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PubMed1992

Preverbal and verbal counting and computation.

We describe the preverbal system of counting and arithmetic reasoning revealed by experiments on numerical representations in animals. In this system, numerosities are represented by magnitudes, which are rapidly but inaccurately generated by the Meck and Church (1983) preverbal counting mechanism. We suggest the following. (1) The preverbal counting mechanism is the source of the implicit principles that guide the acquisition of verbal counting. (2) The preverbal system of arithmetic computation provides the framework for the assimilation of the verbal system. (3) Learning to count involves, in part, learning a mapping from the preverbal numerical magnitudes to the verbal and written number symbols and the inverse mappings from these symbols to the preverbal magnitudes. (4) Subitizing is the use of the preverbal counting process and the mapping from the resulting magnitudes to number words in order to generate rapidly the number words for small numerosities. (5) The retrieval of the number facts, which plays a central role in verbal computation, is mediated via the inverse mappings from verbal and written numbers to the preverbal magnitudes and the use of these magnitudes to find the appropriate cells in tabular arrangements of the answers. (6) This model of the fact retrieval process accounts for the salient features of the reaction time differences and error patterns revealed by experiments on mental arithmetic. (7) The application of verbal and written computational algorithms goes on in parallel with, and is to some extent guided by, preverbal computations, both in the child and in the adult.

Animals↗

PubMed2006

Model-based blood glucose control for Type 1 diabetes via parametric programming.

An advanced model-based control technique for regulating the blood glucose for patients with Type 1 diabetes is presented. The optimal insulin delivery rate is obtained off-line as an explicit function of the current blood glucose concentration of the patient by using novel parametric programming algorithms, developed at Imperial College London. The implementation of the optimal insulin delivery rate, therefore, requires simple function evaluation and minimal on-line computations. The proposed framework also addresses the uncertainty in the model due to interpatient and intrapatient variability by identifying the model parameters which ensure that a feasible control law can be obtained. The developments reported in this paper are expected to simplify the insulin delivery mechanism, thereby enhancing the quality of life of the patient.

Blood Glucose↗

PubMed2003

The informatics of a C57BL/6J mouse brain atlas.

The Mouse Atlas Project (MAP) aims to produce a framework for organizing and analyzing the large volumes of neuroscientific data produced by the proliferation of genetically modified animals. Atlases provide an invaluable aid in understanding the impact of genetic manipulations by providing a standard for comparison. We use a digital atlas as the hub of an informatics network, correlating imaging data, such as structural imaging and histology, with text-based data, such as nomenclature, connections, and references. We generated brain volumes using magnetic resonance microscopy (MRM), classical histology, and immunohistochemistry, and registered them into a common and defined coordinate system. Specially designed viewers were developed in order to visualize multiple datasets simultaneously and to coordinate between textual and image data. Researchers can navigate through the brain interchangeably, in either a text-based or image-based representation that automatically updates information as they move. The atlas also allows the independent entry of other types of data, the facile retrieval of information, and the straight-forward display of images. In conjunction with centralized servers, image and text data can be kept current and can decrease the burden on individual researchers' computers. A comprehensive framework that encompasses many forms of information in the context of anatomic imaging holds tremendous promise for producing new insights. The atlas and associated tools can be found at http://www.loni.ucla.edu/MAP.

Anatomy, Artistic↗

PubMed2006

Distributed virtual experiments in water quality management.

Since the complexity of virtual experiments (VEs) and their underlying models is constantly increasing, computational performance of monolithic software solutions is rapidly becoming insufficient. Examples of VEs are probabilistic design, model calibration, optimal experimental design and scenario analysis. In order to tackle this computational bottleneck, a framework for the distributed execution of VEs on a potentially heterogeneous pool of work nodes has been implemented. This framework was named WDVE (WEST distributed virtual experimentation) and is built on top of technologies such as C++, XML and SOAP. It was designed for stability, expandability, performance, platform-independence and ease of use. Complex VEs are most often composed of mutually independent sub-experiments, which can be run concurrently. With WDVE, a complex VE that is executed on a so-called Master machine will therefore attempt to execute its sub-experiments on Slave machines that have previously registered with the Master. The process of submitting requests for the execution of sub-experiments is transparent and involves the transfer of a description of the experiment to be executed, and the resources that are needed for the execution (i.e., model and input data). WDVE is in many ways similar to the Grid Computing paradigm, which is currently receiving widespread attention. However, WDVE is more geared towards application within the scope of water quality management.

Calibration↗

PubMed1998

[Computer-assisted surgical navigation with a dynamic mobile framework for the nasal fossae, sinuses and base of the skull].

Surgery of the skull base and of the paranasal sinuses is often difficult because of the complex anatomy and the delicate structures; serious complications (loss of vision, cerebral lesion) have been reported. To improve the safety of such operations, computer-assisted navigation surgery is increasingly being put to use. We introduce the system which was developed in Berne. Our computer-assisted system is based on an intraoperative pursuit of the head and instruments which are equipped with infrared diodes and registered by an opto-electronic system-camera. The CT-acquisition of the head is accomplished framelessly without a head-holding device. This allows free movement of the head during surgery. Between March and November 1997, 35 navigation operations were performed for various pathologies at the anterior and lateral skull base. The majority of the cases were endonasal operations. No surgical complications occurred inspite of the complexity of the operations. The measured accuracy of the system between the CT and the actual instrument location in the patient was 0.5-2 mm (mean : < 1 mm) for the anterior skull base and 1-2.5 mm (mean < 1.5 mm) for the lateral skull base. The intraoperative navigation system allows identification of essential anatomical structures and permits safe and efficient surgery without additional loss of time. In addition, such a system allows minimal invasive approaches, and new operations may become possible.

Adult↗

PubMed2026

Dynamic Protein Structure Paradox: An Integrative Framework for Endpoint-Conditioned Evidentiary Sufficiency in Structure-to-Function Claims.

Accurate coordinates for a represented protein state do not, by themselves, establish activity or any other condition-specific function. This article defines the Dynamic Protein Structure Paradox (DPSP) as the apparent conflict between structural accuracy and functional underdetermination and develops it as an integrative evidentiary assessment framework rather than a new theory or paradigm. The underlying problem has been longstanding, since structural genomics, function annotation, allostery, and disorder research each established that fold does not determine function and that function does not determine fold. DPSP consolidates those results into one endpoint-conditioned rule. Once a measurable endpoint is defined, it assesses four coupled dimensions: relevant-state completeness, context completeness, ensemble or kinetic dependence, and chemical dependence. A rubric rates each dimension as adequate, uncertain, or missing, and a materiality test determines which gaps influence the stated decision. The outcome is one of three mutually exclusive modes of utilization: geometry-led, conditional, or function-measured. The deliverable is a concise evidence statement delineating what the structure supports, which decisive variable remains unmeasured, and what corroboration is necessary. DPSP complements, rather than replaces, existing structural, ensemble, and computational approaches. The framework remains unvalidated, its thresholds are provisional, and the studies necessary to confirm or refute it are specified.

Proteins↗

PubMed2005

An evaluation of contrast enhancement techniques for mammographic breast masses.

The main aim of this paper is to propose a novel set of metrics that measure the quality of the image enhancement of mammographic images in a computer-aided detection framework aimed at automatically finding masses using machine learning techniques. Our methodology includes a novel mechanism for the combination of the metrics proposed into a single quantitative measure. We have evaluated our methodology on 200 images from the publicly available digital database for screening mammograms. We show that the quantitative measures help us select the best suited image enhancement on a per mammogram basis, which improves the quality of subsequent image segmentation much better than using the same enhancement method for all mammograms.

Algorithms↗

PubMed2006

Metabolic engineering under uncertainty--II: analysis of yeast metabolism.

Yeast metabolism has been used extensively in scientific investigations and industrial applications. Understanding the properties of the yeast metabolic network is crucial, yet unaccomplished due to its high complexity, the different culture conditions, and the uncertainty associated with kinetic parameters. We recently developed a computational and mathematical framework using Monte Carlo method in which parameter uncertainty can be addressed through large-scale sampling procedure. This framework was applied on the compartmentalized central carbon pathways of Saccharomyces cerevisiae metabolism considering the growth environment of batch and chemostat reactor and integrating information from metabolic flux analysis. Statistical analysis of the results indicates that yeast cells growing in batch culture condition exhibit dramatically different control schemes from those growing in a chemostat. The difference is mainly due to the feedback introduced by the constraints of the chemostat. The control of the enzymes on the rates of the substrate uptake, product excretion, and cell growth and its practical implication are discussed. Clustering of the reaction steps according to the similarity of their responses to enzyme activity perturbations reveals functional coupling of metabolic reactions.

Bioreactors↗

PubMed2005

Tetrahedral distortion and energetic packing penalty in "zeolite" frameworks: linked phenomena?

We report a computational study on the distortion of SiO4 tetrahedra in zeolite frameworks. For all previously observed frameworks, the tetrahedral mismatch was found to span a narrow range (1.0 x 10(-3) to 2.5 x 10(-2) angstroms2) of values, in contrast to the hypothetical frameworks, which were calculated to have a much wider range of mismatch values. The energy of the frameworks was not found to be a function of the tetrahedral distortion for the previously observed and moderately distorted (tetrahedral mismatch <2.5 x 10(-2) angstroms2) hypothetical frameworks. In contrast, the energy of the bulk of the hypothetical frameworks was shown to be a strong function of the tetrahedral distortion. The fact that the framework energies of some hypothetical frameworks lie much higher than both those of the observed frameworks and the values we would expect from our previously developed topological method (the so-called energetic packing penalty) is explained in terms of the tetrahedral distortion contribution to the framework energy which is negligible for the observed frameworks. Finally, it is hypothesized that the absence of tetrahedral distortion is pivotal for a framework to be experimentally realized, in which case a large fraction of hypothetical frameworks are unrealizable and will forever remain in the realms of the abstract.

Letter↗

PubMed2026

Mining the sHSP20 (small heat-shock protein) gene family in finger millet (Eleusine coracana (L.) Gaertn.): structural, evolutionary and predicted abiotic-stress-responsive insights.

Small heat-shock proteins (sHSPs, the HSP20 family) are ATP-independent molecular chaperones that hold partially unfolded substrates and protect the proteome during heat and other abiotic stresses; every member is defined by a conserved α-crystallin domain (ACD). Finger millet (Eleusine coracana) is a climate-resilient, calcium-rich allotetraploid cereal of the semi-arid tropics whose HSP20 repertoire had not been catalogued. The present study is an entirely computational (in silico) analysis of the chromosome-scale reference genome of finger millet (NCBI GenBank assembly GCA_032690845.1, cultivar KNE 796-S). Mining the predicted proteome with the ACD profile (Pfam PF00011) and confirming every candidate by NCBI CD-search recovered 76 non-redundant ACD-bearing HSP20 genes (EcHSP20-1-EcHSP20-76). Based on phylogeny and TargetP-predicted localization, the members were classified into ten subfamilies: seven cytosolic/nuclear classes (C-I to C-VII, 60 members) together with chloroplastic (11), mitochondrial (3) and endoplasmic-reticulum (2) groups. The proteins ranged from 110 to 355 amino acids (12.1-39.2 kDa) with theoretical pI of 4.85-9.69. The 76 loci were distributed over 14 of the 18 chromosomes and were conspicuously absent from chromosomes 8 A, 8B, 9 A and 9B, with pronounced clustering on chromosomes 1, 2, 3 and 6. Duplication analysis detected 149 paralogous pairs (49 homoeologous, 80 segmental/dispersed and 18 tandem); 147 of 148 pairs for which substitution rates could be calculated returned Ka/Ks < 1 (mean 0.20), indicating strong purifying selection consistent with retention after whole-genome/allopolyploid duplication. Promoter analysis (PlantCARE) revealed enrichment of abscisic-acid-responsive (ABRE), MYB/MYC drought-related, STRE, DRE, low-temperature (LTR) and methyl-jasmonate/salicylic-acid elements, whereas canonical heat-shock elements (HSE) were not recovered. Expression profiling against a public drought transcriptome (SRP081350) showed that about half of the genes (39 of 76) are transcribed in leaf tissue, the expressed fraction being dominated by the cytosolic class C-I. This first finger-millet HSP20 catalogue provides a verified, reproducible framework and nominates computationally predicted candidate genes for future functional work on thermotolerance in cereals.

Allotetraploid↗

PubMed2004

Mechanism of the hydrogen transfer from the OH group to oxygen-centered radicals: proton-coupled electron-transfer versus radical hydrogen abstraction.

High-level ab initio electronic structure calculations have been carried out with respect to the intermolecular hydrogen-transfer reaction HCOOH+.OH-->HCOO.+H(2)O and the intramolecular hydrogen-transfer reaction .OOCH2OH-->HOOCH(2)O.. In both cases we found that the hydrogen atom transfer can take place via two different transition structures. The lowest energy transition structure involves a proton transfer coupled to an electron transfer from the ROH species to the radical, whereas the higher energy transition structure corresponds to the conventional radical hydrogen atom abstraction. An analysis of the atomic spin population, computed within the framework of the topological theory of atoms in molecules, suggests that the triplet repulsion between the unpaired electrons located on the oxygen atoms that undergo hydrogen exchange must be much higher in the transition structure for the radical hydrogen abstraction than that for the proton-coupled electron-transfer mechanism. It is suggested that, in the gas phase, hydrogen atom transfer from the OH group to oxygen-centered radicals occurs by the proton-coupled electron-transfer mechanism when this pathway is accessible.

Journal Article↗

PubMed2005

Application of cause-and-effect analysis to potentiometric titration.

A first attempt has been made to interpret physicochemical data from potentiometric titration analysis in accordance with the complete measurement-uncertainty budget approach (bottom-up) of ISO and Eurachem. A cause-and-effect diagram is established and discussed. Titration data for arsenazo III are used as a basis for this discussion. The commercial software Superquad is used and applied within a computer-intensive resampling framework. The cause-and-effect diagram is applied to evaluation of seven protonation constants of arsenazo III in the pH range 2-10.7. The data interpretation is based on empirical probability distributions and their analysis by second-order correct confidence estimates. The evaluated data are applied in the calculation of a speciation diagram including uncertainty estimates using the probabilistic speciation software Ljungskile.

Arsenazo III↗

PubMed1996

Hormone replacement therapy in a risk-benefit perspective.

The relative cost-effectiveness of different treatment strategies for hormone replacement therapy (HRT) was assessed within the framework of a computer model. Where data were lacking, it was necessary to make assumptions about the effects of HRT, particularly in relation to combined oestrogen-progestogen therapy and cardiovascular disease; however, sensitivity analyses were performed to assess the impact of changing these assumptions on the cost-effectiveness equation. It appears that net expenditure by the NHS will depend critically on the direct costs of treatment, rather than on any indirect costs incurred or saved as a result of side-effects. In terms of mortality, a reduction in cardiovascular disease risk would have greatest impact and would overshadow any small increase in breast cancer risk which may be associated with long-term use. If the cardioprotective effect of oestrogen is real, our results suggest that long-term prophylactic treatment of hysterectomised women would be relatively cost-effective. Treatment of symptomatic menopausal women for any period of time appears to offer very good value for money. The lack of data relating to combined oestrogen-progestogen therapy and cardioprotection, and the major importance of the latter in the equation of benefits and risks, make it more difficult to draw conclusions about the cost-effectiveness of treating non-hysterectomised asymptomatic women for prophylactic reasons.

Aged↗

PubMed1993

Exploring the relationship between rationality and bounded rationality in medical knowledge-based systems.

If our goal in Artificial Intelligence in Medicine (AIM) is to engineer systems health-care providers will both use and, in the process, improve their performance, we must concentrate on the development of causal theories of knowledge and problem solving. One broad direction in pursuing this goal is understanding the relationships between existing models of rationality and bounded rationality for similar tasks. Models of rationality refer to those approaches in which the optimal properties of the models are deductively provable, i.e. in which the processing is rational. Representative models of rationality used in AIM are deductive logical models, statistical models such as Bayesian inference models, and decision-analytic models. Models of bounded rationality are those which do not guarantee such optimal properties nor yield to deductive correctness proofs. These models have their roots in cognitive psychology. In this article we show how explicating the relationship between models of rationality and bounded rationality might be done in the case of abductive tasks in medicine. This is done by positioning these modeling approaches within the same framework (an abstract computational model) and interpreting in this context both computational complexity results concerning the nature of the task and empirical results studies of human problem-solving behavior.

Artificial Intelligence↗

PubMed2006

Using engineering control principles to inform the design of adaptive interventions: a conceptual introduction.

The goal of this paper is to describe the role that control engineering principles can play in developing and improving the efficacy of adaptive, time-varying interventions. It is demonstrated that adaptive interventions constitute a form of feedback control system in the context of behavioral health. Consequently, drawing from ideas in control engineering has the potential to significantly inform the analysis, design, and implementation of adaptive interventions, leading to improved adherence, better management of limited resources, a reduction of negative effects, and overall more effective interventions. This article illustrates how to express an adaptive intervention in control engineering terms, and how to use this framework in a computer simulation to investigate the anticipated impact of intervention design choices on efficacy. The potential benefits of operationalizing decision rules based on control engineering principles are particularly significant for adaptive interventions that involve multiple components or address co-morbidities, situations that pose significant challenges to conventional clinical practice.

Drug Administration Schedule↗

PubMed2005

Electron optical phase-shifts by Fourier methods: analytical versus numerical calculations.

The theoretical framework for the computation of electromagnetic fields and electron optical phase-shifts in Fourier space has been recently applied to objects with long-range fringing fields, such as reverse-biased p-n junctions and magnetic stripe domains near a specimen edge. In addition to new analytical results, in this work, we present a critical comparison between numerical and analytical computations. The influence of explicit and implicit boundary conditions on the phase shifts and phase-contrast images is also investigated in detail.

Journal Article↗

PubMed1990

A computational theory of the hippocampal cognitive map.

Evidence from single unit and lesion studies suggests that the hippocampal formation acts as a spatial or cognitive map (O'Keefe and Nadel, 1978). In this chapter, I summarise some of the unit recording data and then outline the most recent computational version of the cognitive map theory. The novel aspects of the present version of the theory are that it identifies two allocentric parameters, the centroid and the eccentricity, which can be calculated from the array of cues in an environment and which can serve as the bases for an allocentric polar co-ordinate system. Computations within this framework enable the animal to identify its location within an environment, to predict the location which will be reached as a result of any specific movement from that location, and conversely, to calculate the spatial transformation necessary to go from the current location to a desired location. Aspects of the model are identified with the information provided by cells in the hippocampus and dorsal presubiculum. The hippocampal place cells are involved in the calculation of the centroid and the presubicular direction cells in the calculation of the eccentricity.

Animals↗

PubMed2001

Pseudo beam's-eye-view as applied to beam orientation selection in intensity-modulated radiation therapy.

PURPOSE: To introduce the concept of pseudo beam's-eye-view (pBEV), to establish a framework for computer-assisted beam orientation selection in intensity-modulated radiation therapy (IMRT), and to evaluate the utility of the proposed technique. METHODS AND MATERIALS: To facilitate the selection of beam orientations for IMRT treatment planning, a scoring of beam direction was introduced. The score function was based on the maximum target dose deliverable by the beam without exceeding the tolerance doses of the critical structures. For the score function calculation, the beam portal at given gantry and couch angles was divided into a grid of beamlets. Each beamlet crossing the target was assigned the maximum intensity that could be used without exceeding the dose tolerances of the organs at risk (OARs) and normal tissue. Thereafter, a score was assigned to the beam according to the target dose delivered. The beams for the treatment were selected among those with the highest scores. In a sense, this technique is similar to the beam's-eye-view approach used in conventional radiation therapy, except that the evaluation by a human is replaced by a score function, and beam modulation is taken into account. RESULTS: The pBEV technique was tested on two clinical cases: a paraspinal treatment and a nasopharyngeal cancer with both coplanar and noncoplanar beam configurations. The plans generated under the guidance of pBEV for the paraspinal treatment offered superior target dose uniformity and reduced OAR doses. For the nasopharyngeal cancer case, it was also found that the pBEV-selected coplanar and noncoplanar beams significantly improved the target coverage without compromising the sparing of the OARs. CONCLUSIONS: The pBEV technique developed in this work provides a comprehensive tool for beam orientation selection in IMRT. It is especially valuable for complicated cases, where the target is surrounded by several sensitive structures and where it is difficult to select a set of good beam orientations. The pBEV technique has considerable potential for simplifying the IMRT treatment planning process and for maximizing the technical capacity of IMRT.

Humans↗