High Throughput Primer Walking of cDNA Clones

Primer walking of cloned DNA is a standard research tool. It has been used in the past to determine the sequence of individual clones of interest. With the expansion of DNA sequencing capacity the need to be able to walk larger numbers of clones has become necessary. Our laboratory is a mid-sized genomics facility. In conjunction with the Advanced Biomedical Computing Center (ABCC) we have developed methods for automating the primer selection, DNA sequencing, contig assembly and sequence analysis for clones arrayed in microtiter format. This approach has allowed us to walk 475 clones (five microtiter plates) selected from a cDNA library.     

Localization of Function Within the Dorsal Hippocampus: The Role of the CA3 Subregion in Paired-Associate Learning.

Computational models and electrophysiological data suggest that the CA3 subregion of the hippocampus supports the formation of arbitrary associations; however, no behavioral studies have been conducted to test this hypothesis. Rats with neurotoxin-induced lesions of dorsal dentate gyrus (DG), CA3, or CA1 were tested on object-place and odor-place paired-associate tasks to test whether the mechanism that supports paired-associate learning is localized to the CA3 subregion of the dorsal hippocampus or whether all hippocampal subregions contribute to paired-associate learning. The data indicate that rats with DG or CA1 lesions learned the tasks as well as controls; however, CA3-lesioned rats were impaired in learning the tasks. Thus, the CA3 subregion of the dorsal hippocampus contains a mechanism to support paired-associate learning. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

PAC-learnability of probabilistic deterministic finite state automata in terms of variation distance

We consider the problem of PAC-learning distributions over strings, represented by probabilistic deterministic finite automata (PDFAs). PDFAs are a probabilistic model for the generation of strings of symbols, that have been used in the context of speech and handwriting recognition, and bioinformatics. Recent work on learning PDFAs from random examples has used the KL-divergence as the error measure; here we use the variation distance. We build on recent work by Clark and Thollard, and show that the use of the variation distance allows simplifications to be made to the algorithms, and also a strengthening of the results; in particular that using the variation distance, we obtain polynomial sample size bounds that are independent of the expected length of strings.     

A case study in SQA audits

Software quality assurance (SQA) audits are becoming a standard practice in corporations seeking to enter contractual relations with other organizations, or just evaluating their own state of readiness. This paper describes one approach to conducting SQA audits. Excerpts from reports of actual audits conducted on several organizations engaged in software development are used to show how an audit is conducted and what can be achieved through the auditing process. The paper is not meant to be a definitive answer or guide to doing SQA audits. Rather, it serves as an annotated case study of how SQA audits can be conducted with an emphasis on data gathering and reporting.Dr Paul W. Oman is an associate professor of computer science at the University of Idaho, and an independent software consultant who specializes in software analysis. He is the director of the Software Engineering Test Lab within the UI College of Engineering, where he conducts research in software development methods, CASE tools, and software maintainability issues. Oman has published over 50 articles and reports on software tools, software development, and computer science education. He has a PhD in computer science and is a member of the IEEE, IEEE Computer Society, and ACM.     

Preexercise meal composition alters plasma large neutral amino acid responses during exercise and recovery

This study was designed to determine metabolic and physical performance responses to ingestion of pre-exercise meals with different macronutrient and fiber profiles. Twelve physically active subjects (6 males and 6 females) were used to investigate the metabolic and physical performance consequences of consuming pre-exercise meals consisting of oat, corn, or wheat cereals. A fasting trial served as the control, and all subjects received each treatment in a Latin-square design. Blood samples were drawn before and 85 min after meal ingestion, during 90 min of cycling exercise (60% VO2peak), after a 6.4 km performance ride, and during 60 min of recovery. Expired air samples were collected to determine nutrient utilization. Resting carbohydrate oxidation rates and plasma insulin concentrations after oat ingestion were less than after wheat, and corn and wheat ingestion, respectively (P < 0.05). During exercise, the change in plasma glucose from pre-exercise was greater after consuming wheat and corn compared with oat (P < 0.05), and it was inversely related to pre-exercise plasma insulin concentration (r = -0.55, P = 0.0001). Plasma free fatty acid concentrations were inversely related to plasma lactate concentrations (r = -0.58, P = 0.0001). Free fatty acid concentrations and fat oxidation were greater in fasting trials than all others, but performance ride times did not differ among treatments. Plasma branched-chain amino acid concentrations resembled their respective meal profiles throughout exercise, the performance ride, and recovery. These results indicate that pre-exercise meal composition can influence glucose homeostasis during early exercise and plasma branched-chain amino acid concentrations over a substantial range of metabolic demands.     

Examination of coping resources and family adaptation in mothers and daughters of incestuous versus nonclinical families.

Mother–daughter dyads from incestuous vs nonclinical families were compared in terms of (1) family life stress, (2) problem-solving appraisal, (3) direct coping behaviors, (4) mother–daughter communication, and (5) family adaptation and cohesion. 15 mother–daughter pairs from an incestuous family involving an adult male caretaker were matched on several variables to 16 mother–daughter pairs from a nonclinical family. The results revealed that mothers from the incest group (compared with the nonclinical group) reported greater amounts of family life stress, had more negative perceptions of their problem-solving appraisal, and reported more communication difficulties. The daughters from the incest group appeared to be quite similar to the nonclinical group daughters, although they did acknowledge more family stress. Implications of the results for therapeutic interventions as well as future research were discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Meta-analyses of age–cognition relations in adulthood: Estimates of linear and nonlinear age effects and structural models.

A meta-analysis was conducted on 91 studies to derive a correlation matrix for adult age, speed of processing, primary–working memory, episodic memory, reasoning, and spatial ability. Structural equation modeling with a single latent common cognitive factor showed that all cognitive measures shared substantial portions of age-related variance. A mediational model revealed that speed of processing and primary–working memory appear to be important mediators of age-related differences in the other measures. However, not all of the age-related influences were mediated. An examination of quadratic age effects and correlational patterns for subsamples under and over 50 years of age revealed that (a) negative age–cognition relations were significant for the 18- to 50-year-old sample and (b) the age-related decline accelerated significantly over the adult life span for variables assessing speed, reasoning, and episodic memory. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Attentional cues in chronic schizophrenia: Abnormal disengagement of attention.

M. I. Possner's 1980 reaction time (RT) paradigm was used to examine the engagement and disengagement operations of visual selective attention in patients with schizophrenia. In the 1st experiment 14 medicated, chronic schizophrenic Ss (diagnosed by criteria of the Diagnostic and Statistical Manual of Mental Disorders [DSM-I]), and 15 age-matched normal and control Ss made a speeded response to a target preceded by a valid, and invalid, or no cue. Control Ss showed the expected advantage and disadvantage in RT for valid and invalid cues, which suggests intact engagement and disengagement operations. For schizophrenic Ss, valid cues also enhanced RT, but invalid cues did not slow RT. Similar results were found in the 2nd experiment. The failure of unpredictable, invalid cues to inhibit RT in chronic schizophrenia may be related to an abnormality in the disengagement operation of selective attention. (PsycINFO Database Record (c) 2010 APA, all rights reserved)