Systematic Behavior Research Articles

G-Networks Based Two Layer Stochastic Modeling of Gene Regulatory Networks with Post-Translational Processes

Background: Thanks to the development of the mathematical/statistical reverse engineering and the high-throughput measuring biotechnology, lots of biologically meaningful gene-gene interaction networks have been revealed. Steady-state analysis of these systems provides an important clue to understand and to predict the systematic behaviours of the biological system. However, modeling such a complex and large-scale system is one of the challenging difficulties in systems biology. Results: We introduce a new stochastic modeling approach that can describe gene regulatory mechanisms by dividing two (DNA and protein) layers. Simple queuing system is employed to explain the DNA layer and the protein layer is modeled using G-networks which enable us to account for the post-translational protein interactions. Our method is applied to a transcription repression system and an active protein degradation system. The steadystate results suggest that the active protein degradation system is more sensitive but the transcription repression system might be more reliable than the transcription repression system. Conclusions: Our two layer stochastic model successfully describes the long-run behaviour of gene regulatory networks which consist of various mRNA/protein processes. The analytic solution of the G-networks enables us to extend our model to a large-scale system. A more reliable modeling approach could be achieved by cooperating with a real experimental study in synthetic biology.

In situ X-ray Diffraction Study of the Swelling of Montmorillonite as Affected by Exchangeable Cations and Temperature

AbstractThe swelling property of smectite is dominated by the hydration of exchangeable cations in the interlayer spacing (‘interlayer hydration’). By investigating systematically the swelling behavior of various exchangeable cations with different valences and ionic radii, the interlayer hydration of smectite was explored. The swelling behavior of Li+-, K+-, Rb+-, Cs+-, Mg2+-, Sr2+-, Ba2+-, and La3+- montmorillonites in undersaturated conditions was measured precisely over the range 50–150°C by in situ X-ray diffraction (XRD) analyses. The systematic swelling behavior of ten homocationic montmorillonites, the aforementioned eight homoionic montmorillonites, plus Na+ and Ca2+ from a previous study, and the cation hydration energies were analysed by studying the changes occurring in the basal spacing and the 001 peak width. With decreasing cation hydration energy, swelling curves (i.e. plots of basal spacing vs. relative humidity (RH)) change from continuous (Mg2+, La3+, and Ca2+) to stepwise (Sr2+, Li+, Ba2+, and Na+) to one-layer only (K+, Rb+, and Cs+). For the first two groups, the RH at the midpoint between the one- and two-layer hydration states increased as the cation hydration energy decreased. Under low RH, with increasing temperature, the basal spacings of Mg-, La-, Ca-, Sr-, Li-, and Ba-montmorillonites decreased continuously to the zero-layer hydration state, whereas Na-, K-, Rb-, and Cs-montmorillonites swelled from the zero-layer hydration state even at the lowest temperature (50°C). A decrease in the basal spacing at the same RH but at different temperatures suggests the existence of metastable states or that the layer-stacking structure changes with temperature. The systematics of the swelling behavior of various homocationic montmorillonites as functions of RH and temperature (<150°C) at 1 atmare reported here.

Iron and magnesium isotopic compositions of peridotite xenoliths from Eastern China

We present high-precision measurements of Mg and Fe isotopic compositions of olivine, orthopyroxene (opx), and clinopyroxene (cpx) for 18 lherzolite xenoliths from east central China and provide the first combined Fe and Mg isotopic study of the upper mantle. δ 56Fe in olivines varies from 0.18‰ to −0.22‰ with an average of −0.01 ± 0.18‰ (2SD, n = 18), opx from 0.24‰ to −0.22‰ with an average of 0.04 ± 0.20‰, and cpx from 0.24‰ to −0.16‰ with an average of 0.10 ± 0.19‰. δ 26Mg of olivines varies from −0.25‰ to −0.42‰ with an average of −0.34 ± 0.10‰ (2SD, n = 18), opx from −0.19‰ to −0.34‰ with an average of −0.25 ± 0.10‰, and cpx from −0.09‰ to −0.43‰ with an average of −0.24 ± 0.18‰. Although current precision (∼±0.06‰ for δ 56Fe; ±0.10‰ for δ 26Mg, 2SD) limits the ability to analytically distinguish inter-mineral isotopic fractionations, systematic behavior of inter-mineral fractionation for both Fe and Mg is statistically observed: Δ 56Fe ol–cpx = −0.10 ± 0.12‰ (2SD, n = 18); Δ 56Fe ol–opx = −0.05 ± 0.11‰; Δ 26Mg ol–opx = −0.09 ± 0.12‰; Δ 26Mg ol–cpx = −0.10 ± 0.15‰. Fe and Mg isotopic composition of bulk rocks were calculated based on the modes of olivine, opx, and cpx. The average δ 56Fe of peridotites in this study is 0.01 ± 0.17‰ (2SD, n = 18), similar to the values of chondrites but slightly lower than mid-ocean ridge basalts (MORB) and oceanic island basalts (OIB). The average δ 26Mg is −0.30 ± 0.09‰, indistinguishable from chondrites, MORB, and OIB. Our data support the conclusion that the bulk silicate Earth (BSE) has chondritic δ 56Fe and δ 26Mg. The origin of inter-mineral fractionations of Fe and Mg isotopic ratios remains debated. δ 56Fe between the main peridotite minerals shows positive linear correlations with slopes within error of unity, strongly suggesting intra-sample mineral–mineral Fe and Mg isotopic equilibrium. Because inter-mineral isotopic equilibrium should be reached earlier than major element equilibrium via chemical diffusion at mantle temperatures, Fe and Mg isotope ratios of coexisting minerals could be useful tools for justifying mineral thermometry and barometry on the basis of chemical equilibrium between minerals. Although most peridotites in this study exhibit a narrow range in δ 56Fe, the larger deviations from average δ 56Fe for three samples likely indicate changes due to metasomatic processes. Two samples show heavy δ 56Fe relative to the average and they also have high La/Yb and total Fe content, consistent with metasomatic reaction between peridotite and Fe-rich and isotopically heavy melt. The other sample has light δ 56Fe and slightly heavy δ 26Mg, which may reflect Fe–Mg inter-diffusion between peridotite and percolating melt.

Production of isomers in compound and transfer reactions with 4He ions

A well-known island of nuclear isomerism appears near A=175–180 due to the deformation alignment of single-particle orbits at high angular momentum. This sometimes results in the formation of multi-quasiparticle states with record spin that are long-lived because of “K-hindrance”, i.e. symmetry re-arrangement. Production methods and spectroscopic studies of these isomers remain a challenge for modern nuclear reaction and nuclear structure physics. In the present work, activities were produced by irradiation of 176Yb (97.6% enriched) and natLu targets with 35 MeV 4He ions from the internal beam of the U-200 cyclotron. Induced activities were analyzed by applying the methods of radiochemistry and gamma spectroscopy. Yields of the compound and nucleon-transfer reactions were measured and the isomer-to-ground state ratios were deduced. Calculated results were obtained using standard procedures to reproduce the (α, xn) cross-sections, and the systematic behavior of the nucleon-transfer yields was established. The isomer-to-ground-state ratios for direct reactions with 4He ions were examined, resulting in a new characterization of the reaction mechanism.

Synthesis, Molecular Structure, and Physical Properties of the Complexes [{PhB(pz)2(CH2SMe)}2M] (M = MnII, FeII; pz = pyrazol‐1‐yl) Containing a Novel [N,N,S]‐Heteroscorpionate Ligand

AbstractTwo transition metal complexes [L2M] {M = FeII (2), MnII (3)} of the novel [N,N,S] scorpionate ligand L = [PhB(pz)2(CH2SMe)]– have been synthesized and characterized by X‐ray crystallography, magnetic measurements, cyclic voltammetry, and various spectroscopic techniques. In the solid state, both complexes 2 and 3 possess a distorted octahedral ligand sphere, but adopt different configurations (2: cis; 3: trans). According to X‐ray diffraction data, Mössbauer spectroscopy, and SQUID measurements, compound 2 exists as low‐spin complex in the solid state at temperatures T ≤ 20 °C (μeff ≈ 0.5 μB). Upon heating, the magnetic moment μeff increases continuously to a value of 1.8 μB at 90 °C, which indicates a temperature dependent high‐spin ↔ low‐spin transition above room temp. Solutions of 2 in CDCl3 showed paramagnetic behavior at 25 °C (μeff = 3.1 μB; Evans NMR method). Cyclic voltammetry (CH2Cl2, [Bu4N][PF6]; vs. FcH/FcH+) on 2 reveals a reversible FeII/FeIII redox transition at E1/2 = –0.16 V. Density functional theory (B3LYP‐D/def2‐TZVPP//B3LYP‐D/SVP level) has been used to evaluate relative energies of the cis and trans isomers of 2 in their high‐spin and low‐spin states. Theoretical and experimental investigations have been extended to the related literature‐known homoleptic FeII complexes [{PhB(pz)3}2Fe], [{PhB(pz)(CH2SMe)2}2Fe], and [{PhB(CH2SMe)3}2Fe]. The following order of ligand‐field strengths has been established: [PhB(CH2SMe)3]– < [PhB(pz)(CH2SMe)2]– < [PhB(pz)2(CH2SMe)]– < [PhB(pz)3]–. The only significant deviation from this systematic behavior became evident for the unexpectedly low solution magnetic moment of [{PhB(CH2SMe)3}2Fe], which finds no parallel in the solid state. Computed spin‐state splittings for the entire series of complexes, however, confirm the trend in solution magnetic moments and we relate the disaccording experimental observations to the presence of a second stereoisomer in crystals of [{PhB(CH2SMe)3}2Fe] which increases the paramagnetism of solid‐state samples of this complex.

Calendar Anomalies In Kuwait Stock Exchange: Anomalous Evidence

<p class="MsoBlockText" style="margin: 0in 0.5in 0pt;"><span style="font-style: normal; mso-bidi-font-style: italic;"><span style="font-size: x-small;"><span style="font-family: Times New Roman;">Calendar anomalies such as January and weekend effects were found to exist in many international stock markets. Explanations of these anomalies are vast and so far are not robust. This paper examines these anomalies in a distinct emerging market, Kuwait stock market (KSE). With Kuwait joining the World Trade Organization treaty (WTO) and by opening its stock market to foreign investors, it becomes important to investigate stock behavior in KSE. The study finds interesting regularities in trading patterns of investors related to the weekend as well as to the day of the week. That is, there exists a weekend effect and is robust to the methodology applied. However, this effect is different from that uncovered in other developed stock markets in the sense that the first trading day (Saturday in KSE) shows positive returns and the second trading day (Sunday in KSE) shows negative returns. Other days show no systematic behavior and if detected, it is insignificant. On the other hand, January effect is not detected in KSE and returns in January are mot different from those in other months. However, returns during summer months (May-September) tend to be significantly higher than returns during other months of the year (October-April) in what is termed as summer effect. The most plausible elucidation relates to human factors as investors in KSE sense no unhealthy information about firms over the weekend and hence make their portfolio acquisition decisions in Saturdays and reverse these decisions on next day to capitalize on their marginal profits.</span></span></span></p>

Decay properties of long-lived isomers in the odd-oddN=81nucleusTb146compared to theHo148andTm150nuclei

Excited states of the $^{146}\mathrm{Tb}$ nucleus have been studied using $\ensuremath{\gamma}$-ray and electron spectroscopy in off-beam and in-beam modes following $^{112}\mathrm{Sn}$($^{40}\mathrm{Ar}$,$3n3p$) reaction with the use of the OSIRIS-II, HPGe detector array and the conversion electron spectrometer. The multipolarity of the 343 keV transition deexciting the $({7}^{\ensuremath{-}})$ level in $^{146}\mathrm{Tb}$ shows mainly an $E2$ nature and the first excited state above the 23 s isomer is assigned as a $({5}^{\ensuremath{-}},{6}^{\ensuremath{-}})$ state. The log $\mathit{ft}$ values have been deduced for 11 ${\ensuremath{\beta}}^{+}/$EC transitions populating excited states in $^{146}\mathrm{Gd}$. The systematic behavior of spins and parities of the long-lived levels at $0+x$ keV and the first excited states above them in the $N=81$ isotones $^{146}\mathrm{Tb}$, $^{148}\mathrm{Ho}$, and $^{150}\mathrm{Tm}$ is discussed.

A Proline Kink in GWALP23

GWALP23 (acetyl-GGALW5LALALALALALALW19LAGA-ethanolamide) is a proven model membrane-spanning peptide (see JACS 130, 12584) that moves “beyond” WALP family peptides by employing, for the purpose of interfacial anchoring, only one tryptophan residue on either end of a central alpha-helical core sequence. Because of its systematic behavior in lipid bilayer membranes of differing thickness (see JBC 285, 31723), we utilize GWALP23 as a framework for introducing guest residues within the transmembrane sequence. For example, we have incorporated a central proline residue to give acetyl-GGALW5LALALAP12ALALALW19LAGA-ethanolamide. We have synthesized the resulting GWALP23-P12 with selected 2H and 15N labels for solid-state NMR spectroscopy, to enable analysis of the peptide orientation and segmental tilt in oriented lipid bilayer membranes using combined (2H)-GALA and (15N/1H)-PISEMA methods. In DMPC bilayer membranes, the peptide segments N-terminal and C-terminal to proline are tilted substantially with respect to the bilayer normal, by about 34°-40° and 27°-29° (± 6°), respectively, with a proline-induced kink angle of 20°-23°. The proline places restrictions on the dynamics of both segments. As has been described previously for GWALP23, the C-terminal helix ends before Ala-21.

Least Squares Spectral Analysis for Detection of Systematic Behaviour of Digital Level Compensator

Least Squares Spectral Analysis for Detection of Systematic Behaviour of Digital Level CompensatorLevelling is the most precise technique for height difference measurements in geomatics engineering. Various systematic errors affect precise levelling observations and reduce the precision of the observed height differences. This study investigates digital levels residual compensator error and observational method for its elimination. For this purpose the levelling data, which was collected with Zeiss DiNi 12 digital levels, was analysed. There are different statistical and spectral methods that can reveal the presence of systematic errors in levelling results. In this study, the Least Squares Spectral Analysis (LSSA) method is used. The analysis confirmed that using alternating pointing method (BFFB, FBBF) instead of usual observation routine (BFFB) will eliminate the Zeiss DiNi 12 digital levels residual compensator error from section height differences and discrepancies. In this way, it does not matter using different instruments in the forward and backward section runs and the discrepancies can be used to investigate other systematic errors.

Limits of observable proton-emitting nuclei between theN=82andZ=82shell closures

The regular systematic behavior of ${Q}_{\mathrm{p}}$ values is analyzed to provide a basis for estimating $Q$ values for as yet unknown proton and $\ensuremath{\alpha}$ decays. These estimates are used in predicting partial half-lives for proton and $\ensuremath{\alpha}$-particle emission from states in Ta, Re, Ir, and Au nuclei beyond the proton drip line. The implications of these predictions for further experimental study in this region are discussed.

Symbol manipulation and rule learning in spiking neuronal networks

It has been claimed that the productivity, systematicity and compositionality of human language and thought necessitate the existence of a physical symbol system (PSS) in the brain. Recent discoveries about temporal coding suggest a novel type of neuronal implementation of a physical symbol system. Furthermore, learning classifier systems provide a plausible algorithmic basis by which symbol re-write rules could be trained to undertake behaviors exhibiting systematicity and compositionality, using a kind of natural selection of re-write rules in the brain, We show how the core operation of a learning classifier system, namely, the replication with variation of symbol re-write rules, can be implemented using spike-time dependent plasticity based supervised learning. As a whole, the aim of this paper is to integrate an algorithmic and an implementation level description of a neuronal symbol system capable of sustaining systematic and compositional behaviors. Previously proposed neuronal implementations of symbolic representations are compared with this new proposal.

Direct Behavior Rating: A Review of the Issues and Research in Its Development

The conceptual foundation for Direct Behavior Rating as a behavior assessment method is reviewed. A contemporary definition of Direct Behavior Rating is framed as combining strengths of systematic direct observation and behavior rating scales, which may result in a usable and defensible assessment tool for educators engaged in formative purposes. The rationale behind development of Direct Behavior Rating Single Item Scales as general outcome measures for school-based behavioral risk is provided. Research related to development of instrumentation and procedures for Direct Behavior Rating Single Item Scales is discussed, along with implications for future research and practice.

Systematic Trading Behavior and Cross-Sectional Stock Returns on the OMXH

Systematic Trading Behavior and Cross-Sectional Stock Returns on the OMXH

Inductive rule learning on the knowledge level

We present an application of the analytical inductive programming system Igor to learning sets of recursive rules from positive experience. We propose that this approach can be used within cognitive architectures to model regularity detection and generalization learning. Induced recursive rule sets represent the knowledge which can produce systematic and productive behavior in complex situations – that is, control knowledge for chaining actions in different, but structural similar situations. We argue, that an analytical approach which is governed by regularity detection in example experience is more plausible than generate-and-test approaches. After introducing analytical inductive programming with Igor we will give a variety of example applications from different problem solving domains. Furthermore, we demonstrate that the same generalization mechanism can be applied to rule acquisition for reasoning and natural language processing.

Modulation of headcut soil erosion in rills due to upstream sediment loads

Headcut erosion can severely accelerate soil loss in upland concentrated flows and lead to significant soil degradation in agricultural areas. Previous experimental work has demonstrated that actively migrating headcuts display systematic morphodynamic behavior and that impinging jet theory can provide an excellent analytic foundation for predicting these erosional phenomena. This research sought to examine systematically the effect of an upstream sediment load on the morphodynamics of actively migrating headcuts in upland concentrated flows. Using a specially designed experimental facility, actively migrating headcuts in packed soil beds were allowed to develop freely when subjected to concentrated, clear‐water flows similar to rills, crop furrows, and ephemeral gullies. After such headcut development and without altering the boundary conditions of the experiment, a sediment load composed of relatively coarser grained sand was introduced into the flow well upstream of the erosional feature. At relatively low upstream sediment loadings, the morphodynamics and sediment discharge of the actively migrating headcuts remained unchanged in time and space. As upstream sediment loadings increased, the size and migration rate of the headcuts decreased markedly, yet sediment discharge was not strongly affected as its sediment texture shifted from headcut‐controlled flux to sediment‐feed flux. The headcut erosion process was completely arrested when the upstream sediment feed rate exceeded a specific magnitude. Analytic arguments are used to explain the reaction time and morphodynamic response of an actively migrating headcut to this upstream sediment loading. This research shows that headcut erosion can be strongly modulated by an upstream sediment load, further complicating the prediction of soil erosion on upland areas dissected by sediment‐laden concentrated flows.

Neutron density distributions ofPb204,206,208deduced via proton elastic scattering atEp=295MeV

Cross sections and analyzing powers for polarized proton elastic scattering from $^{58}\mathrm{Ni}$, and $^{204,206,208}\mathrm{Pb}$ were measured at intermediate energy ${E}_{p}=295$ MeV. An effective relativistic Love-Franey interaction is tuned to reproduce $^{58}\mathrm{Ni}$ scattering data within the framework of the relativistic impulse approximation. The neutron densities of the lead isotopes are deduced using model-independent sum-of-Gaussians distributions. Their error envelopes are estimated by a new ${\ensuremath{\chi}}^{2}$ criterion including uncertainties associated with the reaction model. The systematic behaviors of extracted error envelopes of the neutron density distributions in $^{204,206,208}\mathrm{Pb}$ are presented. The extracted neutron and proton density distribution of $^{208}\mathrm{Pb}$ gives a neutron skin thickness of $\ensuremath{\Delta}{r}_{\mathit{np}}={0.211}_{\ensuremath{-}0.063}^{+0.054}$ fm.

Crystallization of Hen Egg White Lysozyme by Solvent Freeze‐Out: Effect of Cooling Rate on Protein Inclusion in the Ice Layer

AbstractA new technique for crystallizing proteins is introduced. Solvent removal by freezing‐out is employed to crystallize hen egg white lysozyme from aqueous salt solutions. The crystallization is carried out at moderate salt concentrations (1–10 wt % NaCl) and at pH 4.4–5.2. The required supersaturation for nucleation and crystal growth is achieved by removal of the solvent resulting in a concentration increase with respect to salt, buffer, and protein. A simple tube and shell heat exchanger is used to generate the driving force for crystallization of the ice. The enzymatic activity of the resulting crystals is measured after their dissolution and shows large variations with respect to the crystallization conditions, though no systematic behavior is observed. The effect of the cooling rate applied to the cold finger upon the protein concentration in the ice is investigated.

Experimental Determinations of the High-Pressure Crystal Structures of Ca3N2

Using synchrotron angle-dispersive X-ray diffraction and Raman spectroscopy techniques in a diamond anvil cell, we have examined the structural behaviors of the cubic (anti-C) Ca3N2 at high pressures and room temperature. Two first-order phase transformations were observed at 9.6 and 19.5 GPa accompanied by large volume collapses of 7 and 9%, respectively. The two high pressure phases were identified as monoclinic (anti-B) and hexagonal (anti-A) structures by Rietveld refinement. With the pressure derivatives fixed at 4, the bulk modulus of anti-C, anti-B, and anti-A type structures were determined as 53.1(2), 61.6(4), and 83.9(2) GPa, respectively, indicating the increased incompressibility of Ca3N2 under high pressure. The phase sequence observed in Ca3N2 is in accordance with the systematic behavior of C → B → A phase transitions occurring in most sesquioxides.

Do wheat futures returns exhibit long-range dependence?

The efficient market hypothesis, where asset prices follow a random walk and incorporate all relevant information, is often invoked in financial economics. There is some evidence however to suggest that some asset prices do not follow random walks but display long-range dependence. Such systematic behavior of past returns is of interest to traders. This article examines long-range dependence in wheat futures prices using rescaled range analysis and the Hurst exponent. Since this estimate is biased when long-range dependence is absent and its distribution is unknown, a Monte Carlo simulation approach is proposed. Results show that wheat futures prices show no evidence of long-range dependence and there are no profitable trading rules.

The evolution of electronic structure in few-layer graphene revealed by optical spectroscopy

The massless Dirac spectrum of electrons in single-layer graphene has been thoroughly studied both theoretically and experimentally. Although a subject of considerable theoretical interest, experimental investigations of the richer electronic structure of few-layer graphene (FLG) have been limited. Here we examine FLG graphene crystals with Bernal stacking of layer thicknesses N = 1,2,3,...8 prepared using the mechanical exfoliation technique. For each layer thickness N, infrared conductivity measurements over the spectral range of 0.2-1.0 eV have been performed and reveal a distinctive band structure, with different conductivity peaks present below 0.5 eV and a relatively flat spectrum at higher photon energies. The principal transitions exhibit a systematic energy-scaling behavior with N. These observations are explained within a unified zone-folding scheme that generates the electronic states for all FLG materials from that of the bulk 3D graphite crystal through imposition of appropriate boundary conditions. Using the Kubo formula, we find that the complete infrared conductivity spectra for the different FLG crystals can be reproduced reasonably well within the framework a tight-binding model.