Intelligent Assistance for Software Development and Maintenance

This article presents an architecture for controlled automation in software development environments. Controlled automation enables environments to behave as intelligent assistants by answering questions about the software project and automatically invoking tools to further the users’ goal of producing a working software system. The discussion of the architecture focuses primarily on the programming stages of development and maintenance. An environment assists programmers by understanding the technical aspects of the evolving software system and by actively participating in the programming process. The architecture supports these capabilities by providing two kinds of knowledge representation: (1) the knowledge specific to a particular software project is represented as entities in a database and (2) the knowledge that models programming activities in general is represented as rules amenable to forward and backward chaining. These rules enable an environment to automatically carry out each activity sometime between when its conditions are satisfied and its results are required. The rules are grouped into collections called strategies. One or more specific strategies are employed according to each user’s current context and goals, and determine when forward or backward chaining should be applied and which rules are considered during chaining. This architecture has been validated through a prototype implementation that models the capabilities of an existing environment that supports automation

Crystal Structure of a Ube2S-Ubiquitin Conjugate

Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a “donor” ubiquitin and a primary amino group of an “acceptor” ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface

Contribution of Matrix Metalloproteinase-9 to Cerebral Edema and Functional Outcome following Experimental Subarachnoid Hemorrhage

Background: Cerebral edema is an important risk factor for death and poor outcome following subarachnoid hemorrhage (SAH). However, underlying mechanisms are still poorly understood. Matrix metalloproteinase (MMP)-9 is held responsible for the degradation of microvascular basal lamina proteins leading to blood-brain barrier dysfunction and, thus, formation of vasogenic cerebral edema. The current study was conducted to clarify the role of MMP-9 for the development of cerebral edema and for functional outcome after SAH. Methods: SAH was induced in FVB/N wild-type (WT) or MMP-9 knockout (MMP-9(-/-)) mice by endovascular puncture. Intracranial pressure (ICP), regional cerebral blood flow (rCBF), and mean arterial blood pressure (MABP) were continuously monitored up to 30 min after SAH. Mortality was quantified for 7 days after SAH. In an additional series neurological function and body weight were assessed for 3 days after SAH. Subsequently, ICP and brain water content were quantified. Results: Acute ICP, rCBF, and MABP did not differ between WT and MMP-9(-/-) mice, while 7 days' mortality was lower in MMP-9(-/-) mice (p = 0.03; 20 vs. 60%). MMP-9(-/-) mice also exhibited better neurological recovery, less brain edema formation, and lower chronic ICP. Conclusions: The results of the current study suggest that MMP-9 contributes to the development of early brain damage after SAH by promoting cerebral edema formation. Hence, MMP-9 may represent a novel molecular target for the treatment of SAH. Copyright (C) 2011 S. Karger AG, Base

Arecibo Timing and Single Pulse Observations of 18 Pulsars

We present new results of timing and single pulse measurements for 18 radio pulsars discovered in 1993 - 1997 by the Penn State/NRL declination-strip survey conducted with the 305-m Arecibo telescope at 430 MHz. Long-term timing measurements have led to significant improvements of the rotational and the astrometric parameters of these sources, including the millisecond pulsar, PSR J1709+2313, and the pulsar located within the supernova remnant S147, PSR J0538+2817. Single pulse studies of the brightest objects in the sample have revealed an unusual "bursting" pulsar, PSR J1752+2359, two new drifting subpulse pulsars, PSR J1649+2533 and PSR J2155+2813, and another example of a pulsar with profile mode changes, PSR J1746+2540. PSR J1752+2359 is characterized by bursts of emission, which appear once every 3-5 min. and decay exponentially on a ~45 sec timescale. PSR J1649+2533 spends ~30% of the time in a null state with no detectable radio emission.Comment: submitted to Ap

Crystal structures of native cytochrome c 6 from Thermosynechococcus elongatus in two different space groups and implications for its oligomerization

Native cytochrome c (6) was purified from an extract of strain BP-1 of the thermophilic cyanobacterium Thermosynechococcus elongatus. The protein was crystallized, and with only slight modifications of the buffer and vapour-diffusion conditions two different space groups were observed, namely H3 and C2. Both crystal structures were solved; they contained three and six molecules per asymmetric unit and were refined to 1.7 and 2.25 Å resolution, respectively. To date, the structure of native cytochrome c (6) from T. elongatus has only been reported as a monomer using NMR spectroscopy, i.e. without addressing putative oligomerization, and related structures have only previously been solved using X-ray crystallography after recombinant gene overexpression in Escherichia coli. The reported space groups of related cyanobacterial cytochrome c (6) structures differ from those reported here. Interestingly, the protein–protein interfaces that were observed utilizing X-ray crystallography could also explain homo-oligomerization in solution; specifically, trimerization is indicated by infra-red dynamic light scattering and blue native gel electrophoresis in solution. Trimers were also detected by mass spectrometry. Furthermore, there is an indication of post-translational methylation in the crystal structure. Additionally, the possibility of modifying the crystal size and the redox activity in the context of photosynthesis is shaping the investigated cytochrome as a highly suitable model protein for advanced serial crystallography at highly brilliant X-ray free-electron laser sources

Survey of Planetary Nebulae at 30 GHz with OCRA-p

We report the results of a survey of 442 planetary nebulae at 30 GHz. The purpose of the survey is to develop a list of planetary nebulae as calibration sources which could be used for high frequency calibration in future. For 41 PNe with sufficient data, we test the emission mechanisms in order to evaluate whether or not spinning dust plays an important role in their spectra at 30 GHz. The 30-GHz data were obtained with a twin-beam differencing radiometer, OCRA-p, which is in operation on the Torun 32-m telescope. Sources were scanned both in right ascension and declination. We estimated flux densities at 30 GHz using a free-free emission model and compared it with our data. The primary result is a catalogue containing the flux densities of 93 planetary nebulae at 30 GHz. Sources with sufficient data were compared with a spectral model of free-free emission. The model shows that free-free emission can generally explain the observed flux densities at 30 GHz thus no other emission mechanism is needed to account for the high frequency spectra.Comment: 10 pages, 7 Postscript figures, to be published in A&

Double radio peak and non-thermal collimated ejecta in RS Ophiuchi following the 2006 outburst

We report Multi-Element Radio-Linked Interferometer Network, Very Large Array, One-Centimetre Radio Array, Very Long Baseline Array (VLBA), Effelsberg and Giant Metrewave Radio Telescope observations beginning 4.5 days after the discovery of RS Ophiuchi undergoing its 2006 recurrent nova outburst. Observations over the first 9 weeks are included, enabling us to follow spectral development throughout the three phases of the remnant development. We see dramatic brightening on days 4 to 7 at 6 GHz and an accompanying increase in other bands, particularly 1.46 GHz, consistent with transition from the initial ‘free expansion’ phase to the adiabatic expansion phase. This is complete by day 13 when the flux density at 5 GHz is apparently declining from an unexpectedly early maximum (compared with expectations from observations of the 1985 outburst). The flux density recovered to a second peak by approximately day 40, consistent with behaviour observed in 1985. At all times the spectral index is consistent with mixed non-thermal and thermal emission. The spectral indices are consistent with a non-thermal component at lower frequencies on all dates, and the spectral index changes show that the two components are clearly variable. The estimated extent of the emission at 22 GHz on day 59 is consistent with the extended east and west features seen at 1.7 GHz with the VLBA on day 63 being entirely non-thermal. We suggest a two-component model, consisting of a decelerating shell seen in mixed thermal and non-thermal emission plus faster bipolar ejecta generating the non-thermal emission, as seen in contemporaneous VLBA observations. Our estimated ejecta mass of 4 ± 2 × 10−7 M⊙ is consistent with a white dwarf (WD) mass of 1.4 M⊙. It may be that this ejecta mass estimate is a lower limit, in which case a lower WD mass would be consistent with the data

RoboPol: First season rotations of optical polarization plane in blazars

We present first results on polarization swings in optical emission of blazars obtained by RoboPol, a monitoring program of an unbiased sample of gamma-ray bright blazars specially designed for effective detection of such events. A possible connection of polarization swing events with periods of high activity in gamma rays is investigated using the dataset obtained during the first season of operation. It was found that the brightest gamma-ray flares tend to be located closer in time to rotation events, which may be an indication of two separate mechanisms responsible for the rotations. Blazars with detected rotations have significantly larger amplitude and faster variations of polarization angle in optical than blazars without rotations. Our simulations show that the full set of observed rotations is not a likely outcome (probability $\le 1.5 \times 10^{-2}$) of a random walk of the polarization vector simulated by a multicell model. Furthermore, it is highly unlikely ($\sim 5 \times 10^{-5}$) that none of our rotations is physically connected with an increase in gamma-ray activity.Comment: 16 pages, 9 figure

Selective nanomanipulation using optical forces

We present a detailed theoretical study of the recent proposal for selective nanomanipulation of nanometric particles above a substrate using near-field optical forces [Chaumet {\it et al.} Phys. Rev. Lett. {\bf 88}, 123601 (2002)]. Evanescent light scattering at the apex of an apertureless near-field probe is used to create an optical trap. The position of the trap is controlled on a nanometric scale via the probe and small objects can be selectively trapped and manipulated. We discuss the influence of the geometry of the particles and the probe on the efficiency of the trap. We also consider the influence of multiple scattering among the particles on the substrate and its effect on the robustness of the trap.Comment: 12 pages, 17 figure