Absence Of Mix Research Articles

Promoter Recognition by Extracytoplasmic Function σ Factors: Analyzing DNA and Protein Interaction Motifs.

Extracytoplasmic function (ECF) σ factors are the largest and the most diverse group of alternative σ factors, but their mechanisms of transcription are poorly studied. This subfamily is considered to exhibit a rigid promoter structure and an absence of mixing and matching; both -35 and -10 elements are considered necessary for initiating transcription. This paradigm, however, is based on very limited data, which bias the analysis of diverse ECF σ subgroups. Here we investigate DNA and protein recognition motifs involved in ECF σ factor transcription by a computational analysis of canonical ECF subfamily members, much less studied ECF σ subgroups, and the group outliers, obtained from recently sequenced bacteriophages. The analysis identifies an extended -10 element in promoters for phage ECF σ factors; a comparison with bacterial σ factors points to a putative 6-amino-acid motif just C-terminal of domain σ2, which is responsible for the interaction with the identified extension of the -10 element. Interestingly, a similar protein motif is found C-terminal of domain σ2 in canonical ECF σ factors, at a position where it is expected to interact with a conserved motif further upstream of the -10 element. Moreover, the phiEco32 ECF σ factor lacks a recognizable -35 element and σ4 domain, which we identify in a homologous phage, 7-11, indicating that the extended -10 element can compensate for the lack of -35 element interactions. Overall, the results reveal greater flexibility in promoter recognition by ECF σ factors than previously recognized and raise the possibility that mixing and matching also apply to this group, a notion that remains to be biochemically tested. ECF σ factors are the most numerous group of alternative σ factors but have been little studied. Their promoter recognition mechanisms are obscured by the large diversity within the ECF σ factor group and the limited similarity with the well-studied housekeeping σ factors. Here we extensively compare bacterial and bacteriophage ECF σ factors and their promoters in order to infer DNA and protein recognition motifs involved in transcription initiation. We predict a more flexible promoter structure than is recognized by the current paradigm, which assumes rigidness, and propose that ECF σ promoter elements may complement (mix and match with) each other's strengths. These results warrant the refocusing of research efforts from the well-studied housekeeping σ factors toward the physiologically highly important, but insufficiently understood, alternative σ factors.

Perfect Kagomé lattices in YCu3(OH)6Cl3: a new candidate for the quantum spin liquid state

The absence of mixing between Y3+ and Cu2+ results in a more idealized Kagomé lattice in YCu3(OH)6Cl3 compared to hebertsmithite and kapellasite.

Ratner’s property and mild mixing for smooth flows on surfaces

Let${\mathcal{T}}=(T_{t}^{f})_{t\in \mathbb{R}}$be a special flow built over an IET$T:\mathbb{T}\rightarrow \mathbb{T}$of bounded type, under a roof function$f$with symmetric logarithmic singularities at a subset of discontinuities of$T$. We show that${\mathcal{T}}$satisfies the so-called switchable Ratner’s property which was introduced in Fayad and Kanigowski [On multiple mixing for a class of conservative surface flows.Invent. Math.to appear]. A consequence of this fact is that such flows are mildly mixing (before, they were only known to be weakly mixing [Ulcigrai. Weak mixing for logarithmic flows over interval exchange transformations.J. Mod. Dynam.3(2009), 35–49] and not mixing [Ulcigrai. Absence of mixing in area-preserving flows on surfaces.Ann. of Math.(2)173(2011), 1743–1778]). Thus, on each compact, connected, orientable surface of genus greater than one there exist flows that are mildly mixing and not mixing.

Experimental phase equilibria of a Mount St. Helens rhyodacite: a framework for interpreting crystallization paths in degassing silicic magmas

We present isothermal (885 °C) phase equilibrium experiments for a rhyodacite from Mount St. Helens (USA) at variable total pressure (25–457 MPa) and fluid composition (XH2Ofl = 0.6–1.0) under relatively oxidizing conditions (NNO to NNO + 3). Run products were characterized by SEM, electron microprobe, and SIMS. Experimental phase assemblages and phase chemistry are consistent with those of natural samples from Mount St. Helens from the last 4000 years. Our results emphasize the importance of pressure and melt H2O content in controlling phase proportions and compositions, showing how significant textural and compositional variability may be generated in the absence of mixing, cooling, or even decompression. Rather, variations in the bulk volatile content of magmas, and the potential for fluid migration relative to surrounding melts, mean that magmas may take varied trajectories through pressure–fluid composition space during storage, transport, and eruption. We introduce a novel method for projecting isothermal phase equilibria into CO2–H2O space (as conventionally done for melt inclusions) and use this projection to interpret petrological data from Mount St. Helens dacites. By fitting the experimental data as empirical functions of melt water content, we show how different scenarios of isothermal magma degassing (e.g., water-saturated ascent, vapor-buffered ascent, and vapor fluxing) can have quite different textural and chemical consequences. We explore how petrological data might be used to infer degassing paths of natural magmas and conclude that melt CO2 content is a much more useful parameter in this regard than melt H2O.

Solid-Phase Interaction of Depleted Uranium Tetrafluoride with Different History of Production with Silica

The characteristics and behavior of depleted uranium tetrafl uoride obtained by different methods in the process of solid-phase conversion into uranium oxides using mechano-activated crystalline and x-ray amorphous silica in oxygen-containing and inert media in the absence of mixing of the components are compared. It is found that the reactivity of depleted uranium tetrafl uoride obtained by the reduction of depleted uranium hexafl uoride by unsaturated organic halogen derivatives and hydrogen in a fl uorohydrogen fl ame is actually no different, and the solid-phase reaction products UO 2 and U 3 O 8 inherit the morphological features of the initial uranium tetrafl uoride.

Interference-induced magnetoresistance in HgTe quantum wells

We study the quantum interference correction to the conductivity in HgTe quantum wells using the Bernevig-Hughes-Zhang model. This model consists of two independent species (blocks) of massive Dirac fermions. We describe the crossover between the orthogonal and symplectic classes with increasing the carrier concentration and calculate, respectively, weak localization and antilocalization corrections in the absence of the block mixing and assuming the white-noise disorder within each block. We have calculated the interference-induced magnetoresistance in a wide interval of magnetic fields, in particular, beyond the diffusion regime. Remarkably, each Dirac cone taken separately gives a linear contribution to the low-field magnetoresistance, which turns out to be asymmetric in magnetic field $B$. We present an interpretation of this result in terms of the Berry-phase formalism. The contributions of the two blocks are related to each other by replacing $B$ to $\ensuremath{-}B$, so that the total magnetoresistance is symmetric and parabolic in the limit $B\ensuremath{\rightarrow}0$. However, in some range of parameters, field dependence turns out to be strongly nonmonotonous. We also demonstrate that block mixing gives rise to additional singular diffusive modes which do not show up in the absence of mixing.

An evaluation of alternative assessment approaches for intermixing fish populations: a case study with Great Lakes lake whitefish

AbstractWe used simulation modeling to explore how three statistical catch-at-age approaches for assessing intermixed fisheries performed in terms of assessment accuracy and management performance, under differing productivity, mixing, and harvest levels. Simulations were based on intermixing lake whitefish (Coregonus clupeaformis) populations in the upper Laurentian Great Lakes of North America. We found that with intermixing, the “separate” assessment approach, which ignored intermixing and treated mixed populations as unit stocks, produced biased estimates of spawning stock biomass (SSB); however, the “pooled” assessment approach, which lumped populations and assessed them as a single stock, was nearly unbiased in estimating SSB. The “overlap” assessment approach, which estimated the populations in one combined assessment model by incorporating actual mixing rates, was most strongly biased in estimating SSB in the absence of mixing, with bias decreasing as mixing levels increased. With high mixing levels, the overlap method had difficulty converging on unique solutions. The pooled approach provided better management performance than the separate approach with intermixing. When the overlap method could be applied, it provided the greatest SSB with little reductions in yield and the lowest inter-annual variation in yield. Relative performances of the assessment approaches were robust to assumed harvest levels.

Dynamics of hydrogen peroxide in a coral reef: Sources and sinks

AbstractThe dynamics of hydrogen peroxide (H2O2) was studied in the fringing coral reef off the coast of Eilat, Red Sea. Diurnal changes in H2O2 concentrations in the reef lagoon were typical of photochemically produced species. During the daytime H2O2 accumulated in the lagoon at low tide and exceeded open water concentrations by 100–250 nM. Elevated H2O2 decay kinetics (termed hereafter antioxidant activity) were also recorded in the lagoon at low tide. The observed antioxidant activities were high enough to moderate H2O2 accumulation in the lagoon. In pursuit of the antioxidant source, the ability of corals to release antioxidant activity to their surrounding water was examined in both natural and laboratory settings. Water collected in situ from surfaces of individual corals and next to a coral knoll contained high antioxidant activity. Incubation experiments revealed that many Red Sea corals release antioxidant activity to their external milieu. Besides serving a potential antioxidant source to the reef system, the antioxidant activity detected on coral surfaces enabled corals to lower H2O2 concentrations in their vicinity. The ability of corals to offset exogenous H2O2 was validated in incubations with Stylophora pistillata in the absence of mixing. Conversely, corals subjected to mixing in a beaker were found to release H2O2, implying that corals may act as both a sink and a source for H2O2 in the reef. This newly described ability of corals to change H2O2 dynamics by releasing both H2O2 and antioxidants may bare important implications for coral physiology and interactions with the environment.

Calcareous nannofossil paleoecology of the mid-Cretaceous Western Interior Seaway and evidence of oligotrophic surface waters during OAE2

Analysis of calcareous nannofossils, total organic carbon(TOC) values, and carbon isotope records from outcrop and drill cores in the central (Colorado and Kansas) and southern (Texas) Western Interior Basin (WIB) indicates predominantly oligotrophic surface water conditions during the late Cenomanian–Turonian Oceanic Anoxic Event 2(OAE2). High-resolution bio-chemostratigraphy of this interval allows for detailed correlation of changes in nannofossil assemblages and TOC across the WIB and aids comparison with other global records. Prior to and at the onset of OAE2, the A interval in the δ13C positive excursion identified by Pratt and Threlkeld (1984), mesotrophic to eutrophic nannofossil taxa Biscutum and Zeugrhabdotus are relatively high in abundance and foraminiferal assemblages record a high diversity “benthonic zone”. TOC sharply declines at the start of OAE2 despite evidence of high surface productivity and benthic diversity, implying that the seafloor was briefly oxygenated during a period of enhanced mixing in the expanding Western Interior Seaway. During the latter two thirds of OAE2 (intervals B and C in the excursion) TOC periodically increases, suggesting that anoxic conditions returned at the substrate, despite persistently low abundances of Biscutum and Zeugrhabdotus, implying oligotrophic surface water conditions. The divergence of these two proxies suggests a highly stratified water column in the WIB, not higher productivity, which resulted in anoxic conditions during OAE2.If productivity was not the primary cause of increased carbon burial in the WIB it is probable that increased terrestrial runoff and incursion of warm, saline Tethyan waters from the south led to salinity stratification. In the absence of mixing, warm and saline bottom waters would have been isolated from freshened Boreal currents and become stagnant, allowing for preservation of greater amounts of organic material in the substrate. Nannofossil records from Cuba, KS are an exception, and reveal relatively high productivity throughout, suggesting that occasional mixing of nutrients to the surface may have continued along the eastern margin of the central WIB.

Population dynamics during startup of thermophilic anaerobic digesters: The mixing factor

Two thermophilic digesters were inoculated with manure and started-up under mixed and stagnant conditions. The Archaea in the mixed digester (A) were dominated by hydrogenotrophic Methanobateriaceae (61%) with most of the methane being produced via syntrophic pathways. Methanosarcinales (35%) were the only acetoclastic methanogens present. Acetate dissipation seems to depend on balanced hydrogenotrophic-to-acetotrophic abundance, which in turn was statistically correlated to free ammonia levels. Relative abundance of bacterial community was associated with the loading rate. However, in the absence of mixing (digester B), the relationship between microbial composition and operating parameters was not discernible. This was attributed to the development of microenvironments where environmental conditions are significantly different from average measured parameters. The impact of microenvironments was accentuated by the use of a non-acclimated seed that lacks adequate propionate degraders. Failure to disperse the accumulated propionate, and other organics, created high concentration niches where competitive and inhibiting conditions developed and favored undesired genera, such as Halobacteria (65% in B). As a result, digester B experienced higher acid levels and lower allowable loading rate. Mixing was found necessary to dissipate potential inhibitors, and improve stability and loading capacity, particularly when a non-acclimated seed, often lacking balanced thermophilic microflora, is used.

Comparing neutron and X-ray images from NIF implosions

Directly laser driven and X-radiation driven DT filled capsules differ in the relationship between neutron and X-ray images. Shot N110217, a directly driven DT-filled glass micro-balloon provided the first neutron images at the National Ignition Facility. As seen in implosions on the Omega laser, the neutron image can be enclosed inside time integrated X-ray images. HYDRA simulations show the X-ray image is dominated by emission from the hot glass shell while the neutron image arises from the DT fuel it encloses. In the absence of mix or jetting, X-ray images of a cryogenically layered THD fuel capsule should be dominated by emission from the hydrogen rather than the cooler plastic shell that is separated from the hot core by cold DT fuel. This cool, dense DT, invisible in X-ray emission, shows itself by scattering hot core neutrons. Germanium X-ray emission spectra and Ross pair filtered X-ray energy resolved images suggest that germanium doped plastic emits in the torus shaped hot spot, probably reducing the neutron yield.

A test of the advection‐condensation model for subtropical water vapor using stable isotopologue observations from Mauna Loa Observatory, Hawaii

Subtropical humidity plays a critical role in the radiative balance of the planet, and there is a need for adequate description of the controls on water vapor distributions. This study tests whether an advection‐condensation model, combined with Rayleigh distillation, can describe observed humidity and water vapor isotope ratios of the subtropical free troposphere. A field campaign, from 9 October to 6 November, 2008, included continuous in situ measurement of water vapor stable isotope ratios at the NOAA Mauna Loa Observatory (MLO), Hawaii. Last saturation patterns for air at the MLO were determined using both Lagrangian back‐trajectory and Eulerian model techniques. Last saturation occurs primarily along midlatitude storm tracks (∼65%), and secondarily near Hawaii (∼10%) within mesoscale convective systems. Periods of lowerδDvalues at MLO correspond to extra‐tropical last saturation, while elevatedδD corresponds with saturation locations near Hawaii. To a first order, the conditions of last saturation are found to set not only the humidity but also the water vapor isotope ratio. In the absence of mixing, reconstructed q and δD values underestimate the observations. Experimental reconstructions demonstrate that variable amounts of mixing within the free troposphere and about 2% vapor influx mixing per hour from the boundary layer can explain the observed q and δD values. A last saturation model provides a reasonable description of humidity and water vapor isotope ratios of the subtropical free troposphere and results are sensitive to the treatment of mixing of air parcels last saturated in distinctly different regions of the atmosphere.

Looking for evidence of mixing in the solar wind from 0.31 to 0.98 AU

To determine the efficacy of turbulence in the solar wind, the amount of mixing of the solar wind plasma is quantified. If magnetohydrodynamic turbulence in the solar wind acts as does Navier‐Stokes turbulence, the chunk mixture of scalar quantities in the solar wind plasma should evolve with time. In particular, (1) the sizes of plasma chunks should decrease with distance from the Sun owing to the stretching and folding action of turbulence and (2) the occurrence distributions of passive‐scalar values in the plasma should narrow with distance from the Sun owing to homogenization. The evolution of the chunk mix is studied through the use of interface‐crossing statistics. Using Helios 1 and Helios 2 slow‐solar wind measurements from 0.31 to 0.98 AU, temporal jumps in the proton number density, proton specific entropy, and proton beta are used to locate plasma interfaces in the solar wind and the plasma chunk sizes are determined from the distances between the plasma interfaces. No evidence for the evolution of the chunk‐size distribution is seen, indicating an absence of mixing in the solar wind. The distribution of plasma density broadens by 11% with distance, the distribution of proton flux stays constant, while the distribution of proton specific entropy narrows by 14%; collectively the three distributions do not show clear evidence for evolution toward homogeneity, hence they do not show clear evidence for mixing. Implications of the lack of evidence for mixing in the solar wind are discussed.

Preparation and Characterization of Inclusion Complexes of Poly(dimethylsiloxane)s with γ-Cyclodextrin Without Utilizing Sonic Energy

$\upgamma -$ cyclodextrin ( $\upgamma $ -CD) formed inclusion complexes with poly(dimethylsiloxane)s (PDMS) under sonic energy and the products were crystalline compounds. In this study an inclusion complex between PDMS and $\upgamma $ -CD was synthesized at room temperature in the presence of light and mixing, in the absence of light and in the absence of mixing. These inclusion complexes (ICs) were characterized by XRD, DSC, 1H NMR, UV–Vis and FT-IR spectroscopy. The findings suggest that the reaction conditions change the crystalline structure and mole ratios of the complexes (monomer unit/ $\upgamma $ -CD) determined by 1H NMR spectroscopy for all of the ICs with $\upgamma $ -CD; which is 2 at room temperature, 1.5 under sonic energy, 3 without light and mixing. The UV–Vis results indicate an IC between $\upgamma $ -CD and PDMS.

Absence of mixing in area-preserving flows on surfaces

We prove that minimal area-preserving ows locally given by a smooth Hamiltonian on a closed surface of genus g 2 are typically (in the measure-theoretical sense) not mixing. The result is obtained by considering special ows over interval exchange transformations under roof functions with symmetric logarithmic singularities and proving absence of mixing for a full measure set of interval exchange transformations.

On Mixing Conditions for Sequences of Moving Averages

We study whether moving average sequences satisfy classical mixing conditions concerning cases of independent and dependent innovations. In particular, a class of not m-dependent moving averages is given which satisfies the strong mixing condition. Also for some classes of moving averages the absence of mixing is proved.

Evaluation of rate of cyclopentane hydrate formation in an oscillatory baffled column using laser induced fluorescence and energy balance

We report a novel method using laser induced fluorescence (LIF) for observing cyclopentane hydrate formation in an oscillatory baffled column (OBC). In LIF, a dye fluoresces in a hydrate system when induced by a laser; this highlights the areas in which hydrates are present, allowing the hydrate formation regimes to be identified and rates evaluated. Using temperature measurements of the system, the rates of hydrate formation are also determined by a thermal method. The work shows that there is a high correlation between the LIF and the thermal techniques in obtaining kinetic information on cyclopentane hydrate. The results indicate that there are possibly three mechanisms governing hydrate growth. With the absence of mixing, a film formation is observed. At high mixing intensities uniform droplet dispersion is resulted, where fluid mechanics is the controlling parameter. At low mixing conditions a combination of the two mechanisms co-exists, interfacial mechanics is thought to be the dominant factor. The trends in the rates of hydrate formation are different in each of these regimes.

Geothermal heating, diapycnal mixing and the abyssal circulation

Abstract. The dynamical role of geothermal heating in abyssal circulation is reconsidered using three independent arguments. First, we show that a uniform geothermal heat flux close to the observed average (86.4 mW m−2) supplies as much heat to near-bottom water as a diapycnal mixing rate of ~10−4 m2 s−1 – the canonical value thought to be responsible for the magnitude of the present-day abyssal circulation. This parity raises the possibility that geothermal heating could have a dynamical impact of the same order. Second, we estimate the magnitude of geothermally-induced circulation with the density-binning method (Walin, 1982), applied to the observed thermohaline structure of Levitus (1998). The method also allows to investigate the effect of realistic spatial variations of the flux obtained from heatflow measurements and classical theories of lithospheric cooling. It is found that a uniform heatflow forces a transformation of ~6 Sv at σ4=45.90, which is of the same order as current best estimates of AABW circulation. This transformation can be thought of as the geothermal circulation in the absence of mixing and is very similar for a realistic heatflow, albeit shifted towards slightly lighter density classes. Third, we use a general ocean circulation model in global configuration to perform three sets of experiments: (1) a thermally homogenous abyssal ocean with and without uniform geothermal heating; (2) a more stratified abyssal ocean subject to (i) no geothermal heating, (ii) a constant heat flux of 86.4 mW m−2, (iii) a realistic, spatially varying heat flux of identical global average; (3) experiments (i) and (iii) with enhanced vertical mixing at depth. Geothermal heating and diapycnal mixing are found to interact non-linearly through the density field, with geothermal heating eroding the deep stratification supporting a downward diffusive flux, while diapycnal mixing acts to map near-surface temperature gradients onto the bottom, thereby altering the density structure that supports a geothermal circulation. For strong vertical mixing rates, geothermal heating enhances the AABW cell by about 15% (2.5 Sv) and heats up the last 2000 m by ~0.15°C, reaching a maximum of by 0.3°C in the deep North Pacific. Prescribing a realistic spatial distribution of the heat flux acts to enhance this temperature rise at mid-depth and reduce it at great depth, producing a more modest increase in overturning than in the uniform case. In all cases, however, poleward heat transport increases by ~10% in the Southern Ocean. The three approaches converge to the conclusion that geothermal heating is an important actor of abyssal dynamics, and should no longer be neglected in oceanographic studies.

The methodology and results of determination of inorganic arsenic species in mobile fractions of tsunami deposits by a hyphenated technique of HPLC-HG-AAS

A method of extraction has been proposed for the determination of inorganic species of As(III) and As(V) in the exchangeable fraction of sediments left by the 2004 tsunami. The method combines the fractionation of solid samples with speciation analysis by high performance liquid chromatography with hydride generation and atomic absorption spectrometry (HPLC-HG-AAS). The proposed extraction liquid is a phosphate buffer of Na2HPO4 and KH2PO4, with different concentrations of phosphate ranging from 5 to 50 mmol L−1. This method has been tested for different masses of samples as well as for different times of extraction, pH, temperature, and the presence or absence of mixing. The optimum conditions of extraction have been obtained by the use of buffer (50 mmol L−1 under pH from 5.8 to 6.2) at 80°C. The new technique was applied for the analysis of tsunami deposits left on land and sampled shortly after the tsunami (2005) and after the first (2006) and second rainy seasons (2007). The obtained results show that the exchangeable fraction of tsunami deposits was enriched in arsenic in comparison to reference soil samples. The major changes after the rainy seasons were not in the total concentration of inorganic As species, but in the ratio of As(III) to As(V). More toxic As(III) was removed from the deposits or oxidised, and after two years was hardly detectable in the tsunami deposits.

Intensification of interphase mass transfer as a result of radiolysis of liquid-phase components at a gas–liquid interface

The influence of ionizing radiation on interphase transport of noncondensing gases in a liquid water-vapor-gas mixture system is investigated. A mathematical model is developed and computational experiments are performed for the irradiation of water in equilibrium with vapor, in a closed vessel with a free volume in the absence of mixing of the phases and intense heat transfer, and irradiation of a moving liquid in the bubble flow regime. It is shown that when a liquid water-vapor-gas mixture two-phase system is exposed to ionizing radiation the transition of the mixture of hydrogen and oxygen from the vapor-gas phase into the liquid phase becomes more intense. The reason for this is that they undergo an effective radiation-chemical reaction in a layer adjoining the surface separating the phases. This effect is useful for developing a water-chemical regime for future and currently operating nuclear power facilities.