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PubMed2006

Managing and mining protein crystallization data.

The crystallization of macromolecules remains a major bottleneck in structural biology. The routine screening of more than one thousand crystallization conditions and subsequent optimization by fine screening presents a challenge to conventional laboratory notebook keeping. In addition, the development of high-throughput robotic crystallization and imaging systems presents a pressing need for low-cost laboratory information management system (LIMS). Here we describe CLIMS2, a crystallization LIMS that features a simple, user-friendly graphical interface, allowing the storage, management, retrieval and mining of crystallization data. The CLIMS2 executable and documentation is freely available at http://clims.med.monash.edu.au.

Computer Graphics↗
PubMed1997

Steps on the path to the origin of species.

The choice of Charles Darwin to serve as geologist on H.M.S. Beagle came about in a somewhat haphazard fashion, and by modern standards his technical qualifications for the post were not strong. However, during the voyage he was exposed to a wider range of phenomena, both in geology and in natural history, than any previous scientist, and his innate qualities of enquiring critically with an open mind into the why and wherefore of every one of his observations enabled him to make very effective use of his experience. By the end of the voyage he had found himself ready to abandon the doctrine of the fixity of species, and a few months later he opened the first of the series of notebooks on "Transmutation of Species" in which he recorded his private thinking. He quite quickly arrived at the Principle of Natural Selection as a mechanism for the creation of new species, but the process of building up adequate evidence in support of his theory was a slow one, and more than 20 years had passed before his great work was finally ready for publication.

Animals↗
PubMed2000

Information Processing at Successive Stages of Decision Making: Need for Cognition and Inclusion-Exclusion Effects.

Levin and Jasper's (1995) phased narrowing technique for tracking changes in information usage across successive stages of the decision-making process was combined with Huneke's (1996) "pull-down menu" extension of Payne, Bettman, and Johnson's (1988) software package for generating measures of information processing. Because this technique provided considerable data for each individual subject at each stage, we were able to focus on individual differences in information processing across stages, most notably differences related to need for cognition (NC; Cacioppo & Petty, 1982). In a computerized information search and decision task, 60 college students were first asked to narrow their options for purchasing a notebook computer to form a consideration set and were then asked to make a final choice from this set. At the consideration set formation stage, half the subjects were instructed to adopt a mindset to include options while the other half were asked to exclude options. Especially in the inclusion condition where subjects showed greater narrowing of options, high NC subjects processed information in a more focused manner with greater depth and breadth than did low NC subjects, and the quality of their selections tended to be higher. There was no evidence of widespread shifts in strategy as individuals moved from set formation to final choice but, as a group, high NC subjects were more successful at adaptive decision making. Copyright 2000 Academic Press.

Journal Article↗
PubMed1990

Automated measurement of transplantable solid tumors using digital electronic calipers interfaced to a microcomputer.

Data collection for transplantable solid tumors has been automated with electronic digital calipers and a balance which have been coupled through an RS-232 interface to a microcomputer. BASIC programs handle data entry, calculations and data storage. A "PROTOCOL" program accepts keyboard input of sample name, notebook number, submitter and dose along with necessary information on tumor system, and then initial animal weights for treatment groups are sent from balance to computer. Data is stored as an ASCII file on floppy disks, and protocol reports are printed. When the test is to be measured, a "MEASURE" program prompts the user for keyboard entry of toxic deaths in each group. Then the computer requests input of width and length of tumors for each animal. These tumor dimensions are sent to microcomputer by pressing a button on the calipers. When a group is completed, final animal weights are sent from balance to microcomputer. Then tumor weights and percent inhibition as compared to appropriate control groups are calculated, and the data is appended to the file for that test. A hard copy is generated as tumors are measured, and reports including percent inhibition can be printed immediately after a test is measured. The data as an ASCII file is transferred via modem to mainframe computer, where another program transfers the information to a database management program. These automated procedures for tumor measurement save time and lessen the chance for error by eliminating manual recording of solid tumor dimensions and subsequent reentry of this data for calculation.

Animals↗
PubMed1991

A random allocation system with the minimization method for multi-institutional clinical trials.

This paper describes the random allocation system used to perform precise and rapid treatment assignments in multi-institutional clinical trials. This system is based on sophisticated randomization procedures, according to Pocock and Simon's minimization method and Zelen's method for institution balancing. The major advantage of randomized treatment assignments with this system is to balance treatment numbers for each level of various prognostic factors over the entire trial and at the same time balance the allocation of treatments within an institution. Therefore, the randomized treatment assignments by this system can prevent degrading of the statistical power of a particular treatment factor. This system is designed to run on a small-sized notebook computer and therefore can be set up beside a telephone for registration, without occupying a large space. At present, this system is conveniently being used in two clinical trials.

Algorithms↗
PubMed1996

Accuracy and precision of a new, portable, handheld blood gas analyzer, the IRMA.

OBJECTIVE: The accuracy and precision of the new IRMA (Immediate Response Mobile Analysis System, Diametrics, Inc., St. Paul, MN) handheld blood gas analyzer was compared with that of two benchtop blood gas analyzers. The IRMA consists of a notebook-sized machine and disposable cartridges, each containing a pH, a CO2 and an O2 electrode, and provides bedside (point-of-care) blood gas analysis. METHODS: A total of 172 samples (arterial and mixed venous) were obtained from 25 informed, consenting patients undergoing cardiopulmonary bypass. The pH, PCO2 and PO2 of each sample was determined on four blood gas analyzers: NOVA Statlabs Profile 5 (NOVA Biomedical, Waltham, MA), the ABL-50 (Radiometer, West Lake, OH), and two IRMA machines. Linear regression and bias +/- precision were determined, comparing each of the analyzers with the NOVA. RESULTS: All three machines showed a similar, high degree of correlation with the NOVA for pH, PCO2, and PO2. The bias and precision of the IRMA machines compared with the NOVA was similar to that of the ABL compared with the NOVA for pH (NOVA:ABL -0.005 +/- 0.011; NOVA:IRMA 1 = 0.0026 +/- 0.025; NOVA:IRMA 2 = 0.0021 +/- 0.025), for PCO2 (NOVA:ABL = -1.4 +/- 1.3 mmHg; NOVA: IRMA 1 = -1.3 +/- 1.9 mmHg; NOVA: IRMA 2 = -1.2 +/- 2.1 mmHg) and PO2 (NOVA:ABL = 3.6 +/- 21.1 mmHg; NOVA:IRMA 1 = 3.4 +/- 19.9 mmHg; NOVA:IRMA 2 = 6.3 +/- 20.9 mmHg). The bias found for pH, PCO2, and PO2 was not affected by extremes of temperature (range 25.5-40 degrees C) or hematocrit (range 11-44%) for any machine. CONCLUSIONS: The new technology incorporated in the IRMA blood gas analyzer provides results with an accuracy that is similar to that of benchtop analyzers, but with all of the advantages of point-of-care analysis.

Blood Gas Analysis↗
PubMed2005

An innovative and reliable way of measuring health-related quality of life and mental distress in the deaf community.

BACKGROUND: Structured assessment of quality of life and mental distress in deaf people is difficult for various reasons. This paper describes the development and reliability of an interactive computer-based assessment package for measuring quality of life and psychological distress in the deaf population. METHODS: The Brief version of the WHO Quality of Life (WHOQOL) Questionnaire, the 12-item General Health Questionnaire (GHQ-12) and the Brief Symptom Inventory (BSI) had been translated into sign-language and videotaped. A total of 236 members of the deaf community in Upper Austria participated by responding to a programme consisting of self-administered written and videotaped test-items presented to them on a notebook computer. The reliability of the various assessments was established on this large community sample. RESULTS: When reliability of the versions for the deaf was compared with that of written versions of the same measures in general population samples, it was found to be somewhat lower, although still in an acceptable range, for the WHO-QOL and the GHQ-12. For the BSI, the reliability was even higher than that of the general population. CONCLUSIONS: For deaf individuals whose preferred communication is sign language, quality of life and mental distress can be effectively and reliably assessed with the use of carefully translated and adapted common instruments.

Adult↗
PubMed2002

Resting respiration in dysphagic patients following acute stroke.

The aim of this study was to examine respiration characteristics at rest in healthy volunteers and patients with poststroke dysphagia, using a simple notebook computer-based system. Eighteen patients (age range=51-82 years) with dysphagia poststroke and 50 healthy volunteers (age range=20-78 years) were recruited. The patient group had a wide range of stroke severity as assessed using the Scandinavian Stroke Score (SSS 6-51) and Barthel Index (BI 2-20). Length of breathing cycle, rate, and a measure of the variability of the cycle length were examined. The patient group had a shorter mean cycle length (2.93 s compared with 3.91 s, p < 0.01) and hence faster respiration rate (0.35 Hz compared with 0.26 Hz, p < 0.01). The control group showed greater variability in the cycle length (10.78% compared with 6.56%, p = 0.01). There was no correlation between the SSS and BI and resting respiration variables. This suggests that it is not stroke severity alone that affects breathing. The differences observed in resting respiratory rate suggest that respiratory monitoring as a useful adjunct to the clinical bedside assessment warrants further investigation.

Aged↗
PubMed2002

Swallow respiration patterns in dysphagic patients following acute stroke.

The aim of this study was to examine swallow respiratory characteristics using a notebook computer system. A relatively simple system assessing easily identifiable features is more likely to be incorporated into everyday clinical practice. Eighteen patients (age range = 51-82 years) with dysphagia poststroke and 50 healthy volunteers (age range = 20-78 years) were recruited. The patient group was less likely to always breathe out postswallow on water (9/15 cf 46/49), and some did not breathe out immediately postswallow at all (3/15 cf 0/49, p < 0.01). The pattern was similar with yogurt. Multiple swallowing was identified in the patient group and surprisingly with a large number of the volunteers for all bolus types but was more common in the patient group (p < 0.01). This trait is usually attributed to impaired swallows; that it is prevalent in the normal population has implications for using it as a dysphagia marker in clinical assessments. Yogurt has intrinsic features that increase multiple swallowing and caution should be used when identifying an impairment based on multiple swallowing with such a test substance. In the control group there was a high correlation of swallow apnea on 5 mL of water compared with 20 mL of water (r = 0.759, p < 0.01) and 5 mL of yogurt (r = 0.871, p < 0.01), indicating a possible individual swallow respiration pattern. This was also evident in the patient group. No significant difference in length of swallow apnea was found between the two groups. No evidence was found to link swallow respiration characteristics with aspiration as identified on simultaneous videofluoroscopy. The patient group had a wide range of impairments which suggests that stroke severity is not the sole determinant of swallow respiratory changes.

Aged↗
PubMed2001

Real-time display of the stomach slow wave and its parameters in a newly designed electrogastrographic system.

We designed a new three-channel electrogastrographic (EGG) system, which was easily operated on the Windows 95 platform and could automatically provide slow wave parameters. The purpose of the present study was to test its reliability and accuracy in clinical recording. The system included a signal acquisition device assembled on a printed circuit board. Recorded myoelectrical signals were filtered, amplified, digitized, and transmitted via this device into a notebook personal computer (PC). Based on the short-term Fourier transform the software could transfer the time domain of the signal into the frequency domain. Real-time displayed slow wave parameters, including dominant frequency/power, percent of normal frequency (2-4 cpm), instability coefficient in frequency/power, and power ratio, were automatically renewed every 64s. Twenty healthy subjects (M/F, 12/8; age, 23-51 years) were enrolled to measure both fast and postprandial myoelectrical activities for each 30-min recording. Our results indicated that meal ingestion significantly increased dominant frequency (3.15+/-0.20 vs 3.23+/-0.23 cpm; P < 0.05) and power (26.1+/-3.8 vs 28.4+/-3.9 dB; P < 0.05). The power ratio of the meal effect was 2.02+/-2.07. Other parameters, including instability coefficient and percent of normal frequency, remained similar despite food ingestion. This newly designed EGG system is acceptable for clinically measuring gastric myoelectrical activity; the real-time display of many EGG parameters is an advantage with this new system.

Adult↗
PubMed2003

Finger drawing by infant chimpanzees ( Pan troglodytes).

We introduced a new technique to investigate the development of scribbling in very young infants. We tested three infant chimpanzees to compare the developmental processes of scribbling between humans and chimpanzees. While human infants start to scribble on paper at around the age of 18 months, our 13- to 23-month-old infant chimpanzees had never been observed scribbling prior to this study. We used a notebook computer with a touch-sensitive screen. This apparatus was able to record the location of the subjects' touches on the screen. Each touch generated a fingertip-sized dot at the corresponding on-screen location. During spontaneous interactions with this apparatus, all three infants and two mother chimpanzees left scribbles with their fingers on the screen. The scribbles contained not only simple dots or short lines, but also curves and hook-like lines or loops, most of which were observed in the instrumental drawings of adult chimpanzees. The results suggest that perceptual-motor control for finger drawing develops in infant chimpanzees. Two of the infants performed their first scribble with a marker on paper at the age of 20-23 months. Just prior to this, they showed a rapid increase in combinatory manipulation of objects. These findings suggest that the development of combinatory manipulation of objects as well as that of perceptual-motor control may be necessary for the emergence of instrumental drawing on paper.

Animals↗
PubMed1996

Information technology in diabetes care 'Diabeta': 23 years of development and use of a computer-based record for diabetes care.

In this article we have stressed that a diabetes care information system should be useful to, usable and actually used by carers at the point of patient contact. Information resulting from such encounters should, at no extra cost, furnish the needs of communication, audit, research and management. Diabeta is a clinical record system for supporting the management of patients with diabetes. It has grown 'organically' within an academic clinical unit over a period of 23 years. It is used for each and every encounter with the clinicians in our diabetes team and as such, contains an immense amount of objective clinical experience. This experience can be interrogated very easily by computer-naive clinicians using a remarkable interactive program ('Datascan') which contains statistical procedures 'embedded' in the APL computer code, eliminating the need to 'export' the data into a statistical package. The latest PC-based version is incredibly fast and this immense amount of clinical experience can be carried around on a notebook PC and be available for exploration at any time. This makes 'evidence-based medicine' available in a remarkably flexible way since it shares the accumulated objective experience of literally 'dozens' of clinicians over a period which now extends to 23 years. It adds a completely new dimension to the term 'clinical experience' and is unattainable with manual records. It would be naive to assume that such systems are easy to design, build or implement, or that the initial capital outlay required will be small although costs are falling continuously. Medicine is a highly complex activity, the essential basis of which is human interaction. Introduction of a technology into this interaction requires sensitivity to the wishes and requirements of individuals, and protection of their exchanges from third parties. The potential of computers in diabetes care is so great that these issues must be addressed through continuing research, development, evaluation and funding of new systems. This must be led by the medical profession not the computer industry.

Ambulatory Care↗
PubMed1995

Interactive database management (IDM).

Interactive database management (IDM) is a data editing software that provides complete data editing at the time of initial data entry when information is 'fresh at hand'. Under the new interactive system, initial data recording is subjected to instant data editing by the interactive computer software logic. Data are immediately entered in final form to the database and are available for analysis. IDM continuously checks all variables for acceptability, completeness, and consistency. IDM does not allow form duplication. Many functions including backups have been automated. The interactive system can export the database to other systems. The software has been implemented for two Department of Veterans Affairs Cooperative Studies (CCSHS #5 and CSP #385) which collect data for 1400 and 1000 variables, respectively at 28 VA medical centers. IDM is extremely user friendly and simple to operate. Researchers with no computer background can be trained quickly and easily to use the system. IDM is deployed on notebook microcomputers making it portable for use anywhere in the hospital setting.

Clinical Trials as Topic↗
PubMed1991

A computer-aided control, design and image-processing system for electron microscopes.

A computer-control system for electron microscopes is described. The aim is to reduce a complex series of vacuum-system controls to a menu-driven program that simplifies the operation of the microscope. The system also incorporates image processing, notebook, computer-aided design, and communication functions. It is designed around a commercially available computer workstation. This system has been implemented on an institute-built photoelectron microscope of ultrahigh-vacuum design.

Computer Graphics↗
PubMed1983

Construction of a simple spike counter for analysis of electrophysiological recording data.

A method for constructing a simple spike counter from a conventional calculator by taking advantage of the "adding display to memory" function [(M+) key] is described. The modification involves connecting the (M+) key to a dissecting pin and to a metallic notebook binder which is taped on to a transparent plastic sheet. The plastic sheet can then be placed on top of a polygraph record. After entering "1" into the calculator, a spike can be counted by making a single contact between the pin and the metal fastener. The total number of spikes counted can be displayed on the calculator by pressing the key for memory recall. The spike counter described herein is suitable for counting extracellular action potentials recorded on chart paper as well as other biological signals such as the rate of contraction of muscle.

Animals↗
PubMedDate not supplied

Development of a computer-based battery designed to screen adults for neuropsychological impairment.

The initial step in the development of a new computer-based neuropsychological testing system is described. A new hardware-software system and a screening battery consisting of an orientation task and five cognitive tests has been implemented. This novel screening battery is designed for use in identifying individuals among exposed groups who may require more extensive follow-up neuropsychological evaluation. Sophisticated, but currently available, and relatively inexpensive hardware and software technology are employed, introducing an improvement over existing computer-based batteries. Use of a digitized speech production device for producing instructions facilitates testing of illiterate subjects, use of auditory stimulus materials, and relatively easy translation of the testing instructions to other languages. Use of a pen-based notebook computer enables responding by the subject in a manner that is both natural and analogous to that used in existing paper-and-pencil testing instruments. Five neuropsychological tests were developed to cover a range of cognitive domains: 1) verbal list learning and recognition memory, 2) visual memory span, 3) conceptual and motor tracking, 4) psychomotor speed and accuracy, and 5) delayed verbal recognition. The screening instrument has been pilot-tested for feasibility of use among outpatients at an occupational medicine clinic and among community-dwelling older adults. This instrument is intended to provide a standardized efficient, cost-effective method for widespread use in occupational medicine and public health to detect and track subclinical neurotoxic effects and to prevent additional harmful exposure. Additional aspects of development of the computer-based testing system are discussed.

Adult↗
PubMed1992

Implementation of a thermal biosensor in a process environment: on-line monitoring of penicillin V in production-scale fermentations.

The production of penicillin V was monitored in 0.5 m3 and 160 m3 bioreactors. The thermal biosensor was an enzyme thermistor modified for split-flow analysis. The heat signal generated in the enzyme column was corrected for any nonspecific heat with the use of an identical but inactive reference column. The on-line monitoring was performed in the fermentation pilot plant and in a fermentation plant of Novo Nordisk A/S. Immobilized beta-lactamase was used to monitor three consecutive 0.5 m3 penicillin fermentations. Broth samples were continuously filtered through a tangential flow filtration unit in a sterile external loop. The on-line penicillin V values were 10% higher than those obtained by off-line HPLC analysis. Alternatively a polypropylene filtration probe was inserted into a 160 m3 bioreactor and samples were withdrawn at 0.5 ml/min. The same experiments were repeated with purified and immobilized penicillin V acylase. The on-line penicillin V values obtained with this enzyme correlated very well with those from HPLC analysis. The on-line monitoring was controlled and analysed by a software program written in Labtech Notebook.

Biosensing Techniques↗
PubMed1989

The discovery of beta-galactosidase.

The enzyme beta-galactosidase was first mentioned in the literature by Beijerinck exactly a hundred years ago. The Department of Microbiology and Enzymology of the Delft University of Technology keeps the memory of Beijerinck, its first professor, alive by maintaining a 'Beijerinck-room' in the attic of the building. In addition to manuscripts and laboratory notebooks, this room contains some of his chemicals and biological preparations, and it was here that we recently found a 90-year old lactase preparation. Even after storage under suboptimal conditions, the preparation still exhibited measurable enzyme activities.

Galactosidases↗