"Još jedan osvrt na pitanje izbora šarana za daljnji uzgoj"

We extend the live-cell motility Filament Based Lamellipodium Model (FBLM) to incorporate the forces exerted on the lamellipodium of the cells due to cell-cell collision and cadherin induced cell-cell adhesion. We take into account the nature of these forces via physical and biological constraints and modelling assumptions. We investigate the effect these new components have in the migration and morphology of the cells through particular experiments. We exhibit moreover the similarities between our simulated cells and HeLa cancer cells

K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources

The integration of heterogeneous data sources and software systems is a major issue in the biomed ical community and several approaches have been explored: linking databases, on-the- fly integration through views, and integration through warehousing. In this paper we report on our experiences with two systems that were developed at the University of Pennsylvania: an integration system called K2, which has primarily been used to provide views over multiple external data sources and software systems; and a data warehouse called GUS which downloads, cleans, integrates and annotates data from multiple external data sources. Although the view and warehouse approaches each have their advantages, there is no clear winner . Therefore, users must consider how the data is to be used, what the performance guarantees must be, and how much programmer time and expertise is available to choose the best strategy for a particular application

Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database

Databases of experimentally generated and computationally derived transcript sequences are valuable resources for genome analysis and annotation. The utility of such databases is enhanced when the sequences they contain are integrated with such biological information as genomic location, gene function, gene expression and phenotypic variation. We present the analysis and results of a semi-automated process of connecting transcript assemblies with highly curated biological information for mouse genes that is available through the Mouse Genome Informatics (MGI) database

Response of Common and Rare Beetle Species to Tree Species and Vertical Stratification in a Floodplain Forest

Vertical stratification and host tree species are factors with a high influence on the structure of communities of xylobiont beetles. However, little is known about how this influence varies between common and rare species. Based on estimated species richness, we compared alpha and beta diversity patterns of common and rare species in the canopy of the Leipzig floodplain forest to assess their response to vertical stratification and tree species. We used two measures of rarity: threat level in red lists and abundance based on octaves. The understory displayed a significantly higher number of common species than the canopy strata. Conversely, the canopy strata harbored a higher number of rare species. Turnover was always dominant over richness differences in beta diversity partitions. Using Raup–Crick null models and non-metric multidimensional scaling, we found that the vertical strata accounted for 19% of the overall beta diversity of common species and for 15% of the overall beta diversity of rare species. The tree species accounted for 7% of the overall beta diversity of the common species and 3% of the beta diversity of the rare species. Our results indicate that studies carried out in the understory alone do not allow drawing conclusions regarding the biodiversity in the canopy strata, and thus regarding the overall community structure of xylobiont beetles in the canopy.This study is kindly supported by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the German Research Foundation (FZT 118). The Article processing charges were funded by the Open Science Office of the Leipzig University Library.info:eu-repo/semantics/publishedVersio

Mobile continuous-flow isotope-ratio mass spectrometer system for automated measurements of N₂ and N₂O fluxes in fertilized cropping systems

The use of synthetic N fertilizers has grown exponentially over the last century, with severe environmental consequences. Most of the reactive N will ultimately be removed by denitrification, but estimates of denitrification are highly uncertain due to methodical constraints of existing methods. Here we present a novel, mobile isotope ratio mass spectrometer system (Field-IRMS) for in-situ quantification of N2 and N2O fluxes from fertilized cropping systems. The system was tested in a sugarcane field continuously monitoring N2 and N2O fluxes for 7 days following fertilization using a fully automated measuring cycle. The detection limit of the Field-IRMS proved to be highly sensitive for N2 (54 g ha−1 day−1) and N2O (0.25 g ha−1 day−1) emissions. The main product of denitrification was N2 with total denitrification losses of up to 1.3 kg N ha−1 day−1. These losses demonstrate sugarcane systems in Australia are a hotspot for denitrification where high emissions of N2O and N2 can be expected. The new Field-IRMS allows for the direct and highly sensitive detection of N2 and N2O fluxes in real time at a high temporal resolution, which will help to improve our quantitative understanding of denitrification in fertilized cropping systems.</p

Process theory and research: Exploring the dialectic tension

We contest that although the notion of process is increasingly being applied to the study of organizations, these attempts are hampered by significant methodological shortcomings. We claim that the value of process theory is under-utilized because most attempts to apply process theory end up reverting to conventional non-process methods. We suggest that the cause of this reversion is primarily the challenge of making sense, of fixing the world, propelling us from process into the world of substance. To break free of these limitations we propose an approach that takes the researchers? audience alongside the subject processes rather than attempting to clinically intersect them. We illuminate this paper with our own story vignettes concerning the fortunes of an idea that passes by the name of value based management (VBM). 1 These vignettes are meant to both exemplify and disrupt the theoretical narrative

GeneDB--an annotation database for pathogens.

GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource. The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources. GeneDB is primarily a production and annotation database for the genomes of predominantly pathogenic organisms

EuPathDB: the eukaryotic pathogen genomics database resource

The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists &amp; fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions