Reasoning by analogy in the generation of domain acceptable ontology refinements

Refinements generated for a knowledge base often involve the learning of new knowledge to be added to or replace existing parts of a knowledge base. However, the justifiability of the refinement in the context of the domain (domain acceptability) is often overlooked. The work reported in this paper describes an approach to the generation of domain acceptable refinements for incomplete and incorrect ontology individuals through reasoning by analogy using existing domain knowledge. To illustrate this approach, individuals for refinement are identified during the application of a knowledge-based system, EIRA; when EIRA fails in its task, areas of its domain ontology are identified as requiring refinement. Refinements are subsequently generated by identifying and reasoning with similar individuals from the domain ontology. To evaluate this approach EIRA has been applied to the Intensive Care Unit (ICU) domain. An evaluation (by a domain expert) of the refinements generated by EIRA has indicated that this approach successfully produces domain acceptable refinements

An Infrastructure for acquiring high quality semantic metadata

Because metadata that underlies semantic web applications is gathered from distributed and heterogeneous data sources, it is important to ensure its quality (i.e., reduce duplicates, spelling errors, ambiguities). However, current infrastructures that acquire and integrate semantic data have only marginally addressed the issue of metadata quality. In this paper we present our metadata acquisition infrastructure, ASDI, which pays special attention to ensuring that high quality metadata is derived. Central to the architecture of ASDI is a erification engine that relies on several semantic web tools to check the quality of the derived data. We tested our prototype in the context of building a semantic web portal for our lab, KMi. An experimental evaluation omparing the automatically extracted data against manual annotations indicates that the verification engine enhances the quality of the extracted semantic metadata

Risk of Cancer among Commercially Insured HIV-Infected Adults on Antiretroviral Therapy.

The objective of this study was to explore the cancer incidence rates among HIV-infected persons with commercial insurance who were on antiretroviral therapy and compare them with those rates in the general population. Paid health insurance claims for 63,221 individuals 18 years or older, with at least one claim with a diagnostic code for HIV and at least one filled prescription for an antiretroviral medication between January 1, 2006, and September 30, 2012, were obtained from the LifeLink® Health Plan Claims Database. The expected number of cancer cases in the general population for each gender-age group (<30, 30-39, 40-49, 50-59, and >60 years) was estimated using incidence rates from the Surveillance Epidemiology and End Results (SEER) program. Standardized incidence ratios (SIRs) were estimated using their 95% confidence intervals (CIs). Compared to the general population, incidence rates for HIV-infected adults were elevated (SIR, 95% CI) for Kaposi sarcoma (46.08; 38.74-48.94), non-Hodgkin lymphoma (4.22; 3.63-4.45), Hodgkin lymphoma (9.83; 7.45-10.84), and anal cancer (30.54; 25.62-32.46) and lower for colorectal cancer (0.69; 0.52-0.76), lung cancer (0.70; 0.54, 0.77), and prostate cancer (0.54; 0.45-0.58). Commercially insured, treated HIV-infected adults had elevated rates for infection-related cancers, but not for common non-AIDS defining cancers

How Unsplittable-Flow-Covering helps Scheduling with Job-Dependent Cost Functions

Generalizing many well-known and natural scheduling problems, scheduling with job-specific cost functions has gained a lot of attention recently. In this setting, each job incurs a cost depending on its completion time, given by a private cost function, and one seeks to schedule the jobs to minimize the total sum of these costs. The framework captures many important scheduling objectives such as weighted flow time or weighted tardiness. Still, the general case as well as the mentioned special cases are far from being very well understood yet, even for only one machine. Aiming for better general understanding of this problem, in this paper we focus on the case of uniform job release dates on one machine for which the state of the art is a 4-approximation algorithm. This is true even for a special case that is equivalent to the covering version of the well-studied and prominent unsplittable flow on a path problem, which is interesting in its own right. For that covering problem, we present a quasi-polynomial time $(1+\epsilon)$-approximation algorithm that yields an $(e+\epsilon)$-approximation for the above scheduling problem. Moreover, for the latter we devise the best possible resource augmentation result regarding speed: a polynomial time algorithm which computes a solution with \emph{optimal }cost at $1+\epsilon$ speedup. Finally, we present an elegant QPTAS for the special case where the cost functions of the jobs fall into at most $\log n$ many classes. This algorithm allows the jobs even to have up to $\log n$ many distinct release dates.Comment: 2 pages, 1 figur

Microbiological influences on fracture surfaces of intact mudstone and the implications for geological disposal of radioactive waste

The significance of the potential impacts of microbial activity on the transport properties of host rocks for geological repositories is an area of active research. Most recent work has focused on granitic environments. This paper describes pilot studies investigating changes in transport properties that are produced by microbial activity in sedimentary rock environments in northern Japan. For the first time, these short experiments (39 days maximum) have shown that the denitrifying bacteria, Pseudomonas denitrificans, can survive and thrive when injected into flow-through column experiments containing fractured diatomaceous mudstone and synthetic groundwater under pressurized conditions. Although there were few significant changes in the fluid chemistry, changes in the permeability of the biotic column, which can be explained by the observed biofilm formation, were quantitatively monitored. These same methodologies could also be adapted to obtain information from cores originating from a variety of geological environments including oil reservoirs, aquifers and toxic waste disposal sites to provide an understanding of the impact of microbial activity on the transport of a range of solutes, such as groundwater contaminants and gases (e.g. injected carbon dioxide)

The effects of Cstb duplication on APP/amyloid-β pathology and cathepsin B activity in a mouse model

People with Down syndrome (DS), caused by trisomy of chromosome 21 have a greatly increased risk of developing Alzheimer's disease (AD). This is in part because of triplication of a chromosome 21 gene, APP. This gene encodes amyloid precursor protein, which is cleaved to form amyloid-β that accumulates in the brains of people who have AD. Recent experimental results demonstrate that a gene or genes on chromosome 21, other than APP, when triplicated significantly accelerate amyloid-β pathology in a transgenic mouse model of amyloid-β deposition. Multiple lines of evidence indicate that cysteine cathepsin activity influences APP cleavage and amyloid-β accumulation. Located on human chromosome 21 (Hsa21) is an endogenous inhibitor of cathepsin proteases, CYSTATIN B (CSTB) which is proposed to regulate cysteine cathepsin activity in vivo. Here we determined if three copies of the mouse gene Cstb is sufficient to modulate amyloid-β accumulation and cathepsin activity in a transgenic APP mouse model. Duplication of Cstb resulted in an increase in transcriptional and translational levels of Cstb in the mouse cortex but had no effect on the deposition of insoluble amyloid-β plaques or the levels of soluble or insoluble amyloid-β42, amyloid-β40, or amyloid-β38 in 6-month old mice. In addition, the increased CSTB did not alter the activity of cathepsin B enzyme in the cortex of 3-month or 6-month old mice. These results indicate that the single-gene duplication of Cstb is insufficient to elicit a disease-modifying phenotype in the dupCstb x tgAPP mice, underscoring the complexity of the genetic basis of AD-DS and the importance of multiple gene interactions in disease

Safety and preliminary efficacy of vorinostat with R-EPOCH in high-risk HIV-associated non-Hodgkin\u27s lymphoma (AMC-075)

We performed a phase I trial of vorinostat (VOR) given on days 1 to 5 with R-EPOCH (rituximab plus etoposide, prednisone, vincristine, cyclophosphamide, and doxorubicin hydrochloride) in patients with aggressive HIV-associated non-Hodgkin lymphoma. VOR was tolerable at 300 mg and seemingly efficacious with chemotherapy with complete response rate of 83% and 1-year event-free survival of 83%. VOR did not significantly alter chemotherapy steady-state concentrations, CD4+ cell counts, or HIV viral loads. Vorinostat (VOR), a histone deacetylase inhibitor, enhances the anti-tumor effects of rituximab (R) and cytotoxic chemotherapy, induces viral lytic expression and cell killing in Epstein-Barr virus-positive (EBV+) or human herpesvirus-8-positive (HHV-8+) tumors, and reactivates latent human immunodeficiency virus (HIV) for possible eradication by combination antiretroviral therapy (cART). We performed a phase I trial of VOR given with R-based infusional EPOCH (etoposide, prednisone, vincristine, cyclophosphamide, and doxorubicin hydrochloride) (n = 12) and cART in aggressive HIV-associated B-cell non-Hodgkin lymphoma (NHL) in order to identify safe dosing and schedule. VOR (300 or 400 mg) was given orally on days 1 to 5 with each cycle of R-EPOCH for 10 high-risk patients with diffuse large B-cell lymphoma (1 EBV+), 1 EBV+/HHV-8+ primary effusion lymphoma, and 1 unclassifiable NHL. VOR was escalated from 300 to 400 mg using a standard 3 + 3 design based on dose-limiting toxicity observed in cycle 1 of R-EPOCH. The recommended phase II dose of VOR was 300 mg, with dose-limiting toxicity in 2 of 6 patients at 400 mg (grade 4 thrombocytopenia, grade 4 neutropenia), and 1 of 6 treated at 300 mg (grade 4 sepsis from tooth abscess). Neither VOR, nor cART regimen, significantly altered chemotherapy steady-state concentrations. VOR chemotherapy did not negatively impact CD4+ cell counts or HIV viral loads, which decreased or remained undetectable in most patients during treatment. The response rate in high-risk patients with NHL treated with VOR(R)-EPOCH was 100% (complete 83% and partial 17%) with a 1-year event-free survival of 83% (95% confidence interval, 51.6%-97.9%). VOR combined with R-EPOCH was tolerable and seemingly efficacious in patients with aggressive HIV-NHL