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In vitro evolution of a hyperstable Gbeta1 variant.

An in-vitro selection strategy was used to obtain strongly stabilized variants of the beta1 domain of protein G (Gbeta1). In a two-step approach, first candidate positions with a high potential for stabilization were identified in Gbeta1 libraries that were created by error-prone PCR, and then, after randomization of these positions by saturation mutagenesis, strongly stabilized variants were selected. For both steps the in-vitro selection method Proside was employed. Proside links the stability of a protein with the infectivity of a filamentous phage. Ultimately, residues from the two best selected variants were combined in a single Gbeta1 molecule. This variant with the four mutations E15V, T16L, T18I, and N37L showed an increase of 35.1 degrees C in the transition midpoint and of 28.5 kJ mol(-1) (at 70 degrees C) in the Gibbs free energy of stabilization. It was considerably more stable than the best variant from a previous Proside selection, in which positions were randomized that had originally been identified by computational design. Only a single substitution (T18I) was found in both selections. The best variants from the present selection showed a higher cooperativity of thermal unfolding, as indicated by an increase in the enthalpy of unfolding by about 60 kJ mol(-1). This increase is apparently correlated with the presence of Leu residues that were selected at the positions 16 and 37.

Bacterial Proteins↗

Quantitative SPECT of uptake of monoclonal antibodies.

Absolute quantitation of the distribution of radiolabeled antibodies is important to the efficient conduct of research with these agents and their ultimate use for imaging and treatment, but is formidable because of the unrestricted nature of their distribution within the patient. Planar imaging methods have been developed and provide an adequate approximation of the distribution of radionuclide for many purposes, particularly when there is considerable specificity of targeting. This is not currently the case for antibodies and is unlikely in the future. Single photon emission computed tomography (SPECT) provides potential for greater accuracy because it reduces problems caused by superimposition of tissues and non-target contributions to target counts. SPECT measurement of radionuclide content requires: (1) accurate determination of camera sensitivity; (2) accurate determination of the number of counts in a defined region of interest; (3) correction for attenuation; (4) correction for scatter and septal penetration; (5) accurate measurement of the administered dose; (6) adequate statistics; and (7) accurate definition of tissue mass or volume. The major impediment to each of these requirements is scatter of many types. The magnitude of this problem can be diminished by improvements in tomographic camera design, computer algorithms, and methodological approaches.

Antibodies, Monoclonal↗

Quantitative Assessment of Polyethylene Component Position in a Mobile-Bearing Prosthetic Knee, Using a Single Radiograph.

Rationale and Objectives. To reduce tibio-femoral misalignment, the polyethylene bearing-component of a new knee prosthesis was allowed limited motion on the underlying metallic component. The object of the work presented here was to develop a suitable radiographic technique for quantifying the in-vivo position of the bearing. By collecting these data at discrete flexion angles, the functional operation of the prosthesis could be determined. Methods. The known geometries between landmarks on the two components were used to produce algorithms for reconstructing their spatial positions from a single radiograph. A custom-designed computer program utilized these algorithms to determine the relative translation and rotation of the polyethylene component. Results. This technique produced typical errors of 0.54 mm translation and 0.56 degrees rotation between the polyethylene component and the underlying metallic component. Conclusions. A practical method has been developed for assessing mobile-bearing motion, in vivo. This method can be applied to other prosthetic devices, or combinations of components, once the requirement for identifiable landmarks has been addressed. Clinical Relevance. Skeletal and soft-tissue changes in the pathological knee may produce abnormal rotations and translations in the transverse tibial plane. This technique is intended both to validate the design philosophy of a mobile-bearing prosthesis and to provide additional data on any pathological motions, which will have implications for future prosthetic designs.

Journal Article↗

Current developments in esthetic dentistry.

Current developments in esthetic dentistry center around new techniques and materials that improve the clinician's ability to provide esthetic services. These developments include the availability of improved composites for anterior and posterior use, a new generation of dentin bonding agents, bonded ceramic restorations, and more efficient and predictable ways to whiten teeth. There is a better understanding of factors contributing to the esthetic value of restoration as well as their longevity. New bonding techniques to dentin enable practitioners to perform difficult restorative procedures in a conservative manner, producing results that are highly esthetic and physiologically tolerable. The use of dental porcelains has expanded from the traditional applications in crowns and bridges to veneers, inlays, onlays and all-porcelain bridges that are directly bonded to teeth. Computer-designed and fabricated inlays and onlays are now an available treatment modality, with a reported 3-years follow-up looking very promising. The increasing public demand for esthetic dental procedures has made the discipline a significant part of dental practice and boosted interests and understanding of procedures, such as tooth bleaching and peridontal surgery, for improved esthetics.

Composite Resins↗

A computer-assisted technique for 24-hour esophageal monitoring.

Modern computer design offers the opportunity to rapidly and objectively analyze the large quantity of data obtained during prolonged intraesophageal monitoring. The purpose of this study is: (1) to describe a rapid automated technique for acquisition and analysis of esophageal parameters, using a microcomputer; and (2) to compare computerized versus manual analysis of physiograph recordings. Ten normal subjects underwent 24-hr computerized monitoring of intraesophageal function, including: (1) pH recording at 5 and 10 cm above the lower esophageal sphincter (LES); (2) pharyngeal contraction; (3) esophageal contraction at 5 and 10 cm; (4) posteriorly directed LES pressures; and (5) gastric pressure. Segments from several studies were chosen for comparison of physiograph data with that obtained by computer. No significant differences were found except for the number of esophageal contractile events. This difference stems from a problem of shifting baseline related to subject position. Thus, the computer can be used for analysis of large quantities of data obtained from prolonged esophageal monitoring.

Computers↗

Sampling Schemes for Policy Analyses Using Computer Simulation Experiments

/ Evaluating the environmental and economic impacts of agricultural policies is not a simple task. A systematic approach to evaluation would include the effect of policy-dependent factors (such as tillage practices, crop rotations, and chemical use) as well as the effect of policy-independent covariates (such as weather, topography, and soil attributes) on response variables (such as amount of soil eroded or chemical leached into the groundwater). For comparison purposes, the effects of these input combinations on the response variable would have to be assessed under competing policy scenarios. Because the number of input combinations is high in most problems, and because policies to be evaluated are often not in use at the time of the study, practitioners have resorted to simulation experiments to generate data. However, generating data from simulation models is often costly and time consuming; thus, the number of input combinations in a study may be limiting even in simulation experiments. In this paper, we discuss the problem of designing computer simulation experiments that require generating data for just a fraction of the possible input combinations. We propose an approach that is based on subsampling the 1992 National Resources Inventory (NRI) points. We illustrate the procedure by assessing soil erosion in a situation where there are "observed" data [reported by the Natural Resources Conservation Service (NRCS)] for comparison. Estimates for soil erosion obtained using the procedure we propose are in good agreement with NRCS reported values.KEY WORDS: Metamodel; National Resources Inventory; Nonpoint source pollution

Journal Article↗

Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer.

Rapid growth of protein structures database in recent years requires an effective approach for objective comparison and classification of deposited protein structures. We describe a novel method for structure comparison and classification based on the alignment of one-dimensional structure profiles. These profiles are obtained by calculating the OCCO pseudodihedral angles (formed by O-C-C-O atoms of carbonyl groups of consecutive amino acid residues) from protein three-dimensional coordinates. These angle measurements are then converted into a 24 letter alphabet, and the protein structures are represented by sequences of letter from this alphabet. The BioSCAN parallel computer, designed for primary sequence alignment, is used to rapidly align and classify these one-dimensional structure profiles. We have developed and implemented weighted scoring matrix to identify structural classes based on commonly found structural motifs. The results of our experiments are in good agreement with the traditional protein structure classification schemes. One-dimensional structure profiles significantly improve efficiency of structure comparison and classification.

Algorithms↗

Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond.

Single-stranded regions in RNA secondary structure are important for RNA-RNA and RNA-protein interactions. We present a probability profile approach for the prediction of these regions based on a statistical algorithm for sampling RNA secondary structures. For the prediction of phylogenetically-determined single-stranded regions in secondary structures of representative RNA sequences, the probability profile offers substantial improvement over the minimum free energy structure. In designing antisense oligonucleotides, a practical problem is how to select a secondary structure for the target mRNA from the optimal structure(s) and many suboptimal structures with similar free energies. By summarizing the information from a statistical sample of probable secondary structures in a single plot, the probability profile not only presents a solution to this dilemma, but also reveals 'well-determined' single-stranded regions through the assignment of probabilities as measures of confidence in predictions. In antisense application to the rabbit beta-globin mRNA, a significant correlation between hybridization potential predicted by the probability profile and the degree of inhibition of in vitro translation suggests that the probability profile approach is valuable for the identification of effective antisense target sites. Coupling computational design with DNA-RNA array technique provides a rational, efficient framework for antisense oligonucleotide screening. This framework has the potential for high-throughput applications to functional genomics and drug target validation.

Algorithms↗

Repeat femoral arteriography in hyperlipidemic patients. A study of progression and regression of atherosclerosis.

Femoral arteriography was performed in 62 patients with significant hyperlipidemia. Sixty were asymptomatic and two had intermittent claudication. The patients participated in a study aiming to demonstrate whether serum lipid lowering by drugs could influence the development of femoral artery atheromatous disease. Half of the patients were treated with fenofibrate and nicotinic acid and the other half served as a control group. At the first arteriography atherosclerotic lesions were found in 46 of the 62 patients (74%). Arteriography was repeated up to three times without complication. Visual analysis of angiograms revealed considerable inter-observer variation. An attempt was made to assess the angiograms by a computerized method which, however, still needs improvement and a computer designed for image analysis. Most patients had small or moderate atheromatous deposits in the femoral artery at the initial examination, in most cases showing no change during the study period of 18 months. Regression was found in five patients of the treated group, but in none of the control patients as judged by visual gradation (p less than 0.001).

Adult↗

Users as designers: how people cope with poor HCI design in computer-based medical devices.

In this paper we examine how users interact with a computer-based infusion device adapted for terbutaline infusion to treat preterm labor in women experiencing high-risk pregnancies. This study examines (a) the human-computer interaction (HCI) deficiencies in the device as related to this context of use, (b) how the device characteristics increase the potential for error, and (c) the tailoring strategies developed by users to insulate themselves from failure. Interviews with nurses and tests of the behavior of the infusion device in different conditions identified several classic HCI deficiencies: complex and arbitrary sequences of operation, mode errors caused by poor differentiation of multiple operating modes intended for different contexts, ambiguous alarms, getting lost in multiple displays, and poor feedback on device state and behavior.

Drug Therapy, Computer-Assisted↗

[Exchange of information between community and central health authorities. Development of an EDP system for information processing in the communities].

The Ministry of Health and Social Affairs has started a research program introducing information technology into the float of information between central and local authorities. The prospect is to make a better platform for statistics and planning. This article describes the process of designing a computer program designed to meet the needs of the local authorities. The result is a program that integrates sending and receiving of data with preparation of the local annual report. An evaluation revealed that the need of such computer tools and support is greatest in the small municipalities.

Health Planning Support↗

Failures and successes in total hip replacement--why good ideas may not work.

The course of development of total hip replacement (THR) is neither harmonious nor linear. Progress and set-backs alternate. Progress in THR manifests itself through reductions in the number and the severity of complications (infection, aseptic loosening, prematurely worn components, etc.). Innovation is the motor of progress. However, today's innovation may well be tomorrow's revision! Progress has been achieved in part through new implant materials and designs that provide improvements in such things as stress distribution in surrounding bone, tissue compatibility and osseointegration, and resistance to both wear and cyclic fatigue. Of at least equal importance, however, are improvements achieved in operative procedures (e.g., cementing technique) and finally, in clinical quality control: more complete documentation of implant and patient variables, establishment of implant registers, and utilization of outcome studies to guide the course of further development. Causes of failure in THR are numerous. However, unexpected side effects of innovations are the most frequent cause. An innovation may solve one problem, but also creates new ones. Problems in innovation which can lead to failures include: over-generalization of expected patient responses, ignoring past experience or assigning wrong causes to encountered problems, and finally, ignoring the dynamic nature of the living system (which can be described as using "necro-" instead of biomechanical thinking). Quality control in both manufacturing and clinical practice has to be improved. The pioneer times have come to an end. Today's patients should have the right to be operated on by a well trained surgeon and to be provided with well tested, well-understood implant materials and devices. Progress in endoprosthetics has led to the present high level of clinical success. Paradoxically, however, success is the greatest obstacle to further progress. This is because the curve of progress as a result of effort expended has turned asymptotic in endoprosthetics, as it does in many endeavors. In such situations the more a product (e.g., surgical implant and procedure, automobile design, computer program) becomes successful, the more efforts (and finances) are needed for further progress. On the other hand, the "scissors"--created by crossing what might be feasible with what resources are available--open widely and can cut sharply. In fact, financial restrictions may force orthopaedic surgeons and the medical device and technology industry to turn to lower technologies in the future. However, whatever new developments in endoprosthetics may bring (be they sophistications or simplifications), we must remain open-minded and not assume things to be facts until there is evidence to support them.

Arthroplasty, Replacement, Hip↗

A rotating phantom for the study of flow effects in MR imaging.

A common type of phantom used for the study of flow effects in MR imaging is the tube phantom, where a liquid passes through a set of tubes placed in the main magnetic field of an MR scanner. Among the disadvantages with this type of phantom are that a distribution of velocities is present in each tube, and that quantifications of flow effects using tube phantoms may be very time-consuming. In this work, we describe the design and the properties of a rotating wheel flow phantom used for quantification of the effects of flow through the imaging plane as well as in the imaging plane. The proposed phantom is constructed as a rotating gel-filled wheel, surrounded by static volumes filled with the same gel, and the evaluation of the information from rotating and static parts is made with a specially designed computer program. The phantom can be used as a plug flow phantom covering simultaneously an interchangeable velocity interval, which at present has the range -52 mm/s, +52 mm/s. It is shown that the phantom gives adequate information on the dependence of pixel content on first-order motion in MR modulus and phase images. Among the fields of application are rapid calibration of MR imaging units for flow determination using phase information, as well as testing of pulse sequence characteristics and verification of theoretical predictions concerning the flow dependence in MR images.

Electron Spin Resonance Spectroscopy↗

Genetically encoded sensors for metabolites.

BACKGROUND: Metabolomics, i.e., the multiparallel analysis of metabolite changes occurring in a cell or an organism, has become feasible with the development of highly efficient mass spectroscopic technologies. Functional genomics as a standard tool helped to identify the function of many of the genes that encode important transporters and metabolic enzymes over the past few years. Advanced expression systems and analysis technologies made it possible to study the biochemical properties of the corresponding proteins in great detail. We begin to understand the biological functions of the gene products by systematic analysis of mutants using systematic PTGS/RNAi, knockout and TILLING approaches. However, one crucial set of data especially relevant in the case of multicellular organisms is lacking: the knowledge of the spatial and temporal profiles of metabolite levels at cellular and subcellular levels. METHODS: We therefore developed genetically encoded nanosensors for several metabolites to provide a basic set of tools for the determination of cytosolic and subcellular metabolite levels in real time by using fluorescence microscopy. RESULTS: Prototypes of these sensors were successfully used in vitro and also in vivo, i.e., to measure sugar levels in fungal and animal cells. CONCLUSIONS: One of the future goals will be to expand the set of sensors to a wider spectrum of substrates by using the natural spectrum of periplasmic binding proteins from bacteria and by computational design of proteins with altered binding pockets in conjunction with mutagenesis. This toolbox can then be applied for four-dimensional imaging of cells and tissues to elucidate the spatial and temporal distribution of metabolites as a discovery tool in functional genomics, as a tool for high-throughput, high-content screening for drugs, to test metabolic models, and to analyze the interplay of cells in a tissue or organ.

Animals↗

[Noninvasive analysis of cartilage volume and cartilage thickness in the human elbow joint using MRI].

The aim of the study was to non-invasively analyse the cartilage volume and thickness in the human elbow joint with magnetic resonance imaging. 12 fresh frozen specimens (ages 20 to 69 yrs.) were investigated using a 1.5 T magnet, and a water-excitation FLASH-3D sequence at a resolution of 1 x 0.25 x 0.25 mm3. After linear interpolation to 0.125 x 0.125 mm2 in the image plane, the cartilages were segmented interactively with a Snake algorithm. Following three-dimensional reconstruction, the cartilage volumes were determined, and the mean and maximal cartilage thickness computed by Euclidean distance transformation. The total cartilage volume of the human elbow joint amounted to between 3.90 and 7.17 ml (mean 5.5 ml +/- 20%). The humerus occupied 49 to 60%, the radius 15 to 27% and the ulna 20 to 29% of the total volume. The mean cartilage thickness ranged from an average of 0.9 (proximal part of the ulna) to 1.4 mm (capitulum humeri), and the maximal thickness from 2.3 mm (proximal part of the ulna) to 2.9 mm (distal part of the ulna). The ulnar cartilage showed a more inhomogeneous distribution than that of the humerus and radius. The interindividual variability of the cartilage thickness was less than that of the volume. There was no significant relationship of the volume with age (r = 0.11) or body weight (r = 0.51). However, based on the joint size (r = 0.71-medio-lateral extension of the articular surfaces) about 50% of the variability of the total cartilage volume could be predicted. The technique presented is suitable for designing computer models to investigate the load transmission and functional adaptation of diarthrodial joints, and for diagnosing and monitoring joint disease.

Adult↗

Infertility treatment: from cookery to science. The epidemiology of randomised controlled trials.

OBJECTIVES: To review the epidemiology of published randomised controlled trials in infertility treatment over the last 25 years, with special emphasis on the number and quality of trials. DESIGN: Computer literature review by MEDLINE backed up by a manual search of 41 journals. Each trial was classified according to the methodology described and quality criteria. The results were recorded in a computer database. Odds ratios (OR) and confidence intervals (CI) were calculated where the data were sufficient. SUBJECTS: Couples suffering from primary or secondary infertility. The trials studied 33,761 patients overall. SETTING: Institute of Epidemiology and Health Services Research, Leeds. RESULTS: Five hundred and one randomised trials in male and female infertility treatment were identified between 1966 and 1990. Pregnancy was an outcome in 291 (58%) and these were the subject of detailed analysis. Two hundred and twenty-four (77%) and 67 (23%) 'pregnancy trials' were concerned, respectively, with female and male infertility. Four per cent of the trials were preceded by a sample size calculation, and the average sample size was 96 patients (range 5-933); 700 patients per group would be required to demonstrate plausible success rates for most treatments. The method of randomisation was unstated or pseudo-randomised in 206 (71%) of trials where pregnancy was an outcome. Only 29 (5.8%) of studies were multicentre. The method of confirmation of pregnancy was omitted for 70% of papers. Cross-over design was used in 103 (21%) of cases. Meta-analysis is possible for selected topics such as the use of anti-oestrogens in idiopathic oligospermia and unexplained female infertility. Eight cases of double reporting were identified. CONCLUSIONS: Trials using randomised methodology were relatively few in comparison with other branches of medicine, although their use is important in the evaluation of treatment for infertility as treatment-independent pregnancy is common. It was encouraging to note that an exponential increase in the use of this methodology occurred during the last three years, especially in association with assisted conception techniques, and meta-analysis has become possible for selected topics. However, many trials suffer from an unrealistically small sample size, inappropriate use of cross-over design or pseudo-randomisation. The trend towards properly controlled studies should be encouraged but these studies should be of improved quality and organised on a multicentre or even international basis.

Female↗

[A software for comparing ambulatory blood pressure measurements (ABPM)].

The software (MAPA-PC) for personal computers, designed by the author, provides precise and fast studies of ABPM, especially when comparing two anti-hypertensive treatments. It implies strict definitions of groups (e.g. dippers), indices (peak, trough, peak/trough ratio), and the type of smoothing of measured values: means (over 1, 2 or 3 hours) or smoothing by functions (polynomials or trigonometric series). The software calculates standard parameters (nighttime and daytime means, peak, trough...) as well as more original values (nighttime and period from points of inflexion in the curve, slope in these points, coefficients of variation on differences between 2 ABPM of a given subject...). It uses statistical tests (Mann and Whitney's U. Pearson's chi square, Snedecor's F) to compare results of treatment. It provides many types of curves (blood pressure lines, box-plots) which show kinetics and variability of blood pressure. The user can compare various types of smoothing (e.g. 2 vs 3 harmonics in Fourier series). The software was used on 237 records of 79 patients, in a randomized trial. It was written with Turbo Pascal and works on DOS personal computers. It is interesting for epidemiologic studies or clinical trials in which ABPM are used.

Blood Pressure Monitoring, Ambulatory↗

A tensor analysis to evaluate the effect of high-pull headgear on Class II malocclusions.

The inaccuracies inherent in cephalometric analysis of treatment effects are well known. The objective of this article is to present a more reliable research tool in the analysis of cephalometric data. Bookstein introduced a dilation function by means of a homogeneous deformation tensor as a method of describing changes in cephalometric data. His article gave an analytic description of the deformation tensor that permits the rapid and highly accurate calculation of it on a desktop computer. The first part of this article describes the underlying ideas and mathematics. The second part uses the tensor analysis to analyze the cephalometric results of a group of patients treated with high-pull activator (HPA) to demonstrate the application of this research tool. Eight patients with Class II skeletal open bite malocclusions in the mixed dentition were treated with HPA. A control sample consisting of eight untreated children with Class II who were obtained from The Ohio State University Growth Study was used as a comparison group. Lateral cephalograms taken before and at the completion of treatment were traced, digitized, and analyzed with the conventional method and tensor analysis. The results showed that HPA had little or no effect on maxillary skeletal structures. However, reduction in growth rate was found with the skeletal triangle S-N-A, indicating a posterior tipping and torquing of the maxillary incisors. The treatment also induced additional deformation on the mandible in a downward and slightly forward direction. Together with the results from the conventional cephalometric analysis, HPA seemed to provide the vertical and rotational control of the maxilla during orthopedic Class II treatment by inhibiting the downward and forward eruptive path of the upper posterior teeth. The newly designed computer software permits rapid analysis of cephalometric data with the tensor analysis on a desktop computer. This tool may be useful in analyzing growth changes for research data.

Activator Appliances↗