G*Power 3: a flexible statistical power analysis program for the social, behavioral, and biomedical sciences

G*Power (Erdfelder, Faul, & Buchner, 1996) was designed as a general stand-alone power analysis program for statistical tests commonly used in social and behavioral research. G*Power 3 is a major extension of, and improvement over, the previous versions. It runs on widely used computer platforms (i.e., Windows XP, Windows Vista, and Mac OS X 10.4) and covers many different statistical tests of the t, F, and chi2 test families. In addition, it includes power analyses for z tests and some exact tests. G*Power 3 provides improved effect size calculators and graphic options, supports both distribution-based and design-based input modes, and offers all types of power analyses in which users might be interested. Like its predecessors, G*Power 3 is free.

The Psychophysics Toolbox

The Psychophysics Toolbox is a software package that supports visual psychophysics. Its routines provide an interface between a high-level interpreted language (MATLAB on the Macintosh) and the video display hardware. A set of example programs is included with the Toolbox distribution.

The VideoToolbox software for visual psychophysics: transforming numbers into movies

The VideoToolbox is a free collection of two hundred C subroutines for Macintosh computers that calibrates and controls the computer-display interface to create accurately specified visual stimuli. High-level platform-independent languages like MATLAB are best for creating the numbers that describe the desired images. Low-level, computer-specific VideoToolbox routines control the hardware that transforms those numbers into a movie. Transcending the particular computer and language, we discuss the nature of the computer-display interface, and how to calibrate and control it.

Rapid and sensitive protein similarity searches

An algorithm was developed which facilitates the search for similarities between newly determined amino acid sequences and sequences already available in databases. Because of the algorithm's efficiency on many microcomputers, sensitive protein database searches may now become a routine procedure for molecular biologists. The method efficiently identifies regions of similar sequence and then scores the aligned identical and differing residues in those regions by means of an amino acid replacability matrix. This matrix increases sensitivity by giving high scores to those amino acid replacements which occur frequently in evolution. The algorithm has been implemented in a computer program designed to search protein databases very rapidly. For example, comparison of a 200-amino-acid sequence to the 500,000 residues in the National Biomedical Research Foundation library would take less than 2 minutes on a minicomputer, and less than 10 minutes on a microcomputer (IBM PC).

CLUSTAL: a package for performing multiple sequence alignment on a microcomputer

An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. Then the multiple alignment is achieved from a series of pairwise alignments of clusters of sequences, following the order of branching in the tree. The method is sufficiently fast and economical with memory to be easily implemented on a microcomputer, and yet the results obtained are comparable to those from packages requiring mainframe computer facilities.

A pharmacokinetic analysis program (multi) for microcomputer

A nonlinear least squares program (MULTI) for microcomputers was developed. The program is written in BASIC programming language. Four algorithms, (1) Gauss-Newton method, (2) damping Gauss-Newton method, (3) modified Marquardt method and (4) simplex method, can be used for nonlinear curve fitting in MULTI. Up to five pharmacokinetic equations, which are voluntarily defined by the user, are simultaneously fitted to observed time courses. The executions of MULTI are demonstrated for time courses of ampicillin and oxacillin in man.

DMDX: a windows display program with millisecond accuracy

DMDX is a Windows-based program designed primarily for language-processing experiments. It uses the features of Pentium class CPUs and the library routines provided in DirectX to provide accurate timing and synchronization of visual and audio output. A brief overview of the design of the program is provided, together with the results of tests of the accuracy of timing. The Web site for downloading the software is given, but the source code is not available.

Virtual in vivo interactive dissection of white matter fasciculi in the human brain

This work reports the use of diffusion tensor magnetic resonance tractography to visualize the three-dimensional (3D) structure of the major white matter fasciculi within living human brain. Specifically, we applied this technique to visualize in vivo (i) the superior longitudinal (arcuate) fasciculus, (ii) the inferior longitudinal fasciculus, (iii) the superior fronto-occipital (subcallosal) fasciculus, (iv) the inferior frontooccipital fasciculus, (v) the uncinate fasciculus, (vi) the cingulum, (vii) the anterior commissure, (viii) the corpus callosum, (ix) the internal capsule, and (x) the fornix. These fasciculi were first isolated and were then interactively displayed as a 3D-rendered object. The virtual tract maps obtained in vivo using this approach were faithful to the classical descriptions of white matter anatomy that have previously been documented in postmortem studies. Since we have been able to interactively delineate and visualize white matter fasciculi over their entire length in vivo, in a manner that has only previously been possible by histological means, "virtual in vivo interactive dissection" (VIVID) adds a new dimension to anatomical descriptions of the living human brain.

Analysis of radioligand binding experiments. A collection of computer programs for the IBM PC

It is now well accepted that graphic methods are a poor choice of analytical technique for analyzing radioligand binding data given the complexity of some radioligand-binding sites interactions; this is true not only for studies performed at equilibrium but also for those examining kinetic properties of the radioligand. As a consequence the computer plays an important role in all forms of radioligand binding experiments because it reduces the labor-intensive calculations associated with such experiments and it allows the use of more appropriate weighted nonlinear curve-fitting techniques that more accurately describe the radioligand-binding site interaction. This paper describes a collection of four programs (KINETIC, EBDA, LIGAND, and LOWRY) that can be used to analyze most forms of radioligand binding experiments. The programs have been adapted for use on an IBM PC, which is a popular, inexpensive microcomputer and which is well suited to the analysis of radioligand binding data.

Molecular electronics. Synthesis and testing of components

Molecular electronics involves the use of single or small packets of molecules as the fundamental units for computing. While initial targets are the substitution of solid-state wires and devices with molecules, long-range goals involve the development of novel addressable electronic properties from molecules. A comparison of traditional solid-state devices to molecular systems is described. Issues of cost and ease of manufacture are outlined, along with the syntheses and testing of molecular wires and devices.

'DNA Strider': a 'C' program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers

DNA Strider is a new integrated DNA and Protein sequence analysis program written with the C language for the Macintosh Plus, SE and II computers. It has been designed as an easy to learn and use program as well as a fast and efficient tool for the day-to-day sequence analysis work. The program consists of a multi-window sequence editor and of various DNA and Protein analysis functions. The editor may use 4 different types of sequences (DNA, degenerate DNA, RNA and one-letter coded protein) and can handle simultaneously 6 sequences of any type up to 32.5 kB each. Negative numbering of the bases is allowed for DNA sequences. All classical restriction and translation analysis functions are present and can be performed in any order on any open sequence or part of a sequence. The main feature of the program is that the same analysis function can be repeated several times on different sequences, thus generating multiple windows on the screen. Many graphic capabilities have been incorporated such as graphic restriction map, hydrophobicity profile and the CAI plot- codon adaptation index according to Sharp and Li. The restriction sites search uses a newly designed fast hexamer look-ahead algorithm. Typical runtime for the search of all sites with a library of 130 restriction endonucleases is 1 second per 10,000 bases. The circular graphic restriction map of the pBR322 plasmid can be therefore computed from its sequence and displayed on the Macintosh Plus screen within 2 seconds and its multiline restriction map obtained in a scrolling window within 5 seconds.

Java-based graphical user interface for the MRUI quantitation package

This article describes the Java-based version of the magnetic resonance user interface (MRUI) quantitation package. This package allows MR spectroscopists to easily perform time-domain analysis of in vivo MR spectroscopy data. We show that the Java programming language is very well suited for developing highly interactive graphical software applications such as the MRUI software. We have also established that MR quantitation algorithms, programmed in other languages, can easily be embedded into the Java-based MRUI by using the Java native interface (JNI). This new graphical user interface (GUI) has been conceived for the processing of large data sets and uses prior knowledge data-bases to make interactive quantitation algorithms more userfriendly.

Map Manager QTX, cross-platform software for genetic mapping

Map Manager QTX (QTX) is software for analysis of genetic mapping experiments in experimental plants and animals. It includes functions for mapping both Mendelian and quantitative trait loci. QTX is an enhanced version of Map Manager QT, rewritten with the aid of cross-platform libraries (XVT, Boulder Software Foundry, Inc.), which allow it to be compiled for multiple computer platforms. It currently is distributed for Microsoft Windows and Mac OS and is available at http://mapmgr.roswellpark.org/mmQTX.html.

Using the implicit association test to measure self-esteem and self-concept

Experiment 1 used the Implicit Association Test (IAT; A. G. Greenwald, D. E. McGhee, & J. L. K. Schwartz, 1998) to measure self-esteem by assessing automatic associations of self with positive or negative valence. Confirmatory factor analysis (CFA) showed that two IAT measures defined a factor that was distinct from, but weakly correlated with, a factor defined by standard explicit (self-report) measures of self-esteem. Experiment 2 tested known-groups validity of two IAT gender self-concept measures. Compared with well-established explicit measures, the IAT measures revealed triple the difference in measured masculinity-femininity between men and women. Again, CFA revealed construct divergence between implicit and explicit measures. Experiment 3 assessed the self-esteem IAT's validity in predicting cognitive reactions to success and failure. High implicit self-esteem was associated in the predicted fashion with buffering against adverse effects of failure on two of four measures.

Validation of information recorded on general practitioner based computerised data resource in the United Kingdom

OBJECTIVE

To determine the extent of agreement between clinical information recorded on surgery computers of selected general practitioners and similar information in manual records of letters received from hospital consultants and kept in the general practitioners' files.

DESIGN

Hospital consultants' letters in the manual records of selected general practitioners were photocopied and the consultants' clinical diagnoses were compared with diagnoses recorded on computer.

SETTING

General practices in the United Kingdom using computers provided by VAMP Health for recording clinical information.

SUBJECTS

2491 patients who received one of three non-steroidal anti-inflammatory drugs and who attended 58 practices whose computer recorded data were considered after a preliminary review to be of satisfactory quality.

RESULTS

Among 1191 patients for whom consultants' letters were forwarded a clinical diagnosis reflecting the diagnosis noted on a consultant letter was present on the computer record for 1038 (87%).

CONCLUSION

Clinical information available on the computer records of the general practitioners who participated in this study is satisfactory for many clinical studies.

The reliability of the Alcohol Timeline Followback when administered by telephone and by computer

The Alcohol Timeline Followback (TLFB) has been shown to be a psychometrically sound assessment instrument for obtaining retrospective daily estimates of alcohol consumption. These evaluations, however, have been limited to face-to-face paper-and-pencil interviews. As use of the TLFB method has increased, investigators have reported using the method to collect follow-up data by telephone. Also, as with many assessment instruments, a computerized version of the TLFB method has been developed. The psychometric characteristics of the TLFB method under these administration conditions have not been evaluated. This paper presents results from two studies showing that the Alcohol TLFB method can obtain reliable drinking data when administered over the telephone and by computer.

Validity and reliability of the Nintendo Wii Balance Board for assessment of standing balance

Impaired standing balance has a detrimental effect on a person's functional ability and increases their risk of falling. There is currently no validated system which can precisely quantify center of pressure (COP), an important component of standing balance, while being inexpensive, portable and widely available. The Wii Balance Board (WBB) fits these criteria, and we examined its validity in comparison with the 'gold standard'-a laboratory-grade force platform (FP). Thirty subjects without lower limb pathology performed a combination of single and double leg standing balance tests with eyes open or closed on two separate occasions. Data from the WBB were acquired using a laptop computer. The test-retest reliability for COP path length for each of the testing devices, including a comparison of the WBB and FP data, was examined using intraclass correlation coefficients (ICC), Bland-Altman plots (BAP) and minimum detectable change (MDC). Both devices exhibited good to excellent COP path length test-retest reliability within-device (ICC=0.66-0.94) and between-device (ICC=0.77-0.89) on all testing protocols. Examination of the BAP revealed no relationship between the difference and the mean in any test, however the MDC values for the WBB did exceed those of the FP in three of the four tests. These findings suggest that the WBB is a valid tool for assessing standing balance. Given that the WBB is portable, widely available and a fraction of the cost of a FP, it could provide the average clinician with a standing balance assessment tool suitable for the clinical setting.

Brain responses to micro-machined silicon devices

Micro-machined neural prosthetic devices can be designed and fabricated to permit recording and stimulation of specific sites in the nervous system. Unfortunately, the long-term use of these devices is compromised by cellular encapsulation. The goals of this study were to determine if device size, surface characteristics, or insertion method affected this response. Devices with two general designs were used. One group had chisel-shaped tips, sharp angular corners, and surface irregularities on the micrometer size scale. The second group had rounded corners, and smooth surfaces. Devices of the first group were inserted using a microprocessor-controlled inserter. Devices of the second group were inserted by hand. Comparisons were made of responses to the larger devices in the first group with devices from the second group. Responses were assessed 1 day and 1, 2, 4, 6, and 12 weeks after insertions. Tissues were immunochemically labeled for glial fibrillary acidic protein (GFAP) or vimentin to identify astrocytes, or for ED1 to identify microglia. For the second comparison devices from the first group with different cross-sectional areas were analyzed. Similar reactive responses were observed following insertion of all devices; however, the volume of tissue involved at early times, <1 week, was proportional to the cross-sectional area of the devices. Responses observed after 4 weeks were similar for all devices. Thus, the continued presence of devices promotes formation of a sheath composed partly of reactive astrocytes and microglia. Both GFAP-positive and -negative cells were adherent to all devices. These data indicate that device insertion promotes two responses-an early response that is proportional to device size and a sustained response that is independent of device size, geometry, and surface roughness. The early response may be associated with the amount of damage generated during insertion. The sustained response is more likely due to tissue-device interactions.

A comprehensive sequence analysis program for the IBM personal computer

We have developed a versatile program for the analysis of nucleic acid and protein sequences on the IBM Personal Computer. The program is interactive and self-instructing. It contains all the features generally found in sequence analysis programs on large computers, including extensive homology routines, as well as new procedures for the entry of sequence data. The program contains facilities to store and utilize the entire Nucleic Acid Sequence Data Bank. We have devised a new algorithm to find restriction enzyme sites, which allows our microcomputer program to find all sites on a small plasmid for 100 different enzymes in 1 to 2 minutes.

The use of visual analogue scales to assess motivation to eat in human subjects: a review of their reliability and validity with an evaluation of new hand-held computerized systems for temporal tracking of appetite ratings

This present paper reviews the reliability and validity of visual analogue scales (VAS) in terms of (1) their ability to predict feeding behaviour, (2) their sensitivity to experimental manipulations, and (3) their reproducibility. VAS correlate with, but do not reliably predict, energy intake to the extent that they could be used as a proxy of energy intake. They do predict meal initiation in subjects eating their normal diets in their normal environment. Under laboratory conditions, subjectively rated motivation to eat using VAS is sensitive to experimental manipulations and has been found to be reproducible in relation to those experimental regimens. Other work has found them not to be reproducible in relation to repeated protocols. On balance, it would appear, in as much as it is possible to quantify, that VAS exhibit a good degree of within-subject reliability and validity in that they predict with reasonable certainty, meal initiation and amount eaten, and are sensitive to experimental manipulations. This reliability and validity appears more pronounced under the controlled (but more artificial) conditions of the laboratory where the signal:noise ratio in experiments appears to be elevated relative to real life. It appears that VAS are best used in within-subject, repeated-measures designs where the effect of different treatments can be compared under similar circumstances. They are best used in conjunction with other measures (e.g. feeding behaviour, changes in plasma metabolites) rather than as proxies for these variables. New hand-held electronic appetite rating systems (EARS) have been developed to increase reliability of data capture and decrease investigator workload. Recent studies have compared these with traditional pen and paper (P&P) VAS. The EARS have been found to be sensitive to experimental manipulations and reproducible relative to P&P. However, subjects appear to exhibit a significantly more constrained use of the scale when using the EARS relative to the P&P. For this reason it is recommended that the two techniques are not used interchangeably.

Cellular hypertrophy and hyperplasia of airway smooth muscles underlying bronchial asthma. A 3-D morphometric study

In order to study whether hyperplasia or hypertrophy of cells is responsible for the thickening of airway muscles, 3-D morphometry of airway muscle cells was performed on resin-embedded semithin serial sections of autopsied lungs from 10 asthmatics and five control subjects. There were five Type I and five Type II asthmatic lungs, as defined in an earlier study, thickened muscles being found only in the central bronchi in Type I and distributed over the whole airway tree in Type II. The analysis was based on "unbiased" 3-D morphometry to obtain the numerical density NV of muscle cells using a "disector," a spatial probe introduced by Sterio in 1984, which we modified into a stack of serial sections. The mean number NL of cells per unit airway length and the mean volume Vc of a single muscle cell were also determined. In Type I asthmatics, the number of cells increased in the larger bronchi unaccompanied by cellular hypertrophy at any level of the airway tree. In contrast, in Type II asthmatics, hypertrophy was shown to prevail over the whole airway, but it was most remarkable in the bronchioles, whereas hyperplasia was mild and localized only in the bronchi. The two types of asthmatic lungs may therefore result from different pathogeneses.

Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity

We describe a simple algorithm for computing a homology score for Escherichia coli promoters based on DNA sequence alone. The homology score was related to 31 values, measured in vitro, of RNA polymerase selectivity, which we define as the product KBk2, the apparent second order rate constant for open complex formation. We found that promoter strength could be predicted to within a factor of +/-4.1 in KBk2 over a range of 10(4) in the same parameter. The quantitative evaluation was linked to an automated (Apple II) procedure for searching and evaluating possible promoters in DNA sequence files.

MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers

A computer program package called MEGA has been developed for estimating evolutionary distances, reconstructing phylogenetic trees and computing basic statistical quantities from molecular data. It is written in C++ and is intended to be used on IBM and IBM-compatible personal computers. In this program, various methods for estimating evolutionary distances from nucleotide and amino acid sequence data, three different methods of phylogenetic inference (UPGMA, neighbor-joining and maximum parsimony) and two statistical tests of topological differences are included. For the maximum parsimony method, new algorithms of branch-and-bound and heuristic searches are implemented. In addition, MEGA computes statistical quantities such as nucleotide and amino acid frequencies, transition/transversion biases, codon frequencies (codon usage tables), and the number of variable sites in specified segments in nucleotide and amino acid sequences. Advanced on-screen sequence data and phylogenetic-tree editors facilitate publication-quality outputs with a wide range of printers. Integrated and interactive designs, on-line context-sensitive helps, and a text-file editor make MEGA easy to use.