Linear dimensional change, compressive strength and detail reproduction in type IV dental stone dried at room temperature and in a microwave oven

The type IV dental stone is widely used for the fabrication of dyes and master casts for fixed and removable partial prostheses. It is typically normal to wait at least 24 hours for the casts to dry prior to beginning the laboratory procedures. The waiting time has been shown to be greatly reduced by using microwave drying. OBJECTIVE: This study evaluated the influence of drying techniques at room temperature and microwave oven on the linear dimensional change, compressive strength and detail reproduction in type IV dental stones. MATERIAL AND METHODS: Three type IV dental stone brands were selected; Elite Rock, Shera Premium and Durone IV. Two different drying protocols were tested in 4 groups (n=10); G1 - room temperature (25±4ºC) dried for 2 hours; G2 - room temperature dried for 24 hours; G3 - room temperature dried for 7 days and G4 - microwave oven dried at 800 W for 5 minutes and after 2 hours at room temperature. After drying, the samples were assayed for dimensional charges. The sample surface was submitted to the ImageTool 3.0 software for compressive strength in a universal testing machine with a cell load of 50 KN at a crosshead speed of 0.5 mm/minutes and the detail reproduction was analyzed with a stereomicroscope at 25x magnification. The statistical analysis of the linear dimensional change and compressive strength data were conducted by the ANOVA test followed by the Tukey test (p<0.05). Detailed reproduction values were reported in percentages. RESULTS: For the compressive strength test, Elite Rock and Durone IV did not present significant differences between G2 and G4, while Shera Premium did not present differences between G3 and G4. The best reproduction levels were observed for G3. CONCLUSIONS: Dental stone microwave oven drying showed a linear dimensional change similar to after room temperature drying for 24 hours and 7 days. The compressive strength of the stone dried in the microwave oven was similar to those dried at room temperature for 24 hours, with the exception of Shera Premium, which had similar results for microwave and room temperature drying for 7 days. For the microwave drying method the detail reproduction levels for samples dried at room temperature for 24 hours and 7 days were similar, except for the Durone IV

Position dependent mismatch discrimination on DNA microarrays – experiments and model

<p>Abstract</p> <p>Background</p> <p>The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study.</p> <p>Results</p> <p>We observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends) as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results.</p> <p>Conclusion</p> <p>Molecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN) can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.</p

Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays

<p>Abstract</p> <p>Background</p> <p>Current commercial high-density oligonucleotide microarrays can hold millions of probe spots on a single microscopic glass slide and are ideal for studying the transcriptome of microbial genomes using a tiling probe design. This paper describes a comprehensive computational pipeline implemented specifically for designing tiling probe sets to study microbial transcriptome profiles.</p> <p>Results</p> <p>The pipeline identifies every possible probe sequence from both forward and reverse-complement strands of all DNA sequences in the target genome including circular or linear chromosomes and plasmids. Final probe sequence lengths are adjusted based on the maximal oligonucleotide synthesis cycles and best isothermality allowed. Optimal probes are then selected in two stages - sequential and gap-filling. In the sequential stage, probes are selected from sequence windows tiled alongside the genome. In the gap-filling stage, additional probes are selected from the largest gaps between adjacent probes that have already been selected, until a predefined number of probes is reached. Selection of the highest quality probe within each window and gap is based on five criteria: sequence uniqueness, probe self-annealing, melting temperature, oligonucleotide length, and probe position.</p> <p>Conclusions</p> <p>The probe selection pipeline evaluates global and local probe sequence properties and selects a set of probes dynamically and evenly distributed along the target genome. Unique to other similar methods, an exact number of non-redundant probes can be designed to utilize all the available probe spots on any chosen microarray platform. The pipeline can be applied to microbial genomes when designing high-density tiling arrays for comparative genomics, ChIP chip, gene expression and comprehensive transcriptome studies.</p

Hybridization thermodynamics of NimbleGen Microarrays

Background While microarrays are the predominant method for gene expression profiling, probe signal variation is still an area of active research. Probe signal is sequence dependent and affected by probe-target binding strength and the competing formation of probe-probe dimers and secondary structures in probes and targets. Results We demonstrate the benefits of an improved model for microarray hybridization and assess the relative contributions of the probe-target binding strength and the different competing structures. Remarkably, specific and unspecific hybridization were apparently driven by different energetic contributions: For unspecific hybridization, the melting temperature Tm was the best predictor of signal variation. For specific hybridization, however, the effective interaction energy that fully considered competing structures was twice as powerful a predictor of probe signal variation. We show that this was largely due to the effects of secondary structures in the probe and target molecules. The predictive power of the strength of these intramolecular structures was already comparable to that of the melting temperature or the free energy of the probe-target duplex. Conclusions This analysis illustrates the importance of considering both the effects of probe-target binding strength and the different competing structures. For specific hybridization, the secondary structures of probe and target molecules turn out to be at least as important as the probe-target binding strength for an understanding of the observed microarray signal intensities. Besides their relevance for the design of new arrays, our results demonstrate the value of improving thermodynamic models for the read-out and interpretation of microarray signals

Current and prospective pharmacological targets in relation to antimigraine action

Migraine is a recurrent incapacitating neurovascular disorder characterized by unilateral and throbbing headaches associated with photophobia, phonophobia, nausea, and vomiting. Current specific drugs used in the acute treatment of migraine interact with vascular receptors, a fact that has raised concerns about their cardiovascular safety. In the past, α-adrenoceptor agonists (ergotamine, dihydroergotamine, isometheptene) were used. The last two decades have witnessed the advent of 5-HT1B/1D receptor agonists (sumatriptan and second-generation triptans), which have a well-established efficacy in the acute treatment of migraine. Moreover, current prophylactic treatments of migraine include 5-HT2 receptor antagonists, Ca2+ channel blockers, and β-adrenoceptor antagonists. Despite the progress in migraine research and in view of its complex etiology, this disease still remains underdiagnosed, and available therapies are underused. In this review, we have discussed pharmacological targets in migraine, with special emphasis on compounds acting on 5-HT (5-HT1-7), adrenergic (α1, α2, and β), calcitonin gene-related peptide (CGRP 1 and CGRP2), adenosine (A1, A2, and A3), glutamate (NMDA, AMPA, kainate, and metabotropic), dopamine, endothelin, and female hormone (estrogen and progesterone) receptors. In addition, we have considered some other targets, including gamma-aminobutyric acid, angiotensin, bradykinin, histamine, and ionotropic receptors, in relation to antimigraine therapy. Finally, the cardiovascular safety of current and prospective antimigraine therapies is touched upon

Multiple dimensions of biodiversity drive human interest in tide pool communities

Abstract Activities involving observation of wild organisms (e.g. wildlife watching, tidepooling) can provide recreational and learning opportunities, with biologically diverse animal assemblages expected to be more stimulating to humans. In turn, more diverse communities may enhance human interest and facilitate provisioning of cultural services. However, no experimental tests of this biodiversity-interest hypothesis exist to date. We therefore investigated the effects of different dimensions of animal biodiversity (species richness, phyletic richness and functional diversity) on self-reported interest using tide pools as a model system. We performed two experiments by manipulating: (1) the richness of lower (species) and higher taxonomic levels (phyla) in an image based, online survey, and (2) the richness of the higher taxonomic level (phyla) in live public exhibits. In both experiments, we further quantified functional diversity, which varied freely, and within the online experiment we also included the hue diversity and colourfulness arising from the combination of organisms and the background scenes. Interest was increased by phyletic richness (both studies), animal species richness (online study) and functional diversity (online study). A structural equation model revealed that functional diversity and colourfulness (of the whole scene) also partially mediated the effects of phyletic richness on interest in the online study. In both studies, the presence of three of four phyla additively increased interest, supporting the importance of multiple, diverse phyla rather than a single particularly interesting phylum. These results provide novel experimental evidence that multiple dimensions of biodiversity enhance human interest and suggest that conservation initiatives that maintain or restore biodiversity will help stimulate interest in ecosystems, facilitating educational and recreational benefits