A Common Knowledge Engineering Framework for Data Assimilation, Correlation, and Extrapolation (DACE)

The Common Knowledge Engineering Framework for Data Assimilation, Correlation, and Extrapolation (DACE) project is focused on providing a software centric general framework for advanced processing and analysis of data. This translates to researchers, scientists, engineers, and system architects not having to program a new application but rather to define the system configuration, process, and processing that is needed to perform a specific functionality. This makes the limitation of the application the end users ability to fully define the functional requirements and setup the framework accordingly. This doctoral project will provide the details to the system definition, standards, metrics, schedule, and evaluation that were utilized in the performance o f this project. The project’s framework allows multiple analysis methods to be utilized either individually or concurrently depending on the end user’s configuration. The architecture will not provide limitations on what can be done. It will allow the end user to configure and define the analysis method to use

Implementing an Intelligent Retrieval System: The CODER System, Version 1.0

For individuals requiring interactive access to online text, information storage and retrieval systems provide a way to retrieve desired documents and/or text passages. The CODER (COmposite Document Expert/effective/extended Retrieval) system is a testbed for determining how useful various artificial intelligence techniques are for increasing the effectiveness of information storage and retrieval systems. The system, designed previously, has three components: an analysis subsystem for analyzing and storing document contents, a central spine for manipulations and storage of world and domain knowledge, and a retrieval subsystem for matching user queries to relevant documents. This thesis discusses the implementation of the retrieval subsystem and portions of the spine and analysis subsystem. It illustrates that logic programming, specifically with the Prolog language, is suitable for development of an intelligent information retrieval system. Furthermore, it shows that system modularity provides a flexible research testbed, allowing many individuals to work on different parts of the system which may later be quickly integrated. The retrieval subsystem has been implemented in a modular fashion so that new approaches to information can be easily compared to more traditional ones. A powerful knowledge representation language, a comprehensive lexicon, and individually tailored experts using standardized blackboard modules for communication and control allowed rapid prototyping, incremental development and ready adaptability to change. The system executes on a DEC VAX 11/785 running ULTRIX (TM), a variant of 4.2 BSD UNIX. It has been implemented as a set of MU-Prolog and C modules communicating through TCP/IP sockets

Old and Young X-ray Point Source Populations in Nearby Galaxies

We analyzed 1441 Chandra X-ray point sources in 32 nearby galaxies. The total point-source X-ray luminosity L_XP is well correlated with B, K, and FIR+UV luminosities of spiral host galaxies, and with the B and K luminosities for ellipticals. This suggests an intimate connection between L_XP and both the old and young stellar populations, for which K and FIR+UV luminosities are proxies for the galaxy mass M and star-formation rate SFR. We derive proportionality constants 1.3E29 erg/s/Msol and 0.7E39 erg/s/(Msol/yr), which can be used to estimate the old and young components from M and SFR, respectively. The cumulative X-ray luminosity functions for the point sources have quite different slopes for the spirals (gamma ~= 0.5-0.8) and ellipticals (gamma ~= 1.4), implying *the most luminous point sources dominate L_XP* for the spirals. Most of the point sources have X-ray colors that are consistent with either LMXBs or Ultraluminous X-ray sources (ULXs a.k.a. IXOs) and we rule out classical HMXBs (e.g. neutron-star X-ray pulsars) as contributing much to L_XP. Thus, for spirals, the ULXs dominate L_XP. We estimate that >~20% of all ULXs found in spirals originate from the older (pop II) stellar populations, indicating that many of the ULXs that have been found in spiral galaxies are in fact pop II ULXs, like those in elliptical galaxies. The linear dependence of L_XP on the SFR argues for either a steepening in the X-ray luminosity function of the young (pop I) X-ray source population at L_X >~10^(38.5-39) erg/s, or a decreasing efficiency for producing all types of young X-ray point sources as the galaxy SFR increases.Comment: 33 pages AASTEX, ApJ accepted. Please download full version with figures from http://www.pha.jhu.edu/~colbert/chps_accepted.p

Extranuclear X-ray Emission in the Edge-on Seyfert Galaxy NGC 2992

We found several extranuclear (r >~ 3") X-ray nebulae within 40" (6.3 kpc at 32.5 Mpc) of the nucleus of the Seyfert galaxy NGC 2992. The net X-ray luminosity from the extranuclear sources is ~2-3 E39 erg/s (0.3-8.0 keV). The X-ray core itself (r <~ 1") is positioned at 9:45:41.95 -14:19:34.8 (J2000) and has a remarkably simple power-law spectrum with photon index Gamma=1.86 and Nh=7E21 /cm2. The near-nuclear (3" <~ r <~ 18") Chandra spectrum is best modelled by three components: (1) a direct AGN component with Gamma fixed at 1.86, (2) cold Compton reflection of the AGN component, and (3) a 0.5 keV low-abundance (Z < 0.03 Zsolar) "thermal plasma," with ~10% of the flux of either of the first two components. The X-ray luminosity of the 3rd component (the "soft excess") is ~1.4E40 erg/s, or ~5X that of all of the detected extranuclear X-ray sources. We suggest that most (~75-80%) of the soft excess emission originates from 1" < r < 3", which is not imaged in our observation due to severe CCD pile-up. We also require the cold reflector to be positioned at least 1" (158 pc) from the nucleus, since there is no reflection component in the X-ray core spectrum. Much of the extranuclear X-ray emission is coincident with radio structures (nuclear radio bubbles and large-scale radio features), and its soft X-ray luminosity is generally consistent with luminosities expected from a starburst-driven wind (with the starburst scaled from L_FIR). However, the AGN in NGC 2992 seems equally likely to power the galactic wind in that object. Furthermore, AGN photoionization and photoexcitation processes could dominate the soft excess, especially the \~75-80% which is not imaged by our observations.Comment: 34 pages AASTEX, 9 (low-res) PS figures, ApJ, in press. For full-resolution postscript file, visit http://www.pha.jhu.edu/~colbert/n2992_chandra.ps.g

Liposomal Encapsulation of Amoxicillin via Microfluidics with Subsequent Investigation of the Significance of PEGylated Therapeutics

With an increasing concern of global antimicrobial resistance, the efforts to improve the formulation of a narrowing library of therapeutic antibiotics must be confronted. The liposomal encapsulation of antibiotics using a novel and sustainable microfluidic method has been employed in this study to address this pressing issue, via a targeted, lower-dose medical approach. The study focusses upon microfluidic parameter optimisation, formulation stability, cytotoxicity, and future applications. Particle sizes of circa. 130 nm, with viable short-term (28-day) physical stability were obtained, using two different non-cytotoxic liposomal formulations, both of which displayed suitable antibacterial efficacy. The microfluidic method allowed for high encapsulation efficiencies (≈77 %) and the subsequent in vitro release profile suggested high limits of antibiotic dissociation from the nanovessels, achieving 90% release within 72 h. In addition to the experimental data, the growing use of poly(ethylene) glycol (PEG) within lipid-based formulations is discussed in relation to anti-PEG antibodies, highlighting the key pharmacological differences between PEGylated and non-PEGylated formulations and their respective advantages and drawbacks. It's surmised that in the case of the formulations used in this study, the addition of PEG upon the liposomal membrane would still be a beneficial feature to possess owing to beneficial features such as stability, antibiotic efficacy and the capacity to further modify the liposomal membrane.</p

A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression

Background: Psoroptic mange, caused by infestation with the ectoparasitic mite, Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack of P. ovis transcriptomic and genomic resources. Results: Building on the recent publication of the P. ovis draft genome, here we present a genomic analysis and transcriptomic atlas of gene expression in P. ovis revealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis of P. ovis allergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in "fed" mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novel P. ovis multigene families including known allergens and novel genes with high levels of stage-specific expression. Conclusions: The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draft P. ovis genome

The Blue Tip of the Stellar Locus: Measuring Reddening with the SDSS

We present measurements of reddening due to dust using the colors of stars in the Sloan Digital Sky Survey (SDSS). We measure the color of main sequence turn-off stars by finding the "blue tip" of the stellar locus: the prominent blue edge in the distribution of stellar colors. The method is sensitive to color changes of order 18, 12, 7, and 8 mmag of reddening in the colors u-g, g-r, r-i, and i-z, respectively, in regions measuring 90' by 14'. We present maps of the blue tip colors in each of these bands over the entire SDSS footprint, including the new dusty southern Galactic cap data provided by the SDSS-III. The results disfavor the best fit O'Donnell (1994) and Cardelli et al. (1989) reddening laws, but are well described by a Fitzpatrick (1999) reddening law with R_V = 3.1. The SFD dust map is found to trace the dust well, but overestimates reddening by factors of 1.4, 1.0, 1.2, and 1.4 in u-g, g-r, r-i, and i-z, largely due to the adopted reddening law. In select dusty regions of the sky, we find evidence for problems in the SFD temperature correction. A dust map normalization difference of 15% between the Galactic north and south sky may be due to these dust temperature errors.Comment: 18 pages, 22 figure