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PubMedDate not supplied

Optimization and direct comparison of the dimerizer and reverse tet transcriptional control systems.

BACKGROUND: Exogenously controlled gene expression systems are essential for both the in vivo analysis of gene function and the regulated delivery of therapeutic gene products. However, differences in experimental methods used to characterize the various systems prohibit informative comparisons. The purpose of this study was to identify an optimal system for regulated gene expression studies through a rigorous direct comparison of the dimerizer and the reverse tet transactivator (rtTA) transcriptional switch systems. METHODS: An optimized bicistronic rapamycin-dependent dimerizer construct and an optimized rtTA construct (based on rtTA(s)-M2) were developed that utilize a chimeric mammalian activation domain with a flexible interdomain linker. These constructs were reconstituted in identical eukaryotic expression vectors and compared in transient transfection assays employing target gene reporter constructs that differ only in the relevant DNA binding sites. RESULTS: The optimized rtTA(s)-M2 construct, designated rtTAM2.2, exhibited a twofold increase in the magnitude of doxycycline-dependent reporter gene induction and an eightfold increase in sensitivity as compared to the rtTA(s)-M2 construct. This correlated with a significantly higher level of expression of the rtTAM2.2 protein. In direct comparisons the rtTAM2.2 system mediated inducible expression to a level tenfold greater than the bicistronic dimerizer system. However, while the dimerizer system exhibited no detectable rapamycin-independent expression, a low level of doxycycline-independent target gene expression was detectable. CONCLUSIONS: The improved rtTAM2.2 rtTA system described here may prove optimal when the overall magnitude of target gene induction is critical, while the dimerizer system may be advantageous when the complete absence of ligand-independent target gene expression is essential.

Animals↗

PubMed1990

Development and application of a radioimmunoassay for fluphenazine based on monoclonal antibodies and its comparison with alternate assay methods.

The development of a monoclonal antibody towards fluphenazine allows the measurement of plasma concentrations of this highly potent neuroleptic. The method demonstrates sufficient sensitivity to measure 0.02 ng of fluphenazine per milliliter of plasma and employs a 150-microL plasma extract derived from a 2-mL plasma sample. The procedure is linear over the concentration range of 0.02 to 2.5 ng/mL, with a mean overall coefficient of variation of less than 3%. The validity of the described monoclonal-based RIA procedure was confirmed by comparison to alternate assay methods in replicate samples. Comparison to a newly developed HPLC-coulometric procedure in 159 samples showed a strong correlation, with a slope value of close to unity (1.0484) and a coefficient of correlation of 0.8136, while comparison to a previously developed polyclonal-based RIA procedure showed a correlation of 0.95 and a slope of 0.91 (n = 26).

Animals↗

PubMed1991

Acute myocardial infarction: comparison of T2-weighted and T1-weighted gadolinium-DTPA enhanced MR imaging.

Magnetic resonance images were obtained from 32 patients with acute myocardial infarction, using a four-echo technique (echo time (TE) = 30, 60, 90, and 120 ms) pregadolinium(Gd)-DTPA injection and a TE = 30 ms sequence pre- and post-Gd-DTPA. Intensity ratios of infarcted and normal myocardium were calculated, as were contrast-to-noise and signal-to-noise ratios. The four intensity ratios pre-Gd-DTPA were 1.20 +/- 0.15, 1.42 +/- 0.22, 1.78 +/- 0.38, and 1.99 +/- 0.60 for TE = 30, 60, 90, and 120 ms, respectively, and 1.42 +/- 0.19 post-Gd-DTPA (p = NS for post-Gd-DTPA vs TE = 60, p = 0.007 for TE = 90 vs TE = 120, p less than 0.0001 for all other comparisons). The four contrast-to-noise ratios pre-Gd-DTPA were 1.69 +/- 0.97, 2.69 +/- 1.13, 3.17 +/- 1.15, and 2.90 +/- 1.09 for TE = 30, 60, 90, and 120 ms, respectively, and 2.71 +/- 1.26 post-Gd-DTPA (p = NS for post-Gd-DTPA vs TE = 60, 90, and 120, p = NS for TE = 120 vs TE = 60 and 90, p less than 0.01 for all other comparisons). The four signal-to-noise ratios pre-Gd-DTPA were 8.67 +/- 1.47, 6.52 +/- 0.76, 5.20 +/- 0.64, 4.17 +/- 0.53 for TE = 30, 60, 90, and 120 ms, respectively, and 9.17 +/- 1.92 post-Gd-DTPA (p = 0.03 for post-Gd-DTPA vs TE = 30, p less than 0.0001 for all other comparisons). In conclusion, the detectabilities of acute myocardial infarction were similar at TE = 60 ms and at Gd-DTPA enhanced short-TE MR imaging. However, image quality proved to be superior using the Gd-DTPA enhanced short-TE technique.

Adult↗

PubMed2004

The role of social comparison in coping with rheumatoid arthritis: an interview study.

OBJECTIVE: This study aimed to explore the effects of participants' perceptions of support, ways of coping and feelings of control, on their accounts of well-being. METHODS: Semi-structured interviews were conducted with 10 patients with rheumatoid arthritis (RA) and explored the dynamics of participants' accounts of coping with their everyday lives. RESULTS: Four categories of coping mechanisms were evident in all participants' accounts: support during the medical consultation, nurse support, social support, and comparative strategies. This paper focuses on just one of the themes that emerged from our analysis. Further insight into coping mechanisms was provided by the prevalence of comparative coping strategies. A comparison with previous disease states was used by every participant. This comparison enhanced their sense of control and fostered a sense of well-being. Social comparison was used by seven participants to show themselves how fortunate they were in relation to others with RA. CONCLUSION: Comparative coping has been identified as an important strategy adopted by these participants that could be explored in further intervention-based studies of coping.

Journal Article↗

PubMed1984

Quantitation of metabolites in human skeletal muscle during rest and exercise: a comparison of methods.

Quantitation of muscle metabolites in vastus lateralis needle biopsies from human subjects at rest and following exercise is evaluated using three different methods of normalization of the data, i.e., total protein, total creatine, and NAD+. Coefficients of variation between patient analyses are similar when the metabolite data are normalized by any of the descriptors in resting muscle and in muscle samples obtained following vigorous exercise. When multiple samples are taken from individual patients the intrapatient coefficient of variation is less than that for interpatient comparisons. Normalization to total creatine or NAD+ yields significantly smaller coefficients of variation than does normalization to total protein in these intrapatient comparisons (P less than 0.05). Based on these comparisons, we conclude that any of these methods evaluated for normalizing metabolite content is adequate for studying human subjects, but the total creatine and NAD+ methods may offer some advantage because of the lower variability obtained with these analyses.

Creatine↗

PubMed1994

Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding.

We have recently developed a fast approach to comparisons of 3-dimensional structures. Our method is unique, treating protein structures as collections of unconnected points (atoms) in space. It is completely independent of the amino acid sequence order. It is unconstrained by insertions, deletions, and chain directionality. It matches single, isolated amino acids between 2 different structures strictly by their spatial positioning regardless of their relative sequential position in the amino acid chain. It automatically detects a recurring 3D motif in protein molecules. No predefinition of the motif is required. The motif can be either in the interior of the proteins or on their surfaces. In this work, we describe an enhancement over our previously developed technique, which considerably reduces the complexity of the algorithm. This results in an extremely fast technique. A typical pairwise comparison of 2 protein molecules requires less than 3 s on a workstation. We have scanned the structural database with dozens of probes, successfully detecting structures that are similar to the probe. To illustrate the power of this method, we compare the structure of a trypsin-like serine protease against the structural database. Besides detecting homologous trypsin-like proteases, we automatically obtain 3D, sequence order-independent, active-site similarities with subtilisin-like and sulfhydryl proteases. These similarities equivalence isolated residues, not conserving the linear order of the amino acids in the chains. The active-site similarities are well known and have been detected by manually inspecting the structures in a time-consuming, laborious procedure. This is the first time such equivalences are obtained automatically from the comparison of full structures. The far-reaching advantages and the implications of our novel algorithm to studies of protein folding, to evolution, and to searches for pharmacophoric patterns are discussed.

Amino Acid Sequence↗

PubMed2004

Evaluation of protein fold comparison servers.

When a new protein structure has been determined, comparison with the database of known structures enables classification of its fold as new or belonging to a known class of proteins. This in turn may provide clues about the function of the protein. A large number of fold comparison programs have been developed, but they have never been subjected to a comprehensive and critical comparative analysis. Here we describe an evaluation of 11 publicly available, Web-based servers for automatic fold comparison. Both their functionality (e.g., user interface, presentation, and annotation of results) and their performance (i.e., how well established structural similarities are recognized) were assessed. The servers were subjected to a battery of performance tests covering a broad spectrum of folds as well as special cases, such as multidomain proteins, Calpha-only models, new folds, and NMR-based models. The CATH structural classification system was used as a reference. These tests revealed the strong and weak sides of each server. On the whole, CE, DALI, MATRAS, and VAST showed the best performance, but none of the servers achieved a 100% success rate. Where no structurally similar proteins are found by any individual server, it is recommended to try one or two other servers before any conclusions concerning the novelty of a fold are put on paper.

Computational Biology↗

PubMed2004

Alternative alignments from comparison of protein structures.

Comparison of two protein structures often results in not only a global alignment but also a number of distinct local alignments; the latter, referred to as alternative alignments, are however usually ignored in existing protein structure comparison analyses. Here, we used a novel method of protein structure comparison to extensively identify and characterize the alternative alignments obtained for structure pairs of a fold classification database. We showed that all alternative alignments can be classified into one of just a few types, and with which illustrated the potential of using alternative alignments to identify recurring protein substructures, including the internal structural repeats of a protein. Furthermore, we showed that among the alternative alignments obtained, permuted alignments, which included both circular and scrambled permutations, are as prevalent as topological alignments. These results demonstrated that the so far largely unattended alternative alignments of protein structures have implications and applications for research of protein classification and evolution.

Databases, Protein↗

PubMed2006

Comparison of protein active site structures for functional annotation of proteins and drug design.

Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary-sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein's activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand-binding sites to infer biological function and aid in drug discovery. The CPASS database comprises the ligand-defined active sites identified in the protein data bank, where the CPASS program compares these ligand-defined active sites to determine sequence and structural similarity without maintaining sequence connectivity. CPASS will compare any set of ligand-defined protein active sites, irrespective of the identity of the bound ligand.

Adenosine Triphosphate↗

PubMed1995

Size-independent comparison of protein three-dimensional structures.

Protein structures are routinely compared by their root-mean-square deviation (RMSD) in atomic coordinates after optimal rigid body superposition. What is not so clear is the significance of different RMSD values, particularly above the customary arbitrary cutoff for obvious similarity of 2-3 A. Our earlier work argued for an intrinsic cutoff for protein similarity that varied with the number of residues in the polypeptide chains being compared. Here we introduce a new measure, rho, of structural similarity based on RMSD that is independent of the sizes of the molecules involved, or of any other special properties of molecules. When rho is less than 0.4-0.5, protein structures are visually recognized to be obviously similar, but the mathematically pleasing intrinsic cutoff of rho < 1.0 corresponds to overall similarity in folding motif at a level not usually recognized until smoothing of the polypeptide chain path makes it striking. When the structures are scaled to unit radius of gyration and equal principle moments of inertia, the comparisons are even more universal, since they are no longer obscured by differences in overall size and ellipticity. With increasing chain length, the distribution of rho for pairs of random structures is skewed to higher values, but the value for the best 1% of the comparisons rises only slowly with the number of residues. This level is close to an intrinsic cutoff between similar and dissimilar comparisons, namely the maximal scaled rho possible for the two structures to be more similar to each other than one is to the other's mirror image. The intrinsic cutoff is independent of the number of residues or points being compared. For proteins having fewer than 100 residues, the 1% rho falls below the intrinsic cutoff, so that for very small proteins, geometrically significant similarity can often occur by chance. We believe these ideas will be helpful in judging success in NMR structure determination and protein folding modeling.

Computer Graphics↗

PubMed2004

Combination of direct and indirect evidence in mixed treatment comparisons.

Mixed treatment comparison (MTC) meta-analysis is a generalization of standard pairwise meta-analysis for A vs B trials, to data structures that include, for example, A vs B, B vs C, and A vs C trials. There are two roles for MTC: one is to strengthen inference concerning the relative efficacy of two treatments, by including both 'direct' and 'indirect' comparisons. The other is to facilitate simultaneous inference regarding all treatments, in order for example to select the best treatment. In this paper, we present a range of Bayesian hierarchical models using the Markov chain Monte Carlo software WinBUGS. These are multivariate random effects models that allow for variation in true treatment effects across trials. We consider models where the between-trials variance is homogeneous across treatment comparisons as well as heterogeneous variance models. We also compare models with fixed (unconstrained) baseline study effects with models with random baselines drawn from a common distribution. These models are applied to an illustrative data set and posterior parameter distributions are compared. We discuss model critique and model selection, illustrating the role of Bayesian deviance analysis, and node-based model criticism. The assumptions underlying the MTC models and their parameterization are also discussed.

Humans↗

PubMed2005

Pairwise multiple comparison adjustment in survival analysis.

Many clinical studies have as their endpoint the time until some event (such as death) occurs. Often in such studies researchers are interested in comparing several treatment or prognostic groups with one another in terms of their survival curves. When many such pairwise group comparisons are done, the chance of finding a false significance among all of the comparisons is inflated above the usual desired significance level. This paper investigates methods of adjusting the survival analysis for the number of comparisons being made. These methods are applied to a retrospective study conducted by the International Bone Marrow Transplant Registry and compared in a simulation study in terms of the power to detect actual differences in the survival curves between the groups.

Bone Marrow Transplantation↗

PubMed1989

A two-period crossover design for the comparison of two active treatments and placebo.

This paper discusses a two-period crossover design for the comparison of two active treatments (A and B) and placebo (P) for relief of recurrent symptoms of a chronic health disorder. It is based on blocks of ten patients for which the treatment sequences A:B and B:A are each assigned to three patients and the sequences A:P, P:A, B:P, and P:B are each assigned to one patient; thus, treatment periods have a 2:2:1 allocation for A, B, and P. The principal model for analysis of this design involves additive subject effects, period effects, and treatment effects. Analysis of within-patient differences provides an estimate of the comparison between active treatments with variance (2vw/7r) and an estimate of the comparison between an active treatment and placebo with variance (4vw/7r); here vw is the within-patient variance and r is the number of blocks of ten patients. Analyses which address carryover effects and treatment effects adjusted for carryover effects are also described. An example using simulated data on relief of recurrent gastrointestinal pain illustrates the methodology.

Chronic Disease↗

PubMed2001

Efficiency comparisons of rank and permutation tests based on summary statistics computed from repeated measures data.

A popular method of using repeated measures data to compare treatment groups in a clinical trial is to summarize each individual's outcomes with a scalar summary statistic, and then to perform a two-group comparison of the resulting statistics using a rank or permutation test. Many different types of summary statistics are used in practice, including discrete and continuous functions of the underlying repeated measures data. When the repeated measures processes of the comparison groups differ by a location shift at each time point, the asymptotic relative efficiency of (continuous) summary statistics that are linear functions of the repeated measures has been determined and used to compare tests in this class. However, little is known about the non-null behaviour of discrete summary statistics, about continuous summary statistics when the groups differ in more complex ways than location shifts or where the summary statistics are not linear functions of the repeated measures. Indeed, even simple distributional structures on the repeated measures variables can lead to complex differences between the distribution of common summary statistics of the comparison groups. The presence of left censoring of the repeated measures, which can arise when these are laboratory markers with lower limits of detection, further complicates the distribution of, and hence the ability to compare, summary statistics. This paper uses recent theoretical results for the non-null behaviour of rank and permutation tests to examine the asymptotic relative efficiencies of several popular summary statistics, both discrete and continuous, under a variety of common settings. We assume a flexible linear growth curve model to describe the repeated measures responses and focus on the types of settings that commonly arise in HIV/AIDS and other diseases.

Acquired Immunodeficiency Syndrome↗

PubMed2001

Dynamic linear model and SARIMA: a comparison of their forecasting performance in epidemiology.

One goal of a public health surveillance system is to provide a reliable forecast of epidemiological time series. This paper describes a study that used data collected through a national public health surveillance system in the United States to evaluate and compare the performances of a seasonal autoregressive integrated moving average (SARIMA) and a dynamic linear model (DLM) for estimating case occurrence of two notifiable diseases. The comparison uses reported cases of malaria and hepatitis A from January 1980 to June 1995 for the United States. The residuals for both predictor models show that they were adequate tools for use in epidemiological surveillance. Qualitative aspects were considered for both models to improve the comparison of their usefulness in public health. Our comparison found that the two forecasting modelling techniques (SARIMA and DLM) are comparable when long historical data are available (at least 52 reporting periods). However, the DLM approach has some advantages, such as being more easily applied to different types of time series and not requiring a new cycle of identification and modelling when new data become available.

Communicable Disease Control↗

PubMed1999

Pitfalls in the categorization of behaviour: a comparison of dolphin whistle classification methods.

The categorization of behaviour patterns into separate classes is crucial to the study of animal behaviour. Traditionally researchers have classified behaviour patterns through careful observation by eye. Recently this method has been increasingly replaced by computer methods. While the definition and fine scale analysis that can be achieved with computers is desirable, only a few studies have actually looked at how these methods perform in comparison with human observation. I compared the classification of bottlenose dolphin, Tursiops truncatus, whistles by human observers with the performance of three computer methods: (1) a method developed by McCowan (1995, Ethology, 100, 177-193); (2) a comparison of cross-correlation coefficients using hierarchical cluster analysis; and (3) a comparison of average difference in frequency along two whistle contours also using hierarchical cluster analysis. The whistle sample consisted of 104 randomly chosen whistles from a group of four captive bottlenose dolphins recorded both during periods when one was separate from the rest of the group and while they all swam in the same pool. The sample contained five individual-specific signature whistles and several nonsignature whistles. Five human observers, without knowledge of the recording context, were more likely than the computer methods to identify signature whistles that were used only while an animal was isolated from the rest of the group. I discuss the limitations of methods commonly used for pattern recognition in communication studies. The discrepancies between methods show how crucial it is to obtain an external validation of the behaviour classes used in studies of animal behaviour. Copyright 1999 The Association for the Study of Animal Behaviour.

Journal Article↗

PubMed1993

Derivation of a scale-independent parameter which characterizes genetic sequence comparisons.

A new method of quantifying the similarity between genetic sequences is presented. The method makes use of the finding that sequence comparisons expressed in binary vector form have an associated scale-independent parameter, D. This parameter is represented in the function M(S,n) = (N) (en/enD), where S is the vector, n represents the window size which is allowed to vary, N is a constant, and D is the scale-independent measure of homology. By comparing two sequences using this method, a unimodal, symmetric distribution of D values associated with the frameshifted vectors is obtained. The degree of sequence similarity is determined by the distribution of these parameters. A set of sequences of evolutionary interest coding for glyceraldehyde-3-phosphate dehydrogenases and mammalian insulins is compared using this methodology. The results confirm evolutionary tree distances calculated using different procedures. Since a z score can be calculated for each comparison, the method allows for the rapid identification of sequence homologies ranked according to the probability of occurrence. This unique scale-independent measure of similarity allows contrasts and comparisons between any two sequence fragments using all available order information.

Actins↗

PubMedDate not supplied

What makes a man similar to a tie? Stimulus compatibility with comparison and integration.

We argue and show that different properties of stimuli are compatible with different types of processing. Specifically, object pairs from the same taxonomic category (e.g., chair-bed) tend to be alignable and thus compatible with comparison, whereas object pairs that play different roles in thematic relations (e.g., chair-carpenter) tend to be nonalignable and compatible with integration. Using object pairs that varied orthogonally in alignability and thematic relatedness, we demonstrated that stimulus compatibility modulates processing and affects the outcomes of tasks that are currently believed to involve only comparison (similarity ratings, Experiment 1; listing commonalities and differences, Experiment 2) or only integration (thematic relatedness ratings, Experiment 3). Our findings and others that we have reviewed suggest that: (1) many cognitive tasks involve both comparison and integration, and (2) the relative influence of each process is modulated by an interplay between the task-appropriate and the stimulus-compatible process. We believe that single-process models should be extended to take this interplay into account.

Humans↗