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A system for quantitative analysis of associative learning. Part 2. Real-time software for MS-DOS microcomputers.

Microcomputer software was designed and used to control the timing and delivery of sensory stimuli and to acquire and analyze behavioral data during classical conditioning experiments. The software package runs under DOS 4.x through 6.x (earlier versions run under DOS 3.x) on PC AT-compatible microcomputers coupled with appropriate interface hardware (see Thompson et al., 1994). The software controls timed delivery of up to 8 conditional stimuli. It can collect behavioral data from 2 subjects simultaneously performing the same task (e.g., eyeblink responses) or from a single subject performing 2 different tasks (e.g., both eyeblink and conditional discrimination tasks), permitting its use in a number of experimental paradigms. Digital timing signals are adjustable for different stimulus output systems. Behavior is continuously monitored onscreen, ensuring consistent measurement across trials. Real-time performance measures of the presence or absence of conditioned responses allow coordination with external events (e.g., serum sampling, drug delivery, or single-unit recording). Quantitative measures are generated both for each trial and for complete sessions. Records are stored to disk and can be printed or merged for statistical analyses. Data can be archived on standard media, and internal software utilities translate files for export to PC and Macintosh programs. This system and the hardware described in the preceding paper combine ease of use with extremely replicable behavioral measurements across trials, sessions subjects, cohorts, and studies.

Animals↗

How quantitative is quantitative PCR with respect to cell counts?

Quantitative diagnostic PCR systems based upon rDNA targeted primer and probe combinations were developed for the detection of Escherichia coli, Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas alcaligenes, enterococci, Staphylococcus aureus, and Staphylococcus epidermidis. Primers and probes were designed in silico using the ARB software package (TU Munich) in combination with Primer Design software of PE Applied Biosystems. Purified genomic DNA or bacterial cells of target and reference organisms were used for the evaluation of the PCR assays applying the TaqMan technique on an ABI PRISM TM 7700 Sequence Detection System (PE Applied Biosystems). Sensitive, reliable and reproducible quantification of target rDNA could be achieved applying primer-probe combinations that mediate in vitro amplification of DNA fragments smaller than 100 base pairs. Large amounts of non target DNA (1 mg per sample) remarkably affected the quantification potential of the approach resulting in an underestimation of the amounts of target DNA. One of the principal goals was to use quantitative PCR to study the correlation of gene and cell numbers depending on the growth behavior of target organisms and to explore the potential to estimate cell numbers from target DNA quantification. A clear correlation of rDNA quantification and bacterial growth was observed, however, cell numbers cannot directly be estimated from quantitative PCR data, given that the cellular genome content varies with the growth phase of the organisms. In the case of Escherichia coli the cell numbers which could be assigned to a certain number of rDNA targets varied reasonably depending upon the growth phase of batch cultures.

Bacteria↗

Development of a portable closed-loop atracurium infusion system: systems methodology and safety issues.

Safety of closed-loop drug infusion systems is an issue often raised as a matter of concern. As a result, many closed-loop control systems are reported in the literature merely as computer simulation studies and few ever reach the stage of physical realisation and formal clinical evaluation. We address the safety issues involved with such systems by describing the development of a portable closed-loop control system for atracurium-induced muscle relaxation. This is a safety-critical system particularly when applied to brain and eye surgery where movement could have serious deleterious effects. The benefits of closed-loop muscle relaxation in providing stable surgical operating conditions over a wide range of patient sensitivities while infusing the minimum amount of drug makes this a worthwhile aim and serves to demonstrate safety issues which are generally applicable to other closed-loop drug infusion systems. It is hoped that the described methodology will facilitate and encourage the clinical application of closed-loop drug infusion systems so that clinical staff and patients may receive the benefits of closed-loop drug therapy.

Atracurium↗

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

Algorithms↗

Pericranial muscle tenderness and exteroceptive suppression of temporalis muscle activity: a blind study of chronic tension-type headache.

The aim of the present study was to examine the ability of pericranial muscle tenderness and the second exteroceptive suppression period to distinguish chronic tension-type headache sufferers, migraine sufferers, and controls in a young adult population utilizing a blind design. The second exteroceptive suppression periods were assessed using the methodology recommended by the European Headache Federation and were scored with an automated computer software program designed in our laboratory to provide reliable, standardized, and precise quantification of exteroceptive suppression periods and eliminate any influence of experimenter bias that may occur with manual scoring. Our sample consisted of 45 subjects diagnosed according to IHS criteria: 25 with chronic tension-type headache and 20 with migraine without aura. Twenty-three headache-free controls were recruited. Consistent with our previous findings, abnormalities in pericranial muscle tenderness, but not in the second exteroceptive suppression period distinguished chronic tension-type headache sufferers from controls. The chronic tension headache sufferers exhibited the highest pericranial muscle tenderness and the control group exhibited the lowest tenderness (P < .001). Pericranial muscle tenderness was quite successful in distinguishing recurrent headache sufferers from controls, but failed to distinguish chronic tension-type headache sufferers from migraineurs. Our findings raise the possibility that pericranial muscle tenderness is present early in the development of chronic tension-type headache and migraine without aura, and thus might contribute to the etiology of headache disorders. Our findings also indicate that a shortened second exteroceptive suppression period is not a reliable marker for chronic tension-type headache in young adults.

Adolescent↗

Improving software environments through usability and interaction design.

This paper introduces the fields of usability and interaction design in order to highlight their benefits and provide further resources for those that wish to find out more. It is hoped that this review will encourage medical illustrators to adopt certain principles and practices in their own project work, in order to strive towards (and ultimately produce) products and environments that provide more positive interactions for their users. Usability and interaction design are fields of study concerned with aims relating to ensuring that any given interactive product or environment is efficient, effective and safe to use, as well as easy to learn and remember. Of primary importance is the experience of the user whose interactions should be positive, as opposed to frustrating or counter-intuitive.

Equipment Design↗

Principles of web site development and design: powerful educational tools.

Setting up an educational Web site is easy and is a huge benefit to the nursing profession. Although Web sites may radically differ in their audiences and intent, the principles behind a great site are the same. This article provides basic information, terminology, and advice on how to create effective Web sites using concepts of Web design and Web publishing.

Computer Communication Networks↗

M3S: the local network for electric wheelchairs and rehabilitation equipment.

M3S is an open electric network standard for connecting rehabilitation equipment, especially electric modules in a wheelchair. It provides bidirectional communication at 250 kbaud via a CAN bus and extra safety lines for "Dead Man's Switch" and a TURN ON key. In an M3S system, the same input device may be used for controlling many different output devices in different operating modes. It provides flexible configuration tools for adapting the system for the individual user. M3S has been demonstrated and tested in more than ten different European development projects.

Electricity↗

Developing wearable bio-feedback systems: a general-purpose platform.

Microprocessors, even those in PocketPCs, have adequate power for many real-time biofeedback applications for disabled people. This power allows design of portable or wearable devices that are smaller and lighter, and that have longer battery life compared to notebook-based systems. In this paper, we discuss a general-purpose hardware/software solution based on industrial or consumer devices and a C++ framework. Its flexibility and modularity make it adaptable to a wide range of situations. Moreover, its design minimizes system requirements and programming effort, thus allowing efficient systems to be built quickly and easily. Our design has been used to build two brain computer interface systems that were easily ported from the Win32 platform.

Biofeedback, Psychology↗

Development of a computer information management system.

The Department of Veterans Affairs, Social Work Service has designed, developed and implemented the Social Work Information Management System (SWIMS) which provides for both administrative and clinical reporting. The system is clinically based and includes an option for case recording. The social work staff, who will use the system, was integrally involved in all phases of planning. The processes of the design, development, testing and implementation are discussed.

Database Management Systems↗

Database issues in object-oriented clinical information systems design.

A clinical information system (CIS) prototype was created from an Object-Oriented (OO) design. We experienced considerable difficulties when implementing the OO data model in a relational database management system (RDBMS), including lack of semantic power and support for complex objects, inability to encapsulate object methods, and performance degradation due to extensive join operations. This paper reflects on the experiences of a CIS research project and explores issues related to the use of RDBMS and Object-Oriented Database Management Systems (OODBMS) in CIS design and development.

Database Management Systems↗

Design of nutrient removal activated sludge systems.

A mechanistic mathematical model for nutrient and organic matter removal was used to describe the behavior of a nitrification denitrification enhanced biological phosphorus removal (NDEBPR) system. This model was implemented in a user-friendly software DESASS (design and simulation of activated sludge systems). A 484-L pilot plant was operated to verify the model results. The pilot plant was operated for three years over three different sludge ages. The validity of the model was confirmed with data from the pilot plant. Also, the utility of DESASS as a valuable tool for designing NDEBPR systems was confirmed.

Bioreactors↗

A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection.

Separation of complex mixtures of proteins by two-dimensional gel electrophoresis (2-DE) is a fundamental component of current proteomic technology. Quantitative analysis of the images generated by digitization of such gels is critical for the identification of alterations in protein expression within a given biological system. Despite the availability of several commercially available software packages designed for this purpose, image analysis is extremely resource intensive, subjective and remains a major bottleneck. In addition to reducing throughput, the requirement for manual intervention results in the introduction of operator subjectivity, which can limit the statistical significance of the numerical data generated. A key requirement of image analysis is the accurate definition of protein spot boundaries using a suitable method of image segmentation. We describe a method of spot detection applicable to 2-DE image files using a segmentation method involving pixel value collection via serial analysis of the image through its range of density levels. This algorithm is reproducible, sensitive, accurate and primarily designed to be automatic, removing operator subjectivity. Furthermore, it is believed that this method may offer the potential for improved spot detection over currently available software.

Algorithms↗

Software standards improve flow of information.

Many healthcare organizations buy their microcomputers and software packages in a piece-meal fashion. As a result, single microcomputers cannot share information with other microcomputers, networks, or the central computer system. Designating compatible software packages and machines as standards for the institution ensures that hardware and software can communicate. These standards should be implemented across the institution and regularly updated so that users' needs are met.

Computer Communication Networks↗