Information profiles for DNA pattern discovery

Finite-context modeling is a powerful tool for compressing and hence for representing DNA sequences. We describe an algorithm to detect genomic regularities, within a blind discovery strategy. The algorithm uses information profiles built using suitable combinations of finite-context models. We used the genome of the fission yeast Schizosaccharomyces pombe strain 972 h- for illustration, unveilling locations of low information content, which are usually associated with DNA regions of potential biological interest.Comment: Full version of DCC 2014 paper "Information profiles for DNA pattern discovery

JSKETCH: Sketching for Java

Sketch-based synthesis, epitomized by the SKETCH tool, lets developers synthesize software starting from a partial program, also called a sketch or template. This paper presents JSKETCH, a tool that brings sketch-based synthesis to Java. JSKETCH's input is a partial Java program that may include holes, which are unknown constants, expression generators, which range over sets of expressions, and class generators, which are partial classes. JSKETCH then translates the synthesis problem into a SKETCH problem; this translation is complex because SKETCH is not object-oriented. Finally, JSKETCH synthesizes an executable Java program by interpreting the output of SKETCH.Comment: This research was supported in part by NSF CCF-1139021, CCF- 1139056, CCF-1161775, and the partnership between UMIACS and the Laboratory for Telecommunication Science

Effects of pyruvate administration on infarct volume and neurological deficits following permanent focal cerebral ischemia in rats

Recent experimental evidences indicate that pyruvate, the final metabolite of glycolysis, has a remarkable protective effect against different types of brain injury. The purpose of this study was to assess the neuroprotective effect and the neurological outcome after pyruvate administration in a model of ischemic stroke induced by permanent middle cerebral artery occlusion (pMCAO) in rats. Three doses of pyruvate (250, 500 and 1000 mg/kg, i.p.) or vehicle were administered intraperitoneally 30 min after pMCAO. In other set of experiments, pyruvate was given either before, immediately after ischemia or in a long-term administration paradigm. Functional outcome, mortality and infarct volume were determined 24 h after stroke. Even when the lowest doses of pyruvate reduced mortality and neurological deficits, no concomitant reduction in infarct volume was observed. The highest dose of pyruvate increased cortical infarction by 27% when administered 30 min after pMCAO. In addition, when pyruvate was given before pMCAO, a significant increase in neurological deficits was noticed. Surprisingly, on the contrary of what was found in the case of transient global ischemia, present findings do not support a great neuroprotective role for pyruvate in permanent focal cerebral ischemia, suggesting two distinct mechanisms involved in the effects of this glycolytic metabolite in the ischemic brain

On Secure Implementation of an IHE XUA-Based Protocol for Authenticating Healthcare Professionals

The importance of the Electronic Health Record (EHR) has been addressed in recent years by governments and institutions.Many large scale projects have been funded with the aim to allow healthcare professionals to consult patients data. Properties such as confidentiality, authentication and authorization are the key for the success for these projects. The Integrating the Healthcare Enterprise (IHE) initiative promotes the coordinated use of established standards for authenticated and secure EHR exchanges among clinics and hospitals. In particular, the IHE integration profile named XUA permits to attest user identities by relying on SAML assertions, i.e. XML documents containing authentication statements. In this paper, we provide a formal model for the secure issuance of such an assertion. We first specify the scenario using the process calculus COWS and then analyse it using the model checker CMC. Our analysis reveals a potential flaw in the XUA profile when using a SAML assertion in an unprotected network. We then suggest a solution for this flaw, and model check and implement this solution to show that it is secure and feasible

Highly entangled photons from hybrid piezoelectric-semiconductor quantum dot devices

Entanglement resources are key ingredients of future quantum technologies. If they could be efficiently integrated into a semiconductor platform a new generation of devices could be envisioned, whose quantum-mechanical functionalities are controlled via the mature semiconductor technology. Epitaxial quantum dots (QDs) embedded in diodes would embody such ideal quantum devices, but QD structural asymmetries lower dramatically the degree of entanglement of the sources and hamper severely their real exploitation in the foreseen applications. In this work, we overcome this hurdle using strain-tunable optoelectronic devices, where any QD can be tuned for the emission of highly polarization-entangled photons. The electrically-controlled sources violate Bell inequalities without the need of spectral or temporal filtering and they feature the highest degree of entanglement ever reported for QDs, with concurrence as high as 0.75(2). These quantum-devices are at present the most promising candidates for the direct implementation of QD-based entanglement-resources in quantum information science and technology

TG, FT-IR and NMR characterization of n-C16H34 contaminated alumina and silica after mechanochemical treatment

This paper deals with the application of mechanochemistry to model systems composed of alumina or silica artificially contaminated with n-C16H34. The mechanochemical treatment was carried out by means of a ring mill for times ranging from 10 to 40 h. Thermogravimetry and infrared and nuclear magnetic resonance spectroscopies were used for the characterization of the mechanochemical products. The results have indicated that, in the case of alumina, almost all the contaminant n-C16H34 undergoes a complex oxidative reaction path whose end products are strongly held on the surface. These end products are most likely made of crosslinked, partially oxidized hydrocarbon chains bond to the solid surface via COO− groups. In the case of silica, the hydrocarbon undergoes a different, equally complex reaction path, but to a lower extent. In this case the end products are most probably carbonylic compounds and graphitic carbon. Then, for both solid matrices, the mechanochemical treatment promotes significant modification of the chemical nature of the polluting hydrocarbon with end products much more difficult to remove from the surface. As the systems studied are models of sites contaminated by aliphatic hydrocarbon, the results are worthy of consideration in relation to the mobility of the contaminants in the environment