A survey of probabilistic methods used in reliability, risk and uncertainty analysis: Analytical techniques 1

This report provides an introduction to the various probabilistic methods developed roughly between 1956--1985 for performing reliability or probabilistic uncertainty analysis on complex systems. This exposition does not include the traditional reliability methods (e.g. parallel-series systems, etc.) that might be found in the many reliability texts and reference materials (e.g. and 1977). Rather, the report centers on the relatively new, and certainly less well known across the engineering community, analytical techniques. Discussion of the analytical methods has been broken into two reports. This particular report is limited to those methods developed between 1956--1985. While a bit dated, methods described in the later portions of this report still dominate the literature and provide a necessary technical foundation for more current research. A second report (Analytical Techniques 2) addresses methods developed since 1985. The flow of this report roughly follows the historical development of the various methods so each new technique builds on the discussion of strengths and weaknesses of previous techniques. To facilitate the understanding of the various methods discussed, a simple 2-dimensional problem is used throughout the report. The problem is used for discussion purposes only; conclusions regarding the applicability and efficiency of particular methods are based on secondary analyses and a number of years of experience by the author. This document should be considered a living document in the sense that as new methods or variations of existing methods are developed, the document and references will be updated to reflect the current state of the literature as much as possible. For those scientists and engineers already familiar with these methods, the discussion will at times become rather obvious. However, the goal of this effort is to provide a common basis for future discussions and, as such, will hopefully be useful to those more intimate with probabilistic analysis and design techniques. There are clearly alternative methods of dealing with uncertainty (e.g. fuzzy set theory, possibility theory), but this discussion will be limited to those methods based on probability theory

Design and analysis of Bar-seq experiments

High-throughput quantitative DNA sequencing enables the parallel phenotyping of pools of thousands of mutants. However, the appropriate analytical methods and experimental design that maximize the efficiency of these methods while maintaining statistical power are currently unknown. Here, we have used Bar-seq analysis of the Saccharomyces cerevisiae yeast deletion library to systematically test the effect of experimental design parameters and sequence read depth on experimental results. We present computational methods that efficiently and accurately estimate effect sizes and their statistical significance by adapting existing methods for RNA-seq analysis. Using simulated variation of experimental designs, we found that biological replicates are critical for statistical analysis of Bar-seq data, whereas technical replicates are of less value. By subsampling sequence reads, we found that when using four-fold biological replication, 6 million reads per condition achieved 96% power to detect a two-fold change (or more) at a 5% false discovery rate. Our guidelines for experimental design and computational analysis enables the study of the yeast deletion collection in up to 30 different conditions in a single sequencing lane. These findings are relevant to a variety of pooled genetic screening methods that use high-throughput quantitative DNA sequencing, including Tn-seq

Liver fat in adults with GH deficiency: comparison to matched controls and the effect of GH replacement

CONTEXT: Existing data regarding the association between growth hormone deficiency (GHD) and liver fat content are conflicting. OBJECTIVE: We aimed i) to assess intrahepatocellular lipid (IHCL) content in hypopituitary adults with GHD compared to matched controls and ii) to evaluate the effect of growth hormone (GH) replacement on IHCL content. DESIGN: Cross-sectional comparison and controlled intervention study. PATIENTS, PARTICIPANTS: Cross-sectional comparison: 22 hypopituitary adults with GHD and 44 healthy controls matched for age, BMI, gender and ethnicity. Intervention study: 9 GHD patients starting GH replacement (GH Rx group), 9 GHD patients not starting replacement therapy (non-GH Rx group). INTERVENTION: Intervention study:GH replacement for 6 months in the GH Rx group, dosage was titrated to achieve normal IGF-1 levels. MAIN OUTCOME MEASURES: IHCL content determined by proton magnetic resonance spectroscopy (1 H MRS). RESULTS: Cross-sectional comparison: There was no difference in IHCL content between GHD patients and healthy controls (1.89% (0.30, 4.03) vs. 1.14% (0.22, 2.32); p=0.2), the prevalence of patients with hepatic steatosis (IHCL of ≥ 5.56%) was similar in the two groups (22.7% vs. 15.9%; chi square probability = 0.4). Intervention study: The change in IHCL content over 6 months did not differ between the GH Rx group and the non-GH Rx group (-0.63 ± 4.53% vs. +0.11 ± 1.46%; p=0.6). CONCLUSIONS: In our study liver fat content and the prevalence of hepatic steatosis did not differ between hypopituitary adults with GHD and matched controls. In GHD patients GH replacement had no effect on liver fat content

Phosphoproteins and protein-kinase activity in isolated envelopes of pea (Pisum sativum L.) chloroplasts

A protein kinase was found in envelope membranes of purified pea (Pisum sativum L.) chloroplasts. Separation of the two envelope membranes showed that most of the enzyme activity was localized in the outer envelope. The kinase was activated by Mg2+ and inhibited by ADP and pyrophosphate. It showed no response to changes in pH in the physiological range (pH 7-8) or conventional protein substrates. Up to ten phosphorylated proteins could be detected in the envelope-membrane fraction. The molecular weights of these proteins, as determined by polyacrylamide-gel electrophoresis were: two proteins higher than 145 kDa, 97, 86, 62, 55, 46, 34 and 14 kDa. The 86-kDa band being the most pronounced. Experiments with separated inner and outer envelopes showed that most labeled proteins are also localized in the outer-envelope fraction. The results indicate a major function of the outer envelope in the communication between the chloroplast and the parent cell

Effects of land markets and land management on ecosystem function: A framework for modelling exurban land-change

This paper presents the conceptual design and application of a new land-change modelling framework that represents geographical, sociological, economic, and ecological aspects of a land system. The framework provides an overarching design that can be extended into specific model implementations to evaluate how policy, land-management preferences, and land-market dynamics affect (and are affected by) land-use and land-cover change patterns and subsequent carbon storage and flux. To demonstrate the framework, we implement a simple integration of a new agent-based model of exurban residential development and land-management decisions with the ecosystem process model BIOME-BGC. Using a stylized scenario, we evaluate the influence of different exurban residential-land-management strategies on carbon storage at the parcel level over a 48-year period from 1958 to 2005, simulating stocks of carbon in soil, litter, vegetation, and net primary productivity. Results show 1) residential parcels with management practices that only provided additions in the form of fertilizer and irrigation to turfgrass stored slightly more carbon than parcels that did not include management practices, 2) conducting no land-management strategy stored more carbon than implementing a strategy that included removals in the form of removing coarse woody debris from dense tree cover and litter from turfgrass, and 3) the removal practices modelled had a larger impact on total parcel carbon storage than our modelled additions. The degree of variation within the evaluated land-management practices was approximately 42,104 kg C storage on a 1.62 ha plot after 48 years, demonstrating the substantial effect that residential land-management practices can have on carbon storag

Further constraints on electron acceleration in solar noise storms

We reexamine the energetics of nonthermal electron acceleration in solar noise storms. A new result is obtained for the minimum nonthermal electron number density required to produce a Langmuir wave population of sufficient intensity to power the noise storm emission. We combine this constraint with the stochastic electron acceleration formalism developed by Subramanian & Becker (2005) to derive a rigorous estimate for the efficiency of the overall noise storm emission process, beginning with nonthermal electron acceleration and culminating in the observed radiation. We also calculate separate efficiencies for the electron acceleration -- Langmuir wave generation stage and the Langmuir wave -- noise storm production stage. In addition, we obtain a new theoretical estimate for the energy density of the Langmuir waves in noise storm continuum sources.Comment: Accepted for publication in Solar Physic

Computing with Membranes and Picture Arrays

Splicing systems were introduced by Tom Head [3] on biological considerations to model certain recombinant behaviour of DNA molecules. An effective extension of this operation to images was introduced by Helen Chandra et al. [5] and H array splicing systems were considered. A new method of applying the splicing operation on images of hexagonal arrays was introduced by Thomas et al. [12] and generated a new class of hexagonal array languages HASSL. On the other hand, P systems, introduced by Paun [6] generating rectangular arrays and hexagonal arrays have been studied in the literature, bringing together the two areas of theoretical computer science namely membrane computing and picture languages. P system with array objects and parallel splicing operation on arrays is introduced as a simple and effective extension of P system with operation of splicing on strings and this new class of array languages is compared with the existing families of array languages. Also we propose another P system with hexagonal array objects and parallel splicing operation on hexagonal arrays is introduced and this new class of hexagonal array languages is compared with the existing families of hexagonal array languages

Three-dimensional stability of Burgers vortices

Burgers vortices are explicit stationary solutions of the Navier-Stokes equations which are often used to describe the vortex tubes observed in numerical simulations of three-dimensional turbulence. In this model, the velocity field is a two-dimensional perturbation of a linear straining flow with axial symmetry. The only free parameter is the Reynolds number $Re = \Gamma/\nu$, where $\Gamma$ is the total circulation of the vortex and $\nu$ is the kinematic viscosity. The purpose of this paper is to show that Burgers vortex is asymptotically stable with respect to general three-dimensional perturbations, for all values of the Reynolds number. This definitive result subsumes earlier studies by various authors, which were either restricted to small Reynolds numbers or to two-dimensional perturbations. Our proof relies on the crucial observation that the linearized operator at Burgers vortex has a simple and very specific dependence upon the axial variable. This allows to reduce the full linearized equations to a vectorial two-dimensional problem, which can be treated using an extension of the techniques developped in earlier works. Although Burgers vortices are found to be stable for all Reynolds numbers, the proof indicates that perturbations may undergo an important transient amplification if $Re$ is large, a phenomenon that was indeed observed in numerical simulations.Comment: 31 pages, no figur