A Model of Optimal Network Structure for Decentralized Nearest Neighbor Search

One of the approaches for the nearest neighbor search problem is to build a network which nodes correspond to the given set of indexed objects. In this case the search of the closest object can be thought as a search of a node in a network. A procedure in a network is called decentralized if it uses only local information about visited nodes and its neighbors. Networks, which structure allows efficient performing the nearest neighbour search by a decentralised search procedure started from any node, are of particular interest especially for pure distributed systems. Several algorithms that construct such networks have been proposed in literature. However, the following questions arise: "Are there network models in which decentralised search can be performed faster?"; "What are the optimal networks for the decentralised search?"; "What are their properties?". In this paper we partially give answers to these questions. We propose a mathematical programming model for the problem of determining an optimal network structure for decentralized nearest neighbor search. We have found an exact solution for a regular lattice of size 4x4 and heuristic solutions for sizes from 5x5 to 7x7. As a distance function we use L1 , L2 and L_inf metrics. We hope that our results and the proposed model will initiate study of optimal network structures for decentralised nearest neighbour search

Maternal polymorphic loci of rs1979277 serine hydroxymethyl transferase and rs1805087 5-methylenetetrahydrofolate are correlated with the development of fetal growth restriction: A case-control study

Background: Key reactions in folate-mediated single-carbon metabolism are regulated by folate cycle enzymes. Violations of the folate cycle may be associated with the occurrence of fetal growth restriction (FGR) in pregnant women. Objective: To study the relationship between polymorphisms of folate cycle genes in the mother with the development of FGR. Materials and Methods: In this case-control study, 122 pregnant women with FGR and 243 pregnant women with normal newborn weight were enrolled. The polymorphic loci of folate cycle genes including rs1805087 5-methylenetetrahydrofolate (MTR) and rs1979277 serine hydroxymethyl transferase (SHMT1) were examined. The study of polymorphisms was carried out through the TaqMan probe detection method using polymerase chain reaction. Logistic regression was used to analyze the associations of the polymorphisms. Results: It was established that the T allele rs1979277 of the SHMT1 gene was correlated with the development of FGR within the framework of the allelic (OR = 1.67, 95% CI 1.20-2.33, pperm < 0.01), additive (OR = 1.69, 95% CI 1.20-2.37, pperm < 0.01), dominant (OR = 1.81, 95% CI 1.15-2.87, pperm = 0.01) and recessive (OR = 2.34, 95% CI 1.15-4.73, pperm = 0.01) models. The association of the G rs1805087 allele of the MTR gene with the occurrence of FGR was also identified following the recessive model (OR = 3.01, 95% CI 1.05-8.68, pperm = 0.04). Conclusion: Our results indicated that maternal polymorphic loci rs1979277 SHMT1 and rs1805087 MTR may be associated with the development of FGR. Key words: Polymorphism, Associations, Fetal growth restriction, Folic acid

Detecting synchronization of self-sustained oscillators by external driving with varying frequency

We propose a method for detecting the presence of synchronization of self-sustained oscillator by external driving with linearly varying frequency. The method is based on a continuous wavelet transform of the signals of self-sustained oscillator and external force and allows one to distinguish the case of true synchronization from the case of spurious synchronization caused by linear mixing of the signals. We apply the method to driven van der Pol oscillator and to experimental data of human heart rate variability and respiration.Comment: 9 pages, 7 figure

Disruptive Selection of Human Immunostimulatory and Immunosuppressive Genes Both Provokes and Prevents Rheumatoid Arthritis, Respectively, as a Self-Domestication Syndrome

Using our previously published Web service SNP_TATA_Comparator, we conducted a genome-wide study of single-nucleotide polymorphisms (SNPs) within core promoters of 68 human rheumatoid arthritis (RA)-related genes. Using 603 SNPs within 25 genes clinically associated with RA-comorbid disorders, we predicted 84 and 70 candidate SNP markers for overexpression and underexpression of these genes, respectively, among which 58 and 96 candidate SNP markers, respectively, can relieve and worsen RA as if there is a neutral drift toward susceptibility to RA. Similarly, we predicted natural selection toward susceptibility to RA for 8 immunostimulatory genes (e.g., IL9R) and 10 genes most often associated with RA (e.g., NPY). On the contrary, using 25 immunosuppressive genes, we predicted 70 and 109 candidate SNP markers aggravating and relieving RA, respectively (e.g., IL1R2 and TGFB2), suggesting that natural selection can simultaneously additionally yield resistance to RA. We concluded that disruptive natural selection of human immunostimulatory and immunosuppressive genes is concurrently elevating and reducing the risk of RA, respectively. So, we hypothesize that RA in human could be a self-domestication syndrome referring to evolution patterns in domestic animals. We tested this hypothesis by means of public RNA-Seq data on 1740 differentially expressed genes (DEGs) of pets vs. wild animals (e.g., dogs vs. wolves). The number of DEGs in the domestic animals corresponding to worsened RA condition in humans was significantly larger than that in the related wild animals (10 vs. 3). Moreover, much less DEGs in the domestic animals were accordant to relieved RA condition in humans than those in the wild animals (1 vs. 8 genes). This indicates that the anthropogenic environment, in contrast to a natural one, affects gene expression across the whole genome (e.g., immunostimulatory and immunosuppressive genes) in a manner that likely contributes to RA. The difference in gene numbers is statistically significant as confirmed by binomial distribution (p < 0.01), Pearson’s χ2 (p < 0.01), and Fisher’s exact test (p < 0.05). This allows us to propose RA as a candidate symptom within a self-domestication syndrome. Such syndrome might be considered as a human’s payment with health for the benefits received during evolution

Association of matrix metalloproteinase gene polymorphisms with different biological subtypes of breast cancer

Aim. To investigate the associations of matrix metalloproteinase (MMP) MMP3 (rs679620), MMP8 (rs1940475), and MMP9 (rs17576 and rs3787268) gene polymorphisms with different biological subtypes of breast cancer (BC). Materials and methods. The study sample consisted of 285 patients with BC of various biological subtypes (luminal A and B [n=153], triple negative [n=108], and HER2 positive [HER2+, n=24]) and 746 females in the control group. Genotyping of four polymorphic sites of MMP3 (rs679620), MMP8 (rs1940475), and MMP9 (rs17576 and rs3787268) genes was performed in the study groups. Results. The role of MMP gene polymorphisms in the BC development of various biological subtypes differs. The c.836 AG MMP9 polymorphism (rs17576, the odds ratio is 0.670.71 for the G allele) has a protective effect on the development of luminal A- and B-subtypes of BC; susceptibility to triple-negative BC is associated with the polymorphic site c.1331-163 GA MMP9 (rs3787268, OR 4.51 for genotype AA), and two polymorphisms of the MMP3 (c.133 TC, rs679620, OR 0.460.49 for T allele) and MMP8 (c.259 TC, rs1940475, OR 0.370.48 for T allele) genes are associated with HER2+ BC development. According to the in silico data, the above polymorphisms have pronounced functional effects in organs and tissues that are pathogenetically significant for the disease, including the target organ, the breast. Conclusion. The c.836 AG MMP9 (rs17576) polymorphism is associated with luminal A- and B-subtype of BC; c.1331-163 GA MMP9 (rs3787268) is associated with triple negative BC, and c.133 TC MMP3 (rs679620) and c.259 TC MMP8 (rs1940475) are involved in HER2+ BC development

Natural Selection Equally Supports the Human Tendencies in Subordination and Domination: A Genome-Wide Study With in silico Confirmation and in vivo Validation in Mice

We proposed the following heuristic decision-making rule: “IF {an excess of a protein relating to the nervous system is an experimentally known physiological marker of low pain sensitivity, fast postinjury recovery, or aggressive, risk/novelty-seeking, anesthetic-like, or similar agonistic-intolerant behavior} AND IF {a single nucleotide polymorphism (SNP) causes overexpression of the gene encoding this protein} THEN {this SNP can be a SNP marker of the tendency in dominance} WHILE {underexpression corresponds to subordination} AND vice versa.” Using this decision-making rule, we analyzed 231 human genes of neuropeptidergic, non-neuropeptidergic, and neurotrophinergic systems that encode neurotrophic and growth factors, interleukins, neurotransmitters, receptors, transporters, and enzymes. These proteins are known as key factors of human social behavior. We analyzed all the 5,052 SNPs within the 70 bp promoter region upstream of the position where the protein-coding transcript starts, which were retrieved from databases Ensembl and dbSNP using our previously created public Web service SNP_TATA_Comparator (http://beehive.bionet.nsc.ru/cgi-bin/mgs/tatascan/start.pl). This definition of the promoter region includes all TATA-binding protein (TBP)-binding sites. A total of 556 and 552 candidate SNP markers contributing to the dominance and the subordination, respectively, were uncovered. On this basis, we determined that 231 human genes under study are subject to natural selection against underexpression (significance p < 0.0005), which equally supports the human tendencies in domination and subordination such as the norm of a reaction (plasticity) of the human social hierarchy. These findings explain vertical transmission of domination and subordination traits previously observed in rodent models. Thus, the results of this study equally support both sides of the century-old unsettled scientific debate on whether both aggressiveness and the social hierarchy among humans are inherited (as suggested by Freud and Lorenz) or are due to non-genetic social education, when the children are influenced by older individuals across generations (as proposed by Berkowitz and Fromm)

Automatic Adaptive Lossy Compression of Multichannel Remote Sensing Images

In this chapter, we consider lossy compression of multichannel images acquired by remote sensing systems. Two main features of such data are taken into account. First, images contain inherent noise that can be of different intensity and type. Second, there can be essential correlation between component images. These features can be exploited in 3D compression that is demonstrated to be more efficient than component-wise compression. The benefits are in considerably higher compression ratio attained for the same or even less distortions introduced. It is shown that important performance parameters of lossy compression can be rather easily and accurately predicted