Biomedical subjects

G Benson

Publications and source records attributed to G Benson.

At least 19 recordsLinked to original sources

PubMed1999

Tandem repeats finder: a program to analyze DNA sequences.

A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem repeats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm's speed and its ability to detect tandem repeats that have undergone extensive mutational change by analyzing four sequences: the human frataxin gene, the human beta T cellreceptor locus sequence and two yeast chromosomes. These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface atc3.biomath.mssm.edu/trf.html has been established for automated use of the program.

Algorithms↗

PubMed1999

Friction in perspective.

In the past, most frictional resistance studies have been conducted in a steady state condition that does not simulate the dynamics of the oral environment. Various oral functions as chewing, swallowing, speaking, etc, as well as the oral tissues contacting any orthodontic appliances, result in periodic, repetitive, minute relative motion at the bracket/arch wire interfaces several thousand times each day. This in turn affects the normal forces at the interfaces, and because frictional resistance is directly proportional to the normal force, a pilot study was undertaken to emulate the dynamic environment of the oral cavity and its effect on frictional resistance. Tests of a limited sample of stainless steel arch wires and brackets typically used in sliding mechanics revealed that frictional resistance was effectively reduced to zero each time minute relative movements occurred at the bracket/arch wire interfaces. Factors such as the degree of dental tipping, relative arch wire/slot clearances, and method of tying, did not have a measurable effect on frictional resistance in the simulated dynamics of the oral environment.

Dental Stress Analysis↗

PubMed1999

Editorial comment

Explore the source record for details and available documents.

Journal Article↗

PubMed1999

Editorial comment

Explore the source record for details and available documents.

Journal Article↗

PubMed1999

Reconstructing the duplication history of a tandem repeat.

One of the less well understood mutational transformations that act upon DNA is tandem duplication. In this process, a stretch of DNA is duplicated to produce two or more adjacent copies, resulting in a tandem repeat. Over time, the copies undergo additional mutations so that typically, multiple approximate tandem copies are present. An interesting feature of tandem repeats is that the duplicated copies are preserved together, making it possible to do "phylogenetic analysis" on a single sequence. This involves using the pattern of mutations among the copies to determine a minimal or a most likely history for the repeat. A history tries to describe the interwoven pattern of substitutions, indels, and duplication events in such a way as to minimize the number of identical mutations that arise independently. Because the copies are adjacent and ordered, the history problem can not be solved by standard phylogeny algorithms. In this paper, we introduce several versions of the tandem repeat history problem, develop algorithmic solutions and evaluate their performance. We also develop ways to visualize important features of a history with the goal of discovering properties of the duplication mechanism.

Algorithms↗

PubMed1998

Understanding referential expressions in context: use of common ground by children and adolescents with mental retardation.

Listeners interpret utterances against the common ground, or network of presuppositions shared with the speaker. The first purpose of the study was to determine whether individuals with mental retardation use the major sources of common ground (i.e., physical copresence, linguistic copresence, and community membership) to resolve referential ambiguity. The second purpose was to determine whether they seek confirmation of their referent choices in accordance with the certainty of interpretation afforded by the common ground. The third purpose was to determine whether they signal noncomprehension when faced with ambiguity and common ground that is not informative. The final purpose was to evaluate the relationship between within-group variability in common ground use and measures of nonverbal cognition, receptive and expressive language, and social cognition. Participants were school-age individuals with mental retardation and typically developing children matched to them on nonverbal MA. Common ground use was examined in a role-playing task in which the participant responded to ambiguous utterances. Common ground was manipulated within participants. We determined whether referent selections were appropriate for the common ground, whether they were accompanied by confirmation requests, and whether noncomprehension was signaled. Both groups used all sources of common ground to resolve referential ambiguity at better than chance levels but were less successful in using community membership. Both groups also requested confirmation of their referent choices most often when the common ground was based on community membership. Both groups signaled noncomprehension when the common ground was not informative. Different aspects of common ground use were related to different predictors for the group with mental retardation.

Adolescent↗

PubMed1998

On the distribution of k-tuple matches for sequence homology: a constant time exact calculation of the variance.

We study the distribution of a statistic useful in calculating the significance of the number of k-tuple matches detected in biological sequence homology algorithms. The statistic is Rn,k, the total number of heads in head runs of length k or more in a sequence of iid Bernoulli trials of length n. Calculation of the mean is straightforward. Poisson approximation formulas have been used for the variance because they are simple and powerful. Unfortunately, when p = P(Head) is large, the Poisson approximation no longer works well. In our application, p is large, say .75, and we have turned instead to direct calculation of the variance. Surprisingly, we are able to show that the variance, which is based on the interactions of O(n2) random variables, can be computed in constant time, independent of the length of the sequence and probability p. This result can be used to calculate the mean and variance of a number of other head run statistics in constant time. Additionally, we show how to extend the result to sequences generated by a stationary Markov process where the variance can be calculated in O(n) time.

Algorithms↗

PubMed1997

Circadian rest-activity disturbances in seasonal affective disorder.

BACKGROUND: Previous studies hypothesized that seasonal affective disorder (SAD) was caused by a circadian rhythm abnormality. The purpose of this study was to ascertain whether rest-activity rhythms were phase delayed, diminished in amplitude, or more poorly entrained to the 24-hour day. METHOD: Twenty healthy adult controls and 25 outpatients meeting Rosenthal-National Institute of Mental Health criteria for SAD and DSM-III-R criteria for major or bipolar depression with seasonal pattern had their levels of activity recorded for 72 hours (weekdays) using wrist-worn actigraphs. RESULTS: Subjects with SAD had activity levels that were 11% lower than controls (P = .03), and their levels of activity were most attenuated during the first 2 hours after arising (P = .004). The relative amplitude of the circadian rhythm did not differ between groups. Patients with SAD were phase delayed by 50 minutes for the entire period (P = .02). Analysis of each individual day indicated that patients were delayed by up to 70 minutes (P = .007). Interdaily stability, an index of coupling between the rhythm and its zeitigeber was reduced in SAD (P = .01). Compared with controls, patients with SAD had best-fit circadian periods that were 92% more deviated from 24 hours (P = .007) and daily acrophase (time of the peak of the fit circadian rhythm) times that were 110% more variable between days (P < .001). CONCLUSIONS: Patients with SAD have circadian rest-activity rhythms that are significantly phase delayed and more poorly entrained to the 24-hour day.

Activity Cycles↗

PubMed1997

Signaling of noncomprehension by children and adolescents with mental retardation: effects of problem type and speaker identity.

Previous research has demonstrated considerable within-individual and within-group variability in the signaling of noncomprehension by persons with mental retardation. The first purpose of this study was to determine whether within-individual variability in such signaling was related to differences in the nature of the inadequate message and the identity of the speaker. The second purpose was to evaluate the relationship between within-group variability in noncomprehension signaling and measures of cognition, receptive and excessive language ability, speech intelligibility, and social cognition. Participants were school-age individuals with mild mental retardation and typically developing children matched to them on nonverbal MA. Noncomprehension signaling was examined in a direction-following task in which inadequate message type and speaker were manipulated. It was found that message type, but not speaker, influenced noncomprehension signaling, with no difference between the two groups. We also found that performance on a test of receptive language ability was the best predictor of noncomprehension signaling for persons with mental retardation.

Adolescent↗

PubMed1997

Sequence alignment with tandem duplication.

Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of sequences proceeds through any of the operations of substitution, insertion or deletion (the latter two collectively termed indels). While this model has worked fairly well, it has long been apparent that other mutational events occur. In this paper, we introduce a new model, the DSI model which includes another common mutational event, tandem duplication. Tandem duplication produces tandem repeats which are common in DNA, making up perhaps 10% of the human genome. They are responsible for some human diseases and may serve a multitude of functions in DNA regulation and evolution. Using the DSI model, we develop new exact and heuristic algorithms for comparing and aligning DNA sequences when they contain tandem repeats.

Algorithms↗

PubMed1997

Pooling strategies for establishing physical genome maps using FISH.

Often, in biological studies, it is necessary to identify an organism's chromosomes. In some organisms the individual chromosomes can be identified by staining procedures while many other species have a very large number of chromosomes, often of similar size, which defy identification by traditional staining methods. We have devised strategies, based on fluorescent in situ hybridization (FISH), which allow the assignment of a preset number of probes to each chromosome without prior chromosome identification. By hybridizing mixtures of probes labeled with different colored fluorescent molecules, the chromosomal origin of each probe can be determined.

Animals↗

PubMed1997

The measure of success.

Explore the source record for details and available documents.

Centers for Medicare and Medicaid Services, U.S.↗

PubMed1997

Women and heart attack: a study of women's experiences.

Cardiovascular disease in general, and myocardial infarction (MI) in particular, is the major health problem of females after 50 years of age. To date, heart disease research has focused primarily on males. The limited evidence suggests that the physical, psychological, and social ramifications of MI for women are significant, and different from those of men. Since the specific rehabilitation needs of women are not yet clear, this study was designed to explore the unique experiences and needs of women following a first MI. A phenomenological study using focus groups was used to explore the experiences, questions, concerns, and preferred interventions of women after a MI. Participants were female volunteers (n = 14) who had been hospitalized for a MI within the previous 6 months. Focus groups were audio taped and analysed by the investigators. Four major themes emerged: validation; perceived gender differences; role expectations/role tensions; and helps and hindrances to recovery.

Adult↗

PubMed1995

Sexually dimorphic sterility phenotypes in Hoxa10-deficient mice.

The Abdominal B (AbdB) genes constitute a distinct subfamily of homeobox genes that exhibit posterior domains of expression, including the genital imaginal disc in Drosophila and the developing urogenital system in vertebrates. We have mutated the AbdB gene Hoxa10 in mice. We report here that homozygotes are fully viable and show an anterior homeotic transformation of lumbar vertebrae. All male homozygotes manifest bilateral cryptorchidism resulting in severe defects in spermatogenesis and increasing sterility with age. Female homozygotes ovulate normally, but about 80% are sterile because of death of embryos between days 2.5 and 3.5 post coitum. This coincides spatially and temporally with expression of maternal Hoxa10 in distal oviductal and uterine epithelium. These results indicate a role for AbdB Hox genes in male and female fertility and suggest that maternal Hoxa10 is required to regulate the expression of a factor that affects the viability of preimplantation embryos.

Animals↗

PubMed1995

Effects of sampling context on the expressive language of children and adolescents with mental retardation.

This study was designed to determine whether conversational samples of language should be supplemented with samples obtained in narrative, or storytelling, contexts when evaluating the expressive language skills of individuals with mental retardation. Language samples were elicited in both conversational and narrative contexts from 16 school-age individuals with mental retardation and 16 typically developing children matched to them on MA. An analysis of the samples demonstrated that both groups produced more syntactically complex language in narration than in conversation, whereas they were more talkative in conversation than in narration. These results suggest that conversational and narrative contexts should be used together when evaluating the expressive language performance of individuals with mental retardation.

Adolescent↗

PubMed1994

A method for fast database search for all k-nucleotide repeats.

A significant portion of DNA consists of repeating patterns of various sizes, from very small (one, two and three nucleotides) to very large (over 300 nucleotides). Although the functions of these repeating regions are not well understood, they appear important for understanding the expression, regulation and evolution of DNA. For example, increases in the number of trinucleotide repeats have been associated with human genetic disease, including Fragile-X mental retardation and Huntington's disease. Repeats are also useful as a tool in mapping and identifying DNA; the number of copies of a particular pattern at a site is often variable among individuals (polymorphic) and is therefore helpful in locating genes via linkage studies and also in providing DNA fingerprints of individuals. The number of repeating regions is unknown as is the distribution of pattern sizes. It would be useful to search for such regions in the DNA database in order that they may be studied more fully. The DNA database currently consists of approximately 150 million basepairs and is growing exponentially. Therefore, any program to look for repeats must be efficient and fast. In this paper, we present some new techniques that are useful in recognizing repeating patterns and describe a new program for rapidly detecting repeat regions in the DNA database where the basic unit of the repeat has size up to 32 nucleotides. It is our hope that the examples in this paper will illustrate the unrealized diversity of repeats in DNA and that the program we have developed will be a useful tool for locating new and interesting repeats.

Base Sequence↗

PubMed1994

Impact of parental substance use on adolescents: a test of a mediational model.

Tested a mediational model of the relationship between parental substance use and adolescents' substance (tobacco, alcohol, marijuana) use with data from a sample of 1,775 adolescents, mean age 13.3 years, who completed a questionnaire including constructs from three theories of substance use. Mediational analyses identified five constructs involved in the relationship of parental and adolescent use. A structural model with latent constructs for substance use showed indirect effects of parental substance use through greater tolerance for deviance, lower behavioral control, greater perceived coping function of substance use, more negative life events, and more affiliation with peer users, plus a direct effect. Implications for the theory of transmission of risk are considered.

Adaptation, Psychological↗

PubMed1993

A quantitatively controlled method to study prospectively interstitial cystitis and demonstrate the efficacy of pentosanpolysulfate.

A randomized, prospective, double-blind, placebo-controlled study was conducted at 7 clinical centers on 148 patients. Patients received orally either 100 mg. pentosanpolysulfate (a synthetic polysaccharide) 3 times per day or a placebo. Of the patients on drug therapy 32% showed significant improvement compared to 16% of those on placebo (p = 0.01). This study provides a model to assess this disease quantitatively in a prospective manner using a method whereby the patients globally assess their symptoms as either worse or improved by 0, 25, 50, 75 or 100%. Patients on drug therapy also experienced a significant decrease in pain and urgency (p = 0.04 and 0.01) on analogue scales when compared to placebo and also more drug patients showed an average increase of more than 20 ml. in voided volume than did placebo patients (p = 0.02). All adverse effects were minor, with 7 in the drug group and 10 in the placebo group. The results support the concept that some patients with the interstitial cystitis syndrome may have abnormal bladder surface glycosaminoglycans.

Aged↗