzzy regions to efficiently and more accurately solve fuzzy topological relations. Thus, extending the existing research and improving upon the previous work, this paper presents a new method to describe fuzzy topological relations between simple spatial regions in Geographic Information Sciences (GIS) and Artificial Intelligence (AI). Firstly, we propose a new definition for simple fuzzy line segments and simple fuzzy regions based on the computational fuzzy topology. And then, based on the new definitions, we also propose a new combinational reasoning method to compute the topological relations between simple fuzzy regions, moreover, this study has discovered that there are (1) 23 different topological relations between a simple crisp region and a simple fuzzy region; (2) 152 different topological relations between two simple fuzzy regions. In the end, we have discussed some examples to demonstrate the validity of the new method, through comparisons with existing fuzzy models, we showed that the proposed method can compute more than the existing models, as it is more expressive than the existing fuzzy models.     

从植物中寻找农药活性物质

从植物中寻找农药活性物质,判明结构,使之成为创新类型农药有效母体,是创制新农药品种的重要途径之一,受到当今全世界农药界的广泛重视。本文综合性介绍植物与农药的关系,该交叉学科研究的一般程序和方法以及通过对有效母体的结构改造,构一效关系的研究,创制新农药的研究过程。     

A new family-based association test via a least-squares method

To test the association between a dichotomous phenotype and genetic marker based on family data, we propose a least-squares method using the vector of phenotypes and their cross products within each family. This new approach allows covariate adjustment and is numerically much simpler to implement compared to likelihood- based methods. The new approach is asymptotically equivalent to the generalized estimating equation approach with a diagonal working covariance matrix, thus avoiding some difficulties with the working covariance matrix reported previously in the literature. When applied to the data from Collaborative Study on the Genetics of Alcoholism, this new method shows a significant association between the marker rs1037475 and alcoholism.     

Effect of new rules on the correlation between situation parameters and performance in beach volleyball

The aim of the study was to assess the effect of basic technical-tactical elements, i.e. specific motor abilities, on performance in beach volleyball, with special reference to differences between the old and new official rules. Analysis of variance for 6 variables of technical-tactical elements between the winning and defeated teams included a sample of 129 sets played according to the old official rules (1995 and 1996) and 74 sets played according to the new official rules (2003). This was followed by regression analysis between these technical-tactical elements as predictors and a variable, i.e. score difference at which the team won or lost the game, as a criterion. Results of the analysis of variance between the winning and defeated teams showed highest differences in the performance of attack-hit, followed by counterattack-hit and blocking in both game types. However, difference in the performance of serve reception, serve, and field defense between the winning and defeated teams decreased significantly with the use of new rules as compared with the old ones. Results of regression analysis indicated the sets played according to the new rules relative to old ones to increase the predominant impact of technical-tactical elements in the above-net actions, especially attack-hit and block, on the final result in beach volleyball.     

Microarray time course experiments: finding profiles

Time course studies with microarray techniques and experimental replicates are very useful in biomedical research. We present, in replicate experiments, an alternative approach to select and cluster genes according to a new measure for association between genes. First, the procedure normalizes and standardizes the expression profile of each gene, and then, identifies scaling parameters that will further minimize the distance between replicates of the same gene. Then, the procedure filters out genes with a flat profile, detects differences between replicates, and separates genes without significant differences from the rest. For this last group of genes, we define a mean profile for each gene and use it to compute the distance between two genes. Next, a hierarchical clustering procedure is proposed, a statistic is computed for each cluster to determine its compactness, and the total number of classes is determined. For the rest of the genes, those with significant differences between replicates, the procedure detects where the differences between replicates lie, and assigns each gene to the best fitting previously identified profile or defines a new profile. We illustrate this new procedure using simulated data and a representative data set arising from a microarray experiment with replication, and report interesting results.     

New concentration measures as kinds of the quadratic entropy

We introduced two new quadratic entropy indices and performed numerical experimentation on biological data sets to reveal their properties. The difference between two individuals was postulated in both cases on the basis of occurrence probabilities of the species concerned. The new measures summarize a different aspect of community properties than biodiversity indices. They may play a critical role among others in population dynamic models and in the analysis of dominance in ecology. The numerical experimentation was based in part on the characteristics of so-called sensitivity graphs. The graphs related to the new indices are very similar to the opposites of sensitivity graphs of diversity indices, generally used in statistical ecology. Further relations between the new indices and concentration indices were analysed on plot diagrams originating from simulated data. From these analyses, we conclude that the new quadratic entropies are close to concentration measures.     

Cognitive neuroscience of human social behaviour

We are an intensely social species--it has been argued that our social nature defines what makes us human, what makes us conscious or what gave us our large brains. As a new field, the social brain sciences are probing the neural underpinnings of social behaviour and have produced a banquet of data that are both tantalizing and deeply puzzling. We are finding new links between emotion and reason, between action and perception, and between representations of other people and ourselves. No less important are the links that are also being established across disciplines to understand social behaviour, as neuroscientists, social psychologists, anthropologists, ethologists and philosophers forge new collaborations.     

Construction of two recombination yeast two-hybrid vectors by in vitro recombination

Recombination-based restrictionless, ligation-independent cloning has been proven to be advantageous over restriction digestion and ligation cloning. To utilize the recombination cloning and previously constructed two-hybrid cDNA libraries, a new Gateway yeast two-hybrid bait vector, pEZY202, and a new prey vector, pEZY45, were constructed. The two-hybrid vectors were generated by in vitro recombination using a protocol that can be easily adapted for the conversion of other existing vectors. The new vectors were used to assay the interaction between the WW domain of PQBP1 (PQBPww) and the WW domain binding protein WBP11. Both PQBPww and WBP11 were cloned into a Gateway donor vector by in vitro recombination. They were then subcloned into pEZY45 and pEZY202, respectively, by in vitro recombination. The binding between PQBPww and WBP11 was reported in a two-hybrid experiment using the new vectors. The results of testing the new vectors in combination with the original vectors indicated that the new bait vector could be used to screen cDNA libraries that are constructed using the original prey vectors.     

Hemispheric Asymmetry in New Neurons in Adulthood Is Associated with Vocal Learning and Auditory Memory

Many brain regions exhibit lateral differences in structure and function, and also incorporate new neurons in adulthood, thought to function in learning and in the formation of new memories. However, the contribution of new neurons to hemispheric differences in processing is unknown. The present study combines cellular, behavioral, and physiological methods to address whether 1) new neuron incorporation differs between the brain hemispheres, and 2) the degree to which hemispheric lateralization of new neurons correlates with behavioral and physiological measures of learning and memory. The songbird provides a model system for assessing the contribution of new neurons to hemispheric specialization because songbird brain areas for vocal processing are functionally lateralized and receive a continuous influx of new neurons in adulthood. In adult male zebra finches, we quantified new neurons in the caudomedial nidopallium (NCM), a forebrain area involved in discrimination and memory for the complex vocalizations of individual conspecifics. We assessed song learning and recorded neural responses to song in NCM. We found significantly more new neurons labeled in left than in right NCM; moreover, the degree of asymmetry in new neuron numbers was correlated with the quality of song learning and strength of neuronal memory for recently heard songs. In birds with experimentally impaired song quality, the hemispheric difference in new neurons was diminished. These results suggest that new neurons may contribute to an allocation of function between the hemispheres that underlies the learning and processing of complex signals.     

The synthesis of physics and biology

The hypothesis of a qualitative new field permits the prediction of a new fundamental constant. With this constant a relation between c and h can be found. The new constant permits not only a system of physics but also a new transition from physics into biology.     

Multi-QTL Mapping for Quantitative Traits Using Epistatic Distorted Markers

The interaction between segregation distortion loci (SDL) has been often observed in all kinds of mapping populations. However, little has been known about the effect of epistatic SDL on quantitative trait locus (QTL) mapping. Here we proposed a multi-QTL mapping approach using epistatic distorted markers. Using the corrected linkage groups, epistatic SDL was identified. Then, these SDL parameters were used to correct the conditional probabilities of QTL genotypes, and these corrections were further incorporated into the new QTL mapping approach. Finally, a set of simulated datasets and a real data in 304 mouse F₂ individuals were used to validate the new method. As compared with the old method, the new one corrects genetic distance between distorted markers, and considers epistasis between two linked SDL. As a result, the power in the detection of QTL is higher for the new method than for the old one, and significant differences for estimates of QTL parameters between the two methods were observed, except for QTL position. Among two QTL for mouse weight, one significant difference for QTL additive effect between the above two methods was observed, because epistatic SDL between markers C66 and T93 exists (P = 2.94e-4).     

New version of Monte Carlo expanded ensemble method for precise calculations of free energy difference

A new version of Monte Carlo (MC) expanded ensemble (EE) method is proposed for the calculations of free energy difference (FED) between two different systems with close values of the free energy. In order to check the method the FED between simple model systems (fluid of hard spheres and freely jointed polymer chain of hard spheres) was calculated. The free energy of the mentioned above systems was also calculated by a standard MC EE method in order to compare the results of two simulations. It was shown that the accuracy of a new algorithm is the same as of a standard one. At the same time new version of EE allows us to obtain FED between two systems having quite different structures, but similar free energies, during one simulation run.     

Unequal crossingover between homologous chromosomes is not the major mechanism involved in the generation of new alleles at VNTR loci

To investigate the hypothesis that unequal exchange between homologous chromosomes is involved when new alleles are generated at VNTR loci, we used genetic linkage maps to identify flanking markers surrounding a VNTR marker locus. The minisatellite probe lambda MS1 was selected, as the hypervariable locus it detects undergoes spontaneous generation of new alleles in the germline at a rate of approximately 5%. Multipoint linkage analysis placed lambda MS1 within a cluster of polymorphic marker loci on chromosome 1p. Using the two closest flanking markers, CMM8 and YNZ2, we were able to characterize 12 new-allele events in terms of crossingover between the flanking markers. Statistical analysis of these data has allowed us to reject the model that assumes that events generating new alleles always involve unequal exchange between homologous chromosomes at meiosis.     

Universal similarity measure for comparing protein structures

We introduce a new variant of the root mean square distance (RMSD) for comparing protein structures whose range of values is independent of protein size. This new dimensionless measure (relative RMSD, or RRMSD) is zero between identical structures and one between structures that are as globally dissimilar as an average pair of random polypeptides of respective sizes. The RRMSD probability distribution between random polypeptides converges to a universal curve as the chain length increases. The correlation coefficients between aligned random structures are computed as a function of polypeptide size showing two characteristic lengths of 4.7 and 37 residues. These lengths mark the separation between phases of different structural order between native protein fragments. The implications for threading are discussed.