The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007

In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial genomes available in Genbank in April 2007, belong to these lines with high accuracy. The main challenge now is to explain the observed high accuracy. The new phenomenon of complementary symmetry for codon position--specific nucleotide frequencies is observed. The results of analysis of several codon usage models are presented. We demonstrate that the mean--field approximation, which is also known as context--free, or complete independence model, or Segre variety, can serve as a reasonable approximation to the real codon usage. The first two principal components of codon usage correlate strongly with genomic G+C content and the optimal growth temperature respectively. The variation of codon usage along the third component is related to the curvature of the mean-field approximation. First three eigenvalues in codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and archaeal genomes codon usage is clearly distributed along two third order curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct bacterial genomes available in Genbank in April 200

Late Pleistocene insects from the Dubrovino site at Ob River (West Siberia, Russia) and their paleoenvironmental significance

A blue-grey clay loam lens with plant and insect remains was found in an expo-sure of the Ob River, 2 km upper Dubrovino village in Novosibirskaya Oblast of Russia.Conventional radiocarbon dating of the Dubrovino deposit is ca 19,444±159 14C BP(23,234±338 cal yr BP) and coincides with Sartan glaciation period (MIS 2). Ninety-twoColeoptera species, dominated by fragments of Curculionidae and Carabidae are rep-resented in the Dubrovino deposit. Species of the tundra-steppe fauna are dominant,followed by meadow-dwelling taxa and coniferous forest taxa. A comparison of theDubrovino assemblage with the previously studied late Pleistocene Kalistratikha andBunkovo fossil assemblages showed that tundra-steppe landscapes with coniferousgroves and sparse meadow vegetation were typical for this area from the end of Kargininterglacial (MIS 3) through the end of the Sartan glaciation (MIS 2)

Vector Theory of Gravity

We proposed a gravitation theory based on an analogy with electrodynamics on the basis of a vector field. For the first time, to calculate the basic gravitational effects in the framework of a vector theory of gravity, we use a Lagrangian written with gravitational radiation neglected and generalized to the case of ultra-relativistic speeds. This allows us to accurately calculate the values of all three major gravity experiments: the values of the perihelion shift of Mercury, the light deflection angle in the gravity field of the Sun and the value of radar echo delay. The calculated values coincide with the observed ones. It is shown that, in this theory, there exists a model of an expanding Universe.Comment: 9 page

Комплексы жесткокрылых из четвертичных отложений р. Кизиха - самые южные позднеплейстоценовые насекомые Западно-Сибирской равнины

Two sites with insect remains were found in an exposure on the bank of Kizikha river, in the Rubtsovskii District of the Altaiskii Krai of Russia, Kizikha-1 with radiocarbon age 13455±150 14C BP (SPb-1347), and Kizikha-2 with the age 26094±400 14C BP (SPb-1418). This period is coincides with Sartan stadial and Kargin interstadial (MIS 2 and MIS 3). This is the southernmost late Pleistocene insect bearing deposit found in West Siberia. The fragments in both sites are represented mainly by Coleoptera. Beetle fauna from the site Kizikha-1 is represented by 34 species from 9 families. The majority of fragments belong to weevils and ground beetles. 28 species from 8 families are found in Kizikha-2 site, the majority of fragments belong to Carabidae. 7 species found in the sites, Dyschiriodes rufimanus, Cymindis cf. rostowtzowi (Carabidae), Cidnopus cf. parallelus, Pristilophus punctatissimus (Elateridae), Hemitrichapion alexsandri (Brentidae), Paophilus albilaterus and Otiorhynchus sushkini (Curculionidae), are recorded in Pleistocene deposits for the first time. Sub-fossil insect assemblages of the two sites coincides with the late Pleistocene “Otiorhynchus-type” sub-fossil insect fauna from southeastern part of West-Siberian Plain (Zinovyev, 2011; Legalov et al., 2016) with characteristics as follows: dominance of steppe species, presence of halophile species, lack of forest species. Most of these species are absent in the contemporary regional fauna. The complex of eastern species and presence of endemics of Altai-Sayan Mountain system is also characteristic to the both studied sites. Specifics of the deposit assemblages in comparison with the other late Pleistocene fauna of West Siberian Plain is in high share of meadow species that could be explained by taphonomic condition of sedimentation or microclimatic conditions caused by close location to Altai mountains. Analysis of sub-fossil insect fragments showed that open landscapes with zonal steppe and sparse meadow vegetation near rivers and in depressions were typical for this area. In comparison to contemporary conditions climate was dry and cold, but Kizikha-2 (end of MIS 3) was formed in more mild climate conditions than Kizikha-1 (end of MIS 2). Results gained from Kizikha-1 and Kizikha-2 sites are complementing data on latitudinal-zonal distribution of beetles found in late Pleistocene deposits in West Siberian Plain

Palaeoenvironment of the Middle and Upper Neopleistocene at the Gornovo Upper Palaeolithic site (Southern Ural foreland, Russia)

© 2015 Elsevier Ltd and INQUAComplex biostratigraphical methods and radiocarbon dates were used to reconstruct the Middle (late Middle Pleistocene) and Late Neopleistocene (Late Pleistocene) palaeoenvironments covering the Palaeolithic period in the western foreland of the Urals. The Gornovo Palaeolithic settlement is located on the lowest terrace of the Belaya River. From the base to the top, this terrace consists of fluvial and lacustrine deposits of the Belaya horizon (Middle Neopleistocene; 427–364 ka), alluvial and lacustrine deposits of the Larevka horizon (Middle Neopleistocene; 364–334 ka), fluvial and lacustrine deposits of the Tabulda horizon (Late Neopleistocene; 57–24 ka), water-slope deposits of the Kudashevo horizon (Late Neopleistocene; 24–11 ka) and chernozem soil of the Holocene. The small and large mammals, insects, molluscs, and ostracods discovered in the deposits complete the palaeoecological characteristics of these periods. A diverse herbaceous steppe vegetation dominated during the Belaya Interglacial (a mixed coniferous forests with broad-leaved trees occurred in wet areas). The ostracoda species clearly indicate a cooling at the end of this time span. Molluscs inhabited the rivers and shores of freshwater ponds. The large mammals belong to the Middle Pleistocene fauna complex. During Larevka time span vegetation and fauna indicate cold climate conditions. The cold steppe communities typical of the beginning of this period changed gradually into communities that show an increasing role of the taiga. The ostracoda species confirm these cold conditions. Forest-steppe landscapes dominated during the second part of the Tabulda time span. Numerous ostracods as well as molluscs populated the lakes and floodplain basins. Entomological data show that the palaeoenvironment conditions were somewhat cooler than modern environment existing in the Southern Ural foreland. The large mammals of the Gornovo site belong to the Late Palaeolithic complex with the specific presence of Camelus sp. The Gornovo forest-steppe small mammalian fauna developed in cool continental climate conditions when coniferous forests grew in the river valleys and when forest-steppe landscapes dominated in the water interfluves. The artefacts are characteristic of the beginning of the Late Palaeolithic (32–24 ka). The Kudashevo time is correlated with the late Valdai (late Late Pleistocene; 24–11 ka). The herbage-Artemisia-Chenopodiaceae grassland-steppe association covered most of the territory and a Picea forest with Betula and a small quantity of broad-leaved trees grew in wet depressions. The climate at the end of this period became colder. Freshwater and terrestrial molluscs were represented by rare widespread species while the ostracoda species indicate cold conditions

Elastic principal manifolds and their practical applications

Principal manifolds serve as useful tool for many practical applications. These manifolds are defined as lines or surfaces passing through "the middle" of data distribution. We propose an algorithm for fast construction of grid approximations of principal manifolds with given topology. It is based on analogy of principal manifold and elastic membrane. The first advantage of this method is a form of the functional to be minimized which becomes quadratic at the step of the vertices position refinement. This makes the algorithm very effective, especially for parallel implementations. Another advantage is that the same algorithmic kernel is applied to construct principal manifolds of different dimensions and topologies. We demonstrate how flexibility of the approach allows numerous adaptive strategies like principal graph constructing, etc. The algorithm is implemented as a C++ package elmap and as a part of stand-alone data visualization tool VidaExpert, available on the web. We describe the approach and provide several examples of its application with speed performance characteristics.Comment: 26 pages, 10 figures, edited final versio

PCA Beyond The Concept of Manifolds: Principal Trees, Metro Maps, and Elastic Cubic Complexes

Multidimensional data distributions can have complex topologies and variable local dimensions. To approximate complex data, we propose a new type of low-dimensional ``principal object'': a principal cubic complex. This complex is a generalization of linear and non-linear principal manifolds and includes them as a particular case. To construct such an object, we combine a method of topological grammars with the minimization of an elastic energy defined for its embedment into multidimensional data space. The whole complex is presented as a system of nodes and springs and as a product of one-dimensional continua (represented by graphs), and the grammars describe how these continua transform during the process of optimal complex construction. The simplest case of a topological grammar (``add a node'', ``bisect an edge'') is equivalent to the construction of ``principal trees'', an object useful in many practical applications. We demonstrate how it can be applied to the analysis of bacterial genomes and for visualization of cDNA microarray data using the ``metro map'' representation. The preprint is supplemented by animation: ``How the topological grammar constructs branching principal components (AnimatedBranchingPCA.gif)''.Comment: 19 pages, 8 figure

Elastic Maps and Nets for Approximating Principal Manifolds and Their Application to Microarray Data Visualization

Principal manifolds are defined as lines or surfaces passing through ``the middle'' of data distribution. Linear principal manifolds (Principal Components Analysis) are routinely used for dimension reduction, noise filtering and data visualization. Recently, methods for constructing non-linear principal manifolds were proposed, including our elastic maps approach which is based on a physical analogy with elastic membranes. We have developed a general geometric framework for constructing ``principal objects'' of various dimensions and topologies with the simplest quadratic form of the smoothness penalty which allows very effective parallel implementations. Our approach is implemented in three programming languages (C++, Java and Delphi) with two graphical user interfaces (VidaExpert http://bioinfo.curie.fr/projects/vidaexpert and ViMiDa http://bioinfo-out.curie.fr/projects/vimida applications). In this paper we overview the method of elastic maps and present in detail one of its major applications: the visualization of microarray data in bioinformatics. We show that the method of elastic maps outperforms linear PCA in terms of data approximation, representation of between-point distance structure, preservation of local point neighborhood and representing point classes in low-dimensional spaces.Comment: 35 pages 10 figure