Search results for "Trie"
showing 10 items of 4468 documents
A summary of genomic databases: overview and discussion
2009
In the last few years both the amount of electronically stored biological data and the number of biological data repositories grew up significantly (today, more than eight hundred can be counted thereof). In spite of the enormous amount of available resources, a user may be disoriented when he/she searches for specific data. Thus, the accurate analysis of biological data and repositories turn out to be useful to obtain a systematic view of biological database structures, tools and contents and, eventually, to facilitate the access and recovery of such data. In this chapter, we propose an analysis of genomic databases, which are databases of fundamental importance for the research in bioinfo…
BIOfid dataset: publishing a German gold standard for named entity recognition in historical biodiversity literature
2019
The Specialized Information Service Biodiversity Research (BIOfid) has been launched to mobilize valuable biological data from printed literature hidden in German libraries for over the past 250 years. In this project, we annotate German texts converted by OCR from historical scientific literature on the biodiversity of plants, birds, moths and butterflies. Our work enables the automatic extraction of biological information previously buried in the mass of papers and volumes. For this purpose, we generated training data for the tasks of Named Entity Recognition (NER) and Taxa Recognition (TR) in biological documents. We use this data to train a number of leading machine learning tools and c…
Mathematical Modelling of In-sewer Processes as a Tool for Sewer System Design
2018
The objective of this paper is to evaluate the potential impact of in-sewer processes (COD components transformation and hydrogen sulphide production) on the design of sewer systems. The tool used for such analysis is a mathematical model derived from the WATS model (Wastewater Aerobic/anaerobic Transformation in Sewers) able to describe the processes occurring in the sewer system both under aerobic and anaerobic conditions. The model is applied to three synthetic catchments with, respectively, 10,000, 50,000 and 250,000 inhabitants connected to gravity sewer systems different in terms of type (separate or combined), slope, length, travel time, wastewater temperature. The simulation results…
A Coclustering Approach for Mining Large Protein-Protein Interaction Networks
2012
Several approaches have been presented in the literature to cluster Protein-Protein Interaction (PPI) networks. They can be grouped in two main categories: those allowing a protein to participate in different clusters and those generating only nonoverlapping clusters. In both cases, a challenging task is to find a suitable compromise between the biological relevance of the results and a comprehensive coverage of the analyzed networks. Indeed, methods returning high accurate results are often able to cover only small parts of the input PPI network, especially when low-characterized networks are considered. We present a coclustering-based technique able to generate both overlapping and nonove…
Comparative study of phytoplankton in an oligotrophic soft water lake under different pH-phosphate ranges
1998
This work reports phytoplankton changes in a shallow, acidic and oligotrophic lake (Loch Rusky, Scotland) from two different periods: one with artificial phosphate fertilization and neutral pH (SRP 3–18 µg l-1, pH 6.6–7.8, 1972–73) and the other with low phosphate and acidic pH values (SRP <1.5 µg l-1, pH 5.6–6.9, 1985–86). Phosphate enhanced markedly total algal biomass and favoured the presence of cyanophytes, especially in the summer epilimnion, while cryptophytes dominated at this time during unfertilized periods. Anabaena sp. peaked during summer and a higher density of Ceratium hirundinella and Peridinium sp. in mid-summer was also observed during the fertilized period. Otherwise, alg…
Influence of carbon and nutrient additions on a decomposer food chain and the growth of pine seedlings in microcosms
2001
Abstract Because of N deposition plant production is becoming increasingly limited by other nutrients in boreal forests. At the same time more C is suggested to become available for below-ground food webs because of enhanced CO2 fixation. We studied the effects of carbon and nutrient addition on a fungus–nematode food chain and on the growth of mycorrhizal or nonmycorrhizal pine seedlings (Pinus sylvestris L.) in microcosms with N-rich mineral soil and a humus layer. The role of the food chain and mycorrhizal fungi for pine growth was tested in a smaller set-up. The total pine biomass was not N-limited at the scale of two experimental growing seasons. In accordance with established knowledg…
Scientific HIV research in Africa and the Middle East: a socio-economic demographic analysis
2021
Background: In Africa, HIV/AIDS research is concentrated in certain countries, particularly South Africa. This distribution may not accurately reflect the disease prevalence or the true research efforts of countries.Objectives: To identify HIV/AIDS research productivity of countries in Africa and the Middle East, in absolute terms and adjusted for people living with HIV, population size and economic development.Methods: We identified all the articles and reviews on HIV and AIDS in the Web of Science Core Collection in which African or Middle Eastern countries had participated. After determining the number of documents produced by each country, we adjusted the findings for the number of peop…
Biomolecules and nanostructured systems : characterization by Surface Enhanced Raman Scattering (SERS)
2014
This work addressed the study of several kinds of nanostructured systems, biomolecules and inorganic thin films, mainly by Surface Enhanced Raman Spectroscopy (SERS). The aim was to investigate the structure and the chemical bonds. Transmission electron microscopy (TEM) was also used to complete the structural characterization of the different samples.Firstly, the study was conducted on molecules of biological interest. The aim was to study the interaction between silver nanoparticles and proteins. With this aim, silver nanoparticles bioconjugated with different proteins (hemoglobin, cytochrome C, BSA and lysozim) were synthesized. SERS results allowed concluding that proteins are chemisorb…
Quantification of hydrolysis of toxic organophosphates and organophosphonates by diisopropyl fluorophosphatase from Loligo vulgaris by in situ Fourie…
2008
Abstract The enzyme diisopropyl fluorophosphatase (DFPase) from the squid Loligo vulgaris effectively catalyzes the hydrolysis of diisopropyl fluorophosphate (DFP) and a number of organophosphorus nerve agents, including sarin, soman, cyclosarin, and tabun. Up to now, the determination of kinetic data has been achieved by techniques such as pH-stat titration, ion-selective electrodes, and fluorogenic substrate analogs. We report a new assaying method using in situ Fourier transform infrared (FTIR) spectroscopy with attenuated total reflection (ATR) for the real-time determination of reaction rates. The method employs changes in the P–O–R stretching vibration of DFP and nerve agent substrate…
Effect of temperature and organic nutrients on the biodegradation of linear alkylbenzene sulfonate (LAS) during the composting of anaerobically diges…
2004
Limits on the application of biosolids (anaerobically processed sludges from wastewater treatment plants) as fertilizers for the amendment of soil are becoming greater because of the accumulation of recalcitrant substances, making necessary the use of techniques that bring the concentration of xenobiotics to lower concentrations than those permitted. In general, the biosolids composting process is sufficient to reduce the usual concentration of linear alkylbenzene sulfonates (LAS) to low levels. In this work, an assessment is made on the effect of temperature in the capacity of enriched bacterial populations to biodegrade LAS, together with the influence that the available nutrients may hav…