Diffusion of two molecular species in a crowded environment: theory and experiments.

Diffusion of a two component fluid is studied in the framework of differential equations, but where these equations are systematically derived from a well-defined microscopic model. The model has a finite carrying capacity imposed upon it at the mesoscopic level and this is shown to lead to nonlinear cross diffusion terms that modify the conventional Fickean picture. After reviewing the derivation of the model, the experiments carried out to test the model are described. It is found that it can adequately explain the dynamics of two dense ink drops simultaneously evolving in a container filled with water. The experiment shows that molecular crowding results in the formation of a dynamical barrier that prevents the mixing of the drops. This phenomenon is successfully captured by the model. This suggests that the proposed model can be justifiably viewed as a generalization of standard diffusion to a multispecies setting, where crowding and steric interferences are taken into account.

A case report of dyshidrotic bullous pemphigoid developing after partial anterior circulation ischaemic stroke.

Dyshidrotic bullous pemphigoid is a rare form of bullous pemphigoid that affects predominantly a patient's hands and feet. It has been associated in the literature with neurologic, psychiatric and cerebrovascular disorders. We present an interesting case of this rare skin condition developing in a patient following a diagnosis of partial anterior circulation stroke.

First pregnancies in jennies with vitrified donkey semen using a new warming method.

Sperm vitrification has been recently developed, but fertility trials have not been performed yet in equine species. In this study, a new warming technique for vitrified donkey semen was developed and the uterine inflammatory response and fertility were compared to conventional freezing. In Experiment 1, sperm was vitrified in straws and warmed in 3 ml of extender or in a water bath at: 37 °C/30 s; 43 °C/10 s; and 60 °C/5 s. Sperm motility, plasma and acrosome membranes and DNA integrity were compared between treatments. In Experiment 2, jennies were inseminated twice (500 × 106 sperm) in the uterine body either with vitrified or frozen semen (2 cycles/jenny). Pregnancy rates and the uterine inflammatory response (polymorphonuclear neutrophil concentration; PMN) were evaluated after artificial insemination (AI). No differences between warming in extender/water bath were found and 43 °C/10 s was better than lower temperatures in terms of total (53.8 ±â€¯13.2%) and progressive sperm motility (41.4 ±â€¯11.4%). No differences in PMN concentration (×103 PMN/ml) were found between vitrified (276.8 ±â€¯171.6) or frozen (309.7 ±â€¯250.7) semen after AI. However, PMN decreased faster (P < 0.05) using vitrified semen. Pregnancy rates were greater for vitrified (22%) than frozen semen (10%) but not statistically different. In conclusion, donkey sperm vitrified in straws could be directly warmed in a water bath at 43 °C/10 s, reducing the uterine inflammatory response obtained after AI and promoting positive pregnancy outcomes. These findings confirm the possibility to use vitrified semen as an alternative for AI in jennies.

Negative specific heat in the canonical statistical ensemble.

According to thermodynamics, the specific heat of Boltzmannian short-range interacting systems is a positive quantity. Less intuitive properties are instead displayed by systems characterized by long-range interactions. In that case, the sign of specific heat depends on the considered statistical ensemble: Negative specific heat can be found in isolated systems, which are studied in the framework of the microcanonical ensemble; on the other hand, it is generally recognized that a positive specific heat should always be measured in systems in contact with a thermal bath, for which the canonical ensemble is the appropriate one. We demonstrate that the latter assumption is not generally true: One can, in principle, measure negative specific heat also in the canonical ensemble if the system under scrutiny is non-Boltzmannian and/or out-of-equilibrium.

Progressive pearl necklace collapse mechanism for cerato-ulmin aggregation film.

Cerato-ulmin (CU) is a fungal toxin class II hydrophobin, involved in Dutch elm disease. The formation of hydrophobin films at the air-water interface is a key mechanism which plays a role of paramount importance at different stages of the fungal development. We present a study on the precursor stages of growth towards the self-assembly aggregation film of CU. Atomic force microscopy images of CU dropped on mica substrates indicate that the system self-organizes in almost one-dimensional pearl-necklace-like chains, which subsequently collapse and possibly merge to form extended and rather compact planar films. We propose and verify a simple model to describe the self-aggregation mechanism in terms of progressive thickening of the pearl chains due to the successive merging and collapse of the elementary constitutive units.

Cryopreservation of donkey embryos: Comparison of embryo survival rate after in vitro culture between conventional freezing and vitrification.

Embryo cryopreservation ensures that genetic biodiversity is preserved over time. This study evaluates the survival of donkey embryos subjected to slow freezing and vitrification after thawing and in vitro culture. Seven-day-old in vivo produced donkey embryos were subjected to slow freezing (SF, N = 14) or vitrification (VIT, N = 22). After one year of cryopreservation, embryos were warmed, washed and placed in incubation for in vitro culture (IVC). In order to assess the embryo viability, the quality grade and developmental stage were recorded after thawing and after 24 and 48 h of IVC. Eleven embryos (SF = 4 and VIT = 7) were incubated under a time-lapse camera, for up to 68 h, in order to determine the area and growth. The survival rate was not influenced by the procedure but by the developmental stage: after 48 h of IVC blastocyst survival rate (1/8, 12.5%) was significantly lower compared to both morulas (8/12, 66.7%) and early blastocysts (11/16, 68.7%) (P < 0.05). Embryo diameter class at recovery did not significantly influence the survival rate. In terms of the embryos that were judged to be alive after 48 h of IVC, quality grade 1 was observed in 7/8 (88%) and 4/12 (33%) of the SF and VIT embryos, respectively (P < 0.05). After time-lapse analysis, the IVC embryo area as well as growth percentage were statistically higher in the SF than the VIT embryos (P < 0.05). In conclusion, no difference in survival rates was found between the two cryopreservation procedures, although embryo quality was more negatively affected by vitrification.

A stochastic reaction scheme for drug/metabolite interaction.

We present a simplified stochastic model to investigate the mechanisms of action of tramadol, a centrally acting analgesic, used for treating pain. The model accounts for the process of metabolization through the cytochrome CYP2D6 and the interactions between molecules and target receptors. The proposed formulation is stochastic in nature and allows to speculate on the role of finite-size fluctuations. Analytically, the master equation, governing the process under scrutiny, is derived and studied in the mean-field limit. The analysis of the associated asymptotic behavior proves interesting for its potential medical implications. The analysis of fluctuations is carried on via the van Kampen expansion. Numerical simulations are also performed to confirm the adequacy of our theoretical prediction.

Out-of-equilibrium phase re-entrance(s) in long-range interacting systems.

Systems with long-range interactions display a short-time relaxation toward quasistationary states (QSSs) whose lifetime increases with system size. The application of Lynden-Bell's theory of "violent relaxation" to the Hamiltonian Mean Field model leads to the prediction of out-of-equilibrium first- and second-order phase transitions between homogeneous (zero magnetization) and inhomogeneous (nonzero magnetization) QSSs, as well as an interesting phenomenon of phase re-entrances. We compare these theoretical predictions with direct N -body numerical simulations. We confirm the existence of phase re-entrance in the typical parameter range predicted from Lynden-Bell's theory, but also show that the picture is more complicated than initially thought. In particular, we exhibit the existence of secondary re-entrant phases: we find unmagnetized states in the theoretically magnetized region as well as persisting magnetized states in the theoretically unmagnetized region. We also report the existence of a region with negative specific heats for QSSs both in the numerical and analytical caloric curves.

New simplified protocols for timed artificial insemination (TAI) in milk-producing donkeys.

This study compared the outcome of two new timed artificial insemination (TAI) protocols in a milk-producing donkey farm. Ninety Amiata jennies were inseminated at the moment of ovulation induction with hCG, with fresh-transported semen that had been stored at room temperature from 3 up to 6 h, with an approximate average storage time of 4 h and a half. In both protocols, on Day 0 jennies were treated with alfaprostol (PGF2α), and on Day 7 they were checked by ultrasound (US) and, if in estrus, they were treated in order to induce ovulation and were then artificially inseminated. In the slow-short TAI protocol, jennies not already inseminated were treated again with PGF2α at Day 14. On day 21 US was repeated and estrus jennies were induced to ovulate and inseminated. In the fast-long TAI protocol, US was performed once a week in jennies not already inseminated and if found in estrus, they were induced to ovulate and inseminated, while those not in estrus were treated again with PGF2α. This protocol was repeated for up to nine weeks. The rates of inseminated/treated, pregnant/inseminated and pregnant/treated jennies were 76%, 56% and 43% for the slow-short TAI protocol and 94%, 47% and 44% for the fast-long TAI protocol. The age class and the lactation status of the jennies had no significant effect on synchronization success or final pregnancy rate. This study demonstrates that it is possible to achieve reasonable pregnancy rates through simplified TAI protocols in jennies, reducing animal handling to a minimum.

Modelling the pharmacokinetics of tramadol: on the difference between CYP2D6 extensive and poor metabolizers.

In this work we propose a mathematical model for the kinetics of tramadol, a synthetic opioid commonly used for treating moderate to severe pain. This novel theoretical framework could result in an objective criterion on how to adjust the assigned dose, depending on the genetic polymorphisms of CYP2D6. The model describes the coupled dynamics of tramadol and the metabolite O-desmethyltramadol. The effect of diffusion of the drug in the blood is here accounted for and we further hypothesize the existence of a time delay in the process of chemical translation from tramadol into metabolites. The system of coupled differential equations is solved numerically and the free parameters adjusted so to interpolate the experimental time series for the intravenous injection setting. Theoretical curves are shown to reproduce correctly the experimental profiles obtained from clinical trials. This enables in turn to extract an estimate of the metabolization rate. A difference in metabolization rate between CYP2D6 poor and extensive metabolizers is also found, and the stereoselectivity in the O-demethylation of tramadol highlighted. Our results allow one to quantify the dose of (+)-tramadol (resp. (-)-tramadol) administered to poor or extensive metabolizers, if the same effect is sought. The latter is here quantified through the blood concentration of (+)-metabolites (resp. (-)-metabolites).

Dynamics of antibodies from cryo-electron tomography.

The issue of protein dynamics and its implications in the biological function of proteins are arousing greater and greater interest in molecular biology. In cryo-electron tomography experiments one takes several snapshots of a given biological macromolecule. In principle, a large enough collection of snapshots may then be used to calculate its equilibrium configuration in terms of the experimentally accessible degrees of freedom, and hence estimate its potential energy. Consequently, one could analyze the biological functions of biomolecules by directly accessing their dynamics. In this work, we analyze the results of cryo-electron tomography experiments on monoclonal murine IgG2a antibodies. With the aid of a novel software for image processing, we measure the equilibrium distribution of the angles which describe the configuration of the molecule. This helps us shed some critical light on recent results from X-ray crystallography. We then build a model of the antibody dynamics, which enables us to use the measured angular distribution in order to derive an explicit expression of the IgG potential energy. Finally, as a preliminary application of our results, we investigate the dynamical effects in the rate of formation of the antigen-antibody encounter complex. In particular, we suggest that the dynamics of antibodies operates in the direction of decreasing anticooperativity of the two antigen binding arms.

Dynamics and stabilization of the Elettra storage-ring free-electron laser.

The ultimate performance of a storage-ring free-electron laser in terms of light stability and extracted power depends on the possibility of simultaneously controlling the electron-beam and laser dynamics. As a preliminary requirement, the level of longitudinal and transverse electron-beam stability must be high enough to guarantee the laser start-up and growth. This is usually obtained by means of dedicated feedback systems. Once such a requirement is satisfied, the possibility of establishing and maintaining a continuous-wave operation mode finally resides in a deep understanding of the strongly coupled laser-electrons dynamics. For this purpose, we have developed a simple theoretical model which has been proved to be able to provide insight into the evolution of the laser intensity. In this framework, we have also proposed the possibility of utilizing a derivative closed-loop feedback to create or enlarge the region of stable signal. A feedback of this type has been implemented on the Elettra storage-ring free-electron laser. The obtained results, which fully confirm our predictions, are discussed in this paper.

One-dimensional toy model of globular clusters.

We introduce a one-dimensional toy model of globular clusters. The model is a version of the well-known gravitational sheets system, where we also take into account mass and energy loss by evaporation of stars at the boundaries. Numerical integration by the "exact" event-driven dynamics is performed, for initial uniform density and Gaussian random velocities. Two distinct quasistationary asymptotic regimes are attained, depending on the initial energy of the system. We guess the forms of the density and velocity profiles that fit numerical data extremely well and allow us to perform an independent calculation of the self-consistent gravitational potential. Some power laws for the asymptotic number of stars and for the collision times are suggested.

Documenting for patient-focused care.

Hospitals across the country are rethinking the way health care is delivered. With a shift from inpatient to outpatient care, there is an effort to deliver quality, "patient-focused care" in the hospital setting. Multidisciplines have embarked in cross-training to provide immediate services at the bedside. The premise of "nursing" documentation is no longer feasible in multicaregiver environments. One hospital's adaptation to documentation methods to meet the needs of a patient-focused system is described.

Abundance of regular orbits and nonequilibrium phase transitions in the thermodynamic limit for long-range systems.

We investigate the dynamics of many-body long-range interacting systems, taking the Hamiltonian mean-field model as a case study. We show that regular trajectories, associated with invariant tori of the single-particle dynamics, prevail. The presence of such tori provides a dynamical interpretation of the emergence of long-lasting out-of-equilibrium regimes observed generically in long-range systems. This is alternative to a previous statistical mechanics approach to such phenomena which was based on a maximum entropy principle. Previously detected out-of-equilibrium phase transitions are also reinterpreted within this framework.

Resolving the geometry of biomolecules imaged by cryo electron tomography.

In this paper, we describe two methods for computerized analysis of cryo electron tomography reconstructions of biomolecules. Both methods aim at quantifying the degree of structural flexibility of macromolecules and eventually resolving the inner dynamics through automatized protocols. The first method performs a Brownian dynamics evolution of a simplified molecular model into a fictitious force field generated by the tomograms. This procedure enables us to dock the simplified model into the experimental profiles. The second uses a fuzzy framework to delineate the subparts of the proteins and subsequently determine their interdomain relations. The two methods are discussed and their complementarities highlighted with reference to the case of the immunoglobulin antibody. Both artificial maps, constructed from immunoglobulin G entries in the Protein Data Bank and real tomograms are analyzed. Robustness issues and agreement with previously reported measurements are discussed.

Atomic force microscopy images suggest aggregation mechanism in cerato-platanin.

Cerato-platanin (CP), the first member of the "cerato-platanin family", is a moderately hydrophobic protein produced by Ceratocystis fimbriata, the causal agent of a severe plant disease called "canker stain". The protein is localized in the cell wall of the fungus and it seems to be involved in the host-plane interaction and induces both cell necrosis and phytoalexin synthesis (one of the first plant defence-related events). Recently, it has been determined that CP, like other fungal surface protein, is able to self assemble in vitro. In this paper we characterize the aggregates of CP by Atomic Force Microscopy (AFM) images. We observe that CP tends to form early annular-shaped oligomers that seem to constitute the fundamental bricks of a hierarchical aggregation process, eventually resulting in large macrofibrillar assemblies. A simple model, based on the hypothesis that the aggregation is energetically favourable when the exposed surface is reduced, is compatible with the measured aggregates' shape and size. The proposed model can help to understand the mechanism by which CP and many other fungal surface proteins exert their effects.

The social parasite wasp Polistes atrimandibularis does not form host races.

Parasites that exploit the parental behaviour of several host species may be selected to form distinct host-specific genetic lineages. This process is well documented in bird brood parasites, but not in insect social parasites. Polistes atrimandibularis is the only paper-wasp social parasite known to exploit four host species. It does not form genetically distinct host races according to analyses based on microsatellite loci. Also, there were no size-matching between parasites and host species. Instead, P. atrimandibularis queens seemed to be successful as parasites in this population only when they originated from nests of P. dominulus, the largest species. The other host species are a sink for P. atrimandibularis since adult females emerging from those nests appear too small to usurp colonies themselves. Traits that may help P. atrimandibularis infiltrate multiple species may include its nonaggressive usurpation tactics and its ability to acquire host cuticular hydrocarbon recognition labels.

Anti-cooperativity in diffusion-controlled reactions with pairs of anisotropic domains: a model for the antigen-antibody encounter.

The encounter between anisotropic agents in diffusion-controlled reactions is a topic of very general relevance in chemistry and biology. Here we introduce a simplified model of encounter of an isotropic molecule with a pair of partially reacting agents and apply it to the encounter reaction between an antibody and its antigen. We reduce the problem to the solution of dual series relations, which can be solved iteratively, yielding the exact solution for the encounter rate constant at any desired order of accuracy. We quantify the encounter effectiveness by means of a simple indicator and show that the two binding centers systematically behave in an anti-cooperative fashion. However, we demonstrate that a reduction of the binding active sites allows the composite molecule to recover binding effectiveness, in spite of the overall reduction of the rate constant. In addition, we provide a simple formula that enables one to calculate the anti-cooperativity as a function of the size of the binding site for any values of the separation between the two active lobes and of the antigen size. Finally, some biological implications of our results are discussed.

Applications of the sulfinimine-mediated asymmetric strecker synthesis to the synthesis of alpha-alkyl alpha-amino acids.

Addition of Et(2)AlCN and i-PrOH to ketosulfinimines (N-sulfinyl imines) affords corresponding alpha-alkyl alpha-amino nitriles in moderate to good yields. The diastereoselectivity is largely dependent on the E/Z isomer ratio of the ketosulfinimine. Hydrolysis of the diastereomerically pure amino nitriles affords enantiopure alpha-alkyl alpha-amino acids in moderate to good yields.