Progress in the clinical application of evoked potentials. Introduction and methodologic considerations.
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Cerebral Cortex↗
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[Methodological developments in clinical pathology].
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Computers↗
Combination of computational prescreening and experimental library construction can accelerate enzyme optimization by directed evolution.
Chiral compounds can be produced efficiently by using biocatalysts. However, wild-type enzymes often do not meet the requirements of a production process, making optimization by rational design or directed evolution necessary. Here, we studied the lipase-catalyzed hydrolysis of the model substrate 1-(2-naphthyl)ethyl acetate both theoretically and experimentally. We found that a computational equivalent of alanine scanning mutagenesis based on QM/MM methodology can be applied to identify amino acid positions important for the activity of the enzyme. The theoretical results are consistent with concomitant experimental work using complete saturation mutagenesis and high-throughput screening of the target biocatalyst, a lipase from Bacillus subtilis. Both QM/MM-based calculations and molecular biology experiments identify histidine 76 as a residue that strongly affects the catalytic activity. The experiments demonstrate its important influence on enantioselectivity.
Amino Acid Substitution↗
Negative correlates of computer game play in adolescents.
There is some concern that playing computer games may be associated with social isolation, lowered self-esteem, and aggression among adolescents. Measures of these variables were included in a questionnaire completed by 204 year eight students at a North London comprehensive school. Principal components analysis of a scale to assess needs fulfilled by game play provided some support for the notion of 'electronic friendship' among boys, but there was no evidence that game play leads to social isolation. Play was not linked to self-esteem in girls, but a negative relationship was obtained between self-esteem and frequency of play in boys. However, self-esteem was not associated with total exposure to game play. Aggression scores were not related to the number of games with aggressive content named among three favourite games, but they were positively correlated with total exposure to game play. A multiple regression analysis revealed that sex and total game play exposure each accounted for a significant but small amount of the variance in aggression scores. The positive correlation between playing computer games and aggression provides some justification for further investigation of the causal hypothesis, and possible methodologies are discussed.
Adolescent↗
Towards predictive ligand design with free-energy based computational methods?
The accurate prediction of ligand-biopolymer binding affinities is of general interest to medicinal chemistry, as well as to the broader field of molecular recognition. The ability to predict computationally the thermodynamics of these molecular recognition processes has been relatively weak until recently, however, continued developments on several fronts are extending the scope of applicability of these methods. The rapid growth in the number of protein-ligand structures has initially led to the development of a range of empirical scoring functions based on relatively simple descriptions of intermolecular interactions. These methods have had some success in ranking binding affinities when tuned to particular protein systems or in rather qualitative estimates of molecular fit in fast docking calculations. However, they are too unreliable for more detailed, quantitative, assessment and comparison of binding affinities. Physics-based free energy calculations are in principle more general and have the potential to be significantly more accurate. These approaches have seen steady development over many years and rely on carefully calibrated molecular energy functions (force-fields), simulations of the systems with explicit solvent, and the coming-of-age of continuum solvation models. In addition to the initially developped Free Energy Perturbation (FEP) and Thermodynamic Integration (TI) methods, new approaches include the Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) and the Linear Interaction Energy (LIE) approaches. This review concentrates on MM-PBSA and LIE, and their variants. The routine application of these calculations is becoming possible because of enhanced computational hardware and the development of a range of computational chemistry tools. This review addresses: i) the basic principles behind free energy calculations ii) recent methodological advances iii) comparisons of predicted and experimentally determined affinities iv) the uncertainties and limitations of both the computational and experimental data v) areas where progress can be made vi) the practicality of applying the methods at the different stages of the drug discovery and optimization process.
Animals↗
Advanced exact structure searching in large databases of chemical compounds.
Efficient recognition of tautomeric compound forms in large corporate or commercially available compound databases is a difficult and labor intensive task. Our data indicate that up to 0.5% of commercially available compound collections for bioscreening contain tautomers. Though in the large registry databases, such as Beilstein and CAS, the tautomers are found in an automated fashion using high-performance computational technologies, their real-time recognition in the nonregistry corporate databases, as a rule, remains problematic. We have developed an effective algorithm for tautomer searching based on the proprietary chemoinformatics platform. This algorithm reduces the compound to a canonical structure. This feature enables rapid, automated computer searching of most of the known tautomeric transformations that occur in databases of organic compounds. Another useful extension of this methodology is related to the ability to effectively search for different forms of compounds that contain ionic and semipolar bonds. The computations are performed in the Windows environment on a standard personal computer, a very useful feature. The practical application of the proposed methodology is illustrated by several examples of successful recovery of tautomers and different forms of ionic compounds from real commercially available nonregistry databases.
Algorithms↗
Three-dimensional computed tomography-guided multitract aspiration of extensive ganglionic hemorrhage: technical note.
BACKGROUND: We describe a methodology for effectively improving the lysis and drainage of intracerebral hematomas during stereotactic surgery. METHODS: Stereotactic aspiration using a multitrack technique was performed in 20 patients with ganglionic hemorrhages perforating into the subcortex. Using 3-dimensional computed tomography (3D-CT) guidance, the trajectories and targets of hematoma drainage were selected to extract most portions of the irregular and expansive intracerebral hematomas. Volumes ranged from 36 to 60 mL (mean, 45 mL). Four to 5 drains were inserted into the parenchymal and ventricular clots. Aspiration and injections of urokinase (5000 IU) were repeated every 2 to 3 hours until the hematoma was almost completely removed. RESULTS: The intended catheters for hematoma aspiration were placed precisely along the predetermined tracks with the aid of 3D-CT visualization. The deep and subcortical hematomas were totally removed within a mean of 10 hours postoperatively. Multiple catheter placements itself caused no complications. Sixteen patients (80%) recovered with a favorable neurological outcome. CONCLUSIONS: The 3D-CT-based multitrack technique is a rapid and effective method for the stereotactic removal of extensive ganglionic hemorrhages. It has the advantage of giving better neurological recovery than conventional stereotactic or microscopic surgery for selected patients.
Adult↗
[Curietherapy in the carcinoma of the uterine cervix. Comparison of the obtained by computer dosimetric informations. Cooperative study by the European Group of curietherapists (author's transl)].
A cooperative study was taken to comparate the doses, obtained by the different institutes. The European Group had first defined the important points of the irradiated volume. This study has shown the great differencies between the doses of the institutes. First, the reference points for the surrounding structures were examined. The average of the doses at the inferior points of the Fletcher's lymphatic trapezium varies between 500 and 1 500 rads. This at the pelvic wall point is usually more important (10 or 15%). The doses at the delicate organs, the bladder and the rectum were studied in second. The average of the maximal vesical doses varies from 4 000 to 4 900 rads in the preoperative group; the average of the maximal rectal doses between 2 100 and 5 200 rads in the same group. The examination of the mean rectal dose was difficult. Every Institute has his own means of determining it. At last the size of the reference volume was considered. The 6 000 rads isodose was selected for the whole treatment. The height of this volume seems to be essentially dependent of the length of the uterine source. There seems existing some parallelism between the width and the thickness of the reference volume, but there are many differencies from an Institute to another. Now the Group has to determine a dosimetric methodology which may be transmissible.
Brachytherapy↗
A systematic review of human avoidance learning: Cognition, computation, and methods.
Avoidance behaviour is fundamental for survival but can become maladaptive in clinical conditions. A large body of literature has accumulated on the dynamics of human avoidance learning. However, current theories and overviews do not provide an exhaustive account of this evidence. In this systematic review, we identify N = 116 studies on human avoidance learning. We analyse these studies with the goal of distilling robust empirical phenomena as a basis for theory-building, and examine their diagnostic value in differentiating between competing theories. We find that the evidence is difficult to reconcile with foundational two-factor and classical safety-signal accounts, and most strongly supports expectancy- and inference-based views, in which avoidance responses are selected with respect to represented consequences. At the same time, no current framework provides a complete account of the evidence: several findings point to an additional role for operant valuation, Pavlovian influences, and contextual or latent-state control over the expression of avoidance. Methodologically, we observe that the problem setting in the most common experimental paradigms is radically simpler than real-world avoidance and therefore unlikely to expose the limits of inferential or reflective mechanisms. Consequently, we argue that paradigms with greater computational demands and more realistic action affordances are required to identify the mechanisms underlying avoidance learning. Collectively, these insights provide a foundation for theoretical refinement, computational modelling, and methodological innovation, with implications for advancing interventions targeting maladaptive avoidance.
Humans↗
Using ontologies linked with geometric models to reason about penetrating injuries.
OBJECTIVE: Medical assessment of penetrating injuries is a difficult and knowledge-intensive task, and rapid determination of the extent of internal injuries is vital for triage and for determining the appropriate treatment. Physical examination and computed tomographic (CT) imaging data must be combined with detailed anatomic, physiologic, and biomechanical knowledge to assess the injured subject. We are developing a methodology to automate reasoning about penetrating injuries using canonical knowledge combined with specific subject image data. METHODS AND MATERIAL: In our approach, we build a three-dimensional geometric model of a subject from segmented images. We link regions in this model to entities in two knowledge sources: (1) a comprehensive ontology of anatomy containing organ identities, adjacencies, and other information useful for anatomic reasoning and (2) an ontology of regional perfusion containing formal definitions of arterial anatomy and corresponding regions of perfusion. We created computer reasoning services ("problem solvers") that use the ontologies to evaluate the geometric model of the subject and deduce the consequences of penetrating injuries. RESULTS: We developed and tested our methods using data from the Visible Human. Our problem solvers can determine the organs that are injured given particular trajectories of projectiles, whether vital structures--such as a coronary artery--are injured, and they can predict the propagation of injury ensuing after vital structures are injured. CONCLUSION: We have demonstrated the capability of using ontologies with medical images to support computer reasoning about injury based on those images. Our methodology demonstrates an approach to creating intelligent computer applications that reason with image data, and it may have value in helping practitioners in the assessment of penetrating injury.
Diagnosis, Computer-Assisted↗
Unimolecular rovibrational bound and resonance states for large angular momentum: J=20 calculations for HO2.
We explore the calculation of unimolecular bound states and resonances for deep-well species at large angular momentum using a Chebychev filter diagonalization scheme incorporating doubling of the autocorrelation function as presented recently by Neumaier and Mandelshtam [Phys. Rev. Lett. 86, 5031 (2001)]. The method has been employed to compute the challenging J=20 bound and resonance states for the HO2 system. The methodology has firstly been tested for J=2 in comparison with previous calculations, and then extended to J=20 using a parallel computing strategy. The quantum J-specific unimolecular dissociation rates for HO2-->H+O2 in the energy range from 2.114 to 2.596 eV have been reported for the first time, and comparisons with the results of Troe and co-workers [J. Chem. Phys. 113, 11019 (2000) Phys. Chem. Chem. Phys. 2, 631 (2000)] from statistical adiabatic channel method/classical trajectory calculations have been made. For most of the energies, the reported statistical adiabatic channel method/classical trajectory rate constants agree well with the average of the fluctuating quantum-mechanical rates. Near the dissociation threshold, quantum rates fluctuate more severely, but their average is still in agreement with the statistical adiabatic channel method/classical trajectory results.
Journal Article↗
Operating room scheduling data base analysis for scheduling.
A methodology to determine and maintain the schedule times used in a computer-based OR Scheduling System is presented. State-of-the-art equations to be used for different scheduling situations are presented and discussed with the attendant data base reduction methodology to provide the scheduling parameters. An example is given of the data reduction methodology as well as suggestions for maintenance of the data base.
Hospital Information Systems↗
Comparison of artificial neural networks (ANN) with classical modelling techniques using different experimental designs and data from a galenical study on a solid dosage form.
Artificial Neural Networks (ANN) methodology was used to analyse experimental data from a tabletting study and compared both graphically and numerically to classical modelling techniques (i.e. Response surface methodology, RSM). The aim of this investigation was to describe quantitatively the degree of data fitting achieved and the robustness of the developed models using two types of experimental design (i.e. a statistical, highly organised design and a randomised design). To compare goodness of fit, the R(2) coefficient was used, whereas for the robustness of the models the R(2) coefficient of an independent validation data set was computed. Comparable results were achieved for both ANN and RSM methodology when using the statistical plan. However, the robustness of the models when developed based on a randomised plan was clearly better for the ANN methodology. Based on the results of this study, it appears that the ANN methodology is much less sensitive to the organisational level of a trial design and is therefore better adapted to the data analysis of the results of historical or poorly organised trials. All tablet properties determined were largely influenced by the dwell time during compression as well as by concentration of silica aerogel and magnesium stearate, whereas the other factors showed very much weaker effects.
Biopharmaceutics↗
Speechreading and the structure of the lexicon: computationally modeling the effects of reduced phonetic distinctiveness on lexical uniqueness.
A lexical modeling methodology was employed to examine how the distribution of phonemic patterns in the lexicon constrains lexical equivalence under conditions of reduced phonetic distinctiveness experienced by speech-readers. The technique involved (1) selection of a phonemically transcribed machine-readable lexical database, (2) definition of transcription rules based on measures of phonetic similarity, (3) application of the transcription rules to a lexical database and formation of lexical equivalence classes, and (4) computation of three metrics to examine the transcribed lexicon. The metric percent words unique demonstrated that the distribution of words in the language substantially preserves lexical uniqueness across a wide range in the number of potentially available phonemic distinctions. Expected class size demonstrated that if at least 12 phonemic equivalence classes were available, any given word would be highly similar to only a few other words. Percent information extracted (PIE) [D. Carter, Comput. Speech Lang. 2, 1-11 (1987)] provided evidence that high-frequency words tend not to reside in the same lexical equivalence classes as other high-frequency words. The steepness of the functions obtained for each metric shows that small increments in the number of visually perceptible phonemic distinctions can result in substantial changes in lexical uniqueness.
Electronic Data Processing↗
[Computer simulation of protein molecular dynamics].
A review of the works on the computer simulation of the globular protein dynamics is given. Methodological aspects of the simulation procedure are outlined briefly. Main peculiarities of protein dynamics revealed in the course of simulation of pancreatic trypsin inhibitor and cytochrome c are presented. The causes of "anomalous" processes, inherent in the simulated behaviour of model proteins are discussed. These "anomalous" processes are: continuous drift of the structure and its deviation from the experimental one, determined by X-ray analysis. Both processes are supposed to be the consequence of the reduced conformational rigidity of the model protein in comparison to the real one. Among the possible reasons for this reduced rigidity absence of the water molecules, hydrating peptide groups in the real protein, may be mentioned. Analogy between "anomalous" processes in the simulated protein dynamics and some phenomena observed in the real proteins during their functioning is drawn.
Computers↗
Spatio-logical processes in intracellular signalling.
Classical models of intracellular signalling describe how small changes in a cell's external environment can bring about major changes in cellular activity. Recent findings from experimental biology indicate that many intracellular signalling systems show a high level of spatial organisation. This permits the modification, by protein kinase or protein phosphatase action, of specific subsets of intracellular proteins - an attribute that is not addressed in classical signalling models. Here we use ideas and concepts from computer science to describe the information processing nature of intracellular signalling pathways and the impact of spatial heterogeneity of their components (e.g. protein kinases and protein phosphatases) on signalling activity. We argue that it is useful to view the signalling ecology as a vast parallel distributed processing network of agents operating in heterogeneous microenvironments, and we conclude with an overview of the mathematical and semantic methodologies that might help clarify this analogy between biological and computational systems.
Models, Biological↗
Age differences in the performance of computer-based work.
This study investigated the extent to which age had an impact on the performance of computer-based work. Three simulated real-world computer-interactive tasks that varied in complexity and pacing requirements were evaluated. Ss included 65 women, ranging in age from 25 years to 70 years. The methodology encompassed physiological, subjective, and objective performance measures. The data indicated that previous computer experience and age had a significant impact on the performance of the 3 tasks. Increased age was associated with longer response times and a greater number of errors for all 3 tasks. Age also influenced perceptions of fatigue and task difficulty. The findings are discussed in terms of the implications for training and job design.
Adult↗
Space as the final frontier in stochastic simulations of biological systems.
Recent technological and theoretical advances are only now allowing the simulation of detailed kinetic models of biological systems that reflect the stochastic movement and reactivity of individual molecules within cellular compartments. The behavior of many systems could not be properly understood without this level of resolution, opening up new perspectives of using computer simulations to accelerate biological research. We review the modeling methodology applied to stochastic spatial models, also to the attention of non-expert potential users. Modeling choices, current limitations and perspectives of improvement of current general-purpose modeling/simulation platforms for biological systems are discussed.
Animals↗
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