Optimizing anti-gene oligonucleotide ‘Zorro-LNA’ for improved strand invasion into duplex DNA

Zorro-LNA (Zorro) is a newly developed, oligonucleotide (ON)-based, Z-shaped construct with the potential of specific binding to each strand of duplex DNA. The first-generation Zorros are formed by two hybridized LNA/DNA mixmers (2-ON Zorros) and was hypothesized to strand invade. We have now established a method, which conclusively demonstrates that an LNA ON can strand invade into duplex DNA. To make Zorros smaller in size and easier to design, we synthesized 3′–5′–5′–3′ single-stranded Zorro-LNA (ssZorro) by using both 3′- and 5′-phosphoramidites. With ssZorro, a significantly greater extent and rate of double-strand invasion (DSI) was obtained than with conventional 2-ON Zorros. Introducing hydrophilic PEG-linkers connecting the two strands did not significantly change the rate or extent of DSI as compared to ssZorro with a nucleotide-based linker, while the longest alkyl-chain linker tested (36 carbons) resulted in a very slow DSI. The shortest alkyl-chain linker (3 carbons) did not reduce the extent of DSI of ssZorro, but significantly decreased the DSI rate. Collectively, ssZorro is smaller in size, easier to design and more efficient than conventional 2-ON Zorro in inducing DSI. Analysis of the chemical composition of the linker suggests that it could be of importance for future therapeutic considerations

Non-pathologic components are associated with reduced visual acuity in myopes after spectacle correction

Purpose: To find the association between reduced best-corrected visual acuity and non-pathologic components after optical correction in individuals with low to high myopia. Methods: Myopic children under 16 years of age were reviewed using electronic medical records and the following data were extracted and recorded: participant's age, gender, uncorrected visual acuity (UCVA), manifest refraction, and best corrected visual acuity (BCVA). Spherical equivalent and cylinder were classified into low, moderate, and high categories based on the magnitude range. Similarly, astigmatism was defined into with-the-rule, against-the-rule, and oblique based on the location of the steepest meridian. Reduced BCVA was defined when the decimal visual acuity was less than 0.66 (equivalent to Snellen's acuity of 6/9 or 20/30). Logistic regression was performed to test the factors associated with reduced visual acuity after optical correction in the absence of myopic pathologic changes. Statistical significance was considered if P < 0.05. Results: Overall 44.9% (N = 242/538) of myopes had reduced best-corrected visual acuity (BCVA) and none of the patients had pathologic myopic lesions. Using logistic regression, we found that high spherical refraction (OR 27.98, 95% CI 14.43–54.25, P < 0.001) and moderate spherical refraction (OR 5.52, 95% CI 2.56–11.91, P < 0.001) were significantly associated with reduced best corrected visual acuity despite any pathological lesions. Additionally, oblique and ATR astigmatism were associated with reduced visual acuity in myopic children with (OR 2.05, 95% CI 0.77–5.42) and (OR 1.59, 95% CI 0.82–3.08). Conclusion: Higher magnitude of refractive error components causes reduced visual acuity in the absence of pathologic changes

Automated Abstraction Refinement for Model Checking Large State Spaces using SAT based Conflict Analysis

Abstract. We introduce a SAT based automatic abstraction refinement framework for model checking systems with several thousand state variables in the cone of influence of the specification. The abstract model is constructed by designating a large number of state variables as invisible. In contrast to previous work where invisible variables were treated as free inputs we describe a computationally more advantageous approach in which the abstract transition relation is approximated by pre-quantifying invisible variables during image computation. The abstract counterexamples obtained from model-checking the abstract model are symbolically simulated on the concrete system using a state-of-the-art SAT checker. If no concrete counterexample is found, a subset of the invisible variables is reintroduced into the system and the process is repeated. The main contribution of this paper are two new algorithms for identifying the relevant variables to be reintroduced. These algorithms monitor the SAT checking phase in order to analyze the impact of individual variables. Our method is complete for safety properties (AG p) in the sense that – performance permitting – a property is either verified or disproved by a concrete counterexample. Experimental results are given to demonstrate the power of our method on real-world designs.

Automated Abstraction Refinement for Model Checking Large Spaces using SAT based Conflict Analysis

We introduce a SAT based automatic abstraction refinement framework for model checking systems with several thousand state variables in the cone of influence of the specification. The abstract model is constructed by designating a large number of state variables as invisible. In contrast to previous work where invisible variables were treated as free inputs we describe a computationally more advantageous approach in which the abstract transition relation is approximated by pre-quantifying invisible variables during image computation. The abstract counterexamples obtained from model-checking the abstract model are symbolically simulated on the concrete system using a state-of-the-art SAT checker. If no concrete counterexample is found, a subset of the invisible variables is reintroduced into the system and the process is repeated. The main contribution of this paper are two new algorithms for identifying the relevant variables to be reintroduced. These algorithms monitor the SAT checking phase in order to analyze the impact of individual variables. Our method is complete for safety properties (AG p) in the sense that-performance permitting - a property is either verified or disproved by a concrete counterexample. Experimental results are given to demonstrate the power of our method on real-world designs