Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring- and autumn-spawners confined to early postglacial arrival

Presence of sympatric populations may reflect local diversification or secondary contact of already distinct forms. The Baltic cisco (Coregonus albula) normally spawns in late autumn, but in a few lakes in Northern Europe sympatric autumn and spring- or winter-spawners have been described. So far, the evolutionary relationships and taxonomic status of these main life history forms have remained largely unclear. With microsatellites and mtDNA sequences, we analyzed extant and extinct spring- and autumn-spawners from a total of 23 Swedish localities, including sympatric populations. Published sequences from Baltic ciscoes in Germany and Finland, and Coregonus sardinella from North America were also included together with novel mtDNA sequences from Siberian C.sardinella. A clear genetic structure within Sweden was found that included two population assemblages markedly differentiated at microsatellites and apparently fixed for mtDNA haplotypes from two distinct clades. All sympatric Swedish populations belonged to the same assemblage, suggesting parallel evolution of spring-spawning rather than secondary contact. The pattern observed further suggests that postglacial immigration to Northern Europe occurred from at least two different refugia. Previous results showing that mtDNA in Baltic cisco is paraphyletic with respect to North American C.sardinella were confirmed. However, the inclusion of Siberian C.sardinella revealed a more complicated pattern, as these novel haplotypes were found within one of the two main C.albula clades and were clearly distinct from those in North American C.sardinella. The evolutionary history of Northern Hemisphere ciscoes thus seems to be more complex than previously recognized

Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis

<p>Abstract</p> <p>Background</p> <p>One of the challenges of bioinformatics remains the recognition of short signal sequences in genomic DNA such as donor or acceptor splice sites, splicing enhancers or silencers, translation initiation sites, transcription start sites, transcription factor binding sites, nucleosome binding sites, miRNA binding sites, or insulator binding sites. During the last decade, a wealth of algorithms for the recognition of such DNA sequences has been developed and compared with the goal of improving their performance and to deepen our understanding of the underlying cellular processes. Most of these algorithms are based on statistical models belonging to the family of Markov random fields such as position weight matrix models, weight array matrix models, Markov models of higher order, or moral Bayesian networks. While in many comparative studies different learning principles or different statistical models have been compared, the influence of choosing different prior distributions for the model parameters when using different learning principles has been overlooked, and possibly lead to questionable conclusions.</p> <p>Results</p> <p>With the goal of allowing direct comparisons of different learning principles for models from the family of Markov random fields based on the <it>same a-priori information</it>, we derive a generalization of the commonly-used product-Dirichlet prior. We find that the derived prior behaves like a Gaussian prior close to the maximum and like a Laplace prior in the far tails. In two case studies, we illustrate the utility of the derived prior for a direct comparison of different learning principles with different models for the recognition of binding sites of the transcription factor Sp1 and human donor splice sites.</p> <p>Conclusions</p> <p>We find that comparisons of different learning principles using the same a-priori information can lead to conclusions different from those of previous studies in which the effect resulting from different priors has been neglected. We implement the derived prior is implemented in the open-source library Jstacs to enable an easy application to comparative studies of different learning principles in the field of sequence analysis.</p

Unifying generative and discriminative learning principles

<p>Abstract</p> <p>Background</p> <p>The recognition of functional binding sites in genomic DNA remains one of the fundamental challenges of genome research. During the last decades, a plethora of different and well-adapted models has been developed, but only little attention has been payed to the development of different and similarly well-adapted learning principles. Only recently it was noticed that discriminative learning principles can be superior over generative ones in diverse bioinformatics applications, too.</p> <p>Results</p> <p>Here, we propose a generalization of generative and discriminative learning principles containing the maximum likelihood, maximum a posteriori, maximum conditional likelihood, maximum supervised posterior, generative-discriminative trade-off, and penalized generative-discriminative trade-off learning principles as special cases, and we illustrate its efficacy for the recognition of vertebrate transcription factor binding sites.</p> <p>Conclusions</p> <p>We find that the proposed learning principle helps to improve the recognition of transcription factor binding sites, enabling better computational approaches for extracting as much information as possible from valuable wet-lab data. We make all implementations available in the open-source library Jstacs so that this learning principle can be easily applied to other classification problems in the field of genome and epigenome analysis.</p

Modelling of the vertical migration process of phosphogypsum components in the soil profile

This paper focuses on the study of the process of vertical migration of phosphogypsum components according to the soil profile. The qualitative and quantitative identification of main biogenic elements (phosphorus, sulphur, calcium etc) and heavy metals in lysimetric solutions from various horizons while getting on the surface of soil solutions containing phosphogypsum components is carried out by means of designed laboratory and experimental complex. The mineral hard soil fraction is also analysed. According to the results of the X-ray diffractometrical researches, the carbonates with heavy metals in their structure, caused by the ion-exchange with Са2+, were found in the mineral structure of the illuvial horizon soil samples. The results of experimental modeling indicate significant changes in the chemical parameters of groundwater, which are obtained by passing water with phosphogypsum particles on a model soil profile, which makes it easy to track the input data. In the upper part of the profile after 1 000 hours and for the first speed of the infiltration process, the constant moisture level was 25,6%, after the second speed of infiltration, it rose to 29.1 %. Noted that the highest concentration of biogenic elements (calcium, sulfur, potassium) was found in lysimetric solutions obtained from the humus and eluvial horizons. In addition, it is determined that iron is present up to 5 %, nickel – within the range of 1–3 %, and copper – up to 1 %. It should be noted that the biochemical transformations of silicon influence the fractional distribution of heavy metals, which can be fixed by sorption-sedimentation mechanisms in silica, oligo and polysilicon compounds, as well as in crystalline lattice structures of clay minerals, quartz, etc. The model of soil and geochemical situation was formed according to the soil profile under the influence of the phosphogypsum within the three-dimensional surface, developed with the help of the stochastic reconstructions based on the images of the scan electron microscopes

A Picture is Worth a Thousand Tags: Automatic Web Based Image Tag Expansion

Abstract. We present an approach to automatically expand the annotation of images using the internet as an additional information source. The novelty of the work is in the expansion of image tags by automatically introducing new unseen complex linguistic labels which are collected unsupervised from associated webpages. Taking a small subset of existing image tags, a web based search retrieves additional textual information. Both a textual bag of words model and a visual bag of words model are combined and symbolised for data mining. Association rule mining is then used to identify rules which relate words to visual contents. Unseen images that fit these rules are re-tagged. This approach allows a large number of additional annotations to be added to unseen images, on average 12.8 new tags per image, with an 87.2 % true positive rate. Results are shown on two datasets including a new 2800 image annotation dataset of landmarks, the results include pictures of buildings being tagged with the architect, the year of construction and even events that have taken place there. This widens the tag annotation impact and their use in retrieval. This dataset is made available along with tags and the 1970 webpages and additional images which form the information corpus. In addition, results for a common state-of-the-art dataset MIRFlickr25000 are presented for comparison of the learning framework against previous works.

Electrophoretic identification of allozyme variation in natural population of ticks Ixodes persulcatus Schulze (Acari: Ixodidae) in Irkutsk suburbs

Allozyme structure of the tick population Ixodes persulcatus coded by nine enzyme gene loci has been studied using two subsamples of ticks from Irkutsk suburban areas. Nine loci out of fourteen were polymorphic in ticks of Baikal highway population, whereas five loci were polymorphic in tics sampled from Goloustnoye highway. High level of intra-population heterogeneity of ticks has been revealed. No distinction between two populations from different nidi of infection has been recorded. It was probably due to the high rate of gene migration between the studied populations and to their high genetic similarity

Research of Plate Granulator Operation Modes in the Production of Coarse Carbamide Granules

The object of research is granulation of mineral fertilizers by the rolling method. One of the most problematic places is the uncertainty of the conditions of the temperature regime of granulation. The paper considers the technology for obtaining enlarged urea granules of prolonged action. It is indicated that an increase in the diameter of the granules to 7–10 mm increases the efficiency of the use of mineral fertilizers by the consumer. It is proposed to obtain large carbamide granules by rolling in a plate granulator. It is indicated that the setting of the optimal operating parameters of the tray granulator is an important factor in the efficient operation of the equipment. A scheme of a pilot plant for granulating mineral fertilizers is presented, a methodology for conducting experimental studies and design parameters of a plate granulator are described. It is indicated that in the process of experimental studies, the design parameters changed: the tilt angle of the plate, the height of the side and the frequency of rotation of the plate, the angle of opening of the spray jet by the hydraulic nozzle. In the process of research, the influence of regime and technological parameters, namely, the temperature of the layer on the plate is studied. As a result of experimental studies, the optimal ranges of design and regime-technological parameters for obtaining enlarged carbamide granules in a plate granulator were revealed. The influence of the location of the nozzle for spraying the melt on the layer relative to the plane of the plate is shown, which results in the particle size distribution of the granular product. It is indicated that a higher content of the commercial fraction in the finished product is observed when the layer in the left sector of the upper part of the plate is irrigated by the rising melt. A technique for determining the static strength of the obtained carbamide granules is given. A calculation equation for determining the static strength of a granule is presented. A diagram of a laboratory device for determining the static strength of granules is presented, which made it possible to determine the values of the static strength of granules for individual fractions, namely: for coarse, fine and commercial fractions. It is shown that the obtained values correlate well with standardized indicators

Research of Plate Granulator Operation Modes in the Production of Coarse Carbamide Granules

The object of research is granulation of mineral fertilizers by the rolling method. One of the most problematic places is the uncertainty of the conditions of the temperature regime of granulation. The paper considers the technology for obtaining enlarged urea granules of prolonged action. It is indicated that an increase in the diameter of the granules to 7–10 mm increases the efficiency of the use of mineral fertilizers by the consumer. It is proposed to obtain large carbamide granules by rolling in a plate granulator. It is indicated that the setting of the optimal operating parameters of the tray granulator is an important factor in the efficient operation of the equipment. A scheme of a pilot plant for granulating mineral fertilizers is presented, a methodology for conducting experimental studies and design parameters of a plate granulator are described. It is indicated that in the process of experimental studies, the design parameters changed: the tilt angle of the plate, the height of the side and the frequency of rotation of the plate, the angle of opening of the spray jet by the hydraulic nozzle. In the process of research, the influence of regime and technological parameters, namely, the temperature of the layer on the plate is studied. As a result of experimental studies, the optimal ranges of design and regime-technological parameters for obtaining enlarged carbamide granules in a plate granulator were revealed. The influence of the location of the nozzle for spraying the melt on the layer relative to the plane of the plate is shown, which results in the particle size distribution of the granular product. It is indicated that a higher content of the commercial fraction in the finished product is observed when the layer in the left sector of the upper part of the plate is irrigated by the rising melt. A technique for determining the static strength of the obtained carbamide granules is given. A calculation equation for determining the static strength of a granule is presented. A diagram of a laboratory device for determining the static strength of granules is presented, which made it possible to determine the values of the static strength of granules for individual fractions, namely: for coarse, fine and commercial fractions. It is shown that the obtained values correlate well with standardized indicators

Debt detection in social security by sequence classification using both positive and negative patterns

Debt detection is important for improving payment accuracy in social security. Since debt detection from customer transactional data can be generally modelled as a fraud detection problem, a straightforward solution is to extract features from transaction sequences and build a sequence classifier for debts. The existing sequence classification methods based on sequential patterns consider only positive patterns. However, according to our experience in a large social security application, negative patterns are very useful in accurate debt detection. In this paper, we present a successful case study of debt detection in a large social security application. The central technique is building sequence classification using both positive and negative sequential patterns. © 2009 Springer Berlin Heidelberg