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The comparison of the genomes of two very closely related human mucosal pathogens, Mycoplasma genitalium and Mycoplasma pneumoniae, has helped define the essential functions of a self-replicating minimal cell, as well as what constitutes a mycoplasma. Here we report the complete sequence of a more distant phylogenetic relative of those bacteria, Ureaplasma(More)
Using the recently introduced BigDye terminators, large-template DNA can be directly sequenced with custom primers on automated instruments. Cycle sequencing conditions are presented to sequence DNA samples isolated from a number of microbial genomes including 750-kb Ureaplasma urealyticum, 1.2-Mb Mycoplasma fermentans, 2.3-Mb Streptococcus pneumoniae, and(More)
A basic question in mining data from an intelligent tutoring system is, " What happened when…? " We identify requirements for a tool to help answer such questions by finding occurrences of specified phenomena and browsing them in human-understandable form. We describe an implemented tool and how it meets the requirements. The tool applies to MySQL databases(More)
DNA comprising 219 447 bp was sequenced in nine cosmids and verified at > 99.9% precision. Of the standard repetitive elements, 187 Alus make up 20.6% of the sequence, but there were only 27 MERs (2.9%) and 17 L1 fragments (1.6%). This may be characteristic of such high GC (57%) regions. The sequence also includes an 11.3 kb tract duplicated with 99.2%(More)
We have used two new dye sets for automated dye-labeled terminator DNA sequencing. One set consists of four, 4,7-dichlororhodamine dyes (d-rhodamines). The second set consists of energy-transfer dyes that use the 5-carboxy-d-rhodamine dyes as acceptor dyes and the 5- or 6-carboxy isomers of 4'-aminomethylfluorescein as the donor dye. Both dye sets utilize a(More)
We have synthesized a set of four energy transfer dyes and demonstrated their use in automated DNA sequencing. The donor dyes are the 5- or 6-carboxy isomers of 4'-aminomethylfluorescein and the acceptor dyes are a novel set of four 4,7-dichloro-substituted rhodamine dyes which have narrower emission spectra than the standard, unsubstituted rhodamines. A(More)
Some tutoring system projects have completed empirical studies of student-tutor interaction by manually collecting data while observing fewer than a hundred students. Analyzing larger, automatically collected data sets requires new methods to address new problems. We share lessons on design, analysis, presentation, and iteration. Our lessons are based on(More)
When do students interrupt help to request different help? To study this question, we embedded a within-subject experiment in the 2003-2004 version of Project LISTEN's Reading Tutor. We analyze 168,983 trials of this experiment, randomized by help type, and report patterns in when students choose to interrupt help. Using the amount of prior help, we fit an(More)
A basic question in mining data from an intelligent tutoring system is, " What happened when…? " A generic tool to answer such questions should let the user specify which phenomenon to explore; explore selected events and the context in which they occurred; and require minimal effort to adapt the tool to new versions, to new users, or to other tutors. We(More)