A Study of Spiders (Araneae) on Maple Trees (Acer Spp.)

We began this study to determine whether spider species occur randomly on maple species or whether they are selective in picking either their host species or their position on that host. Several papers have been published on habitat selection of spiders in relation to structural components or microclimate (Barnes, 1953; Barnes & ,Barnes, 1954, 1955; Cherrett, 1964; Duffey, 1962a. 1962b, 1966; Hackmann, 1957; Kuenzler, 1958; Norgaard, 1951). Duffey (1956) and Kuenzler (1958) also discussed the influence of microclimate on the activities of spiders. None of the above, however, dealt with arboreal spiders with the exception of Duffey (1956) who discussed aerial dispersal rather than habitat selection

Fast Ejection Chain Algorithms for Vehicle Routing with Time Windows

This paper introduces new ejection chain strategies to effectively target vehicle routing problems with time window constraints (VRPTW). Ejection chain procedures are based on the idea of compound moves that allow a variable number of solution components to be modified within any single iteration of a local search algorithm. The yardstick behind such procedures is the underlying reference structure, which is the structure that is used to coordinate the moves that are available for the local search algorithm. The main contribution of the paper is a new reference structure that is particularly suited in order to handle the asymmetric aspects in a VRPTW. The new reference structure is a generalization of the doubly rooted reference structure introduced by Glover, resulting in a new, powerful neighborhood for the VRPTW. We use tabu search for the generation of the ejection chains. On a higher algorithmic level, we study the effect of different meta heuristics to steer the tabu chain ejection process. Computational results confirm that our approach leads to very fast algorithms that can compete with the current state of the art algorithms for the VRPTW.operations research and management science;

Scale free networks from a Hamiltonian dynamics

Contrary to many recent models of growing networks, we present a model with fixed number of nodes and links, where it is introduced a dynamics favoring the formation of links between nodes with degree of connectivity as different as possible. By applying a local rewiring move, the network reaches equilibrium states assuming broad degree distributions, which have a power law form in an intermediate range of the parameters used. Interestingly, in the same range we find non-trivial hierarchical clustering.Comment: 4 pages, revtex4, 5 figures. v2: corrected statements about equilibriu

Reproductive isolation between two populations of Aglaoctenus lagotis , a funnel-web wolf spider

Aglaoctenus lagotis (Lycosidae: Sosippinae) is a spider that, in contrast to the predominant wandering habit of the family, constructs funnel webs. The species is widely distributed throughout the Neotropics and is credited with high levels of intraspecific variation. Here, we evaluate whether reproductive isolating barriers operate between some populations of A. lagotis. We used heterotypic encounters between individuals from two distant localities: southern Uruguay (SU) and Central Argentina (CA). Additionally, we used spiders from an ntermediate locality, western Uruguay (WU), where both forms of the species overlap (SU.WU was used to describe individuals from WU reminiscent of those from SU; and CA.WU was used to describe individuals from WU reminiscent of those from CA). No copulations occurred between SU and CA individuals, whereas a single and atypical copulation occurred between SU.WU and CA.WU individuals. Attacks (only by females on males) were rare. In tests of choice based on silk cues, SU males did not prefer homotypic cues but almost did not court CA females, whereas CA males preferred homotypic cues but usually courted heterotypic females. These findings, with a previously reported temporal asynchrony between populations, suggest the occurrence of reproductive isolation between both spider forms and a speciation process favoured by the wide distribution and plasticity of the species.Fil: González Pérez, María de la Macarena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Cátedra de Diversidad Animal I; ArgentinaFil: Peretti, Alfredo Vicente. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Cátedra de Diversidad Animal I; ArgentinaFil: Costa, Fernando G.. Instituto de Investigaciones Biológicas "Clemente Estable"; Urugua

MCL-CAw: A refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure

Abstract Background The reconstruction of protein complexes from the physical interactome of organisms serves as a building block towards understanding the higher level organization of the cell. Over the past few years, several independent high-throughput experiments have helped to catalogue enormous amount of physical protein interaction data from organisms such as yeast. However, these individual datasets show lack of correlation with each other and also contain substantial number of false positives (noise). Over these years, several affinity scoring schemes have also been devised to improve the qualities of these datasets. Therefore, the challenge now is to detect meaningful as well as novel complexes from protein interaction (PPI) networks derived by combining datasets from multiple sources and by making use of these affinity scoring schemes. In the attempt towards tackling this challenge, the Markov Clustering algorithm (MCL) has proved to be a popular and reasonably successful method, mainly due to its scalability, robustness, and ability to work on scored (weighted) networks. However, MCL produces many noisy clusters, which either do not match known complexes or have additional proteins that reduce the accuracies of correctly predicted complexes. Results Inspired by recent experimental observations by Gavin and colleagues on the modularity structure in yeast complexes and the distinctive properties of "core" and "attachment" proteins, we develop a core-attachment based refinement method coupled to MCL for reconstruction of yeast complexes from scored (weighted) PPI networks. We combine physical interactions from two recent "pull-down" experiments to generate an unscored PPI network. We then score this network using available affinity scoring schemes to generate multiple scored PPI networks. The evaluation of our method (called MCL-CAw) on these networks shows that: (i) MCL-CAw derives larger number of yeast complexes and with better accuracies than MCL, particularly in the presence of natural noise; (ii) Affinity scoring can effectively reduce the impact of noise on MCL-CAw and thereby improve the quality (precision and recall) of its predicted complexes; (iii) MCL-CAw responds well to most available scoring schemes. We discuss several instances where MCL-CAw was successful in deriving meaningful complexes, and where it missed a few proteins or whole complexes due to affinity scoring of the networks. We compare MCL-CAw with several recent complex detection algorithms on unscored and scored networks, and assess the relative performance of the algorithms on these networks. Further, we study the impact of augmenting physical datasets with computationally inferred interactions for complex detection. Finally, we analyse the essentiality of proteins within predicted complexes to understand a possible correlation between protein essentiality and their ability to form complexes. Conclusions We demonstrate that core-attachment based refinement in MCL-CAw improves the predictions of MCL on yeast PPI networks. We show that affinity scoring improves the performance of MCL-CAw.http://deepblue.lib.umich.edu/bitstream/2027.42/78256/1/1471-2105-11-504.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/2/1471-2105-11-504-S1.PDFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/3/1471-2105-11-504-S2.ZIPhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/4/1471-2105-11-504.pdfPeer Reviewe

Sister species diverge in modality-specific courtship signal form and function

Understanding the relative importance of different sources of selection (e.g., the environment, social/sexual selection) on the divergence or convergence of reproductive communication can shed light on the origin, maintenance, or even disappearance of species boundaries. Using a multistep approach, we tested the hypothesis that two presumed sister species of wolf spider with overlapping ranges and microhabitat use, yet differing degrees of sexual dimorphism, have diverged in their reliance on modality- specific courtship signaling. We predicted that male Schizocosa crassipalpata (no ornamentation) rely predominantly on diet-dependent vibratory signaling for mating success. In contrast, we predicted that male S. bilineata (black foreleg brushes) rely on diet-dependent visual signaling. We first tested and corroborated the sister-species relationship between S. crassipalpata and S. bilineata using phylogenomic scale data. Next, we tested for species-specific, diet-dependent vibratory and visual signaling by manipulating subadult diet and subsequently quantifying adult morphology and mature male courtship signals. As predicted, vibratory signal form was diet-dependent in S. crassipalpata, while visual ornamentation (brush area) was diet-dependent in S. bilineata. We then compared the species-specific reliance on vibratory and visual signaling by recording mating across artificially manipulated signaling environments (presence/absence of each modality in a 2 × 2 full factorial design). In accordance with our diet dependence results for S. crassipalpata, the presence of vibratory signaling was important for mating success. In contrast, the light and vibratory environment interacted to influence mating success in S. bilineata, with vibratory signaling being important only in the absence of light. We found no differences in overall activity patterns. Given that these species overlap in much of their range and microhabitat use, we suggest that competition for signaling space may have led to the divergence and differential use of sensory modalities between these sister species

Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins

Motivation: Protein–protein interactions (PPIs) are critical for virtually every biological function. Recently, researchers suggested to use supervised learning for the task of classifying pairs of proteins as interacting or not. However, its performance is largely restricted by the availability of truly interacting proteins (labeled). Meanwhile, there exists a considerable amount of protein pairs where an association appears between two partners, but not enough experimental evidence to support it as a direct interaction (partially labeled)