A Method for Assaying Deubiquitinating Enzymes

A general method for the assay of deubiquitinating enzymes was described in detail using (125)I-labeled ubiquitin-fused αNH-MHISPPEPESEEEEEHYC (referred to as Ub-PESTc) as a substrate. Since the tyrosine residue in the PESTc portion of the fusion protein was almost exclusively radioiodinated under a mild labeling condition, such as using IODO-BEADS, the enzymes could be assayed directly by simple measurement of the radioactivity released into acid soluble products. Using this assay protocol, we could purify six deubiquitinating enzymes from chick skeletal muscle and yeast and compare their specific activities. Since the extracts of E. coli showed little or no activity against the substrate, the assay protocol should be useful for identification and purification of eukaryotic deubiquitinating enzymes cloned and expressed in the cells

How spiking neurons give rise to a temporal-feature map

A temporal-feature map is a topographic neuronal representation of temporal attributes of phenomena or objects that occur in the outside world. We explain the evolution of such maps by means of a spike-based Hebbian learning rule in conjunction with a presynaptically unspecific contribution in that, if a synapse changes, then all other synapses connected to the same axon change by a small fraction as well. The learning equation is solved for the case of an array of Poisson neurons. We discuss the evolution of a temporal-feature map and the synchronization of the single cells’ synaptic structures, in dependence upon the strength of presynaptic unspecific learning. We also give an upper bound for the magnitude of the presynaptic interaction by estimating its impact on the noise level of synaptic growth. Finally, we compare the results with those obtained from a learning equation for nonlinear neurons and show that synaptic structure formation may profit from the nonlinearity

Hyaluronic Acid Binding Sperm Selection for assisted reproduction treatment (HABSelect): Study protocol for a multicentre randomised controlled trial

© Published by the BMJ Publishing Group Limited.Introduction The selection of a sperm with good genomic integrity is an important consideration for improving intracytoplasmic sperm injection (ICSI) outcome. Current convention selects sperm by vigour and morphology, but preliminary evidence suggests selection based on hyaluronic acid binding may be beneficial. The aim of the Hyaluronic Acid Binding Sperm Selection (HABSelect) trial is to determine the efficacy of hyaluronic acid (HA)-selection of sperm versus conventionally selected sperm prior to ICSI on live birth rate (LBR). The mechanistic aim is to assess whether and how the chromatin state of HA-selected sperm corresponds with clinical outcomes - clinical pregnancy rate (CPR), LBR and pregnancy loss (PL). Methods and analysis Couples attending UK Centres will be approached, eligibility screening performed and informed consent sought. Randomisation will occur within 24 hours prior to ICSI treatment. Participants will be randomly allocated 1:1 to the intervention arm (physiological intracytoplasmic sperm injection, PICSI) versus the control arm using conventional methods (ICSI). The primary clinical outcome is LBR ≥37 weeks' gestation with the mechanistic study determining LBR's relationship with sperm DNA integrity. Secondary outcomes will determine this for CPR and PL. Only embryologists performing the procedure will be aware of the treatment allocation. Steps will be taken to militate against biases arising from embryologists being non-blinded. Randomisation will use a minimisation algorithm to balance for key prognostic variables. The trial is powered to detect a 5% difference (24-29%: p=0.05) in LBR ≥37 weeks' gestation. Selected residual sperm samples will be tested by one or more assays of DNA integrity. Ethics and dissemination HABSelect is a UK NIHR-EME funded study (reg no 11/14/34; IRAS REF. 13/YH/0162). The trial was designed in partnership with patient and public involvement to help maximise patient benefits. Trial findings will be reported as per CONSORT guidelines and will be made available in lay language via the trial web site (http://www.habselect.org.uk/). Trial registration number ISRCTN99214271; Pre-results

Three-dimensional general relativistic hydrodynamics II: long-term dynamics of single relativistic stars

This is the second in a series of papers on the construction and validation of a three-dimensional code for the solution of the coupled system of the Einstein equations and of the general relativistic hydrodynamic equations, and on the application of this code to problems in general relativistic astrophysics. In particular, we report on the accuracy of our code in the long-term dynamical evolution of relativistic stars and on some new physics results obtained in the process of code testing. The tests involve single non-rotating stars in stable equilibrium, non-rotating stars undergoing radial and quadrupolar oscillations, non-rotating stars on the unstable branch of the equilibrium configurations migrating to the stable branch, non-rotating stars undergoing gravitational collapse to a black hole, and rapidly rotating stars in stable equilibrium and undergoing quasi-radial oscillations. The numerical evolutions have been carried out in full general relativity using different types of polytropic equations of state using either the rest-mass density only, or the rest-mass density and the internal energy as independent variables. New variants of the spacetime evolution and new high resolution shock capturing (HRSC) treatments based on Riemann solvers and slope limiters have been implemented and the results compared with those obtained from previous methods. Finally, we have obtained the first eigenfrequencies of rotating stars in full general relativity and rapid rotation. A long standing problem, such frequencies have not been obtained by other methods. Overall, and to the best of our knowledge, the results presented in this paper represent the most accurate long-term three-dimensional evolutions of relativistic stars available to date.Comment: 19 pages, 17 figure

Net Fisher information measure versus ionization potential and dipole polarizability in atoms

The net Fisher information measure, defined as the product of position and momentum Fisher information measures and derived from the non-relativistic Hartree-Fock wave functions for atoms with Z=1-102, is found to correlate well with the inverse of the experimental ionization potential. Strong direct correlations of the net Fisher information are also reported for the static dipole polarizability of atoms with Z=1-88. The complexity measure, defined as the ratio of the net Onicescu information measure and net Fisher information, exhibits clearly marked regions corresponding to the periodicity of the atomic shell structure. The reported correlations highlight the need for using the net information measures in addition to either the position or momentum space analogues. With reference to the correlation of the experimental properties considered here, the net Fisher information measure is found to be superior than the net Shannon information entropy.Comment: 16 pages, 6 figure

Renormalization of the mass gap

The full gluon propagator relevant for the description of the truly non-perturbative QCD dynamics, the so-called intrinsically non-perturbative gluon propagator has been derived in our previous work. It explicitly depends on the regularized mass gap, which dominates its structure at small gluon momentum. It is automatically transversal in a gauge invariant way. It is characterized by the presence of severe infrared singularities at small gluon momentum, so the gluons remain massless, and this does not depend on the gauge choice. In this paper we have shown how precisely the renormalization program for the regularized mass gap should be performed. We have also shown how precisely severe infrared singularities should be correctly treated. This allowed to analytically formulate the exact and gauge-invariant criteria of gluon and quark confinement. After the renormalization program is completed, one can derive the gluon propagator applicable for the calculation of physical observables processes, etc., in low-energy QCD from first principles.Comment: 16 pages, no figures, no tables, some minor changes are introduce

Ab initio Quantum and ab initio Molecular Dynamics of the Dissociative Adsorption of Hydrogen on Pd(100)

The dissociative adsorption of hydrogen on Pd(100) has been studied by ab initio quantum dynamics and ab initio molecular dynamics calculations. Treating all hydrogen degrees of freedom as dynamical coordinates implies a high dimensionality and requires statistical averages over thousands of trajectories. An efficient and accurate treatment of such extensive statistics is achieved in two steps: In a first step we evaluate the ab initio potential energy surface (PES) and determine an analytical representation. Then, in an independent second step dynamical calculations are performed on the analytical representation of the PES. Thus the dissociation dynamics is investigated without any crucial assumption except for the Born-Oppenheimer approximation which is anyhow employed when density-functional theory calculations are performed. The ab initio molecular dynamics is compared to detailed quantum dynamical calculations on exactly the same ab initio PES. The occurence of quantum oscillations in the sticking probability as a function of kinetic energy is addressed. They turn out to be very sensitive to the symmetry of the initial conditions. At low kinetic energies sticking is dominated by the steering effect which is illustrated using classical trajectories. The steering effects depends on the kinetic energy, but not on the mass of the molecules. Zero-point effects lead to strong differences between quantum and classical calculations of the sticking probability. The dependence of the sticking probability on the angle of incidence is analysed; it is found to be in good agreement with experimental data. The results show that the determination of the potential energy surface combined with high-dimensional dynamical calculations, in which all relevant degrees of freedon are taken into account, leads to a detailed understanding of the dissociation dynamics of hydrogen at a transition metal surface.Comment: 15 pages, 9 figures, subm. to Phys. Rev.