The Commercialisation of Public Data - How Does Participatory Data-mining Look on a Global Scale?

The commercialisation of local spatial knowledge is an emerging problem across communities all around the world. Users creating spatial and  attributive data through the use of commercial tools such as Google Map Maker, are extending corporate databases, but aren’t able to use the very same data freely when they need to. Open-source and participatory  mapping projects such as OpenStreetMap are designed to support  community empowerment and to ensure that high quality data are  available to everyone regardless of their origin, social status and position within the power structure. The article points out the danger of  commercialisation of public data using the example of community  development projects. It also shows the advantages of participatory data-mining, using as an example the OpenStreetMap project in the Kibera slum, Nairobi Kenya and shows the possibilities of such an initiative in  Koffiekraal, NW province of South Africa.Keywords:Participatory GIS, PGIS, OpenStreetMap, Google Map Maker, local spatial knowledge (LSK), Koffiekraal, Kiber

Implications of spatial distribution of rockfall reconstructed by dendrogeomorphological methods

Rockfall is a dangerous geomorphological process. The prediction of potentially threatened areas requires thorough reconstruction of spatial rockfall activity. Dendrogeomorphic methods allow precise determination of both temporal and spatial occurrences of rockfall without the necessity of long-term monitoring. At the case-study site of Taraktash, located among southern slopes of the Crimean Mountains, 114 Crimean pine trees (Pinus nigra ssp. pallasiana) were sampled on a talus slope located under a 150 m high rockwall. Based on their age, the trees were divided into two distinct groups (young and old trees). Considerable disturbance in the age structure of the trees on the talus was probably caused by a series of strong earthquakes. Major differences were identified in the ability of young and old trees to record a rockfall event. We found that in the first decades of their growth, the ability of the studied P. nigra to record rockfall events gradually increased. The trees showed the highest sensitivity at the age of 80 to 90 yr; after that age their sensitivity gradually decreases. Two indicators were selected for the spatial reconstruction of rockfall events (the number of rockfall events per tree and recurrence interval). The highest activity was identified on the talus using selected indicators

Synthetic RNA Silencing of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2)

We demonstrate the first application of synthetic RNA gene silencers in Streptomyces coelicolor A3(2). Peptide nucleic acid and expressed antisense RNA silencers successfully inhibited actinorhodin production. Synthetic RNA silencing was target-specific and is a new tool for gene regulation and metabolic engineering studies in Streptomyces.Peer reviewe

Phylogenomics and Morphological Reconstruction of Arcellinida Testate Amoebae Highlight Diversity of Microbial Eukaryotes in the Neoproterozoic

Life was microbial for the majority of Earth's history, but as very few microbial lineages leave a fossil record, the Precambrian evolution of life remains shrouded in mystery. Shelled (testate) amoebae stand out as an exception with rich documented diversity in the Neoproterozoic as vase-shaped microfossils (VSMs). While there is general consensus that most of these can be attributed to the Arcellinida lineage in Amoebozoa, it is still unclear whether they can be used as key fossils for interpretation of early eukaryotic evolution. Here, we present a well-resolved phylogenomic reconstruction based on 250 genes, obtained using single-cell transcriptomic techniques from a representative selection of 19 Arcellinid testate amoeba taxa. The robust phylogenetic framework enables deeper interpretations of evolution in this lineage and demanded an updated classification of the group. Additionally, we performed reconstruction of ancestral morphologies, yielding hypothetical ancestors remarkably similar to existing Neoproterozoic VSMs. We demonstrate that major lineages of testate amoebae were already diversified before the Sturtian glaciation (720 mya), supporting the hypothesis that massive eukaryotic diversification took place in the early Neoproterozoic and congruent with the interpretation that VSM are arcellinid testate amoebae

Assessing the positional accuracy of perceptual landscape data: A study from Friuli Venezia Giulia, Italy

Online GIS-based applications that combine mapping and public participation to collect citizens' voices on their surrounding environment are a way to collect original spatial data that do not already figure in authoritative data sets. However, these applications, relying on non-expert users, might produce spatial data of insufficient quality for the purpose for which they are collected. This article presents an approach for assessing the positional accuracy of vague landscape features, using the results from a map-based survey completed by a group of volunteers in the Friuli Venezia Giulia region of Italy. The spatial section of the survey, gathering both georeferenced data and textual information on the mapping activity, allows the assessment of whether there is a correspondence between the mapped features and the intended map locations. The findings reveal a greater accuracy among participants in completing the mapping activity relating to degraded sites than to those of beauty

Machine learning on normalized protein sequences

<p>Abstract</p> <p>Background</p> <p>Machine learning techniques have been widely applied to biological sequences, e.g. to predict drug resistance in HIV-1 from sequences of drug target proteins and protein functional classes. As deletions and insertions are frequent in biological sequences, a major limitation of current methods is the inability to handle varying sequence lengths.</p> <p>Findings</p> <p>We propose to normalize sequences to uniform length. To this end, we tested one linear and four different non-linear interpolation methods for the normalization of sequence lengths of 19 classification datasets. Classification tasks included prediction of HIV-1 drug resistance from drug target sequences and sequence-based prediction of protein function. We applied random forests to the classification of sequences into "positive" and "negative" samples. Statistical tests showed that the linear interpolation outperforms the non-linear interpolation methods in most of the analyzed datasets, while in a few cases non-linear methods had a small but significant advantage. Compared to other published methods, our prediction scheme leads to an improvement in prediction accuracy by up to 14%.</p> <p>Conclusions</p> <p>We found that machine learning on sequences normalized by simple linear interpolation gave better or at least competitive results compared to state-of-the-art procedures, and thus, is a promising alternative to existing methods, especially for protein sequences of variable length.</p

nocoRNAc: Characterization of non-coding RNAs in prokaryotes

<p>Abstract</p> <p>Background</p> <p>The interest in non-coding RNAs (ncRNAs) constantly rose during the past few years because of the wide spectrum of biological processes in which they are involved. This led to the discovery of numerous ncRNA genes across many species. However, for most organisms the non-coding transcriptome still remains unexplored to a great extent. Various experimental techniques for the identification of ncRNA transcripts are available, but as these methods are costly and time-consuming, there is a need for computational methods that allow the detection of functional RNAs in complete genomes in order to suggest elements for further experiments. Several programs for the genome-wide prediction of functional RNAs have been developed but most of them predict a genomic locus with no indication whether the element is transcribed or not.</p> <p>Results</p> <p>We present <smcaps>NOCO</smcaps>RNAc, a program for the genome-wide prediction of ncRNA transcripts in bacteria. <smcaps>NOCO</smcaps>RNAc incorporates various procedures for the detection of transcriptional features which are then integrated with functional ncRNA loci to determine the transcript coordinates. We applied RNAz and <smcaps>NOCO</smcaps>RNAc to the genome of <it>Streptomyces coelicolor </it>and detected more than 800 putative ncRNA transcripts most of them located antisense to protein-coding regions. Using a custom design microarray we profiled the expression of about 400 of these elements and found more than 300 to be transcribed, 38 of them are predicted novel ncRNA genes in intergenic regions. The expression patterns of many ncRNAs are similarly complex as those of the protein-coding genes, in particular many antisense ncRNAs show a high expression correlation with their protein-coding partner.</p> <p>Conclusions</p> <p>We have developed <smcaps>NOCO</smcaps>RNAc, a framework that facilitates the automated characterization of functional ncRNAs. <smcaps>NOCO</smcaps>RNAc increases the confidence of predicted ncRNA loci, especially if they contain transcribed ncRNAs. <smcaps>NOCO</smcaps>RNAc is not restricted to intergenic regions, but it is applicable to the prediction of ncRNA transcripts in whole microbial genomes. The software as well as a user guide and example data is available at <url>http://www.zbit.uni-tuebingen.de/pas/nocornac.htm</url>.</p

Small non-coding RNAs in Streptomyces coelicolor

In bacteria, small RNAs (sRNAs) make important regulatory contributions to an ever increasing number of cellular processes. To expand the repertoire of known sRNAs, we sought to identify novel sRNAs in the differentiating, multicellular bacterium Streptomyces coelicolor. We describe a combined bioinformatic and experimental approach that enabled the identification and characterization of nine novel sRNAs in S. coelicolor, including a cis-encoded antisense sRNA. We examined sRNA expression throughout the S. coelicolor developmental cycle, which progresses from vegetative mycelium formation, to aerial mycelium formation and finally sporulation. We further determined the effects of growth medium composition (rich versus minimal medium) on sRNA gene expression, and compared wild-type sRNA expression profiles with those of four developmental mutants. All but two of the sRNAs exhibited some degree of medium dependence, with three sRNAs being expressed exclusively during growth on one medium type. Unlike most sRNAs characterized thus far, several sRNA genes in S. coelicolor were expressed constitutively (apart from during late sporulation), suggesting a possible housekeeping role for these transcripts. Others were expressed at specific developmental stages, and their expression profiles were altered in response to developmental mutations. Expression of one sRNA in particular was dependent upon the sporulation-specific sigma factor σWhiG

Integrating anaerobic digestion and pyrolysis for treating digestates derived from sewage sludge and fat wastes

P. 32603-32614The coupling of biological and thermal technologies allows for the complete conversion of wastes into energy and biochar eliminating the problem of sludge disposal. The valorisation of fatty residues as co-substrate in a mesophilic digester of a wastewater treatment plant was studied considering an integrated approach of co-digestion and pyrolysis. Four digested samples obtained from co-digestion of sewage sludge and butcher’s fat waste were studied by thermogravimetric analysis. The activation energy corresponding to the sludge pyrolysis was calculated by a non-isothermal kinetic. Arrhenius activation energy was lower for the pyrolysis of a digested grease sample (92 kJ mol−1 obtained by OFW and 86 kJ mol−1 obtained by Vyazovkin) than for the pyrolysis of sewage sludge and its blends (164–190 kJ mol−1 obtained by OFW and 162–190 kJ mol−1 obtained by Vyazovkin). The analysis of the integrated approach of anaerobic co-digestion and pyrolysis of digestates demonstrated that the addition of 3% (w/v) of fat to the feeding sludge results in a 25% increase in the electricity obtained from biogas (if a combined heat and power unit is considered for biogas valorisation) and increasing the fat content to 15% allows for covering all thermal needs for drying of digestate and more than doubles (2.4 times) the electricity production when the scenario of digestion and pyrolysis is contemplated.S