β-Decay and the origin of optical purity

Improving Keszthelyis simple model the evolutionary appearance of concentration difference of enanthiomeric compounds due to their differential decomposition by -rays is investigated taking into account the racemization as well. It is shown that if the difference in the cross sections is very small then the resulting concentration difference will never exceed the statistical fluctuations, while in the case of a sufficiently large difference in the cross sections the concentration difference can overgrow the statistical fluctuations in an evolutionary reasonable period of time. The relative difference of the concentrations, however, will be generally much smaller than that of the cross sections. Therefore some other, amplifying mechanism must be postulated in order to explain the optical purity of living beings.     

Small angle neutron scattering, total cross-sections and mass density measurements of concentrated NaCl and KCl solutions in H2O or D2O

The mass densities, total cold neutron cross sections and small angle scattering of concentrated NaCl and KCl solutions in H2O or D2O (2H2O) were measured at 20 degrees C. The partial specific volumes of both salts increase with salt concentration and are significantly smaller in D2O than in H2O, showing that these salt solutions cannot be considered as isomorphous in H2O and D2O. As salt concentration increases for both salts, the total coherent cross sections for neutrons of the solutions also increase while the coherent small angle scattering decreases-observations that are consistent, respectively, with increasing correlations involving the ion and water components and a decrease in the particle number density and/or concentration fluctuations, in the solutions. Changes in incoherent scattering with salt concentration are essentially those expected from the solution compositions and densities.     

Method to classify xylem cell types using cross sectionsof 1-year-old branches in Mediterranean woody species

Measurements of anatomical parameters of wood are of great interest both for eco-physiological purposes and for technological applications. The aim of this paper is to describe a new method for classifying and measuring cell lumen of xylem, analysing cross sections under the light microscope. The proposed method is based on the application of digital image analysis on images of the cross sections of xylem in combination with graphical and statistical methods. The methodology was tested on 1-year-old branches of several woody species, both trees and shrubs, occurring in a Mediterranean natural ecosystem in southern Italy. The development of the procedure was based on statistical comparison between data collected according to four procedures: (a) manual identification and measurement of lumen diameter of conduits on longitudinal sections; (b) manual identification and measurement of lumen diameter of conduits on cross sections; (c) manual identification and measurement of lumen area of conduits on cross sections; and (d) automatic measurement of lumen area of conduits on cross sections. The influence of image resolution and that of the position of the selected area on cell classification and measurements were ascertained. The proposed method was proved to be specific to woody structures and allowed the construction of a model-graph that is species-specific. Interpretation of the model-graphs allows classification and hence measurement of identified cells.     

Toroidal inhomogeneity of plasma density fluctuations during ECR plasma heating in the L-2M stellarator

Correlation between short-wavelength (k_⊥ ≈ 20–30 cm^–1) and long-wavelength (k_⊥ ≈ 1–2 cm^–1) plasma density fluctuations in two poloidal cross sections of the stellarator chamber separated by 1/14 or 5/14 of the torus perimeter was studied using collective scattering of radiation of two 75-GHz gyrotrons and radiation of a 37-GHz Doppler reflectometer at an ECR heating power density of 1.6–3.2 MW/m³. It is found that excitation of turbulent fluctuations is bursty in character and that fluctuations excited in different L-2M cross sections are uncorrelated. It is shown that the energy of turbulent fluctuations is modulated by a low frequency of 5–20 kHz. An idea is put forward that anomalous transport is toroidally inhomogeneous.     

A Monte Carlo code for the simulation of heavy-ion tracks in water

TILDA, a new Monte Carlo track structure code for ions in gaseous water that is valid for both high-LET (approximately 10(4) keV/microm) and low-LET ions, is presented. It is specially designed for a comparison of the patterns of energy deposited by a large range of ions. Low-LET ions are described in a perturbative frame, whereas heavy ions with a very high stopping power are treated using the Lindhard local density approximation and the Russek and Meli statistical method. Ionization cross sections singly differential with energy compare well with the experiment. As an illustration of the non-perturbative interaction of high-LET ions, a comparison between the ion tracks of light and heavy ions with the same specific energy is presented (1.4 MeV/nucleon helium and uranium ions). The mean energy for ejected electrons was found to be approximately four times larger for uranium than for helium, leading to a much larger track radius in the first case. For electrons, except for the excitation cross sections that are deduced from experimental fits, cross sections are derived analytically. For any orientation of the target molecule, the code calculates multiple differential cross sections as a function of the ejection and scattering angles and of the energy transfer. The corresponding singly differential and total ionization cross sections are in good agreement with experimental data. The angular distribution of secondary electrons is shown to depend strongly on the orientation of the water molecule.     

Contingency and statistical laws in replicate microbial closed ecosystems

Contingency, the persistent influence of past random events, pervades biology. To what extent, then, is each course of ecological or evolutionary dynamics unique, and to what extent are these dynamics subject to a common statistical structure? Addressing this question requires replicate measurements to search for emergent statistical laws. We establish a readily replicated microbial closed ecosystem (CES), sustaining its three species for years. We precisely measure the local population density of each species in many CES replicates, started from the same initial conditions and kept under constant light and temperature. The covariation among replicates of the three species densities acquires a stable structure, which could be decomposed into discrete eigenvectors, or "ecomodes." The largest ecomode dominates population density fluctuations around the replicate-average dynamics. These fluctuations follow simple power laws consistent with a geometric random walk. Thus, variability in ecological dynamics can be studied with CES replicates and described by simple statistical laws.     

Analysis of the distribution of chemical elements in Adelie penguin bone using synchrotron radiation X-ray fluorescence

We performed synchrotron radiation X-ray fluorescence (SR-XRF) analysis of Adelie penguin bones, collected in the maritime Antarctic. This method enabled us to determine the microscopic concentration profiles of chemical elements in transverse bone sections. Results show that: (1) there are different concentration profiles for elements in the bones; (2) the inter-correlation of elements in the bones is complex; (3) some trace elements, including toxic ones like Rb, Sr, Fe, Mn, Cu, Co, Ni, Ti, Zr, Br, As, Hg, and Cr, are also detected somewhere in the cross section of the bones. It is suggested that further studies be conducted to establish an SR-XRF database for polar and non-polar animals. This will be greatly beneficial for characterizing penguins by the microscopic distribution of elements in bone and for the understanding of elements' roles in animal metabolism.     

On inherited fertility in biological systems: a model of correlated fluctuations in the stochastic branching process.

A new evolutionary model with hereditary modes considered as correlated fluctuations of fertility has been proposed. It has been demonstrated that the model allows the global statistical properties of the system to be evaluated, e.g. the ensemble average and the probability of extinction. The results obtained show the increase of instability of a population with the enhancement of inheritance efficiency. The existence of at least an exponential stratification in the population has also been shown. Possible applications of the present model are discussed.     

A non-parametric method for the reconstruction of age- and time-dependent incidence from the prevalence data of irreversible diseases with differential mortality.

A method is proposed for reconstructing the time and age dependence of incidence rates from successive age-prevalence cross sections taken from the sentinel surveys of irreversible diseases when there is an important difference in mortality between the infected and susceptible subpopulations. The prevalence information at different time-age points is used to generate a surface; the time-age variations along the life line profiles of this surface and the difference in mortality rates are used to reconstruct the time and age dependence of the incidence rate. Past attempts were based on specified parametric forms for the incidence or on the hypothesis of time-invariant forms for the age-prevalence cross sections. The proposed method makes no such assumptions and is thus capable of coping with rapidly evolving prevalence situations. In the simulations carried out, it is found to be resilient to important random noise components added to a prescribed incidence rate input. The method is also tested on a real data set of successive HIV age-prevalence cross sections from Burundi coupled to differential mortality data on HIV(+) and HIV(-) individuals. The often-made assumption that the incidence rate can be written as the product of a calendar time component and an age component is also examined. In this case, a pooling procedure is proposed to estimate the time and the age profiles of the incidence rate using the reconstructed incidence rates at all time-age points.     

Statistics and truth in phylogenomics

Phylogenomics refers to the inference of historical relationships among species using genome-scale sequence data and to the use of phylogenetic analysis to infer protein function in multigene families. With rapidly decreasing sequencing costs, phylogenomics is becoming synonymous with evolutionary analysis of genome-scale and taxonomically densely sampled data sets. In phylogenetic inference applications, this translates into very large data sets that yield evolutionary and functional inferences with extremely small variances and high statistical confidence (P value). However, reports of highly significant P values are increasing even for contrasting phylogenetic hypotheses depending on the evolutionary model and inference method used, making it difficult to establish true relationships. We argue that the assessment of the robustness of results to biological factors, that may systematically mislead (bias) the outcomes of statistical estimation, will be a key to avoiding incorrect phylogenomic inferences. In fact, there is a need for increased emphasis on the magnitude of differences (effect sizes) in addition to the P values of the statistical test of the null hypothesis. On the other hand, the amount of sequence data available will likely always remain inadequate for some phylogenomic applications, for example, those involving episodic positive selection at individual codon positions and in specific lineages. Again, a focus on effect size and biological relevance, rather than the P value, may be warranted. Here, we present a theoretical overview and discuss practical aspects of the interplay between effect sizes, bias, and P values as it relates to the statistical inference of evolutionary truth in phylogenomics.     

MHD diagnostics in the T-11M tokamak

An MHD diagnostic system for investigating the dynamics of disruption and the preceding phase of the discharge in the T-11M tokamak is described. This system makes it possible to study the structure of magnetic fluctuations in the plasma column. The diagnostic system includes a set of magnetic pick-up loops (Mirnov coils) arranged in several poloidal cross sections of the tokamak, a data acquisition system that provides synchronous recording of Mirnov coil signals, a synchronization system for triggering the data acquisition system during a disruption, and a system for processing and representation of the experimental data on magnetic fluctuations in the plasma column. Examples of how the MHD diagnostic system operates in the T-11M tokamak are presented.     

Nuclear fragmentation of clinical silicon beam

Heavy ions used for biomedical studies fragment when they pass through matter. It is known that different fragments cause different types of biological damage. In this paper, results pertaining to different kinds of secondary fragments produced by a 28Si beam at 463 MeV/nucleon in its interaction with nuclear emulsion are presented. It is observed that the production frequencies of secondary fragments are independent of the target. Partial production cross sections and fluences of the secondary fragments are also discussed. The partial production cross sections for different fragments at three lower energy ranges are practically the same within their statistical errors except for the cross section for Li fragments, which is larger by almost a factor of 1.5 at the lowest energy investigated. The dose contributions of the primary Si beam and its components at different points of the Bragg curve are presented for two different energy regions.     

Visibility of the impact of environmental noise: a response to Kaitala and Ranta

Based on simulation modelling, Kaitala and Ranta (2001 Proc. R. Soc. Lond. B 268, 1769-1774) have argued that detecting the statistical relationships between environmental variability and population fluctuations will be difficult. However, their study was limited in that only one pattern of density dependence and one detection method were used. Here, we show that their conclusion is in part a consequence of their choice of population model and in part a consequence of using relatively weak or inappropriate statistical methods. Other patterns of density dependence respond differently to environmental fluctuations, and the impact of the disturbance on these is clearly visible using their methods. For some patterns of population dynamics, environmental impacts are more readily detectable by correlating running-average environmental conditions with the population time-series or by correlating the first differences of the population time-series with environmental noise. When more appropriate statistical methods are used, environmental forcing is detectable in the majority of cases used by Kaitala and Ranta. The interplay between environmental stochasticity and density-dependent population growth means that there is no single best method to detect the influence of environmental forcing, even when population dynamics are approximately linear. But environmental forcing will often be detectable, contrary to Kaitala and Ranta's assertions.     

Effect of vascular endothelial growth factor and testis tissue culture on spermatogenesis in bovine ectopic testis tissue xenografts

Bovine ectopic testis tissue grafting is a technique that can be used to study bovine spermatogenesis and for the production of germ cells for a variety of applications. Approximately 10% of seminiferous tubule cross sections in testis grafts contain spermatids, providing a unique tool to investigate what regulates germ cell differentiation. We hypothesized that manipulation of testis tissue grafts would increase the percentage of seminiferous tubule cross sections undergoing complete germ cell differentiation. To test this hypothesis, bovine testis tissue was treated with vascular endothelial growth factor (VEGF) at the time of grafting or explant cultured for 1 wk prior to grafting. For the VEGF experiment, 8-wk donor tissue and graft sites were treated with 1 microg of VEGF in order to increase angiogenesis at the graft site. For the testis tissue culture experiment, 4-wk-old donor testis was cultured for 1 wk prior to grafting to stimulate spermatogonial stem cell proliferation. Testis tissue grafts were removed from the mice 24 wk after grafting. VEGF treatment increased graft weight and the percentage of seminiferous tubule cross sections with elongating spermatids at the time of graft removal. Cultured testis tissue grafts were smaller and had fewer seminiferous tubules per graft. However, there was no difference in the percentage of seminiferous tubule cross sections that contained any germ cell type between groups. These data indicate for the first time that bovine testis tissue can be manipulated to better support germ cell differentiation in grafted tissue.     

Stochastic fluctuations in frequency-dependent selection: a one-locus, two-allele and two-phenotype model

Stochastic fluctuations in a simple frequency-dependent selection model with one-locus, two-alleles and two-phenotypes are investigated. The steady-state statistics of allele frequencies for an interior stable phenotypic equilibrium are shown to be similar to the stochastic fluctuations in standard evolutionary game dynamics [Tao, Y., Cressman, R., 2007. Stochastic fluctuations through intrinsic noise in evolutionary game dynamics. Bull. Math. Biol. 69, 1377-1399]. On the other hand, for an interior stable phenotypic or genotypic equilibrium, our main results show that the deterministic model cannot be used to predict the expectation of phenotypic frequency. The variance of phenotypic frequency for an interior stable genotypic equilibrium is more sensitive to the expected population size than for an interior stable phenotypic equilibrium. Furthermore, the stochastic fluctuations of allele frequency and phenotypic frequency can be considered approximately independent of each other for these genotypic equilibria, but not for phenotypic.     

Ultraviolet resonance Raman and absorption difference spectroscopy of myoglobins: titration behavior of individual tyrosine residues

The UV resonance Raman spectra of horse and sperm whale myoglobin excited at 240 nm show bands between 600 and 1700 cm-1 which derive from tyrosyl and tryptophyl residues. No significant contribution from phenylalanine and peptide backbone vibrations occurs at this excitation wavelength. We examine the pH dependence of the UV resonance Raman and UV absorption difference spectra of these myoglobins to correlate the local protein environment of the tyrosyl residues as given by the protein crystal structure to their pKa values, molar absorptivities, and Raman cross sections. Some of our pKa values for the tyrosinate residues of horse Mb differ from those of previous studies. We show that the lambda max values, the molar absorptivities, and the Raman cross sections are sensitive to the local environment of the tyrosinate residues in the protein. We relate differences in the tyrosyl absorption spectra to differences in Raman cross sections. In addition, we discuss the importance to the Raman cross sections of the local electromagnetic field enhancement due to the dielectric environment of the tyrosinate residues in the protein. This local field should scale the Raman cross sections in a way useful as a probe of the average aromatic amino acid residue environment.     

Fluctuation Induces Evolutionary Branching in a Mathematical Model of Ecosystems

Ecological systems are always subjected to various environmental fluctuations. They evolve under these fluctuations and the resulting systems are robust against them. The diversity in ecological systems is also acquired through the evolution. How do the fluctuations affect the evolutionary processes? Do the fluctuations have direct impact on the species diversity in ecological systems? In the present paper, we investigate the relation between the environmental fluctuation and the evolution of species diversity with a mathematical model of evolutionary ecology. In the model, individual organisms compete for a single restricted resource and the temporal fluctuation in the resource supply is introduced as the environmental fluctuation. The evolutionary process is represented by the mutational change of genotypes which determines their resource utilization strategies. We found that when the environmental state is switched form static to fluctuating conditions, the initial closely related population distributed around the genotype adapted for the static environment is destabilized and divided into two groups in the genotype space; i.e., the evolutionary branching is induced by the environmental fluctuation. The consequent multiple species structures is evolutionary stable at the presence of the fluctuation. We perform the evolutionary invasion analysis for the phenomena and illustrate the mechanisms of the branchings. The results indicate a novel process of increasing the species diversity via evolutionary branching, and the analysis reveals the mechanisims of the branching preocess as the response to the environmental fluctuation. The robustness of the evolutionary process is also discussed.     

Fluctuations in continuous mammalian cell bioreactors with retention.

Continuous flow bioreactors with cell retention have been increasingly used for the cultivation of mammalian cells. The potential advantages of such bioreactors are high cell concentrations and volumetric productivities. In many reported cases, these systems have shown fluctuations in cell concentrations of various frequency and magnitude. To analyze the dynamics of the fluctuations, a model-based approach is followed. Simulations showed that large fluctuations in biomass resulted in response to fluctuations in the retention ratio when the system is operated at high dilution rate and high cell retention. The dependence of cell concentration fluctuations on variations in dilution rate and retention ratio was established by a cross-correlation statistical analysis on available experimental data. The slower dynamics and the fluctuation propensity of retention systems suggest that continuous culture without retention is more convenient for kinetic studies. In all likelihood, continuous culture with retention can be stabilized by controlling both the retention ratio and the dilution rate.     

Adaptation to Stochastic Temporal Variations in Intratumoral Blood Flow: The Warburg Effect as a Bet Hedging Strategy

While most cancers promote ingrowth of host blood vessels, the resulting vascular network usually fails to develop a mature organization, resulting in abnormal vascular dynamics with stochastic variations that include slowing, cessation, and even reversal of flow. Thus, substantial spatial and temporal variations in oxygen concentration are commonly observed in most cancers. Cancer cells, like all living systems, are subject to Darwinian dynamics such that their survival and proliferation are dependent on developing optimal phenotypic adaptations to local environmental conditions. Here, we consider the environmental stresses placed on tumors subject to profound, frequent, but stochastic variations in oxygen concentration as a result of temporal variations in blood flow. While vascular fluctuations will undoubtedly affect local concentrations of a wide range of molecules including growth factors (e.g., estrogen), substrate (oxygen, glucose, etc.), and metabolites (\(\hbox {H}^{+})\), we focus on the selection forces that result solely from stochastic fluctuations in oxygen concentration. The glucose metabolism of cancer cells has been investigated for decades following observations that malignant cells ferment glucose regardless of oxygen concentration, a condition termed the Warburg effect. In contrast, normal cells cease fermentation under aerobic conditions and this physiological response is termed the Pasteur effect. Fermentation is markedly inefficient compared to cellular respiration in terms of adenosine triphosphate (ATP) production, generating just 2 ATP/glucose, whereas respiration generates 38 ATP/glucose. This inefficiency requires cancer cells to increase glycolytic flux, which subsequently increases acid production and can significantly acidify local tissue. Hence, it initially appears that cancer cells adopt a disadvantageous metabolic phenotype. Indeed, this metabolic “hallmark” of cancer is termed “energy dysregulation.” However, if cancers arise through an evolutionary optimization process, any common observed property must confer an adaptive advantage. In the present work, we investigate the hypothesis that aerobic glycolysis represents an adaptation to stochastic variations in oxygen concentration stemming from disordered intratumoral blood flow. Using mathematical models, we demonstrate that the Warburg effect evolves as a conservative metabolic bet hedging strategy in response to stochastic fluctuations of oxygen. Specifically, the Warburg effect sacrifices fitness in physoxia by diverting resources from the more efficient process of respiration, but preemptively adapts cells to hypoxia because fermentation produces ATP anaerobically. An environment with sufficiently stochastic fluctuations of oxygen will select for the bet hedging (Warburg) phenotype since it is modestly successful irrespective of oxygen concentration.