Research on knowledge representation, machine learning, and knowledge acquisition

Research in knowledge representation, machine learning, and knowledge acquisition performed at Knowledge Systems Lab. is summarized. The major goal of the research was to develop flexible, effective methods for representing the qualitative knowledge necessary for solving large problems that require symbolic reasoning as well as numerical computation. The research focused on integrating different representation methods to describe different kinds of knowledge more effectively than any one method can alone. In particular, emphasis was placed on representing and using spatial information about three dimensional objects and constraints on the arrangement of these objects in space. Another major theme is the development of robust machine learning programs that can be integrated with a variety of intelligent systems. To achieve this goal, learning methods were designed, implemented and experimented within several different problem solving environments

THE IMPACT OF POPULATION GROWTH ON RESIDENTIAL PROPERTY TAXES

A multivariate model of the effect of population on local fiscal behavior, assessed value of property and average single family home values is estimated using cross-sectional data from Oregon. Regression results suggest that property tax levies are unit elastic with respect to population, that the total assessed value of property increases less than proportionally with population, and that the average value of a single family home increases with population. These results imply a positive relationship between population and both property tax rates and the tax bill of the average single family homeowner. Ceteris paribus, increases in average residential property taxes are associated with increases in population.Public Economics,

Spitzer IRS Spectra of Luminous 8 micron Sources in the Large Magellanic Cloud: Testing color-based classifications

We present archival Spitzer IRS spectra of 19 luminous 8 micron selected sources in the Large Magellanic Cloud (LMC). The object classes derived from these spectra and from an additional 24 spectra in the literature are compared with classifications based on 2MASS/MSX (J, H, K, and 8 micron) colors in order to test the "JHK8" classification scheme (Kastner et al. 2008). The IRS spectra confirm the classifications of 22 of the 31 sources that can be classified under the JHK8 system. The spectroscopic classification of 12 objects that were unclassifiable in the JHK8 scheme allow us to characterize regions of the color-color diagrams that previously lacked spectroscopic verification, enabling refinements to the JHK8 classification system. The results of these new classifications are consistent with previous results concerning the identification of the most infrared-luminous objects in the LMC. In particular, while the IRS spectra reveal several new examples of asymptotic giant branch (AGB) stars with O-rich envelopes, such objects are still far outnumbered by carbon stars (C-rich AGB stars). We show that Spitzer IRAC/MIPS color-color diagrams provide improved discrimination between red supergiants and oxygen-rich and carbon-rich asymptotic giant branch stars relative to those based on 2MASS/MSX colors. These diagrams will enable the most luminous IR sources in Local Group galaxies to be classified with high confidence based on their Spitzer colors. Such characterizations of stellar populations will continue to be possible during Spitzer's warm mission, through the use of IRAC [3.6]-[4.5] and 2MASS colors.Comment: 31 pages, 10 figures, to be published in A

Automatic Annotation of Protein Motif Function with Gene Ontology terms

Background: Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist for identifying candidate protein motifs at the whole genome level. However, a much needed and important task is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO) project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results: This paper presents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifs is viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and a GO term association is found to be a very useful feature. We take advantage of the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correct association. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions: In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about the functions of newly discovered candidate protein motifs

Muscle preservation in long duration space missions: The eccentric factor

In our quest to understand, and eventually prevent, the loss of muscle strength and mass that occurs during prolonged periods in microgravity, we have organized our research approach by systems and useful terrestrial analogs. Our hypothesis was that: The eccentric movement, or lengthening component, of dynamic, resistive exercise, is required for the production of the greatest gains in strength and muscle hypertrophy in the most metabolically efficient, and time effective manner. The exercises selected were leg presses, leg (knee) extensions, and hamstring curls. In this 30 week study, 38 male subjects, between the ages of 25 and 50, were divided into four groups. One group performed 5 sets of 8-12 repetitions per set of conventional concentric/eccentric (CON/ECC) exercises. Another group performed only the concentric (CON) movement on the same schedule. The third group performed twice the number of sets in the concentric only mode (CON/CON), and the last group served as controls. We interpret these data as convincing evidence that the eccentric component of heavy resistance training is required along with the concentric for the most effective increase in strength and muscle fiber size in the least time. We also conclude that such heavy exercise of any such muscle group need not consume inordinately long periods of time, and is quite satisfactorily effective when performed on 72 hour centers

Accelerated Partial Breast Irradiation: Using the CyberKnife as the Radiation Delivery Platform in the Treatment of Early Breast Cancer

We evaluate the CyberKnife (Accuray Incorporated, Sunnyvale, CA, USA) for non-invasive delivery of accelerated partial breast irradiation (APBI) in early breast cancer patients. Between 6/2009 and 5/2011, nine patients were treated with CyberKnife APBI. Normal tissue constraints were imposed as outlined in the National Surgical Adjuvant Breast and Bowel Project B-39/Radiation Therapy Oncology Group 0413 (NSABP/RTOG) Protocol (Vicini and White, 2007). Patients received a total dose of 30 Gy in five fractions (group 1, n = 2) or 34 Gy in 10 fractions (group 2, n = 7) delivered to the planning treatment volume (PTV) defined as the clinical target volume (CTV) +2 mm. The CTV was defined as either the lumpectomy cavity plus 10 mm (n = 2) or 15 mm (n = 7). The cavity was defined by a T2-weighted non-contrast breast MRI fused to a planning non-contrast thoracic CT. The CyberKnife Synchrony system tracked gold fiducials sutured into the cavity wall during lumpectomy. Treatments started 4–5 weeks after lumpectomy. The mean PTV was 100 cm3 (range, 92–108 cm3) and 105 cm3 (range, 49–241 cm3) and the mean PTV isodose prescription line was 70% for groups 1 and 2, respectively. The mean percent of whole breast reference volume receiving 100 and 50% of the dose (V100 and V50) for group 1 was 11% (range, 8–13%) and 23% (range, 16–30%) and for group 2 was 11% (range, 7–14%) and 26% (range, 21–35.0%), respectively. At a median 7 months follow-up (range, 4–26 months), no acute toxicities were seen. Acute cosmetic outcomes were excellent or good in all patients; for those patients with more than 12 months follow-up the late cosmesis outcomes were excellent or good. In conclusion, the lack of observable acute side effects and current excellent/good cosmetic outcomes is promising. We believe this suggests the CyberKnife is a suitable non-invasive radiation platform for delivering APBI with achievable normal tissue constraints

Geographic variation in the PRNP gene and its promoter, and their relationship to chronic wasting disease in North American deer

PRNP genotypes, number of octarepeats (PHGGGWGQ) and indels in the PRNP promoter can influence the progression of prion disease in mammals. We found no relationship between presence of promoter indels in white-tailed deer and mule deer from Nebraska and CWD presence. White-tailed deer with the 95 H allele and G20D mule deer were more likely to be CWD- free, but unlike other studies white-tailed deer with the 96S allele(s) were equally likely to be CWD-free. We provide the first information on PRNP genotypes and indels in the promoter for Key deer (all homozygous 96SS) and Coues deer (lacked 95 H and 96S alleles, but possessed a uniquely high frequency of 103 T). All deer surveyed were homozygous for three tandem octarepeats

Factors affecting use of unscheduled care for people with advanced cancer:a retrospective cohort study in Scotland

BACKGROUND: People with advanced cancer frequently attend unscheduled care, but little is known about the factors influencing presentations. Most research focuses on accident and emergency (A&amp;E) and does not consider GP out-of-hours (GPOOH).AIM: To describe the frequency and patterns of unscheduled care use by people with cancer in their last year of life and to examine the associations of demographic and clinical factors with unscheduled care attendance.DESIGN AND SETTING: Retrospective cohort study of all 2443 people who died from cancer in Tayside, Scotland, during 2012-2015. Clinical population datasets were linked to routinely collected clinical data using the Community Health Index (CHI) number.METHOD: Anonymised CHI-linked data were analysed in SafeHaven, with descriptive analysis, using binary logistic regression for adjusted associations.RESULTS: Of the people who died from cancer, 77.9% (n = 1904) attended unscheduled care in the year before death. Among unscheduled care users, most only attended GPOOH (n = 1070, 56.2%), with the rest attending A&amp;E only (n = 204, 10.7%), or both (n = 630, 33.1%). Many attendances occurred in the last week (n =1360, 19.7%), last 4 weeks (n = 2541, 36.7%), and last 12 weeks (n = 4174, 60.3%) of life. Age, sex, deprivation, and cancer type were not significantly associated with unscheduled care attendance. People living in rural areas were less likely to attend unscheduled care: adjusted odds ratio (aOR) 0.64 (95% confidence interval = 0.50 to 0.82). Pain was the commonest coded clinical reason for presenting (GPOOH: n = 482, 10.5%; A&amp;E: n = 336, 28.8%). Of people dying from cancer, n = 514, 21.0%, were frequent users (≥5 attendances/year), and accounted for over half (n = 3986, 57.7%) of unscheduled care attendances.CONCLUSION: Unscheduled care attendance by people with advanced cancer was substantially higher than previously reported, increased dramatically towards the end of life, was largely independent of demographic factors and cancer type, and was commonly for pain and palliative care.</p