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PubMed1997

Effects of season, herd size, and geographic region on the composition and quality of milk in the northeast.

Our objectives were to describe the milkshed comprising herds in New York, western New Jersey, and central and eastern Pennsylvania in regard to milk yield, composition, and quality and also to estimate the effects of season, herd size, and geographic area on those same variables. Data were collected from July 1993 through June 1994 from 3450 herds. The effect of a somatic cell count (SCC) limit of 500,000/ml on milk yield and the composition of monthly bulk tank milk for all marketed milk was estimated as was the frequency of deliveries of milk that contained SCC that were greater than this limit. All general linear models for mean monthly yield of milk and milk components (fat and protein) and SCC were significant for fixed effects of month and herd size within quartiles for herd size (defined by the number of lactating cows) and significant absorbed effects of herds within quartiles for herd size within subregion. Milk yield, milk components (kilograms), true protein percentage, and SCC were significantly higher in spring than in fall for both data files (complete data file and data file containing only herds with SCC < 500,000/ml). Thirty-five percent of herds with < 27 lactating cows but only 15.3% of herds with > 62 lactating cows had > or = 1 mo with an SCC > 500,000/ml. For herds in the subregions, percentages of shipments with an SCC > or = 500,000/ml ranged from 10.5 to 20.2%. Herds with < 27 lactating cows contributed to the milkshed a disproportionate percentage of SCC (11%) compared with their percentage of contribution of milk (5%).

Animals↗

PubMed1994

Availability of nuclear decay data in electronic form, including beta spectra not previously published.

The unabridged data used in preparing ICRP Publication 38 (1983) and a monograph of the Medical Internal Radiation Dose (MIRD) Committee (Weber et al. 1989) are now available in electronic form. The "ICRP38 collection" contains data on the energies and intensities of radiations emitted by 825 radionuclides (those in ICRP Publication 38 plus 13 from the MIRD monograph), and the "MIRD collection" contains data on 242 radionuclides. Each collection consists of a radiations data file and a beta spectra data file. The radiations data file contains the complete listing of the emitted radiations, their types, mean or unique energies, and absolute intensities for each radionuclide. The beta spectra file contains, for each beta-emitting radionuclide, the probability that a beta particle will be emitted with kinetic energies defined by a standard energy grid. Although summary information from the radiations data files has been published, neither the unabridged data nor the beta spectra have been published. These data files and a data extraction utility, which runs on a personal computer, are available from the Radiation Shielding Information Center at Oak Ridge National Laboratory.

Databases, Factual↗

PubMed1992

[Management of personal health examination data for a population by use of a portable computer].

A new system was developed for processing annual personal health examination data with a portable microcomputer utilizing commercial software by converting the IBM formatted data file of the law mandated health examination for adults into an MS-DOS file. The sequential data file was further transferred into a random access data file by a simple program and software was developed for the presentation of annual personal data by table and graphs. Printout of data and selected comments filed on disc by the public health nurse or physician could become retrievable. This system is easily operated by a beginner in micro-computers from conversion of the original data to actual demonstration. This system was utilized for a small village of about 700 adults. By using part of the main memory as a RAM disc, presentation of 5 years' data was possible. File capacity was dependent on population size and also on the type of software for Japanese language input. In the case of a larger population, use of hard disc or expansion of memory may be recommended to shorten computer start-up time. Once necessary data has been placed into the field buffer's memory, retrieval of data requires less than one second. The results of health examination were usually provided by hard copies to village. But by use of this system, a more effective transfer of data between computerized systems by using a floppy disc is possible.

Humans↗

PubMedDate not supplied

The use of machine learning program LERS-LB 2.5 in knowledge acquisition for expert system development in nursing.

LERS-LB (Learning from Examples using Rough Sets Lower Boundaries) is a computer program based on rough set theory for knowledge acquisition, which extracts patterns from real-world data in generating production rules for expert system development. From LERS-LB evaluation of an SPSS-X data file containing data for recovery room patients, it was concluded that both statistical data files and existing databases can be converted to decision-table format needed by LERS-LB, but it is less desirable to work with statistical files than a well-developed database. It was also concluded that choosing a well-developed database and checking it thoroughly for accuracy and completeness should be done before running LERS-LB, or other learning programs, to avoid problems with data errors. Using rough set theory and a technique called 'dropping conditions' LERS-LB offers, at least in theory, a possible method for identifying which data items are critical to nursing practice. Further research and continued LERS-LB program enhancements still may help with identifying critical data items versus redundant data for nursing practice. LERS-LB, and other learning programs, offer techniques which will help reduce the knowledge acquisition bottleneck in nursing expert system development. It is doubtful, however, that learning programs will eliminate the need for involving domain experts in evaluating rules and expert systems for clinical decision support.

Artificial Intelligence↗

PubMed2001

CT data storage reduction by means of compressing projection data instead of images: feasibility study.

The authors developed and evaluated a technique of compressing raw projection data at computed tomography (CT). Raw projection data acquired at CT were compressed and decompressed and then used for image reconstruction. For comparison, original images were compressed by comparable ratios. Projection data files were more compressible than image files. Projection data compression is a promising, efficient method to reduce data file size and thus to facilitate retrospective image reconstruction.

Algorithms↗

PubMed2000

Nuclear-labeling index analysis (NLIA), a software package used to perform accurate automation of cell nuclear-labeling index analysis on immunohistochemically stained rat liver samples.

The nuclear labeling index (labeled nuclei/100 nuclei) and the apoptotic index (apoptotic cells/100 cells) are important parameters of cell growth and death. Automatic counting of labeled nuclei is desirable since manual counting is tedious, time-consuming, and with a greater potential for inaccuracies. A nuclear-labeling index analysis (NLIA) software package was developed in this laboratory to perform the counting process automatically and accurately. This software package consists of an application program NLIA and a set of macros for obtaining nuclear data that is used in Scion Image. It is designed to work cooperatively with Scion Image, Adobe Photoshop, and Microsoft Office. NLIA has two basic functions: building nuclear data files and analyzing nuclear data. A color image captured from an immunohistochemically stained or autoradiographic sample is loaded into NLIA. Nuclear data can be entered into the program manually, automatically, or in combination. In the manual data entering mode, NLIA acts as an object-counting tool, while in the automatic mode it acts as a data picker: picking up the data generated by Scion Image into memory. A method to enter nuclear data (both labeled nuclei and unlabeled nuclei) in the automatic mode is described. The color image is processed in Adobe Photoshop, where the interested color ranges are selected and separated. These are then analyzed in Scion Image with the help of the macros for obtaining nuclear data. Since the advanced particle analysis function is used, the counting process is automatic and rapid. Data from thousands of nuclei can be obtained within seconds. To ensure the accuracy of the analysis, a nuclear data checking and edit feature is employed in NLIA: results of computer-generated counting can be compared with the original color image by overlaying the plot of counting results onto the original color image. In this way any computer counting mistakes can be easily discovered and corrected by the operator. Corrected nuclear data (including nuclear size, location, shape) are then stored in data files. These data files can be used in NLIA to obtain cell density and nuclear labeling indices. Because criteria for obtaining nuclear data (truncation diameter, shape factor) can be set by the operator in NLIA, nuclear size distribution and shape variation can be analyzed. This method provides a fast and accurate way to determine cell nuclear-labeling indices. Currently, Scion Image is a freeware on the internet, and NLIA software package is available from our lab home page. Methods presented here expand the Scion Image ability to analyze color images by using color separation techniques in a commercial graphic application. The instrumentation required can be relatively inexpensive, and the methods described may be useful in studies of cell kinetics, lesion growth, and tumor therapy.

Animals↗

PubMed2004

A low-cost digital filing system for echocardiography data with MPEG4 compression and its application to remote diagnosis.

The high cost of digital echocardiographs and the large size of data files hinder the adoption of remote diagnosis of digitized echocardiography data. We have developed a low-cost digital filing system for echocardiography data. In this system, data from a conventional analog echocardiograph are captured using a personal computer (PC) equipped with an analog-to-digital converter board. Motion picture data are promptly compressed using a moving pictures expert group (MPEG) 4 codec. The digitized data with preliminary reports obtained in a rural hospital are then sent to cardiologists at distant urban general hospitals via the internet. The cardiologists can evaluate the data using widely available movie-viewing software (Windows Media Player). The diagnostic accuracy of this double-check system was confirmed by comparison with ordinary super-VHS videotapes. We have demonstrated that digitization of echocardiography data from a conventional analog echocardiograph and MPEG 4 compression can be performed using an ordinary PC-based system, and that this system enables highly efficient digital storage and remote diagnosis at low cost.

Analog-Digital Conversion↗

PubMed1994

Association of deficiency of uridine monophosphate synthase with production and reproduction.

Interaction between genotype at locus for uridine monophosphate synthase and parity was reexamined for 305-d mature equivalent milk and fat production and calving interval. Three lactations for cows of known genotype defined two data files corresponding to different sampling procedures. The first data file selected by herd contained records on 23 cows that were deficient in activity of uridine monophosphate synthase and on 1081 cows with normal activity; the second data file contained records on 19 cows with deficient activity and on 17 cows with normal activity, all daughters of bulls known to be heterozygous at the locus for uridine monophosphate synthase. Results from the mutually exclusive data files were determined independently and then pooled. Genotype and parity interaction, tested against mean square error, was not supported for any of the three traits. Mean differences of the two genotypes, averaged across data files, were, for first, second, and third parities, respectively, 360, 568, and 299 kg for milk; 6, 9, and 8 kg for fat; and 22, 9, and 12 d for calving interval. Main effect of genotype indicated a 417-kg advantage for heterozygotes but 17-d longer calving interval. The main effect of genotype on milk production adjusted for calving interval was 343 kg but was nonsignificant.

Animals↗

PubMed1995

Object-oriented approach to fast display of electrophysiological data under MS-windows.

Microcomputers provide neuroscientists an alternative to a host of laboratory equipment to record and analyze electrophysiological data. Object-oriented programming tools bring an essential link between custom needs for data acquisition and analysis with general software packages. In this paper, we outline the layout of basic objects that display and manipulate electrophysiological data files. Visual inspection of the recordings is a basic requirement of any data analysis software. We present an approach that allows flexible and fast display of large data sets. This approach involves constructing an intermediate representation of the data in order to lower the number of actual points displayed while preserving the aspect of the data. The second group of objects is related to the management of lists of data files. Typical experiments designed to test the biological activity of pharmacological products include scores of files. Data manipulation and analysis are facilitated by creating multi-document objects that include the names of all experiment files. Implementation steps of both objects are described for an MS-Windows hosted application.

Animals↗

PubMedDate not supplied

A method for detecting errors in data of growth studies.

The paper describes a new method used for data cleaning in growth and development studies. The method is essentially based on the assumption that an extreme value of a certain variable might be suspicious if other highly correlated variables show low compatibility with it and that, on the other hand, an extreme but possible value tends not to be erroneous if it is reinforced by another extreme but possible value of a highly correlated variable. Each variable was therefore included in at least two ratios with the highest correlated variables. A program was designed to detect extreme values of individual variables and extreme ratio values. This procedure with ratios was used to help to detect possible errors and discriminate them from true extreme values. Seen in the light of corrected data files against existing data files, the number of corrections was approximately 4.4%. If the real number of corrected errors is compared to the total number of subjects, this percentage reached 5.5%. If, when correcting, the real value was not detected with certainty, the erroneous value was then simply deleted. From our results, there is reason to believe that with this method few detectable errors will escape from the cleaning procedure. Conclusions for future correction procedures and for future growth studies in general, are also given in the paper.

Anthropometry↗

PubMed1990

[Study on the simulation in planning for orthognathic surgery by using a personal computer].

This study was made in order to develop and evaluate three-dimensional simulation programs in planning for orthognathic surgery by using microcomputer system. Microcomputer system is composed of CPU (NEC, PC-9801), high resolutional color display, color printer, image scanner, and MOUSE. This simulation is composed of four procedures. 1. Data input Three-dimensional coordinate data on tracing obtained from CT films is inputted. One data file is made from one outline of structures. 2. Three dimensional reconstruction A control file is made to arrange data files constructing structures. 3. Simulation This procedure is composed of cutting and movement. The horizontal projection of mandible is displayed. After cutting simulated orthognathic surgery is designed, new data files and new control file are made. A movement consists of parallel translation and rotation. A movement data is combined with movements designed on each of three projections. 4. Three-dimensional graphic display Three-dimensional graphics of the mandible before and after a simulation for orthognathic surgery are displayed by perspective views with treated hidden lines and accurate pictures (COSMOZONE 2SA, NIKON). These simulation programs were carried out with the asymmetrical patient. The simulation was supposed that the operation was combined with sagittal splitting osteotomy of the right mandibular ramus and body ostectomy of the left lower first premolar part. Three-dimensional graphics of the mandible before and after the simulation were presented. Its three-dimensional mandibular position and form after orthognathic surgery were predicted. These three-dimensional simulation programs may be important procedure, when a treatment planning in asymmetrical prognathic case is discussed.

Computer Graphics↗

PubMed1997

Transformation and average as handy tools for pressure measurement data analysis.

INTRODUCTION:: Pressure measurement data underneath[Table: see text] the foot represent usually a large number of data files which is equal to double product of the number of the subjects in study and of the number of the trials for each foot. Besides, 'normal' parameters are necessary to compare the results for the controls and for the subjects in study. Statistical parameters (mean values and standard deviations) are not very convenient when it is required to establish cartographical and geometrical parameters or peak pressures, maximum forces, contact areas, contact time and others for foot typing or as a standard. Sometimes it is reasonable to obtain average pressure data as a base for further data analysis. But taking into account that pressure distribution pattern may differ by its length, width and angle of the inclination of the foot axis to the horizontal it was necessary to solve a problem of transformation of any pressure picture to the given length and width (for vertical location of the foot axis). METHODS:: The transformed coordinates X(*) and Y(*) are defined from the following system of equations: X = Y(*) x width/width(*) x sina + X(*) x length/length(*) x cosa + X(o) Y = Y(*) x width/width(*) x cosa - X(*) x length/length(*) x sina + Y(o) where X(o), Y(o) -- the coordinates of the origin; width, length, a -- parameters of the initial pressure picture; width(*), length(*) -- parameters of the transformed pressure picture. X, Y -- are real values but the values of pressure are defined only in the integer coordinates. One of the main parts of average is a reduction of the time process to any number of frames. If N(max) is a maximum number of frames in one of the data files than all other data files must be transformed with accordance to the following formulas: for j-th frame the value of pressure for sensor with coordinates x, y is: P(*1)(xy) (j) = P(1)(xy) (i) x ki + P(1)(xy) (i+1) x k(i+1), where P(1)(xy) (i) -- pressure for sensor with coordinates x, y of the 1-th initial time process; j = 0, ellipsis, N(max) -1; j-th frame corresponds to i-th frame in the initial time process as i = integer(j) x (N -1)/(N(max) -1), N -- a number of frames in initial time process; coefficients k(i) and k(i+1) are equal to k(i) = j x (N -1)/(N(max) -1) -- I, k(i+1) = 1 - ki. Then the values of pressure are averaged: P(*)(xy) (j) = 1 / L x S P(1)(xy) (j), where L is a number of data files. Corresponding software was developed. RESULTS AND DISCUSSION:: 38 files of pressure measurement data of the teenagers from military school were chosen for transformation and average. Statistical errors of transformation and average were calculated for each data file (for peak pressure, force and area) and for all parameters from two software packages: Novel-win v.95.121 and Novel-ortho v.95.121. The maximum errors are for peak pressures (about 7%-10%) and contact areas (about 6%). CONCLUSION:: Transformation and average programs can be successfully used for data analysis additionally to traditional statistical software: groupmask evaluation program.

Journal Article↗

PubMed1985

PCS System I: point counting stereology programs for cell biology.

PCS System I (PCS) is a set of four software modules designed to simplify the application of stereology to problems in cell biology. It is written in BASIC for the Tektronix 4052A microcomputer (Beaverton, OR). A Counting Module collects raw data counts in either a Density Mode (points, intersections, transections, profiles) or a Boundary Mode (intersections with complete nuclear profiles). This information is stored on tape or disk data files and can also be printed. Three analysis modules use data files created with the Counting Module. The Density Module uses Density Mode data files to calculate volume, surface, length, and numerical densities. The B Numerical Density Module uses both Boundary Mode and Density Mode data to calculate the means for the boundary, diameter, and surface area of a nuclear compartment. The mean nuclear surface area is then used with the nuclear surface density to estimate the nuclear numerical density, which, in turn, is used to calculate surface areas of membrane compartments in average cells and in 10(6) cells. The Format Module reformats raw data files for analysis with Tektronix statistical software.

Biometry↗

PubMed1992

A file format for the exchange of nuclear medicine image data: a specification of Interfile version 3.3.

Working Group 1 of the European project COST-B2 on quality assurance of nuclear medicine software has been concerned with the development of an appropriate mechanism for the transfer of nuclear medicine image data files between computer systems from different vendors. To this end a protocol based upon Report No. 10 of the American Association of Physicists in Medicine (AAPM) [1] was adopted. A previous publication [2] gave a specification (V3.2) for an intermediate file format with a list of key-value pairs for the header data associated with nuclear medicine image data files. This paper presents a revised specification for the intermediate file format and associated keys, now called V3.3, which has evolved from the experience in using the earlier version. It is hoped that the modifications proposed will improve the definition and usability of the file format as given in the earlier version.

European Union↗

PubMed1990

Parallel line analysis: multifunctional software for the biomedical sciences.

An easy to use, interactive FORTRAN program for analyzing the results of parallel line assays is described. The program is menu driven and consists of five major components: data entry, data editing, manual analysis, manual plotting, and automatic analysis and plotting. Data can be entered from the terminal or from previously created data files. The data editing portion of the program is used to inspect and modify data and to statistically identify outliers. The manual analysis component is used to test the assumptions necessary for parallel line assays using analysis of covariance techniques and to determine potency ratios with confidence limits. The manual plotting component provides a graphic display of the data on the terminal screen or on a standard line printer. The automatic portion runs through multiple analyses without operator input. Data may be saved in a special file to expedite input at a future time.

Data Interpretation, Statistical↗

PubMed2002

PDB Goodies--a web-based GUI to manipulate the Protein Data Bank file.

PDB Goodies is a web-based graphical user interface (GUI) to manipulate the Protein Data Bank file containing the three-dimensional atomic coordinates of protein structures. The program also allows users to save the manipulated three-dimensional atomic coordinate file on their local client system. These fragments are used in various stages of structure elucidation and analysis. This software is incorporated with all the three-dimensional protein structures available in the Protein Data Bank, which presently holds approximately 18 000 structures. In addition, this program works on a three-dimensional atomic coordinate file (Protein Data Bank format) uploaded from the client machine. The program is written using CGI/PERL scripts and is platform independent. The program PDB Goodies can be accessed over the World Wide Web at http://144.16.71.11/pdbgoodies/.

Computer Graphics↗

PubMed1990

The use of laboratory microcomputers to hold NMR data bases.

Computer-based data bases are essential tools for NMR spectroscopists working with complex mixtures such as tissue extracts. Algorithms are described which are easily implemented on a small laboratory microcomputer and which can be used to make, edit, and query personalized laboratory data files. The data are stored in a series of small files accessed by pointers to overcome inherent redundancy in the information. Performance times are tabulated for a BBC Model B microcomputer working in the BASIC language and using 5.25-in. floppy discs as virtual memory.

Algorithms↗

PubMed1996

Analysis of neuro-behavioral Discovery data on the Macintosh computer.

This paper describes a suite of routines using IgorPro, a powerful analysis and graphing software package for the Macintosh computer, to enhance the ability to analyze, manipulate, and display data recorded with the Discovery acquisition software marketed by DataWave Technologies. The routines are able to time-align fast and slow data channels, and are especially useful for analyses that involve both neural and behavioral data. The software was designed for eyeblink conditioning and vocalization experiments, but it can easily be used for analyzing other types of neurobehavioral data. The data are first prepared on the PC with routines that inspect the header of the data file and translate the data file into a compact binary format that can be read by IgorPro. An option is also available to splice out data from unnecessary portions of an intertrial interval. The new file is then put on the Macintosh computer for display and analysis by IgorPro. These routines enable both neural and behavioral data to be quickly and easily reduced, manipulated, and statistically and graphically summarized.

Analysis of Variance↗