Lifecycle-Support in Architectures for Ontology-Based Information Systems

Ontology-based applications play an increasingly important role in the public and corporate Semantic Web. While today there exist a range of tools and technologies to support specific ontology engineering and management activities, architectural design guidelines for building ontology-based applications are missing. In this paper, we present an architecture for ontology-based applications—covering the complete ontology-lifecycle—that is intended to support software engineers in designing and developing ontology based-applications. We illustrate the use of the architecture in a concrete case study using the NeOn toolkit as one implementation of the architecture

Rotation-tunneling spectrum and astrochemical modeling of dimethylamine, CH3_3NHCH3_3, and searches for it in space

Methylamine has been the only simple alkylamine detected in the interstellar medium for a long time. With the recent secure and tentative detections of vinylamine and ethylamine, respectively, dimethylamine has become a promising target for searches in space. Its rotational spectrum, however, has been known only up to 45 GHz until now. Here we investigate the rotation-tunneling spectrum of dimethylamine in selected regions between 76 and 1091 GHz using three different spectrometers in order to facilitate its detection in space. The quantum number range is extended to $J = 61$ and $K_a = 21$, yielding an extensive set of accurate spectroscopic parameters. To search for dimethylamine, we refer to the spectral line survey ReMoCA carried out with the Atacama Large Millimeter/submillimeter Array toward the high-mass star-forming region Sagittarius B2(N) and a spectral line survey of the molecular cloud G+0.693$-$0.027 employing the IRAM 30 m and Yebes 40 m radio telescopes. We report nondetections of dimethylamine toward the hot molecular cores Sgr B2(N1S) and Sgr B2(N2b) as well as G+0.693$-$0.027 which imply that dimethylamine is at least 14, 4.5 and 39 times less abundant than methylamine toward these sources, respectively. The observational results are compared to computational results from a gas-grain astrochemical model. The modeled methylamine to dimethylamine ratios are compatible with the observational ratios. However, the model produces too much ethylamine compared with methylamine which could mean that the already fairly low levels of dimethylamine in the models may also be too high.Comment: Mon. Not. R. Astron. Soc., accepted. 33 pages including tables, figures, and appendi

Investigation of the rotational spectrum of CD3_3OD and an astronomical search toward IRAS 16293−-2422

Solar-type prestellar cores and protostars display large amounts of deuterated organic molecules. Recent findings on CHD$_2$OH and CD$_3$OH toward IRAS 16293-2422 suggest that even fully deuterated methanol, CD$_3$OD, may be detectable as well. However, searches for CD$_3$OD are hampered in particular by the lack of intensity information from a spectroscopic model. The objective of the present investigation is to develop a spectroscopic model of CD$_3$OD in low-lying torsional states that is sufficiently accurate to facilitate searches for this isotopolog in space. We carried out a new measurement campaign for CD$_3$OD involving two spectroscopic laboratories that covers the 34 GHz-1.1 THz range. A torsion-rotation Hamiltonian model based on the rho-axis method was employed for our analysis. Our resulting model describes the ground and first excited torsional states of CD$_3$OD well up to quantum numbers $J \leq 51$ and $K_a \leq 23$. We derived a line list for radio-astronomical observations from this model that is accurate up to at least 1.1 THz and should be sufficient for all types of radio-astronomical searches for this methanol isotopolog. This line list was used to search for CD$_3$OD in data from the Protostellar Interferometric Line Survey of IRAS 16293$-$2422 obtained with the Atacama Large Millimeter/submillimeter Array. While we found several emission features that can be attributed largely to CD$_3$OD, their number is still not sufficiently high enough to establish a clear detection. Nevertheless, the estimate of 2$\times 10^{15}$ cm$^{-2}$ derived for the CD$_3$OD column density may be viewed as an upper limit that can be compared to column densities of CD$_3$OH, CH$_3$OD, and CH$_3$OH. The comparison indicates that the CD$_3$OD column density toward IRAS 16293-2422 is in line with the enhanced D/H ratios observed for multiply deuterated complex organic molecules.Comment: 10 pages total, including figures, tables, and references; abstract slightly shortened; Astron. Astrophys., accepte

Interstellar detection of CCC and high-precision laboratory measurements near 2THz

ABSTRACT We describe more fully our original tentative interstellar detection of the triatomic pure carbon chain molecule, CCC, in absorption toward the Galactic center source Sgr B2

Coding Efficiency of Fly Motion Processing Is Set by Firing Rate, Not Firing Precision

To comprehend the principles underlying sensory information processing, it is important to understand how the nervous system deals with various sources of perturbation. Here, we analyze how the representation of motion information in the fly's nervous system changes with temperature and luminance. Although these two environmental variables have a considerable impact on the fly's nervous system, they do not impede the fly to behave suitably over a wide range of conditions. We recorded responses from a motion-sensitive neuron, the H1-cell, to a time-varying stimulus at many different combinations of temperature and luminance. We found that the mean firing rate, but not firing precision, changes with temperature, while both were affected by mean luminance. Because we also found that information rate and coding efficiency are mainly set by the mean firing rate, our results suggest that, in the face of environmental perturbations, the coding efficiency is improved by an increase in the mean firing rate, rather than by an increased firing precision

Accurate laboratory rest frequencies of vibrationally excited CO up to varv=3varv = 3 and up to 2 THz

Astronomical observations of (sub)millimeter wavelength pure rotational emission lines of the second most abundant molecule in the Universe, CO, hold the promise of probing regions of high temperature and density in the innermost parts of circumstellar envelopes. The rotational spectrum of vibrationally excited CO up to \varv = 3 has been measured in the laboratory between 220 and 1940 GHz with relative accuracies up to $5.2 \times 10^{-9}$, corresponding to $\sim 5$ kHz near 1 THz. The rotational constant $B$ and the quartic distortion parameter $D$ have been determined with high accuracy and even the sextic distortion term $H$ was determined quite well for \varv = 1 while reasonable estimates of $H$ were obtained for \varv = 2 and 3. The present data set allows for the prediction of accurate rest frequencies of vibrationally excited CO well beyond 2 THz.Comment: Astron. Astrophys, accepted; 5 pages, 2 Figures, 2 Table

Comparative assessment of phototherapy protocols for reduction of oxidative stress in partially transected spinal cord slices undergoing secondary degeneration

Background: Red/near-infrared light therapy (R/NIR-LT) has been developed as a treatment for a range of conditions, including injury to the central nervous system (CNS). However, clinical trials have reported variable or sub-optimal outcomes, possibly because there are few optimized treatment protocols for the different target tissues. Moreover, the low absolute, and wavelength dependent, transmission of light by tissues overlying the target site make accurate dosing problematic. Results: In order to optimize light therapy treatment parameters, we adapted a mouse spinal cord organotypic culture model to the rat, and characterized myelination and oxidative stress following a partial transection injury. The ex vivo model allows a more accurate assessment of the relative effect of different illumination wavelengths (adjusted for equal quantal intensity) on the target tissue. Using this model, we assessed oxidative stress following treatment with four different wavelengths of light: 450 nm (blue); 510 nm (green); 660 nm (red) or 860 nm (infrared) at three different intensities: 1.93 × 10¹⁶ (low); 3.85 × 10¹⁶ (intermediate) and 7.70 × 10¹⁶ (high) photons/cm²/s. We demonstrate that the most effective of the tested wavelengths to reduce immunoreactivity of the oxidative stress indicator 3-nitrotyrosine (3NT) was 660 nm. 860 nm also provided beneficial effects at all tested intensities, significantly reducing oxidative stress levels relative to control (p ≤ 0.05). Conclusions: Our results indicate that R/NIR-LT is an effective antioxidant therapy, and indicate that effective wavelengths and ranges of intensities of treatment can be adapted for a variety of CNS injuries and conditions, depending upon the transmission properties of the tissue to be treated.12 page(s

Neutrophil depletion reduces edema formation and tissue loss following traumatic brain injury in mice

Background: Brain edema as a result of secondary injury following traumatic brain injury (TBI) is a major clinical concern. Neutrophils are known to cause increased vascular permeability leading to edema formation in peripheral tissue, but their role in the pathology following TBI remains unclear. Methods: In this study we used controlled cortical impact (CCI) as a model for TBI and investigated the role of neutrophils in the response to injury. The outcome of mice that were depleted of neutrophils using an anti-Gr-1 antibody was compared to that in mice with intact neutrophil count. The effect of neutrophil depletion on blood-brain barrier function was assessed by Evan's blue dye extravasation, and analysis of brain water content was used as a measurement of brain edema formation (24 and 48 hours after CCI). Lesion volume was measured 7 and 14 days after CCI. Immunohistochemistry was used to assess cell death, using a marker for cleaved caspase-3 at 24 hours after injury, and microglial/macrophage activation 7 days after CCI. Data were analyzed using Mann-Whitney test for non-parametric data. Results: Neutrophil depletion did not significantly affect Evan's blue extravasation at any time-point after CCI. However, neutrophil-depleted mice exhibited a decreased water content both at 24 and 48 hours after CCI indicating reduced edema formation. Furthermore, brain tissue loss was attenuated in neutropenic mice at 7 and 14 days after injury. Additionally, these mice had a significantly reduced number of activated microglia/macrophages 7 days after CCI, and of cleaved caspase-3 positive cells 24 h after injury. Conclusion: Our results suggest that neutrophils are involved in the edema formation, but not the extravasation of large proteins, as well as contributing to cell death and tissue loss following TBI in mice

Biomarkers for Severity of Spinal Cord Injury in the Cerebrospinal Fluid of Rats

One of the major challenges in management of spinal cord injury (SCI) is that the assessment of injury severity is often imprecise. Identification of reliable, easily quantifiable biomarkers that delineate the severity of the initial injury and that have prognostic value for the degree of functional recovery would significantly aid the clinician in the choice of potential treatments. To find such biomarkers we performed quantitative liquid chromatography-mass spectrometry (LC-MS/MS) analyses of cerebrospinal fluid (CSF) collected from rats 24 h after either a moderate or severe SCI. We identified a panel of 42 putative biomarkers of SCI, 10 of which represent potential biomarkers of SCI severity. Three of the candidate biomarkers, Ywhaz, Itih4, and Gpx3 were also validated by Western blot in a biological replicate of the injury. The putative biomarkers identified in this study may potentially be a valuable tool in the assessment of the extent of spinal cord damage