Absence Of Direct Interactions Research Articles

Linkages between pelagic and benthic biota in a deteriorated coastal lake after restoration, Maruit, Egypt

Until the 1960s, Lake Maruit was one of Egypt’s most productive coastal brackish lakes. Continuous polluted discharge from Alexandria city resulted in long-term deterioration. The Egyptian government started a lake restoration program in 2010. Biological linkages between pelagic and benthic communities were assessed in November 2012 using parasitism and predation. This study examined ectoparasites infesting tilapia fish from 300 samples. The platyhelminth ectoparasite, Monogenea, and parasitic-copepod Ergasilus lizae were detected. Platyhelminthes parasitized Oreochromis niloticus and Oreochromis aureus, whereas the crustacean parasitized Coptodon zillii. The parasitic prevalence was low for Cichlidogyrus sp. and Ergasilus lizae. Benthic biotas were similar across basins. Fish abundance does not respond directly to benthic biotic components. Phytoplankton and benthic microalgae were not the main fish diet. Data on Halacaridae and fish clustered, indicating that either Halacaridae responds to their environment like fish or fish prey upon them because of their size. Linear correlations between pelagic, benthic biota, and parasite-infected fish indicate parasites may control their hosts. Some bioindicators indicate that stressed ecosystems differ from unstressed ecosystems. Fish species and biota abundances were low. Inconsistency in the food web and an absence of direct interactions between prey and predators are bioindicators of disturbed ecosystems. The low prevalence of ectoparasites and lack of heterogenous distribution of the various examined biota are bioindicators of habitat rehabilitation. Ongoing biomonitoring to better understand habitat rehabilitation is suggested.

Effect of Fuel Cetane Number on the Performance of Catalyst-Heating Operation in a Medium-duty Diesel Engine

<div class="section abstract"><div class="htmlview paragraph">To comply with increasingly stringent pollutant emissions regulations, diesel engine operation in a catalyst-heating mode is critical to achieve rapid light-off of exhaust aftertreatment catalysts during the first minutes of cold starting. Current approaches to catalyst-heating operation typically involve one or more late post injections to retard combustion phasing and increase exhaust temperatures. The ability to retard post injection timing(s) while maintaining acceptable pollutant emissions levels is pivotal for improved catalyst-heating calibrations. Higher fuel cetane number has been reported to enable later post injections with increased exhaust heat and decreased pollutant emissions, but the mechanism is not well understood. The purpose of this experimental and numerical simulation study is to provide further insight into the ways in which fuel cetane number affects combustion and pollutant formation in a medium-duty diesel engine.</div><div class="htmlview paragraph">Three full boiling-range diesel fuels with cetane numbers of approximately 45, 50, and 55 are employed in this study with a well-controlled set of calibrations employing a five-injection strategy. The two post injections are block-shifted to increasingly retarded timings, and the effects on exhaust heat and pollutant emissions are quantified for each fuel. For a given injection strategy calibration, increasing cetane number enables increased exhaust temperature and decreased hydrocarbon and carbon monoxide emissions for a fixed load. The increase in exhaust temperature is attributed to an increased fueling requirement to compensate for additional wall heat losses caused by earlier, more robust pilot combustion with the more reactive fuels. Formaldehyde is predicted to form in the fuel-lean periphery of the first pilot injection spray and can persist until exhaust valve opening in the absence of direct interactions with subsequent injections. Unreacted fuel-air mixture in the fuel-rich interior of the first-pilot spray is likely too cool for any significant reactions, and can persist until exhaust valve opening in the absence of turbulence/chemistry interactions and/or direct heating through interactions with subsequent injections.</div></div>

Heralded quantum-entanglement transfer based on photon absorption of nitrogen-vacancy centers in diamond

As a kind of hybrid spin system, nitrogen-vacancy (NV) centers in diamond have shown great advantages in implementing quantum registers for quantum information processing (QIP). When scaling up quantum registers to quantum networks for long-distance quantum communication and distributed quantum computation, determining how to entangle two registers in distant nodes is a basic challenge in the absence of direct interactions. In this paper, we present a scheme for entangling two distant NV centers based on the special optical absorption and emission of NV centers. In this demonstration, we transfer the entanglement information of a pair of photons to nuclear spins in NV centers and create remote NV–NV entanglement mediated by entangled photons. We then explain how to extract the entangled information from NV centers to prepare on-demand entangled photons for optical quantum information processing. The strategy of entanglement transfer between spins and photons demonstrated herein may pave the way for an NV-center-based quantum network.

A simple theory for molecular chemotaxis driven by specific binding interactions.

Recent experiments have suggested that enzymes and other small molecules chemotax toward their substrates. However, the physical forces driving this chemotaxis are currently debated. In this work, we consider a simple thermodynamic theory for molecular chemotaxis that is based on the McMillan-Mayer theory of dilute solutions and Schellman's theory for macromolecular binding. Even in the absence of direct interactions, the chemical binding equilibrium introduces a coupling term into the relevant free energy, which then reduces the chemical potential of both enzymes and their substrates. Assuming a local thermodynamic equilibrium, this binding contribution to the chemical potential generates an effective thermodynamic force that promotes chemotaxis by driving each solute toward its binding partner. Our numerical simulations demonstrate that, although small, this thermodynamic force is qualitatively consistent with several experimental studies. Thus, our study may provide additional insight into the role of the thermodynamic binding free energy for molecular chemotaxis.

Gestatten: Estimation of User's Attention in Mobile MOOCs From Eye Gaze and Gaze Gesture Tracking

The rapid proliferation of Massive Open Online Courses (MOOC) has resulted in many-fold increase in sharing the global classrooms through customized online platforms, where a student can participate in the classes through her personal devices, such as personal computers, smartphones, tablets, etc. However, in the absence of direct interactions with the students during the delivery of the lectures, it becomes difficult to judge their involvements in the classroom. In academics, the degree of student's attention can indicate whether a course is efficacious in terms of clarity and information. An automated feedback can hence be generated to enhance the utility of the course. The precision of discernment in the context of human attention is a subject of surveillance. However, visual patterns indicating the magnitude of concentration can be deciphered by analyzing the visual emphasis and the way an individual visually gesticulates, while contemplating the object of interest. In this paper, we develop a methodology called Gestsatten which captures the learner's attentiveness from his visual gesture patterns. In this approach, the learner's visual gestures are tracked along with the region of focus. We consider two aspects in this approach -- first, we do not transfer learner's video outside her device, so we apply in-device computing to protect her privacy; second, considering the fact that a majority of the learners use handheld devices like smartphones to observe the MOOC videos, we develop a lightweight approach for in-device computation. A three level estimation of learner's attention is performed based on these information. We have implemented and tested Gestatten over 48 participants from different age groups, and we observe that the proposed technique can capture the attention level of a learner with high accuracy (average absolute error rate is 8.68%), which meets her ability to learn a topic as measured through a set of cognitive tests.

Generation of heralded entanglement between distant hole spins

Quantum entanglement emerges naturally in interacting quantum systems and plays a central role in quantum information processing. Remarkably, it is possible to generate entanglement even in the absence of direct interactions: provided that which path information is erased, weak spin-state dependent light scattering can be used to project two distant spins onto a maximally entangled state upon detection of a single photon. Even though this approach is necessarily probabilistic, successful generation of entanglement is heralded by the photon detection event. Here, we demonstrate heralded quantum entanglement of two quantum dot heavy-hole spins separated by 5 meters using single-photon interference. Thanks to the long coherence time of hole spins and the efficient spin-photon interface provided by self-assembled quantum dots embedded in leaky microcavity structures, we generate 2300 entangled spin pairs per second, which represents an improvement approaching three orders of magnitude as compared to prior experiments. Delayed two-photon interference scheme we developed allows for efficient verification of quantum correlations. Our results lay the groundwork for the realization of quantum networks in semiconductor nanostructures. Combined with schemes for transferring quantum information to a long-lived memory qubit, fast entanglement generation we demonstrate could also impact quantum repeater architectures.

No Evidence for Activity Adjustment in Response to Increased Density in Daphnia magna.

Increased population density may lead to a decrease in energy available for growth and reproduction via effects on the activity level of individuals. Whilst this may be of particular importance for organisms that compete for defendable resources and/or have a high frequency of social interactions, it is less obvious how individual activity should covary with population density when food resources are not defendable or direct interactions among individuals are negligible. Based on observations that there is a general negative relationship between population density and metabolism it has been suggested that organisms actively reduce activity under increased density to accommodate an expected decrease in food availability. However, in the absence of direct activity measurements the validity of this hypothesis is unclear. Here we test for such anticipatory adjustments of activity levels in the planktonic cladoceran Daphnia magna Straus, a filter feeder whose food resources are not defendable, meaning that density responses can be evaluated in the absence of direct interactions. We tested for changes in activity in response to two separate density cues, one being the direct physical and visual stimuli resulting from being in the vicinity of conspecifics (‘direct density experiment’), and the other being the detection of olfactory cues in their environment (‘olfactory cue experiment’). Ten genetically distinct clones were used to evaluate the potential for genetic variation in these responses. Our measures of activity were highly repeatable, and there was significant variation in activity among clones. Furthermore, this clonal variation was consistent in the ‘direct density’ and ‘olfactory cue’ experiments. The estimated evolvability of the trait (1.3–3.2%) was within the range typically observed in behavioural traits. However, there was no indication that the activity level of individuals respond to population density, either directly to actual density or to olfactory cues representing high density. In this case, the energetic influence of density on population dynamics is sufficiently described by effects on per capita resource availability.

Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arrays

Heterochromatin protein 1 (HP1) participates in establishing and maintaining heterochromatin via its histone-modification-dependent chromatin interactions. In recent papers HP1 binding to nucleosomal arrays was measured in vitro and interpreted in terms of nearest-neighbour cooperative binding. This mode of chromatin interaction could lead to the spreading of HP1 along the nucleosome chain. Here, we reanalysed previous data by representing the nucleosome chain as a 1D binding lattice and showed how the experimental HP1 binding isotherms can be explained by a simpler model without cooperative interactions between neighboring HP1 dimers. Based on these calculations and spatial models of dinucleosomes and nucleosome chains, we propose that binding stoichiometry depends on the nucleosome repeat length (NRL) rather than protein interactions between HP1 dimers. According to our calculations, more open nucleosome arrays with long DNA linkers are characterized by a larger number of binding sites in comparison to chains with a short NRL. Furthermore, we demonstrate by Monte Carlo simulations that the NRL dependent folding of the nucleosome chain can induce allosteric changes of HP1 binding sites. Thus, HP1 chromatin interactions can be modulated by the change of binding stoichiometry and the type of binding to condensed (methylated) and non-condensed (unmethylated) nucleosome arrays in the absence of direct interactions between HP1 dimers.

Signaling at Crossroads: The Dialogue between PDEs and PKA is Spoken in Multiple Languages

Signaling at Crossroads: The Dialogue between PDEs and PKA is Spoken in Multiple Languages

Leptophilic dark matter withZ′interactions

We consider a scenario where dark matter (DM) interacts exclusively with Standard Model (SM) leptons at tree level. Due to the absence of tree-level couplings to quarks, the constraints on leptophilic dark matter arising from direct detection and hadron collider experiments are weaker than those for a generic WIMP. We study a simple model in which interactions of DM with SM leptons are mediated by a leptophilic $Z'$ boson, and determine constraints on this scenario arising from relic density, direct detection, and other experiments. We then determine current LHC limits and project the future discovery reach. We show that, despite the absence of direct interactions with quarks, this scenario can be strongly constrained.

Dynamic density functional theory with hydrodynamic interactions and fluctuations.

We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, "Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps," Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absence of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, "A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law," J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions.

A proposed voltage dependence of the ionic strength of a confined electrolyte based on a grand canonical ensemble model

Electrodes with highly porous morphologies are of great technological interest, as their exceptionally high specific surface areas make them ideal for use in capacitors, battery electrodes and electrochemical sensors. There is a large body of research focusing on the structure of confined electrolytes in these systems, but the majority of these studies focus on cases where the length scale of the porous domain is equal to or less than the Debye screening length of the electrolyte. In this work, we use a thermodynamic model to consider the structure of electrolytes in mesoscale domains, where the pore dimensions are significantly larger than the Debye screening length. In this limit, the interface is screened by the electrochemical double layer and the enclosed volume primarily consists of an electroneutral ‘bulk liquid’ domain. Despite the absence of direct interactions between ions in the bulk domain and the charged interface, we show that minimization of the free energy of the system leads to a reduction in the ionic strength of the electrolyte within the bulk liquid domain of the pore. Based on our model studies, we anticipate that this depletion will apply for porous domains with widths of the order of 50–200 nm even under mild experimental conditions and low applied voltages. The results imply relationships between electrolyte strength, surface morphology and applied voltage that may be important in device design.

TRAF Binding Is Required for a Distinct Subset of In Vivo B Cell Functions of the Oncoprotein LMP1

EBV-encoded latent membrane protein 1 (LMP1) is important for EBV contributions to B cell transformation and many EBV-associated malignancies, as well as EBV-mediated exacerbation of autoimmunity. LMP1 functionally mimics TNF receptor (TNFR) superfamily member CD40, but LMP1 signals and downstream effects are amplified and sustained compared with CD40. CD40 and LMP1 both use TNFR-associated factor (TRAF) adaptor proteins, but in distinct ways. LMP1 functions require TRAFs 3, 5, and 6, which interact with LMP1. However, TRAFs can also contribute to signaling in the absence of direct interactions with cell surface receptors, so we investigated whether their roles in LMP1 in vivo functions require direct association. We show in this study that the LMP1 TRAF binding site was required for LMP1-mediated autoantibody production, the germinal center response to immunization, and optimal production of several isotypes of Ig, but not LMP1-dependent enlargement of secondary lymphoid organs in transgenic mice. Thus, LMP1 in vivo effects can be mediated via both TRAF binding-dependent and -independent pathways. Together with our previous findings, these results indicate that TRAF-dependent receptor functions may not always require TRAF-receptor binding. These data suggest that TRAF-mediated signaling pathways, such as those of LMP1, may be more diverse than previously appreciated. This finding has significant implications for receptor and TRAF-targeted therapies.

Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase: SUBSTRATE CLEAVAGE, ENOLATE STABILIZATION, AND SUBSTRATE SPECIFICITY

Crystal structures of divalent metal-dependent pyruvate aldolase, HpaI, in complex with substrate and cleavage products were determined to 1.8-2.0 Å resolution. The enzyme·substrate complex with 4-hydroxy-2-ketoheptane-1,7-dioate indicates that water molecule W2 bound to the divalent metal ion initiates C3-C4 bond cleavage. The binding mode of the aldehyde donor delineated a solvent-filled capacious binding locus lined with predominantly hydrophobic residues. The absence of direct interactions with the aldehyde aliphatic carbons accounts for the broad specificity and lack of stereospecific control by the enzyme. Enzymatic complex structures formed with keto acceptors, pyruvate, and 2-ketobutyrate revealed bidentate interaction with the divalent metal ion by C1-carboxyl and C2-carbonyl oxygens and water molecule W4 that is within close contact of the C3 carbon. Arg(70) assumes a multivalent role through its guanidinium moiety interacting with all active site enzymatic species: C2 oxygen in substrate, pyruvate, and ketobutyrate; substrate C4 hydroxyl; aldehyde C1 oxygen; and W4. The multiple interactions made by Arg(70) stabilize the negatively charged C4 oxygen following proton abstraction, the aldehyde alignment in aldol condensation, and the pyruvate enolate upon aldol cleavage as well as support proton exchange at C3. This role is corroborated by loss of aldol cleavage ability and pyruvate C3 proton exchange activity and by a 730-fold increase in the dissociation constant toward the pyruvate enolate analog oxalate in the R70A mutant. Based on the crystal structures, a mechanism is proposed involving the two enzyme-bound water molecules, W2 and W4, in acid/base catalysis that facilitates reversible aldol cleavage. The same reaction mechanism promotes decarboxylation of oxaloacetate.

Sol gel transitions during acid gelation of milk containing modified waxy maize starch. Differences between chemical and bacterial acidification measured using rheological and spectroscopic techniques

Modified waxy maize starch (1%, w/v) was added to skim milk and the mixtures were heated and homogenized. Acidification was conducted at 40 °C, using either glucono-δ-lactone (GDL) or a commercial starter culture. The physico-chemical changes occurring during acidification were monitored using small oscillatory rheology, diffusing wave spectroscopy and ultrasound spectroscopy. A similar gelling behaviour was noted for GDL and bacterial-induced gels; however, a difference was noted in the values of storage modulus (G′). The presence of starch did not seem to affect the development of the gel structure, nor the mobility and positional correlations of the casein micelles during acidification. On the other hand, starch increased the final storage modulus, G′ of the acid milk gels. These results indicate the absence of direct interactions between micelles and the modified starch granules.

Modeling the gel electrophoresis of short duplex DNA by Brownian dynamics: cubic gel lattice with direct interaction.

The technique of Brownian dynamics is used to model the electrophoretic mobility of spherical and rod-like particles in a three-dimensional cubic gel lattice. In addition to excluded volume interactions between the migrating particle and the gel, direct interactions are also included. The methodology is first applied to spherical particles in the absence of direct interactions and the resulting mobilities are shown to agree with independent studies. The methodology is then applied to rod-like models of short duplex DNA fragments 10-50 base pairs in length. In the absence of direct interactions between gel and DNA, calculated mobilities show a much weaker dependence on gel concentration than observed in experiments of DNA in Tris-acetate buffer and polyacrylamide gels. When an attractive interaction between gel and DNA of approximately -0.3 k(B)T per base pair at contact is included, good agreement between calculated and experimental mobilities is achieved.

Effect of Sugars on Headgroup Mobility in Freeze-Dried Dipalmitoylphosphatidylcholine Bilayers: Solid-State 31P NMR and FTIR Studies

The effect of the carbohydrates trehalose, glucose, and hydroxyethyl starch (HES) on the motional properties of the phosphate headgroup of freeze-dried dipalmitoylphosphatidylcholine (DPPC) liposomes was studied by means of 31P NMR, Fourier transform infrared spectroscopy (FTIR), and differential scanning calorimetry (DSC). The results show that trehalose, which is a strong glass former ( T g = 115°C), elevates the onset of the lipid headgroup rotations and preserves some rotational mobility of the phosphate headgroups after cooling from the liquid-crystalline state. Glucose ( T g = 30°C), a very effective depressant of the phase transition temperature of freeze-dried DPPC, markedly elevates the initiation of the temperature of headgroup rotations. On the other hand, the monosaccharide does not preserve the headgroup disordering when cooled from the liquid-crystalline state. These effects are consistent with formation of hydrogen bonds between the OH groups of the sugar and the polar headgroups of DPPC. They show, however, that hydrogen bonding is not sufficient for preservation of the dynamic properties of freeze-dried DPPC. HES, although a very good glass former ( T g > 110°C), does not depress the phase transition temperature and affects only slightly the rotational properties of freeze-dried DPPC. This lack of effect of HES is associated with the absence of direct interactions with the lipid phosphates, as evidenced by the FTIR results. These data show that vitrification of the additive is not sufficient to affect the dynamic properties of dried DPPC.

Structural aspects and evolutionary implications of the recognition between tRNAs and aminoacyl-tRNA synthetases

Recent structural discoveries in the fields of tRNAs and aminoacyl-tRNA synthetases (aaRS), such as the existence of two classes of aminoacyl tRNA synthetases, the modular character of aaRS with domains homologous to other existing proteins, and the absence of direct interactions between the catalytic site containing the aminoacid binding pocket and the anticodon point the way to an understanding of the origin of the genetic code.

Effects of interactions with older males on behavior and reproductive development in first-year male red-winged blackbirds Agelaius phoeniceus.

Male red-winged blackbirds Agelaius phoeniceus in their first year normally do not establish territories or breed. To investigate the possibility that interactions with older males might inhibit reproductive development of young males, we compared the behavior of first-year males in the presence and absence of older males. For three months during the first half of the breeding season, we studied mixed- and single-age groups of three males in standardized outdoor aviaries: two groups of three first-year males (FFF groups), two groups of one older and two first-year males (AFF groups), and one group of three older males (AAA group). In all groups one male established clear dominance, invariably the older male in AFF groups. The dominant male in FFF groups displaced subordinates less frequently than did the dominant older male in AFF groups early in the season, but equally frequently later. In May the largest testies weights of males in FFF groups were significantly lower than those of dominant older males in AFF groups. First-year males in the absence of direct interactions with older males can achieve levels of aggressive behavior comparable to those of a dominant older male in similar social environments but the seasonal development of their aggressive behavior occurs later and their testes in May are smaller than dominant adults'. This delay in the seasonal development of aggressive behavior in first-year males, independent of the immediate social environment, suggests that the age-dependent territoriality of males in this species is not strongly regulated by effects of older males on the development of younger males.

Spectral considerations in two-dimensional incompressible flow

The spectrum of two-dimensional incompressible motion is studied with particular attention paid to non-linear interactions. Conditions for the absence of direct interactions between high and low wave numbers are developed. The non-linear tendency of an initial spectrum is computed to illustrate these points. The importance of the angular distribution of the spectrum is illustrated in a spectral stability problem for an isotropic stream function spectrum. Finally, a special inertial equilibrium spectrum is derived exhibiting the properties of an energy barrier in wave number space. DOI: 10.1111/j.2153-3490.1962.tb00126.x