Computational inference in systems biology

Parameter inference in mathematical models of biological pathways, expressed as coupled ordinary differential equations (ODEs), is a challenging problem. The computational costs associated with repeatedly solving the ODEs are often high. Aimed at reducing this cost, new concepts using gradient matching have been proposed. This paper combines current adaptive gradient matching approaches, using Gaussian processes, with a parallel tempering scheme, and conducts a comparative evaluation with current methods used for parameter inference in ODEs

Alexander representation of tangles

A tangle is an oriented 1-submanifold of the cylinder whose endpoints lie on the two disks in the boundary of the cylinder. Using an algebraic tool developed by Lescop, we extend the Burau representation of braids to a functor from the category of oriented tangles to the category of Z[t,t^{-1}]-modules. For (1,1)-tangles (i.e., tangles with one endpoint on each disk) this invariant coincides with the Alexander polynomial of the link obtained by taking the closure of the tangle. We use the notion of plat position of a tangle to give a constructive proof of invariance in this case.Comment: 13 pages, 5 figure

Analysis of No-Difference Findings in Evaluation Research

Conclusions of no difference are becoming increasingly important in evaluation research. We delineate three major uses of no-difference findings and analyze their meanings. (1) No-differ ence findings in randomized experiments can be interpreted as support for conclusions of the absence of a meaningful treatment effect, but only if the proper analytic methods are used. (2) Statistically based conclusions in quasi-experiments do not allow causal statements about the treatment impact but do provide a metric to judge the size of the resulting difference. (3) Using no-difference findings to conclude equivalence on control variables is inefficient and potentially misleading. The final section of the article presents alternative methods by which conclusions of no difference may be supported when applicable. These methods include the use of arbitrarily high alpha levels, interval estimation, and power analysis.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67182/2/10.1177_0193841X8901300604.pd

Studying the vertical extent of the ground layer turbulence using sonic-anemometers

The optical turbulence above Dome C in winter is mainly concentrated in the first tens of meters above the ground. The properties of this so-called surface layer were investigated during the last two winterover by a set of sonics anemometers placed on a 45 m high tower. These anemometers provide measurements of the temperature and the wind speed vector. The sampling rate of 10 Hz allows to derivate the refractive index structure constant C_n^2. We report here the first analysis of these data

Neuropsychological constraints to human data production on a global scale

Which are the factors underlying human information production on a global level? In order to gain an insight into this question we study a corpus of 252-633 Million publicly available data files on the Internet corresponding to an overall storage volume of 284-675 Terabytes. Analyzing the file size distribution for several distinct data types we find indications that the neuropsychological capacity of the human brain to process and record information may constitute the dominant limiting factor for the overall growth of globally stored information, with real-world economic constraints having only a negligible influence. This supposition draws support from the observation that the files size distributions follow a power law for data without a time component, like images, and a log-normal distribution for multimedia files, for which time is a defining qualia.Comment: to be published in: European Physical Journal

The Taming of Closed Time-like Curves

We consider a $R^{1,d}/Z_2$ orbifold, where $Z_2$ acts by time and space reversal, also known as the embedding space of the elliptic de Sitter space. The background has two potentially dangerous problems: time-nonorientability and the existence of closed time-like curves. We first show that closed causal curves disappear after a proper definition of the time function. We then consider the one-loop vacuum expectation value of the stress tensor. A naive QFT analysis yields a divergent result. We then analyze the stress tensor in bosonic string theory, and find the same result as if the target space would be just the Minkowski space $R^{1,d}$, suggesting a zero result for the superstring. This leads us to propose a proper reformulation of QFT, and recalculate the stress tensor. We find almost the same result as in Minkowski space, except for a potential divergence at the initial time slice of the orbifold, analogous to a spacelike Big Bang singularity. Finally, we argue that it is possible to define local S-matrices, even if the spacetime is globally time-nonorientable.Comment: 37 pages, LaTeX2e, uses amssymb, amsmath and epsf macros, 8 eps and 3 ps figures; (v2): Two additional comments + one reference added; (v3): corrections in discussion of CTCs + some clarification

Magnetic Resonance Imaging of Plantar Plate Rupture

Degenerative plantar plate failure is an under-recognized cause of lesser metatarsalgia. We performed magnetic resonance imaging (MRI) with a small receiver coil in 13 patients in whom plantar plate ruptures of the second or third metatarsophalangeal joint were clinically suspected. In eight patients, MRI showed focal hyperintensity in the plantar plate that was interpreted as a rupture of the plate. Ruptures were confirmed in all five patients who underwent an operative procedure to treat the unstable, painful metatarsophalangeal joint. MRI is a noninvasive technique that can visualize plantar plate abnormalities and aid the clinical evaluation of problematic lesser metatarsalgia

Multi-Leg One-Loop Gravity Amplitudes from Gauge Theory

By exploiting relations between gravity and gauge theories, we present two infinite sequences of one-loop n-graviton scattering amplitudes: the `maximally helicity-violating' amplitudes in N=8 supergravity, and the `all-plus' helicity amplitudes in gravity with any minimally coupled massless matter content. The all-plus amplitudes correspond to self-dual field configurations and vanish in supersymmetric theories. We make use of the tree-level Kawai-Lewellen-Tye (KLT) relations between open and closed string theory amplitudes, which in the low-energy limit imply relations between gravity and gauge theory tree amplitudes. For n < 7, we determine the all-plus amplitudes explicitly from their unitarity cuts. The KLT relations, applied to the cuts, allow us to extend to gravity a previously found `dimension-shifting' relation between (the cuts of) the all-plus amplitudes in gauge theory and the maximally helicity-violating amplitudes in N=4 super-Yang-Mills theory. The gravitational version of the relation lets us determine the n < 7 N=8 supergravity amplitudes from the all-plus gravity amplitudes. We infer the two series of amplitudes for all n from their soft and collinear properties, which can also be derived from gauge theory using the KLT relations.Comment: Minor errors corrected, Latex, 53 page