On the Estimation of Nonrandom Signal Coefficients from Jittered Samples

This paper examines the problem of estimating the parameters of a bandlimited signal from samples corrupted by random jitter (timing noise) and additive iid Gaussian noise, where the signal lies in the span of a finite basis. For the presented classical estimation problem, the Cramer-Rao lower bound (CRB) is computed, and an Expectation-Maximization (EM) algorithm approximating the maximum likelihood (ML) estimator is developed. Simulations are performed to study the convergence properties of the EM algorithm and compare the performance both against the CRB and a basic linear estimator. These simulations demonstrate that by post-processing the jittered samples with the proposed EM algorithm, greater jitter can be tolerated, potentially reducing on-chip ADC power consumption substantially.Comment: 11 pages, 8 figure

Adaptive evolution is substantially impeded by Hill–Robertson interference in Drosophila

Hill–Robertson interference (HRi) is expected to reduce the efficiency of natural selection when two or more linked selected sites do not segregate freely, but no attempt has been done so far to quantify the overall impact of HRi on the rate of adaptive evolution for any given genome. In this work, we estimate how much HRi impedes the rate of adaptive evolution in the coding genome of Drosophila melanogaster. We compiled a data set of 6,141 autosomal protein-coding genes from Drosophila, from which polymorphism levels in D. melanogaster and divergence out to D. yakuba were estimated. The rate of adaptive evolution was calculated using a derivative of the McDonald–Kreitman test that controls for slightly deleterious mutations. We find that the rate of adaptive amino acid substitution at a given position of the genome is positively correlated to both the rate of recombination and the mutation rate, and negatively correlated to the gene density of the region. These correlations are robust to controlling for each other, for synonymous codon bias and for gene functions related to immune response and testes. We show that HRi diminishes the rate of adaptive evolution by approximately 27%. Interestingly, genes with low mutation rates embedded in gene poor regions lose approximately 17% of their adaptive substitutions whereas genes with high mutation rates embedded in gene rich regions lose approximately 60%. We conclude that HRi hampers the rate of adaptive evolution in Drosophila and that the variation in recombination, mutation, and gene density along the genome affects the HRi effect

Gene duplicability of core genes is highly consistent across all angiosperms

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes

Sorption Thermodynamics of CO2, H2O, and CH3OH in a Glassy Polyetherimide: A Molecular Perspective

In this paper, the sorption thermodynamics of low-molecular-weight penetrants in a glassy polyetherimide, endowed with specific interactions, is addressed by combining an experimental approach based on vibrational spectroscopy with thermodynamics modeling. This modeling approach is based on the extension of equilibrium theories to the out-of-equilibrium glassy state. Specific interactions are accounted for in the framework of a compressible lattice fluid theory. In particular, the sorption of carbon dioxide, water, and methanol is illustrated, exploiting the wealth of information gathered at a molecular level from Fourier-transform infrared (FTIR) spectroscopy to tailor thermodynamics modeling. The investigated penetrants display a different interacting characteristic with respect to the polymer substrate, which reflects itself in the sorption thermodynamics. For the specific case of water, the outcomes from molecular dynamics simulations are compared with the results of the present analysis

Ranked Sparse Signal Support Detection

This paper considers the problem of detecting the support (sparsity pattern) of a sparse vector from random noisy measurements. Conditional power of a component of the sparse vector is defined as the energy conditioned on the component being nonzero. Analysis of a simplified version of orthogonal matching pursuit (OMP) called sequential OMP (SequOMP) demonstrates the importance of knowledge of the rankings of conditional powers. When the simple SequOMP algorithm is applied to components in nonincreasing order of conditional power, the detrimental effect of dynamic range on thresholding performance is eliminated. Furthermore, under the most favorable conditional powers, the performance of SequOMP approaches maximum likelihood performance at high signal-to-noise ratio.Comment: 13 page

Adaptive detection of a signal known only to lie on a line in a known subspace, when primary and secondary data are partially homogeneous

This paper deals with the problem of detecting a signal, known only to lie on a line in a subspace, in the presence of unknown noise, using multiple snapshots in the primary data. To account for uncertainties about a signal's signature, we assume that the steering vector belongs to a known linear subspace. Furthermore, we consider the partially homogeneous case, for which the covariance matrix of the primary and the secondary data have the same structure but possibly different levels. This provides an extension to the framework considered by Bose and Steinhardt. The natural invariances of the detection problem are studied, which leads to the derivation of the maximal invariant. Then, a detector is proposed that proceeds in two steps. First, assuming that the noise covariance matrix is known, the generalized-likelihood ratio test (GLRT) is formulated. Then, the noise covariance matrix is replaced by its sample estimate based on the secondary data to yield the final detector. The latter is compared with a similar detector that assumes the steering vector to be known