Parameter reference immutability: formal definition, inference tool, and comparison

Knowing which method parameters may be mutated during a method’s execution is useful for many software engineering tasks. A parameter reference is immutable if it cannot be used to modify the state of its referent object during the method’s execution. We formally define this notion, in a core object-oriented language. Having the formal definition enables determining correctness and accuracy of tools approximating this definition and unbiased comparison of analyses and tools that approximate similar definitions. We present Pidasa, a tool for classifying parameter reference immutability. Pidasa combines several lightweight, scalable analyses in stages, with each stage refining the overall result. The resulting analysis is scalable and combines the strengths of its component analyses. As one of the component analyses, we present a novel dynamic mutability analysis and show how its results can be improved by random input generation. Experimental results on programs of up to 185 kLOC show that, compared to previous approaches, Pidasa increases both run-time performance and overall accuracy of immutability inference.     

The principle cause for lower plate numbers in capillary zone electrophoresis with most organic solvents.

With longitudinal diffusion as an unavoidable source of peak broadening, the peak efficiency (expressed by the plate number, N) in capillary zone electrophoresis depends on the ratio of electrophoretic mobility, mu, and tracer- or self-diffusion coefficient, D. Both parameters are functions of the ionic strength of the electrolyte solution. According to theory, the mobility is decreased with increasing ionic strength by the relaxation effect (depending on the relative permittivity) and the electrophoretic effect (depending on the relative permittivity and the viscosity of the solvent), whereas the diffusion coefficient is decreased only by the relaxation effect. This allows the theoretical predictions that the plate number, which is proportional to the ratio mu/D, decreases with increasing ionic strength and that the magnitude of this reduction depends on the solvent. Taking the values for relative permittivity and viscosity allows forecasting that, in general, water as a solvent exhibits the smallest lowering of the plate number, as compared to organic solvents. The theoretical predictions are confirmed by the data for the ratio calculated from measured mobilities and diffusion coefficients for iodide as the analyte ion in water, methanol, and acetonitrile with ionic strength of the background electrolyte varying between 0.005 and 0.080 mol L(-1). Whereas the experimentally observed plate number per volt is reduced from its "ultimate value" of about 20 (analyte charge number z = 1, zero ionic strength) in water by only 10%, the decrease at the same ionic strength in methanol and acetonitrile reaches 25 to 30%. Thus, the maximum plate number should read Nmax approximately equals 13 zU (with U being the effective voltage) for these solvents with ionic strengths normally applied in capillary electrophoresis. This reduction is not stemming from inappropriate experimental conditions, but has fundamental physicochemical causes.     

Characterization of seasonal variation of forest canopy in a temperate deciduous broadleaf forest, using daily MODIS data

In this paper, we present an improved procedure for collecting no or little atmosphere- and snow-contaminated observations from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor. The resultant time series of daily MODIS data of a temperate deciduous broadleaf forest (the Bartlett Experimental Forest) in 2004 show strong seasonal dynamics of surface reflectance of green, near infrared and shortwave infrared bands, and clearly delineate leaf phenology and length of plant growing season. We also estimate the fractions of photosynthetically active radiation (PAR) absorbed by vegetation canopy (FAPAR_canopy), leaf (FAPAR_leaf), and chlorophyll (FAPAR_chl), respectively, using a coupled leaf-canopy radiative transfer model (PROSAIL-2) and daily MODIS data. The Markov Chain Monte Carlo (MCMC) method (the Metropolis algorithm) is used for model inversion, which provides probability distributions of the retrieved variables. A two-step procedure is used to estimate the fractions of absorbed PAR: (1) to retrieve biophysical and biochemical variables from MODIS images using the PROSAIL-2 model; and (2) to calculate the fractions with the estimated model variables from the first step. Inversion and forward simulations of the PROSAIL-2 model are carried out for the temperate deciduous broadleaf forest during day of year (DOY) 184 to 201 in 2005. The reproduced reflectance values from the PROSAIL-2 model agree well with the observed MODIS reflectance for the five spectral bands (green, red, NIR₁, NIR₂, and SWIR₁). The estimated leaf area index, leaf dry matter, leaf chlorophyll content and FAPAR_canopy values are close to field measurements at the site. The results also showed significant differences between FAPAR_canopy and FAPAR_chl at the site. Our results show that MODIS imagery provides important information on biophysical and biochemical variables at both leaf and canopy levels.     

An overview of JML tools and applications

The Java Modeling Language (JML) can be used to specify the detailed design of Java classes and interfaces by adding annotations to Java source files. The aim of JML is to provide a specification language that is easy to use for Java programmers and that is supported by a wide range of tools for specification typechecking, runtime debugging, static analysis, and verification.This paper gives an overview of the main ideas behind JML, details about JML’s wide range of tools, and a glimpse into existing applications of JML.     

Sliding simulation for adhesion problems in micro gear trains based on an atomistic simplified model

The objective of this research work is to provide a systematic method to perform molecular dynamics simulation or evaluation for adhesion of micro/nano gear train during sliding friction in MEMS. In this paper, molecular dynamics simulations of adhesion problems in micro gear train are proposed. The perfect MEMS gear train model is very complicated by considering the computing time. A simplified model to simulate surface sliding between metals by molecular dynamics (MD) is proposed because the surface property is a dominant factor for the performance of gear systems. Based on analysis of sliding friction and the transmitting characteristics of micro gear train, a model is established by utilizing the Morse potential function. The Verlet algorithm is employed to solve atom trajectories. The simulation results show that adhesion tends to occur between two micro gears after certain cycles and such adhesion accounts for the friction force and the temperature increase. The simulation results are in consistence with the experimental results in the literature. The model is meaningful to prolong the lifetime of micro gear train by selecting proper parameters.     

Solid-state NMR studies of the prion protein H1 fragment

Conformational changes in the prion protein (PrP) seem to be responsible for prion diseases. We have used conformation-dependent chemical-shift measurements and rotational-resonance distance measurements to analyze the conformation of solid-state peptides lacking long-range order, corresponding to a region of PrP designated H1. This region is predicted to undergo a transformation of secondary structure in generating the infectious form of the protein. Solid-state NMR spectra of specifically 13C-enriched samples of H1, residues 109-122 (MKHMAGAAAAGAVV) of Syrian hamster PrP, have been acquired under cross-polarization and magic-angle spinning conditions. Samples lyophilized from 50% acetonitrile/50% water show chemical shifts characteristic of a beta-sheet conformation in the region corresponding to residues 112-121, whereas samples lyophilized from hexafluoroisopropanol display shifts indicative of alpha-helical secondary structure in the region corresponding to residues 113-117. Complete conversion to the helical conformation was not observed and conversion from alpha-helix back to beta-sheet, as inferred from the solid-state NMR spectra, occurred when samples were exposed to water. Rotational-resonance experiments were performed on seven doubly 13C-labeled H1 samples dried from water. Measured distances suggest that the peptide is in an extended, possibly beta-strand, conformation. These results are consistent with the experimental observation that PrP can exist in different conformational states and with structural predictions based on biological data and theoretical modeling that suggest that H1 may play a key role in the conformational transition involved in the development of prion diseases.     

Wasserstoffinduzierte Spannungsrißkorrosion an unverzinkten und verzinkten Baustählen

Hydrogen induced stress corrosion cracking of non galvanized and galvanized construction steels The processes of atmospheric corrosion and corrosion in collected water which may lead to hydrogen induced stress corrosion cracking of high-strength reinforcing steels in casing tubes before injection with concrete are discussed. Hydrogen uptake during corrosion occurs in weakly acid solutions as well as in neutral or alkaline aqueous solutions. The hydrogen uptake by proton discharge in acid solutions decreases with increasing pH of the electrolyte. Hydrogen can also be absorbed in neutral to weakly alkaline solutions if steels are plastically deformed and water reacts with the fresh iron surface. In alkaline solutions, hydrogen uptake is possible if, at the generally passivated steel surface, localized corrosion (pitting or crevice corrosion), local galvanic cells and a sufficient decrease in the pH of the pit electrolyte occurs. In the case of galvanized steels with damaged zinc layers, hydrogen uptake may result from the cathodic polarization of the free steel surface by zinc dissolution. The absorbed hydrogen interacts with the microstructure of the steels and weakens the bonds between the iron atoms. The influence of the microstructure of high-strength steels on the fracture behaviour is discussed on the basic of the so-called decohesion theory.     

Proton spectroscopy in myotonic dystrophy: correlations with CTG repeats

We have previously reported inhibition of cell-free activation of the neutrophil superoxide-generating NADPH oxidase by a soluble cationic protein of neutrophil granules and by low concentrations of human defensin. Subcellular fractionation carried out in the current study indicated that the inhibitory substance was derived from azurophilic granules, was released into the medium on cell stimulation, and was resistant to phenylmethylsulfonyl fluoride (PMSF). Phorbol ester was the most effective stimulus for the release of the blocking activity. The possibility was raised that granule protein(s) act in vivo as negative modulators of superoxide production. Gel filtration of granule extract revealed a markedly retarded protein peak exhibiting oxidase-blocking activity and containing lysozyme as the main protein. Because lysozyme did not exert inhibitory effects on oxidase activation, association of the inhibitory protein with lysozyme was assumed. Indeed a column of immobilized lysozyme retained a fraction of the granule extract's oxidase-blocking activity. Elution with a low-pH buffer recovered a component capable of inhibition of the NADPH oxidase in stimulated neutrophils and in the cell-free system. The main 29-kDa protein band in the eluted fraction was identified as proteinase 3, a serine protease of azurophilic granules. Enzymatically active as well as PMSF-blocked conventionally purified proteinase 3 interfered with phorbol myristate acetate-induced superoxide release. These findings support the hypothesis that exocytosed granule constituents may prevent excessive activation of the NADPH oxidase.