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At least 937 records · Page 52Linked to original sources

Comfort climate evaluation with thermal manikin methods and computer simulation models.

With increasing demand for acceptable environment in the modern workplace is it necessary, already in the construction phase, to estimate what effect different environmental factors have on the occupants. Thermal sensation is affected by many factors in the work place environment, especially thermal factors and effects from air movement caused by different ventilation principles. A series of full scale measurements as well as numerical calculations have been carried out in order to investigate whether Computational Fluid Dynamics (CFD) calculations and measurements with a thermal manikin are able to predict the perceived thermal climate. When human thermal sensation is linked together in measurements and calculations, the thermal situation in the work place environment is visualized. The results show relatively good agreement with the measurements made in the real environment. However, numerical and experimental methods need to be further developed. Evaluation methods of this type, will enable engineers to make better predictions and early decisions in the design and construction process. This also opens possibilities to use results from a number of full scale tests providing means to improve the comfort, health and productivity in working life.

Air Movements↗

Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes.

BACKGROUND: Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation. RESULTS: The method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulatory sequence was determined. CONCLUSIONS: We have described and successfully tested a simple computational method to identify upstream motifs relevant to gene regulation in eukaryotes by studying the statistical correlation between overepresented upstream motifs and gene expression levels.

5' Flanking Region↗

A maximum entropy method to compute the 13NH3 pulmonary transit time from right to left ventricle in cardiac PET studies.

The distribution function of pulmonary transit times (fPTTs) contains information on the transit time of blood through the lungs and the dispersion in transit times. Most of the previous studies have used specific functional forms with adjustable parameters to characterize the fPTT. It is the purpose here to investigate the possibility of estimating the fPTT in a model-free way. The method employs the maximum entropy principle and is used, in particular, on cardiac positron emission tomographic (PET) studies but is believed to be more generally applicable. Using this principle in a test case, we were able to accurately identify a two-peaked transfer function, which may theoretically be seen in patients with pulmonary disease confined to one lung. Transit time values for [13N]-ammonia were produced by applying the algorithm to PET studies from normal volunteers.

Algorithms↗

A structural model of EmrE, a multi-drug transporter from Escherichia coli.

Using a recently reported computational method, we describe an approach to model the structure of EmrE, a proton coupled multi-drug transporter of Escherichia coli. EmrE is the smallest ion-coupled transporter known; it functions as an oligomer and each monomer comprises four transmembrane segments. Because of its size, EmrE provides a unique experimental paradigm. The computational method does not afford a unique solution for the monomer. The experimental constraints available were used to select the most likely structure and to dock two monomers together to yield a dimer. The model is further validated by modeling of Hsmr, an EmrE homolog with a remarkable amino acid composition with over 40% of Ala and Val. The Hsmr model is similar to that of EmrE, with the majority of the Ala or Val residues facing the lipid. In addition, the model of EmrE features a putative substrate-binding site very similar to that observed in BmrR, a transcription activator of multi-drug transporters, with a similar substrate profile. The two crucial residues that couple proton fluxes with substrate binding in the homo-dimer of EmrE, Glu-14, have a spatial arrangement that agrees with proposed molecular mechanisms of transport.

Alanine↗

Development of a computer-assisted method for the collection, organization, and use of patient health history information in physical therapy.

Screening a patient's general health prior to instituting physical therapy management is generally acknowledged as important. However, neither the specific content nor the optimal method of performing this part of patient examination has received much attention. One method that uses a computerized information management system to assemble relevant clinical literature and to guide the collection, organization, and use of patient health history data in clinical decision-making is described. The philosophy and rationale for performance of general health screenings by physical therapists, justification for the use of computers in the screening process, and the development and application of one type of computer-assisted health history screening system for physical therapy are presented.

Decision Making, Computer-Assisted↗

A computer-aided method for the quantitative analysis of dendritic arborizations reconstructed from serial sections.

We present a methodology for measuring precisely defined morphological parameters on complete dendritic arborizations. Brains are sectioned through anatomical planes which are defined with reference to ventricular landmarks. For each neuron, drawn through the camera lucida, dendritic points are defined and identified by means of a numerical topological codification. The 3-dimensional coordinates of each point are measured on a video computer microscope with reference to a cartesian system of axes which are oriented with reference to the anatomical planes of the brain. The data points from several serial sections are stored section by section and re-ordered by a computer program. Quantitative data concerning the diameters of the dendrites and the number and the dimensions of their spines are also stored. From these data, various quantitative morphological parameters may be computed. The accuracy of the video computer microscope is measured. The different existing computerized systems and the contribution of computerized techniques are discussed.

Animals↗

A computer assisted method to control the steady state of an ATP-regenerating assay.

A mathematical procedure is presented which permits to calculate the steady-state concentrations of AMP, ADP and ATP in an ATP-regenerating assay containing pyruvate kinase and lactate dehydrogenase as auxiliary enzymes. The accuracy of this procedure is demonstrated by the agreement of the calculated concentrations with the experimental data obtained in measurements of mitochondrial ATPase activities. The computer-assisted procedure can be employed (a) to determine extremely low adenine nucleotide concentrations which are difficult to obtain by direct measurements and (b) to adjust and to optimize the assay conditions according to the specific requirements of the experiment, including high concentrations of ATP and prescribed ATP/ADP ratios.

Adenosine Diphosphate↗

A computer-based method for comparisons of continuous intracranial pressure recordings within individual cases.

BACKGROUND: This study assessed two strategies of comparing continuous intracranial pressure (ICP) recordings within individual cases, namely either by calculation of differences in mean ICP or by calculation of differences in numbers of ICP elevations. METHODS: Continuous ICP recordings before and after cranial surgery were both presented as mean ICP and as numbers of ICP elevations of different levels (20 and 25 mmHg lasting either 0.5 or 1 minute). Since the length of pressure recordings differed somewhat between individuals, the numbers of ICP elevations were standardised by computing the numbers of elevations during a 10 hours period. The ICP recordings were analysed by the Sensometrics Pressure Analyser software. The ICP curves included here were selected from a group of 15 children undergoing calvarial expansion surgery for craniosynostosis, in whom continuous ICP monitoring was performed both before and after surgery as part of the diagnostic workout to rule out lasting intracranial hypertension. FINDINGS: After surgery, mean ICP during sleep was reduced by 5 mmHg or more in 5 cases, minimally changed (i.e. 2 mmHg or less) in 6 cases, and variably increased in the other 4 cases. In one of these 4 latter cases, numbers of ICP elevations were increased after surgery, but in all other 14 cases the numbers of ICP elevations were significantly reduced. Reduction of mean ICP by more than 2 mmHg associated with good outcome was observed in 3 of 15 cases (20%), whereas marked and significant reductions in numbers of ICP elevations during sleep combined with good outcome was observed in 12 of 15 cases (80%). INTERPRETATION: Outcome after the 2nd ICP monitoring was more reliably predicted by computing differences in numbers of ICP elevations than by calculation of mean ICP.

Adolescent↗

A method of computing restricted best linear unbiased prediction of breeding values for some animals in a population.

Restricted BLUP (R-BLUP) is derived by imposing restrictions directly within a multiple-trait mixed model. As a result, the R-BLUP procedure requires the solution of high-order simultaneous equations. If restrictions are imposed on breeding values for only some animals in a population, calculations become more complex. A new procedure for computing the R-BLUP of breeding values was derived when constraints were imposed on the additive genetic values of only some animals in a population. Rules for including records when proportional constraints are imposed were developed based on the traits that are recorded for an animal. The technique was better than the previous method in both memory requirement and central processing unit time.

Algorithms↗

[Effects of tandospirone citrate on frozen gait in patients with early stage of progressive supranuclear palsy, investigated by walk-induced activation single photon emission computed tomography method].

We reported a 64-year-old woman in the early stage of progressive supranuclear palsy presenting as pure akinesia syndrome who showed marked improvement with tandospirone citrate. She revealed bradykinesia, severe frozen gait and disturbance of postural reflex without rigidity or tremor. Treatment with L-dopa and L-threo DOPS was not effective, but tandospirone citrate at a daily dosage of 30 mg significantly lessened the severity of frozen gait. Activation single photon emission computed tomography study with 99mTc-ethyl cysteinate dimer during gait revealed a significant increase in brain activity in the right cingulate cortex after tandospirone citrate treatment. The effect lasted ten months until neck rigidity and ventricular supranuclear palsy were evident.

Brain↗

Interaction of local anesthetics with a peptide encompassing the IV/S4-S5 linker of the Na+ channel.

The peptide pIV/S4-S5 encompasses the cytoplasmic linker between helices S4-S5 in domain IV of the voltage-gated Na+ channel, residues 1644-1664. The interaction of two local anesthetics (LA), lidocaine and benzocaine, with pIV/S4-S5 has been studied by DOSY, heteronuclear NMR 1H-15N-HSQC spectroscopy and computational methods. DOSY indicates that benzocaine, a neutral ester, exhibits stronger interaction with pIV/S4-S5 than lidocaine, a charged amine-amide. Weighted average chemical shifts, Deltadelta(1H-15N), show that benzocaine affects residues L1653, M1655 and S1656 while lidocaine slightly perturbs residues I1646, L1649 and A1659, L1660, near the N- and C-terminus, respectively. Computational methods confirmed the stability of the benzocaine binding and the existence of two binding sites for lidocaine. Even considering that the approach of studying the peptide in the presence of a co-solvent (TFE/H2O, 30%/70% v/v) has an inherently limited implication, our data strongly support the existence of multiple LA binding sites in the IV/S4-S5 linker, as suggested in the literature. In addition, we consider that LA can bind to the S4-S5 linker with diverse binding modes and strength since this linker is part of the receptor for the "inactivation gate particle". Conditions for devising new functional studies, aiming to better understand Na+ channel functionality as well as the various facets of LA pharmacological activity are proposed in this work.

Amino Acid Sequence↗

Comparison of two methods for computing abduction moment arms of the rotator cuff.

Biomechanical models of the shoulder mechanism require estimates of muscle moment arm magnitude. Some shoulder models have estimated muscle moment arms by assuming an idealized minimum distance path from the origin to insertion that passes around the bony geometry. Alternatively, the principle of virtual work can be used to estimate moment arms from tendon excursion and joint-angle data. The purpose of this study was to determine if these two methods give different estimates of abduction moment arms for the supraspinatus, infraspinatus, and subscapularis muscles. Muscle moment arms were estimated for these muscles on ten fresh frozen cadaver specimens. The results showed a significant difference between the two estimation methods. Average differences were 3.1 mm (10.6%), 3.9 mm (43.9%), and 7.2 mm (70.3%) for the supraspinatus, subscapularis, and infraspinatus muscles, respectively. These results suggest that shoulder models based on the origin-insertion method may give higher rotator cuff muscle force estimates than methods using the slope of the tendon excursion vs joint angle relationship.

Adult↗

Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function.

To determine which of seven library design algorithms best introduces new protein function without destroying it altogether, seven combinatorial libraries of green fluorescent protein variants were designed and synthesized. Each was evaluated by distributions of emission intensity and color compiled from measurements made in vivo. Additional comparisons were made with a library constructed by error-prone PCR. Among the designed libraries, fluorescent function was preserved for the greatest fraction of samples in a library designed by using a structure-based computational method developed and described here. A trend was observed toward greater diversity of color in designed libraries that better preserved fluorescence. Contrary to trends observed among libraries constructed by error-prone PCR, preservation of function was observed to increase with a library's average mutation level among the four libraries designed with structure-based computational methods.

Combinatorial Chemistry Techniques↗

Interobserver and intraobserver variability in the assessment of pulmonary nodule size on CT using film and computer display methods.

RATIONALE AND OBJECTIVES: A critical element in determining biologic behavior of pulmonary nodules is volume and temporal volume change. We evaluate variability in nodule volume among readers and measuring methods. MATERIALS AND METHODS: 55 small (<2 cm) lung nodules were measured in long- and short-axis dimensions independently by 4 radiologists, using 3 methods: 1) hard copy, 2) GE Advantage Windows workstation (GE Healthcare, Milwaukee, WI), 3) Siemens IMACS workstation (Siemens Medical Systems, Iselan, NJ). Nodule margin was recorded as smooth, lobulated, or spiculated. Volume was calculated from diameter measurements. Variability in nodule volume was evaluated within each reader, between readers, and across measurement tools. RESULTS: Mean nodule short-axis diameter was 5.3 mm; mean long-axis diameter 7.2 mm. There was statistically significant variation among readers and measurement method for nodule volume. Volume was significantly larger using hard-copy measurements (51.9%-54.1% variation; P < .0001) than either workstation, and not different between workstations. There was greater intraobserver variability in volume using the hard-copy method, and no difference between workstation methods. Volumes based on measurements from one reader were consistently lower than those from other readers (P = < .001, .003, and .02); volume was consistently larger for another reader (P < .0001, .03, and .12). Reader agreement for nodule margin was good to excellent. CONCLUSION: Considerable interobserver and intraobserver variability in measuring nodules exists using hard-copy and computer tools. Since a small change in diameter indicates a much larger change in volume, this may be significant when using early repeat CT to follow small pulmonary nodules. Computer-aided diagnostic tools that reproducibly measure nodule volume are strongly needed.

Humans↗

A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.

The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.

Epidermal Growth Factor↗

In silico genetics: identification of a functional element regulating H2-Ealpha gene expression.

Computational tools can markedly accelerate the rate at which murine genetic models can be analyzed. We developed a computational method for mapping phenotypic traits that vary among inbred strains onto haplotypic blocks. This method correctly predicted the genetic basis for strain-specific differences in several biologically important traits. It was also used to identify an allele-specific functional genomic element regulating H2-Ealpha gene expression. This functional element, which contained the binding sites for YY1 and a second transcription factor that is probably serum response factor, is located within the first intron of the H2-Ealpha gene. This computational method will greatly improve our ability to identify the genetic basis for a variety of phenotypic traits, ranging from qualitative trait information to quantitative gene expression data, which vary among inbred mouse strains.

Alleles↗

A computer-based method to quantify the classic pattern of choroidal neovascularization in order to monitor photodynamic therapy.

BACKGROUND: Photodynamic therapy (PDT) is a new treatment modality which relies on a nonthermal light exposure of choroidal neovascularization (CNV) which has accumulated a photosensitizer, to produce a photochemical thrombosis. The aim of the present study was to develop a more quantitative outcome parameter that can be used to optimize a number of treatment parameters which in PDT are larger than many other modalities. METHODS: Nine patients underwent up to four standardized fluorescein angiography (FA) examinations on a Zeiss 30 degrees retinograph using Kodak Trimax film. The 35-mm pictures were digitized. The CNV size was evaluated using the NIH Image 1.60 software, comparing the CNV surface to the disk area. The fluorescence intensity was measured comparing the grayscale fluorescence levels of the CNV classic pattern with the mean grayscale level of control areas. A combination of the CNV size parameter with the fluorescence contrast parameter was called "integrated contrast" (IC). The IC amplitude was then used to describe and compare the fluorescence before and after PDT. RESULTS: FAs on three normal patients defined the normal range of the IC. IC measurements on two patients with a classic CNV who underwent FA examinations respectively 1 and 3 months apart demonstrated the robustness and the reproducibility of the method. IC measurements on three patients who underwent PDT with three different treatment parameters demonstrated the feasibility of using this IC measurement as a PDT outcome criteria. CONCLUSION: We have developed a method to transform a qualitative clinical evaluation of CNV leakage into a more quantitative grading.

Choroid↗

[The differential diagnosis of sarcoidosis of the respiratory organs using mathematical methods and computers].

A system for detecting sarcoidosis has been proposed on the basis of the results of a primary examination, which comprises a combination of programs for determining whether sarcoidosis may occur in various X-ray syndromes (enlarged intrathoracic lymph nodes, disseminated process, infiltrative or pneumonia-like shadow and cavity formation). The system has been developed with the help of a program-algorithm complex which enables one to make the dialogue system of the decision-make support on the basis of statistical methods of "image recognition" containing basic structural elements of the expert systems. Program development proceeds from the findings obtained in 406 patients with sarcoidosis of respiratory organs and 723 patients having similar clinical and X-ray picture of the disease. The diagnostic efficiency of the system was 89% in disseminated processes, 90% in enlarged intrathoracic lymph nodes and cavitary changes, and 96.2% in infiltrative changes.

Diagnosis, Differential↗