Formal ontology for biomedical knowledge systems integration

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications

Ontological theory for ontological engineering: Biomedical systems information integration

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date

Meaningful vocabulary practice in third grade reading,

Thesis (M.A.)--Boston Universit

System-performance analysis of optimized gain-switched pulse source employed in 40-and 80-Gb/s OTDM systems

The development of ultrashort optical pulse sources, exhibiting excellent temporal and spectral profiles, will play a crucial role in the performance of future optical time division multiplexed (OTDM) systems. In this paper, we demonstrate the difference in performance in 40- and 80-Gb/s OTDM systems between optical pulse sources based on a gain-switched laser whose pulses are compressed by a nonlinearly and linearly chirped fiber Bragg grating. The results achieved show that nonlinear chirp in the wings of the pulse leads to temporal pedestals formed on either side of the pulse when using the linearly chirped grating, whereas with the nonlinearly chirped grating, pedestals are essentially eliminated. In an OTDM system, these pedestals cause coherent interaction between neighboring channels, resulting in intensity fluctuations that lead to a power penalty of 1.5 dB (40 Gb/s) and 3.5 dB (80 Gb/s) in comparison to the case where the nonlinearly chirped grating is used. Simulations carried out with the aid of Virtual Photonics Inc. verify the results achieved

Temporal and spatial trends in stranding records of cetaceans on the Irish coast, 2002–2014

Using Irish strandings data collected between 2002 and 2014, seasonal and annual trends in the number of strandings for all strandings identified to species level (N ¼ 1480), and for the five most frequently reported species: common dolphin (25.7% of records), harbour porpoise (22.2%), long-finned pilot whale (8.8%), striped dolphin (6.9%) and bottlenose dolphin (6.9%) were investigated. With the exception of bottlenose dolphins, there was a significant linear increase in the number of strandings across years for all species and for all strandings collectively, that were identified to species-level. Only common dolphins demonstrated a significant increase in the proportion of records relative to all other strandings, which may be indicative of a real rise in the number of strandings of this species. Common dolphins and harbour porpoises showed a similar significant difference in monthly strandings, with more strandings occurring during the earlier months of the year.\ud Significant differences in the gender of stranded animals were found in common, striped, bottlenose and Atlantic white-sided dolphins and sperm and pygmy sperm whales. Live and mass stranding events were primarily comprised of pelagic species. Most strandings occurred on the south and west coasts, with two hotspots for live and mass strandings identified. The patterns and trends identified are discussed in relation to the caveats in interpreting strandings data. Specifically to Ireland, the findings highlight the urgent need to build on the current volunteer reporting network and augment this comprehensive dataset with post-mortem examinations to better understand the cause of the trends identified. The importance of strandings data in informing conservation and management guidelines of these species’ is discussed

FROG characterisation of SOA-based wavelength conversion using XPM in conjunction with shifted filtering up to line rates of 80 GHz

The work we present here builds on recent work where we obtained 80 Gb/s error free performance using cross phase modulation (XPM) in an SOA in conjunction with a blue shifted bandpass filter. Here we present a detailed characterisation of this wavelength conversion scheme using a Frequency Resolved Optical Gating (FROG) measurement scheme for both red and blue shifted filtering. This type of characterisation has not been provided before to the best of our knowledge and is an important analysis firstly to achieve a full understanding of the gain and phase dynamics exploited by the wavelength conversion scheme presented and secondly to design a filter so that an optimum performance can be obtaine

Mid-Infrared and Submillimeter Observations of the Illuminating Source of McNeil's Variable Nebula

We present post-outburst observations of the mid-infrared spectrum and submillimeter continuum of the illuminating source of the newly-discovered McNeil's Nebula in the L1630 region of Orion. The 12 micron flux of this source has increased by a factor of 25 after the outburst, whereas the submillimeter continuum remains at its pre-outburst level. The bolometric luminosity has increased by at least an order of magnitude, to ~34 L_sun, and is likely less than 90 L_sun. The mid-infrared spectrum exhibits a strong and red continuum with no emission or absorption features. The infrared slope of the spectral energy distribution characterizes the illuminating source as a flat-spectrum protostar, in both its active and quiescent states. New CO spectral line observations show no evidence for a molecular outflow.Comment: submitted to ApJ

Asymptotic Neutrality of Large-Z Ions

Let N(Z) denote the number of electrons that a nucleus of charge Z binds in nonrelativistic quantum theory. It is proved that (N(Z))/Z → 1 as Z → ∞. The Pauli principle plays a critical role

Analysis of bit rate dependence up to 80 Gbit/s of a simple wavelength converter based on XPM in a SOA and a shifted filtering

This paper provides the analysis of wavelength converted pulses obtained with a simple semiconductor optical amplifier (SOA)-based wavelength conversion scheme, which exploits cross phase modulation (XPM) in an SOA in conjunction with shifted filtering. The analysis includes experimental measurements of the back-to-back system performances as well as frequency-resolved optical gating (FROG) characterisations of the wavelength converted pulses. These measurements are implemented at different bit rates up to 80 Gbit/s and for both red and blue-shifted filtering, particularly showing different patterning effect dependencies of red and blue-shifting techniques. This analysis is developed by the addition of a numerical study which corroborates the experimental results. A further understanding of the different performances of red and blue filtering techniques, presented in the literature, can thus be proposed. The placement of the filter to undertake red-shifted filtering (RSF) allows us to achieve very short pulse widths but high bit rate operation is limited by pattern effects. The blue-shifted filtering (BSF) technique shows optimum performance as regards to patterning effects even if the wavelength converted pulses can be larger

80-Gb/s OTDM system analysis of a vertical microcavity-based saturable absorber for the enhancement of pulse pedestal suppression

In future high-speed optical time-division-multiplexed (OTDM) systems, an important factor that needs to be considered for optical pulse generation schemes is the impact of pulse pedestals on the overall system performance. The results presented in this letter are two-fold; first, the impact due to the height of pulse pedestals in an 80-Gb/s OTDM system are established. Second, a solution is provided to overcome these high pedestal levels through the use of a vertical microcavity saturable absorber, which can significantly reduce the pulse pedestal level and give enhanced system performanc