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The evolution of proline synthesis transcriptional regulation in gammaproteobacteria

2010
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Moscow University Biological Sciences Bulletin
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We report a conserved motif in the upstream region of the proA and proB genes, which are widely found among γ proteobacteria, particularly in the genera Pseudomonas, Marinobacter, and Shewanella. The conserved protein-DNA binding sites are 8 bp long. Some genes have double sites for cooperative factor binding. The phylogenetic profiles of binding sites and all protein factors were compared. We identify the tetR family protein, an ortholog of the NP_249058 protein from P. aeruginosa PAO1, as a

doi:10.3103/s0096392510040255
fatcat:4tcr4zecg5hmflihrwwnv7qmju
## more »

... anscription factor. Our algorithm was applied to construct the species tree with predicted regulation of the pro genes. The phylogeny of pro genes, transcription factor phylogeny, and a phylogeny of their binding sites were mapped onto the spe cies tree with our algorithm. The obtained scenario displays important HGT and related events.##
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Lichen planus follicularis tumidus

2019
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Vestnik Dermatologii i Venerologii
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Fig. 1 . 1 Patient

doi:10.25208/0042-4609-2019-95-1-46-51
fatcat:7hqlqcyqsfbjhhihhpya6bzbmq
*K*. 65 y.o., brown-purple plaques with multiple cysts on the surface Рис. 2. ... Patient*K*. 65 y.o., scar alopecia focus in the scalp with dimension of 3.0 × 5.0 cm in diameter Fig. 3 . 3 Multiple partially fused infundibular cysts filled with horn masses and surrounded by dense ...##
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An Almost Exact Linear Complexity Algorithm of the Shortest Transformation of Chain-Cycle Graphs
[article]

2020
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arXiv
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pre-print

Let us denote the beginning of a gene with name

arXiv:2004.14351v1
fatcat:fscogpzas5gsnovovk4yrp3y4m
*k*by k1, and its end, by k2. ... [8] and*Gorbunov*and Lyubetsky [21] . We define five operations over a+b. These are as follows. ...##
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Reconstructing the evolution of genes along the species tree

2009
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Molecular Biology (Moscow)
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Then two approximate estimates of x are

doi:10.1134/s0026893309050197
fatcat:7hyzfzpfp5apravhb2obfssx6q
*k*1 l 1 and*k*2 l 2 , where*k*1 = f 11 /f 1 ,*k*2 = f 12 /f 1 , l 1 = a 1r(v 11 ), l 2 = a 1r(v 12 ). ... Designate*k*= f 2 /f 1 . ...##
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Reconstruction of ancestral regulatory signals along a transcription factor tree

2007
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Molecular Biology (Moscow)
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A model and an algorithm were developed to reconstruct the ancestral regulatory signals, first and foremost, for DNA-protein interactions, at inner nodes of a transcription factor phylogenetic tree on the basis of the modern signal distribution. The algorithm simultaneously infers the evolutionary scenario as a set of tree edges along which the signal diverged to the greatest extent. The model and algorithm were tested with simulation data and biological findings on the NrdR, MntR, and LacI signals.

doi:10.1134/s0026893307050172
fatcat:ajaibny6t5albe2l7eeue2dq6m
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THERMAL ACID INTEGRATION OF SULFURIC ACID VAPORIZATION

2020
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Integrated Technologies and Energy Saving
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*Gorbunov*

*K*., Selikhov

*Yu*., Kotsarenko V., Ponomarenko H., Gorbunova O. THERMAL ACID INTEGRATION OF SULFURIC ACID VAPORIZATION Currently, Ukraine is an issue of energy conservation. ...

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Identification of Ancestral Genes That Introduce Incongruence between Protein- and Species Trees

2005
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Molecular Biology (Moscow)
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In the case of small

doi:10.1007/s11008-005-0089-6
fatcat:axvwdm4kz5dhvgjbaeg3a6637e
*K*'\*K*, the genes from*K*' \*K*=*K*' \(*K*∩*K*') did not descend from the common ancestral gene*K*but were transferred to*K*' or emerged in*K*' later. ... These two sets M =*K*\*K*' and M' =*K*' \*K*will be referred to as components of clades*K*and*K*', respectively. ...##
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The tree nearest on average to a given set of trees

2011
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Problems of Information Transmission
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Hence, in this path there are neighboring vertices

doi:10.1134/s0032946011030069
fatcat:spukmaoisrfcta6geqwtwufwbe
*k*+ and*k*− for which f (*k*+ ) < s < f(*k*− ), i.e., the edge*k*+ ,*k*− and the vertex s form a loss for f . ... By (7) and by the assumption, we have {*k*| h(*k*) is a tube} = {*k*| f (*k*) is a tube}; ( 8 ) then h(g) is a tube. Consider a vertex s for which h(g) < s < f(g). ...##
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INTEGRATION OF A HEATER POWER PLANT ON RENEWABLE ENERGY SOURCES

2020
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Integrated Technologies and Energy Saving
*

.,

doi:10.20998/2078-5364.2020.1.07
fatcat:oprlvdl5cbg77a7z44y7b6ohfu
*Gorbunov*K.A., Rossikhin V.V. ...##
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Modeling evolution of the bacterial regulatory signals involving secondary structure

2009
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Molecular Biology (Moscow)
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This functional H ( σ ) = H 1 ( σ ) + H 2 ( σ ) comprises two conditions (constraints) for the desired configuration σ : (1) for each sequence σ (

doi:10.1134/s0026893309030170
fatcat:kmijzw3ytjbjfazl6isce2yyuy
*k*) (i.e., for the value of σ in the*k*th tree node) and ...*GORBUNOV*et al. serv.html, where the available software for constructing phylogenetic trees and the reconstruction of ancestral sequences are listed). ...##
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The method of normal splines for linear DAEs on the number semi-axis

2009
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Applied Numerical Mathematics
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The method of normal spline-collocation for ordinary linear integral, differential and integro-differential equations, including implicit equations, has been created by

doi:10.1016/j.apnum.2008.03.009
fatcat:fq5dfq4wkvhppaikckduxamihu
*Gorbunov*in the eighties. ... functional (LCF) l ik (x) = n j =1 a ij (t*k*)ẍ j (t*k*) + b ij (t*k*)ẋ j (t*k*) + c ij (t*k*)x j (t*k*) . (13) The boundary/initial conditions also define composite functionals. ... t*k*) + C(t*k*)x(t*k*) = f (t*k*),*k*= 1, . . . , m. (12) The required z-normal solution x z satisfies this finite system, consisting of the n * m scalar equations, and the corresponding 2n conditions ...##
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An Estimate of the Tree-Width of a Planar Graph Which Has Not a Given Planar Grid as a Minor
[chapter]

1998
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Lecture Notes in Computer Science
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Then we suppose that

doi:10.1007/10692760_30
fatcat:2qcisq7r45dthlps4hxaicgiv4
*K*can be partitioned into two (unknown) parts*K*1 and*K*2 being n-divisible by ≤ m dividing. ... Let*K*=*K*\(O 1 O 2 ). We call a path clear if all its vertices except, maybe, ends lie in*K*\ (P 1 P 2 ). For each vertex a in*K*consider two the following conditions. 1. ...##
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Cardiac tumors: analysis of surgical treatment

2021
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Russian Journal of Cardiology
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ORCID: 0000-0003-2977-1792,

doi:10.15829/1560-4071-2021-4598
fatcat:bkiaexaxgvhxlewalehqtccp2a
*Gorbunov*D. N. ORCID: 0000-0003-1424-683Х, Buyankov D. I. ORCID: 0000-0001-9774-7888, Gross*Yu*. V. ORCID: 0000-0003-2657-8049, Verkhoturov M.*K*. ... A.,*Gorbunov*D. N., Buya nkov D. I., Gross*Yu*. V., Verkhoturov M.*K*., Stavtseva M. A. Cardiac tumors: analysis of surgical treatment. Russian Journal of Cardiology. 2021;26(8):4598. (In Russ.) ...##
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An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers
[chapter]

2010
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Lecture Notes in Computer Science
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Given a subset of leaves

doi:10.1007/978-3-642-16181-0_9
fatcat:uy2tgtu5xbhjfmrmr4u5copjlq
*K*⊆ L(T ), the homeomorphic tree of T connecting*K*, denoted T*K*, is the smallest binary tree induced from T such that L( T*K*)=*K*. ... G is the homeomorphic tree G o*K*, where*K*= L C (G o ). from one of its descendant leaves (which leaf does not matter as they are all at the same distance from x). ...##
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Transverse muon polarization in $K^+\to\mu^+\nu_\mu\gamma$ : scanning over the Dalitz plot

2003
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European Physical Journal C: Particles and Fields
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We study the potential of the measurement of the transverse muon polarization P_T in the

doi:10.1140/epjc/s2003-01297-x
fatcat:bvg5hgv5prbozcd6jqt4hobrwy
*K*->mu nu gamma decay with the sensitivity of δ P_T 10^-4. ... (R) , (5) where N*K*µ2γ (R) is the number of*K*µ2γ events in the region R. ... In this paper, we study the T -odd muon polarization in the decay*K*+ → µ + ν µ γ (*K*µ2γ ). ...
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