New host and country records for European Tachinidae (Diptera)

The paper presents host records for 17 species of Tachinidae (of subfamilies Exoristinae and Tachininae) from the Czech Republic, Slovakia, Austria, Croatia, Macedonia, Italy, Spain, Portugal, and Bulgaria. New parasitoid-host couples are Exorista larvarum — Melanchra pisi; Exorista segregata — Catocala nymphaea; Sturmia bella — Hadena compta; Spallanzania multisetosa — Cycnia sordida (first host record); Tachina praeceps — Cucullia bubaceki; and Bithia modesta — Bembecia megillaeformis. New country records of tachinid species Rhacodinella apicata from the Czech Republic, Masicera pavoniae from Macedonia and Bithia demotica from Portugal are presented

Target prediction and a statistical sampling algorithm for RNA-RNA interaction

It has been proven that the accessibility of the target sites has a critical influence for miRNA and siRNA. In this paper, we present a program, rip2.0, not only the energetically most favorable targets site based on the hybrid-probability, but also a statistical sampling structure to illustrate the statistical characterization and representation of the Boltzmann ensemble of RNA-RNA interaction structures. The outputs are retrieved via backtracing an improved dynamic programming solution for the partition function based on the approach of Huang et al. (Bioinformatics). The $O(N^6)$ time and $O(N^4)$ space algorithm is implemented in C (available from \url{http://www.combinatorics.cn/cbpc/rip2.html})Comment: 7 pages, 10 figure

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

Annotated host catalogue for the Tachinidae (Diptera) of the Czech Republic

An annotated host catalogue is given for the Tachinidae of the Czech Republic. It comprises 149 of 476 tachinid species which are currently known from this country (included the two new records cited below). 195 hosts are listed. The first host records of Tachinidae date back to the second half of the 19th century. The bibliography for the host records consists of 116 papers of 55 researchers. Several records of hitherto unpublished material are included. Phryxe setifacies and Anthomyiopsis plagioderae are first records for the Czech Republic

Probabilistic sequence alignments: realistic models with efficient algorithms

Alignment algorithms usually rely on simplified models of gaps for computational efficiency. Based on an isomorphism between alignments and physical helix-coil models, we show in statistical mechanics that alignments with realistic laws for gaps can be computed with fast algorithms. Improved performances of probabilistic alignments with realistic models of gaps are illustrated. Probabilistic and optimization formulations are compared, with potential implications in many fields and perspectives for computationally efficient extensions to Markov models with realistic long-range interactions

The acute effects of mental fatigue on balance performance in healthy young and older adults:A systematic review and meta-analysis

Cognitive resources contribute to balance control. There is evidence that mental fatigue reduces cognitive resources and impairs balance performance, particularly in older adults and when balance tasks are complex, for example when trying to walk or stand while concurrently performing a secondary cognitive task. We conducted a systematic literature search in PubMed (MEDLINE), Web of Science and Google Scholar to identify eligible studies and performed a random effects meta-analysis to quantify the effects of experimentally induced mental fatigue on balance performance in healthy adults. Subgroup analyses were computed for age (healthy young vs. healthy older adults) and balance task complexity (balance tasks with high complexity vs. balance tasks with low complexity) to examine the moderating effects of these factors on fatigue-mediated balance performance. We identified 7 eligible studies with 9 study groups and 206 participants. Analysis revealed that performing a prolonged cognitive task had a small but significant effect (SMDwm = −0.38) on subsequent balance performance in healthy young and older adults. However, age- and task-related differences in balance responses to fatigue could not be confirmed statistically. Overall, aggregation of the available literature indicates that mental fatigue generally reduces balance in healthy adults. However, interactions between cognitive resource reduction, aging and balance task complexity remain elusive

Corona: Die Rolle der Stadtplanung für die Krisenbewältigung am Beispiel Wien

Die Auswirkungen von Covid-19 betrafen wie kaum eine Krise der jüngeren Vergangenheit alle Lebensbereiche in drastischer Weise. Auf Grund der schwerwiegenden Gesundheitsfolgen und pandemischen Bedrohung musste überdurchschnittlich rasant und einschneidend gehandelt werden. Die Stadtplanung und -entwicklung, als Disziplin mit einem längerfristigen Zeithorizont von mehreren Jahren bis Jahrzehnten, stellte dies vor eine ungewohnte Aufgabe. Dabei lassen die Entwicklungen der vergangenen Jahre vermuten, dass es sich bei Krisen wie der aktuellen wohl nicht um singuläre Ereignisse handelt, sondern um Ausprägungen zunehmend volatiler Rahmenbedingungen, die sich durch bereits jetzt eintretende klimatische oder ökonomische Umwälzungen tendenziell noch verschärfen werden. Entsprechend steigt das Interesse der planenden Disziplinen an der Auseinandersetzung mit Notfällen, Krisen und Katastrophen und zeitnahen Reaktionsmöglichkeiten. Nichtsdestoweniger ist die Stadtplanung und -entwicklung gefordert ihre Kernkompetenz nicht außer Acht zu lassen und auch zukünftig langfristige und vorausschauende Strategien zu verfolgen. Der vorliegende Text wirft einen Blick auf die Wiener Stadtplanung und Stadtentwicklung. Dabei werden Fragen zu den Auswirkungen durch Covid-19 in den Monaten März bis Juni 2020 in den unterschiedlichen Planungsaspekten, -sektoren und -disziplinen aufgegriffen. Ausgangspunkt ist die Frage welche Bedeutung langfristige, strategische Ansätze und die kontinuierliche Weiterentwicklung einer robusten Stadtentwicklung in Zeiten von akuten Krisen aufweisen. Es wird weiters beleuchtet, welche bestehendenArgumentationen der Wiener Stadtentwicklung im Zuge der Erfahrungen der letzten Monate gestärkt oder geschwächt wurden. Dabei wird auch auf das Verhältnis von taktischen Adhoc-Lösungen und langfristigen Strategien eingegangen. Zu Grunde liegend ist das Verständnis, dass jede Entwicklung und Veränderung in der Stadtplanung ins Verhältnis zur globalen Klimakrise und dem Umgang damit gesetzt werden muss

Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics

The thermodynamics of RNA-RNA interaction consists of two components: the energy necessary to make a potential binding region accessible, i.e., unpaired, and the energy gained from the base pairing of the two interaction partners. We show here that both components can be efficiently computed using an improved variant of RNAup. The method is then applied to a set of bacterial small RNAs involved in translational control. In all cases of biologically active sRNA target interactions, the target sites predicted by RNAup is in perfect agreement with literature. In addition to prediction of target site location, RNAup can be also be used to determine the mode of sRNA action. Using information about target site location and the accessibility change resulting form sRNA binding we can discriminate between positive and negative regulators of translation

Partition function and base pairing probabilities of RNA heterodimers

Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. Methods: The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs. Results: We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures

Thermodynamics of RNA-RNA binding

Background: Reliable prediction of RNA–RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA–mRNA binding and antisense interactions. The thermodynamics of such RNA–RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to ‘open’ the binding site and (2) the energy gained from hybridization. Methods: We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired. Results: Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable with a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding energies of siRNAs to their respective mRNA target