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Introduction to genomic information retrieval

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Abstract

This article presents an efficient algorithm for DNA sequence compression, which achieves the best compression ratios reported over a test set commonly used for evaluating DNA compression programs. The algorithm introduces many refinements to a compression ...

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There are growing concerns over noise exposure via personal music system use by young adults. One purpose of this study was to evaluate the prevalence of personal music system use and the listening patterns associated with these systems in a large sample of young adults. A second purpose of this study was to measure the dB SPL in the ear canal of young adults while they blindly set the volume of a personal music system to four settings. In the first study, the personal music system use survey was completed by 1016 students at various locations on the San Diego State University campus. Questions included sex, age, ethnicity, race, and whether or not they used a personal music system. Students who answered Yes to using a personal music system were instructed to complete the remaining 11 closed-set questions. These questions dealt with type of earphones used with the system, most common listening environment, length of time per day the system was used, and the volume setting. The differences between women and men and across ethnicity and race were evaluated for the questions. In the second study, a probe microphone placed in the ear canal of 32 participants was used to determine the dB SPL of four loudness categories at which the participants blindly set the level of a personal music system: low, medium or comfortable, loud, and very loud. In study 1, over 90% of the participants who completed the survey reported using a personal music system. Over 50% of those who use a personal music system reported listening between 1 and 3 hrs and almost 90% reported listening at either a medium or loud volume. Men were significantly more likely to report listening to their system for a longer duration compared with women and more likely to report listening at a very loud volume. There was a trend for Hispanic or Latino students to report listening for longer durations compared with Not Hispanic or Latino students, but this difference was not statistically significant. Black or African American students were significantly more likely to report listening to their personal music system between 3 and 5 hrs and more than 5 hrs and to report listening at a very loud volume compared with other racial groups. In study 2, the mean dB SPL values for low, medium or comfortable, loud, and very loud were 62.0, 71.6, 87.7, and 97.8 dB SPL, respectively. Men set the level of very loud significantly higher than women. It is clear that a vast majority of young adults who completed the personal music system use survey listen to a system using earphones. Most of the respondents listen between 1 and 3 hrs a day at a medium or loud volume. Based on the probe microphone measurement results, the volume settings for reported durations may not be hazardous for hearing. Long-term use of personal music systems, however, in combination with other noise exposures (i.e., recreational, occupational), and their effect on hearing remains a question for additional research.
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To investigate the damages to the extracellular matrix in articular cartilage due to cryopreservation, the depth-dependent concentration profiles of glycosaminoglycans (GAGs) in 34 cartilage specimens from canine humeral heads were imaged at 13-mum pixel resolution using the in vitro version of the dGEMRIC protocol in microscopic MRI (microMRI). In addition, a biochemical assay was used to determine the GAG loss from the tissue to the solution where the tissue was immersed. For specimens that had been frozen at -20 degrees C or -80 degrees C without any cryoprotectant, a significant loss of GAG (as high as 56.5%) was found in cartilage, dependent upon the structural zones of the tissue and the conditions of cryopreservation. The cryoprotective abilities of dimethyl sulfoxide (DMSO) as a function of its concentration in saline and storage temperature were also investigated. A 30% DMSO concentration was sufficient in preventing the reduction of GAG in the tissue at the -20 degrees C storage temperature, but a 50% concentration of DMSO was necessary for the -80 degrees C cryopreservation. These imaging results were verified by the biochemical analysis.
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Predicting forest-tree seed dispersal across a landscape is useful for estimating gene flow from genetically engineered (GE) or transgenic trees. The question of biocontainment has yet to be resolved, although field-trial permits for transgenic forest trees are on the rise. Most current field trials in the United States occur in the Southeast where Pinus taeda L., an indigenous species, is the major timber commodity. Seed dispersal distances were simulated using a model where the major determinants were: (1) forest canopy height at seed release, (2) terminal velocity of the seeds, (3) absolute seed release, and (4) turbulent-flow statistics, all of which were measured or determined within a P. taeda plantation established from seeds collected from wild forest-tree stands at the Duke Forest near Durham, North Carolina, USA. In plantations aged 16 and 25 years our model results showed that most of the seeds fell within local-neighborhood dispersal distances, with estimates ranging from 0.05 to 0.14 km from the source. A fraction of seeds was uplifted above the forest canopy and moved via the long-distance dispersal (LDD) process as far as 11.9-33.7 km. Out of 10(5) seeds produced per hectare per year, roughly 440 seeds were predicted to be uplifted by vertical eddies above the forest canopy and transported via LDD. Of these, 70 seeds/ha traveled distances in excess of 1 km from the source, a distance too great to serve as a biocontainment zone. The probability of LDD occurrence of transgenic conifer seeds at distances exceeding 1 km approached 100%.
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