COLLISION PUMPED SOFT-X-RAY LASERS - PROGRESS AT RAL

Recent developments and progress on collision pumped soft X-ray lasers using the VULCAN glass laser at Rutherford-Appleton Laboratory are presented. This includes saturated output operation of a double target germanium system within a low Fresnel number half-cavity, measurement of the spatial coherence of the output beam in the above and other geometries, use of the beam to demonstrate almost-equal-to 0.15 mum spatial resolution in a full-field microscope and initial studies of other Ne-like and Ni-like systems. Future directions, in the light of new developments of VULCAN facilities, are outlined.

Multiple proton translocation in biomolecular systems: concerted to stepwise transition in a simple model

In this paper we study a simple model potential energy surface (PES) useful for describing multiple proton translocation mechanisms. The approach presented is relevant to the study of more complex biomolecular systems like enzymes. In this model, at low temperatures, proton tunnelling favours a concerted proton transport mechanism, while at higher temperatures there is a crossover from concerted to stepwise mechanisms; the crossover temperature depends on the energetic features of the PES. We illustrate these ideas by calculating the crossover temperature using energies taken from ab initio calculations on specific systems. Interestingly, typical crossover temperatures lie around room temperature; thus both concerted and stepwise reaction mechanisms should play an important role in biological systems, and one can be easily turned into another by external means such as modifying the temperature or the pH, thus establishing a general mechanism for modulation of the biomolecular function by external effectors.

Mutational analysis of the active centre of coronavirus 3C-like proteases.

Formation of the coronavirus replication-transcription complex involves the synthesis of large polyprotein precursors that are extensively processed by virus-encoded cysteine proteases. In this study, the coding sequence of the feline infectious peritonitis virus (FIPV) main protease, 3CL(pro), was determined. Comparative sequence analyses revealed that FIPV 3CL(pro) and other coronavirus main proteases are related most closely to the 3C-like proteases of potyviruses. The predicted active centre of the coronavirus enzymes has accepted unique replacements that were probed by extensive mutational analysis. The wild-type FIPV 3CL(pro) domain and 25 mutants were expressed in Escherichia coli and tested for proteolytic activity in a peptide-based assay. The data strongly suggest that, first, the FIPV 3CL(pro) catalytic system employs His(41) and Cys(144) as the principal catalytic residues. Second, the amino acids Tyr(160) and His(162), which are part of the conserved sequence signature Tyr(160)-Met(161)-His(162) and are believed to be involved in substrate recognition, were found to be indispensable for proteolytic activity. Third, replacements of Gly(83) and Asn(64), which were candidates to occupy the position spatially equivalent to that of the catalytic Asp residue of chymotrypsin-like proteases, resulted in proteolytically active proteins. Surprisingly, some of the Asn(64) mutants even exhibited strongly increased activities. Similar results were obtained for human coronavirus (HCoV) 3CL(pro) mutants in which the equivalent Asn residue (HCoV 3CL(pro) Asn(64)) was substituted. These data lead us to conclude that both the catalytic systems and substrate-binding pockets of coronavirus main proteases differ from those of other RNA virus 3C and 3C-like proteases.

Neuropeptide signalling systems in flatworms

Two distinct families of neuropeptides are known to endow platyhelminth nervous systems-the FMRFamide-like peptides (FLPs) and the neuropepticle Fs (NPFs). Flatworm FLPs are strusturally simple, each 4-6 amino acids in length with a carboxy terminal aromatic-hydropliobic-Arg-Phe-amide motif. Thus far, four distinct flatworm FLPs have been characterized, with only one of these from a parasite. They have a widespread distribution within the central and peripheral nervous system of every flatworm examined, including neurones serving the attachment organs, the somatic Musculature and the reproductive system. The only physiological role that has been identified for flatworm FLPs is myoexcitation. Flatworm NPFs are believed to be invertebrate homologues of the vertebrate neuropeptide Y (NPY) family of peptides. Flatworm NPFs are 36-39 amino acids in length and are characterized by a caboxy terminal GRPRFarnide signature and conserved tyrosine residues at positions 10 and 17 from the carboxy terminal. Like FLPs, NPF occurs throughout flatworm nervous systems, although less is known about its biological role. While there is some evidence for a myoexcitatory action in cestodes and flukes, more compelling physiological data indicate that flatworm NPF inhibits cAMP levels in a manner that is characteristic of NPY action in vertebrates. The widespread expression of these neuropeptides in flanworm parasites highlights the potential of these signalling systems to yield new targets for novel anthelmintics. Although platyhelminth FLP and NPF receptors await identification, other molecules that play pivotal roles in neuropeptide signalling have been uncovered. These enzymes, involved in the biosynthesis and processing of flatworm neuropeptides, have recently been described and offer other distinct and attractive targets for therapeutic interference.

Intermedin (Adrenomedullin-2) a novel counter-regulatory peptide in the cardiovascular and renal systems

Intermedin (IMD) is a novel peptide related to calcitonin gene-related peptide (CGRP) and adrenomedullin (AM). Proteolytic processing of a larger precursor yields a series of biologically active C-terminal fragments, IMD1–53, IMD1–47 and IMD8–47. IMD shares a family of receptors with AM and CGRP composed of a calcitonin-receptor like receptor (CALCRL) associated with one of three receptor activity modifying proteins (RAMP). Compared to CGRP, IMD is less potent at CGRP1 receptors but more potent at AM1 receptors and AM2 receptors; compared to AM, IMD is more potent at CGRP1 receptors but less potent at AM1 and AM2 receptors. The cellular and tissue distribution of IMD overlaps in some aspects with that of CGRP and AM but is distinct from both. IMD is present in neonatal but absent or expressed sparsely, in adult heart and vasculature and present at low levels in plasma. The prominent localization of IMD in hypothalamus and pituitary and in kidney is consistent with a physiological role in the central and peripheral regulation of the circulation and water-electrolyte homeostasis. IMD is a potent systemic and pulmonary vasodilator, influences regional blood flow and augments cardiac contractility. IMD protects myocardium from the deleterious effects of oxidative stress associated with ischaemia-reperfusion injury and exerts an anti-growth effect directly on cardiomyocytes to oppose the influence of hypertrophic stimuli. The robust increase in expression of the peptide in hypertrophied and ischaemic myocardium indicates an important protective role for IMD as an endogenous counter-regulatory peptide in the heart.

Immunocytochemical localization of glutamate-like immunoreactivity within the nervous system of the cestode Mesocestoides corti and the trematode Fasciola hepatica

The localization and distribution of glutamate-like immunoreactivity (IR) in the nervous system of both the cestode Mesocestoides corti and the trematode Fasciola hepatica has been determined by an indirect immunofluorescent technique, in conjunction with confocal scanning laser microscopy (CSLM). Immunostaining was widespread in the central (CNS) and peripheral (PNS) nervous systems of both species examined. In the CNS, IR was evident in nerve cells and fibres in the cerebral ganglia, the cerebral commissure and the dorsal, ventral and longitudinal nerve cords. In the peripheral nervous system (PNS) of M. corti, IR was apparent in nerve plexuses associated with the subtegmental musculature and the musculature associated with the anteriorly positioned suckers. In F. hepatica, IR was evident in the innervation of both the oral and the ventral suckers, In the reproductive system of F. hepatica, glutamate-IR was observed around the ootype/Mehlis' gland complex.

Comparative analysis of the distribution of bradykinin-, GYIRFamide- and neuropeptide F-like immunoreactivities in the monogenean, Diclidophora merlangi

An indirect immunocytochemical technique combined with confocal scanning laser microscopy has been used to demonstrate immunoreactivities to the nonapeptide, RPPGFSPFR (bradykinin, BK) and the endogenous flatworm regulatory peptide, GYIRFamide in the nervous system of the monogenean, Diclidophora merlangi. In addition, a simultaneous double-labelling technique was employed to examine possible co-localization of GYIRFamide- and neuropeptide F (NPF) immunoreactivities, using antisera to the C-terminal nonapeptide-amide of NPF (Moniezia expansa, FAIIGRPRF.NH2). BK immunostaining was restricted to a small population of nerve cells and associated fibres within the Ventral nerve cords and to 2 pairs of nerve cells innervating the cirrus and the pharynx, respectively. No immunopositive nerve cells and fibres were identified within the brain or in association with the female reproductive apparatus. In contrast, GYIRFamide staining was abundant throughout the central and peripheral nervous systems, and appeared similar to the staining pattern revealed using an FMRFamide antiserum. GYIRFamide immunoreactivity was localized to nerve cells and fibres within the paired cerebral ganglia and the longitudinal ventral, dorsal and lateral nerve cords and their numerous interconnecting transverse commissures. The plexuses of the buccal suckers, pharynx and clamps of the haptor were strongly immunopositive for GYIRFamide, as were nerve cells innervating the ootype, the oviduct and the vitelline reservoir of the reproductive apparatus. Double-labelling experiments indicated an apparent co-localization of GYIRFamide and NPF immunoreactivities.

LOCALIZATION OF DIPLOPTERA-PUNCTATA ALLATOSTATIN-LIKE IMMUNOREACTIVITY IN HELMINTHS - AN IMMUNOCYTOCHEMICAL STUDY

The nervous systems of helminths are predominantly peptidergic in nature, although it is likely that the full range of regulatory peptides used by these organisms has yet to be elucidated. Attempts to identify novel helminth neuropeptides are being made using immunocytochemistry with antisera raised against peptides isolated originally from insects. One of these antisera was raised against allatostatin III, a peptide isolated originally from the cockroach, Diploptera punctata, and a member of a family of related peptides found in insects. Allatostatin immunoreactivity was found throughout the nervous systems of Mesocestoides corti tetrathyridia, and adult Moniezia expansa, Diclidophora merlangi, Fasciola hepatica, Schistosoma mansoni, Ascaris suum and Panagrellus redivivus. Immunostaining was observed in the nerve cords and anterior ganglia of all the helminths. It was also apparent in the subtegumental nerves and around the reproductive apparatus of the flatworms, in neurones in the pharynx of D. merlangi, F. hepatica, A. suum and P. redivivus, and in fibres innervating the anterior sense organs in the nematodes. Immunostaining in all species was both reproducible and specific in that it could be abolished by pre-absorption of the antiserum with allatostatins I-IV. These results suggest that molecules related to the D. punctata allatostatins are important components in the nervous systems of a number of helminth parasites, and a free-living nematode. Their distribution within the nervous system suggests they function as neurotransmitters/ neuromodulators with roles in locomotion, feeding, reproduction and sensory perception.

The geometry and ionization structure of the wind in the eclipsing nova-like variables RW Tri and UX UMa

The UV spectra of nova-like variables are dominated by emission from the accretion disk, modified by scattering in a wind emanating from the disk. Here, we model the spectra of RW Tri and UX UMa, the only two eclipsing nova-like variables which have been observed with the Hubble Space Telescope in the far-ultraviolet, in an attempt to constrain the geometry and the ionization structure of their winds. Using our Monte Carlo radiative transfer code, we computed spectra for simply parameterized axisymmetric biconical outflow models and were able to find plausible models for both systems. These reproduce the primary UV resonance lines-N v, Si iv, and C iv-in the observed spectra in and out of eclipse. The distribution of these ions in the wind models is similar in both cases as is the extent of the primary scattering regions in which these lines are formed. The inferred mass-loss rates are 6%-8% of the mass accretion rates for the systems. We discuss the implication of our point models for our understanding of accretion disk winds in cataclysmic variables. © 2010. The American Astronomical Society. All rights reserved.

Detection of Avian Influenza Virus with PCR-Like Sensitivity by Fluorescent DNA Barcode-Based Immunoassay

In this paper, we report a coupling of fluorophore-DNA barcode and bead-based
immunoassay for the detection of Avian Influenza Virus (AIV), a potential pandemic threat for human health and enormous economic losses. The detection strategy is based on the use of sandwich immunoassay and fluorophore-tagged oligonucleotides as representatively fluorescent barcodes. Despite its simplicity the assay has sensitivity comparable to RT-PCR amplification, and possesses a great potential as a rapid and sensitive on-chip detection format.

Constitutive model for localized Lüders-like stress-induced martensitic transformation and super-elastic behaviors of laser-welded NiTi wires

The application of the shape memory alloy NiTi in micro-electro-mechanical-systems (MEMSs) is extensive nowadays. In MEMS, complex while precise motion control is always vital. This makes the degradation of the functional properties of NiTi during cycling loading such as the appearance of residual strain become a serious problem to study, in particular for laser micro-welded NiTi in real applications. Although many experimental efforts have been put to study the mechanical properties of laser welded NiTi, surprisingly, up to the best of our understanding, there has not been attempts to quantitatively model the laser-welded NiTi under mechanical cycling in spite of the accurate prediction required in applications and the large number of constitutive models to quantify the thermo-mechanical behavior of shape memory alloys. As the first attempt to fill the gap, we employ a recent constitutive model, which describes the localized SIMT in NiTi under cyclic deformation; with suitable modifications to model the mechanical behavior of the laser welded NiTi under cyclic tension. The simulation of the model on a range of tensile cyclic deformation is consistent with the results of a series of experiments. From this, we conclude that the plastic deformation localized in the welded regions (WZ and HAZs) of the NiTi weldment can explain most of the extra amount of residual strain appearing in welded NiTi compared to the bare one. Meanwhile, contrary to common belief, we find that the ability of the weldment to memorize its transformation history, sometimes known as ‘return point memory’, still remains unchanged basically though the effective working limit of this ability reduces to within 6% deformation.

1-D constitutive model for evolution of stress-induced R-phase and localized Lüders-like stress-induced martensitic transformation of super-elastic NiTi wires

NiTi alloys have been widely used in the applications for micro-electro-mechanical-systems (MEMS), which often involve some precise and complex motion control. However, when using the NiTi alloys in MEMS application, the main problem to be considered is the degradation of functional property during cycling loading. This also stresses the importance of accurate prediction of the functional behavior of NiTi alloys. In the last two decades, a large number of constitutive models have been proposed to achieve the task. A portion of them focused on the deformation behavior of NiTi alloys under cyclic loading, which is a practical and non-negligible situation. Despite of the scale of modeling studies of the field in NiTi alloys, two experimental observations under uniaxial tension loading have not received proper attentions. First, a deviation from linearity well before the stress-induced martensitic transformation (SIMT) has not been modeled. Recent experiments confirmed that it is caused by the formation of stress-induced R phase. Second, the influence of the well-known localized Lüders-like SIMT on the macroscopic behavior of NiTi alloys, in particular the residual strain during cyclic loading, has not been addressed. In response, we develop a 1-D phenomenological constitutive model for NiTi alloys with two novel features: the formation of stress-induced R phase and the explicit modeling of the localized Lüders-like SIMT. The derived constitutive relations are simple and at the same time sufficient to describe the behavior of NiTi alloys. The accumulation of residual strain caused by R phase under different loading schemes is accurately described by the proposed model. Also, the residual strain caused by irreversible SIMT at different maximum loading strain under cyclic tension loading in individual samples can be explained by and fitted into a single equation in the proposed model. These results show that the proposed model successfully captures the behavior of R phase and the essence of localized SIMT.

Enhancing non-classicality in mechanical systems

We study the effects of post-selection measurements on both the non-classicality of the state of a mechanical oscillator and the entanglement between two mechanical systems that are part of a distributed optomechanical network. We address the cases of both Gaussian and non-Gaussian measurements, identifying in which cases simple photon counting and Geiger-like measurements are effective in distilling a strongly non-classical mechanical state and enhancing the purely mechanical entanglement between two elements of the network.

A Hamiltonian approach to simulation of acoustic systems involving nonlinear interactions

Nonlinear interactions take place in most systems that arise in music acoustics, usually as a result of player-instrument coupling. Several time-stepping methods exist for the numerical simulation of such systems. These methods generally involve the discretization of the Newtonian description of the system. However, it is not always possible to prove the stability of the resulting algorithms, especially when dealing with systems where the underlying force is a non-analytic function of the phase space variables. On the other hand, if the discretization is carried out on the Hamiltonian description of the system, it is possible to prove the stability of the derived numerical schemes. This Hamiltonian approach is applied to a series of test models of single or multiple nonlinear collisions and the energetic properties of the derived schemes are discussed. After establishing that the schemes respect the principle of conservation of energy, a nonlinear single-reed model is formulated and coupled to a digital bore, in order to synthesize clarinet-like sounds.

Establishing Metrics for Assessing the Performance of Directional Modulation Systems

In this paper metrics for assessing the performance of directional modulation (DM) physical-layer secure wireless systems are discussed. In the paper DM systems are shown to be categorized as static or dynamic. The behavior of each type of system is discussed for QPSK modulation. Besides EVM-like and BER metrics, secrecy rate as used in information theory community is also derived for the purpose of this QPSK DM system evaluation.