miRGen: a database for the study of animal microRNA genomic organization and function

miRGen is an integrated database of (i) positional relationships between animal miRNAs and genomic annotation sets and (ii) animal miRNA targets according to combinations of widely used target prediction programs. A major goal of the database is the study of the relationship between miRNA genomic organization and miRNA function. This is made possible by three integrated and user friendly interfaces. The Genomics interface allows the user to explore where whole-genome collections of miRNAs are located with respect to UCSC genome browser annotation sets such as Known Genes, Refseq Genes, Genscan predicted genes, CpG islands and pseudogenes. These miRNAs are connected through the Targets interface to their experimentally supported target genes from TarBase, as well as computationally predicted target genes from optimized intersections and unions of several widely used mammalian target prediction programs. Finally, the Clusters interface provides predicted miRNA clusters at any given inter-miRNA distance and provides specific functional information on the targets of miRNAs within each cluster. All of these unique features of miRGen are designed to facilitate investigations into miRNA genomic organization, co-transcription and targeting. miRGen can be freely accessed at

Numerical and experimental evaluation of sonic resonance against ultrasonic pulse velocity and compression tests on concrete core samples

Destructive Testing, like core drilling, remains today the only reliable method to calculate with accuracy concrete’s strength parameters. However, the damage of the constructions is always a limitation. On the contrary, Non-Destructive Tests (NDT) are fast and cost-effective which make them attractive nowadays. Nevertheless, the results of Ultrasonic Pulse Velocity (UPV) test are highly dispersed. Therefore, it is necessary to combine them along with destructive tests. The purpose of this study is to investigate the feasibility to adopt the Sonic Resonance (SR) test to determine the strength parameters of the concrete. UPV and SR were used in conjunction with the Uniaxial Compression Test. Experimental and numerical analysis were conducted. More than 200 concrete cores from existing constructions were tested and more than 70 Finite Element Method (FEM) models were simulated. The results were correlated, and two empirical equations derived. It was observed that the dispersion of the of SR alone is smaller than the UPV, but also the UPV dispersion can be narrowed as long as the Poisson’s ratio is known

Isoform Specific Gene Auto-Regulation via miRNAs: A Case Study on miR-128b and ARPP-21

In this study, we investigate whether miRNAs located within “host” protein-coding genes may regulate the expression of their host genes. We find that 43 of 174 miRNAs encoded within RefSeq genes are predicted to target their host genes. Statistical analysis of this phenomenon suggests that gene auto-regulation via miRNAs may be under positive selective pressure. Our analysis also indicates that several of the 43 miRNAs have a much lower expectation of targeting their host genes by chance than others. Among these examples, we identify miR-128b:ARPP-21 (cyclic AMP-regulated phosphoprotein, 21 kD) as a case in which both the miRNA and the target site are also evolutionarily conserved. We provide experimental support for this miRNA:target interaction via reporter silencing assays, and present evidence that this isoform-specific gene auto-regulation has been preserved in vertebrate species in order to prevent detrimental consequences of ARPP-21 over-expression in brain

The DIANA-mirExTra Web Server: From Gene Expression Data to MicroRNA Function

Background: High-throughput gene expression experiments are widely used to identify the role of genes involved in biological conditions of interest. MicroRNAs (miRNA) are regulatory molecules that have been functionally associated with several developmental programs and their deregulation with diverse diseases including cancer. Methodology/Principal Findings: Although miRNA expression levels may not be routinely measured in high-throughput experiments, a possible involvement of miRNAs in the deregulation of gene expression can be computationally predicted and quantified through analysis of overrepresented motifs in the deregulated genes 39 untranslated region (39UTR) sequences. Here, we introduce a user-friendly web-server, DIANA-mirExTra (www.microrna.gr/mirextra) that allows the comparison of frequencies of miRNA associated motifs between sets of genes that can lead to the identification of miRNAs responsible for the deregulation of large numbers of genes. To this end, we have investigated different approaches and measures, and have practically implemented them on experimental data. Conclusions/Significance: On several datasets of miRNA overexpression and repression experiments, our proposed approaches have successfully identified the deregulated miRNA. Beyond the prediction of miRNAs responsible for the deregulation of transcripts, the web-server provides extensive links to DIANA-mirPath, a functional analysis tool incorporating miRNA targets in biological pathways. Additionally, in case information about miRNA expression changes i

Earthquake design for controlled structures

An alternative design philosophy, for structures equipped with control devices, capable to resist an expected earthquake while remaining in the elastic range, is described. The idea is that a portion of the earthquake loading is undertaken by the control system and the remaining by the structure which is designed to resist elastically. The earthquake forces assuming elastic behavior (elastic forces) and elastoplastic behavior (design forces) are first calculated according to the codes. The required control forces are calculated as the difference from elastic to design forces. The maximum value of capacity of control devices is then compared to the required control force. If the capacity of the control devices is larger than the required control force then the control devices are accepted and installed in the structure and the structure is designed according to the design forces. If the capacity is smaller than the required control force then a scale factor, ?, reducing the elastic forces to new design forces is calculated. The structure is redesigned and devices are installed. The proposed procedure ensures that the structure behaves elastically (without damage) for the expected earthquake at no additional cost, excluding that of buying and installing the control devices

Direct damage controlled seismic design of plane steel degrading frames

A new method for seismic design of plane steel moment resisting framed structures is developed. This method is able to control damage at all levels of performance in a direct manner. More specifically, the method: (a) can determine damage in any member or the whole of a designed structure under any given seismic load, (b) can dimension a structure for a given seismic load and desired level of damage and (c) can determine the maximum seismic load a designed structure can sustain in order to exhibit a desired level of damage. In order to accomplish these things, an appropriate seismic damage index is used that takes into account the interaction between axial force and bending moment at a section, strength and stiffness degradation as well as low cycle fatigue. Then, damage scales are constructed on the basis of extensive parametric studies involving a large number of frames exhibiting cyclic strength and stiffness degradation and a large number of seismic motions and using the above damage index for damage determination. Some numerical examples are presented to illustrate the proposed method and demonstrate its advantages against other methods of seismic design. © 2014, Springer Science+Business Media Dordrecht

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

As the relevant literature and the number of experiments increase at a super linear rate, databases that curate and collect experimentally verified microRNA (miRNA) targets have gradually emerged. These databases attempt to provide efficient access to this wealth of experimental data, which is scattered in thousands of manuscripts. Aim of TarBase 6.0 (http://www.microrna.gr/tarbase) is to face this challenge by providing a significant increase of available miRNA targets derived from all contemporary experimental techniques (gene specific and high-throughput), while incorporating a powerful set of tools in a user-friendly interface. TarBase 6.0 hosts detailed information for each miRNA–gene interaction, ranging from miRNA- and gene-related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. All database entries are enriched with function-related data, as well as general information derived from external databases such as UniProt, Ensembl and RefSeq. DIANA microT miRNA target prediction scores and the relevant prediction details are available for each interaction. TarBase 6.0 hosts the largest collection of manually curated experimentally validated miRNA–gene interactions (more than 65 000 targets), presenting a 16.5–175-fold increase over other available manually curated databases

The database of experimentally supported targets: a functional update of TarBase

TarBase5.0 is a database which houses a manually curated collection of experimentally supported microRNA (miRNA) targets in several animal species of central scientific interest, plants and viruses. MiRNAs are small non-coding RNA molecules that exhibit an inhibitory effect on gene expression, interfering with the stability and translational efficiency of the targeted mature messenger RNAs. Even though several computational programs exist to predict miRNA targets, there is a need for a comprehensive collection and description of miRNA targets with experimental support. Here we introduce a substantially extended version of this resource. The current version includes more than 1300 experimentally supported targets. Each target site is described by the miRNA that binds it, the gene in which it occurs, the nature of the experiments that were conducted to test it, the sufficiency of the site to induce translational repression and/or cleavage, and the paper from which all these data were extracted. Additionally, the database is functionally linked to several other relevant and useful databases such as Ensembl, Hugo, UCSC and SwissProt. The TarBase5.0 database can be queried or downloaded from http://microrna.gr/tarbase