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PubMedDate not supplied

MOLMAKER: de novo generation of 3D databases for use in drug design.

A program, MOLMAKER, is described which, in conjunction with a 2D-3D conversion program and 3D database software, can generate de novo 3D databases to aid in drug design. MOLMAKER is based upon graph-theoretical techniques for vertex degree set generation and constructive enumeration of molecular graphs. The generated molecular graphs are then functionalised in a probabilistic manner but in accordance with various constraints specified by the user. The resulting connection tables can be converted into 3D structures by commercial software and loaded into a 3D database for pharmacophore searching. The utility of MOLMAKER is illustrated by two examples of interest from the recent scientific literature: the design of novel protein kinase C agonists and of a bridging ligand for cyclophilin-calcineurin.

Amino Acid Isomerases↗
PubMed2000

On numerical characterization of cyclicity

We propose characterizing the cyclicity of molecular graphs by considering their D/DD matrix. Each nondiagonal element of D/DD is a quotient of the corresponding elements of the distance matrix D and the detour matrix DD of a graph. In particular, we are using the leading eigenvalue of the D/DD matrix as a descriptor of cyclicity and are investigating for monocyclic graphs Cn how this eigenvalue depends on the number of vertexes n, as n approaches infinity.

Journal Article↗
PubMed2003

Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.

Cellular functions result from intricate networks of molecular interactions, which involve not only proteins and nucleic acids but also small chemical compounds. Here we present an efficient algorithm for comparing two chemical structures of compounds, where the chemical structure is treated as a graph consisting of atoms as nodes and covalent bonds as edges. On the basis of the concept of functional groups, 68 atom types (node types) are defined for carbon, nitrogen, oxygen, and other atomic species with different environments, which has enabled detection of biochemically meaningful features. Maximal common subgraphs of two graphs can be found by searching for maximal cliques in the association graph, and we have introduced heuristics to accelerate the clique finding and to detect optimal local matches (simply connected common subgraphs). Our procedure was applied to the comparison and clustering of 9383 compounds, mostly metabolic compounds, in the KEGG/LIGAND database. The largest clusters of similar compounds were related to carbohydrates, and the clusters corresponded well to the categorization of pathways as represented by the KEGG pathway map numbers. When each pathway map was examined in more detail, finer clusters could be identified corresponding to subpathways or pathway modules containing continuous sets of reaction steps. Furthermore, it was found that the pathway modules identified by similar compound structures sometimes overlap with the pathway modules identified by genomic contexts, namely, by operon structures of enzyme genes.

Algorithms↗
PubMed2005

Experimental X-ray charge density studies on the binary carbonyls Cr(CO)6, Fe(CO)5, and Ni(CO)4.

The experimental charge densities in the binary carbonyls Cr(CO)(6) (1), Fe(CO)(5) (2), and Ni(CO)(4) (3) have been investigated on the basis of high-resolution X-ray diffraction data collected at 100 K. The nature of the metal-ligand interactions has been studied by means of deformation densities and by topological analyses using the Atoms in Molecules (AIM) approach of Bader. A detailed comparison between the experimental results and theoretical results from previous work and from gas-phase and periodic DFT/B3LYP calculations shows excellent agreement, both on a qualitative and quantitative level. An examination of the kappa-restricted multipole model (KRMM) for Cr(CO)(6), using theoretically derived structure factors, showed it to provide a somewhat worse fit than a model with freely refined kappa' values. The experimental atomic graphs for the metal atoms in 2 and 3 were found to be dependent on the multipole model used for that atom. In the case of compound 2, restriction of the multipole populations according to idealized site symmetry of D(3h) gave an atomic graph in essential agreement with the theoretical gas-phase study. For compound 3, all multipole models fail to reproduce the atomic graph obtained from the theoretical gas-phase study. The atomic quadrupole moments for the C atoms in all compounds were consistent with significant pi back-donation from the metal atoms.

Journal Article↗
PubMed1998

Dipodascus capitatus, Dipodascus spicifer and Geotrichum clavatum: genomic characterization.

The G + C contents of 25 strains of Dipodascus capitatus, Dipodascus spicifer and Geotrichum clavatum were found to be heterogeneous on basis of derivative graphs of the melting profiles. Strains showing similar derivative graphs of the melting curve exhibited high levels of DNA homology (80-100%); strains showing dissimilar derivative graphs exhibited low levels of DNA homology (5 to 45%). Being considered separate taxa on basis of these parameters, D. capitatus, D. spicifer and G. clavatum could be identified by a combination of the key characteristics growth on xylose, cellobiose, salicin and arbutin.

Base Composition↗
PubMed2000

Tonality of suntan vs sunless tanning with dihydroxyacetone.

BACKGROUND/AIMS: Although there is an increasing awareness of the detrimental effects of solar irradiation on skin, a tanned look is still in fashion. To achieve the tanned look without sun exposure various sunless tanning formulations have become available. Most of these contain dihydroxyacetone (DHA) which binds to the proteins of the stratum cornium and imparts a brown color to skin. This color is similar to a suntan but can be somewhat more yellow, making it appear unnatural. The aim of this study was to determine a quantitative method to define a "natural" tan and to study methods to improve the tonality of sunless tanning on skin. METHODS: Tonality of suntan was determined as the marker for a "natural" tan. In order to achieve this, human volunteers were exposed to the sun and the change in skin color was observed after 3 days. Color measurements obtained with the Minolta Chromameter were plotted in two standard graphs labeled as the "natural universe of tan", which depicted a balance between Chroma and change in reflectance, while the "natural universe of color" determined the balance between changes in yellow and red components of the suntan. Change in skin color after treatment with DHA was then inserted in these graphs to observe how "natural" the tonality of sunless tan appeared relative to suntan. RESULTS: Results show a good balance between Chroma and change in reflectance for suntanned skin in the "natural universe of tan". Conversely, the "natural universe of color" exhibited a good balance between increase in yellow and red components of suntan. Sunless tan data inserted in these graphs showed that for several subjects with skin types I-II the tonality is not within the realm of "natural" but is unnaturally yellow. Addition of antioxidants, especially caffeic acid phenethyl ester (CAPE) in DHA formulation significantly shifted the tonality towards the center of the "natural universe of color". CONCLUSIONS: The "natural universes of tan and color" exhibit a simple and quantitative assessment of tonality of suntan and sunless tan. Although skin tonality from DHA-induced sunless tan can often lie outside the realm of the "natural" tan, it is possible to improve this tonality to a more "natural" look by addition of strong antioxidants in the DHA formulations.

Journal Article↗
PubMed1989

Kinetic and chemometric studies of the determination of creatinine using the Jaffé reaction. Part 2. Application to human serum samples: kinetic behaviour and chemometric evaluation of the determination.

The kinetic behaviour of the reaction of alkaline picrate with creatinine in human serum samples was found to be similar to that for standard creatinine solutions containing albumin. A chemometric evaluation of the kinetic determination of creatinine using the Jaffé reaction was carried out. The analysis of variance (ANOVA) method applied to the delta A45,180 values, obtained from two replicates of three different serum samples over a period of 10 d, showed that the between-day and between-replicate variations added a component to the total variability, the residual error (delta R2) being 5 X 10(-5). A study of the accuracy of the determination was carried out by means of percentage recovery experiments, Youden's method and the standard additions method. Percentage recovery experiments showed that albumin has a marked effect on the results obtained. The application of Youden's method to four serum samples indicated that the method does not have a constant bias error, but, by applying the standard additions method it was concluded that the method has a proportional bias error. The recovery factor, defined as the ratio of the slope of the standard additions graph to that of the standard response graph, was also calculated for the four serum samples. The best values were obtained with different standard response graphs (7.7, 15.4 and 25.6 g l-1 of albumin) for each sample. A modification of the routine procedure used in clinical laboratories is proposed. This modification is based on the principles of the standard additions method and gives better results for creatinine content than those obtained with the routine procedure.

Creatinine↗
PubMed1993

Flux control coefficients determined by inhibitor titration: the design and analysis of experiments to minimize errors.

This paper is a study into the effects of experimental error on the estimated values of flux control coefficients obtained using specific inhibitors. Two possible techniques for analysing the experimental data are compared: a simple extrapolation method (the so-called graph method) and a non-linear function fitting method. For these techniques, the sources of systematic errors are identified and the effects of systematic and random errors are quantified, using both statistical analysis and numerical computation. It is shown that the graph method is very sensitive to random errors and, under all conditions studied, that the fitting method, even under conditions where the assumptions underlying the fitted function do not hold, outperformed the graph method. Possible ways of designing experiments to minimize the effects of experimental errors are analysed and discussed.

Enzyme Inhibitors↗
PubMed2000

Computerized infrared thermographic imaging and pulpal blood flow: Part 2. Rewarming of healthy human teeth following a controlled cold stimulus.

AIM: To investigate the rewarming pattern and rewarming rate of clinically healthy teeth following a controlled cold stimulus using TI techniques. METHODOLOGY: A controlled cold stimulus was developed using an air stream at 20 degrees C. Gingival and incisal sites on 12 healthy maxillary lateral incisors in six patients were imaged under rubber dam following 20 s cooling. Images were captured at 10 s intervals during a 3-min rewarming period and the data used to construct graphs of the rewarming rate. Log transformation of the data was used to produce 'best fit' straight line graphs. Linear regression analysis was used to examine three variables, viz. the side of the mouth (right or left), the site of measurement (gingival or incisal) and the phase of rewarming (early 0-90 s, late 91-180 s). RESULTS: The mean temperature change (delta t degree C) during rewarming was 8.5 degrees C (SD 1.0 degree C) for gingival sites and 7.2 degrees C (SD 1.1 degrees C) for incisal sites. The slope of the 'best fit' straight line data enabled a rewarming index to be calculated for each site on each tooth. Linear regression analysis showed that the phase of rewarming was highly significant but the other variables were not. A one-way ANOVA showed no significant differences between or within groups. CONCLUSIONS: Three min is an appropriate time to record rewarming of teeth cooled for 20 s with an airstream at 20 degrees C. The side or site used to record surface temperatures using this technique is not significant. Rewarming is exponential and log transformation of the data produces a well-fitting straight line graph. The slope of this line provides a rewarming index which should enable comparison of TI and laser Doppler flowmetry in determining pulpal blood flow as a measure of tooth vitality.

Adult↗
PubMed2004

Falls prevention revisited: a call for a new approach.

BACKGROUND: Patient falls constitute a major threat to health services' ability to provide care. Previous studies confirm that nurses can identify patients at risk and that a preventative programme can reduce the rate of falls but few studies have been evaluated over time. AIMS AND OBJECTIVES: A study was undertaken to test a Falls Prevention Programme in an acute medical area that was re-evaluated 5 years later to determine if the effects were sustainable. DESIGN: The design included two groups of patients admitted before and after the programme. Variables such as staffing, equipment, environment and routines were controlled. However, because of ethical approval constraints, some variables such as age, mental status, mobility and gender were not. METHODS: The programme included a risk assessment tool, a choice of interventions, a graphic that alerted others to 'at risk patients' and simple patient and staff education. Data were collected using incident forms and a formula was used to calculate a rate of falls. A non-paired t-test compared rates and anova examined the relationship of age, gender, mobility and mental status on the incidence of falls. Control graphs determined the stability of the process. RESULTS: The falls rate was significantly reduced. Control graphs demonstrate that the process achieved greater control with less variation. In the next 5 years the falls rate increased to preprogramme levels and control graphs demonstrated that the process was no longer controlled. Compliance with the programme had deteriorated. CONCLUSIONS: The practice review considered skill mix, patient activity and acuity but provided no definitive answers to explain non-compliance. The implications to nursing are discussed. RELEVANCE TO CLINICAL PRACTICE: Clinicians are called to conduct more rigorous research into falls prevention but it may be more useful to direct research towards examining nursing work and increasing nurse autonomy in falls prevention.

Accidental Falls↗
PubMed2003

Estimation of glomerular filtration rate and bladder capacity: the effect of maturation, ageing, gender and size.

OBJECTIVE: To show that glomerular filtration rate (GFR) and bladder capacity (BC) develop isometrically, and to provide graphs for estimating GFR and BC for specific individuals of any age, sex, height and weight, for cystometric purposes. MATERIALS AND METHODS: GFR and BC data were collected from published reports; graphs relating GFR and BC to age, sex, height and weight were obtained by using a computerized curve-fitting technique that minimizes the 1.1 power of the absolute error. RESULTS: The plots show the GFR and BC for individuals of 10th, 50th and 90th percentile height and weight as a function of age and sex for different physiological conditions. GFR increases up to age 20 years and thereafter declines, whereas GFR per unit body surface area reaches a maximum at 3.25 years old and declines thereafter. CONCLUSIONS: The clinical management strategy to preserve or enhance renal function in paediatric and adult nephrological disease should incorporate the present data on development, growth, ageing and deterioration of function. These data should be used when interpreting cystometrograms and evaluating compliance. The graphs are useful for clinically estimating GFR and BC, especially when estimating infusion rate and BC for individual patients. BC and GFR develop isometrically with a proportionality constant of 4.56 min, except from birth to 1.5 years of age. Accordingly, individuals with healthy urinary systems, irrespective of age, sex and size, in the same physiological conditions have, on average, the same time to reach BC, ranging from 7 h at a normal 1% GFR to 41 min at the maximum diuresis of 10% GFR.

Adolescent↗
PubMed2001

Using survival curve comparisons to inform patient decision making can a practice exercise improve understanding?

BACKGROUND: Patients often face medical decisions that involve outcomes that occur and change over time. Survival curves are a promising communication tool for patient decision support because they present information about the probability of an outcome over time in a simple graphic format. However, previous studies of survival curves did not measure comprehension, used face-to-face explanations, and focused on a VA population. METHODS: In this study, 246 individuals awaiting jury duty at the Philadelphia County Courthouse were randomized to receive one of two questionnaires. The control group received a questionnaire describing two hypothetical treatments and a graph with two survival curves showing the outcomes of each treatment. The practice group received the same questionnaire preceded by a practice exercise asking questions about a graph containing a single curve. Subjects' ability to interpret survival from a curve and ability to calculate change in survival over time were measured. RESULTS: Understanding of survival at a single point in time from a graph containing two survival curves was high overall, and was improved by the use of a single curve practice exercise. With a practice exercise, subjects were over 80% accurate in interpreting survival at a single point in time. Understanding of changes in survival over time was lower overall, and was not improved by the use of a practice exercise. With or without a practice exercise, subjects were only 55% accurate in calculating changes in survival. CONCLUSION: The majority of the general public can interpret survival at a point in time from self-administered survival curves. This understanding is improved by a single curve practice exercise. However, a significant proportion of the general public cannot calculate change in survival over time. Further research is necessary to determine the effectiveness of survival curves in improving risk communication and patient decision making.

Adult↗
PubMed1991

[Lack of fatigue of the musculature in patients after immobilization--a paradox?].

The isometric strength of knee extensors was measured in patients six weeks after cruciate ligament surgery over a contraction period of 30 sec. The characteristics of the graph obtained form the measurement system were compared to the graphs of uninjured knee extensor muscles. Apart from strength reductions, as expected for atrophic muscle, the pattern of the strength graph led to the impression that these muscles did not fatigue during prolonged contraction. This paradoxical phenomenon can be explained by the existence of central inhibitory mechanisms.

Anterior Cruciate Ligament↗
PubMed1997

Alpha-fetoprotein (AFP) levels in normal children.

Alpha-fetoprotein (AFP) is an important tumor marker for yolk sac tumor and hepatoblastoma in childhood. We have been using the graph of the normal range of serum AFP made by Tsuchida et al, when we evaluate the serum AFP levels in early infancy. We measured the serum AFP levels by an immunoradiometric assay in 163 normal infants under 2 years of age, in order to make a more precise graph. Our normal range was a little wider than that of Tsuchida et al. According to our graph, false-positive cases would be fewer. Referring to the half-lives of serum AFP levels in normal infancy is also useful, when it is difficult to evaluate the AFP level.

Age Factors↗
PubMed2002

Chaotic maps derived from trajectory data.

We assume that we have the following information from observed trajectory data about a discrete time dynamical process: (1) a rough graph of the phase plot, (2) the probability density function and (3) the metric entropy. We describe a method for constructing a nonlinear map whose graph is "within" the rough graph of the phase plot, and which has the observed probability density function and entropy.(c) 2002 American Institute of Physics.

Journal Article↗
PubMed2005

Nucleation-controlled multiphase transitions.

Thermodynamics and kinetics of phase transitions in multiphase systems have been discussed. Thermodynamically admissible transitions have been identified and transition kinetics described in terms of the extended Kolmogoroff-Avrami-Evans model. Different combinations of transitions have been described as directed graphs. Graph nodes represented individual phases, graph edges--transitions. Superposition of parallel transitions in various mother phases, simultaneous transition of the same mother phase into different target phases, and successive (chain) transitions have been analyzed. Detailed solutions for a three-phase system consisting of one liquid phase and two polymorphic solid phases have been presented.

Journal Article↗
PubMed2006

Synchronization in asymmetrically coupled networks with node balance.

We study global stability of synchronization in asymmetrically connected networks of limit-cycle or chaotic oscillators. We extend the connection graph stability method to directed graphs with node balance, the property that all nodes in the network have equal input and output weight sums. We obtain the same upper bound for synchronization in asymmetrically connected networks as in the network with a symmetrized matrix, provided that the condition of node balance is satisfied. In terms of graphs, the symmetrization operation amounts to replacing each directed edge by an undirected edge of half the coupling strength. It should be stressed that without node balance this property in general does not hold.

Action Potentials↗
PubMed2002

Remnant amount and cleanup for 3 adhesives after debracketing.

The cleanup of remnant bonding adhesive from the enamel surface after debonding is an important factor for clinicians. The purposes of this study were to compare the weight, the surface area, and the cleanup times of remnant adhesive for a composite resin, Transbond (TB); a resin-modified glass ionomer, Fuji ORTHO LC bonded to enamel both conditioned (FOC) and nonconditioned (FONC); and a fluoride-releasing composite resin, Advance (ADV), bonded to nonetched enamel. In addition, 2 qualitative methods for scoring remnant adhesive were compared with the quantitative weight and area data. Forty extracted human incisors were weighed, bonded with brackets, debonded, weighed, and photographed. Area was measured from the photographs with a sonic digitizer. Mean adhesive remnant weights differed between groups (analysis of variance [ANOVA], P =.02): The remnants from ADV and FOC were equal and both significantly heavier than the remnants from FONC; the weights of the TB remnants were intermediate between the heavier ADV and FOC remnants and the lighter FONC remnants. Mean remnant areas differed between groups (ANOVA, P =.03): The remnants from ADV were significantly larger than the remnants from TB and FONC, which were equal; the areas of the FOC remnants were intermediate between the larger ADV remnants and the smaller remnants from TB and FONC. Mean cleanup times also differed between groups (ANOVA, P <.001): TB and FOC had equal times that were significantly longer than the times for ADV and FONC, which were equal. Adhesives bonded to acid-etched or conditioned enamel took about 1 and a half times longer to clean up than did those bonded to nonetched enamel. When bonded to conditioned enamel, the resin-modified glass ionomer had mean remnant adhesive weights, areas, and cleanup times statistically equivalent to TB. ADV had the fastest mean cleanup time per amount of remnant (ANOVA, P <.002). The graphs of scores for 2 qualitative methods used for scoring remnant amount did not closely resemble the graphs based on weight and area. The graph of a newly introduced qualitative method better reflected the area data. Weighing may be a useful method for quantifying remnant adhesive.

Acrylic Resins↗