bluuebunny/crossref_metadata_2025_split huggingface dataset:
LibSBGN: Electronic Processing of SBGN maps
Authors: Demir Emek , Dogrusoz Ugur , Le Novère Nicolas , Matsuoka Yukiko , Sorokin Anatoly , Funahashi Akira , Mi Huaiyu , Kitano Hiroaki , Aladjem Mirit , van Iersel Martijn , Blinov Michael , Boyd Sarah , Villéger Alice , Bergmann Frank , Moodie Stuart , Schreiber Falk , Luna Augustin , Czauderna Tobias 
Published: October 2010

AbstractIntroduction Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that enables diagram exchange while preserving biological meaning and relations.
Results
To meet this need, we are developing an Extensible Markup Language (XML) schema definition. In addition we are developing a software library called LibSBGN. Besides reading and writing files, this library will also be used to validate SBGN maps against the specifications, and convert to and from related systems biology standards, such as SBML and BioPAX.LibSBGN is still under development, but is already being adopted by several tools (See the LibSBGN project page for an up-to-date list of client software). The early adoption of LibSBGN by those tools helps to ensure that LibSBGN is independent of a specific software application, and does not contain artifacts for specific tools. LibSBGN is currently implemented in Java, a parallel C++ version is planned for the future.A test-suite of dozens of LibSBGN documents, covering every possible feature of SBGN maps, was created. This test-suite can be used by developers to check for compliance with the standard, and compare rendering capabilities with other tools.LibSBGN is a community effort, involving people from institutes all around the world, representing a wide selection of pathway tools. The community is organized around a sourceforge project site (http://libsbgn.sourceforge.net), a mailing list and monthly online meetings.A first release of LibSBGN, covering only the Process Description (PD) language, is planned in October 2010. Support for all three languages of SBGN is planned for a later release.
Searching BioModels Database
Authors: Henkel Ron , Waltemath Dagmar , Peters Andre , Endler Lukas , le Novère Nicolas 
Published: October 2010

Abstract*Aim*The increasing number of computational models of biological systems demands a better support for search facilities. One possible improvement is to enable ranked retrieval of models based on existing model annotation. Applying existing Information Retrieval (IR) techniques to computational models, we have implemented a new search strategy in BioModels Database. In this search strategy the index of search terms contains not only the model descriptions in the database, but is expanded by including ontological and textual information about a model and its constituents retrieved from external sources. To add more background knowledge, we additionally index the abstracts of the reference publications.
Results
The new search system was integrated into BioModels Database and is based on a Lucene implementation. The model index includes 454 models and 154854 terms, the semantic index 2353 constituents and 437244 terms. Different sources are incorporated in the retrieval and ranking process, the most important of them via MIRIAM annotations to models and model constituents.The search results are sorted with regard to different aspects, i.e. model authors, dates, constituents, or SBML elements. Several state-of-the-art information retrieval features are supported, such as fuzzy, proximity or range search. As a result the user is enabled to specify the criteria relevant for a search, and is provided with a ranked result set of relevant models. The search was implemented in the demo version of BioModels Database and is available at http://www.ebi.ac.uk/biomodels-demo/.A detailed description of the technical realisation is given in:[Henkel et al., 2010]: Henkel, R., Endler, L., Peters, A., Novere, N., and Waltemath, D. (2010). Ranked retrieval of computational biology models. BMC Bioinformatics, 11(1):423+..
CellML 1.1 modularity
Authors: Nielsen Poul 
Published: October 2010

AbstractCellML 1.1 is an open XML-based language designed to store and exchange computer-based mathematical models. It has a simple facility to import existing models in order to create new models. The import facility encourages the development of hierarchical models and model reuse through the creation of well-curated model components in public model repositories. This presentation describes some of the features of CellML 1.1 and best practices for taking advantage of these features.
Inferring a Transcriptional Regulatory Network from Gene Expression Data Using Nonlinear Manifold Embedding
Authors: Zare Hossein , Kaveh Mostafa , Khodursky Arkady 
Published: October 2010

AbstractTranscriptional networks consist of multiple regulatory layers corresponding to the activity of global regulators, specialized repressors and activators of transcription as well as proteins and enzymes shaping the DNA template. Such intrinsic multi-dimensionality makes uncovering connectivity patterns difficult and unreliable and it calls for adoption of methodologies commensurate with the underlying organization of the data source. Here we present a new computational method that predicts interactions between transcription factors and target genes using a compendium of microarray gene expression data and the knowledge of known interactions between genes and transcription factors. The proposed method called Kernel Embedding of REgulatory Networks (KEREN) is based on the concept of gene-regulon association and it captures hidden geometric patterns of the network via manifold embedding. We applied KEREN to reconstruct gene regulatory interactions in the model bacteria E.coli on a genome-wide scale. Our method not only yields accurate prediction of verifiable interactions, which outperforms on certain metrics comparable methodologies, but also demonstrates the utility of a geometric approach to the analysis of high-dimensional biological data. We also describe the general application of kernel embedding techniques to some other function and network discovery algorithms.
Validating the use of woodrat (Neotoma) middens for documenting natural invasions
Authors: Lyford Mark E. , Jackson Stephen T. , Gray Stephen T. , Eddy Robert G. 
Published: October 2010

AbstractAim  Plant macrofossils in fossil woodrat (Neotoma) middens are the primary source of information on late Quaternary biogeographical history of plants in arid and semi‐arid regions of North America. Macrofossil records from middens are playing particularly important roles in documenting spatial and temporal patterns of plant migrations and invasions since the last glacial maximum 21,000 years ago. However, relatively few actualistic studies comparing contents of modern middens with surrounding flora and vegetation have been carried out. The primary aim of this study is to assess the reliability of midden assemblages in detecting the presence of tree, shrub and several other plant species growing on the surrounding landscape. The secondary aims are to determine whether probability of occurrence of species in middens is related to abundance in vegetation, and whether representation of individual species in middens is contingent on presence/absence or abundance of other species.Location  Our five study sites were bedrock escarpments or canyons in the central Rocky Mountains (north‐eastern Utah, central Wyoming and south‐central Montana). All sites were in conifer woodland or forest/woodland variously dominated by Juniperus osteosperma, J. scopulorum, Pinus edulis, P. flexilis and Pseudotsuga menziesii. Neotoma cinerea is the only woodrat species in the region.Methods  Macrofossil assemblages from 59 modern middens (all showing clear signs of recent or ongoing woodrat activity) were compared with floristic composition of vegetation within 50 m of the middens, and with percent cover of vegetation within 30 m of the middens.Results  Coniferous trees and shrubs were well‐represented in middens, occurring consistently even when abundance in the local vegetation was very low. Juniperus osteosperma and J. scopulorum were particularly well‐represented, occurring in middens regardless of local abundance. Other conifers (P. edulis, P. flexilis, P. ponderosa, Pseudotsuga menziesii) were occasionally absent from middens when abundance in vegetation was low (< 20% canopy cover). Occurrence of dicot shrubs and graminoids was less consistent.Main conclusions  Middens constructed by N. cinerea are highly reliable sensors of presence/absence of J. osteosperma and J. scopulorum, and hence can be used to infer invasions and past biogeographical distributions of these species. The middens are also reliable in registering populations of other conifers, although presence in middens may be contingent on local abundance. Additional comparative studies are needed to develop a sound empirical basis for using middens of N. cinerea and other species to infer past presence/absence of plant species on the landscape, and to explore the vegetation‐sensing properties of midden assemblages.
Do we need land‐cover data to model species distributions in Europe?
Authors: Thuiller Wilfried , Araújo Miguel B , Lavorel Sandra 
Published: October 2010

AbstractAim  To assess the influence of land cover and climate on species distributions across Europe. To quantify the importance of land cover to describe and predict species distributions after using climate as the main driver.Location  The study area is Europe.Methods  (1) A multivariate analysis was applied to describe land‐cover distribution across Europe and assess if the land cover is determined by climate at large spatial scales. (2) To evaluate the importance of land cover to predict species distributions, we implemented a spatially explicit iterative procedure to predict species distributions of plants (2603 species), mammals (186 species), breeding birds (440 species), amphibian and reptiles (143 species). First, we ran bioclimatic models using stepwise generalized additive models using bioclimatic variables. Secondly, we carried out a regression of land cover (LC) variables against residuals from the bioclimatic models to select the most relevant LC variables. Finally, we produced mixed models including climatic variables and those LC variables selected as decreasing the residual of bioclimatic models. Then we compared the explanatory and predictive power of the pure bioclimatic against the mixed model.Results  (1) At the European coarse resolution, land cover is mainly driven by climate. Two bioclimatic axes representing a gradient of temperature and a gradient of precipitation explained most variation of land‐cover distribution. (2) The inclusion of land cover improved significantly the explanatory power of bioclimatic models and the most relevant variables across groups were those not explained or poorly explained by climate. However, the predictive power of bioclimatic model was not improved by the inclusion of LC variables in the iterative model selection process.Main conclusion  Climate is the major driver of both species and land‐cover distributions over Europe. Yet, LC variables that are not explained or weakly associated with climate (inland water, sea or arable land) are interesting to describe particular mammal, bird and tree distributions. However, the addition of LC variables to pure bioclimatic models does not improve their predictive accuracy.
Effects of climate and local aridity on the latitudinal and habitat distribution of Arvicanthis niloticus and Arvicanthis ansorgei (Rodentia, Murinae) in Mali
Authors: Sicard B. , Catalan J. , Ag'Atteynine S. , Abdoulaye D. , Britton‐Davidian J. 
Published: October 2010

AbstractIntroduction  The genus Arvicanthis (Lesson 1842) (Rodentia: Murinae), usually referred to as the unstriped grass rat, is mainly distributed in savanna and grassland habitats of Sub‐Saharan Africa. Among the four chromosomal forms of Arvicanthis recently differentiated in Western and Central Africa, the one with a diploid chromosomal number (2n) of 62 and an autosomal fundamental number (NFa) of 62 or 64 is ascribed to Arvicanthis niloticus (Demarest 1822), while the one with 2n = 62 and a NFa between 74 and 76 is referred to A. ansorgei (Thomas 1910). Despite the broad area of sympatry recently uncovered along the inner delta of the Niger river in Mali [details in Volobouev et al. (2002) Cytogenetics and Genome Research, 96, 250–260], the distribution of the two species is largely parapatric and follows the latitudinal patterns of the West‐African biogeographical domains, which are related to the latitudinal patterns of annual rainfall in this region. Here, we analyse the suggestion that the two species show specific adaptations to differences in climate aridity.Methods  Karyologically screened animals were sampled in 19 localities in seasonally flooded regions located along the ‘Niger’ river in Mali and extending from 1100 to 200 mm of mean annual rainfall. The analysis of trapping success (TS) data allowed us to investigate the respective effects of climate (i.e. annual rainfall) and local (i.e. duration of the green herbaceous vegetation) aridity on the latitudinal and habitat distribution of the two species.Conclusions  The broad zone of sympatry was found to correspond to a northward expansion of the recognized distribution area of A. ansorgei. TS values indicated that the two species responded very differently to climatic and local conditions of aridity. Arvicanthis ansorgei decreased in TS as regional conditions became more arid; a similar trend was also observed within regions where habitat occupancy decreased with local aridity. The higher TS observed in the most humid habitat relative to the others persisted throughout the latitudinal rainfall gradient. In contrast, TS of A. niloticus increased with latitudinal aridity. This species was present in more arid habitats than A. ansorgei from 1000 mm down to 400 mm of mean annual rainfall where a shift to the most humid habitat occurred. These opposite trends in TS distribution between species suggest that A. ansorgei is less adapted than A. niloticus to arid environments at both a regional and habitat level; thus, A. ansorgei would be able to invade dry regions only along the extensive floodplains bordering the inner delta of the ‘Niger’ river. Several biological traits that may be involved in limiting the southward distribution of A. niloticus are discussed.
The distribution of South American galaxiid fishes: the role of biological traits and post‐glacial history
Authors: Cussac Víctor , Ortubay Silvia , Iglesias Gustavo , Milano Daniela , Lattuca María E. , Barriga Juan P. , Battini Miguel , Gross Miguel 
Published: October 2010

AbstractAim  The aim of this work is to update the distribution data of Galaxiidae in South America, relating extant distribution to physiological and reproductive characteristics of the species, latitude, temperature, and post‐glacial opportunities for colonization.Location  Lakes and rivers of Patagonia.Methods  We compared, and eventually reconsidered, general data about distribution based on the original literature about capture sites, incorporating several published and unpublished data to the analysis of the biological traits and distribution of Galaxiidae.Results  The more consistent issue in the comprehension of galaxiid biogeography in South America is the ability to establish landlocked populations. Different founding events in landlocked populations of Galaxias maculatus suggest the possible existence of older and younger landlocked populations. This difference in the time since the establishment of lacustrine populations could have been expressed in their ability for colonization of post‐glacial areas. Galaxias maculatus, Aplochiton and Brachygalaxias are more clearly excluded from the post‐glacial area than G. platei. For all the species we could note a more abundant record of lake populations at the area of glacial refuges. It could be noted that the most successful species, Galaxias platei, is a specialized deep bottom dweller. Deep bottom dwelling helps to endure winter constraints and it appears to be an alternative to the colonization of the littoral and limnetic zones of post‐glacial lakes, the prefered habitat of the other Patagonian fish species.Main conclusions  At the end of this process of post‐glacial colonization, in the beginning of twentieth century, man introduced several salmonid species in Patagonia. In addition, antropogenic actions had its more recent consequences in global warming. Nowadays we were able to observe new localities for Brazilian fishes into the Austral Subregion and expect some changes in the distribution of Galaxiidae. Northern limits for all species and southern limits for landlocked G. maculatus, Brachigalaxias bullocki and Aplochiton zebra, could be displaced southward. Probably, the species less affected by the changes will be G. platei. These predictions could be accurately formulated using the model of B.J. Shuter & J.R. Post (1990) Transactions of the American Fisheries Society119, 314–336, when biological database on these species are completed.
Low diversity but high differentiation: the population genetics of Aglaope infausta (Zygaenidae: Lepidoptera)
Authors: Schmitt Thomas , Seitz Alfred 
Published: October 2010

AbstractAim  Aglaope infausta is a thermophilous Zygaenid of Atlanto‐Mediterranean origin, distributed in Portugal, Spain, France and north‐western Italy reaching its north‐eastern distribution limit in western Germany. The local, regional and inter‐regional genetic structure of this species is studied in this analysis.Location and methods  The allozymes of 456 individuals from 12 populations (11 from western Germany and one from southern Portugal) were studied by electrophoresis.Results  Six of the 19 loci analysed were monomorphic. Genetic differentiation between populations was high (FST: 0.404), while the mean genetic diversity was low (He: 3.4%). Most (96.5%) of the genetic variance between populations was between the Portuguese and the German samples, but also the differentiation within Germany was considerable (FSR: 0.101).In Germany, A. infausta occurs in two major regions (middle Rhine and Nahe) that are geographically separated, and 55.5% of the genetic variance was found between these two regions. The populations of both areas do not differ in their genetic diversity, but those of the middle Rhine have significantly higher genetic distances among them than the Nahe populations (0.020 and 0.015, respectively). FST was also higher in the middle Rhine region than in the Nahe region (0.089 and 0.045, respectively).Main conclusions  Aglaope infausta shows a very low level of genetic heterogeneity for a lepidopteran species. However, this genetic poverty is not affecting the species’ viability. During the ice ages, differentiation into two genetic lineages occurred, most probably in a south‐western and a south‐eastern differentiation centre in Iberia. The gap in the distribution range in Germany is clearly reflected in the genetic structure. This differentiation must have developed relatively quickly because western Germany most probably was colonized during the climatic optimum 6000 years ago.
Fern species richness along a central Himalayan elevational gradient, Nepal
Authors: Bhattarai Khem R. , Vetaas Ole R. , Grytnes John A. 
Published: October 2010

AbstractAim  The study explores fern species richness patterns along a central Himalayan elevational gradient (100–4800 m a.s.l.) and evaluates factors influencing the spatial increase and decrease of fern richness.Location  The Himalayas stretch from west to east by 20°, i.e. 75–95° east, and Nepal is located from 80 to 88° east in this range.Methods  We used published data of the distribution of ferns and fern allies to interpolate species elevational ranges. Defining species presence between upper and lower elevation limit is the basis for richness estimates. The richness pattern was regressed against the total number of rainy days, and gradients that are linearly related to elevation, such as length of the growing season, potential evapotranspiration (PET, energy), and a moisture index (MI = PET/mean annual rainfall). The regressions were performed by generalized linear models.Results  A unimodal relationship between species richness and elevation was observed, with maximum species richness at 2000 m. Fern richness has a unimodal response along the energy gradients, and a linear response with moisture gradients.Main conclusions  The study confirms the importance of moisture on fern distributions as the peak coincides spatially with climatic factors that enhance moisture levels; the maximum number of rainy days and the cloud zone. Energy‐related variables probably control species richness directly at higher elevations but at the lower end the effect is more probably related to moisture.