198 research outputs found
Observations - Planet Mars in 1967
Visual Mars observations by Volgograd Observatory in 1966-196
The cooperation of Russian and German metal forming scientific schools to develop the new energy-efficient materials and technologies
The future scientific orientation of Katedra PDSS is in the area of materials forming and materials development with a focus on efficient processes regarding the use of energy and resources. Current research in the department PDSS is based on fundamental works on thermo-mechanical treatment of metals and on the modeling of nano-materials, rolled material and medical materials. This includes research on the relevant microstructural and macroscopic effects on the materials behavior. Together with its international research partners PDSS has excellent foundations for experimental research as well. With its international focus and its educational programs for students and skilled employees PDSS is an important partner of the Russian metal processing industry which supports Russian companies to compete on a world-class level
PCA and K-Means decipher genome
In this paper, we aim to give a tutorial for undergraduate students studying
statistical methods and/or bioinformatics. The students will learn how data
visualization can help in genomic sequence analysis. Students start with a
fragment of genetic text of a bacterial genome and analyze its structure. By
means of principal component analysis they ``discover'' that the information in
the genome is encoded by non-overlapping triplets. Next, they learn how to find
gene positions. This exercise on PCA and K-Means clustering enables active
study of the basic bioinformatics notions. Appendix 1 contains program listings
that go along with this exercise. Appendix 2 includes 2D PCA plots of triplet
usage in moving frame for a series of bacterial genomes from GC-poor to GC-rich
ones. Animated 3D PCA plots are attached as separate gif files. Topology
(cluster structure) and geometry (mutual positions of clusters) of these plots
depends clearly on GC-content.Comment: 18 pages, with program listings for MatLab, PCA analysis of genomes
and additional animated 3D PCA plot
Principal manifolds and graphs in practice: from molecular biology to dynamical systems
We present several applications of non-linear data modeling, using principal
manifolds and principal graphs constructed using the metaphor of elasticity
(elastic principal graph approach). These approaches are generalizations of the
Kohonen's self-organizing maps, a class of artificial neural networks. On
several examples we show advantages of using non-linear objects for data
approximation in comparison to the linear ones. We propose four numerical
criteria for comparing linear and non-linear mappings of datasets into the
spaces of lower dimension. The examples are taken from comparative political
science, from analysis of high-throughput data in molecular biology, from
analysis of dynamical systems.Comment: 12 pages, 9 figure
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
Translational control of gene expression via interacting feedback loops
Translation is a key step in the synthesis of proteins. Accordingly, cells
have evolved an intricate array of control mechanisms to regulate this process.
By constructing a multi-component mathematical framework for translation we
uncover how translation may be controlled via interacting feedback loops. Our
results reveal that this interplay gives rise to a remarkable range of protein
synthesis dynamics, including oscillations, step-change and bistability. This
suggests that cells may have recourse to a much richer set of control
mechanisms than was previously understood.Comment: Supplementary Material Available on Reques
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