The Vienna RNA Websuite

The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides a web interface to the most commonly used programs of the Vienna RNA package. Among them, we find folding of single and aligned sequences, prediction of RNA–RNA interactions, and design of sequences with a given structure. Additionally, we provide analysis of folding landscapes using the barriers program and structural RNA alignments using LocARNA. The web server together with software packages for download is freely accessible at http://rna.tbi.univie.ac.at/

GIOVE, a shallow laboratory Ge-spectrometer with 100 μBq/kg sensitivity

A new germanium gamma spectrometer called GIOVE ( G ermanium spectrometer with I nner and O uter V eto) has been set up at the underground/shallow laboratory (15 m w.e.) of MPI-K. Its double plastic scintillator veto system and neutron moderation interlayer lower the background by more than one order of magnitude compared to the other existing spectrometer at this facility. The integral (40-2700 keV) background rate of about 290 counts (day kg)−1 is just a factor 4 to 8 above that of the GeMPI spectrometers operated at LNGS (3800 m w.e.) and thus proves that even under shallow overburden sub mBq/kg sensitivities are achievable. Extended material screening and neutron attenuation studies preceded the final design of the spectrometer. The technical realization of the spectrometer is described in detail with special emphasis on the inner veto system. For its optimisation a simulation model was developed for light collection on small low activity PMT’s under various geometrical conditions. Radon suppression is accomplished by employing a gas tight sample container and a nitrogen flushed glove-box system with an airlock. The active volume of the crystal was modelled by absorption scanning measurements and Monte Carlo simulations. The complete shield is implemented in a Geant4 based simulation framework

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures

Many non-coding RNA genes and cis-acting regulatory elements of mRNAs contain RNA secondary structures that are critical for their function. Such functional RNAs can be predicted on the basis of thermodynamic stability and evolutionary conservation. We present a web server that uses the RNAz algorithm to detect functional RNA structures in multiple alignments of nucleotide sequences. The server provides access to a complete and fully automatic analysis pipeline that allows not only to analyze single alignments in a variety of formats, but also to conduct complex screens of large genomic regions. Results are presented on a website that is illustrated by various structure representations and can be downloaded for local view. The web server is available at: rna.tbi.univie.ac.at/RNAz

Strategies for measuring evolutionary conservation of RNA secondary structures

<p>Abstract</p> <p>Background</p> <p>Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential.</p> <p>Results</p> <p>We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons.</p> <p>Conclusion</p> <p>Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.</p

Qualification Tests of 474 Photomultiplier Tubes for the Inner Detector of the Double Chooz Experiment

The hemispherical 10" photomultiplier tube (PMT) R7081 from Hamamatsu Photonics K.K. (HPK) is used in various experiments in particle and astroparticle physics. We describe the test and calibration of 474 PMTs for the reactor antineutrino experiment Double Chooz. The unique test setup at Max-Planck-Institut f\"ur Kernphysik Heidelberg (MPIK) allows one to calibrate 30 PMTs simultaneously and to characterize the single photo electron response, transit time spread, linear behaviour and saturation effects, photon detection efficiency and high voltage calibration

Qualification Tests of 474 Photomultiplier Tubes for the Inner Detector of the Double Chooz Experiment

The hemispherical 10" photomultiplier tube (PMT) R7081 from Hamamatsu Photonics K.K. (HPK) is used in various experiments in particle and astroparticle physics. We describe the test and calibration of 474 PMTs for the reactor antineutrino experiment Double Chooz. The unique test setup at Max-Planck-Institut f\"ur Kernphysik Heidelberg (MPIK) allows one to calibrate 30 PMTs simultaneously and to characterize the single photo electron response, transit time spread, linear behaviour and saturation effects, photon detection efficiency and high voltage calibration

Qualification Tests of 474 Photomultiplier Tubes for the Inner Detector of the Double Chooz Experiment

The hemispherical 10" photomultiplier tube (PMT) R7081 from Hamamatsu Photonics K.K. (HPK) is used in various experiments in particle and astroparticle physics. We describe the test and calibration of 474 PMTs for the reactor antineutrino experiment Double Chooz. The unique test setup at Max-Planck-Institut f\"ur Kernphysik Heidelberg (MPIK) allows one to calibrate 30 PMTs simultaneously and to characterize the single photo electron response, transit time spread, linear behaviour and saturation effects, photon detection efficiency and high voltage calibration

R-chie: a web server and R package for visualizing RNA secondary structures

Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R-chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems

What makes information in online consumer reviews diagnostic over time? The role of review relevancy, factuality, currency, source credibility and ranking score

Online consumer reviews (OCRs) have become one of the most helpful and influential information in consumers purchase decisions. However, the proliferation of OCRs has made it difficult for consumers to orientate themselves with the wealth of reviews available. Therefore, it is paramount for online organizations to understand the determinants of perceived information diagnosticity in OCRs. In this study, we investigate consumer perceptions and we adopt the Elaboration Likelihood Model to analyze the influence of central (long, relevant, current, and factual OCRs) and peripheral cues (source credibility, overall ranking scores) on perceived information diagnosticity (PID). We consider the potential moderating effect of consumer involvement, and tested the robustness of the theoretical framework across time. Based on two surveys carried out in 2011 and in 2016, this study demonstrates the dynamic nature of the antecedents of PID in e-WOM. We found that long reviews are not perceived as helpful, while relevant and current reviews as well as overall ranking scores are perceived as diagnostic information in both samples. The significance of the predicting power of review factuality and source credibility has evolved over time. Both central (review quality dimensions) and peripheral cues (ranking score) were found to influence PID in high-involvement decisions

Multiple sequence alignments of partially coding nucleic acid sequences

BACKGROUND: High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared to their encoded protein sequences due to the redundancy of the genetic code. It is desirable, therefore, to make use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however, only a part of the sequence of interest is translated. On the other hand, overlapping reading frames may encode multiple alternative proteins, possibly with intermittent non-coding parts. Examples are, in particular, RNA virus genomes. RESULTS: The standard scoring scheme for nucleic acid alignments can be extended to incorporate simultaneously information on translation products in one or more reading frames. Here we present a multiple alignment tool, codaln, that implements a combined nucleic acid plus amino acid scoring model for pairwise and progressive multiple alignments that allows arbitrary weighting for almost all scoring parameters. Resource requirements of codaln are comparable with those of standard tools such as ClustalW. CONCLUSION: We demonstrate the applicability of codaln to various biologically relevant types of sequences (bacteriophage Levivirus and Vertebrate Hox clusters) and show that the combination of nucleic acid and amino acid sequence information leads to improved alignments. These, in turn, increase the performance of analysis tools that depend strictly on good input alignments such as methods for detecting conserved RNA secondary structure elements