On pairwise distances and median score of three genomes under DCJ

In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a resulting genome is called median genome). In contrast to the rearrangement distance between two genomes which can be computed in linear time, computing the median score for three genomes is NP-hard. This inspires a quest for simpler and faster approximations for the median score, the most natural of which appears to be the halved sum of pairwise distances which in fact represents a lower bound for the median score. In this work, we study relationship and interplay of pairwise distances between three genomes and their median score under the model of Double-Cut-and-Join (DCJ) rearrangements. Most remarkably we show that while a rearrangement may change the sum of pairwise distances by at most 2 (and thus change the lower bound by at most 1), even the most "powerful" rearrangements in this respect that increase the lower bound by 1 (by moving one genome farther away from each of the other two genomes), which we call strong, do not necessarily affect the median score. This observation implies that the two measures are not as well-correlated as one's intuition may suggest. We further prove that the median score attains the lower bound exactly on the triples of genomes that can be obtained from a single genome with strong rearrangements. While the sum of pairwise distances with the factor 2/3 represents an upper bound for the median score, its tightness remains unclear. Nonetheless, we show that the difference of the median score and its lower bound is not bounded by a constant.Comment: Proceedings of the 10-th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG), 2012. (to appear

Disturbance of Thermodynamic Equilibrium of the Quartz-Water System and Silica Separation from the Liquid Phase at a Small Temperature Gradient

AbstractIn electric furnaces destined for experimental geochemical investigations, a small temperature gradient (TG) always exists, and it is difficult to avoid it. In our electric furnaces (from bottom to top) the temperature rises in the lower part (TG = 0.25°/cm) and falls in the upper part (TG = -0.16°/cm). Long-term runs with quartz and water at 300°C have shown the attainment of equilibrium at TG equal to -0.16°/cm. At TG equal to 0.25°/cm, the silica re- precipitated from the ampoule bottom onto its walls above the meniscus, and the aqueous silica concentration was reduced and became 300 times lower than quartz solubility. The obtained results were explained by the combined action of slow convection of water and thermal diffusion of silica. The efficient mechanism of fractionation revealed by us can be extended to other substances and has geochemical and technological importance

Metrological characterization of the pulsed Rb clock with optical detection

We report on the implementation and the metrological characterization of a vapor-cell Rb frequency standard working in pulsed regime. The three main parts that compose the clock, physics package, optics and electronics, are described in detail in the paper. The prototype is designed and optimized to detect the clock transition in the optical domain. Specifically, the reference atomic transition, excited with a Ramsey scheme, is detected by observing the interference pattern on a laser absorption signal. \ The metrological analysis includes the observation and characterization of the clock signal and the measurement of frequency stability and drift. In terms of Allan deviation, the measured frequency stability results as low as $1.7\times 10^{-13} \ \tau^{-1/2}$, $\tau$ being the averaging time, and reaches the value of few units of $10^{-15}$ for $\tau=10^{4}$ s, an unprecedent achievement for a vapor cell clock. We discuss in the paper the physical effects leading to this result with particular care to laser and microwave noises transferred to the clock signal. The frequency drift, probably related to the temperature, stays below $10^{-14}$ per day, and no evidence of flicker floor is observed. \ We also mention some possible improvements that in principle would lead to a clock stability below the $10^{-13}$ level at 1 s and to a drift of few units of $10^{-15}$ per day

Limited Lifespan of Fragile Regions in Mammalian Evolution

An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals (Ma et al. (2006) Genome Research 16, 1557-1565) raised some doubts about their existence. We demonstrate that fragile regions are subject to a "birth and death" process, implying that fragility has limited evolutionary lifespan. This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome

Towards the electron EDM search: Theoretical study of HfF+

We report first ab initio relativistic correlation calculations of potential curves for ten low-lying electronic states, effective electric field on the electron and hyperfine constants for the ^3\Delta_1 state of cation of a heavy transition metal fluoride, HfF^+, that is suggested to be used as the working state in experiments to search for the electric dipole moment of the electron. It is shown that HfF^+ has deeply bound ^1\Sigma^+ ground state, its dissociation energy is D_e=6.4 eV. The ^3\Delta_1 state is obtained to be the relatively long-lived first excited state lying about 0.2 eV higher. The calculated effective electric field E_eff=W_d|\Omega| acting on an electron in this state is 5.84*10^{24}Hz/(e*cm)Comment: 4 page

Social portrait of a police officer today

Objective: to study the social portrait of a police officer at the present stage, their attitude to work (promotion, labor intensity, psychological atmosphere), family, marriage, financial status, recreation, and retirement.Methods: dialectic approach to cognition of social phenomena allowing to analyze them in their historical development and functioning in the context of a set of objective and subjective factors, which determined the choice of the following research methods: formal-logical, comparative-legal, sociological.Results: the paper analyzes the social profile of police officers, their views on the future, family, and career. Special attention is paid to the problems of police officers in the service and at home - bureaucracy in the workplace, financial difficulties, situation with housing, attitude to family and marriage. The positive and negative coefficients of police officers’ agreement with the proposed questions are analyzed. The questions with maximum coefficient of agreement were: a) the monetary allowance of employees is the main means of their material provision; b) the life and health of a police officer is insured at the expense of budgetary funds; c) family members of a police officer are proud of their profession. The questions with maximum coefficient of disagreement included the following: a) neighbors are alert when communicating with family members of a police officer; b) I am completely satisfied with the amount of bonuses to the official salary for performing complex tasks; c) a police officer is forced to be friends only with other police officers.Scientific novelty: the paper concludes that currently employees of internal affairs agencies perceive stability and confidence in their position. As positive aspects of their work, the police officers note the high level of professionalism of the team, long vacation, and early retirement. However, there are a number of problems that need to be addressed. These include an excessive amount of paperwork, high stress levels, and financial problems.Practical significance: the main provisions and conclusions of the article can be used in scientific, educational and law enforcement activities when considering issues related to guarantees of social protection of police officers: remuneration, mandatory state insurance, provision of housing for police officers, medical care and other guarantees

Configuration interaction calculation of hyperfine and P,T-odd constants on ^{207}PbO excited states for the electron EDM experiments

We report first configuration interaction calculations of hyperfine constants A_\parallel and the effective electric field W_d acting on the electric dipole moment of the electron, in two excited electronic states of ^{207}PbO. The obtained hyperfine constants, A_\parallel = -3826 MHz for the a(1) state and A_\parallel = 4887 MHz for the B(1) state, are in very good agreement with the experimental data, -4113 MHz and 5000 \pm 200 MHz, respectively. We find W_d = -(6.1 ^{+1.8}_{-0.6}) 10^{24} Hz/(e cm) for a(1), and W_d = (8.0 \pm 1.6) 10^{24} Hz/(e cm) for B(1). The obtained values are analyzed and compared to recent relativistic coupled cluster results and a semiempirical estimate of W_d for the a(1) state.Comment: 6 pages, REVTeX4 style, submitted to Pthys.Rev.

Таргетная терапия распространенного рака почки Сутентом®: побочные эффекты и их коррекция

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