The effects of weak selection on neutral diversity at linked sites

The effects of selection on variability at linked sites have an important influence on levels and patterns of within-population variation across the genome. Most theoretical models of these effects have assumed that selection is sufficiently strong that allele frequency changes at the loci concerned are largely deterministic. These models have led to the conclusion that directional selection for new selectively favorable mutations, or against recurrent deleterious mutations, reduces nucleotide site diversity at linked neutral sites. Recent work has shown, however, that fixations of weakly selected mutations, accompanied by significant stochastic changes in allele frequencies, can sometimes cause higher diversity at linked sites when compared with the effects of fixations of neutral mutations. The present paper extends this work by deriving approximate expressions for the mean times to loss and fixation of mutations subject to selection, and analysing the conditions under which selection increases rather than reduces these times. Simulations are used to examine the relations between diversity at a neutral site and the fixation and loss times of mutations at a linked site subject to selection. It is shown that the long-term level of neutral diversity can be increased over the equilibrium expectation in the absence of selection by recurrent fixations and losses of linked, weakly selected dominant or partially dominant favorable mutations, and by linked recessive or partially recessive deleterious mutations. The results are used to examine the conditions under which associative overdominance, as opposed to background selection, is likely to operate.

Development of a new rain attenuation model for tropical location

This study proposes a new rain attenuation prediction model (RAM) based on the rain cell concept for tropical locations. The new model addresses the research gap in the international telecommunications union (ITU) model. Results obtained show that the proposed RAM predicted the possibility of signal across seven (7) out of thirteen (13) stations monitored. The predicted attenuation values were 18.3427 dB, 18.8106 dB, 18.3921 dB, 13.8062 dB, 20.8803 dB, 9.4519 dB, and 19.6018 dB for Jalingo, Jos, Makurdi, Mubi, Otukpo, Sokoto, and Abuja respectively. However, the RAM predicted outage across six stations with predicted attenuation values of 31.7040 dB, 26.8302 dB, 28.6635 dB, 29.6562 dB, 28.8827 dB, and 30.0614 dB for Akwa-Ibom, Benin, Donga, Port-Harcourt, Owerri, and Aba respectively. The proposed RAM hence suggests an additional Ku-band spot beam power of at least 331.97 watts for Nigeria's Nigerian communication satellite-1 (NIGCOMSAT-1R) Ku-band transponder to overcome the predicted attenuation across the six stations which recorded signal outage. The results from this study can be used by network engineers for the implementation of fade mitigation techniques (FMTs) such as site diversity and power control to aid telecommunication networks anticipate changes and allocate resources accordingly.

Field-theoretic density estimation for biological sequence space with applications to 5′ splice site diversity and aneuploidy in cancer

Density estimation in sequence space is a fundamental problem in machine learning that is also of great importance in computational biology. Due to the discrete nature and large dimensionality of sequence space, how best to estimate such probability distributions from a sample of observed sequences remains unclear. One common strategy for addressing this problem is to estimate the probability distribution using maximum entropy (i.e., calculating point estimates for some set of correlations based on the observed sequences and predicting the probability distribution that is as uniform as possible while still matching these point estimates). Building on recent advances in Bayesian field-theoretic density estimation, we present a generalization of this maximum entropy approach that provides greater expressivity in regions of sequence space where data are plentiful while still maintaining a conservative maximum entropy character in regions of sequence space where data are sparse or absent. In particular, we define a family of priors for probability distributions over sequence space with a single hyperparameter that controls the expected magnitude of higher-order correlations. This family of priors then results in a corresponding one-dimensional family of maximum a posteriori estimates that interpolate smoothly between the maximum entropy estimate and the observed sample frequencies. To demonstrate the power of this method, we use it to explore the high-dimensional geometry of the distribution of 5′ splice sites found in the human genome and to understand patterns of chromosomal abnormalities across human cancers.

Robust, data-driven bioregionalizations emerge from diversity concordance

Aim: Despite the increasing interest in developing new bioregionalizations and assessing the most widely accepted biogeographic frameworks, no study to date has sought to systematically define a system of small bioregions nested within larger ones that better reflect the distribution and patterns of biodiversity. Here, we examine how an algorithmic, data-driven model of diversity patterns can lead to an ecologically interpretable hierarchy of bioregions. Location: Australia. Time period: Present. Major taxa studied: Terrestrial vertebrates and vascular plants. Methods: We compiled information on the biophysical characteristics and species occupancy of Australia′s geographic conservation units (bioregions). Then, using cluster analysis to identify groupings of bioregions representing optimal discrete-species areas, we evaluated what a hierarchical bioregionalization system would look like when based empirically on the within- and between-site diversity patterns across taxa. Within an information-analytical framework, we then assessed the degree to which the World Wildlife Fund′s (WWF) biomes and ecoregions and our suite of discrete-species areas are spatially associated and compared those results among bioregionalization scenarios. Results: Information on biodiversity patterns captured was moderate for WWF′s biomes (50–58% for birds′ beta, and plants′ alpha and beta diversity, of optimal discrete areas, respectively) and ecoregions (additional 4–25%). Our plants and vertebrate optimal areas retained more information on alpha and beta diversity across taxa, with the two algorithmically derived biogeographic scenarios sharing 86.5% of their within- and between-site diversity information. Notably, discrete-species areas for beta diversity were parsimonious with respect to those for alpha diversity. Main conclusions: Nested systems of bioregions must systematically account for the variation of species diversity across taxa if biodiversity research and conservation action are to be most effective across multiple spatial or temporal planning scales. By demonstrating an algorithmic rather than subjective method for defining bioregionalizations using species-diversity concordances, which reliably reflects the distributional patterns of multiple taxa, this work offers a valuable new tool for systematic conservation planning.

Performance of Micro-Scale Transmission & Reception Diversity Schemes in High Throughput Satellite Communication Networks

The use of Ka and Q/V bands could be a promising solution in order to accommodate higher data rate, interactive services; however, at these frequency bands signal attenuation due to the various atmospheric phenomena and more particularly due to rain could constitute a serious limiting factor in system performance and availability. To alleviate this possible barrier, short- and large-scale diversity schemes have been proposed and examined in the past; in this paper a micro-scale site diversity system is evaluated in terms of capacity gain using rain attenuation time series generated using the Synthetic Storm Technique (SST). Input to the SST was 4 years of experimental rainfall data from two stations with a separation distance of 386 m at the National Technical University of Athens (NTUA) campus in Athens, Greece. Additionally, a novel multi-dimensional synthesizer based on Gaussian Copulas parameterized for the case of multiple-site micro-scale diversity systems is presented and evaluated. In all examined scenarios a significant capacity gain can be observed, thus proving that micro-scale site diversity systems could be a viable choice for enterprise users to increase the achievable data rates and improve the availability of their links.

Research and Development of a Transportable Optical Ground Station in NICT: The Results of the First Performance Test

In recent years, the necessity of free-space optical (FSO) communications has increased as a method for realizing high-speed communications between satellites and the ground. However, one disadvantage of FSO communications is the significant influence of the atmosphere. Specifically, FSO communications cannot be utilized under certain atmospheric conditions, especially in the presence of clouds. One of the solutions to this problem is the site diversity technique, which makes it possible to select a given ground station with better atmospheric conditions among a number of fixed ground stations. The other solution is to prepare a ground station that can be moved to a place with better atmospheric conditions. We applied the latter method and developed a transportable optical ground station in NICT. We utilize a realistic telescope diameter, which is about 30 cm at the maximum, capable of being set up quickly, and with a pointing accuracy of about 100 µrad. In addition, it is necessary to prepare a fine-pointing optical system that performs tracking with about 1/10 of the pointing accuracy of the telescope. In this paper, we report the results of the first performance test of the transportable optical ground station in NICT.