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At least 325 records · Page 18Linked to original sources

Probability density estimation for the interpretation of neural population codes.

1. Electrophysiological recording data from multiple cells in motor cortex and elsewhere often are interpreted using the population vector method pioneered by Georgopoulos and coworkers. This paper proposes an alternative method for interpreting coding across populations of cells that may succeed under circumstances in which the population vector fails. 2. Population codes are analyzed using probability theory to find the complete conditional probability density of a movement parameter given the firing pattern of a set of cells. 3. The conditional probability density when a single cell fires is proportional to the shape of the cell's tuning curve of firing rate in response to different movement parameters. 4. The conditional density when multiple cells fire is proportional to the product of their tuning curves. 5. Movement parameters can be estimated from the conditional density using statistical maximum likelihood or minimum mean-squared error methods. 6. Simulations show that density estimation correctly finds movement directions for nonuniform distributions of preferred directions and noncosine cell tuning curves, whereas the population vector method fails for these cases. 7. Probability methods thus provide a statistically based alternative to the population vector for interpreting electrophysiological recording data from multiple cells.

Cell Count↗

[Left-handed helix conformation of poly-L-proline II type in globular proteins. Statistics of incidence and a role of sequence].

Regions of left-handed polyproline II type conformation in globular proteins were studied throughout the PDB bank. The length and sequence of corresponding fragments were analyzed. It was found that a lot of tetrapeptides (from combinatorial possible ones) show the tendency to be included in the left-handed helices. Much more tetrapeptides do not occur in this structure type.

Amino Acid Sequence↗

The harm done by tests of significance.

Three historical episodes in which the application of null hypothesis significance testing (NHST) led to the mis-interpretation of data are described. It is argued that the pervasive use of this statistical ritual impedes the accumulation of knowledge and is unfit for use.

Accidents, Traffic↗

Dealing with large data sets.

Collection, storage and retrieval of large amounts of data from multiple experiments for subsequent reduction, graphing and statistical analysis need not be a burdensome task. Although turnkey systems may offer significant economies for single well-defined and repetitive tasks, they may not permit sufficient flexibility to achieve the diverse aims required by many research programs. Using popular microcomputers to run one or a few experimental subjects may confront the investigator not only with significant bookkeeping problems, but also with an allocation of labor resources to computer maintenance and support that might be better invested in research effort. By using networked minicomputers, economies of scale emerge both in data collection, transfer, reduction, and analysis, as well as in maintenance, support, and scientific effort.

Data Collection↗

The reading, writing, and arithmetic of the medical literature, part 2: critical evaluation of statistical reporting.

OBJECTIVE: To offer suggestions to help improve clinicians' understanding of the statistical analyses in the literature and their use of these methods in their own medical writings. DATA SOURCES: Literature searches began at the National Library of Medicine's online database and were traced to primary sources. STUDY SELECTION: All referenced information in this article was cited from primary sources. RESULTS: Physicians should be able to determine the variables studied and how they were measured, the comparisons that were made, the difference (with 95% confidence interval) between the groups, the exact P value for the difference, the statistical test used in the analysis, whether the data conformed to the assumptions of the test, whether the study had adequate statistical power, and the clinical importance of the difference. CONCLUSION: Clinicians should know how to interpret statistical results so that they can use medical science to its full extent in treating patients.

Biomedical Research↗

Summary measures of population health: methods for calculating healthy life expectancy.

This report is one of several appearing as Healthy People Statistical Notes that evaluate methodological issues pertaining to summary measures. Summary measures of population health are statistics that combine mortality and morbidity to represent overall population health in a single number--in this report, health expectancy measures. This report presents a comprehensive discussion of the methods for calculation and methodologic issues related to the interpretation of healthy life expectancy. These measures combine both mortality and morbidity using an abridged life-table procedure. Data from the National Center for Health Statistics and other sources will be used to illustrate the calculation of the statistics and the associated statistical tests.

Age Factors↗

Using multiple imputation for analysis of incomplete data in clinical research.

BACKGROUND: Sample loss and missing data are inevitable in multivariate and longitudinal research. Ad hoc approaches such as analysis of incomplete data or substituting the group mean for missing data, while common, may unnecessarily reduce statistical power and threaten study validity. Multiple imputation for missing data is a newly accessible, methodologically rigorous approach to dealing with the problem of missing data. APPROACH: To (a) discuss the problem of missing data in clinical research, and (b) describe the technique of multiple imputation. A case of analysis of multivariate psychosocial data is presented to illustrate the practice of multiple imputation. RESULTS: The advantages of multiple imputation are it (a) results in unbiased estimates, providing more validity than ad hoc approaches to missing data; (b) uses all available data, preserving sample size and statistical power; (c) may be used with standard statistical software; and, (d) results are readily interpreted. DISCUSSION: Accessible, user-friendly computer programs are available to perform multiple imputation for missing data making ad hoc approaches to missing data obsolete.

Data Interpretation, Statistical↗

Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turns.

A new and more accurate method has been developed for predicting the backbone U-turn positions (where the chain reverses global direction) and the dominant secondary structure elements between U-turns in globular proteins. The current approach uses sequence-specific secondary structure propensities and multiple sequence information. The latter plays an important role in the enhanced success of this approach. Application to two sets (total 108) of small to medium-sized, single-domain proteins indicates that approximately 94% of the U-turn locations are correctly predicted within three residues, as are 88% of dominant secondary structure elements. These results are significantly better than our previous method (Kolinski et al., Proteins 27:290-308, 1997). The current study strongly suggests that the U-turn locations are primarily determined by local interactions. Furthermore, both global length constraints and local interactions contribute significantly to the determination of the secondary structure types between U-turns. Accurate U-turn predictions are crucial for accurate secondary structure predictions in the current method. Protein structure modeling, tertiary structure predictions, and possibly, fold recognition should benefit from the predicted structural data provided by this new method.

Amino Acid Sequence↗

Diagnostic statistical procedures in medical meta-analyses.

The number of published meta-analyses in medicine has had phenomenal growth, to a point where over 300 meta-analyses in medicine are published yearly. Because meta-analyses tend to lead to policy decisions, it is extremely important that the analyses be robust and that alternative analyses yield consistent results. We herein provide a discussion of diagnostic statistical procedures.

Confidence Intervals↗

Family-Wise Error Rate Control in Clinical Trials With Overlapping Populations.

We consider clinical trials with multiple, overlapping patient populations that test multiple treatment policies specifically tailored to these populations. Such designs may lead to multiplicity issues, as false statements will affect several populations. For type I error control, often the family-wise error rate (FWER) is controlled, which is the probability to reject at least one true null hypothesis. If the joint distribution of the test statistics is known, the FWER level can be exhausted by determining critical values or adjusted-levels. The adjustment is typically done under the common ANOVA assumptions. However, the performed tests are then only valid under the rather strong assumption of homogeneous null effects, that is, when the null hypothesis applies to all subpopulations and their intersections. We show that under cancelling null effects, when heterogeneous effects cancel out in some or all subpopulations, this procedure does not provide FWER control. We also suggest different alternatives and compare them in terms of FWER control and their power.

Humans↗

Evaluation of numerical analysis of random amplified polymorphic DNA (RAPD)-PCR as a method to differentiate Lactobacillus plantarum and Lactobacillus pentosus.

Lactobacillus plantarum and Lactobacillus pentosus grouped into one protein profile cluster at r > or = 0.70, separate from Lactobacillus casei, Lactobacillus sake, and Lactobacillus curvatus. Similar sugar fermentation reactions were recorded for representative strains of L. plantarum and L. pentosus. Representative strains, including the type of each species, were selected from the different protein profile clusters and their genetic relatedness determined by using numerical analysis of random amplified polymorphic DNA (RAPD)-PCR. The type strains of L. plantarum (ATCC 14917T) and L. pentosus (NCFB 363T) displayed different RAPD profiles and grouped into two independent clusters, well separated from L. casei, L. curvatus, and L. sake. Numerical analysis of RAPD-PCR proved a reliable and accurate method to distinguish between strains of L. plantarum and L. pentosus.

Base Sequence↗

An optical scan/statistical package for clinical data management in C-L psychiatry.

This paper explores aspects of the need for clinical database management systems that permit ongoing service management, measurement of the quality and appropriateness of care, databased administration of consultation liaison (C-L) services, teaching/educational observations, and research. It describes an OPTICAL SCAN databased management system that permits flexible form generation, desktop publishing, and linking of observations in multiple files. This enhanced MICRO-CARES software system--Medical Application Platform (MAP)--permits direct transfer of the data to ASCII and SAS format for mainframe manipulation of the clinical information. The director of a C-L service may now develop his or her own forms, incorporate structured instruments, or develop "branch chains" of essential data to add to the core data set without the effort and expense to reprint forms or consult with commercial vendors.

Computer Systems↗

Amino acid sequences of P1 protamines and the phylogeny of eutherian mammals: a cladistic study.

Amino acid and cDNA sequences of eutherian P1 protamines, known from publications of other authors, were compared by a cladistic method. Fish, toad and bird protamines were used for the pertinent "outgroup comparisons", i.e. they provided relevant data for the comparative alignment of the sequences and for the recognition of evolutionary trends. In the sequence positions compared, each amino acid was individually assigned as a plesiomorphic or apomorphic character state (qualitative treatment). The resulting phylogenetic tree (Fig. 2) is only partially in accordance with common ideas on eutherian phylogeny. Disagreements refer to the branching points of Perissodactyla, Lagomorpha and Rodentia.

Amino Acid Sequence↗

Inactivation and destruction by KMnO4 of Escherichia coli RNA polymerase open transcription complex: recommendations for footprinting experiments.

Potassium permanganate oxidation of pyrimidine residues in single-stranded DNA is commonly used in footprinting studies on formation of open transcription complex (RPo) by RNA polymerases (RNAP) at cognate promoters. Our own experience and literature search led us to conclude that KMnO4 doses often used in such studies might cause multiple-hit oxidation of promoter DNA and oxidative damage to RNAP in RPo and lead to false interpretation of footprints. We have therefore studied as a function of KMnO4 dose (i) transcription activity of RPo formed by Escherichia coli RNAP at a model cognate promoter Pa and (ii) RPo's structural integrity, by gel electrophoresis and footprinting assays. Kinetics of formation of this complex and melting of DNA in the transcription bubble region were thoroughly characterized by us previously. Here we show that (i) RPo becomes completely inactivated at oxidant doses much lower than those needed to cause a detectable footprint of the melted DNA region, (ii) footprinting patterns of the melted promoter region remain practically unaffected by RNAP oxidation within a range of low oxidant doses causing single-hit oxidation of DNA, and (iii) at higher oxidant doses, corresponding to multiple-hit DNA oxidation, the gross structure of RPo changes progressively until its complete collapse and dissociation into constituent components, so that only approximate interpretation of the footprinting data for the melted DNA region is possible. A protocol for accurate RPo footprinting with low single-hit KMnO4 doses and interpretation of the footprinting data in terms of kinetics of oxidation of pyrimidine residues in promoter DNA is recommended.

Base Sequence↗