Recurrence-mediated suprathreshold stochastic resonance

It has previously been shown that the encoding of time-dependent signals by feedforward networks (FFNs) of processing units exhibits suprathreshold stochastic resonance (SSR), which is an optimal signal transmission for a finite level of independent, individual stochasticity in the single units. In this study, a recurrent spiking network is simulated to demonstrate that SSR can be also caused by network noise in place of intrinsic noise. The level of autonomously generated fluctuations in the network can be controlled by the strength of synapses, and hence the coding fraction (our measure of information transmission) exhibits a maximum as a function of the synaptic coupling strength. The presence of a coding peak at an optimal coupling strength is robust over a wide range of individual, network, and signal parameters, although the optimal strength and peak magnitude depend on the parameter being varied. We also perform control experiments with an FFN illustrating that the optimized coding fraction is due to the change in noise level and not from other effects entailed when changing the coupling strength. These results also indicate that the non-white (temporally correlated) network noise in general provides an extra boost to encoding performance compared to the FFN driven by intrinsic white noise fluctuations.Deutsche ForschungsgemeinschaftHumboldt-Universität zu Berlin (1034)Peer Reviewe

Individual filamentous phage imaged by electron holography

An in-line electron hologram of an individual f1.K phage was recorded with a purpose-built low energy electron point source (LEEPS) microscope. Cryo-microscopic methods were employed to prepare the specimen so that a single phage could be presented to the coherent low energy electrons: An aqueous phage suspension was applied to a thin carbon membrane with micro-machined slits. The membrane was rapidly cooled to freeze the remaining water as an amorphous ice sheet, which was then sublimated at low temperatures and pressures to leave individual free-standing phages suspended across slits. An image of a phage particle, depicted as the amplitude of the object wave, was reconstructed numerically from a digitized record of the hologram, obtained using 88eV coherent electrons. The reconstructed image shows a single phage suspended across a slit in a supporting carbon membrane, magnified by a factor of 100,000. The width and shape in the reconstructed image compared well with a TEM image of the same filament. It is thus possible to record and reconstruct electron holograms of an individual phage. The challenge now is to improve the resolution of reconstructed images obtained by this method and to extend these structural studies to other biological molecule

Development of a fully automatic shape model matching (FASMM) system to derive statistical shape models from radiographs: application to the accurate capture and global representation of proximal femur shape

SummaryObjectiveTo evaluate the accuracy and sensitivity of a fully automatic shape model matching (FASMM) system to derive statistical shape models (SSMs) of the proximal femur from non-standardised anteroposterior (AP) pelvic radiographs.DesignAP pelvic radiographs obtained with informed consent and appropriate ethical approval were available for 1105 subjects with unilateral hip osteoarthritis (OA) who had been recruited previously for The arcOGEN Study. The FASMM system was applied to capture the shape of the unaffected (i.e., without signs of radiographic OA) proximal femur from these radiographs. The accuracy and sensitivity of the FASMM system in calculating geometric measurements of the proximal femur and in shape representation were evaluated relative to validated manual methods.ResultsDe novo application of the FASMM system had a mean point-to-curve error of less than 0.9 mm in 99% of images (n = 266). Geometric measurements generated by the FASMM system were as accurate as those obtained manually. The analysis of the SSMs generated by the FASMM system for male and female subject groups identified more significant differences (in five of 17 SSM modes after Bonferroni adjustment) in their global proximal femur shape than those obtained from the analysis of conventional geometric measurements. Multivariate gender-classification accuracy was higher when using SSM mode values (76.3%) than when using conventional hip geometric measurements (71.8%).ConclusionsThe FASMM system rapidly and accurately generates a global SSM of the proximal femur from radiographs of varying quality and resolution. This system will facilitate complex morphometric analysis of global shape variation across large datasets. The FASMM system could be adapted to generate SSMs from the radiographs of other skeletal structures such as the hand, knee or pelvis

Investigation of Association Between Hip Osteoarthritis Susceptibility Loci and Radiographic Proximal Femur Shape

Objective: To test whether previously reported hip morphology or osteoarthritis (OA) susceptibility loci are associated with proximal femur shape as represented by statistical shape model (SSM) modes and as univariate or multivariate quantitative traits. Methods: We used pelvic radiographs and genotype data from 929 subjects with unilateral hip OA who had been recruited previously for the Arthritis Research UK Osteoarthritis Genetics Consortium genome-wide association study. We built 3 SSMs capturing the shape variation of the OA-unaffected proximal femur in the entire mixed-sex cohort and for male/female-stratified cohorts. We selected 41 candidate single-nucleotide polymorphisms (SNPs) previously reported as being associated with hip morphology (for replication analysis) or OA (for discovery analysis) and for which genotype data were available. We performed 2 types of analysis for genotype–phenotype associations between these SNPs and the modes of the SSMs: 1) a univariate analysis using individual SSM modes and 2) a multivariate analysis using combinations of SSM modes. Results: The univariate analysis identified association between rs4836732 (within the ASTN2 gene) and mode 5 of the female SSM (P = 0.0016) and between rs6976 (within the GLT8D1 gene) and mode 7 of the mixed-sex SSM (P = 0.0003). The multivariate analysis identified association between rs5009270 (near the IFRD1 gene) and a combination of modes 3, 4, and 9 of the mixed-sex SSM (P = 0.0004). Evidence of associations remained significant following adjustment for multiple testing. All 3 SNPs had previously been associated with hip OA. Conclusion: These de novo findings suggest that rs4836732, rs6976, and rs5009270 may contribute to hip OA susceptibility by altering proximal femur shape

The formation of voids in a universe with cold dark matter and a cosmological constant

A spherical Lagrangian hydrodynamical code has been written to study the formation of cosmological structures in the early Universe. In this code we take into account the presence of collisionless non-baryonic cold dark matter (CDM), the cosmological constant and a series of physical processes present during and after the recombination era, such as photon drag resulting from the cosmic background radiation and hydrogen molecular production. We follow the evolution of the structure since the recombination era until the present epoch. As an application of this code we study the formation of voids starting from negative density perturbations which evolved during and after the recombination era. We analyse a set of COBE-normalized models, using different spectra to see their influence on the formation of voids. Our results show that large voids with diameters ranging from 10h^{-1} Mpc up to 50h^{-1} Mpc can be formed in a universe model dominated by the cosmological constant (\Omega_\Lambda ~ 0.8). This particular scenario is capable of forming large and deep empty regions (with density contrasts \delta < -0.6). Our results also show that the physical processes acting on the baryonic matter produce a transition region where the radius of the dark matter component is greater than the baryonic void radius. The thickness of this transition region ranges from about tens of kiloparsecs up to a few megaparsecs, depending on the spectrum considered. Putative objects formed near voids and within the transition region would have a different amount of baryonic/dark matter when compared with \Omega_b/\Omega_d. If one were to use these galaxies to determine, by dynamical effects or other techniques, the quantity of dark matter present in the Universe, the result obtained would be only local and not representative of the Universe as a whole.Comment: MNRAS (in press); 9 pages, no figure

DXA-derived hip shape is related to osteoarthritis:findings from in the MrOS cohort

BF conducted this research whilst on a clinical research primer fellowship awarded by the Elizabeth Blackwell Institute, University of Bristol, UK. This study was funded by Arthritis Research UK project grant ref 20244. CG is funded by Arthritis Research UK grant ref 20000. The Osteoporotic Fractures in Men (MrOS) Study is supported by National Institutes of Health funding. The following institutes provide support: the National Institute on Aging (NIA), the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), the National Center for Advancing Translational Sciences (NCATS), and NIH Roadmap for Medical Research under the following grant numbers: R01 AR052000, K24 AR048841, U01 AG027810, U01 AG042124, U01 AG042139, U01 AG042140, U01 AG042143, U01 AG042145, U01 AG042168, U01 AR066160, and UL1 TR000128.Peer reviewedPostprin

Formation of voids in the Universe within the Lemaitre-Tolman model

We develop models of void formation starting from a small initial fluctuation at recombination and growing to a realistic present day density profile in agreement with observations of voids. The model construction is an extension of previously developed algorithms for finding a Lemaitre-Tolman metric that evolves between two profiles of either density or velocity specified at two times. Of the 4 profiles of concern -- those of density and velocity at recombination and at the present day -- two can be specified and the other two follow from the derived model. We find that, in order to reproduce the present-day void density profiles, the initial velocity profile is more important than the initial density profile. Extrapolation of current CMB observations to the scales relevant to proto-voids is very uncertain. Even so, we find that it is very difficult to make both the initial density and velocity fluctuation amplitudes small enough, and still obtain a realistic void by today.Comment: MN2e LaTeX style file, 17 pages, 16 figures, 22 figure files; replecement has minor changes in reference

The cosmic web for density perturbations of various scales

We follow the evolution of galaxy systems in numerical simulation. Our goal is to understand the role of density perturbations of various scales in the formation and evolution of the cosmic web. We perform numerical simulations with the full power spectrum of perturbations, and with spectrum cut at long wavelengths. Additionally, we have one model, where we cut the intermediate waves. We analyze the density field and study the void sizes and density field clusters in different models. Our analysis shows that the fine structure (groups and clusters of galaxies) is created by small-scale density perturbations of scale $\leq 8$ \Mpc. Filaments of galaxies and clusters are created by perturbations of intermediate scale from $\sim 8$ to $\sim 32$ \Mpc, superclusters of galaxies by larger perturbations. We conclude that the scale of the pattern of the cosmic web is determined by density perturbations of scale up to $\sim 100$ \Mpc. Larger perturbations do not change the pattern of the web, but modulate the richness of galaxy systems, and make voids emptier. The stop of the increase of the scale of the pattern of the cosmic web with increasing scale of density perturbations can probably be explained as the freezing of the web at redshift $z\simeq 0.7$.Comment: 12 pages, 7 figures, accepted for publication in Astronomy and Astrophysic