Bounded-time fault-tolerant rule-based systems

Two systems concepts are introduced: bounded response-time and self-stabilization in the context of rule-based programs. These concepts are essential for the design of rule-based programs which must be highly fault tolerant and perform in a real time environment. The mechanical analysis of programs for these two properties is discussed. The techniques are used to analyze a NASA application

Long-term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (1) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation, and; (2) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky-islands (the Transmexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains, and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow

AVENS - A Novel Flying Ad Hoc Network Simulator with Automatic Code Generation for Unmanned Aircraft System

The wireless communication has played a significant impact on our daily lives introducing simplicity and making life more comfortable. \ As a result of faster technological advances in electronics and communications, the development of different types of unmanned aerial vehicles (UAVs) has become possible. \ Recently, many efforts have been made to develop more efficient inter- and intra-vehicle communication protocols introducing new challenges, e. g. multiple-UAV communication and Flying Ad Hoc Networks (FANETs). \ However, most of the experiments using real prototypes or systems are not feasible due to the costs and risks involved. \ Thus, simulating network protocol behavior in FANET scenarios is increasingly required to evaluate the applicability of developed network protocols. \ Thereby, we have been developing AVENS, a hybrid aerial network simulation framework, which merges LARISSA Architectural Model, X-Plane Flight Simulator and OMNeT++ Discrete Event Simulator. \ In a proof-of-concept study, we highlighted its advantages. \ Using AVENS, we can advance in the state-of-the-art concerning performance evaluation of intelligent aerial vehicles and provide means to evaluate the development of protocols, codes and systems more accurately

Geography, climate and shifts in host plants distribution explain the genomic variation in the cactus moth

Landscape heterogeneity and the host plant use are factors suggested to play determinant roles in shaping the evolutionary history of herbivorous insects. However, the role of the reconfiguration of host plants distributions linked to Quaternary climate oscillations as drivers of contemporary population genetic structure is still poorly understood. Here, we formally examine the relative contribution of such factors on intraspecific diversification using the South American cactus moth, Cactoblastis cactorum, an herbivore insect specialized in the use of cacti as host plants. We assessed genomic variation using genome-wide SNPs and mitochondrial data in populations sampled across a broad geographical gradient where moths feed on different cactus species. We integrated demographic simulations and ecological niche modeling into a landscape genomics framework, to test alternative hypotheses of past and current population connectivity for both C. cactorum and its host plants. Regions exhibiting higher genomic diversity were evaluated for congruence with areas where suitable climatic conditions remained stable through time. Our results revealed that past spatial configuration of suitable habitat conditions and shifts of host plants distributions are the factors that better explain the intraspecific diversification. Genomic data also supported the hypothesis that areas of long-term habitat stability served as refugia for C. cactorum, enabling the maintenance of high levels of genetic diversity over time. Overall, our study highlights the importance of integrating inter-specific interactions and their spatio-temporal dynamics to better understand the relative importance of abiotic and biotic factors driving the diversification processes in herbivorous insects with broad geographical and restricted host ranges

Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data

RNA sequencing (RNA-Seq) is the current method of choice for characterizing transcriptomes and quantifying gene expression changes. This next generation sequencing-based method provides unprecedented depth and resolution. The negative binomial (NB) probability distribution has been shown to be a useful model for frequencies of mapped RNA-Seq reads and consequently provides a basis for statistical analysis of gene expression. Negative binomial exact tests are available for two-group comparisons but do not extend to negative binomial regression analysis, which is important for examining gene expression as a function of explanatory variables and for adjusted group comparisons accounting for other factors. We address the adequacy of available large-sample tests for the small sample sizes typically available from RNA-Seq studies and consider a higher-order asymptotic (HOA) adjustment to likelihood ratio tests. We demonstrate that 1) the HOA-adjusted likelihood ratio test is practically indistinguishable from the exact test in situations where the exact test is available, 2) the type I error of the HOA test matches the nominal specification in regression settings we examined via simulation, and 3) the power of the likelihood ratio test does not appear to be affected by the HOA adjustment. This work helps clarify the accuracy of the unadjusted likelihood ratio test and the degree of improvement available with the HOA adjustment. Furthermore, the HOA test may be preferable even when the exact test is available because it does not require ad hoc library size adjustments.Keywords: Regression, RNA-Seq, Overdispersion, Extra- Poisson variation, Negative binomial, Higher-order asymptotic

Spatial and seasonal variability of the air-sea equilibration timescale of carbon dioxide

The exchange of carbon dioxide between the ocean and the atmosphere tends to bring waters within the mixed layer toward equilibrium by reducing the partial pressure gradient across the air-water interface. However, the equilibration process is not instantaneous; in general, there is a lag between forcing and response. The timescale of air-sea equilibration depends on several factors involving the depth of the mixed layer, wind speed, and carbonate chemistry. We use a suite of observational data sets to generate climatological and seasonal composite maps of the air-sea equilibration timescale. The relaxation timescale exhibits considerable spatial and seasonal variations that are largely set by changes in mixed layer depth and wind speed. The net effect is dominated by the mixed layer depth; the gas exchange velocity and carbonate chemistry parameters only provide partial compensation. Broadly speaking, the adjustment timescale tends to increase with latitude. We compare the observationally derived air-sea gas exchange timescale with a model-derived surface residence time and a data-derived horizontal transport timescale, which allows us to define two nondimensional metrics of equilibration efficiency. These parameters highlight the tropics, subtropics, and northern North Atlantic as regions of inefficient air-sea equilibration where carbon anomalies are relatively likely to persist. The efficiency parameters presented here can serve as simple tools for understanding the large-scale persistence of air-sea disequilibrium of CO2 in both observations and models

Cheddar: analysis and visualisation of ecological communities in R

There has been a lack of software available to ecologists for the management, visualisation and analysis of ecological community and food web data. Researchers have been forced to implement their own data formats and software, often from scratch, resulting in duplicated effort and bespoke solutions that are difficult to apply to future analyses and comparative studies. We introduce Cheddar – an R package that provides standard, transparent implementations of a wide range of food web and community-level analyses and plots, focussing on ecological network data that are augmented with estimates of body mass and/or numerical abundance. The package allows analysis of individual communities, as well as collections of communities, allowing examination of changes in structure through time, across environmental gradients, or due to experimental manipulations. Several commonly analysed food web data sets are included and used in worked examples. This is the first time these important features have been combined in a single package that helps improve research efficiency and serves as a unified framework for future development