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PubMed2004

Computerized symptom and quality-of-life assessment for patients with cancer part I: development and pilot testing.

PURPOSE/OBJECTIVES: To develop and test an innovative computerized symptom and quality-of-life (QOL) assessment for patients with cancer who are evaluated for and treated with radiation therapy. DESIGN: Descriptive, longitudinal prototype development and cross-sectional clinical data. SETTING: Department of radiation oncology in an urban, academic medical center. SAMPLE: 101 outpatients who were evaluated for radiation therapy, able to communicate in English (or through one of many interpreters available at the University of Washington), and competent to understand the study information and give informed consent. Six clinicians caring for the patients in the sample were enrolled. METHODS: Iterative prototype development was conducted using a standing focus group of clinicians. The software was developed based on survey markup language and implemented in a wireless, Web-based format. Patient participants completed the computerized assessment prior to consultation with the radiation physician. Graphical output pages with flagged areas of symptom distress or troublesome QOL issues were made available to consulting physicians and nurses. MAIN RESEARCH VARIABLES: Pain intensity, symptoms, QOL, and demographics. INSTRUMENTS: Computerized versions of a 0 to 10 Pain Intensity Numerical Scale (PINS), Symptom Distress Scale, and Short Form-8. FINDINGS: Focus group recommendations included clinician priorities of brevity, flexibility, and simplicity for both input interface and output and that the assessment output contain color graphic display. Patient participants included 45 women and 56 men with a mean age of 52.7 years (SD = 13.8). Fewer than half of the participants (40%) reported using a computer on a regular basis (weekly or daily). Completion time averaged 7.8 minutes (SD = 3.7). Moderate to high levels of distress were reported more often for fatigue, pain, and emotional issues than for other symptoms or concerns. CONCLUSIONS: Computerized assessment of cancer symptoms and QOL is technically possible and feasible in an ambulatory cancer clinic. A wireless, Web-based system facilitates access to results and data entry and retrieval. The symptom and QOL profiles of these patients new to radiation therapy were comparable to other samples of outpatients with cancer. IMPLICATIONS FOR NURSING: The ability to capture an easily interpreted illustration of a patients symptom and QOL experience in less than 10 minutes is a potentially useful adjunct to traditional face-to-face interviewing. Ultimately, electronic patient-generated data could produce automated red flags directed to the most appropriate clinicians (e.g., nurse, pain specialist, social worker, nutritionist) for further evaluation. Such system enhancement could greatly facilitate oncology nurses coordination role in caring for complex patients with cancer.

Academic Medical Centers↗

PubMed1999

5-Hydroxytryptamine and glutamate modulate velocity and extent of intercellular calcium signalling in hippocampal astroglial cells in primary cultures.

The effects of 5-hydroxytryptamine or glutamate treatment on mechanically induced intercellular calcium waves were studied in gap junction-coupled astroglial cells using rat astroglial-neuronal primary cultures from hippocampus. Imaging software was developed to study amplitude, velocity and extent of wave propagation. Velocity software was designed to find the cell contours automatically and to calculate travelled distance and time-delay of the calcium wave as it propagates from the stimulated cell to all other cells. Propagation analyses were performed to calculate the area of wave propagation. Mechanical stimulation of a single astroglial cell induced an intercellular calcium wave spreading from cell to cell in the astroglial syncytium. When registering the appearances of calcium signals in individual cells along the wave path upon re-stimulation of the same cell, 44.7% of the cells responded with similar calcium signal appearances the second time as the first time. A second wave from the opposite direction resulted in similar calcium signal appearances in 27.3% of the studied cells. Both amplitude and velocity of the calcium signal decreased most prominently in the first part and showed a later flattening out. Treatment with 5-hydroxytryptamine or glutamate for 20-30 s before mechanical stimulation increased the velocity of the calcium waves. 5-Hydroxytryptamine treatment for varying times decreased the propagation area of the calcium waves. In contrast, glutamate treatment increased the propagation area.

Animals↗

PubMed2000

Preoperative radiochemotherapy in locally advanced or recurrent rectal cancer: regional radiofrequency hyperthermia correlates with clinical parameters.

PURPOSE: Preoperative radiochemotherapy (RCT) is a widely used means of treatment for patients suffering from primary, locally advanced, or recurrent rectal cancer. We evaluated the efficacy of treatment due to additional application of regional hyperthermia (HRCT) to this conventional therapy regime in a Phase II study, employing the annular phased-array system BSD-2000 (SIGMA-60 applicator). The clinical results of the trial were encouraging. We investigated the relationship between a variety of thermal and clinical parameters in order to assess the adequacy of thermometry, the effectiveness of hyperthermia therapy, and its potential contribution to clinical endpoints. METHODS AND MATERIALS: A preoperative combination of radiotherapy (1.8 Gy for 5 days a week, total dose 45 Gy applied over 5 weeks) and chemotherapy (low-dose 5-fluorouracil [5-FU] plus leucovorin in the first and fourth week) was administered to 37 patients with primary rectal cancer (PRC) and 18 patients with recurrent rectal cancer (RRC). Regional hyperthermia (RHT) was applied once a week prior to the daily irradiation fraction of 1.8 Gy. Temperatures were registered along rectal catheters using Bowman thermistors. Measurement points related to the tumor were specified after estimating the section of the catheter in near contact with the tumor. Three patients with local recurrence after abdominoperineal resection, had their catheters positioned transgluteally under CT guidance, where the section of the catheter related to the tumor was estimated from the CT scans. Index temperatures (especially T(max), T(90)) averaged over time, cumulative minutes (cum min) (here for T(90) > reference temperature 40.5 degrees C), and equivalent minutes (equ min) (with respect to 43 degrees C) were derived from repetitive temperature-position scans (5- to 10-min intervals) utilizing software specially developed for this purpose on a PC platform. Using the statistical software package SPSS a careful analysis was performed, not only of the variance of thermal parameters with respect to clinical criteria such as toxicity, response, and survival but also its dependency on tumor characteristics. RESULTS: The rate of resectability (89%) and response (59%) were high for the PRC group, and a clear positive correlation existed between index temperatures (T(90)) and thermal doses (cum min T(90) >/= 40.5 degrees C). Even though the overall 5-year survival was encouraging (60%) and significantly associated with response, there was no statistically significant relationship between temperature parameters and long-term survival for this limited number of patients. However, nonresectable tumors with higher thermal parameters (especially cum min T(90) >/= 40.5 degrees C) had a tendency for better overall survival. We found even higher temperatures in patients with recurrences (T(90) = 40.7 degrees C versus T(90) = 40.2 degrees C). However, these conditions for easier heating did not involve a favorable clinical outcome, since surgical resectability (22%) and response rate (28%) for the RRC group were low. We did not notice any other dependency of thermal parameters to a specific tumor or patient characteristics. Finally, neither acute toxicity (hot spots) induced by hyperthermia or RCT nor perioperative morbidity were correlated with temperature-derived parameters. Only a higher probability for the occurrence of hot spots was found during treatment with elevated power levels. CONCLUSION: In this study with two subgroups, i.e., patients with PRC (n = 37) and RRC (n = 18), there exists a positive interrelationship between thermal parameters (such as T(90), cum min T(90) >/= 40,5 degrees C) and clinical parameters concerning effectiveness. Additional hyperthermia treatment does not seem to enhance toxicity or subacute morbidity. Procedures to measure temperatures and to derive thermal parameters, as well as the hyperthermia technique itself appear adequate enough to classify heat treatments in

Age Factors↗

PubMedDate not supplied

Computer-assisted analysis of three-dimensional MR angiograms.

The software tools required for postprocessing of magnetic resonance (MR) angiograms include the following functions: data handling, image visualization, and vascular analysis. A custom postprocessing software called Magnetic Resonance Angiography Computer Assisted Analysis (MARACAS) has been developed. This software combines the most commonly used three-dimensional visualization techniques with image processing methods for analysis of vascular morphology on MR angiograms. The main contributions of MARACAS are (a) implementation of a fast method for stenosis quantification on three-dimensional MR angiograms, which is clinically applicable in a personal computer-based system; and (b) portability to the most widespread platforms. The quantification is performed in three steps: extraction of the vessel centerline, detection of vessel boundaries in planes locally orthogonal to the centerline, and calculation of stenosis parameters on the basis of the resulting contours. Qualitative results from application of the method to data from patients showed that the vessel centerline correctly tracked the vessel path and that contours were correctly estimated. Quantitative results obtained from images of phantoms showed that the computation of stenosis severity was accurate.

Algorithms↗

PubMed2002

PGAAS: a prokaryotic genome assembly assistant system.

MOTIVATION: In order to accelerate the finishing phase of genome assembly, especially for the whole genome shotgun approach of prokaryotic species, we have developed a software package designated prokaryotic genome assembly assistant system (PGAAS). The approach upon which PGAAS is based is to confirm the order of contigs and fill gaps between contigs through peptide links obtained by searching each contig end with BLASTX against protein databases. RESULTS: We used the contig dataset of the cyanobacterium Synechococcus sp. strain PCC7002 (PCC7002), which was sequenced with six-fold coverage and assembled using the Phrap package. The subject database is the protein database of the cyanobacterium, Synechocystis sp. strain PCC6803 (PCC6803). We found more than 100 non-redundant peptide segments which can link at least 2 contigs. We tested one pair of linked contigs by sequencing and obtained satisfactory result. PGAAS provides a graphic user interface to show the bridge peptides and pier contigs. We integrated Primer3 into our package to design PCR primers at the adjacent ends of the pier contigs. AVAILABILITY: We tested PGAAS on a Linux (Redhat 6.2) PC machine. It is developed with free software (MySQL, PHP and Apache). The whole package is distributed freely and can be downloaded as UNIX compress file: ftp://ftp.cbi.pku.edu.cn/pub/software/unix/pgaas1.0.tar.gz. The package is being continually updated.

Algorithms↗

PubMed2004

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

Biochemistry↗

PubMed2001

[Pharmaceutical traceability integrated with the patient file. Development of a computerized hospital application].

The Clinical Pharmacy Department (CPD) of the Gustave Roussy Institute, has developed a traceability software package that is integrated with the patient file. The Traceability & Medical Devices Functional Unit manages the Blood Derivative Medicinal Product traceability circuits, the circuits of over 400 Sterile Medical Devices and, generally speaking, those for all pharmaceutical goods for which traceability is imperative. The SIMBAD-TRACE software package has been developed in situ and was first open for access in March 1999. It enables pharmaceutical traceability data to be accessed from 500 networked workstations. The references tracked generated about 10,000 movements per year. In terms of performance, the system achieves three complementary objectives: 1) reporting traceability scores which reflect the ability of CPD and the establishment to pertinently respond to a complex regulatory requirement on a daily basis; 2) the contribution of the tool to cost containment with respect to allocating rare goods; the contribution of the software package to the implementation of medical device vigilance inquiries, particularly descending inquiries. Finally, SIMBAD-TRACE is one of the pillars of our Quality Assurance Program (QAP).

Equipment and Supplies↗

PubMed2004

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.

BACKGROUND: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. RESULTS: We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficiently and accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solves the appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. CONCLUSIONS: We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

Algorithms↗

PubMed2002

Nuclear cardiology patient tracking using a palm-based device: methods and clinician satisfaction.

Handheld personal computers are popular, easy to use, inexpensive, portable, and can share data among different operating systems. In our institution, nuclear cardiology testing is performed in the nuclear medicine department and jointly reported by radiologists and cardiologists. The objective of this article is to describe a system for recording nuclear cardiology data and to assess clinician satisfaction using handheld computers with the Palm Operating System. We devised a Palm-based relational database/ using commercially available software (HanDBase) that requires minimal computer expertise to implement and maintain. Data are collected by the cardiologist and synchronized to a single central relational database compatible with Microsoft Access. We assessed cardiologists' satisfaction with this system. Cardiologists unanimously agreed that this system had a positive impact on patient management and cardiology fellow education. They were satisfied with ease of data input, sharing, retrieval, and clarity of data display. The cardiologist with the least experience in using the software took longer to input data and thought that it prolonged the nuclear cardiology rounds. The idea to develop this software was to ease data entry using shortcuts and lists, limiting data stored to that essential for patient management and also to transmit data easily between staff. The cardiologist with the most experience in using the software felt more comfortable and satisfied with it. This was perhaps due to his continuous involvement in the development of this system. Like any new system, there is a learning curve in using this software. The software was easy to customize, and support and tutorials were found on the manufacturer's Web site. The system of collecting data using handheld computers with the Palm Operating System is easy to use, relatively inexpensive, accurate, and secure. The user-friendly system provides prompt, complete, and accurate data, enhancing the education of fellows while facilitating the job of cardiologists.

Attitude of Health Personnel↗

PubMed2004

Decision support systems in nuclear emergencies: a scenario-based comparison of domestic and reference tools.

The article reports selective results of a comparison between RODOS-an emerging decision support system for the management of nuclear emergencies in Europe developed by an international research consortium under EEC aegis, and a resident software package developed and maintained for similar purposes at IFIN-HH, Bucharest. Reproducible similarity patterns obtained in the output data distributions provide for simple normalising procedures that may ensure convergent radiological assessments. When properly consolidated on a sufficient scenario casuistry, such procedures could lend a certain resilience to domestic decision support tools over the interim lead time required by the full implementation of RODOS, or other major league, internationally accepted reference systems.

Decision Support Techniques↗

PubMed2004

Diagnostic and prognostic use of DNA image cytometry in cervical squamous intraepithelial lesions and invasive carcinoma.

In the fight against cervical malignancy and its precursors, several adjuvant diagnostic methods have been proposed to increase the accuracy of cytologic and histologic diagnoses. Because chromosomal aneuploidy has been accepted as an early key event in tumorigenesis caused by genetic instability, the cytometric equivalent of chromosomal aneuploidy detected by DNA image cytometry (DNA-ICM) may serve as a marker of neoplasia. During the last decade, the appearance of a new generation of hardware with high processing and storage capacities, together with the development of appropriate software, has facilitated the development of high-performance DNA-ICM systems. International consensus on the clinical application of DNA-ICM has been reached. According to the statements of Task Force 8 of the International Consensus Conference on the Fight Against Cervical Cancer, indications for DNA-ICM include the identification of prospectively malignant cells in squamous intraepithelial lesions (SILs) and atypical squamous cells of undetermined significance (ASCUS). The European Society of Analytical Cellular Pathology consensus reports on DNA-ICM have provided standardized technical details on performance, terms, and algorithms for diagnostic data interpretation and quality-assurance procedures. Increasing biologic evidence and clinical data have confirmed the utility of DNA-ICM as an adjuvant method suitable for determining the diagnosis and prognosis of cervical intraepithelial lesions and invasive carcinoma. Patients with ASCUS and low-grade SIL diagnoses that reveal DNA euploidy may return for normal screening intervals, whereas the detection of DNA aneuploidy indicates that these lesions should be removed. Formerly a research tool, today, standardized DNA-ICM has become a useful and low-cost laboratory method to establish objectively and reproducibly an early diagnosis of prospectively progressive cervical intraepithelial lesions at a high-quality level. DNA-ICM may further contribute to the monitoring of treatment in patients with invasive cervical malignancies.

Adult↗

PubMed1991

A programmable digital video pattern generator controlled by microprocessor for basic research and clinical applications.

A programmable digital video pattern generator controlled by a microprocessor is described as a part of any commercial or specific visual evoked potential analysis system. The generator handles all kinds of patterns (uniform, orthogonal and radial) with all known presentation modes (onset, offset and reversal) and resolution 640 x 200 square pixels. The frame rate of the generator is adjusted to be compatible to either low cost 50 Hz video monitor or expensive ones of higher frame rate. The operation parameters defined by software are: pattern selection, trigger mode, field selection and stimulation rate. The development of software applications for special research demands is desirable because of the control of the generator by a microprocessor.

Computer Graphics↗

PubMed1994

Application of a bi-directional associative memory (BAM) network in computer assisted learning in chemistry.

A computer assisted learning software based on a bi-directional associative memory (BAM) network was developed. The software was implemented to assist students in associating the names of the elements in the periodic table with their chemical symbols. The use of the BAM facilitates the analysis and interpretation of students' responses. The software package can be modified easily as an educational tool for other disciplines.

Algorithms↗

PubMed1999

Automated and simultaneous identification of microsatellite instability by fluorescence-based polymerase chain reaction (PCR) in four loci.

Genomic instability is sometimes due to impairment of DNA repair systems, which results in a change in the number of microsatellite repeats in tumor cells, produced by slippage during DNA replication. Such abnormal repeats are manifested as microsatellite instability (MSI). We have devised a simple assay using four-color fluorescence for the detection of MSI by an automatic sequencer. Using this method, MSI and loss of heterozygosity (LOH) at four microsatellite loci can be identified simultaneously. We have also developed an algorithm and software for automated analysis of MSI and LOH with this method. Using our method for the detection of MSI in four microsatellite loci and the algorithm and software that we developed, 18 (94.7%) of 19 patients with hereditary nonpolyposis colorectal cancer (HNPCC), meeting the Amsterdam Minimum Criteria, were found to exhibit MSI.

Colorectal Neoplasms, Hereditary Nonpolyposis↗

PubMed2003

Determination of antioxidant efficacy of cosmetic formulations by non-invasive measurements.

BACKGROUND/AIMS: Antioxidants have been proposed, over the last decade, as functional ingredients for anti aging preparations and to prevent and modulate oxidative skin damages. Up to date, beside the photo-induced oxidative skin damages model, none in vivo protocols have shown sufficient reproducibility for the validation of the antioxidant claim for a cosmetic finished product. To this aim, we have recently anticipated a new in vivo protocol based on a microinflammatory model, driven by reactive oxygen species. In the present study our model was validated by comparison with four different instrumental methods. METHODS: The effects of a pre-treatment of two different formulations based on antioxidant functional ingredients, were investigated on forearm skin of 15 healthy volunteers, and compared to a cosmetic base and control area. The instruments considered in the study were Chromameter (CR-300 Minolta), Tewameter TM 210 (Courage-khazaka, Cologne, Germany), Laser Doppler Perfusion Imager (PIM1.0 Lisca Development AB, Sweden), in comparison to DermAnalyzer(R), an easy to use software program developed by us, using the CIE L*a*b* color space parameters. RESULTS: The comparative measurements showed that the antioxidant formulations tested were all able to reduce, in different but statistically significant extent, the intensity of skin redness, and of cutaneous blood flow, when compared to control area (P < 0.0001). CONCLUSIONS: The methyl nicotinate (MN) based microinflammatory model, in conjunction with objective measure- ments, resulted an effective tool for in vivo assessment of oxidative skin injuries. In view of the high level of repeatability, short time of answer and simplicity, the procedure by us developed, is proposed as a possible protocol for the evaluation of in vivo efficacy of antioxidant functional ingredients in cosmetic formulations.

Adult↗

PubMed2006

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).

In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors.

Genomics↗

PubMed2004

Automatic Discrimination of Abnormal Subjects Using the Visual Evoked Potential Spectral Components.

Study of visual evoked potential (VEP) is one of the utilized methods in clinical diagnosis of ophthalmology and neurological disorders. The automatic detection of VEP spectral components is an important tool in the diagnosis of mental activity. This paper presents a novel computational approach using feedforward neural network to identify abnormal subjects from changes in spectral components. The output vector from the feedforward neural network is based on the VEP spectral components. The software was developed to identify mental state from the VEP spectral components using Matlab software package. Using this approach, it is possible to perform real-time abnormality identification accurately on personal computers.

Journal Article↗

PubMed1991

Computer-assisted compounding of neonatal/pediatric parenteral nutrition solutions.

A computer software package was developed to perform the calculations involved in compounding neonatal/pediatric parenteral nutrition (PN) solutions. A 16-bit micro-computer was used to develop and evaluate the software. The program requires a minimum of user input and is menu-driven. It performs the calculations, prints appropriate labels, a preparation card and a summary of the nutritional content of the solution. Error check routines and a check for calcium-phosphate compatibility are imbedded in the program. The effect of the package on PN compounding was evaluated using a computer model. The evaluation indicated the computer-assisted system was more efficient than a manual system and the possibility of computational error was reduced. The increase in efficiency with the computer-assisted system was between 12-15% compared to a manual system. Computer modeling appeared to be a useful tool in both evaluating the software package and determining the effect it would have on work flow.

Canada↗