SEARCH · PubMed Health

Results for “Software development”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources

PubMed1994

The genetic data environment an expandable GUI for multiple sequence analysis.

An X-Windows-based graphic user interface is presented which allows the seamless integration of numerous existing biomolecular programs into a single analysis environment. This environment is based on a core multiple sequence editor that is linked to external programs by a user-expandable menu system and is supported on Sun and DEC workstations. There is no limitation to the number of external functions that can be linked to the interface. The length and number of sequences that can be handled are limited only by the size of virtual memory present on the workstation. The sequence data itself is used as the reference point from which analysis is done, and scalable graphic views are supported. It is suggested that future software development utilizing this expandable, user-defined menu system and the I/O linkage of external programs will allow biologists to easily integrate expertise from disparate fields into a single environment.

Algorithms↗

PubMed2004

Preventing provider errors: online total parenteral nutrition calculator.

OBJECTIVE: To describe the development of a pragmatic low-cost medical information system that reduces errors in the ordering of total parenteral nutrition (TPN) in the newborn intensive care unit at the Johns Hopkins Hospital. METHODS: We designed an online total parenteral nutrition order entry system (TPNCalculator) using Internet technologies. Utilization, impact on medical errors, and user satisfaction were evaluated prior to and immediately after introduction of TPNCalculator (intervention 1) and after 2 years (intervention 2). RESULTS: Total software development time was 3 weeks. The number of orders was similar during the 3 periods: 0.39 orders per patient per day (N = 557) were received compared with 0.35 and 0.43 orders per patient per day (N = 471 and N = 656) in 2 intervention periods. During the control period, an average of 10.8 errors were detected per 100 TPN orders compared with 4.2 per 100 orders in the first intervention period (61% reduction of error rate) and 1.2 per 100 orders after 2 years and some redesign of TPNCalculator (89% reduction of error rate). We found a reduction in the following types of problems (intervention 1; intervention 2): calculation errors (100%; 100%), osmolality outside the allowed range (88%; 91%), and other knowledge problems (84%; 100%). There was a 35% increase in the number of incomplete forms in the first intervention period and a 100% reduction in the second. Rapid cycle development was used in the development of this application. Users of the system were enthusiastic and supportive and compared it favorably to the previous paper-based system. CONCLUSION: Low-cost, pragmatic approaches using Internet technology in the design of medical information systems can reduce medical errors and might pose a viable option for the prevention of adverse drug events.

Baltimore↗

PubMed2001

The need for open geographical information systems in medicine.

This paper presents a promising approach of using component-oriented geographical information systems (GIS) to facilitate improved medical and ecological applications. The integration of administrative geographical and medical data (map overlay) allows sophisticated and advanced analysis. This can serve as a basis to detect undiscovered relationships. We hope to increase the usage of geographical information by the creation of a general framework. This approach is mainly supported by two advances in recent years. Geographical data (e.g. administrative areas) is up-to-date, consistent and covers Germany completely. In addition, enormous technological improvements in the area of high-bandwidth networks and component-based software development have been made. These advances allowed to define our general framework for the integration of GIS functions into existing and already accepted applications.

Germany↗

PubMed1999

Propylnitrosourea-induced T-lymphomas in LEXF RI strains of rats: genetic analysis.

Oral administration of propylnitrosourea (PNU) in drinking water induces high incidence of lympho-haemopoietic malignancies in rats. Previously we reported that F344 strain rats were highly susceptible to T-lymphomas, and LE/Stm rats, to erythro- or myeloid leukaemias. For analysis of the genetic factors determining types of diseases, we have established LEXF recombinant inbred strains of rats comprising 23 substrains, each derived from intercross between F344 and LE/Stm rats. Rats of 23 LEXF substrains were given PNU, and the development of tumours was observed. The overall incidence of haemopoietic tumours ranged from 100% to 66.7%, and the fractions of T-lymphomas, from 100% to 4%, showing a continuous spectrum. Based on the genetic profile published as a strain distribution pattern table for the LEXF, we screened the potential quantitative trait loci involved in determination of the types of disease and length of the latency period. Statistical calculation was performed using the Map Manager QT software developed by Manly. Four loci, on chromosome 4, 7, 10 and 18, were suggested to associate with the T-lymphoma susceptibility and three loci, on chromosome 1, 5 and 16, with the length of the latency period. These putative loci were further examined in backcross (F344 x LE)F1 x LE. Among seven loci suggested by the recombinant inbred study, three loci, on chromosome 5, 7 and 10, were significantly associated with T-lymphomas and another locus on chromosome 1, just weakly. These observations indicate that PNU-induced lymphomagenesis is a multifactorial genetic process involving a number of loci linked with susceptibility and resistance.

Animals↗

PubMed2002

Use of a computerized tuberculosis register for automated generation of case finding, sputum conversion, and treatment outcome reports.

SETTING: Tuberculosis (TB) rates in southern Africa have increased dramatically in recent years. Provision of accurate data for surveillance, program management, and supervision is increasingly essential. OBJECTIVE: To develop software that would provide more efficient collection, compilation, and analysis of TB data on an ongoing basis. DESIGN: The 'Electronic TB Register' is a user-friendly, Epi-Info based software program based on the WHO/IUATLD format of recording and reporting. Individual records from the TB registry are entered in a program that provides interactive support. The software provides several patient management and supervision functions, such as lists of defaulters. Finally, it generates standard quarterly and annual reports on case-finding, sputum conversion, and cohort analysis, and provides graphs of trends and maps of TB indicators. RESULTS: The 'Electronic TB Register' software has been successfully implemented in five pilot projects in southern Africa. User acceptance has been high and quality of data has improved, although timeliness remains unchanged. Factors critical for success include a functioning, paper-based system, involvement of staff from the TB program, health information systems, and health facilities, ongoing training, and backup support. CONCLUSIONS: The 'Electronic TB Register' is a potentially powerful tool for surveillance, management, and supervision for countries with well-functioning paper-based recording and reporting systems.

Confidentiality↗

PubMed2004

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.

BACKGROUND: Many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition. It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation. RESULTS: This work explores a new approach to gene-prediction, based on the Self-Organizing Map, which has the ability to automatically identify multiple gene models within a genome. The current implementation, named RescueNet, uses relative synonymous codon usage as the indicator of protein-coding potential. CONCLUSIONS: While its raw accuracy rate can be less than other methods, RescueNet consistently identifies some genes that other methods do not, and should therefore be of interest to gene-prediction software developers and genome annotation teams alike. RescueNet is recommended for use in conjunction with, or as a complement to, other gene prediction methods.

Chromosome Mapping↗

PubMed2002

Kappa and Hirschberg ratio measured with an automated video gaze tracker.

PURPOSE: To develop a fast automated procedure to measure kappa and the Hirschberg ratio for immediate use in a video gaze tracker. METHODS: Using the hardware platform of the PowerRefractor and a 200 mm lens, the pupil was imaged with a resolution of 57 pixels/mm, at a camera distance of 90 cm. Both the positions of the first Purkinje image and the edges of the pupil were located at 25 Hz sampling rate with subpixel resolution using video image processing software developed under Borland C++. Subjects fixated on a red spot on the left side of the monitor. If their fixation was stable (standard deviation <0.2 degrees in 25 subsequent measurements evaluated in 1 s), the fixation spot appeared automatically on the right side, and the procedure was repeated. Data on the angular position of the optical axis for both targets were stored and provided kappa and the Hirschberg ratio with a standard deviation of about 0.2 degrees or better. This enabled the system to track fixation with a resolution of about 0.2 degrees. RESULTS: (1) Kappa was +3.91+/-2.73 degrees (right eyes), -3.93+/-2.68 degrees (left eyes, mean +/- SD from 24 young adults). Kappa was highly correlated in both eyes (r = 0.8996), but there were significant asymmetries between both eyes in three subjects (delta up to 3 degrees). (2) The Hirschberg ratios were 12.93+/-1.23 degrees/mm = 22.56 delta/mm (right eyes) and 12.82+/-1.49 degrees/mm = 22.38 delta/mm (left eyes). They were also highly correlated in both eyes (r = 0.931). (3) Neither kappa nor the Hirschberg ratios were correlated to refractive errors (range +0.50 to -7.75 D, mean -1.73+/-2.29 D [spherical equivalents]). CONCLUSIONS: (1) The video gaze tracker measured fixation with an angular resolution high enough to display the eye position during reading of individual words on the computer screen. (2) The applicable Hirschberg ratio changed with the power of the spectacles of the subjects by about 3% per diopter. (3) In some subjects, there were significant differences in the geometry of both eyeballs, which may be important in the analysis of strabismus. (4) Consistent with the assumption of retinal stretching, the linear distance of the fovea from the optical axis appeared to increase in myopia.

Adult↗

PubMed2007

Prediction of absorbed dose to normal organs in thyroid cancer patients treated with 131I by use of 124I PET and 3-dimensional internal dosimetry software.

UNLABELLED: The objective of this work was to determine normal organ (131)I dosimetry in patients undergoing radioiodide therapy for thyroid cancer by use of serial scanning with (124)I PET. METHODS: A total of 26 patients who had papillary and follicular metastatic thyroid cancer and who were already enrolled in a Memorial Sloan-Kettering Cancer Center (131)I thyroid cancer protocol were selected for this study. Imaging before (131)I therapy consisted of multiple, whole-body (124)I PET studies over a period of 2-8 d, an (18)F-FDG PET scan and, for some, a diagnostic CT scan. With a set of in-house-developed software tools (3-dimensional internal dosimetry [3D-ID] and Multiple Image Analysis Utility [MIAU]), the following procedures were performed: all PET emission and transmission and CT image sets were aligned; half-life-corrected tomographic images of (131)I activity were integrated voxel by voxel to produce cumulated (131)I activity images; and the latter images were, in turn, convolved with a (131)I electron-photon point kernel to produce images of (131)I dose distribution. Cumulated activity values and calculated residence times obtained from our patient-specific dosimetry software (3D-ID) were used as inputs to OLINDA, and volume difference-adjusted comparisons were made between the mean dose estimates. RESULTS: With 3D-ID, dose volume histograms and mean doses were calculated for 14 organs, and results were expressed in Gy/GBq. The highest mean dose, 0.26 Gy/GBq, was seen in the right submandibular gland, whereas the lowest mean dose, 0.029 Gy/GBq, was seen in the brain. CONCLUSION: This is the first comprehensive study of normal organ dosimetry in patients by use of a quantitative tomographic imaging modality.

Adult↗

PubMed1984

Microcomputer interface for computer-controlled enzyme kinetic studies with the monolayer technique.

A microcomputer interface for computer-assisted monolayer experiments was developed, tested, and used for analysis of the enzymatic hydrolysis by pancreatic phospholipases A2 (EC 3.1.1.4) of 1,2-didodecanoyl-sn-glycero-3-sulfate monitored under constant surface pressure. The interface described multiplexes two different analog signals onto one set of 12 data input lines to the computer. One signal is obtained from an electromicrobalance which measures surface pressure of a monomolecular substrate layer in a two-compartment trough. The second signal comes from a 10-turns precision potentiometer which measures the position of a surface barrier. Both signals together determine a velocity value which is output via four data lines to a DC motor that drives the barrier. Software developed specifically to drive the interface, to store data, and to keep pressure constant is described.

Animals↗

PubMed1995

Filter wheel equalization for chest radiography: a computer simulation.

A chest radiographic equalization system using lung-shaped templates mounted on filter wheels is under development. Using this technique, 25 lung templates for each lung are available on two computer controlled wheels which are located in close proximity to the x-ray tube. The large magnification factor (> 10X) of the templates assures low-frequency equalization due to the blurring of the focal spot. A low-dose image is acquired without templates using a (generic) digital receptor, the image is analyzed, and the left and right lung fields are automatically identified using software developed for this purpose. The most appropriate left and right lung templates are independently selected and are positioned into the field of view at the proper location under computer control. Once the templates are positioned, acquisition of the equalized radiographic image onto film commences at clinical exposure levels. The templates reduce the exposure to the lung fields by attenuating a fraction of the incident x-ray fluence so that the exposure to the mediastinum and diaphragm areas can be increased without overexposing the lungs. A data base of 824 digitized chest radiographs was used to determine the shape of the specific lung templates, for both left and right lung fields. A second independent data base of 208 images was used to test the performance of the templates using computer simulations. The template shape characteristics derived from the clinical image data base are demonstrated. The detected exposure in the lung fields on conventional chest radiographs was found to be, on average, three times the detected exposure behind the diaphragm and mediastinum.(ABSTRACT TRUNCATED AT 250 WORDS)

Biophysical Phenomena↗

PubMed1990

Generating precise mechanical stimuli and recording chordotonal organ discharge patterns using a microcomputer.

A computer-controlled system for the investigation of the response properties of the tibio-femoral chordotonal organ in the locust is described. The computer is used to generate small amplitude sinusoidal movements of the tibia via a small servo-controlled motor. The resulting response recorded via a suction electrode is simultaneously detected, processed and stored on disk. Full constructional details for all hardware required are given. The software, developed for a BBC microcomputer, in addition to controlling all the hardware, has graphics and analysis routines enabling the operator to display and manipulate the stored data.

Action Potentials↗

PubMed2004

Quantitative fish determination of chromosome 3 arm imbalances in lung tumors by automated image cytometry.

BACKGROUND: Clonal heterogeneity is a major difficulty in the analysis of chromosome rearrangements within tumor tissue. Using in situ hybridization, a cell-to-cell analysis can be performed and should allow a better understanding of the genetic process. In addition, detection of pre-neoplastic lesions with only a few cells involved may improve the diagnosis of such lesions and their precocious treatment. MATERIAL/METHODS: Automated analysis was performed on tissue sections with our previously described two-color fluorescence in situ hybridization-based method for quantitative determination of chromosome arm imbalance. The imbalance between the long and short arms of chromosome 3 was determined in 24 cases of non-small-cell and small-cell lung cancers in which only small snap-frozen sections were used, allowing other simultaneous molecular analyses, such as TP53 gene mutation detection. RESULTS: Specifically developed software allowed localization of each nucleus within the section with regard to its chromosome imbalance and to reconstitute a multi-clonal panel within an apparently homogeneous sample. In some cases, discrepancies in the imbalance values were observed between the biopsy and the tumor obtained after surgery from the same patient. CONCLUSIONS: The discrepancies observed between biopsies and tumors, likely linked to the samples' heterogeneity, demonstrate the necessity to analyze tissue sections collected at various locations. The fully automated approach developed in this study rendered such investigations possible.

Cell Transformation, Neoplastic↗

PubMed2001

ArrayExplorer, a program in Visual Basic for robust and accurate filter cDNA array analysis.

Determining the dynamics in the global regulation of gene expression holds the promise of bringing a better understanding of the processes that govern physiological cell growth regulation and its disruption during the development of disease. The advent for cDNA arrays has created the possibility for the parallel analysis of expression of thousands of genes in a given cell population, simultaneously. The level of expression of a given set of genes within the studied tissue corresponds to the intensity of a labeled cDNA probe synthesized from the studied tissue RNA and bound specifically to the cDNAs of the genes spotted on the array. The accurate extraction of gene expression intensity values is essential for further data analysis and the interpretation of the obtained results. Here, we describe a new array image-processing software developed in Microsoft Visual Basic, the ArrayExplorer, which provides a user-friendly, multiple-window interface and a number of automatic and manual features that facilitate a reliable, robust, and accurate extraction of gene intensity values from filter-array images.

Biotechnology↗

PubMed1996

Fractals for multicyclic synthesis conditions of biopolymers. Examples of oligonucleotide synthesis measured by high-performance capillary electrophoresis and ion-exchange high-performance liquid chromatography.

We have developed models of patterns for nucleotide chain growth. These patterns are measurable by high-performance capillary electrophoresis and ion-exchange high-performance liquid chromatography in crude products of solid-phase synthesized 30mer and 65mer oligodeoxyribonucleotide target sequences N. We introduce mathematical methods for finding characteristic values d(o) and p(o) for constant chemical modes of growth as well as d and p for non-constant chemical modes of growth (d = probability of propagation, p = probability of termination). These methods are employed by presenting the accompanying computer software developed by us in C code, Mathematica R languages, and Fortran. Characteristic values of the parameters d, p, and the target nucleotide length N describe the complete composition of the crude product. From this we have developed the relation 2 - [N/(N - 1)]/Da, measurable(N,d) as a universal quantitative measure for multicyclic synthesis conditions (D, fractal dimension and similarity exponent, respectively). We use this mathematical treatment to compare the efficiency of oligodeoxyribonucleotide syntheses of different target length N on polymer support materials. Further, we analyze selected syntheses of short and long oligodeoxyribonucleotides as well as single-stranded DNA sequences by well-known empirical autocorrelation, fast Fourier transformation, and embedding dimension techniques.

Base Sequence↗

PubMed1984

Computer-assisted morphometry and microdensitometry of transmitter- identified neurons with special reference to the mesostriatal dopamine pathway. Methodological aspects.

New morphometrical and microdensitometrical approaches for evaluation of transmitter-identified neurons in the central nervous system have been developed. These rely at the presynaptic level on the use of immunocytochemistry and at the postsynaptic level on the use of receptor autoradiography. The immunocytochemical analysis involves the indirect immunofluorescence method and the indirect immunoperoxidase method utilizing cryostat and vibratome sections, respectively. In the postsynaptic analysis cryostat sections and tritium-sensitive film were employed. A block diagram representation of the system of the image analyzer used and its connection with its host computer is given. Furthermore, flow charts of the original software developed by our group in presented. The morphometrical analysis has been performed on coronal sections of rat brain resulting in determinations of cell body and cell group parameters. Based on this information, objective criteria have been introduced to assess the existence of a cell group of transmitter-identified neurons in a three-dimensional frame and to give a morphometrical description of this group in the space. Moreover, new quantitative approaches to describe the dendritic and terminal fields have been introduced and for the first time in this type of morphometrical analysis, the Lorenz curves and the Gini index have been utilized in the description of the pattern of dendritic and terminal networks. By means of these morphometrical approaches it became possible to analyze topological and biochemical heterogeneities within cell groups defined in the rostrocaudal frame. In particular, it has been possible to develop a quantitative method for the evaluation of coexistence in nerve cell bodies. This method has been called the overlap method and allows an analysis cell by cell of the possible coexistence of two or more antigens.

Animals↗

PubMed1991

Migrating a clinical laboratory information system between technologies.

The technical revolution that has strongly driven events in the clinical laboratory for the last thirty years is now threatening to make obsolete what has become the central pillar of operation in many laboratories, the minicomputer-based laboratory information system. Some of its functions could easily be absorbed by the personal computers which are proliferating in the laboratory, but any single step leap between systems risks replacing order with chaos. Appropriate use of networking tools, together with essential software development, can provide a systematic migrational path for both the administrative and technical computer support from one environment to another without the trauma of a massive replacement step.

Clinical Laboratory Information Systems↗

PubMed2002

Evaluation of the internal auditory canal with virtual endoscopy.

OBJECTIVE: Three-dimensional imaging can improve the understanding and comprehension of complex anatomy. Recent advances in software development allow the construction of a virtual endoscopic view of anatomic structures. This report applies virtual endoscopic capabilities to imaging of the internal auditory canal. STUDY DESIGN, SETTING, AND PATIENTS: We conducted a retrospective case review at a tertiary referral center of patients with abnormal internal auditory canal anatomy on computed tomography. INTERVENTIONS: Computed tomography images were obtained using conventional clinical algorithms involving multiple, 1-mm-thick slices through the temporal bone. Three-dimensional reconstructions were made using General Electric Advantage Windows Navigator software. The virtual endoscopic image-processing algorithm used selected image intensity threshold levels to visualize internal auditory canal anatomy from an endoscopic perspective. RESULTS: Eleven cases of abnormalities of the internal auditory canal were retrospectively identified. Clinical applications using the virtual endoscopic images are presented. The virtual endoscopic images supported prior clinical decision making in 6 of the 11 cases evaluated. CONCLUSION: This technique shows promise for the diagnosis, surgical planning, and teaching of temporal bone anatomy. Usefulness is dependent on acquisition parameters and clinical indications for examination.

Algorithms↗

PubMed2000

Online tools help agencies cope with PPS.

A flurry of software development, much of it web-based, offers alternatives for agencies to address PPS requirements, streamline operations, and improve agency performance. PPS changes everything--dramatically altering the home care community's financial incentives and focusing attention on technologies that will enable agencies to succeed in this new environment.

Home Care Agencies↗