Baseline correction for NMR spectroscopic metabolomics data analysis.

BackgroundWe propose a statistically principled baseline correction method, derived from a parametric smoothing model. It uses a score function to describe the key features of baseline distortion and constructs an optimal baseline curve to maximize it. The parameters are determined automatically by using LOWESS (locally weighted scatterplot smoothing) regression to estimate the noise variance.ResultsWe tested this method on 1D NMR spectra with different forms of baseline distortions, and demonstrated that it is effective for both regular 1D NMR spectra and metabolomics spectra with over-crowded peaks.ConclusionCompared with the automatic baseline correction function in XWINNMR 3.5, the penalized smoothing method provides more accurate baseline correction for high-signal density metabolomics spectra

Distributed Algorithms for Spectrum Allocation, Power Control, Routing, and Congestion Control in Wireless Networks

We develop distributed algorithms to allocate resources in multi-hop wireless networks with the aim of minimizing total cost. In order to observe the fundamental duplexing constraint that co-located transmitters and receivers cannot operate simultaneously on the same frequency band, we first devise a spectrum allocation scheme that divides the whole spectrum into multiple sub-bands and activates conflict-free links on each sub-band. We show that the minimum number of required sub-bands grows asymptotically at a logarithmic rate with the chromatic number of network connectivity graph. A simple distributed and asynchronous algorithm is developed to feasibly activate links on the available sub-bands. Given a feasible spectrum allocation, we then design node-based distributed algorithms for optimally controlling the transmission powers on active links for each sub-band, jointly with traffic routes and user input rates in response to channel states and traffic demands. We show that under specified conditions, the algorithms asymptotically converge to the optimal operating point.Comment: 14 pages, 5 figures, submitted to IEEE/ACM Transactions on Networkin

Optimization of Quantum Monte Carlo Wave Functions Using Analytical Energy Derivatives

An algorithm is proposed to optimize quantum Monte Carlo (QMC) wave functions based on New ton's method and analytical computation of the first and second derivatives of the variati onal energy. This direct application of the variational principle yields significantly low er energy than variance minimization methods when applied to the same trial wave function. Quadratic convergence to the local minimum of the variational parameters is achieved. A g eneral theorem is presented, which substantially simplifies the analytic expressions of de rivatives in the case of wave function optimization. To demonstrate the method, the ground state energies of the first-row elements are calculated.Comment: 8 pages, 3 figure

Switchable resonant coupling of flux qubits

We propose a coupling scheme, where two or more flux qubits with different eigenfrequencies share Josephson junctions with a coupler loop devoid of its own quantum dynamics. Switchable two-qubit coupling is realized by tuning the frequency of the AC magnetic flux through the coupler to a combination frequency of two of the qubits. The coupling allows any or all of the qubits to be simultaneously at the degeneracy point and can change sign.Comment: REVTeX 4, 4 pages, 2 figures, v2: reference added, v3: final version published in Phys. Rev.

An age-of-allele test of neutrality for transposable element insertions

How natural selection acts to limit the proliferation of transposable elements (TEs) in genomes has been of interest to evolutionary biologists for many years. To describe TE dynamics in populations, many previous studies have used models of transposition-selection equilibrium that rely on the assumption of a constant rate of transposition. However, since TE invasions are known to happen in bursts through time, this assumption may not be reasonable in natural populations. Here we propose a test of neutrality for TE insertions that does not rely on the assumption of a constant transposition rate. We consider the case of TE insertions that have been ascertained from a single haploid reference genome sequence and have subsequently had their allele frequency estimated in a population sample. By conditioning on the age of an individual TE insertion (using information contained in the number of substitutions that have occurred within the TE sequence since insertion), we determine the probability distribution for the insertion allele frequency in a population sample under neutrality. Taking models of varying population size into account, we then evaluate predictions of our model against allele frequency data from 190 retrotransposon insertions sampled from North American and African populations of Drosophila melanogaster. Using this non-equilibrium model, we are able to explain about 80% of the variance in TE insertion allele frequencies based on age alone. Controlling both for nonequilibrium dynamics of transposition and host demography, we provide evidence for negative selection acting against most TEs as well as for positive selection acting on a small subset of TEs. Our work establishes a new framework for the analysis of the evolutionary forces governing large insertion mutations like TEs, gene duplications or other copy number variants.Comment: 40 pages, 6 figures, Supplemental Data available: [email protected]

Analytic thermodynamics and thermometry of Gaudin-Yang Fermi gases

We study the thermodynamics of a one-dimensional attractive Fermi gas (the Gaudin-Yang model) with spin imbalance. The exact solution has been known from the thermodynamic Bethe ansatz for decades, but it involves an infinite number of coupled nonlinear integral equations whose physics is difficult to extract. Here the solution is analytically reduced to a simple, powerful set of four algebraic equations. The simplified equations become universal and exact in the experimental regime of strong interaction and relatively low temperature. Using the new formulation, we discuss the qualitative features of finite-temperature crossover and make quantitative predictions on the density profiles in traps. We propose a practical two-stage scheme to achieve accurate thermometry for a trapped spin-imbalanced Fermi gas.Comment: 4 pages, 2 figures; published version (v2