Characteristic Length Scale of Electric Transport Properties of Genomes

A tight-binding model together with a novel statistical method are used to investigate the relation between the sequence-dependent electric transport properties and the sequences of protein-coding regions of complete genomes. A correlation parameter $\Omega$ is defined to analyze the relation. For some particular propagation length $w_{max}$, the transport behaviors of the coding and non-coding sequences are very different and the correlation reaches its maximal value $\Omega_{max}$. $w_{max}$ and \omax are characteristic values for each species. The possible reason of the difference between the features of transport properties in the coding and non-coding regions is the mechanism of DNA damage repair processes together with the natural selection.Comment: 4 pages, 4 figure

Statistical analysis of the DNA sequence of human chromosome 22

We study statistical patterns in the DNA sequence of human chromosome 22, the first completely sequenced human chromosome. We find that (i) the 33.4 x 10(6) nucleotide long human chromosome exhibits long-range power-law correlations over more than four orders of magnitude, (ii) the entropies H-n of the frequency distribution of oligonucleotides of length n (n-mers) grow sublinearly with increasing n, indicating the presence of higher-order correlations for all of the studied lengths 1 less than or equal to n less than or equal to 10, and (iii) the generalized entropies H-n(q) of n-mers decrease monotonically with increasing q and the decay of H-n(q) with q becomes steeper with increasing n less than or equal to 10, indicating that the frequency distribution of oligonucleotides becomes increasingly nonuniform as the length n increases. We investigate to what degree known biological features may explain the observed statistical patterns. We find that (iv) the presence of interspersed repeats may cause the sublinear increase of H-n with n, and that (v) the presence of monomeric tandem repeats as well as the suppression of CG dinucleotides may cause the observed decay of H-n(q) with q

Single-photon single ionization of W+^{+} ions: experiment and theory

Experimental and theoretical results are reported for photoionization of Ta-like (W$^{+}$) tungsten ions. Absolute cross sections were measured in the energy range 16 to 245 eV employing the photon-ion merged-beam setup at the Advanced Light Source in Berkeley. Detailed photon-energy scans at 100 meV bandwidth were performed in the 16 to 108 eV range. In addition, the cross section was scanned at 50 meV resolution in regions where fine resonance structures could be observed. Theoretical results were obtained from a Dirac-Coulomb R-matrix approach. Photoionization cross section calculations were performed for singly ionized atomic tungsten ions in their $5s^2 5p^6 5d^4({^5}D)6s \; {^6}{\rm D}_{J}$, $J$=1/2, ground level and the associated excited metastable levels with $J$=3/2, 5/2, 7/2 and 9/2. Since the ion beams used in the experiments must be expected to contain long-lived excited states also from excited configurations, additional cross-section calculations were performed for the second-lowest term, $5d^5 \; ^6{\rm S}_{J}$, $J$=5/2, and for the $^4$F term, $5d^3 6s^2 \; ^4{\rm F}_{J}$, with $J$ = 3/2, 5/2, 7/2 and 9/2. Given the complexity of the electronic structure of W$^+$ the calculations reproduce the main features of the experimental cross section quite well.Comment: 23 pages, 7 figures, 1 table: Accepted for publication in J. Phys. B: At. Mol. & Opt. Phy

Finite-sample frequency distributions originating from an equiprobability distribution

Given an equidistribution for probabilities p(i)=1/N, i=1..N. What is the expected corresponding rank ordered frequency distribution f(i), i=1..N, if an ensemble of M events is drawn?Comment: 4 pages, 4 figure

Environmental cues and constraints affecting the seasonality of dominant calanoid copepods in brackish, coastal waters: a case study of Acartia, Temora and Eurytemora species in the south-west Baltic

Information on physiological rates and tolerances helps one gain a cause-and-effect understanding of the role that some environmental (bottom–up) factors play in regulating the seasonality and productivity of key species. We combined the results of laboratory experiments on reproductive success and field time series data on adult abundance to explore factors controlling the seasonality of Acartia spp., Eurytemora affinis and Temora longicornis, key copepods of brackish, coastal and temperate environments. Patterns in laboratory and field data were discussed using a metabolic framework that included the effects of ‘controlling’, ‘masking’ and ‘directive’ environmental factors. Over a 5-year period, changes in adult abundance within two south-west Baltic field sites (Kiel Fjord Pier, 54°19′89N, 10°09′06E, 12–21 psu, and North/Baltic Sea Canal NOK, 54°20′45N, 9°57′02E, 4–10 psu) were evaluated with respect to changes in temperature, salinity, day length and chlorophyll a concentration. Acartia spp. dominated the copepod assemblage at both sites (up to 16,764 and 21,771 females m−3 at NOK and Pier) and was 4 to 10 times more abundant than E. affinis (to 2,939 m−3 at NOK) and T. longicornis (to 1,959 m−3 at Pier), respectively. Species-specific salinity tolerance explains differences in adult abundance between sampling sites whereas phenological differences among species are best explained by the influence of species-specific thermal windows and prey requirements supporting survival and egg production. Multiple intrinsic and extrinsic (environmental) factors influence the production of different egg types (normal and resting), regulate life-history strategies and influence match–mismatch dynamics

The response of temperate aquatic ecosystems to global warming: novel insights from a multidisciplinary project

This article serves as an introduction to this special issue of Marine Biology, but also as a review of the key findings of the AQUASHIFT research program which is the source of the articles published in this issue. AQUASHIFT is an interdisciplinary research program targeted to analyze the response of temperate zone aquatic ecosystems (both marine and freshwater) to global warming. The main conclusions of AQUASHIFT relate to (a) shifts in geographic distribution, (b) shifts in seasonality, (c) temporal mismatch in food chains, (d) biomass responses to warming, (e) responses of body size, (f) harmful bloom intensity, (f), changes of biodiversity, and (g) the dependence of shifts to temperature changes during critical seasonal windows

Experimental investigation of left-right asymmetry in photon-atom interaction

Single ionization of noble gas atoms by linearly polarized synchrotron radiation has been studied by employing angle- and energy-resolved photoelectron spectroscopy. The measurements were carried out in the plane defined by the momentum and polarization vectors of the photon. Parameters describing the left-right asymmetry (LRA) (relative to the photon propagation direction) of the photoelectron angular distribution were determined experimentally for the s-shells of He, Ne, Ar, Kr and Xe atoms and H2 molecules and for the p-shells of Ne, Ar, Kr and Xe atoms. The values of the left-right asymmetry differ significantly from zero for both subshells. The photon and photoelectron energy dependence of the LRA parameters are presented also. Possible experimental and instrumental sources that could generate asymmetry are discussed and excluded as well

Entropy estimates of small data sets

Estimating entropies from limited data series is known to be a non-trivial task. Naive estimations are plagued with both systematic (bias) and statistical errors. Here, we present a new 'balanced estimator' for entropy functionals Shannon, R\'enyi and Tsallis) specially devised to provide a compromise between low bias and small statistical errors, for short data series. This new estimator out-performs other currently available ones when the data sets are small and the probabilities of the possible outputs of the random variable are not close to zero. Otherwise, other well-known estimators remain a better choice. The potential range of applicability of this estimator is quite broad specially for biological and digital data series.Comment: 11 pages, 2 figure