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

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

Resonant Amplification of Electroweak Baryogenesis at Preheating

We explore viable scenarios for parametric resonant amplification of electroweak (EW) gauge fields and Chern-Simons number during preheating, leading to baryogenesis at the electroweak (EW) scale. In this class of scenarios time-dependent classical EW gauge fields, essentially spatially-homogeneous on the horizon scales, carry Chern-Simons number which can be amplified by parametric resonance up to magnitudes at which unsuppressed topological transitions in the Higgs sector become possible. Baryon number non-conservation associated with the gauge sector and the highly non-equilibrium nature of preheating allow for efficient baryogenesis. The requisite large CP violation can arise either from the time dependence of a slowly varying Higgs field (spontaneous baryogenesis), or from a resonant amplification of CP violation induced in the gauge sector through loops. We identify several CP violating operators in the Standard Model and its minimal extensions that can facilitate efficient baryogenesis at preheating, and show how to overcome would-be exponential suppression of baryogenesis associated with tunneling barriers.Comment: 51 pages, 8 figues; minor corrections; references adde

Representative transcript sets for evaluating a translational initiation sites predictor

<p>Abstract</p> <p>Background</p> <p>Translational initiation site (TIS) prediction is a very important and actively studied topic in bioinformatics. In order to complete a comparative analysis, it is desirable to have several benchmark data sets which can be used to test the effectiveness of different algorithms. An ideal benchmark data set should be reliable, representative and readily available. Preferably, proteins encoded by members of the data set should also be representative of the protein population actually expressed in cellular specimens.</p> <p>Results</p> <p>In this paper, we report a general algorithm for constructing a reliable sequence collection that only includes mRNA sequences whose corresponding protein products present an average profile of the general protein population of a given organism, with respect to three major structural parameters. Four representative transcript collections, each derived from a model organism, have been obtained following the algorithm we propose. Evaluation of these data sets shows that they are reasonable representations of the spectrum of proteins obtained from cellular proteomic studies. Six state-of-the-art predictors have been used to test the usefulness of the construction algorithm that we proposed. Comparative study which reports the predictors' performance on our data set as well as three other existing benchmark collections has demonstrated the actual merits of our data sets as benchmark testing collections.</p> <p>Conclusion</p> <p>The proposed data set construction algorithm has demonstrated its property of being a general and widely applicable scheme. Our comparison with published proteomic studies has shown that the expression of our data set of transcripts generates a polypeptide population that is representative of that obtained from evaluation of biological specimens. Our data set thus represents "real world" transcripts that will allow more accurate evaluation of algorithms dedicated to identification of TISs, as well as other translational regulatory motifs within mRNA sequences. The algorithm proposed by us aims at compiling a redundancy-free data set by removing redundant copies of homologous proteins. The existence of such data sets may be useful for conducting statistical analyses of protein sequence-structure relations. At the current stage, our approach's focus is to obtain an "average" protein data set for any particular organism without posing much selection bias. However, with the three major protein structural parameters deeply integrated into the scheme, it would be a trivial task to extend the current method for obtaining a more selective protein data set, which may facilitate the study of some particular protein structure.</p

Accurate microRNA target prediction correlates with protein repression levels

MicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pairing of the microRNA to sites in the messenger RNA of protein coding genes. Since experimental identification of miRNA target genes poses difficulties, computational microRNA target prediction is one of the key means in deciphering the role of microRNAs in development and diseas

Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations

MicroRNAs (miRNAs) suppress gene expression by forming a duplex with a target messenger RNA (mRNA), blocking translation or initiating cleavage. Computational approaches have proven valuable for predicting which mRNAs can be targeted by a given miRNA, but currently available prediction methods do not address the extent of duplex formation under physiological conditions. Some miRNAs can at low concentrations bind to target mRNAs, whereas others are unlikely to bind within a physiologically relevant concentration range. Here we present a novel approach in which we find potential target sites on mRNA that minimize the calculated free energy of duplex formation, compute the free energy change involved in unfolding these sites, and use these energies to estimate the extent of duplex formation at specified initial concentrations of both species. We compare our predictions to experimentally confirmed miRNA-mRNA interactions (and non-interactions) in Drosophila melanogaster and in human. Although our method does not predict whether the targeted mRNA is degraded and/or its translation to protein inhibited, our quantitative estimates generally track experimentally supported results, indicating that this approach can be used to predict whether an interaction occurs at specified concentrations. Our approach offers a more-quantitative understanding of post-translational regulation in different cell types, tissues, and developmental conditions

MetWAMer: eukaryotic translation initiation site prediction

<p>Abstract</p> <p>Background</p> <p>Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations.</p> <p>Results</p> <p>MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the <it>k</it>-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage.</p> <p>Conclusion</p> <p>We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.</p