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PubMed2004

Hemosoft: a new software for blood bank and apheresis management.

BACKGROUND: Blood banks (BB) generate large volumes of information relating to patients and blood products sometimes stored indefinitely. Today computers are the main keys used to manage this task. BB information systems are developed mainly to assist BB specialists. MATERIALS AND METHODS: We developed a new software, Hemosoft, in our blood bank. We have carried out a great deal of research into BB programs around the world in terms of program features. Using the latest technology, Hemosoft has been designed to run on a multi-user platform on the basis of a modular structure, and high security levels. RESULTS: Hemosoft's structural advantages are: (1) its modular structure and client/server architecture reduce initial hardware costs. (2) Relational database structure provides consistent and secure data access, (3) user-friendly graphical interface, (4) according to operational needs, Hemosoft can be expanded and transferred on to different platforms. As a MS Windows based program with graphical user interfacing, Hemosoft has all the functions and advantages of windows based applications. Barcode printing is available to ISBT 128 standard. Hemosoft's integrated modules are: blood donation, transfusion, product management, administrative follow-up, apheresis, stock management, staff-management, inter-center communication, statistics, archive, internet and video-conferencing systems, accounts, integration and security. CONCLUSION: It fulfills international transfusion medicine requirements, legislative measures and guidelines. We believe that Hemosoft is a high quality, competitive program developed to meet international standards. It is our hope that it will enforce transfusion medicine and blood banking nationwide.

Blood Banks↗

PubMed2005

Real-time software processing and audio reproduction of directional Doppler signals.

In ultrasound Doppler systems, directional signals are typically obtained by processing quadrature demodulated data with dedicated analog or digital circuits. In this paper, a software approach is proposed, that allows fully exploiting the reproduction and recording capabilities of low-cost personal computer sound cards and/or embedded chips. Forward/reverse signals are separated through a wideband Hilbert filter. No limitations are imposed on the input signal sample rate, which is matched to the standard output format of sound cards through a band-limited interpolation filter controlled in a feedback loop. The digital audio streaming is performed in real-time in a Windows-based application. The processed data are in a standard format compatible with real-time recording in waveform or compressed files, as requested in many research applications. Simulations and in vivo tests show a typical cross talk of -50 dB between forward and reverse components, with low latency time (39 ms) and central processing unit load compatible to currently available personal computers.

Equipment Design↗

PubMed2002

The food intake recording software system is valid among fourth-grade children.

OBJECTIVES: To assess the validity of the Food Intake Recording Software System (FIRSSt) against observation of school lunch and a 24-hour dietary recall (24hDR); and to test the effects of sequencing, observation and a hair sample as a bogus pipeline on accuracy of dietary report. DESIGN: Six-group design systematically varying sequence of self-report (FIRSSt vs 24hDR), observation of school lunch and hair sample as a bogus pipeline manipulation, with random assignment of participants. SUBJECTS/SETTING: 138 fourth-grade students in 2 elementary schools. MAIN OUTCOME MEASURES: Accuracy of reported food consumption was measured in terms of matches, intrusions, and omissions among the FIRSSt, 24hDR, and as observed at school lunch. Students also completed self-report of performance with FIRSSt. STATISTICAL ANALYSIS PERFORMED: t tests, Pearson correlations, analysis of variance, factor analysis. RESULTS: When compared with school lunch observation for one meal, FIRSSt attained 46% match, 24% intrusion and 30% omission rates, while a dietitian-conducted 24hDR obtained 59% match, 17% intrusion, and 24% omission rates. FIRSSt attained 60% match, 15% intrusion, and 24% omission rates against 24hDR for all meals in the previous day. There was no evidence of sequence of assessment affecting accuracy indicators, but there was a weak effect of school lunch observation on percent intrusions. Obtaining a hair sample reduced the omission rate for FIRSSt vs 24hDR and increased the match rate for 24hDR vs observation, thereby enhancing this as a bogus pipeline procedure. Children generally enjoyed completing FIRSSt. Hispanic children were more likely to report problems using FIRSSt. APPLICATIONS/CONCLUSIONS: FIRSSt is somewhat less accurate than a dietitian-conducted 24hDR. However, this lower-cost procedure provides a promising method for assessing diet among children. Observation of consumption at school lunch may be reactive and artificially increase agreement. Obtaining a hair sample as a bogus pipeline may be a valuable technique for enhancing the accuracy of dietary assessment among children.

Child↗

PubMed2002

Software tools for high-throughput analysis and archiving of immunohistochemistry staining data obtained with tissue microarrays.

The creation of tissue microarrays (TMAs) allows for the rapid immunohistochemical analysis of thousands of tissue samples, with numerous different antibodies per sample. This technical development has created a need for tools to aid in the analysis and archival storage of the large amounts of data generated. We have developed a comprehensive system for high-throughput analysis and storage of TMA immunostaining data, using a combination of commercially available systems and novel software applications developed in our laboratory specifically for this purpose. Staining results are recorded directly into an Excel worksheet and are reformatted by a novel program (TMA-Deconvoluter) into a format suitable for hierarchical clustering analysis or other statistical analysis. Hierarchical clustering analysis is a powerful means of assessing relatedness within groups of tumors, based on their immunostaining with a panel of antibodies. Other analyses, such as generation of survival curves, construction of Cox regression models, or assessment of intra- or interobserver variation, can also be done readily on the reformatted data. Finally, the immunoprofile of a specific case can be rapidly retrieved from the archives and reviewed through the use of Stainfinder, a novel web-based program that creates a direct link between the clustered data and a digital image database. An on-line demonstration of this system is available at http://genome-www.stanford.edu/TMA/explore.shtml.

Cluster Analysis↗

PubMed2003

Determination of dissociation constants of (4RS)-[4-carboxy-5,8,11-tris(carboxymethyl)-1-phenyl-2-oxa-5,8,11-triazatridecan-13-oic acid] in water and biological fluids by means of nuclear magnetic resonance spectroscopy and the DISCO software package.

The pK(A) values of (4RS)-[4-carboxy-5,8,11-tris(carboxymethyl)-1-phenyl-2-oxa-5,8,11-triazatridecan-13-oic acid] (BOPTA), a polyprotic molecule whose gadolinium complex is an important magnetic resonance imaging contrast agent for clinical use, have been determined in water, in physiologic solution (PS), in serum (S), and in cerebrospinal fluid (CSF), by means of 13C nuclear magnetic resonance spectroscopy data processed by a dedicated software package called DISCO. The aim of this study was to supply the BOPTA pK(A) values in media very similar to the in vivo environment and, consequently, to get a picture of the in vivo behavior of its Gd complex, whose thermodynamic stability is directly linked to the pK(A) values. The pK(A) values appeared to be almost equal both in D(2)O and in PS, while pK(1) and pK(5) values in CSF differ a little. In S, only pK(2) and pK(3) were calculated due to the narrow pH range used for data collection. However, these pK(A) values were found equal to those in the other media. These results represent the first direct spectroscopic evidence of a substantial invariability of BOPTA behavior in different media and they justify the extrapolation to biological fluids of the data obtained in water. The values also confirmed the high-quality performance of DISCO in calculating pK(A) values of polyprotic molecules in complex media.

Carbon Isotopes↗

PubMed2001

Java-based graphical user interface for MRUI, a software package for quantitation of in vivo/medical magnetic resonance spectroscopy signals.

This article describes a Java-based graphical user interface for the magnetic resonance user interface (MRUI) quantitation package. This package allows MR spectroscopists to easily perform time-domain analysis of in vivo/medical MR spectroscopy data. We have found that the Java programming language is very well suited for developing highly interactive graphical software applications such as the MRUI system. We also have established that MR quantitation algorithms, programmed in the past in other languages, can easily be embedded into the Java-based MRUI by using the Java native interface (JNI).

Algorithms↗

PubMed2001

ANTHEPROT: an integrated protein sequence analysis software with client/server capabilities.

Programs devoted to the analysis of protein sequences exist either as stand-alone programs or as Web servers. However, stand-alone programs can hardly accommodate for the analysis that involves comparisons on databanks, which require regular updates. Moreover, Web servers cannot be as efficient as stand-alone programs when dealing with real-time graphic display. We describe here a stand-alone software program called ANTHEPROT, which is intended to perform protein sequence analysis with a high integration level and clients/server capabilities. It is an interactive program with a graphical user interface that allows handling of protein sequence and data in a very interactive and convenient manner. It provides many methods and tools, which are integrated into a graphical user interface. ANTHEPROT is available for Windows-based systems. It is able to connect to a Web server in order to perform large-scale sequence comparison on up-to-date databanks. ANTHEPROT is freely available to academic users and may be downloaded at http://pbil.ibcp.fr/ANTHEPROT.

Algorithms↗

PubMed1998

A software package for non-invasive, real-time beat-to-beat monitoring of stroke volume, blood pressure, total peripheral resistance and for assessment of autonomic function.

The goal of the present study was to develop and evaluate algorithms for non-invasive, real-time, beat-to-beat monitoring of stroke index (SI), blood pressure (BP) and total peripheral resistance index (TPRI) which has a menu-driven interface, suitable for routine use by unskilled staff. In addition, it was our aim to include a meta-analysis for the evaluation of autonomic function derived from the above haemodynamic data. This includes spectral analysis of heart rate (HR), BP, SI and TPRI and the automatic calculation of baroreceptor reflex sensitivity. Impedance cardiography was used for beat-to-beat SI determination, Finapres corrected by an oscillometric blood pressure measurement (Dinamap) on the upper arm for beat-to-beat BP measurement. We demonstrate noise free recordings during physiological (head up tilt) and pharmacological intervention (alpha 1-, beta 2-adrenoreceptor agonists, insulin induced hypoglycemia). The newly developed software should prove valuable for physiological, pharmacological and clinical studies.

Adult↗

PubMed1995

Superimposed Image Analysis System (SIAS) software: a new approach to sperm motility assessment.

OBJECTIVE: To apply Superimposed Image Analysis System (SIAS) software (Delta Sistemi, Rome, Italy) to the objective analysis of sperm motility. DESIGN: To test a new procedure for sperm motility assessment based on image superimposition. RESULTS: The system can superimpose six sequential frames onto a monitor producing a final image with a motion effect similar to the multiple exposure photography method, but bypassing the film processing stage. Viewing the final image of a complete series of six superimposed frames allows the evaluation of the percentage of motile spermatozoa and their kinetic characteristics. Compared with multiple exposure photography, SIAS has the following main advantages: [1] the procedure is quick; [2] projecting the first frame alone allows the easy evaluation of sperm concentration; and [3] the system allows quick and easy analysis and measurement of each sperm trajectory frame by frame, thus avoiding misleading interpretations because of crossing sperm trajectories, collisions, and overlapping of motile spermatoza with round cells or immotile spermatozoa. CONCLUSIONS: Superimposed image analysis is a new approach to sperm motility assessment. It seems to be useful particularly in selected situations, such as oligozoospermia or in cases of increased round cell concentration. In these situations, SIAS can even serve as a support or an alternative to the computer-aided sperm analysis system widely used for objective sperm analysis.

Humans↗

PubMed2003

Software sensors for bioprocesses.

State estimation is a significant problem in biotechnological processes, due to the general lack of hardware sensor measurements of the variables describing the process dynamics. The objective of this paper is to review a number of software sensor design methods, including extended Kalman filters, receding-horizon observers, asymptotic observers, and hybrid observers, which can be efficiently applied to bioprocesses. These several methods are illustrated with simulation and real-life case studies.

Algorithms↗

PubMed2002

Computerized design of separation strategies by reversed-phase liquid chromatography: development of DryLab software.

The development of DryLab software is a special achievement in analytical HPLC which took place in the last 16 years. This paper tries to collect some of the historical mile stones and concepts. DryLab, being always subject to change according to the needs of the user, never stopped being developed. Under the influence of an ever changing science market, the DryLab development team had to consider not just scientific improvements, but also new technological achievements, such as the introduction of Windows 1.0 and 3.1, and later Windows NT and 2000. The recent availability of new 32-bit programming tools allowed calculations of chromatograms to be completed more quickly so as to show peak movements which result for example from slight changes in eluent pH. DryLab is a great success of interdisciplinary and intercontinental cooperation by many scientists.

Chromatography, High Pressure Liquid↗

PubMed1992

Implementation of a new DDDR algorithm for tachycardia prevention and treatment utilizing an implantable RAM-based software-controlled pacemaker.

Reentry within the atrioventricular node or over accessory pathways are common causes of symptomatic tachycardia. These arrhythmias are frequently initiated by a spontaneous atrial or ventricular premature beat. Appropriately timed atrial or ventricular extrastimuli can, in some patients, render one limb of the reentrant circuit refractory and prevent induction of tachycardia. Currently available implantable devices are not suitable for this application. The authors have implemented a new implantable pacing algorithm capable of extremely short atrial and ventricular refractory periods, rapid triggered ventricular pacing rates, protection against encroachment on the ventricular vulnerable period, protection against tachycardia induction by ventricular premature beats, automated antitachycardia pacing in either atrium and ventricle, as well as an extensive event storage capability. This application has been made possible by a new, RAM-based microprocessor controlled dual chamber pacemaker (Medtronic Prometheus Model 6100). Its use in intraatrial tachycardia with atrioventricular block as well as Wolff-Parkinson-White syndrome is demonstrated. This device is capable of prevention of tachycardia induction in some patients. Where prevention is not feasible or fails, it is backed up by automated or manually activated antitachycardia pacing. The great flexibility of a completely reprogrammable software based pacemaker has enabled the implementation of a very complex experimental pacemaker that will permit evaluation in the implanted setting of this new pacing strategy.

Algorithms↗

PubMed2003

New methods and software tools for high throughput CDR3 spectratyping. Application to T lymphocyte repertoire modifications during experimental malaria.

Immune repertoires of T or B cells are very often studied by Complementary Determining Region 3 (CDR3) spectratyping. However, data obtained with this method is usually subject to a biased eye analysis. We developed recently the ISEApeaks software package to retrieve and handle peak data from automated sequencers, from which CDR3 spectratype data is obtained. We describe a general strategy for CDR3 spectratype analysis based on two new specific modules and multivariate statistics. The first module addresses the crucial problem of peak smoothing. The second is a toolbox for the analysis of CDR3 spectratypes, which includes perturbation computation, recurrent peak finding, expansion assessment and datamining. To illustrate our approach, we assessed the complex TCRB repertoire modifications induced by Plasmodium berghei ANKA (PbA) infection. This global and exhaustive repertoire analysis approach is of general interest for T- and B-lymphocyte repertoire studies and is currently used in human cohorts in various pathologies and during clinical trials.

Algorithms↗

PubMed2002

Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated assignment of the NOESY spectra. CANDID uses an iterative approach with multiple cycles of NOE cross-peak assignment and protein structure calculation using the fast DYANA torsion angle dynamics algorithm, so that the result from each CANDID cycle consists of exhaustive, possibly ambiguous NOE cross-peak assignments in all available spectra and a three-dimensional protein structure represented by a bundle of conformers. The input for the first CANDID cycle consists of the amino acid sequence, the chemical shift list from the sequence-specific resonance assignment, and listings of the cross-peak positions and volumes in one or several two, three or four-dimensional NOESY spectra. The input for the second and subsequent CANDID cycles contains the three-dimensional protein structure from the previous cycle, in addition to the complete input used for the first cycle. CANDID includes two new elements that make it robust with respect to the presence of artifacts in the input data, i.e. network-anchoring and constraint-combination, which have a key role in de novo protein structure determinations for the successful generation of the correct polypeptide fold by the first CANDID cycle. Network-anchoring makes use of the fact that any network of correct NOE cross-peak assignments forms a self-consistent set; the initial, chemical shift-based assignments for each individual NOE cross-peak are therefore weighted by the extent to which they can be embedded into the network formed by all other NOE cross-peak assignments. Constraint-combination reduces the deleterious impact of artifact NOE upper distance constraints in the input for a protein structure calculation by combining the assignments for two or several peaks into a single upper limit distance constraint, which lowers the probability that the presence of an artifact peak will influence the outcome of the structure calculation. CANDID test calculations were performed with NMR data sets of four proteins for which high-quality structures had previously been solved by interactive protocols, and they yielded comparable results to these reference structure determinations with regard to both the residual constraint violations, and the precision and accuracy of the atomic coordinates. The CANDID approach has further been validated by de novo NMR structure determinations of four additional proteins. The experience gained in these calculations shows that once nearly complete sequence-specific resonance assignments are available, the automated CANDID approach results in greatly enhanced efficiency of the NOESY spectral analysis. The fact that the correct fold is obtained in cycle 1 of a de novo structure calculation is the single most important advance achieved with CANDID, when compared with previously proposed automated NOESY assignment methods that do not use network-anchoring and constraint-combination.

Algorithms↗

PubMed2000

A GPS logger and software for analysis of homing in pigeons and small mammals.

A detailed analysis of homing in pigeons and small mammals has remained difficult because the paths of the animals could not be reconstructed precisely. Here, we describe a lightweight global position system (GPS) data logger (35 g including battery and casing; 40 x 68 x 18 mm) that records the flight of pigeons and the path of dogs with an accuracy of +/-12 m. With one battery, the logger runs in continuous mode (1 fix/s) for 3.5 h and in power-saving mode (1 fix/5 s) for about 16 h, and stores a maximum of 100,000 data points that are downloaded to a PC. A module of our public domain software WINTRACK permits a detailed numerical and graphical analysis of path geometry, phases of resting and moving, and path similarity. The device can be adapted to different species provided that satellite signals can be received reliably and that the loggers can be recovered. We expect it to be useful for testing hypotheses about pigeon homing, assessing natural spatial behavior and orientation of many species, and anticipate further miniaturization.

Animals↗

PubMed2001

Extended analysis of path data from mutant mice using the public domain software Wintrack.

Animal tracking by means of videocameras has made considerable progress over the past several years and is now being used in a large number of studies. However, the precision and frequency at which xy path data can be recorded using personal computers contrast with the relative simplicity of the analyses commonly conducted with this type of data. In order to achieve more analytical power and flexibility in numerical and graphical path analysis, we have developed Wintrack, a Windows application that processes data from a variety of commercially available tracking systems. The application provides an intuitive drag-and-drop interface to increase ease and speed of standard analysis and graphical representation of data. A flexible scripting language allows the advanced user to extend the capabilities of the program by defining custom arenas and specialized parameters. For example, this permits to integrate path data with events recorded through the keyboard or to adapt the program for the processing of GPS data from outdoors experiments. A macro language allows for fully automated and database-controlled large-scale data analysis. We are using this feature to develop new analysis parameters for water maze and open-field experiments and to evaluate them retrospectively with reference data from several thousand mice tested in our laboratory. For noncommercial use, the software can be downloaded free of charge at www.dpwolfer.ch/wintrack.

Animals↗

PubMedDate not supplied

Actigraphic assessment of sleep in insomnia: application of the Actigraph Data Analysis Software (ADAS).

The usefulness of the actigraph methodology has been demonstrated in normal individuals. However, the validity of actigraphy has been questioned in insomnia patients because of the considerable measurement error that has been reported between actigraphy (ACT) and polysomnography (PSG). Two independent investigations have reported errors of 48 and 49 min in total sleep time between ACT and PSG. With a new scoring method called the Actigraph Data Analysis Software, a reanalysis of one of these studies was conducted. Based on this reanalysis, we have obtained a measurement error of only 25 min between the two methods. This finding may be an indication of the advantage of this new scoring method. A strong correlation coefficient (r = 0.82, p < 0.0001) was noted between ACT and PSG for total sleep time, thus suggesting a high degree of accuracy of the actigraph methodology in assessing the sleep/wake profile of insomniacs.

Arousal↗

PubMed2003

Predicting logP of pesticides using different software.

We compared experimental and calculated logP values using a data set of 235 pesticides and experimental values from four different sources: The Pesticide Manual, Hansch Manual, ANPA and KowWin databases. LogP were calculated with four softwares: HyperChem, Pallas, KowWin and TOPKAT. Crossed comparison of the experimental and calculated values proved useful, especially for pesticides. These are harder to study than simpler organic compounds. Structurally they are complex, heterogeneous and similar to drugs from a chemical point of view. They offer an interesting way to verify the goodness of the different methods. Other studies compared several logP predictors using a single set of experimental values taken as a reference. Here we discuss the utility of the different logP predictors, with reference to experimental data found in different databases. This offers three advantages: (1) it avoids bias due to the assumption that one single data set is correct; (2) a given predictor can be developed on the same data set used for evaluation; (3) it takes account of experimental variability and can compare it with the predictor's variability. In our study Pallas and KowWin gave the best results for prediction, followed by TOPKAT.

1-Octanol↗