02868nas a2200229   4500008004100000245005300041210005100094260001200145300001600157490000700173520225200180653001602432653000702448653001502455653001602470100002002486700002002506700002202526700001602548700002202564856005202586       2006                        eng d00aBio-Ontology and text: bridging the modeling gap0 aBioOntology and text bridging the modeling gap  cOctober  a2421–24290 v223 aMotivation: Natural language processing (NLP) techniques are increasingly being used in biology to automate the capture of new biological discoveries in text, which are being reported at a rapid rate. Yet, information represented in NLP data structures is classically very different from information organized with ontologies as found in model organisms or genetic databases. To facilitate the computational reuse and integration of information buried in unstructured text with that of genetic databases, we propose and evaluate a translational schema that represents a comprehensive set of phenotypic and genetic entities, as well as their closely related biomedical entities and relations as expressed in natural language. In addition, the schema connects different scales of biological information, and provides mappings from the textual information to existing ontologies, which are essential in biology for integration, organization, dissemination and knowledge management of heterogeneous phenotypic information. A common comprehensive representation for otherwise heterogeneous phenotypic and genetic datasets, such as the one proposed, is critical for advancing systems biology because it enables acquisition and reuse of unprecedented volumes of diverse types of knowledge and information from text. Results: A novel representational schema, PGschema, was developed that enables translation of phenotypic, genetic and their closely related information found in textual narratives to a well-defined data structure comprising phenotypic and genetic concepts from established ontologies along with modifiers and relationships. Evaluation for coverage of a selected set of entities showed that 90% of the information could be represented (95% confidence interval: 86-93%; n = 268). Moreover, PGschema can be expressed automatically in an XML format using natural language techniques to process the text. To our knowledge, we are providing the first evaluation of a translational schema for NLP that contains declarative knowledge about genes and their associated biomedical data (e.g. phenotypes). Availability: http://zellig.cpmc.columbia.edu/PGschema Contact: Friedman@dbmi.columbia.edu or Lussier@uchicago.edu 10.1093/bioinformatics/btl40510adata-mining10ait10aontologies10atext-mining1 aFriedman, Carol1 aBorlawsky, Tara1 aShagina, Lyudmila1 aXing, Rosie1 aLussier, Yves, A.  uhttp://dx.doi.org/10.1093/bioinformatics/btl40502006nas a2200205   4500008004100000245009400041210006900135260001000204300001400214490000700228520140900235653001401644653001801658653001301676653001101689653001501700100002101715700001601736856004801752       2006                        eng d00aClose-range acoustic signaling and mate choice in Hawaiian crickets (Gryllidae: Laupala )0 aCloserange acoustic signaling and mate choice in Hawaiian cricke  cApril  a770–7760 v593 aAbstract&nbsp;&nbsp;Evolution of the mate recognition system (MRS) can play a central role in animal speciation. One dramatic consequence of changes in the MRS is the failure of individuals from divergent lineages to successfully court and mate, thereby reducing gene flow between these groups. Here, we test the role of an acoustic mating signal on mate choice in a Hawaiian cricket genus (Gryllidae: Laupala). Speciation in Laupala is proceeding at an extremely rapid rate, apparently driven by divergence in aspects of the mate recognition system, most conspicuously the pulse rate of male calling song. Previous studies demonstrate that females prefer the pulse rate of a conspecific male's song when perceived at long range, in laboratory phonotaxis trials. In this study, we examined mate choice in two species that differ dramatically in pulse rate: Laupala paranigra and Laupala kohalensis. We tested the female's preference in both species for pulse rates at close range, by providing females an opportunity to mate with hybrid males producing a range of intermediate pulse rates. Results of our study demonstrate that while strong behavioral barriers exist between these two species, variation in the pulse rate of male calling song did not predict female mate choice at close range. These results suggest a more complex architecture to mate recognition in Laupala than previously hypothesized.10abehaviour10acommunication10acrickets10ahawaii10aorthoptera1 aMendelson, Tamra1 aShaw, Kerry  uhttp://dx.doi.org/10.1007/s00265-005-0107-702087nas a2200193   4500008004100000245003900041210003900080260001300119300001400132490000800146520159200154653001701746653001201763653001401775653001201789100002201801700001601823856005401839       2006                        eng d00aComparing species abundance models0 aComparing species abundance models  cNovember  a153–1630 v1993 aFive regression models (Poisson, negative binomial, quasi-Poisson, the hurdle model and the zero-inflated Poisson) were used to assess the relationship between the abundance of a vulnerable plant species, Leionema ralstonii, and the environment. The methods differed in their capacity to deal with common properties of ecological data. They were assessed theoretically, and their predictive performance was evaluated with correlation, calibration and error statistics calculated within a bootstrap evaluation procedure that simulated performance for independent data.The hurdle model performed best, with the highest correlations between the observed and predicted abundances. This model was also well calibrated, giving the closest agreement between observed and predicted abundances. The negative binomial was the worst performing model. It had weaker correlations than the other models and resulted in a strong, inconsistent bias in predictions. The standard Poisson model which accommodates neither zero-inflation nor over-dispersion gave accurate estimates of regional population abundance, but at the individual population level they were inconsistent and biased.The strong performance of the hurdle model, coupled with theoretical properties that suit it for these data and for the ecology of this species, suggest that it is a useful alternative to other modelling methods. The gains in performance have practical advantages where predictions are used by conservation planners to understand population dynamics or to assess the relative risks of alternative management scenarios.10adistribution10aecology10amodelling10apoisson1 aPotts, Joanne, M.1 aElith, Jane  uhttp://dx.doi.org/10.1016/j.ecolmodel.2006.05.02500532nas a2200169   4500008004100000022001400041245006400055210006400119260003100183300001400214490000700228653001700235653001700252653001500269100002300284856005500307       2006                        eng d  a0888-889200aCommon Ground between Anthropology and Conservation Biology0 aCommon Ground between Anthropology and Conservation Biology  bBlackwell PublishingcJune  a683–6850 v2010aanthropology10aconservation10alandrights1 aBrosius, Peter, J.  uhttp://dx.doi.org/10.1111/j.1523-1739.2006.00463.x01631nas a2200193   4500008004100000245006500041210006500106260001000171300001600181490000800197520108200205653001101287653001401298653001101312100002401323700002301347700002101370856004601391       2006                        eng d00aExotic taxa less related to native species are more invasive0 aExotic taxa less related to native species are more invasive  cApril  a5841–58450 v1033 aSome species introduced into new geographical areas from their native ranges wreak ecological and economic havoc in their new environment. Although many studies have searched for either species or habitat characteristics that predict invasiveness of exotic species, the match between characteristics of the invader and those of members of the existing native community may be essential to understanding invasiveness. Here, we find that one metric, the phylogenetic relatedness of an invader to the native community, provides a predictive tool for invasiveness. Using a phylogenetic supertree of all grass species in California, we show that highly invasive grass species are, on average, significantly less related to native grasses than are introduced but noninvasive grasses. The match between the invader and the existing native community may explain why exotic pest species are not uniformly noxious in all novel habitats. Relatedness of invaders to the native biota may be one useful criterion for prioritizing management efforts of exotic species. 10.1073/pnas.050807310310aaliens10ainvasions10atheory1 aStrauss, Sharon, Y.1 aWebb, Campbell, O.1 aSalamin, Nicolas  uhttp://dx.doi.org/10.1073/pnas.050807310300778nas a2200241   4500008004100000022001400041245015000055210006900205260003200274300001400306490000700320653001700327653002700344653001600371653001400387653001400401653001500415653000800430653000900438100001300447700002100460856005500481       2006                        eng d  a1010-061X00aDivergence in the calling songs between sympatric and allopatric populations of the southern wood cricket Gryllus fultoni (Orthoptera: Gryllidae)0 aDivergence in the calling songs between sympatric and allopatric  bBlackwell PublishingcMarch  a459–4720 v1910abioacoustics10acharacter-displacement10acompetition10aevolution10agryllidae10aorthoptera10arcd10asong1 aJang, Y.1 aGerhardt, H., C.  uhttp://dx.doi.org/10.1111/j.1420-9101.2005.01014.x02087nas a2200205   4500008004100000245011900041210006900160260001200229300001600241490000800257520143200265653001701697653001801714653001201732653001401744100002901758700002301787700002601810856004501836       2006                        eng d00aEvidence that female preferences have shaped male signal evolution in a clade of specialized plant-feeding insects0 aEvidence that female preferences have shaped male signal evoluti  cOctober  a2585–25930 v2733 a10.1098/rspb.2006.3635 Mate choice is considered an important influence in the evolution of mating signals and other sexual traits, and—since divergence in sexual traits causes reproductive isolation—it can be an agent of population divergence. The importance of mate choice in signal evolution can be evaluated by comparing male signal traits with female preference functions, taking into account the shape and strength of preferences. Specifically, when preferences are closed (favouring intermediate values), there should be a correlation between the preferred values and the trait means, and stronger preferences should be associated with greater preference–signal correspondence and lower signal variability. When preferences are open (favouring extreme values), signal traits are not only expected to be more variable, but should also be shifted towards the preferred values. We tested the role of female preferences in signal evolution in the species complex of treehoppers, a clade of plant-feeding insects hypothesized to have speciated in sympatry. We found the expected relationship between signals and preferences, implicating mate choice as an agent of signal evolution. Because differences in sexual communication systems lead to reproductive isolation, the factors that promote divergence in female preferences—and, consequently, in male signals—may have an important role in the process of speciation.10abioacoustics10acommunication10ainsects10avibration1 aRodr\'ıguez, Rafael, L.1 aRamaswamy, Karthik1 aCocroft, Reginald, B.  uhttp://dx.doi.org/10.1098/rspb.2006.363501686nas a2200217   4500008004100000022001400041245005400055210004900109260001400158300001400172490000600186520110700192653001701299653002901316653001601345653000901361653001001370100002301380700002401403856004101427       2006                        eng d  a1467-546300aThe Life Sciences Semantic Web is Full of Creeps!0 aLife Sciences Semantic Web is Full of Creeps  cSeptember  a275–2860 v73 aThe Semantic Web for the Life Sciences (SWLS), when realized, will dramatically improve our ability to conduct bioinformatics analyses using the vast and growing stores of web-accessible resources. This ability will be achieved through the widespread acceptance and application of standards for naming, representing, describing and accessing biological information. The W3C-led Semantic Web initiative has established most, if not all, of the standards and technologies needed to achieve a unified, global SWLS. Unfortunately, the bioinformatics community has, thus far, appeared reluctant to fully adopt them. Rather, we are seeing what could be described as semantic creep'–timid, piecemeal and ad hoc adoption of parts of standards by groups that should be stridently taking a leadership role for the community. We suggest that, at this point, the primary hindrances to the creation of the SWLS may be social rather than technological in nature, and that, like the original Web, the establishment of the SWLS will depend primarily on the will and participation of its consumers. 10.1093/bib/bbl02510abiodiversity10abiodiversity-informatics10ainformatics10alsid10aweb201 aGood, Benjamin, M.1 aWilkinson, Mark, D.  uhttp://dx.doi.org/10.1093/bib/bbl02501929nas a2200241   4500008004100000020001800041245009400059210006900153260002700222300001200249520123000261653001101491653000801502653001701510653001601527653001101543653001601554100001701570700001801587700001601605700002001621856004601641       2006                        eng d  a1-59593-343-300aThe design and implementation of a self-calibrating distributed acoustic sensing platform0 adesign and implementation of a selfcalibrating distributed acous  aNew York, NY, USAbACM  a71–843 aWe present the design, implementation, and evaluation of the Acoustic Embedded Networked Sensing Box (ENSBox), a platform for prototyping rapid-deployable distributed acoustic sensing systems, particularly distributed source localization. Each ENSBox integrates an ARM processor running Linux and supports key facilities required for source localization: a sensor array, wireless network services, time synchronization, and precise self-calibration of array position and orientation. The ENSBox's integrated, high precision self-calibration facility sets it apart from other platforms. This self-calibration is precise enough to support acoustic source localization applications in complex, realistic environments: e.g., 5 cm average 2D position error and 1.5 degree average orientation error over a partially obstructed 80x50 m outdoor area. Further, our integration of array orientation into the position estimation algorithm is a novel extension of traditional multilateration techniques. We present the result of several different test deployments, measuring the performance of the system in urban settings, as well as forested, hilly environments with obstructing foliage and 20-30 m distances between neighboring nodes.10aamibio10aasr10abioacoustics10acalibration10aensbox10ameasurement1 aGirod, Lewis1 aLukac, Martin1 aTrifa, Vlad1 aEstrin, Deborah  uhttp://dx.doi.org/10.1145/1182807.1182815