Automated methods of predicting the function of biological sequences using GO and BLAST

BACKGROUND: With the exponential increase in genomic sequence data there is a need to develop automated approaches to deducing the biological functions of novel sequences with high accuracy. Our aim is to demonstrate how accuracy benchmarking can be used in a decision-making process evaluating competing designs of biological function predictors. We utilise the Gene Ontology, GO, a directed acyclic graph of functional terms, to annotate sequences with functional information describing their biological context. Initially we examine the effect on accuracy scores of increasing the allowed distance between predicted and a test set of curator assigned terms. Next we evaluate several annotator methods using accuracy benchmarking. Given an unannotated sequence we use the Basic Local Alignment Search Tool, BLAST, to find similar sequences that have already been assigned GO terms by curators. A number of methods were developed that utilise terms associated with the best five matching sequences. These methods were compared against a benchmark method of simply using terms associated with the best BLAST-matched sequence (best BLAST approach). RESULTS: The precision and recall of estimates increases rapidly as the amount of distance permitted between a predicted term and a correct term assignment increases. Accuracy benchmarking allows a comparison of annotation methods. A covering graph approach performs poorly, except where the term assignment rate is high. A term distance concordance approach has a similar accuracy to the best BLAST approach, demonstrating lower precision but higher recall. However, a discriminant function method has higher precision and recall than the best BLAST approach and other methods shown here. CONCLUSION: Allowing term predictions to be counted correct if closely related to a correct term decreases the reliability of the accuracy score. As such we recommend using accuracy measures that require exact matching of predicted terms with curator assigned terms. Furthermore, we conclude that competing designs of BLAST-based GO term annotators can be effectively compared using an accuracy benchmarking approach. The most accurate annotation method was developed using data mining techniques. As such we recommend that designers of term annotators utilise accuracy benchmarking and data mining to ensure newly developed annotators are of high quality

Cryoprobe-induced apical lesions in the chinchilla. I. Morphological effects of lesioning parameters

To create experimental lesions localized to the low frequency region of the organ of Corti, a cryoprobe was applied to the apical area of 37 cochleas from 26 adult chinchillas. Twenty cochleas were exposed to single applications of a cryoprobe for 2.5, 3.0 and 3.5 min; 17 cochleas were exposed to two applications of 1.5, 2.0 and 3.0 min each with about a 3 min interval between applications. Cryoprobe tip temperature rose from about -140[deg]C when placed on the apex to about -80[deg]C after a continuous 3.5 min application. Survival time after lesioning was from 2 to 75 days, with most being 12 days or less. All cochleas except one sustained regions of damage characterized by complete absence of the organ of Corti and by missing hair cells indicated by extensive scarring. Inner hair cells were less susceptible to damage than were outer hair cells. Well-defined lesions which were continuous over the apical organ of Corti were found in some cochleas exposed to single probe applications, but such applications more often resulted in lesions which had areas of less damage. Of the various application protocols used, two applications of 1.5 min each, with an interval to allow the tissue to warm, most consistently produced severe and discrete apical lesions. In 9 of 13 cochleas exposed to two 1.5 min probe applications, such lesions extended about 35% or less of the distance from the apex. In most cochleas, regardless of the severity of the apical lesion, the pattern of hair cell rows and stereocilia configuration appeared normal in the basal 40-50% of the organ of Corti.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/26940/1/0000506.pd

The Ursinus Weekly, April 26, 1954

Class officer, MSGA petitions to start today • IRC delegates visit Alfred U. • Y retreat begins this weekend • Pre-med society sponsors advice for co-ed pre-meds • H. Smith elected \u2755 Lantern editor • Greek columns • Eugene P. Bentin to speak to FTA • Chi Alpha elects officers • Curtain Club elections to be held on May 3 • Fisher, Harris, Gillespie to lead WSGA, WAA, YW • Dr. Schoonover spoke; Moslem ideas, culture • U.C. debaters gain 14 wins, tie, drop 5 • Ethel Lutz elected pres. of Future Teachers • Beemer, German, Pasfield, McLaughlin U.C. bridge champs • Kampus Karnival a success • Spring play features comedy and confusion • Campus poll results • Queen, court, Cub & Key awards revealed at Jr. prom • Meistersingers\u27 Music for you fine presentation, well received • A professor says • Collegeville-Trappe story: Famous people • ZX edges APE tracksters in 50 3/4 - 47 4 event rally • Bears set records, win disputed game • Slotter\u27s 5-hit shut-out stalls Ford stickmen 7-0 • Ehlers, Carter shine on mound, beat E-town, F-M • Batsmen crush Pharmacy 20-0; Slotter victor • Strength in middle distance, dashes, gives Fords 70-56 win • Girls\u27 tennis team loses; Three matches this week • Elizabethtown first prey; Racquetmen lose opener • Softball league led by Curtis II, Brodbeck I teams • Playoffs begin tonight in girls\u27 intramural basketballhttps://digitalcommons.ursinus.edu/weekly/1495/thumbnail.jp

Anesthesia and surgical traum: their influence on the guinea pig compound action potential

A chronic implant consisting of a fine thermocouple placed on the round window permitted measurement of temperature and of the compound action potential (CAP) of the cochlear nerve in guinea pigs. Thresholds and latencies of the CAP, in response to tone bursts (2-40 kHz), were measured when the animal was awake and unrestrained, and again after several hours of anesthesia. The CAP remained unchanged with a variety of common anesthetics when precise control of round window temperature was maintained. However, when anesthesia was accompanied by several hours of slight cochlear cooling, thresholds were elevated for CAPs evoked by frequencies above 24 kHz and latencies were increased for CAPs evoked by all frequencies tested.The effects of surgery on CAP threshold and latency were also examined. Guinea pigs were tested while still anesthetized at the conclusion of the implantation procedure, and then again several days later while awake. Thresholds and latencies were unchanged. In two anesthetized guinea pigs already implanted with thermocouples, ventral and post-auricular surgery to expose the middle ear had no effect on the CAP, when low-speed drilling was used to open the auditory bulla. However, when small portions of the bulla were broken away with forceps, the CAP in response to high-frequency tone bursts immediately showed elevated thresholds. This alteration of the CAP was clearly different from that produced by lowered temperature, since the latencies at threshold were significantly decreased.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25208/1/0000648.pd

Inner hair cell responses to the velocity of basilar membrane motion in the guinea pig

Triangular wave acoustic stimulation at 200 Hz produced the expected square wave cochlear microphonic at the round window membrane and within the scala media. Intracellular recordings from inner hair cells (IHC) of the first cochlear turn showed a combination waveform having both spike impulse and square wave features. The IHC response suggests a sensitivity of these cells to both the displacement and to the velocity of basilar membrane motion.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24391/1/0000661.pd

The persistent store as an enabling technology for integrated project support environments

The software engineering community has recognised the need for integrated project support environments (IPSEs) for some time. With such a system the user is provided with an integrated set of software tools with which to operate. Given this set of integrated software tools rather than a set of ad hoc tools the cost of software and project support throughout its life cycle is reduced. The technique of integration as a method of cost saving, applies to all levels in the hierarchy of problem solving, both hardware and software. This paper discusses one such level, that in which the IPSE is implemented and in particular the use of a persistent store as an enabling technology for IPSEs. The facilities of the language PS-algol necessary to support an IPSE are illustrated by example and it is demonstrated how an IPSE's base may be provided by a persistent store that supports first class procedures as data objects. The need for a type secure object system which allows static and dynamic binding is demonstrated and finally the secure transactional base of PS-algol is shown to be a necessary and sufficient condition to provide secure version control and concurrent access to both programs and data.Othe

The Lantern Vol. 1, No. 1, May 1933

• Remember: Translation of Rappelle-toi by Alfred de Musset • Lighting the Lantern • Footfalls • To a Lovely Lady • The Sons of Martha • Strategy • Lumine Lunae • Poetry in Retrospect • Nirvana • A Domestic Episode • At Night • Haman and Hitler • This is What He Said • Bookocracy • Four Loves • Cities and Personalitieshttps://digitalcommons.ursinus.edu/lantern/1000/thumbnail.jp

Sorption of organic gases in a furnished room

We present experimental data and semi-empirical models describing the sorption of organic gases in a simulated indoor residential environment. Two replicate experiments were conducted with 20 volatile organic compounds (VOCs) in a 50-m{sup 3} room finished with painted wallboard, carpet and cushion, draperies and furnishings. The VOCs span a wide volatility range and include ten Hazardous Air Pollutants. VOCs were introduced to the static chamber as a pulse and their gas-phase concentrations were measured during a net adsorption period and a subsequent net desorption period. Three sorption models were fit to the measured concentrations for each compound to determine the simplest formulation needed to adequately describe the observed behavior. Sorption parameter values were determined by fitting the models to adsorption period data then checked by comparing measured and predicted behavior during desorption. The adequacy of each model was evaluated using a goodness of fit parameter calculated for each period. Results indicate that sorption usually does not greatly affect indoor concentrations of methyl-tert-butyl ether, 2-butanone, isoprene and benzene. In contrast, sorption appears to be a relevant indoor process for many of the VOCs studied, including C{sub 8}-C{sub 10} aromatic hydrocarbons (HC), terpenes, and pyridine. These compounds sorbed at rates close to typical residential air change rates and exhibited substantial sorptive partitioning at equilibrium. Polycyclic aromatic HCs, aromatic alcohols, ethenylpyridine and nicotine initially adsorbed to surfaces at rates of 1.5 to >6 h{sup -1} and partitioned 95 to >99% in the sorbed phase at equilibrium

Bostonia: The Boston University Alumni Magazine. Volume 12

Founded in 1900, Bostonia magazine is Boston University’s main alumni publication