Annual prediction of shoreline erosion and subsequent recovery

publisher: Elsevier articletitle: Annual prediction of shoreline erosion and subsequent recovery journaltitle: Coastal Engineering articlelink: http://dx.doi.org/10.1016/j.coastaleng.2017.09.008 content_type: article copyright: Crown Copyright © 2017 Published by Elsevier B.V. All rights reserved

Combinatorial RNA Design: Designability and Structure-Approximating Algorithm

In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete characterizations for the structures that can be designed using restricted alphabets. Under a classic four-letter alphabet, we provide a complete characterization of designable structures without unpaired bases. When unpaired bases are allowed, we provide partial characterizations for classes of designable/undesignable structures, and show that the class of designable structures is closed under the stutter operation. Membership of a given structure to any of the classes can be tested in linear time and, for positive instances, a solution can be found in linear time. Finally, we consider a structure-approximating version of the problem that allows to extend bands (helices) and, assuming that the input structure avoids two motifs, we provide a linear-time algorithm that produces a designable structure with at most twice more base pairs than the input structure.Comment: CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun 2015, Ischia Island, Italy. LNCS, 201

A novel real-world ecotoxicological dataset of pelagic microbial community responses to wastewater.

Real-world observational datasets that record and quantify pressure-stressor-response linkages between effluent discharges and natural aquatic systems are rare. With global wastewater volumes increasing at unprecedented rates, it is urgent that the present dataset is available to provide the necessary information about microbial community structure and functioning. Field studies were performed at two time-points in the Austral summer. Single-species and microbial community whole effluent toxicity (WET) testing was performed at a complete range of effluent concentrations and two salinities, with accompanying environmental data to provide new insights into nutrient and organic matter cycling, and to identify ecotoxicological tipping points. The two salinity regimes were chosen to investigate future scenarios based on a predicted salinity increase at the study site, typical of coastal regions with rising sea levels globally. Flow cytometry, amplicon sequencing of 16S and 18S rRNA genes and micro-fluidic quantitative polymerase-chain reactions (MFQPCR) were used to determine chlorophyll-a and total bacterial cell numbers and size, as well as taxonomic and functional diversity of pelagic microbial communities. This strong pilot dataset could be replicated in other regions globally and would be of high value to scientists and engineers to support the next advances in microbial ecotoxicology, environmental biomonitoring and estuarine water quality modelling

Spontaneous Uterine Rupture in the First Trimester: A Case Report

Uterine rupture is one of the most feared obstetric complications affecting the pregnant woman and fetus. Most of the cases have various risk factors and mainly occur during the second or third trimester. However, spontaneous uterine rupture during the first trimester is extremely rare. We experienced a case of spontaneous uterine rupture in a 36-yr-old multiparous woman without definite risk factors. The initial impression was a hemoperitoneum of an unknown origin with normal early pregnancy. Intensive surgical method would be needed for accurate diagnosis and immediate management in bad situation by hemoperitoneum even though a patient was early pregnancy

Are groups more rational than individuals? A review of interactive decision making in groups

Many decisions are interactive; the outcome of one party depends not only on its decisions or on acts of nature but also on the decisions of others. In the present article, we review the literature on decision making made by groups of the past 25 years. Researchers have compared the strategic behavior of groups and individuals in many games: prisoner's dilemma, dictator, ultimatum, trust, centipede and principal-agent games, among others. Our review suggests that results are quite consistent in revealing that groups behave closer to the game-theoretical assumption of rationality and selfishness than individuals. We conclude by discussing future research avenues in this area

RNA Accessibility in cubic time

<p>Abstract</p> <p>Background</p> <p>The accessibility of RNA binding motifs controls the efficacy of many biological processes. Examples are the binding of miRNA, siRNA or bacterial sRNA to their respective targets. Similarly, the accessibility of the Shine-Dalgarno sequence is essential for translation to start in prokaryotes. Furthermore, many classes of RNA binding proteins require the binding site to be single-stranded.</p> <p>Results</p> <p>We introduce a way to compute the accessibility of all intervals within an RNA sequence in <inline-formula><graphic file="1748-7188-6-3-i1.gif"/></inline-formula>(<it>n</it>³) time. This improves on previous implementations where only intervals of one defined length were computed in the same time. While the algorithm is in the same efficiency class as sampling approaches, the results, especially if the probabilities get small, are much more exact.</p> <p>Conclusions</p> <p>Our algorithm significantly speeds up methods for the prediction of RNA-RNA interactions and other applications that require the accessibility of RNA molecules. The algorithm is already available in the program RNAplfold of the ViennaRNA package.</p

ViennaRNA Package 2.0

<p>Abstract</p> <p>Background</p> <p>Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties.</p> <p>Results</p> <p>The <monospace>ViennaRNA</monospace> Package has been a widely used compilation of RNA secondary structure related computer programs for nearly two decades. Major changes in the structure of the standard energy model, the <it>Turner 2004 </it>parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic variants prompted a major technical overhaul of both the underlying <monospace>RNAlib</monospace> and the interactive user programs. New features include an expanded repertoire of tools to assess RNA-RNA interactions and restricted ensembles of structures, additional output information such as <it>centroid </it>structures and <it>maximum expected accuracy </it>structures derived from base pairing probabilities, or <it>z</it>-<it>scores </it>for locally stable secondary structures, and support for input in <monospace>fasta</monospace> format. Updates were implemented without compromising the computational efficiency of the core algorithms and ensuring compatibility with earlier versions.</p> <p>Conclusions</p> <p>The <monospace>ViennaRNA Package 2.0</monospace>, supporting concurrent computations <monospace>via OpenMP</monospace>, can be downloaded from <url>http://www.tbi.univie.ac.at/RNA</url>.</p

Organizing to counter terrorism: sensemaking amidst dynamic complexity

publication-status: Acceptedtypes: ArticlePre-print draft (version 1). ‘The final, definitive version of this paper has been published in Human Relations September 2013 66(9): 1201–1223, by SAGE Publications Ltd, All rights reserved. © [The Author]Organizations increasingly find themselves contending with circumstances that are suffused with dynamic complexity. So how do they make sense of and contend with this? Using a sensemaking approach, our empirical case analysis of the shooting of Mr Jean Charles de Menezes shows how sensemaking is tested under such conditions. Through elaborating the relationship between the concepts of frames and cues, we find that the introduction of a new organizational routine to anticipate action in changing circumstances leads to discrepant sensemaking. This reveals how novel routines do not necessarily replace extant ones but instead, overlay each other and give rise to novel, dissonant identities which in turn can lead to an increase in equivocality rather than a reduction. This has important implications for sensemaking and organizing amidst unprecedented circumstances