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PubMed2006

[Multiple analysis of the relationship between correlation of gene function and expression by GeneHub software].

GeneHub software developed by us can be applied to evaluate the significance of expression similarity of genes in each functional unit of different gene function classification systems, and thus to select experiment condition related gene functional units. With different expression similarity measurement and different experiment data, we have applied GeneHub to analyze the expression correlation of functional related genes classified respectively with gene chromosome location, celluar location and interaction, metabolic pathway and signal transduction pathway relationship of protein products of genes. Genes classified according to these multiple ways all showed significant experimental condition related co-expression in our analysis. Our results provide further evidence for the assumption that functional related genes express similarly, which is widely adopted in gene expression profile analysis.

Chromosome Mapping↗

PubMed2006

A simple pharmacokinetics subroutine for modeling double peak phenomenon.

Double peak absorption has been described with several orally administered drugs. Numerous reasons have been implicated in causing the double peak. DRUG-KNT--a pharmacokinetic software developed previously for fitting one and two compartment kinetics using the iterative curve stripping method--was modified and a revised subroutine was incorporated to solve double-peak models. This subroutine considers the double peak as two hypothetical doses administered with a time gap. The fitting capability of the presented model was verified using four sets of data showing double peak profiles extracted from the literature (piroxicam, ranitidine, phenazopyridine and talinolol). Visual inspection and statistical diagnostics showed that the present algorithm provided adequate curve fit disregarding the mechanism involved in the emergence of the secondary peaks. Statistical diagnostic parameters (RSS, AIC and R2) generally showed good fitness in the plasma profile prediction by this model. It was concluded that the algorithm presented herein provides adequate predicted curves in cases of the double peak phenomenon.

Algorithms↗

PubMed1992

Semiautomatic quantification of silver-stained nucleolar organizer regions in tissue sections and cellular smears.

Silver staining of nucleoli reveals argyrophilic proteins associated with nucleolar organizer region (Ag-NOR) proteins. Argyrophilic components appear as dots about 1 micron in diameter dispersed throughout the nucleolus (Ag-NOR dots). The count of Ag-NOR dots is a useful index for improving the cancer diagnosis and determination of prognosis. Here we describe software developed on a medium-cost image analyzer in order to evaluate the mean area of NORs and their number relative to an internal reference, the number and areas of clusters of NORs and the area of the nucleus. Statistical analysis of the data was performed during counting. The first application concerned counting NOR dots during mitosis in cell imprints; those counts were 2.3, 15.3 and 55.56 for the metaphase, telophase and interphase, respectively (relative to unitary dots of metaphase cells). In the second application we demonstrated a significant difference in NOR numbers between two groups of prostatic cancers with good and poor prognoses (6.05 +/- 2.79 SD and 7.96 +/- 3.01, respectively; with Student's t test, = 1.999; P = .05).

Animals↗

PubMed2006

On-line supervision and control of an aerobic SBR process.

This paper presents a new software developed in MATLAB for analyzing on-line data of an aerobic SBR, detecting faults and, in this case, proposing the most probable causes of fault. Process diagnosis is achieved using a statistical method divided in two main phases: off-line model building and on-line data diagnosis. The off-line model identifies the correct working conditions of the system (standard operative conditions). It includes the characterization of the deviation of the system from these standard conditions in the case of changing in the biomass properties or carbon and nitrogen load characteristics. The on-line diagnosis aims at collecting and analyzing all the available data available through industrial sensors, and at classifying the behavior of each treatment cycle. The diagnosis performance of the proposed method is tested using a data set of an aerobic SBR pilot plant.

Bacteria, Aerobic↗

PubMed1998

Interactive image-guided surgical resection of intracranial arteriovenous malformations.

Surgical excision is the only treatment method that immediately prevents increased morbidity or mortality as a result of hemorrhage from arteriovenous malformations (AVMs). For those lesions located deep within the cerebral hemispheres or near eloquent areas, conventional surgical resection may be associated with an unacceptable degree of morbidity and mortality. Herein we report our experience in the resection of these lesions using interactive image guidance. There were five women and five men in the patient group. Their age ranged from 16 to 73 years (mean = 41). Clinical presentation included hemorrhage (n = 7), headaches (n = 2), and seizures (n = 1). All lesions were classified using the Spetzler-Martin grading system as follows: grade I (n = 4), grade II (n = 5), and grade III (n = 1). The locations of the lesions were supratentorial (9) and infratentorial (1). Surgical planning was carried out using the Neurological Surgery Planning System software developed at Wayne State University. An infrared-based system was used to locate and define the lesion intraoperatively. For those lesions located near or within eloquent areas, an awake craniotomy with functional mapping was carried out. Clinical follow-up ranged from 3 to 62 months (mean = 34). Complete surgical excision was achieved in all patients, which was demonstrated postoperatively by digital substraction angiography. The preoperative neurological status remained unchanged in seven patients and improved in three. There was no associated morbidity and mortality with this technique. Image-guided surgical resection of arteriovenous malformations represents a valuable technique, especially in small deep-seated lesions and in those near eloquent areas.

Adolescent↗

PubMed1994

Portable software tools for 3D radiation therapy planning.

PURPOSE: Produce a collection of software tools (computer programs) that support three-dimensional (3D) radiation therapy planning. The tools are not a complete 3D planning system. Instead, they work with any 3D planning system that meets certain minimal specifications. The tools assist in deriving anatomic data from images, generating target volume contours, evaluating treatment plans, and verifying accurate treatment delivery. The tools are portable: they can run without source code changes in any computing environment that provides a library of functions and data definitions called the Foundation. The Foundation couples the portable tools to the (usually nonportable) file system and dose calculation associated with a particular 3D planning system. METHODS AND MATERIALS: Tools were written at three different (geographically separated) institutions. Software developers from all three sites specified the Foundation. The programmers' interface to the Foundation is portable, but a Foundation implementation need not be portable. Each group implemented a Foundation adapted to the (different) 3D planning system used at their site. RESULTS: All tools run at all three sites without source code changes. Each Foundation was implemented in a few person-months of programming effort. The program text and documentation for the tools have been placed in the public domain. CONCLUSIONS: It is practical and economical to produce portable radiotherapy treatment planning tools. Providers of 3D planning programs should offer Foundations for their systems, so they can be used with tools. Researchers considering new computer programs should write them as tools, so they can work with any 3D planning system.

Costs and Cost Analysis↗

PubMed2005

Radiation doses to patients during selected CT procedures at four hospitals in Tanzania.

The dose characteristics of CT scanners from local scanning protocols were investigated on the basis of questionnaire information provided by four hospitals conducting CT procedures in Tanzania. The information included scanner model, scanner manufacturer, number of most frequent CT examinations and the employed scanning parameters to previously diagnosed patients. For each scan technique, patient doses were estimated in terms of computerized tomography dose index, dose length product and effective dose using the software developed by the ImPACT scan group in conjunction with the NRPB conversion coefficients data. The results show that the mean CTDI_w,100, DLP and effective dose ranged from 8.5 +/- 2.8 to 79.3 +/- 23.7mGy, 145 +/- 5 to 1400 +/- 812.5 mGy cm and 3 +/- 2.3 to 15.7 +/- 10.4 mSv, respectively. On average, the observed CT doses are however roughly higher than the reported literature data such as 30 to 60 mGy, 570 to 1050 mGy cm and 2.4 to 11.7 mSv recommended by European Commission for similar CT examinations. The higher dose levels, which are possibly associated with significant risks, justify extensive similar studies at the national level in order to unify different approaches towards optimisation of CT examinations. In pursue of this noble objective, the need to train the radiology personnel, establish and using protocols and continuously monitor the performance of CT equipment to control patient CT doses is of utmost importance.

Humans↗

PubMed2005

A new retrieval system for a database of 3D facial images.

A new retrieval system for a 3D facial image database was designed and its reliability was experimentally examined. This system has two steps, firstly to automatically adjust the orientation of all 3D facial images in a database to that of the 2D facial image of a target person, and then to identify the facial image of the target person from the adjusted 3D facial images in the database using a graph-matching method. From the experimental study [M. Yoshino, K. Imaizumi, T. Tanijiri, J.G. Clement, Automatic adjustment of facial orientation in 3D face image database, Jpn. J. Sci. Tech. Iden. 8 (2003) 41-47], it is concluded that the software developed for the first step will be applicable to the automatic adjustment of facial orientation in the 3D facial image database. In 28 out of 110 sets (25.5%), the 3D image of the target person was chosen as the best match (from a database of 132 3D facial images) according to the similarity of the facial image characteristics based on the graph matching. The 3D facial image of the target person was ranked in the top of 10 of the database in 75 out of 110 sets (68.2%). These results suggest that this system is inadequate for the identification level, but may be feasible for screening method in a small database. It will be necessary to further pursue the possibility of realization of a facial image retrieval system for a large database such as suspects' facial images in future.

Adult↗

PubMed1993

[Application of fuzzy inference to personal identification--sex determination from teeth].

Fuzzy inference has received much attention recently as a new type of computer control technology for application in various fields. In this study I applied fuzzy inference to personal identification in medical jurisprudence. Sex determination program was constructed from teeth using the fuzzy inference technique and was compared with known discriminant analysis. The materials examined were mandibular and maxillary dental plaster models of 100 adult males and females, and 80 infant males and females. For the permanent teeth, measurements were made on crown width and thickness of the mandibular and maxillary central incisors, canines, first premolars, and first molars, and of the width and length of the maxillary dental arch. For the deciduous teeth, measurements were made on crown width and thickness of all teeth. Stepwise discriminant analysis was conducted using these values. The values from 5 selected upper-ranked items were set as input objects of the fuzzy inference program and the probability of maleness obtained from the discriminant analysis was set as the output object. Finally, sex determination program for both permanent and deciduous teeth was constructed using a fuzzy inference software development tool. Each measured value was input into this program and the output results were compared with those of discriminant analysis. The percentages of correct determinations for permanent teeth were 83.0% for males and 86.0% for females using stepwise discriminant analysis, however it increased to 93.0% for males and 89.0% for females using the fuzzy inference program. The percentages of correct determinations for deciduous teeth models were 67.5% for males and 75.0% for females using stepwise discriminant analysis, and increased to 86.3% for males and 81.3% for females using the fuzzy inference program. Among samples with probabilities between 40% and 60%, 3 out of 14 males and 4 out of 13 females were misjudged using stepwise discriminant analysis in cases of permanent teeth. However using fuzzy inference program, it reduced to 0 for males and 3 for females. In case of deciduous teeth, 9 out of 20 males and 9 out of 23 females were misjudged using stepwise discriminant analysis. But it reduced to 5 for males and 4 for females using the fuzzy inference program.

Adult↗

PubMed2000

[Development and application of the software measuring the size of injured body surface].

A software to measure the area, length and angle of injured body surface is introduced. It is suitable for evaluating injury degrees with 2 or 3 dimension measurement. The software is developed by Visual Basic 6.0 on Windows 98 terrace, supporting digital video camera, digital camera and scanner input. It is easy to use and has been applied in more than 200 cases.

Diagnosis, Computer-Assisted↗

PubMed2002

Quantitative assessment of the clavicle radiostructure as a tool for estimation of the osteopathic effect of breast cancer chemotherapy.

Radiological structure (trabeculation) of the clavicle was quantitatively evaluated using the chest X-ray images obtained in 36 pre-menopausal women subjected to CMF (cyclophosphamide, methotrexate, fluorouracil) chemotherapy. For comparison, the values of the quantitative radiostructural indices were estimated from the X-ray images obtained in 65 age-matched pre-menopausal healthy women and 19 post-menopausal women with clinically confirmed osteoporosis. For the analyses, the high-quality routine chest P-A films were used in which the central segment of the clavicle was well visualised. Evaluation of the skeletal radiostructure was carried out using the original software developed by K.W. Zieliński which, in addition to standardising the quality of the image, calculated the structural density as well as the arrangement and mean thickness of the trabeculae. The results demonstrate in a reproducible way that structural density and mean thickness of the clavicular trabeculae were significantly (p < 0.01) lower in pre-menopausal, CMF-treated and post-menopausal, osteoporotic patients than in healthy, control women. Likewise, the relative radiological density of the clavicle was reduced in the former two groups of women as compared to their control counterparts and the difference approached statistical significance. When the X-ray films were compared in each breast cancer patient before and after the chemotherapy the values of all the three parameters were decreased in up to 86% of the treated patients. Overall, the obtained results demonstrate the significant osteopathic side effect of the CMF chemotherapy in pre-menopausal breast cancer patients.

Adult↗

PubMed1997

Corneal topography using the Holladay Diagnostic Summary.

PURPOSE: To describe new software developments in videokeratography and illustrate their application in patients with corneal disease or patients who have had keratorefractive surgery. METHODS: The Holladay Diagnostic Summary provides 4 maps and 15 corneal parameters for the clinician. The maps include 2 refractive power maps on standard and auto scales, a profile difference map for determining the corneal shape relative to normal asphericity, and a distortion map to display the optical quality of the cornea. The 15 corneal parameters provide quantitative information about the cornea for a 3.0 mm pupil; e.g., effective refractive power, regular astigmatism, asphericity, and predicted corneal acuity. The maps and parameters are used to analyze a calibration ball and five clinical examples. RESULTS: Patients with diseases such as keratoconus or patients who have had keratorefractive surgery have characteristic changes in the 4 maps and the 15 corneal parameters. CONCLUSION: When true refractive power maps, a profile difference map, a distortion map, and 15 corneal parameters are analyzed, characteristic changes are found that can help clinicians recognize and monitor corneal disease and refractive surgery and correlate these changes with patients' visual symptoms.

Adult↗

PubMed2005

[Correlation between the area of arterial blood gases graph and the acid-base disturbance in 92 cases with chronic obstructive pulmonary disease].

OBJECTIVE: To study the correlation between the area of arterial blood gases graph (ABGG) and the acid-base disturbance (ABD). METHODS: Using the software developed by ourselves, the results of arterial blood gases and concomitant electrolyte (K(+), Na(+), Cl(-), HCO(3)(-)) determination in 313 episodes were analyzed in 92 cases with chronic obstructive pulmonary diseases (COPD) during hospitalization, and the correlation was studied. RESULTS: (1)On admission, among 92 cases, in 9 cases the results of blood gas analysis were in the area of compensated ventilation and deranged gas exchange (area IV), in 82 cases the results were in the area of insufficient ventilation and deranged gas exchange (area V), and 1 case in the area of excessive ventilation and deranged gas exchange (area VI). There were 8 types of the ABDs, and respiratory acidosis (RAC)+metabolic alkalosis (MAL), RAC, RAC+metabolic acidosis (MAC) with increase in anion gap (AG) ranked in above order. (2)At the time of discharge, in 2 cases the distribution of ABGG was in the normal area (area I), 5 cases in the area IV, 20 cases in the area V, and 1 case in the area VI. There were 5 types of the ABDs. RAC+MAL and RAC ranked in the first two positions. (3)During hospitalization, the correlations between the area of ABGG and ABD in 313 episodes were as follows: ABD normal and MAC of AG increased in the area I; ABD normal and MAL, MAC with AG increased, RAC+MAC, respiratory alkalosis (RAL)+MAL, MAL+MAC of AG increased, RAC+MAL+MAC of AG increased and RAL+MAL+MAC of AG increased in the area IV; RAC, MAL, RAC+MAL, RAC+MAC of AG increased, MAL+MAC of AG increased, and RAC+MAL+MAC of AG increased in the area V; MAC of AG increased, RAC+MAC, RAL+MAL, MAL+MAC of AG increased, and RAL+MAL+MAC of AG increased in the area VI. No ABD occurred in the areas II and III. CONCLUSION: The correlation between ABGG and ABD can be analyzed easily and quickly and the accuracy of results is ensured by using the software.

Acid-Base Equilibrium↗

PubMed2005

Three-dimensional simulation of ultrasound propagation through trabecular bone structures measured by synchrotron microtomography.

Three-dimensional numerical simulations of ultrasound transmission were performed through 31 trabecular bone samples measured by synchrotron microtomography. The synchrotron microtomography provided high resolution 3D mappings of bone structures, which were used as the input geometry in the simulation software developed in our laboratory. While absorption (i.e. the absorption of ultrasound through dissipative mechanisms) was not taken into account in the algorithm, the simulations reproduced major phenomena observed in real through-transmission experiments in trabecular bone. The simulated attenuation (i.e. the decrease of the transmitted ultrasonic energy) varies linearly with frequency in the MHz frequency range. Both the speed of sound (SOS) and the slope of the normalized frequency-dependent attenuation (nBUA) increase with the bone volume fraction. Twenty-five out of the thirty-one samples exhibited negative velocity dispersion. One sample was rotated to align the main orientation of the trabecular structure with the direction of ultrasonic propagation, leading to the observation of a fast and a slow wave. Coupling numerical simulation with real bone architecture therefore provides a powerful tool to investigate the physics of ultrasound propagation in trabecular structures. As an illustration, comparison between results obtained on bone modelled either as a fluid or a solid structure suggested the major role of mode conversion of the incident acoustic wave to shear waves in bone to explain the large contribution of scattering to the overall attenuation.

Algorithms↗

PubMed1984

Automation of chromogenic substrate Limulus amebocyte lysate assay method for endotoxin by robotic system.

The chromogenic substrate Limulus amebocyte lysate (LAL) assay method for the detection of endotoxin was automated by a Zymate robotic system. The software developed enables the robot to automatically dilute a stock reference endotoxin standard (20,000 endotoxin units per ml) for the construction of a five-point standard curve, make sample dilutions to the proper testing concentration, and perform chromogenic substrate LAL assays in duplicate. The linearity of the standard curve and the endotoxin concentration in each sample are calculated and results are printed automatically. In 48 min the automated system assays three samples and a reference standard in duplicate along with a water blank. Sensitivity of the assay is a function of incubation time. The assay is linear (r greater than 0.99) in the region of 0 to 1.0 endotoxin units per ml or 0 to 0.2 endotoxin units per ml with incubation times of 10 or 16 min, respectively. The method can be made very sensitive, detecting as low as 0.003 endotoxin units per ml with 30 min of incubation. The precision of the assay method, determined by assaying an endotoxin reference solution eight times, is ca. 6%. The LAL reagent designed for gel-clot assay was modified for the chromogenic substrate assay. We describe the optimum conditions for the performance of the chromogenic substrate LAL assay and stability of the LAL reagent.

Automation↗

PubMed2005

The determinants of quality in procedural rural medical care.

INTRODUCTION: A substantial proportion of health services for rural Australians is provided in rural health facilities by rurally based generalist health professionals. These services include procedural care within smaller rural hospitals, where teams of health professionals--medical practitioners, nurses and other support staff--work in teams to deliver a range of procedural services, both elective and urgent, that reduce the need for rural people to travel to major centres. Recent debate over the training of rural medical practitioners has focused on whether or not they need to provide procedural services, because current health service management policy appears to support the rationalisation and centralisation of service delivery in larger centres to contain costs and ensure high quality. Hence there is an assumption, without much evidence, that the quality of care in rural hospitals is lower than that provided in larger urban hospitals, although there is little agreement on just what aspects of care should be measured to indicate its quality. This article reports an exploration of multiple perspectives on what constitutes quality of care in rural procedural medical practice, as part of a broader study of the quality of care of a series of real clinical cases. METHODS: During the collection of a series of 91 individual patient cases involving anaesthetic, obstetric or surgical procedures conducted in small rural hospitals, interviews were conducted with several participants in each case: the rural doctors; rural nurses; the rural patients; and family members of those patients. In addition to issues pertaining to each case, interviews explored the perspectives of individuals in each group on the broader question of what constitutes quality of care in a general sense. Their comments were subjected to qualitative thematic analysis using Atlas.ti software (Muhr T, ATLAS.ti Scientific Software Development; Berlin, Germany). In order to consider how to measure rural health care, the thematic comments were then applied to a Donabedian structure/process/outcome model. RESULTS: The different groups produced different views on what might determine the quality of health care in rural hospitals. The health professionals tended to focus on technical aspects of care, although the doctors and nurses had some different emphases, while the patients and their families were more concerned with access, interpersonal communication, convenience and cost. These themes appeared to be consistent with previous literature from general healthcare settings. A list of indicators is suggested for measuring the quality of rural health care. CONCLUSION: This study has improved understanding of the differing views held by rural health professionals and rural patients in thinking about the quality of care provided in rural hospitals. Consideration of the quality of procedural rural medical care should include the needs and expectations of those living and working in a smaller, more familiar environment. This has implications for health planners, and suggests that there is a continuing need for rural health professionals to be trained to provide procedural medical services in rural hospitals, and for rural hospitals to be maintained at a standard necessary to support quality service provision.

Adult↗

PubMed1994

The potential and limitations of the inverse radiotherapy technique.

The objective of the work presented in this paper is to explore the scope of the applicability of the inverse radiotherapy technique for designing optimized intensity distributions to achieve a desired dose distribution. A specified desired uniform dose to the target volume is inverted, subject to constraints on the surrounding normal tissue dose, to produce optimum intensity distributions in a set of beams arranged around the target volume. We employed the inverse technique and software developed by Bortfeld and evaluated results both qualitatively and quantitatively using dose distribution displays, dose-volume histograms and biological indices including tumor control probability and normal tissue complication probabilities. So far we have applied this methodology to prostate and lung treatment plans. For prostate the inverse technique produces satisfactory approximations of the desired dose distributions. However, for lung its performance is considerably inferior. Our investigations point to a number of factors for this difference, the primary ones being differences in the tolerance doses of neighboring normal tissues, magnitudes of volume effect, tissue architectures, and the achievability of the specified desired dose distributions. We conclude that, for certain clinical situations, it is not sufficient to specify the objectives of optimization purely in terms of the desired pattern of the dose. The objectives must also include dose-volume effects and biological indices. Furthermore, the mathematics of optimization must be able to incorporate these factors into the process. We find that the inverse technique is not suitable for situations where dose-volume considerations and biological indices are important and that other methods of optimization of intensity distributions should be explored.

Adenocarcinoma↗

PubMed2003

Dispersion of odour: a case study with a municipal solid waste landfill site in North London, United Kingdom.

Municipal solid waste (MSW) landfills are a potential source of offensive odours that can create annoyance within communities. Dispersion modelling was used to quantify the potential odour strength causing an impact on the community around a particular MSW landfill site north of the London area in the United Kingdom. The case studies were completed with the short-term mode of COMPLEX-I, software developed by the US-EPA. The year 1998 was chosen as a source of baseline data. It was observed that by 2004, when the landfill will progress towards the west and a big band of the area towards the north would be partly/fully restored, the maximum contribution of the new sources giving higher odour concentrations would be in the southwesterly regions away from the landfill. Concentrations as high as 25.0 ou(E)/m(3) were observed with 3 min averaging time in the southwesterly areas as compared to concentrations of 20.0 ou(E)/m(3) at 10 min averaging times. However, the percentage frequency of such critical events occurring would be low. All other surrounding farms and small villages would be exposed to the concentration of 3.0 ou(E)/m(3) on certain occasions. In the year 2008, the majority of the filling fronts would be filled with wastes with no contributions from the active and operational cells. The maximum odour concentration around the landfill site for 1 h averaging time would be approximately 3 ou(E)/m(3) about 1.0 km north and 500 m west of the landfill site. For 3 min averaging time, the stretch of 5 ou(E)/m(3) band would be up to 2.5 km towards the north of the landfill site. It is argued that further analysis of the model calculations considering effects of wind direction, frequency of wind direction, stability of the atmosphere, selected odour threshold, integration time of the model, etc. would form a basis for calculating the separation distances of the landfill site from the surrounding community.

Air Movements↗