Bounded Model Checking of State-Space Digital Systems: The Impact of Finite Word-Length Effects on the Implementation of Fixed-Point Digital Controllers Based on State-Space Modeling

The extensive use of digital controllers demands a growing effort to prevent design errors that appear due to finite-word length (FWL) effects. However, there is still a gap, regarding verification tools and methodologies to check implementation aspects of control systems. Thus, the present paper describes an approach, which employs bounded model checking (BMC) techniques, to verify fixed-point digital controllers represented by state-space equations. The experimental results demonstrate the sensitivity of such systems to FWL effects and the effectiveness of the proposed approach to detect them. To the best of my knowledge, this is the first contribution tackling formal verification through BMC of fixed-point state-space digital controllers.Comment: International Symposium on the Foundations of Software Engineering 201

Spectroscopic Studies of the Iron and Manganese Reconstituted Tyrosyl Radical in Bacillus Cereus Ribonucleotide Reductase R2 Protein

Ribonucleotide reductase (RNR) catalyzes the rate limiting step in DNA synthesis where ribonucleotides are reduced to the corresponding deoxyribonucleotides. Class Ib RNRs consist of two homodimeric subunits: R1E, which houses the active site; and R2F, which contains a metallo cofactor and a tyrosyl radical that initiates the ribonucleotide reduction reaction. We studied the R2F subunit of B. cereus reconstituted with iron or alternatively with manganese ions, then subsequently reacted with molecular oxygen to generate two tyrosyl-radicals. The two similar X-band EPR spectra did not change significantly over 4 to 50 K. From the 285 GHz EPR spectrum of the iron form, a g1-value of 2.0090 for the tyrosyl radical was extracted. This g1-value is similar to that observed in class Ia E. coli R2 and class Ib R2Fs with iron-oxygen cluster, suggesting the absence of hydrogen bond to the phenoxyl group. This was confirmed by resonance Raman spectroscopy, where the stretching vibration associated to the radical (C-O, ν7a = 1500 cm−1) was found to be insensitive to deuterium-oxide exchange. Additionally, the 18O-sensitive Fe-O-Fe symmetric stretching (483 cm−1) of the metallo-cofactor was also insensitive to deuterium-oxide exchange indicating no hydrogen bonding to the di-iron-oxygen cluster, and thus, different from mouse R2 with a hydrogen bonded cluster. The HF-EPR spectrum of the manganese reconstituted RNR R2F gave a g1-value of ∼2.0094. The tyrosyl radical microwave power saturation behavior of the iron-oxygen cluster form was as observed in class Ia R2, with diamagnetic di-ferric cluster ground state, while the properties of the manganese reconstituted form indicated a magnetic ground state of the manganese-cluster. The recent activity measurements (Crona et al., (2011) J Biol Chem 286: 33053–33060) indicates that both the manganese and iron reconstituted RNR R2F could be functional. The manganese form might be very important, as it has 8 times higher activity

A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical Ultracentrifugation

Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies

Inorganic Mass Spectrometry

To establish a method for sensitive, accurate, and precise determination of Se in real samples, isotope dilution analysis using high-power nitrogen microwave-induced plasma mass spectrometry (N 2 MIP-IDMS) was conducted. In this study, freeze-dried human blood serum (Standard Reference Material, NIES No. 4) provided by NIES (National Institute for Environmental Studies) was used as a real sample. The measured isotopes of Se were 78 Se and 80 Se which are the major isotopes of Se. The appropriate amount of a Se spike solution was theoretically calculated by using an error multiplication factor (F) and was confirmed experimentally for the isotope dilution analysis. The mass discrimination effect was corrected for by using a standard Se solution for the measurement of Se isotope ratios in the spiked sample. However, the sensitivity for the detection of Se was not so good and the precision of the determination was not improved (2-3%) by N 2 MIP-IDMS with use of the conventional nebulizer. Therefore, a hydride generation system was connected to N 2 MIP-IDMS as a sample introduction system (HG-N 2 MIP-IDMS) in order to establish a more sensitive detection and a more precise determination of Se. A detection limit (3σ) of 10 pg mL -1 could be achieved, and the RSD was less than 1% at the concentration level of 5.0-10.0 ng mL -1 by HG-N 2 MIP-IDMS. The analytical results were found to be in a good agreement with those obtained by the standard addition method using conventional Ar ICPMS. It is well-known that Se is an essential element for all mammals. Se deficiency leads to deficiency syndromes, for example, Keshan disease, which is known for cardiac insufficiency that occurred in children and pregnant women in China. Problems also occur if the concentration of Se is too high; for example, gastroenteric disorders, dermatitis, and neurotic disorders are caused by excessive intake of Se. Moreover, it is well-known that the range of permissive intake amounts of Se is very narrow for human beings. Therefore, it is restricted as a toxic element in environmental standards. There are several sources of environmental Se pollution: the processes of Se refinement and the production processes of Se-containing products. For these reasons, the accurate and precise determination of trace levels of Se in environmental and biological samples is required, and studies of Se determination have been reported by several groups. [1][2][3][4][5][6][7][8][9][10][11] Because Ar ICPMS can measure multiple elements at a concentration range from ng mL -1 to fg mL -1 , it has widespread use in the determination of trace elements in various samples. 12-25 However

Potassium and Sodium Transport in Yeast

[EN] As the proper maintenance of intracellular potassium and sodium concentrations is vital for cell growth, all living organisms have developed a cohort of strategies to maintain proper monovalent cation homeostasis. In the model yeast Saccharomyces cerevisiae, potassium is accumulated to relatively high concentrations and is required for many aspects of cellular function, whereas high intracellular sodium/potassium ratios are detrimental to cell growth and survival. The fact that S. cerevisiae cells can grow in the presence of a broad range of concentrations of external potassium (10 M–2.5 M) and sodium (up to 1.5 M) indicates the existence of robust mechanisms that have evolved to maintain intracellular concentrations of these cations within appropriate limits. In this review, current knowledge regarding potassium and sodium transporters and their regulation will be summarized. 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Speech, truth and liberty: Bentham to John Stuart Mill

Bentham’s Utilitarianism transforms earlier free speech doctrine in the service of the pursuit of truth and the control of government, preserving the distinction between statements of opinion and of fact and awarding the latter a lesser degree of protection. The work of James Mill and the early writings of John Stuart Mill retain this distinction, but their accounts are weighed down by the problems of a direct Utilitarian approach, in their consequentialist balancing of different values against each other, and in their dependence on a majoritarian epistemology and their commitment to a naive progressive optimism. Mill goes on in On Liberty to address and resolve these problems on the basis of a new justification for free speech as free deliberative thought. I argue that, contrary to most interpretations, his new justification leaves untouched the basic distinction between absolutely protected expressions of opinion and only functionally and contingently protected assertions of fact, leaving room for restrictions on factual statements, especially when untrue

Outer membrane protein folding from an energy landscape perspective

The cell envelope is essential for the survival of Gram-negative bacteria. This specialised membrane is densely packed with outer membrane proteins (OMPs), which perform a variety of functions. How OMPs fold into this crowded environment remains an open question. Here, we review current knowledge about OFMP folding mechanisms in vitro and discuss how the need to fold to a stable native state has shaped their folding energy landscapes. We also highlight the role of chaperones and the β-barrel assembly machinery (BAM) in assisting OMP folding in vivo and discuss proposed mechanisms by which this fascinating machinery may catalyse OMP folding