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PubMed1993

Network models for sequence evolution.

We introduce a general class of models for sequence evolution that includes network phylogenies. Networks, a generalization of strictly tree-like phylogenies, are proposed to model situations where multiple lineages contribute to the observed sequences. An algorithm to compute the probability distribution of binary character-state configurations is presented and statistical inference for this model is developed in a likelihood framework. A stepwise procedure based on likelihood ratios is used to explore the space of models. Starting with a star phylogeny, new splits (nontrivial bipartitions of the sequence set) are successively added to the model until no significant change in the likelihood is observed. A novel feature of our approach is that the new splits are not necessarily constrained to be consistent with a treelike mode of evolution. The fraction of invariable sites is estimated by maximum likelihood simultaneously with other model parameters and is essential to obtain a good fit to the data. The effect of finite sequence length on the inference methods is discussed. Finally, we provide an illustrative example using aligned VP1 genes from the foot and mouth disease viruses (FMDV). The different serotypes of the FMDV exhibit a range of treelike and network evolutionary relationships.

Aphthovirus↗
PubMed2006

A boolean network modelling of receptor mosaics relevance of topology and cooperativity.

In the last five years data have been obtained showing that a functional cross-talk among G Protein Coupled receptors (GPCR) exists at the plasma membrane level where they can dimerise and are able to generate high order oligomers. These findings are in agreement with the receptor mosaic (RM) hypothesis that claims the existence of clusters of receptor proteins at the plasma membrane level, where they establish mutual interactions and work as 'intelligent interfaces' between the extra-cellular and the intra-cellular environments. Individual receptor dimers can be considered to have two stable conformational states with respect to the macromolecular effectors: one active, one inactive. Owing to receptor-receptor interactions, however, a state change of a given receptor will change the probability of changing the state for the adjacent receptors in the RM and the effect will propagate throughout the cluster, leading to a complex cooperative behaviour. In this study we explore the properties of a RM on the basis of an equivalence with a Boolean network, a mathematical framework able to describe how complex properties may emerge from systems characterized by deterministic local interactions of many simple components acting in parallel. Computer simulations of receptor clusters arranged according to topologies consistent with available experimental ultrastructural data were performed. They indicated that RMs after a stimulation can achieve a limited number of specific temporary equilibrium configurations (attractors), characterized by the presence of receptor units frozen in the active state. They could be interpreted as a form of information storage and a role of RM in learning and memory could be hypothesized. Moreover, they seem to be at the basis of very common 'macroscopical' properties of a receptor system, such as a sigmoidal response curve to an extracellular ligand, the sensitivity of the mosaic being modulated by changes in the topology and/or in the level of cooperativity among receptors.

Allosteric Regulation↗
PubMed1994

A software engineering approach for medical workstations development.

Multimedia medical workstations represent the natural tool for accessing the hospital information system environment. They are complex medical systems that have to gather, in a single framework, a large collection of components dealing with multimedia medical objects. To remain current with both medical practice and with advances in the computer science field, they have to allow the iterative addition of new functions to the set of existing ones. In this paper, after a survey of commonly required medical workstation functional components, we shall try to discuss how a software engineering approach can streamline the development of a medical workstation. Different software engineering tools needed to build the functional components of a workstation are described. Their integration in a single dedicated environment is considered through four perspectives: data, presentation, communication and control. Benefits and limitations of an object-oriented approach are discussed.

Computer Communication Networks↗
PubMed2006

Mentalizing and Marr: an information processing approach to the study of social cognition.

To interact successfully, individuals must not only recognize one another as intentional agents driven primarily by internal mental states, but also possess a system for making reliable and useful inferences about the nature of those beliefs, feelings, goals, and dispositions. The ability to make such mental state inferences (i.e., to mentalize or mindread) is the central accomplishment of human social cognition. The present article suggests that our understanding of how humans go about making mental state inferences will benefit from treating social cognition primarily as an information processing system that comprises a set of mechanisms for elaborating more basic social information into an understanding of another's mind. Following Marr's [Marr, D., 1982. Vision. W. H. Freeman, San Francisco, CA] framework for the study of such information processing systems, I suggest that questions about social cognition might profitably be asked at three levels--computation, algorithm, and implementation--and outline a number of ways in which a description of social cognition at the middle level (i.e., the step-by-step processes that give rise to mental state inferences) can be informed by analysis at the other two.

Cognition↗
PubMed2026

Data-driven approaches in green microbiology: strategies for plant growth-promoting bacteria.

Plant growth-promoting bacteria (PGPB) are gaining attention as scalable biological solutions to enhance crop productivity and resilience. However, accurately identifying and characterizing PGPB remains challenging, particularly under variable environmental conditions where microbial functions are context-dependent and shaped by complex plant-microbe interactions. Advances in high-throughput sequencing have shifted the field from culture-dependent approaches to genome-informed strategies, enabling large-scale taxonomic and functional profiling. Although trait-based databases support the prediction of plant-beneficial genes, they capture only a fraction of the underlying biological complexity and often require labor-intensive analyses. Machine learning (ML) and deep learning (DL) have emerged as powerful tools to integrate genomic, physiological, and ecological data, enabling the prioritization of candidate strains with plant growth-promoting potential. To evaluate advances in the field, we conducted a systematic review of studies integrating ML and DL with PGPB characterization, assessing algorithm selection, performance, and target plant systems. Across 248 observations, only 6.0% of studies directly addressed PGPB screening, whereas the majority (77.4%) focused on plant disease detection, revealing a substantial gap in the application of AI to beneficial microorganisms for plant growth. Convolutional neural networks (CNNs) were the most frequently applied algorithms, largely driven by image-based phenotyping tasks. Overall, the field is constrained by limited datasets, high computational demands, and challenges in modeling multispecies and host-associated interactions. We highlight the need for integrative and interpretable ML and DL frameworks that bridge genomic data and functional validation. Such approaches represent a promising path toward scalable, data-driven discovery and deployment of bioinoculants in sustainable agriculture.

Agriculture↗
PubMed2005

Thermodynamic functions of liquid water calculated from the temperature evolution of the vibration spectrum contour.

Configurational contributions of hydrogen bonds to thermodynamic properties of water (internal energy, entropy, and heat capacity) are calculated on the basis of statistical distributions of frequencies of the OH vibrations of liquid water, calculated earlier from the experimental Raman spectra in frameworks of the fluctuation theory of hydrogen bonding. Distributions of the energy of hydrogen bonds are determined. It is shown by comparison with computer experiments that previously established dependence of energy on frequency, E(nu), must be considered in this formalism as the effective energy of hydrogen bonding averaged over those configurations of hydrogen bridge O-H...O which lead to the given frequency nu in the vibrational spectrum. Contribution of van der Waals interactions not affecting the frequency shift to heat capacity is evaluated.

Entropy↗
PubMedDate not supplied

Development, implementation, and evaluation of a multicenter pharmaceutical care outcomes study.

OBJECTIVES: To: (1) develop a pharmaceutical care multicenter outcomes research project using clinical pharmacy residents and preceptors; (2) develop two research protocols to document pharmacists' impact on clinical, economic, and humanistic outcomes of therapy; (3) develop and implement a data collection process and methodology for outcomes research; (4) evaluate the effectiveness of the multicenter outcomes research process; and (5) prepare clinical pharmacy preceptors and residents to conduct outcomes research. DESIGN AND SETTING: Two research protocols were developed, each a randomized, parallel, open-label evaluation of patients at 10 Department of Veterans Affairs and 1 university medical center. One protocol focused on patients with chronic obstructive pulmonary disease (COPD) and the other on patients with hypertension. The study evaluated pharmacists' management of these two patient groups. PATIENTS AND OTHER PARTICIPANTS: 133 patients with hypertension and 98 patients with COPD; 33 pharmacy directors and preceptors; 45 pharmacy residents. MAIN OUTCOME MEASURES: Clinical, economic, and humanistic outcomes of pharmacists' interventions. The processes of developing a multicenter outcomes study were evaluated, including the data collection process. RESULTS: The two study protocols and an educational program for study participants were developed. A data collection process was developed and implemented, with the paper process being successful and the computer data collection process not implemented due to time constraints. Overall, the multicenter outcomes research process was successful. CONCLUSION: The study provides a framework of processes and sites for the future development of other outcomes research studies. Clinical, economic, and humanistic outcomes are reported in Parts 2 and 3.

Data Collection↗
PubMed2006

Redox enzymes immobilized on electrodes with solution cosubstrates. General procedure for simulation of time-resolved catalytic responses.

In view of the existing and potential applications of electrochemical enzymatic catalysis with redox enzymes immobilized on the electrode surface in biosensors, a numerical calculation procedure for simulating their cyclic voltammetric responses is presented. It is applicable to systems involving a redox cosubstrate in solution. The cosubstrates, substrates, products, and inhibitors are assumed to diffuse linearly (planar electrode) between the electrode and the solution. The reactions in which the various forms of the immobilized enzyme participate may be as numerous and intricate as required by the simulation with no other restriction than the computing time. They may, at will, follow or not follow Michaelis-Menten kinetics. Slow charge-transfer cosubstrates are treated in the framework of Butler-Volmer kinetic law.

Catalysis↗
PubMed2005

Large amplitude quantum mechanics in polyatomic hydrides. I. A particles-on-a-sphere model for XH(n).

A framework is presented for converged quantum mechanical calculations on large amplitude dynamics in polyatomic hydrides (XH(n)) based on a relatively simple, but computationally tractable, "particles-on-a-sphere" (POS) model for the intramolecular motion of the light atoms. The model assumes independent two-dimensional (2D) angular motion of H atoms imbedded on the surface of a sphere with an arbitrary interatomic angular potential. This assumption permits systematic evolution from "free rotor" to "tunneling" to "quasi-rigid" polyatomic molecule behavior for small, but finite, values of total angular momentum J. This work focuses on simple triatom (n=2) and tetratom (n=3) systems as a function of interatomic potential stiffness, with explicit consideration of H2O, NH3, and H3O+ as limiting test cases. The POS model also establishes the necessary mathematical groundwork for calculations on dynamically much more challenging XH(n) species with n>3 (e.g., models of CH5+) where such a reduced dimensionality approach offers prospects for being quantum mechanically tractable at low J values (i.e., J=0, 1, 2) characteristic of supersonic jet expansion conditions.

Journal Article↗
PubMed2006

Automatic integration of the reaction path using diagonally implicit Runge-Kutta methods.

The diagonally implicit Runge-Kutta framework is shown to be a general form for constructing stable, efficient steepest descent reaction path integrators, of any order. With this framework tolerance driven, adaptive step-size methods can be constructed by embedding methods to obtain error estimates of each step without additional computational cost. There are many embedded and nonembedded, diagonally implicit Runge-Kutta methods available from the numerical analysis literature and these are reviewed for orders two, three, and four. New embedded methods are also developed which are tailored to the application of reaction path following. All integrators are summarized and compared for three systems: the Muller-Brown [Theor. Chem. Acta 53, 75 (1979)] potential and two gas phase chemical reactions. The results show that many of the methods are capable of integrating efficiently while reliably keeping the error bound within the desired tolerance. This allows the reaction path to be determined through automatic integration by only specifying the desired accuracy and transition state.

Algorithms↗
PubMed2000

An investigation of the dynamics of aggression: direct observations in ice hockey and basketball.

There have been significant problems in the study of sports aggression, and they are linked to how aggression has been defined, measured, and analyzed. Following a review of the whole domain, this study aimed to construct a theoretically coherent and ecologically valid framework for research on processes underlying sports aggression and to contribute to the advancement of knowledge in the area. An exploratory method using computer observational analysis as the primary research method, along with complementary questionnaires and personal reflections, considered aggression in two comparison sports: ice hockey and basketball. Data were compiled and classified by involved and independent experts relative to factors and behaviors associated with sports aggression derived from a comprehensive review of the literature. Among the study's findings were that: (a) aggression was instrumental in nature two-thirds of the time; (b) aggressive acts typically occurred in clusters and varied in frequency according to game circumstances; and (c) multiple variables and aggression theories were related to severely aggressive acts. The complex dynamics of sports aggression via similar naturalistic methodologies is discussed.

Adolescent↗
PubMed2003

Intrinsic profiles beyond the capillary wave theory: a Monte Carlo study.

We develop and test an operational definition of the intrinsic surface for liquid-vapor interfaces. The application to the microscopic configurations along Monte Carlo computer simulations gives the statistical properties of the intrinsic surfaces and the intrinsic density profiles for simple fluid models. The results open a framework of quantitative description to close the gap between the mesoscopic capillary wave theory and the sharpest level of resolution for the intrinsic density distribution, relative to the first atomic layer in the liquid surface, as done in the interpretation of experimental x-ray reflectivity.

Journal Article↗
PubMedDate not supplied

HDR VolVis: high dynamic range volume visualization.

In this paper, we present an interactive high dynamic range volume visualization framework (HDR VolVis) for visualizing volumetric data with both high spatial and intensity resolutions. Volumes with high dynamic range values require high precision computing during the rendering process to preserve data precision. Furthermore, it is desirable to render high resolution volumes with low opacity values to reveal detailed internal structures, which also requires high precision compositing. High precision rendering will result in a high precision intermediate image (also known as high dynamic range image). Simply rounding up pixel values to regular display scales will result in loss of computed details. Our method performs high precision compositing followed by dynamic tone mapping to preserve details on regular display devices. Rendering high precision volume data requires corresponding resolution in the transfer function. To assist the users in designing a high resolution transfer function on a limited resolution display device, we propose a novel transfer function specification interface with nonlinear magnification of the density range and logarithmic scaling of the color/ opacity range. By leveraging modern commodity graphics hardware, multiresolution rendering techniques and out-of-core acceleration, our system can effectively produce an interactive visualization of large volume data, such as 2,048(3).

Algorithms↗
PubMed2006

Space-time relativity in self-motion reproduction.

Experiments on reproducing imposed self-motion showed that not only final distance or angle of motion, but also the temporal profile are reproduced. Reproduction errors have been attributed to sensory inputs, inaccurate memorization of the motion variable, or motor errors. However, another possible source of error has so far been neglected. The internal time base for path integration or movement memorization may be distorted and thus not reflect physical time. Because additional cognitive load was previously shown to affect subjective estimation of duration, we used a dual-task paradigm during either the stimulation or reproduction phase of three different movement reproduction tasks. We asked subjects 1) on a rotating chair to reproduce imposed passive whole body rotations by controlling the chair with a joystick, 2) on a treadmill to actively reproduce locomotion with respect to the treadmill, and 3) while blindfolded to reproduce a previously walked straight trajectory. The cognitive load changed the distance of reproduced self-motion by about 25% depending on whether the mental task was performed while experiencing or reproducing the motion. Although imposed velocity was reproduced accurately in all conditions, reproduced movement duration was affected in the same way as distance. This result implies that for the perception of distance traveled, perceptual space and time are closely interrelated. The findings are consistent with shared processing of temporal and spatial information. A computational model of motion reproduction including a discrete path integrator is proposed that is able to explain the experimental results within one coherent framework.

Adult↗
PubMed1999

Pruning using parameter and neuronal metrics.

In this article, we introduce a measure of optimality for architecture selection algorithms for neural networks: the distance from the original network to the new network in a metric defined by the probability distributions of all possible networks. We derive two pruning algorithms, one based on a metric in parameter space and the other based on a metric in neuron space, which are closely related to well-known architecture selection algorithms, such as GOBS. Our framework extends the theoretically range of validity of GOBS and therefore can explain results observed in previous experiments. In addition, we give some computational improvements for these algorithms.

Algorithms↗
PubMed2006

Assessment of imaging studies used with radiosurgery: a volumetric algorithm and an estimation of its error. Technical note.

The Gamma Knife has played an increasingly important role in the neurosurgical treatment of patients. Intracranial lesions are not removed by radiosurgery. Rather, the goal of treatment is to induce tumor control. During planning, the creation of dose-volume histograms requires an accurate volumetric analysis of intracranial lesions selected for radiosurgery. In addition, an accurate follow-up imaging analysis of tumor volume is essential for assessing the results of radiosurgery. Nevertheless, sources of volumetric error and their expected magnitudes must be properly understood so that the operator may correctly interpret apparent changes in tumor volume. In this paper, the authors examine the often-neglected contributions of imaging geometry (principally image slice thickness and separation) to overall volumetric error. One of the fundamental sources of volumetric error is that resulting from the geometry of the acquisition protocol. The authors consider the image sampling geometry of tomographic modalities and its contribution to volumetric error through a simulation framework in which a synthetic digital tumor is taken as the primary model. Because the exact volume of the digital phantom can be computed, the volume estimates derived from tomographic "slicing" can be directly compared precisely and independently from other error sources. In addition to providing empirical bounds on volumetric error, this approach provides a tool for guiding the specification of imaging protocols when a specific volumetric accuracy, or volume change sensitivity, for particular structures is sought a priori. Using computational geometry techniques, the volumetric error associated with image acquisition geometry was shown to be dependent on the number of slices through the region of interest (ROI) and the lesion volume. With a minimum of five slices through the ROI, the volume of a compact lesion could be calculated accurately with less than 10% error, which was the predetermined goal for the purposes of computing accurate dose-volume histograms and determining follow-up changes in tumor volume. Accurate dose-volume histograms can be generated and follow-up volumetric assessments performed, assuming accurate lesion delineation, when the object is visualized on at least five axial slices. Volumetric analysis based on fewer than five slices yields unacceptably larger errors (that is, > 10%). These volumetric findings are particularly relevant for radiosurgical treatment planning and follow-up analysis. Through the application of this volumetric methodology and a greater understanding of the error associated with it, neurosurgeons can better perform radiosurgery and assess its outcome.

Algorithms↗
PubMed1999

Nursing information systems: a survey of current practices.

This article reports the results of a recent survey on usefulness of computer-based nursing information systems (NISs). To assess their usefulness, three research questions were asked: Are computer-based NISs useful to most nurses? What accounts for the nurses' assessment of NISs? What factors influence the usefulness of NISs? This framework can serve to guide empirical investigations into various aspects of information systems in hospitals. The findings lead to implications for nursing care management, as well as suggestions for nursing quality research opportunities.

Attitude of Health Personnel↗
PubMed2000

[Construction, expression and activity test of a reshaping single-chain antibody against human CD3].

Monoclonal antibody (McAb) against human CD3 can adjust human body's immune statement in various ways, so that its clinical potential is highly regarded. In order to overcome the immunogenecity related to the murine McAb, this research effort was focused on constructing a reshaping single-chain antibody(scFv) against human CD3 employing antibody engineering. First, the CDRs of the murine McAb against human CD3 OKT3 was transplanted into the light-chain framework regions (FRs) of human McAb LS1 and the heavy-chain FRs of human McAb Nd respectively, spatial conformation was predicted by computer analysis. Then some particular residues were replaced in FRs basing on the result of conformational prediction to draw out the amino acid sequences of the reshaped VL and VH. The genes were chemically synthesize and inserted into an expression vector pROH80 to construct the reshaping scFv. Inducing the expression of reshaping scFv, the products are mainly as inclusion bodies. The reshaping scFv was expressed in another vector pALM. The inclusion bodies were denatured and then renatured by gel filtration. The renatured products were purified by immobilized metal affinity chromatograph (IMAC). Finally, the antigen-binding activily of the reshaping scFv against human CD3 was testified by the Compelitire in hibilory fluorescenceactivated cell sorting (FACS). The competitive inhibition rate is 18%.

Amino Acid Sequence↗