Reference and empty reference

The stage setting for the thesis is the intimate connection between the problem of reference and that of intensionality. The thesis is a survey of attempts to arrive at an account of truth and meaning for languages'containing empty singular terms. We begin with a general account of intensional predicates.We give reasons to doubt that intensional verbs can take direct objects, and adopt Quine's strategy for intensional predicates like "seek", "worship", "refer". We discover certain complexities in verbs like "love", "hate". When we examine the standard formal semantics we discover that to accommodate empty reference, we have to modify that approach. There are several ways to take in empty names. They fall broadly into two categories: theories without truth value gaps and theories with them. None of the theories which we examine is without difficulty. To dispose of empty reference would mean losing an important part of our discourse about the universe. We attempt to give an account based on the Kripkean theory of truth. This allows truth value gaps but retains the equivalence. Our proposal is not successful.This leaves no choice but to return to the standard formal semantical framework without gaps and to a theory of Tyler Burge. This is unfortunately incomplete. It may not be completable. Many semantically significant occurrences of empty names can be got into opaque contexts. For these we give an account which is inspired by Frege's account of "als ob" in "Ausfuhrungen Uber Sinn und Bedeutung" in the Nachrelasscne Schriften and by Davidson's analysis of oratio obliqua. Existential statements we put on one side as a special problem. Residual occurrences of empty names in transparent contexts are explained metalinguistically.<p

IRESite—a tool for the examination of viral and cellular internal ribosome entry sites

The IRESite (http://www.iresite.org) presents carefully curated experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions. At the time of submission, IRESite stored >600 records. The IRESite gradually evolved into a robust tool providing (i) biologically meaningful information regarding the IRESs and their experimental background (including annotation of IRES secondary structures and IRES trans-acting factors) as well as (ii) thorough concluding remarks to stored database entries and regularly updated evaluation of the reported IRES function. A substantial portion of the IRESite data results purely from in-house bioinformatic analyses of currently available sequences, in silico attempts to repeat published cloning experiments, DNA sequencing and restriction endonuclease verification of received plasmid DNA. We also present a newly implemented tool for displaying RNA secondary structures and for searching through the structures currently stored in the database. The supplementary material contains an updated list of reported IRESs

Accurate and efficient reconstruction of deep phylogenies from structured RNAs

Ribosomal RNA (rRNA) genes are probably the most frequently used data source in phylogenetic reconstruction. Individual columns of rRNA alignments are not independent as a consequence of their highly conserved secondary structures. Unless explicitly taken into account, these correlation can distort the phylogenetic signal and/or lead to gross overestimates of tree stability. Maximum likelihood and Bayesian approaches are of course amenable to using RNA-specific substitution models that treat conserved base pairs appropriately, but require accurate secondary structure models as input. So far, however, no accurate and easy-to-use tool has been available for computing structure-aware alignments and consensus structures that can deal with the large rRNAs. The RNAsalsa approach is designed to fill this gap. Capitalizing on the improved accuracy of pairwise consensus structures and informed by a priori knowledge of group-specific structural constraints, the tool provides both alignments and consensus structures that are of sufficient accuracy for routine phylogenetic analysis based on RNA-specific substitution models. The power of the approach is demonstrated using two rRNA data sets: a mitochondrial rRNA set of 26 Mammalia, and a collection of 28S nuclear rRNAs representative of the five major echinoderm groups

GraphClust: alignment-free structural clustering of local RNA secondary structures

Motivation: Clustering according to sequence–structure similarity has now become a generally accepted scheme for ncRNA annotation. Its application to complete genomic sequences as well as whole transcriptomes is therefore desirable but hindered by extremely high computational costs

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

<p>Abstract</p> <p>Background</p> <p>Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized.</p> <p>Results</p> <p>We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1) pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2) a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage.</p> <p>Conclusion</p> <p>The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS) criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.</p

A 3D Print Process For Inexpensive Plastic Parts

Many of the currently available RP-Systems are suitable for building design models of arbitrarily shaped parts. However, most of these RP processes use sophisticated and expensive equipment which is not well suited for an office environment. In this paper we present a method and an experimental device for building design models by a modified 3D print process using plastic powder and a photopolymeric binder.Mechanical Engineerin