Data mining on large data warehouses is becoming increasingly important.In support of this trend, we consider a spectrum of architectural alternatives for coupling mining with database systems. These alternatives include: loosecoupling through a SQL cursor interface; encapsulation of a mining algorithm in a stored procedure; caching the data to a file system on-the-fly and mining; tight-coupling using primarily user-defined functions; and SQL implementations for processing in the DBMS. We comprehensively study the option of expressing the mining algorithm in the form of SQL queries using Association rule mining as a case in point. We consider four options in SQL-92 and six options in SQL enhanced with object-relational extensions (SQL-OR).Our evaluation of the different architectural alternatives shows that from a performance perspective, the Cache-Mine option is superior, although the performance of the SQL-OR option is within a factor of two. Both the Cache-Mine and the SQL-OR approaches incur a higher storage penalty than the loose-coupling approach which performance-wise is a factor of 3 to 4 worse than Cache-Mine. The SQL-92 implementations were too slow to qualify as a competitive option. We also compare these alternatives on the basis of qualitative factors like automatic parallelization, development ease, portability and inter-operability.
We previously demonstrated (M. M. Exner, P. Doig, T. J. Trust, and R. E. W. Hancock, Infect. Immun. 63: 1567-1572, 1995) that Helicobacter pylori has at least one nonspecific porin, HopE, which has a low abundance in the outer membrane but forms large channels. H. pylori is relatively susceptible to most antimicrobial agents but less susceptible to the polycationic antibiotic polymyxin B. We demonstrate here that H. pylori is able to take up higher basal levels of the hydrophobic fluorescent probe 1-N-phenylnaphthylamine (NPN) than Pseudomonas aeruginosa or Escherichia coli, consistent with its enhanced susceptibility to hydrophobic agents. Addition of polymyxin B led to a further increase in NPN uptake, indicative of a self-promoted uptake pathway, but it required a much higher amount of polymyxin B to yield a 50% increase in NPN uptake in H. pylori (6 to 8 g/ml) than in P. aeruginosa or E. coli (0.3 to 0.5 g/ml), suggesting that H. pylori has a less efficient selfpromoted uptake pathway. Since intrinsic resistance involves the collaboration of restricted outer membrane permeability and secondary defense mechanisms, such as periplasmic -lactamase (which H. pylori lacks) or efflux, we examined the possible role of efflux in antibiotic susceptibility. We had previously identified in H. pylori 11637 the presence of portions of three genes with homology to potential restriction-nodulationdivision (RND) efflux systems. It was confirmed that H. pylori contained only these three putative RND efflux systems, named here hefABC, hefDEF, and hefGHI, and that the hefGHI system was expressed only in vivo while the two other RND systems were expressed both in vivo and in vitro. In uptake studies, there was no observable energy-dependent tetracycline, chloramphenicol, or NPN efflux activity in H. pylori. Independent mutagenesis of the three putative RND efflux operons in the chromosome of H. pylori had no effect on the in vitro susceptibility of H. pylori to 19 antibiotics. These results, in contrast to what is observed in E. coli, P. aeruginosa, and other clinically important gram-negative bacteria, suggest that active efflux does not play a role in the intrinsic resistance of H. pylori to antibiotics.
As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html
With ongoing healthcare payment reforms in the USA, radiology is moving from its current state of a revenue generating department to a new reality of a cost-center. Under bundled payment methods, radiology does not get reimbursed for each and every inpatient procedure, but rather, the hospital gets reimbursed for the entire hospital stay under an applicable diagnosis-related group code. The hospital case mix index (CMI) metric, as defined by the Centers for Medicare and Medicaid Services, has a significant impact on how much hospitals get reimbursed for an inpatient stay. Oftentimes, patients with the highest disease acuity are treated in tertiary care radiology departments. Therefore, the average hospital CMI based on the entire inpatient population may not be adequate to determine department-level resource utilization, such as the number of technologists and nurses, as case length and staffing intensity gets quite high for sicker patients. In this study, we determine CMI for the overall radiology department in a tertiary care setting based on inpatients undergoing radiology procedures. Between April and September 2015, CMI for radiology was 1.93. With an average of 2.81, interventional neuroradiology had the highest CMI out of the ten radiology sections. CMI was consistently higher across seven of the radiology sections than the average hospital CMI of 1.81. Our results suggest that inpatients undergoing radiology procedures were on average more complex in this hospital setting during the time period considered. This finding is relevant for accurate calculation of labor analytics and other predictive resource utilization tools.
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