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PubMed2002

Molecular dynamics simulations of mixed micelles modeling human bile.

Extensive molecular dynamics (MD) simulations of binary systems of phospholipids and bile salts, a model for human bile, have been performed. Recent progress in hardware and software development allows simulation of the spontaneous aggregation of the constituents into small mixed micelles, in agreement with experimental observations. The MD simulations reveal the structure of these micelles at atomic detail. The phospholipids are packed radially with their headgroups at the surface and the hydrophobic tails pointing toward the micellar center. The bile salts act as wedges between the phospholipid headgroups, with their hydrophilic sides exposed to the aqueous environment. The structure of the micelles strongly resembles the previously proposed radial shell model. Simulations including small fractions of cholesterol reveal how cholesterol is solubilized inside these mixed micelles without changing their overall structure.

Bile↗

PubMedDate not supplied

A novel approach to high-throughput quality control of parallel synthesis libraries.

Combinatorial chemistry is a powerful tool to enhance drug discovery efforts in the pharmaceutical industry. One type of combinatorial chemistry, parallel synthesis, is now widely used to prepare numerous compounds of structural diversity. A novel high-throughput method for quality control of parallel synthesis libraries has been developed. The method uses flow injection MS, for proof of structure and estimation of purity, and a novel direct injection CLND technique for quantitation of amount. Following the synthesis of a small molecule library, compounds analyzed using this technique were characterized by mass spectrometry, and an accurate concentration of the compound was assessed by CLND. Characterization of one compound is completed in 60 s, allowing for up to 1000 compounds to be analyzed in a single day. The data is summarized using pass/fail criteria using internally developed software.

Chemistry, Organic↗

PubMedDate not supplied

Traditional topological indices vs electronic, geometrical, and combined molecular descriptors in QSAR/QSPR research.

A comparison of the performance of molecular descriptors of different types was conducted. The study was concentrated on determining which descriptors are included in the best linear multivariate regression models constructed for modeling various physicochemical properties (melting point, boiling point, refractive index, molar volume, and density) and biological activities (anaesthetic activity, narcotic activity, sweetness intensity). A total of 84 molecular descriptors published over the past 2 decades was included in this study, plus some of their normalized and squared forms. It was shown that, for the estimation of physicochemical properties, the best small regression models with one to four parameters are mainly comprised of "classical" topological indices such as the Randić index, Wiener index, and molecular connectivity indices. For the correlation of biological activity, combinations of topological indices with geometrical descriptors produced regression models of the best quality. In-house developed software was used for generation of the molecular descriptors (the GROUND program) and for the statistical QSAR/QSPR analysis (the GROUNDSTAT program).

Anesthetics, Local↗

PubMed1991

Computer-aided dosage form design. III. Feasibility assessment for an oral prolonged-release phenytoin product.

Previous publications described computer-aided methodology for assessing the feasibility of designing prolonged release oral dosage forms containing linear-disposition drugs. Those methods determined all useful release rates and examined those rates to decide whether product development was warranted. The present study developed software to obtain similar information for phenytoin, which exhibits Michaelis-Menten disposition. The values for Vmax, Km, and Vd in 27 patients were employed to assess the ability of prolonged absorption to maintain steady-state plasma concentrations between 10 and 20 mg/liter following oral administration at 8-, 12-, and 24-hr intervals. Phenytoin steady-state plasma concentrations in this range were controlled by elimination and were not extended by prolonged absorption. Furthermore, single i.v. bolus doses resulting in an initial plasma level of 20 mg/liter provided concentrations above 10 mg/liter for approximately 1 to 3 days. When an oral multiple-dose regimen was found to maintain steady-state concentrations between 10 and 20 mg/liter, that dose and interval produced concentrations within that range regardless of the absorption rate. While absorption rate was not important, each patient's dose ranges were extremely narrow, emphasizing that dose size was the dominant factor in the control of phenytoin levels.

Absorption↗

PubMed2003

Introduction to the special section on structural equation modeling.

Structural equation modeling (SEM) is a frequently used data-analytic technique in psychopathology research. This popularity is due to the unique capabilities and broad applicability of SEM and to recent advances in model and software development. Unfortunately, the popularity and accessibility of SEM is matched by its complexities and ambiguities. Thus, users are often faced with difficult decisions regarding a variety of issues. This special section is designed to increase the effective use of SEM by reviewing recently developed modeling capabilities, identifying common problems in application, and recommending appropriate strategies for analysis and evaluation.

Humans↗

PubMed2000

Statistical power and optimal design for multisite randomized trials.

The multisite trial, widely used in mental health research and education, enables experimenters to assess the average impact of a treatment across sites, the variance of treatment impact across sites, and the moderating effect of site characteristics on treatment efficacy. Key design decisions include the sample size per site and the number of sites. To consider power implications, this article proposes a standardized hierarchical linear model and uses rules of thumb similar to those proposed by J. Cohen (1988) for small, medium, and large effect sizes and for small, medium, and large treatment-by-site variance. Optimal allocation of resources within and between sites as a function of variance components and costs at each level are also considered. The approach generalizes to quasiexperiments with a similar structure. These ideas are illustrated with newly developed software.

Health Care Rationing↗

PubMed2001

Four-dimensional imaging and quantitative reconstruction to analyse complex spatiotemporal processes in live cells.

Live-cell imaging technology using fluorescent proteins (green fluorescent protein and its homologues) has revolutionized the study of cellular dynamics. But tools that can quantitatively analyse complex spatiotemporal processes in live cells remain lacking. Here we describe a new technique--fast multi-colour four-dimensional imaging combined with automated and quantitative time-space reconstruction--to fill this gap. As a proof of principle, we apply this method to study the re-formation of the nuclear envelope in live cells. Four-dimensional imaging of three spectrally distinct fluorescent proteins is used to simultaneously visualize three different cellular compartments at high speed and with high spatial resolution. The highly complex data, comprising several thousand images from a single cell, were quantitatively reconstructed in time-space by software developed in-house. This analysis reveals quantitative and qualitative insights into the highly ordered topology of nuclear envelope formation, in correlation with chromatin expansion - results that would have been impossible to achieve by manual inspection alone. Our new technique will greatly facilitate study of the highly ordered dynamic architecture of eukaryotic cells.

Animals↗

PubMed2001

Food consumption patterns in Italy: the INN-CA Study 1994-1996.

OBJECTIVES: The present study was aimed at surveying the Italian food consumption patterns in the 90s. It represented the second nationwide food intake survey that was carried out by the Istituto Nazionale di Ricerca per gli Alimenti e la Nutrizione (INRAN). DESIGN: Cross-sectional study. SETTING: Free-living households. SUBJECTS: Sampled subjects: 1147 households randomly selected to be representative of the four main geographical areas (North-West, North-East, Centre, South). Analysed subjects: 1978 individuals out of 2734 initially collected in 15 Collaborative Centres strategically scattered through the national territory. METHODS: A mixed 7-day based survey technique was applied in order to survey both individual and household consumption. At individual level, food intake was recorded by a self-compiled diary. At household level food data collection was by compilation of a food inventory by the dietician, a purchased/wasted foods diary and a recipes form both compiled by the person responsible for food related activities (decision of purchase, purchase, preparation of meals) in the household. All recorded data were monitored by the dieticians who visited the households participating in the study, at least three times. Household members were interviewed in order to collect socio-demographic, lifestyle and motivational information. Furthermore, field-workers performed the food coding and the input of data by an ad hoc developed software. The survey design allowed an internal quantitative check of food data. Several check steps were centrally performed RESULTS: The complex methodology caused the 46.8% response rate and afterwards a reduction of the analysed units (72% of the surveyed individuals). However, the analysed sample provided sufficiently reliable data for outlining the most relevant aspects of dietary patterns in Italy. In order to better interpret the results, controversial aspects are also illustrated and discussed in the text. The disparity analysis found that traditional diversities among Italian regions are still alive. In general, males eat more than females. Analysis according to the age class (children: 1-9 years old; adolescents: 10-17; adults: 18-64; elderly: >64) showed differences especially between the group of children vs all the others, but also in the two groups of young individuals vs adults and the elderly, that could represent clues of an incorrect way of eating. CONCLUSIONS: Taking into account the different methodology, the comparison with previous results showed changes in the Italian average diet complying with an increasing attention to healthy aspects by large sectors of the population, but also opposite tendencies that should be carefully monitored. SPONSORSHIP: Minister delle Politiche Agricole e Forestali (Mi.P.A.F.).

Adolescent↗

PubMed2004

A transmission disequilibrium test for general pedigrees that is robust to the presence of random genotyping errors and any number of untyped parents.

Two issues regarding the robustness of the original transmission disequilibrium test (TDT) developed by Spielman et al are: (i) missing parental genotype data and (ii) the presence of undetected genotype errors. While extensions of the TDT that are robust to items (i) and (ii) have been developed, there is to date no single TDT statistic that is robust to both for general pedigrees. We present here a likelihood method, the TDT(ae), which is robust to these issues in general pedigrees. The TDT(ae) assumes a more general disease model than the traditional TDT, which assumes a multiplicative inheritance model for genotypic relative risk. Our model is based on Weinberg's work. To assess robustness, we perform simulations. Also, we apply our method to two data sets from actual diseases: psoriasis and sitosterolemia. Maximization under alternative and null hypotheses is performed using Powell's method. Results of our simulations indicate that our method maintains correct type I error rates at the 1, 5, and 10% levels of significance. Furthermore, a Kolmorogov-Smirnoff Goodness of Fit test suggests that the data are drawn from a central chi2 with 2 df, the correct asymptotic null distribution. The psoriasis results suggest two loci as being significantly linked to the disease, even in the presence of genotyping errors and missing data, and the sitosterolemia results show a P-value of 1.5 x 10(-9) for the marker locus nearest to the sitosterolemia disease genes. We have developed software to perform TDT(ae) calculations, which may be accessed from our ftp site.

Computer Simulation↗

PubMed1992

Preliminary study of metals in proteins by high-performance liquid chromatography-inductively coupled plasma mass spectrometry using multi-element time-resolved analysis.

The feasibility of multi-element and multi-isotope determinations during the on-line chromatographic separation of protein matrices was investigated using time-resolved software with inductively coupled plasma mass spectrometry. Size-exclusion chromatography was used to separate a mixture of known proteins and the behaviour of associated elements was monitored. It was possible to scan either the entire mass range or a selected number of isotopes. Reversed-phase chromatography was used to separate Zn-containing species in chicken meat that had been intrinsically and extrinsically labelled with stable isotopes of Zn. The ratio obtained for the intrinsic label agreed with that obtained by other workers using thermal ionization mass spectrometry. Time-resolved analysis permitted rapid data acquisition, thus reducing the number of chromatographic runs required. However, at present, data handling can be time consuming. Further software developments will add to the advantages that this technique offers.

Animals↗

PubMed2004

Dielectrophoresis-based programmable fluidic processors.

Droplet-based programmable processors promise to offer solutions to a wide range of applications in which chemical and biological analysis and/or small-scale synthesis are required, suggesting they will become the microfluidic equivalents of microprocessors by offering off-the-shelf solutions for almost any fluid based analysis or small scale synthesis problem. A general purpose droplet processor should be able to manipulate droplets of different compositions (including those that are electrically conductive or insulating and those of polar or non-polar nature), to control reagent titrations accurately, and to remain free of contamination and carry over on its reaction surfaces. In this article we discuss the application of dielectrophoresis to droplet based processors and demonstrate that it can provide the means for accurately titrating, moving and mixing polar or non-polar droplets whether they are electrically conductive or not. DEP does not require contact with control surfaces and several strategies for minimizing surface contact are presented. As an example of a DEP actuated general purpose droplet processor, we show an embodiment based on a scaleable CMOS architecture that uses DEP manipulation on a 32 x 32 electrode array having built-in control and switching circuitry. Lastly, we demonstrate the concept of a general-purpose programming environment that facilitates droplet software development for any type of droplet processor.

Electrophoresis↗

PubMed2001

Effects of four Ni-Ti preparation techniques on root canal geometry assessed by micro computed tomography.

AIM: The aim of this study was to compare the effects of four preparation techniques on canal volume and surface area using three-dimensionally reconstructed root canals in extracted human maxillary molars. In addition, micro CT data was used to describe morphometric parameters related to the four preparation techniques. METHODOLOGY: A micro computed tomography scanner was used to analyse root canals in extracted maxillary molars. Specimens were scanned before and after canals were prepared using Ni-Ti - K-Files, Lightspeed instruments, ProFile.04 and GT rotary instruments. Differences in dentine volume removed, canal straightening, the proportion of unchanged area and canal transportation were calculated using specially developed software. RESULTS: Instrumentation of canals increased volume and surface area. Prepared canals were significantly more rounded, had greater diameters and were straighter than unprepared canals. However, all instrumentation techniques left 35% or more of the canals' surface area unchanged. Whilst there were significant differences between the three canal types investigated, very few differences were found with respect to instrument types. CONCLUSIONS: Within the limitations of the micro CT system, there were few differences between the four canal instrumentation techniques used. By contrast, a strong impact of variations of canal anatomy was demonstrated. Further studies with 3D-techniques are required to fully understand the biomechanical aspects of root canal preparation.

Analysis of Variance↗

PubMed2002

Smooth flexible versus active tapered shaft design using NiTi rotary instruments.

AIM: The aim of this study was to evaluate the influence of a smooth flexible versus active tapered shaft design on canal preparation by NiTi rotary techniques. METHODOLOGY: A XMCT-scanner (SkyScan 1072) and developed software (Bergmans et al. 2001) were used to nondestructively analyze the mesial canals of 10 extracted mandibular molars in 3D with a spatial resolution of 30 microm. Specimens (n = 10 per group) were scanned before (PRE) and after (POST) preparation using Lightspeed (smooth flexible) or GT-rotary (active tapered) files. Numerical values for volumes, dentine removal (net) transportation and centring ability were obtained in addition to a visual inspection on canal aberrations. Data were analyzed by Shapiro Wilk test, multiway factorial anova, Tukey-Kramer test, Wilcoxon test and t-test. RESULTS: Results indicated that the active tapered shaft removed significantly more dentine in the middle to apical portion of the root compared to the smooth flexible design. Both groups demonstrated some straightening, but no significant differences were found with respect to instrument types. However, absolute values for net transportation and centering ratio were small and no canal aberrations could be found. CONCLUSIONS: The smooth flexible shaft design did not improve the morphological characteristics of canal preparation by NiTi rotary instruments when compared with the active tapered design. Therefore, system selection should be based upon other criteria.

Analysis of Variance↗

PubMed2001

Computer-based patient record systems.

OBJECTIVES: To provide oncology nurses with an overview of computer-based patient record (CPR) systems, a key infrastructure requirement in information management that is essential to maintaining a scientific basis for health care. DATA SOURCES: Published articles, research studies, and review articles pertaining to CPR systems. CONCLUSIONS: Progress in hardware development, software applications, and interfaces combine to bring us multimedia patient record systems. Many obstacles have been overcome as standards have emerged and technologies conform to those standards. However, there has been limited success in implementation of such systems. Early acceptance of structured data and problem-oriented documentation set the framework for charting in the electronic record. IMPLICATIONS FOR NURSING PRACTICE: Oncology clinicians and cancer patients alike will realize greater efficiencies and increased quality in health care when the CPR is fully implemented.

Attitude to Computers↗

PubMed2001

A computerized system for tracking practice and prescriptive patterns of family nurse practitioner students.

Decisions about the fit between advanced practice nursing curricula and the real world of primary care practice should be based on data and not on intuition. The purpose of this article is to describe a computerized database system that can be used to: 1) track practice (including prescribing) patterns of nurse practitioner (NP) students; 2) address data issues that commonly arise; and 3) describe NP students' practice during their education to prospective employers. The database system uses both the Family Nurse Practitioners Log (FNPLOG), a faculty-developed software program, and Epi Info, a companion public domain software program. Variables are categorized as being related to sociodemographic, diagnostic, or prescriptive components of primary care. The system provides a simple, efficient, and feasible way of computerizing, analyzing, and evaluating students' clinical experience and practice patterns. The implications for advanced practice nursing education will be illustrated along with other potential uses of the database system.

Data Collection↗

PubMed1999

[Diagnostic value of signal-enhanced color Doppler ultrasound in space-occupying lesions of the skin and skin appendages].

PURPOSE: Prospective evaluation of the diagnostic outcome of plain and signal-enhanced color Doppler sonography for the differentiation between benign and malignant cutis-involving lesions. MATERIALS AND METHODS: 39 patients with 40 suspected malignant skin lesions received an preoperative ultrasound examination before and after application of 4 g Levovist i.v. Spectral Doppler, conventional color and power Doppler were performed. The images were analyzed semiquantitatively using a specially developed software. The diagnoses were confirmed by histological analysis (37 cases) or by follow up controls (3 cases). RESULTS: Whereas the B-mode criteria such as echogenoity, borderline and homogenecity, and the spectral Doppler analysis were not useful for differentiation between malignant and benign lesions, the analysis of the intratumorously visible number of vessels and of the ratio of the vascularized area using a special software, especially after injection of the signal enhancing agent, provided valuable information. In 10 of 18 benign but only in 1 of 22 malignant lesions, no intratumorous vessels were visible after application of Levovist (plain: 10/18 benign and 6/22 malignant lesions). The number of visible vessels increased strongly after signal enhancement. Using a "ratio of the vascularized area (percentage vessel area) > 5%" as a criterion of malignancy, 2 false positive and 2 false negative results were observed after application of Levovist (without/with Levovist sensitivity 73%/91%, specificity 89%/89%). CONCLUSIONS: The signal-enhanced color Doppler sonography provides useful additional information for the differentiation between benign and malignant cutis-involving lesions, especially the semiquantitative vascularization analysis. The latter is superior to B-mode ultrasound and to spectral Doppler analysis. The signal enhancer increases the sensitivity, whereas the specificity remains unchanged.

Adolescent↗

PubMed2002

[Ophthalmology "Made in Switzerland" -- Swiss papers listed in Medline].

BACKGROUND: Publications are one of the most important tools to measure scientific production in a particular sphere. Hence, the aim of this study was to identify the quantitative and (through Journal Impact Factor) qualitative amount of ophthalmological articles coming from Switzerland. MATERIALS AND METHODS: With a specifically developed software we searched 70 ophthalmological Journals indexed by Medline for articles from Switzerland. RESULTS: Not counting the publications related to the annual meeting of the Swiss Ophthalmological Society, the amount of Swiss papers in ophthalmological journals indexed by Medline, increased between 1988 and 1999 by a factor of four. In proportion to the global amount of ophthalmological publications we calculated an increase by a factor of 2.6. The amount of publications grew particularly during the analysed time period in journals with high impact factors. In 1999 a total of 1.8 % of the indexed ophthalmological articles originated from Swiss research institutes and hospitals. The average amount of authors of Swiss publications increased, thereby following an international trend. CONCLUSIONS: The increased amount of publications may rely on the growing role of Swiss research in ophthalmology as well as on a broadened and deepened international orientation of Swiss ophthalmology. The increased number of authors can be explained by the growing complexity and interdisciplinary nature of research projects. Both, the amount of publications and the number of authors, can be linked to the "publish or perish" paradigm.

Forecasting↗

PubMed1993

[Prevention of human birth trauma I. Computer-assisted simulation of delivery using magnetic resonance tomography and finite element analysis].

Imaging procedures suitable for diagnosis of cephalopelvic disproportion, such as radiological pelvimetry, computer- or magnetic resonance imaging (MRI) fail to reflect the dynamics of delivery, including deformations of the birth channel as well as of foetal structures. In order to validate findings of imaging procedures in this respect, a method has been developed to perform dynamic, biomechanical postprocessing of the static information obtained from MRI. Using a specially developed software MRI pixel, matrices of the maternal pelvis and the foetal head were colour-coded and--according to the principle of equal density--line data were created. After sectional attribution of the resulting polygones, a three-dimensional mesh of so called Finite Elements (FE) was created, which can then be used for deformation analysis. The foetal head was then moved through the birth channel by means of computed simulation. This allows not only ongoing deformations to be visualised, but also resulting forces can be calculated at any time of the delivery process for any point of the anatomical model. Furthermore, these calculations can be performed assuming various conditions such as different cephalopelvic dimensions and various labour forces or biomechanical properties of the tissues involved. This paper aims at presenting the method and its mode of working by means of one example of a computed birth simulation.

Adult↗