Abundance of mesozooplankton in the western part of the Black Sea in summer 2005 during Phase 2: Leg1 from the GEF Project

The sampling area was extended to the Western-South area off the Black Sea coast from Kaliakra cape toward the Bosforous. Samples were collected along four transects. The whole dataset is composed of 17 samples (from 10 stations) with data of mesozooplankton species composition abundance and biomass. Sampling for zooplankton was performed from bottom up to the surface at depths depending on water column stratification and the thermocline depth. These data are organized in the "Control of eutrophication, hazardous substances and related measures for rehabilitating the Black Sea ecosystem: Phase 2: Leg I: PIMS 3065". Data Report is not published. Zooplankton samples were collected with vertical closing Juday net,diameter - 36cm, mesh size 150 µm. Tows were performed from surface down to bottom meters depths in discrete layers. Samples were preserved by a 4% formaldehyde sea water buffered solution. Sampling volume was estimated by multiplying the mouth area with the wire length. Mesozooplankton abundance: The collected material was analysed using the method of Domov (1959). Samples were brought to volume of 25-30 ml depending upon zooplankton density and mixed intensively until all organisms were distributed randomly in the sample volume. After that 5 ml of sample was taken and poured in the counting chamber which is a rectangle form for taxomomic identification and count. Large (> 1 mm body length) and not abundant species were calculated in whole sample. Counting and measuring of organisms were made in the Dimov chamber under the stereomicroscope to the lowest taxon possible. Taxonomic identification was done at the Institute of Oceanology by Kremena Stefanova using the relevant taxonomic literature (Mordukhay-Boltovskoy, F.D. (Ed.). 1968, 1969,1972). Taxon-specific abundance: The collected material was analysed using the method of Domov (1959). Samples were brought to volume of 25-30 ml depending upon zooplankton density and mixed intensively until all organisms were distributed randomly in the sample volume. After that 5 ml of sample was taken and poured in the counting chamber which is a rectangle form for taxomomic identification and count. Copepods and Cladoceras were identified and enumerated; the other mesozooplankters were identified and enumerated at higher taxonomic level (commonly named as mesozooplankton groups). Large (> 1 mm body length) and not abundant species were calculated in whole sample. Counting and measuring of organisms were made in the Dimov chamber under the stereomicroscope to the lowest taxon possible. Taxonomic identification was done at the Institute of Oceanology by Kremena Stefanova using the relevant taxonomic literature (Mordukhay-Boltovskoy, F.D. (Ed.). 1968, 1969,1972).

Thermodynamical Phase Noise in Oscillators Based on L-C Resonators

Using a new Admittance-based model for electrical noise able to handle Fluctuations and Dissipations of electrical energy, we explain the phase noise of oscillators that use feedback around L-C resonators. We show that Fluctuations produce the Line Broadening of their output spectrum around its mean frequency f0 and that the Pedestal of phase noise far from f0 comes from Dissipations modified by the feedback electronics. The charge noise power 4FkT/R C2/s that disturbs the otherwise periodic fluctuation of charge these oscillators aim to sustain in their L-C-R resonator, is what creates their phase noise proportional to Leeson’s noise figure F and to the charge noise power 4kT/R C2/s of their capacitance C that today’s modelling would consider as the current noise density in A2/Hz of their resistance R. Linked with this (A2/Hz?C2/s) equivalence, R becomes a random series in time of discrete chances to Dissipate energy in Thermal Equilibrium (TE) giving a similar series of discrete Conversions of electrical energy into heat when the resonator is out of TE due to the Signal power it handles. Therefore, phase noise reflects the way oscillators sense thermal exchanges of energy with their environment.

Thermodynamical Phase Noise in Oscillators Based on L-C Resonators (Foundations)

Using a new Admittance-based model for electrical noise able to handle Fluctuations and Dissipations of electrical energy, we explain the phase noise of oscillators that use feedback around L-C resonators. We show that Fluctuations produce the Line Broadening of their output spectrum around its mean frequency f0 and that the Pedestal of phase noise far from f0 comes from Dissipations modified by the feedback electronics. The charge noise power 4FkT/R C2/s that disturbs the otherwise periodic fluctuation of charge these oscillators aim to sustain in their L-C-R resonator, is what creates their phase noise proportional to Leeson’s noise figure F and to the charge noise power 4kT/R C2/s of their capacitance C that today’s modelling would consider as the current noise density in A2/Hz of their resistance R. Linked with this (A2/Hz?C2/s) equivalence, R becomes a random series in time of discrete chances to Dissipate energy in Thermal Equilibrium (TE) giving a similar series of discrete Conversions of electrical energy into heat when the resonator is out of TE due to the Signal power it handles. Therefore, phase noise reflects the way oscillators sense thermal exchanges of energy with their environment

Cell cycle-dependent colocalization of BARD1 and BRCA1 proteins in discrete nuclear domains

Germ-line mutations of the BRCA1 gene predispose women to early-onset breast and ovarian cancer by compromising the gene’s presumptive function as a tumor suppressor. Although the biochemical properties of BRCA1 polypeptides are not understood, their expression pattern and subcellular localization suggest a role in cell-cycle regulation. When resting cells are induced to proliferate, the steady-state levels of BRCA1 increase in late G1 and reach a maximum during S phase. Moreover, in S phase cells, BRCA1 polypeptides are hyperphosphorylated and accumulate into discrete subnuclear foci termed “BRCA1 nuclear dots.” BRCA1 associates in vivo with a structurally related protein termed BARD1. Here we show that the steady-state levels of BARD1, unlike those of BRCA1, remain relatively constant during cell cycle progression. However, immunostaining revealed that BARD1 resides within BRCA1 nuclear dots during S phase of the cell cycle, but not during the G1 phase. Nevertheless, BARD1 polypeptides are found exclusively in the nuclear fractions of both G1- and S-phase cells. Therefore, progression to S phase is accompanied by the aggregation of nuclear BARD1 polypeptides into BRCA1 nuclear dots. This cell cycle-dependent colocalization of BARD1 and BRCA1 indicates a role for BARD1 in BRCA1-mediated tumor suppression.

The importance of being discrete: Life always wins on the surface

Many systems in chemistry, biology, finance, and social sciences present emerging features that are not easy to guess from the elementary interactions of their microscopic individual components. In the past, the macroscopic behavior of such systems was modeled by assuming that the collective dynamics of microscopic components can be effectively described collectively by equations acting on spatially continuous density distributions. It turns out that, to the contrary, taking into account the actual individual/discrete character of the microscopic components of these systems is crucial for explaining their macroscopic behavior. In fact, we find that in conditions in which the continuum approach would predict the extinction of all of the population (respectively the vanishing of the invested capital or the concentration of a chemical substance, etc.), the microscopic granularity insures the emergence of macroscopic localized subpopulations with collective adaptive properties that allow their survival and development. In particular it is found that in two dimensions “life” (the localized proliferating phase) always prevails.

Monitoring S phase progression globally and locally using BrdU incorporation in TK+ yeast strains

Eukaryotic chromosome replication is initiated from numerous origins and its activation is temporally controlled by cell cycle and checkpoint mechanisms. Yeast has been very useful in defining the genetic elements required for initiation of DNA replication, but simple and precise tools to monitor S phase progression are lacking in this model organism. Here we describe a TK+ yeast strain and conditions that allow incorporation of exogenous BrdU into genomic DNA, along with protocols to detect the sites of DNA synthesis in yeast nuclei or on combed DNA molecules. S phase progression is monitored by quantification of BrdU in total yeast DNA or on individual chromosomes. Using these tools we show that yeast chromosomes replicate synchronously and that DNA synthesis occurs at discrete subnuclear foci. Analysis of BrdU signals along single DNA molecules from hydroxyurea-arrested cells reveals that replication forks stall 8–9 kb from origins that are placed 46 kb apart on average. Quantification of total BrdU incorporation suggests that 190 ‘early’ origins have fired in these cells and that late replicating territories might represent up to 40% of the yeast genome. More generally, the methods outlined here will help understand the kinetics of DNA replication in wild-type yeast and refine the phenotypes of several mutants.

Identification and characterization of an immunophilin expressed during the clonal expansion phase of adipocyte differentiation.

Mouse 3T3-L1 cells differentiate into fat-laden adipocytes in response to a cocktail of adipogenic hormones. This conversion process occurs in two discrete steps. During an early clonal expansion phase, confluent 3T3-L1 cells proliferate and express the products of the beta and delta members of the CCAAT/enhancer binding protein (C/EBP) family of transcription factors. The cells subsequently arrest mitotic growth, induce the expression of the alpha form of C/EBP, and acquire the morphology of fully differentiated adipocytes. Many of the genes induced during the terminal phase of adipocyte conversion are directly activated by C/EBP alpha, and gratuitous expression of this transcription factor is capable of catalyzing adipose conversion in a number of different cultured cell lines. The genetic program undertaken during the clonal expansion phase of 3T3-L1 differentiation, controlled in part by C/EBP beta and C/EBP delta, is less clearly understood. To study the molecular events occurring during clonal expansion, we have identified mRNAs that selectively accumulate during this phase of adipocyte conversion. One such mRNA encodes an immunophilin hereby designated FKBP51. In this report we provide the initial molecular characterization of FKBP51.

Adsorption of benzene on graphitized thermal carbon black: Reduction of the quadrupole moment in the adsorbed phase

The performance of intermolecular potential models on the adsorption of benzene on graphitized thermal carbon black at various temperatures is investigated. Two models contain only dispersive sites, whereas the other two models account explicitly for the dispersive and electrostatic sites. Using numerous data in the literature on benzene adsorption on graphitized thermal carbon black at various temperatures, we have found that the effect of surface mediation on interaction between adsorbed benzene molecules must be accounted for to describe correctly the adsorption isotherm as well as the isosteric heat. Among the two models with partial charges tested, the WSKS model of Wick et at. I that has only six dispersive sites and three discrete partial charges is better than the very expensive all-atom model of Jorgensen and Severance.(2) Adsorbed benzene molecules on graphitized thermal carbon black have a complex orientation with respect to distance from the surface and also with respect to loading. At low loadings, they adopt the parallel configuration relative to the graphene surface, whereas at higher loadings (still less than monolayer coverage) some molecules adopt a slant orientation to maximize the fluid-fluid interaction. For loadings in the multilayer region, the orientation of molecules in the first layer is influenced by the presence of molecules in the second layer. The data that are used in this article come from the work of Isirikyan and Kiselev,(3) Pierotti and Smallwood,(4) Pierce and Ewing,(5) Belyakova, Kiselev, and Kovaleva,(6) and Carrott et al.(7)

Phase separation, porous structure, and cure kinetics in aliphatic epoxy resin containing hyperbranched polyester

Thermosetting blends of an aliphatic epoxy resin and a hydroxyl-functionalized hyperbranched polymer (HBP), aliphatic hyperbranched polyester Boltorn H40, were prepared using 4,4'-diaminodiphenylmethane (DDM) as the curing agent. The phase behavior and morphology of the DDM-cured epoxy/HBP blends with HBP content up to 40 wt% were investigated by differential scanning calorimetry (DSC), dynamic mechanical analysis (DMA), and scanning electron microscopy (SEM). The cured epoxy/HBP blends are immiscible and exhibit two separate glass transitions, as revealed by DMA. The SEM observation showed that there exist two phases in the cured blends, which is an epoxy-rich phase and an HBP-rich phase, which is responsible for the two separate glass transitions. The phase morphology was observed to be dependent on the blend composition. For the blends with HBP content up to 10 wt%, discrete HBP domains are dispersed in the continuous cured epoxy matrix, whereas the cured blend with 40 wt% HBP exhibits a combined morphology of connected globules and bicominuous phase structure. Porous epoxy thermosets with continuous open structures on the order of 100-300 nm were formed after the HBP-rich phase was extracted with solvent from the cured blend with 40 wt% HBP. The DSC study showed that the curing rate is not obviously affected in the epoxy/HBP blends with HBP content up to 40 wt %. The activation energy values obtained are not remarkably changed in the blends; the addition of HBP to epoxy resin thus does not change the mechanism of cure reaction of epoxy resin with DDM. (c) 2006 Wiley Periodicals, Inc.

Transition from time-continuous systems to discrete mappings

Detailed transport studies in plasmas require the solution of the time evolution of many different initial positions of test particles in the phase space of the systems to be investigated. To reduce this amount of numerical work, one would like to replace the integration of the time-continues system with a mapping.

Lattice approach to the dynamics of phase-coded soliton trains

We address the collective dynamics of a soliton train propagating in a medium described by the nonlinear Schrödinger equation. Our approach uses the reduction of train dynamics to the discrete complex Toda chain (CTC) model for the evolution of parameters for each train constituent: such a simplification allows one to carry out an approximate analysis of the dynamics of positions and phases of individual interacting pulses. Here, we employ the CTC model to the problem which has relevance to the field of fibre optics communications where each binary digit of transmitted information is encoded via the phase difference between the two adjacent solitons. Our goal is to elucidate different scenarios of the train distortions and the subsequent information garbling caused solely by the intersoliton interactions. First, we examine how the structure of a given phase pattern affects the initial stage of the train dynamics and explain the general mechanisms for the appearance of unstable collective soliton modes. Then we further discuss the nonlinear regime concentrating on the dependence of the Lax scattering matrix on the input phase distribution; this allows one to classify typical features of the train evolution and determine the distance where the soliton escapes from its slot. In both cases, we demonstrate deep mathematical analogies with the classical theory of crystal lattice dynamics.

Neural population coding is optimized by discrete tuning curves

The sigmoidal tuning curve that maximizes the mutual information for a Poisson neuron, or population of Poisson neurons, is obtained. The optimal tuning curve is found to have a discrete structure that results in a quantization of the input signal. The number of quantization levels undergoes a hierarchy of phase transitions as the length of the coding window is varied. We postulate, using the mammalian auditory system as an example, that the presence of a subpopulation structure within a neural population is consistent with an optimal neural code.

Phase shift keyed systems based on a gain switched laser transmitter

Return-to-Zero (RZ) and Non-Return-to-Zero (NRZ) Differential Phase Shift Keyed (DPSK) systems require cheap and optimal transmitters for widespread implementation. The authors report on a gain switched Discrete Mode (DM) laser that can be employed as a cost efficient transmitter in a 10.7 Gb/s RZ DPSK system and compare its performance to that of a gain switched Distributed Feed-Back (DFB) laser. Experimental results show that the gain switched DM laser readily provides error free performance and a receiver sensitivity of -33.1 dBm in the 10.7 Gbit/s RZ DPSK system. The standard DFB laser on the other hand displays an error floor at 10(-1) in the same RZ DPSK system. The difference in performance, between the two types of gain switched transmitters, is analysed by investigating their linewidths. We also demonstrate, for the first time, the generation of a highly coherent gain switched pulse train which displays a spectral comb of approximately 13 sidebands spaced by the 10.7 GHz modulation frequency. The filtered side-bands are then employed as narrow linewidth Continuous Wave (CW) sources in a 10.7 Gb/s NRZ DPSK system.

Lattice approach to the dynamics of phase-coded soliton trains

We address the collective dynamics of a soliton train propagating in a medium described by the nonlinear Schrödinger equation. Our approach uses the reduction of train dynamics to the discrete complex Toda chain (CTC) model for the evolution of parameters for each train constituent: such a simplification allows one to carry out an approximate analysis of the dynamics of positions and phases of individual interacting pulses. Here, we employ the CTC model to the problem which has relevance to the field of fibre optics communications where each binary digit of transmitted information is encoded via the phase difference between the two adjacent solitons. Our goal is to elucidate different scenarios of the train distortions and the subsequent information garbling caused solely by the intersoliton interactions. First, we examine how the structure of a given phase pattern affects the initial stage of the train dynamics and explain the general mechanisms for the appearance of unstable collective soliton modes. Then we further discuss the nonlinear regime concentrating on the dependence of the Lax scattering matrix on the input phase distribution; this allows one to classify typical features of the train evolution and determine the distance where the soliton escapes from its slot. In both cases, we demonstrate deep mathematical analogies with the classical theory of crystal lattice dynamics.

Anomalies in stiffness and damping of a 2D discrete viscoelastic system due to negative stiffness components

The recent development of using negative stiffness inclusions to achieve extreme overall stiffness and mechanical damping of composite materials reveals a new avenue for constructing high performance materials. One of the negative stiffness sources can be obtained from phase transforming materials in the vicinity of their phase transition, as suggested by the Landau theory. To understand the underlying mechanism from a microscopic viewpoint, we theoretically analyze a 2D, nested triangular lattice cell with pre-chosen elements containing negative stiffness to demonstrate anomalies in overall stiffness and damping. Combining with current knowledge from continuum models, based on the composite theory, such as the Voigt, Reuss, and Hashin-Shtrikman model, we further explore the stability of the system with Lyapunov's indirect stability theorem. The evolution of the microstructure in terms of the discrete system is discussed. A potential application of the results presented here is to develop special thin films with unusual in-plane mechanical properties. © 2006 Elsevier B.V. All rights reserved.