Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection

SummaryMammalian CpG islands are key epigenomic elements that were first characterized experimentally as genomic fractions with low levels of DNA methylation. Currently, CpG islands are defined based on their genomic sequences alone. Here, we develop evolutionary models to show that several distinct evolutionary processes generate and maintain CpG islands. One central evolutionary regime resulting in enriched CpG content is driven by low levels of DNA methylation and consequentially low rates of CpG deamination. Another major force forming CpG islands is biased gene conversion that stabilizes constitutively methylated CpG islands by balancing rapid deamination with CpG fixation. Importantly, evolutionary analysis and population genetics data suggest that selection for high CpG content is not a significant factor contributing to conservation of CpGs in differentially methylated regions. The heterogeneous, but not selective, origins of CpG islands have direct implications for the understanding of DNA methylation patterns in healthy and diseased cells

Safety at what price? : setting anti-terrorist policies for checked luggage on US domestic aircraft

Thesis (S.M.)--Massachusetts Institute of Technology, Sloan School of Management, Operations Research Center, 2000.Includes bibliographical references (leaves 45-46).In this thesis, we considered the costs and benefits of implementing Positive Passenger Bag Match (PPBM) - an anti-terrorist measure to keep bombs out of checked luggage - on US domestic passenger flights. We constructed a stochastic model for comparing the cost-effectiveness of three alternative approaches to PPBM: no PPBML implementation; a PPBM implementation that is applied to 5% of passengers; and a full (100%) implementation of PPBM. We made ranges of estimates concerning the level of terrorist risk, the costs of PPBM operation, the consequences of successful terrorist bombings, and the anti-terrorist effectiveness of both the partial and full PPBM implementations. Calculations showed that there were circumstances under which each policy was the most cost-effective of the three. Of the three options, not implementing PPBM at all was the most cost-effective approach for the largest percentage of the scenarios considered. We found that 5% PPBM captured the next largest portion of the scenarios, and was generally the optimal strategy when annual PPBMI operation costs were low, when 5% PPBM anti-terrorist effectiveness was high, and when the consequences of successful bombings were severe. We found 100%(. PPBM to be the optimal strategy for most scenarios which involved highly costly terrorist bombings, a high level of terrorist risk, and a 100% PPBM policy that provided much added security over 5% PPBM.by Jonathan E.W. Cohen.S.M

Nonradiative interaction and entanglement between distant atoms

We show that nonradiative interactions between atomic dipoles placed in a waveguide can give rise to deterministic entanglement at ranges much larger than their resonant wavelength. The range increases as the dipole-resonance approaches the waveguide's cutoff frequency, caused by the giant density of photon modes near cutoff, a regime where the standard (perturbative) Markov approximation fails. We provide analytical theories for both the Markovian and non-Markovian regimes, supported by numerical simulations, and discuss possible experimental realizations.Comment: 9 pages, 2 figure

From "best practice" to "best fit": a framework for designing and analyzing pluralistic agricultural advisory services worldwide

"The paper develops a framework for the design and analysis of pluralistic agricultural advisory services and reviews research methods from different disciplines that can be used when applying the framework. Agricultural advisory services are defined in the paper as the entire set of organizations that support and facilitate people engaged in agricultural production to solve problems and to obtain information, skills and technologies to improve their livelihoods and well-being... To classify pluralistic agricultural advisory services, the paper distinguishes between organizations from the public, the private and the third sector that can be involved in (a) providing and (b) financing of agricultural advisory services. The framework for analyzing pluralistic agricultural advisory services presented in the paper addresses the need for analytical approaches that help policy-makers to identify those reform options that best fit country-specific frame conditions. Thus, the paper supports a shift from a “one-size-fits-all” to a “best fit” approach in the reform of public services... Based on a review of the literature, the paper presents a variety of quantitative and qualitative methodological approaches derived from different disciplines that can be applied when using the framework in empirical research projects. The disciplines include agricultural and institutional economics, communication theory, adult education, and public administration and management. The paper intends to inform researchers as well as practitioners, policy-makers and development partners who are interested in supporting evidence-based reform of agricultural advisory services. from Authors' AbstractAgricultural extension work, Pro-poor growth, Capacity strengthening,

Wavelet speech enhancement based on time-scale adaptation

Abstract : We propose a new speech enhancement method based on time and scale adaptation of wavelet thresholds. The time dependency is introduced by approximating the Teager Energy of the wavelet coefficients, while the scale dependency is introduced by extending the principle of level dependent threshold to Wavelet Packet Thresholding. This technique does not require an explicit estimation of the noise level or of the apriori knowledge of the SNR, as is usually needed in most of the popular enhancement methods. Performance of the proposed method is evaluated on speech recorded in real conditions (plane, sawmill, tank, subway, babble, car, exhibition hall, restaurant, street, airport, and train station) and artificially added noise. MELscale decomposition based on wavelet packets is also compared to the common wavelet packet scale. Comparison in terms of Signal-to-Noise Ratio (SNR) is reported for time adaptation and time-scale adaptation thresholding of the wavelet coefficients thresholding. Visual inspection of spectrograms and listening experiments are also used to support the results. Hidden Markov Models Speech recognition experiments are conducted on the AURORA–2 database and show that the proposed method improves the speech recognition rates for low SNRs

Qubit Coherent Control with Squeezed Light Fields

We study the use of squeezed light for qubit coherent control and compare it with the coherent state control field case. We calculate the entanglement between a short pulse of resonant squeezed light and a two-level atom in free space and the resulting operation error. We find that the squeezing phase, the phase of the light field and the atomic superposition phase, all determine whether atom-pulse mode entanglement and the gate error are enhanced or suppressed. However, when averaged over all possible qubit initial states, the gate error would not decrease by a practicably useful amount and would in fact increase in most cases. We discuss the possibility of measuring the increased gate error as a signature of the enhancement of entanglement by squeezing.Comment: 12 pages, 6 figure

Reconstruction-based speech enhancement from robust acoustic features

This paper proposes a method of speech enhancement where a clean speech signal is reconstructed from a sinusoidal model of speech production and a set of acoustic speech features. The acoustic features are estimated from noisy speech and comprise, for each frame, a voicing classification (voiced, unvoiced or non-speech), fundamental frequency (for voiced frames) and spectral envelope. Rather than using different algorithms to estimate each parameter, a single statistical model is developed. This comprises a set of acoustic models and has similarity to the acoustic modelling used in speech recognition. This allows noise and speaker adaptation to be applied to acoustic feature estimation to improve robustness. Objective and subjective tests compare reconstruction-based enhancement with other methods of enhancement and show the proposed method to be highly effective at removing noise

Recreating living experiences from past memories through virtual worlds for people with dementia

This paper describes a study aimed to understand the use of 3D virtual world (VW) technology to support life engagement for people with dementia in long-term care. Three versions of VW prototypes (reminiscence room, virtual tour and gardening) utilising gestured-base interaction were developed iteratively. These prototypes were tested with older residents (80+) with dementia in care homes and their caregivers. Data collection was based on observations of how the residents and care staff interacted collaboratively with the VW. We discussed in depth the use of VWs in stimulating past memories and how this technology could help enhance their sense of self through various means. We also highlighted key approaches in designing VWs to sustain attention, create ludic experiences and facilitate interaction for older people with dementia