The renormalization group and the implicit function theorem for amplitude equations

This article lays down the foundations of the renormalization group (RG) approach for differential equations characterized by multiple scales. The renormalization of constants through an elimination process and the subsequent derivation of the amplitude equation [Chen, Phys. Rev. E 54, 376 (1996)] are given a rigorous but not abstract mathematical form whose justification is based on the implicit function theorem. Developing the theoretical framework that underlies the RG approach leads to a systematization of the renormalization process and to the derivation of explicit closed-form expressions for the amplitude equations that can be carried out with symbolic computation for both linear and nonlinear scalar differential equations and first order systems but independently of their particular forms. Certain nonlinear singular perturbation problems are considered that illustrate the formalism and recover well-known results from the literature as special cases. © 2008 American Institute of Physics.

Extending FORK-256 attack to the full hash function

In a paper published in FSE 2007, a way of obtaining near-collisions and in theory also collisions for the FORK-256 hash function was presented [8]. The paper contained examples of near-collisions for the compression function, but in practice the attack could not be extended to the full function due to large memory requirements and computation time. In this paper we improve the attack and show that it is possible to find near-collisions in practice for any given value of IV. In particular, this means that the full hash function with the prespecified IV is vulnerable in practice, not just in theory. We exhibit an example near-collision for the complete hash function.

Functional impairments characterising mild, moderate and severe hallux valgus

Objective Hallux valgus has been linked to functional disability and increased falls risk, but mechanisms underpinning functional disability are unclear. This study investigated functional performance, muscle strength and plantar pressures in adults with mild, moderate, and severe HV compared to controls, while considering the influence of foot pain. Methods Sixty adults with hallux valgus (classified as mild, moderate and severe on dorsalplantar radiographs) and 30 controls participated. Measures included: hallux plantarflexion and abduction strength, walking performance, postural sway and forefoot plantar pressures. Multiple analysis of covariance and pairwise comparisons (p<0.05, Bonferroni adjustment) were used to investigate differences between groups, adjusting for age, sex, body mass index and foot pain. Results Hallux plantarflexion and abduction strength was significantly reduced in those with moderate (mean differences: plantarflexion -45.8N, abduction -12.3N, p<0.001) and severe hallux valgus (plantarflexion -50.1N, p<0.001; abduction -11.2N, p=0.01) compared to controls. A significant reduction in hallux peak pressure and pressure-time integral was evident in moderate (peak pressure -90.8kPa, p<0.001) and severe hallux valgus (peak pressure -106.2kPa, p<0.001) compared to controls. Those with severe hallux valgus also demonstrated increased mediolateral postural sway in single leg stance compared to controls (3.5cm, p=0.01). Conclusion Moderate to severe hallux valgus is associated with reduced hallux plantar pressures and strength measures, while relatively normal function compared to controls was found in those with mild deformity. Greater understanding of specific functional deficits associated with different stages of hallux valgus will help inform clinical management and future research.

Minimum cost of transport in human running is not ubiquitous

Purpose This study explores recent claims that humans exhibit a minimum cost of transport (CoTmin) for running which occurs at an intermediate speed, and assesses individual physiological, gait and training characteristics. Methods Twelve healthy participants with varying levels of fitness and running experience ran on a treadmill at six self-selected speeds in a discontinuous protocol over three sessions. Running speed (km[middle dot]hr-1), V[spacing dot above]O2 (mL[middle dot]kg-1[middle dot]km-1), CoT (kcal[middle dot]km-1), heart rate (beats[middle dot]min-1) and cadence (steps[middle dot]min-1) were continuously measured. V[spacing dot above]O2 max was measured on a fourth testing session. The occurrence of a CoTmin was investigated and its presence or absence examined with respect to fitness, gait and training characteristics. Results Five participants showed a clear CoTmin at an intermediate speed and a statistically significant (p < 0.05) quadratic CoT-speed function, while the other participants did not show such evidence. Participants were then categorized and compared with respect to the strength of evidence for a CoTmin (ClearCoTmin and NoCoTmin). The ClearCoTmin group displayed significantly higher correlation between speed and cadence; more endurance training and exercise sessions per week; than the NoCoTmin group; and a marginally non-significant but higher aerobic capacity. Some runners still showed a CoTmin at an intermediate speed even after subtraction of resting energy expenditure. Conclusion The findings confirm the existence of an optimal speed for human running, in some but not all participants. Those exhibiting a COTmin undertook a higher volume of running, ran with a cadence that was more consistently modulated with speed, and tended to be aerobically fitter. The ability to minimise the energetic cost of transport appears not to be ubiquitous feature of human running but may emerge in some individuals with extensive running experience.

Electron energy distribution function in low-pressure complex plasmas

The effect of density and size of dust grains on the electron energy distribution function (EEDF) in low-temperature complex plasmas is studied. It is found that the EEDF depends strongly on the dust density and size. The behavior of the electron temperature can differ significantly from that of a pristine plasma. For low-pressure argon glow discharge, the Druyvesteyn-like EEDF often found in pristine plasmas can become nearly Maxwellian if the dust density and/or sizes are large. One can thus control the plasma parameters by the dust grains.

Delivery of nitric oxide for analysis of the function of cytochrome c'

On delivery of nitric oxide (NO) to protein samples (e.g., cytochrome c'), for spectroscopic experiments it is important to avoid exposure to oxygen and to remove contaminants from the NO gas. We describe a number of techniques for steady-state UV/Vis spectrophotometry and pre-steady-state stopped-flow spectrophotometry analysis of cytochrome c'.

Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging

Cryo-electron tomography together with averaging of sub-tomograms containing identical particles can reveal the structure of proteins or protein complexes in their native environment. The resolution of this technique is limited by the contrast transfer function (CTF) of the microscope. The CTF is not routinely corrected in cryo-electron tomography because of difficulties including CTF detection, due to the low signal to noise ratio, and CTF correction, since images are characterised by a spatially variant CTF. Here we simulate the effects of the CTF on the resolution of the final reconstruction, before and after CTF correction, and consider the effect of errors and approximations in defocus determination. We show that errors in defocus determination are well tolerated when correcting a series of tomograms collected at a range of defocus values. We apply methods for determining the CTF parameters in low signal to noise images of tilted specimens, for monitoring defocus changes using observed magnification changes, and for correcting the CTF prior to reconstruction. Using bacteriophage PRDI as a test sample, we demonstrate that this approach gives an improvement in the structure obtained by sub-tomogram averaging from cryo-electron tomograms.

Speckle-type POZ protein mutations interrupt tumor suppressor function of speckle-type POZ protein in prostate cancer by affecting androgen receptor degradation

Large scale exome sequencing studies have revealed regions of the genome, which contribute to the castrate resistant prostate cancer (CRPC) phenotype. [1],[2],[3] Such studies have identified mutations in genes, which may have diagnostic/prognostic potential, or which may be targeted therapeutically. Two of these genes include the androgen receptor (AR) and speckle-type POZ protein (SPOP) genes. However, the findings from these exome sequencing studies can only be translated therapeutically once the functional consequences of these mutations have been determined. Here, we highlight the recent study by An et al. [4] which investigated the functional effects of mutations in the SPOP gene that were identified in the aforementioned exome sequencing studies, particularly in the context of SPOP-mediated degradation of the AR.

Structure and function of DsbA, a key bacterial oxidative folding catalyst

Since its discovery in 1991, the bacterial periplasmic oxidative folding catalyst DsbA has been the focus of intense research. Early studies addressed why it is so oxidizing and how it is maintained in its less stable oxidized state. The crystal structure of Escherichia coli DsbA (EcDsbA) revealed that the oxidizing periplasmic enzyme is a distant evolutionary cousin of the reducing cytoplasmic enzyme thioredoxin. Recent significant developments have deepened our understanding of DsbA function, mechanism, and interactions: the structure of the partner membrane protein EcDsbB, including its complex with EcDsbA, proved a landmark in the field. Studies of DsbA machineries from bacteria other than E. coli K-12 have highlighted dramatic differences from the model organism, including a striking divergence in redox parameters and surface features. Several DsbA structures have provided the first clues to its interaction with substrates, and finally, evidence for a central role of DsbA in bacterial virulence has been demonstrated in a range of organisms. Here, we review current knowledge on DsbA, a bacterial periplasmic protein that introduces disulfide bonds into diverse substrate proteins and which may one day be the target of a new class of anti-virulence drugs to treat bacterial infection. Antioxid. Redox Signal. 14, 1729–1760.

Genotoxicity of inorganic lead salts and disturbance of microtubule function

Lead compounds are known genotoxicants, principally affecting the integrity of chromosomes. Lead chloride and lead acetate induced concentration-dependent increases in micronucleus frequency in V79 cells, starting at 1.1 μM lead chloride and 0.05 μM lead acetate. The difference between the lead salts, which was expected based on their relative abilities to form complex acetato-cations, was confirmed in an independent experiment. CREST analyses of the micronuclei verified that lead chloride and acetate were predominantly aneugenic (CREST-positive response), which was consistent with the morphology of the micronuclei (larger micronuclei, compared with micronuclei induced by a clastogenic mechanism). The effects of high concentrations of lead salts on the microtubule network of V79 cells were also examined using immunofluorescence staining. The dose effects of these responses were consistent with the cytotoxicity of lead(II), as visualized in the neutral-red uptake assay. In a cell-free system, 20-60 μM lead salts inhibited tubulin assembly dose-dependently. The no-observed-effect concentration of lead(II) in this assay was 10 μM. This inhibitory effect was interpreted as a shift of the assembly/disassembly steady-state toward disassembly, e.g., by reducing the concentration of assembly-competent tubulin dimers. The effects of lead salts on microtubule-associated motor-protein functions were studied using a kinesin-gliding assay that mimics intracellular transport processes in vitro by quantifying the movement of paclitaxel-stabilized microtubules across a kinesin-coated glass surface. There was a dose-dependent effect of lead nitrate on microtubule motility. Lead nitrate affected the gliding velocities of microtubules starting at concentrations above 10 μM and reached half-maximal inhibition of motility at about 50 μM. The processes reported here point to relevant interactions of lead with tubulin and kinesin at low dose levels.