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PubMed2002

Continuous time transfer using GPS carrier phase.

The Astronomical Institute of the University of Berne is hosting one of the Analysis Centers (AC) of the International GPS Service (IGS). A network of a few GPS stations in Europe and North America is routinely analyzed for time transfer purposes, using the carrier phase observations. This work is done in the framework of a joint project with the Swiss Federal Office of Metrology and Accreditation (METAS). The daily solutions are computed independently. The resulting time transfer series show jumps of up to 1 ns at the day boundaries. A method to concatenate the daily time transfer solutions to a continuous series was developed. A continuous time series is available for a time span of more than 4 mo. The results were compared with the time transfer results from other techniques such as two-way satellite time and frequency transfer. This concatenation improves the results obtained in a daily computing scheme because a continuous time series better reflects the characteristics of continuously working clocks.

Calibration↗
PubMedDate not supplied

The therapeutic relationship: dead or merely impeded by technology?

The ways in which current nurse education is delivered, combined with rapid increases in technological advances in health care, are having a major impact on the delivery of care to patients. This article focuses on one aspect of that care: the establishment, development and maintenance of the therapeutic relationship. The authors argue that the changes in education delivery and the rapid introduction of technologies are contributing to the possible demise of the contemporary nurse-patient relationship and, therefore, the loss of that essence of nursing which is essential to the patients' well-being and the nurses' professional satisfaction. The article explores the requisite knowledge and skills competences essential for the formation of the therapeutic relationship and asks whether these are being impeded by simulated educational activities and the advent of ubiquitous computing. The authors acknowledge the difficulties associated with the assessment of an effective therapeutic relationship and suggest a possible framework in which a performance of understanding of the formation of a therapeutic relationship can be established.

Clinical Competence↗
PubMed2026

The Mechanism of Celosiae Semen in the Treatment of Diabetic Cataract: Based on Network Pharmacology.

INTRODUCTION: Diabetes mellitus can be complicated by a variety of ocular diseases, among which the postoperative complications of diabetic cataract (DC) are significantly higher than those of non-DC patients. Therefore, finding drugs with natural active ingredients is an urgent challenge in the prevention and treatment of DC. Discovering the potential molecular mechanism of celosiae semen (CS) for the treatment of DC and providing new ideas and programs for the treatment and prevention of DC. METHODS: In this study, network pharmacology, molecular docking, and molecular dynamics simulations were utilized to predict the binding and functional enrichment of the main active ingredients of CS with DC-related targets, and to explore the potential pathways and mechanisms of CS for the treatment of DC. RESULTS: Through database searching and screening, a total of 45 potential targets of CS for the treatment of DC were identified, functionally enriched, and a protein-protein interaction network was constructed, and the key target, SRC, was finally found. The results of molecular docking and molecular dynamics simulation showed that the main active ingredient of CS, stigmasterol, could bind stably to the key target SRC protein. DISCUSSION: This study not only elucidates the phyto-pharmacological basis of CS in DC management but also provides a framework for developing natural product-derived targeted therapies against diabetic ocular complications. The integration of modern genomics and computational chemistry to deconstruct the therapeutic effects of traditional Chinese herbal medicines has great clinical significance in expanding the scope of traditional Chinese medicines for the treatment of DC and promoting precision targeting. However, this requires verification through basic experiments. CONCLUSION: These computational findings suggest that CS may exert its anti-cataract effects through the multi-target modulation of diabetic metabolic pathways and SRC-mediated signaling cascades.

Humans↗
PubMed1990

The Ch21 protein, developmentally regulated in chick embryo, belongs to the superfamily of lipophilic molecule carrier proteins.

Ch21, a developmentally regulated low molecular weight protein observed in chick embryo skeletal tissues, is expressed "in vitro" by differentiating chondrocytes at a late stage of development. Here we report the complete amino acid sequence of the protein. 86% of the total amino acid sequence was deduced by sequences of 17 high performance liquid chromatography-separated proteolytic fragments and 33 amino acid residues at the amino-terminal end of protein purified from spent culture medium of hypertrophic chondrocytes. Furthermore we isolated by molecular cloning the corresponding cDNA and determined its nucleotide sequence. By combining protein and nucleotide sequence data we determined the primary structure of the entire Ch21. It consists of 158 amino acids and has a molecular mass of 18.065 kDa. Computer-assisted analysis showed that the Ch21 belongs to the superfamily of low molecular weight proteins sharing a basic framework for binding and transport of small hydrophobic molecules.

Amino Acid Sequence↗
PubMed1998

[Evaluation and comparison of tobacco control legislation in member states of the European Union].

BACKGROUND: Nowadays, tobacco use represents the main cause of avoidable deaths in Europe. Public health authorities have several means at their disposal to fight against this epidemic. For instance, legislative action can operate on the supply side as well as on the demand side, with the aim of reducing tobacco consumption in the targetted populations. METHODS: A systematic data collection of all legislative texts dealing with tobacco control was carried out within the framework of the EuroLego project. This was done, either through direct contact with the countries or through a systematic computer and manual search of data bases concerning the 15 member states of the European Union. RESULTS: At present, the legislative context varies widely from one country to another, whether regarding the number of texts adopted or the subject that is covered. Since the 1950s, a marked increase in the number of legislative texts has been noted as well as a trend towards harmonization of the texts among the different member states. CONCLUSIONS: Several health recommendations can be put forward in the context of public health activities with priority to be given to the protection of the children and the young and to the defense of the rights of non-smokers.

Europe↗
PubMed2004

Multi-criteria decision analysis for the optimal management of nitrate contamination of aquifers.

We present an integrated methodology for the optimal management of nitrate contamination of ground water combining environmental assessment and economic cost evaluation through multi-criteria decision analysis. The proposed methodology incorporates an integrated physical modeling framework accounting for on-ground nitrogen loading and losses, soil nitrogen dynamics, and fate and transport of nitrate in ground water to compute the sustainable on-ground nitrogen loading such that the maximum contaminant level is not violated. A number of protection alternatives to stipulate the predicted sustainable on-ground nitrogen loading are evaluated using the decision analysis that employs the importance order of criteria approach for ranking and selection of the protection alternatives. The methodology was successfully demonstrated for the Sumas-Blaine aquifer in Washington State. The results showed the importance of using this integrated approach which predicts the sustainable on-ground nitrogen loadings and provides an insight into the economic consequences generated in satisfying the environmental constraints. The results also show that the proposed decision analysis framework, within certain limitations, is effective when selecting alternatives with competing demands.

Costs and Cost Analysis↗
PubMed2005

Framework-based design of a new all-purpose molecular simulation application: the Adun simulator.

Here we present Adun, a new molecular simulator that represents a paradigm shift in the way scientific programs are developed. The traditional algorithm centric methods of scientific programming can lead to major maintainability and productivity problems when developing large complex programs. These problems have long been recognized by computer scientists; however, the ideas and techniques developed to deal with them have not achieved widespread adoption in the scientific community. Adun is the result of the application of these ideas, including pervasive polymorphism, evolutionary frameworks, and refactoring, to the molecular simulation domain. The simulator itself is underpinned by the Adun Framework, which separates the structure of the program from any underlying algorithms, thus giving a completely reusable design. The aims are twofold. The first is to provide a platform for rapid development and implementation of different simulation types and algorithms. The second is to decrease the learning barrier for new developers by providing a rigorous and well-defined structure. We present some examples on the use of Adun by performing simple free-energy simulations for the adiabatic charging of a single ion, using both free-energy perturbation and the Bennett's method. We also illustrate the power of the design by detailing the ease with which ASEP/MD, an elaborated mean field QM/MM method originally written in FORTRAN 90, was implemented into Adun.

Algorithms↗
PubMed2026

Accurately Deciphering Tissue Heterogeneity From Spatial Multi-Modal and Multi-Omics With STransformer.

Advances in spatially resolved technologies enable the simultaneous acquisition of diverse data modalities within a tissue slice while preserving critical spatial context, which presents unprecedented opportunities to decipher intricate tissue heterogeneity. However, existing computational approaches lack the intrinsic flexibility to universally process both spatial multi-modal and multi-omics data. Here, we introduce STransformer, a unified deep learning framework designed to seamlessly accommodate a comprehensive landscape of spatial data. By simultaneously capturing short-range cellular interactions and tissue-wide semantic patterns, it extracts robust representations to accurately dissect complex tissue heterogeneity. Systematic evaluations across diverse species, tissue types, and data modalities highlight its profound versatility. For spatial multi-modal data, STransformer delineates intricate anatomical structures in the human cortex, uncovers pathological mechanisms in Alzheimer's disease, and characterizes dynamic spatiotemporal developmental trajectories during chicken cardiogenesis. Scaling to spatial multi-omics data, STransformer synergizes spatial transcriptomic and proteomic profiles to decipher intricate immune microenvironments within the human tonsil, and jointly analyzes spatial epigenomic and transcriptomic data to infer regulatory mechanisms in the mouse embryonic brain. Consequently, STransformer serves as a highly versatile and robust analytical framework for advancing our understanding of tissue heterogeneity and disease pathogenesis.

Multiomics↗
PubMed2006

Grammatical representations of macromolecular structure.

Since the first application of context-free grammars to RNA secondary structures in 1988, many researchers have used both ad hoc and formal methods from computational linguistics to model RNA and protein structure. We show how nearly all of these methods are based on the same core principles and can be converted into equivalent approaches in the framework of tree-adjoining grammars and related formalisms. We also propose some new approaches that extend these core principles in novel ways.

Algorithms↗
PubMed2006

Filter learning: application to suppression of bony structures from chest radiographs.

A novel framework for image filtering based on regression is presented. Regression is a supervised technique from pattern recognition theory in which a mapping from a number of input variables (features) to a continuous output variable is learned from a set of examples from which both input and output are known. We apply regression on a pixel level. A new, substantially different, image is estimated from an input image by computing a number of filtered input images (feature images) and mapping these to the desired output for every pixel in the image. The essential difference between conventional image filters and the proposed regression filter is that the latter filter is learned from training data. The total scheme consists of preprocessing, feature computation, feature extraction by a novel dimensionality reduction scheme designed specifically for regression, regression by k-nearest neighbor averaging, and (optionally) iterative application of the algorithm. The framework is applied to estimate the bone and soft-tissue components from standard frontal chest radiographs. As training material, radiographs with known soft-tissue and bone components, obtained by dual energy imaging, are used. The results show that good correlation with the true soft-tissue images can be obtained and that the scheme can be applied to images from a different source with good results. We show that bone structures are effectively enhanced and suppressed and that in most soft-tissue images local contrast of ribs decreases more than contrast between pulmonary nodules and their surrounding, making them relatively more pronounced.

Absorptiometry, Photon↗
PubMed1998

A computational theory of visual attention.

A computational theory of visual attention is presented. The basic theory (TVA) combines the biased-choice model for single-stimulus recognition with the fixed-capacity independent race model (FIRM) for selection from multi-element displays. TVA organizes a large body of experimental findings on performance in visual recognition and attention tasks. A recent development (CTVA) combines TVA with a theory of perceptual grouping by proximity. CTVA explains effects of perceptual grouping and spatial distance between items in multi-element displays. A new account of spatial focusing is proposed in this paper. The account provides a framework for understanding visual search as an interplay between serial and parallel processes.

Attention↗
PubMed1995

Cloning and expression of mamba toxins.

Mamba venoms contain pharmacologically active proteins that interfere with neuromuscular transmission by binding to and altering the normal functioning of neuronal proteins involved, directly or indirectly, with regulating nerve transmission. Of the mamba toxins studied to date, many act on voltage-sensitive K+ channels, nicotinic or muscarinic acetylcholine receptors, or acetylcholinesterase. In an attempt to clone, characterize, and express the genes encoding these toxins, as well as other genes specifying activities not completely elucidated as yet, a cDNA library was constructed from mRNA isolated from the glands of the black mamba. Clones from the library harboring sequences encoding 14 different mamba toxins were isolated and characterized by nucleotide sequence analysis. Genes coding for three proteins, dendrotoxins (DTX) K, I, and E, were expressed as maltose-binding (MBP) fusion proteins in the periplasmic space of Escherichia coli. The DTXK-MBP fusion protein was affinity purified, cleaved from its chaperon, and the recombinant DTXK purified from MBP. Recombinant DTXK was shown to be identical to native DTXK in its N-terminal sequence, chromatographic behavior, convulsion-inducing activity, and binding to voltage-activated K+ channels in bovine synaptic membranes. Computer modeling was employed to create three-dimensional structures of DTXK and DTX1 from the X-ray crystal structure of alpha-DTX utilizing both structural and sequence homologies. Comparisons were made between the three toxins, providing a framework for site-directed mutagenesis.

Amino Acid Sequence↗
PubMed2006

M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species.

BACKGROUND: Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic sequencing projects. This increase in related genomic data will allow for in depth studies of evolution in closely related species through multiple whole genome comparisons. RESULTS: To facilitate such comparisons, we present an interactive multiple genome comparison and alignment tool, M-GCAT, that can efficiently construct multiple genome comparison frameworks in closely related species. M-GCAT is able to compare and identify highly conserved regions in up to 20 closely related bacterial species in minutes on a standard computer, and as many as 90 (containing 75 cloned genomes from a set of 15 published enterobacterial genomes) in an hour. M-GCAT also incorporates a novel comparative genomics data visualization interface allowing the user to globally and locally examine and inspect the conserved regions and gene annotations. CONCLUSION: M-GCAT is an interactive comparative genomics tool well suited for quickly generating multiple genome comparisons frameworks and alignments among closely related species. M-GCAT is freely available for download for academic and non-commercial use at: http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html.

Algorithms↗
PubMed2004

Multielectron chemistry of zinc porphyrinogen: a ligand-based platform for two-electron mixed valency.

The synthesis, electronic structure, and oxidation-reduction chemistry of a homologous series of Zn(II) porphyrinogens are presented. The fully reduced member of the series, [LZn](2-), was prepared in two steps from pyrrole and acetone. The compound undergoes consecutive two-electron, ligand-based, oxidations at +0.21 and +0.63 V vs NHE to yield [L(Delta)Zn] and [L(Delta Delta)Zn](2+), which also have been independently prepared by chemical means. X-ray diffraction analysis of the redox intermediary, [L(Delta)Zn], shows that the partly oxidized macrocycle is composed of a methylene-bridged dipyrrole that is doubly strapped to a two-electron oxidized dipyrrole bridged by a cyclopropane ring (L(Delta)). The localization of two hole equivalents on the oxidized side of the porphyrinogen framework is consistent with a two-electron mixed valency formulation for the [L(Delta)Zn] species. Electronic structure calculations and electronic spectroscopy support this formalism. Density functional theory computations identify the HOMO to be localized on the reduced half of the macrocycle and the LUMO to be localized on its oxidized half. As implicated by the energy level diagram, the lowest energy transition in the absorption spectrum of [L(Delta)Zn] exhibits charge-transfer character. Taken together, these results establish the viability of using a ligand framework as a two- and four-electron/hole reservoir in the design of multielectron redox schemes.

Journal Article↗
PubMed2005

Width of the extended facial recess: a numerical study of ultrahigh-resolution computed tomography and its implications in minimally invasive otologic surgery.

BACKGROUND: Methods of minimally invasive computer-assisted otologic surgery lag behind other fields. The reason seems to be the extremely small dimensions of the corridors between important structures in the temporal bone and the fact that these structures are encased in bony frameworks, are obscured before drilling, and are not movable. The extended facial recess is a surgical pass to the tympanic cavity. It is bounded medially by the facial nerve and laterally by the tympanic annulus, and varies among individuals. For computer-assisted, minimally invasive temporal bone surgery, high-resolution definition is critically important. AIMS: To determine the width of the extended facial recess and evaluate the computerized findings as a pre- and intraoperative aid to otologic surgery planning. METHODS: Bilateral temporal bone high-resolution computed tomographic images of 100 male and 100 female patients were measured twice at five levels (caudal to cephalic), first using a window-independent algorithm (extended facial recess, full-width at half-maximum), implemented in a computed tomographic image-processing workstation, and then manually with calipers on the same axial computed tomographic images. RESULTS: As expected, the extended facial recess, full-width at half-maximum method yielded the widest values superiorly (4.15 +/- 0.41 mm in the female patients and 4.32 +/- 0.54 mm in the male patients). From this level down, the extended facial recess, full-width at half-maximum method yielded values that tapered gradually to 2.50 +/- 0.56 mm in the female patients and 2.42 +/- 0.46 mm in the male patients at the most interior level. The manual method (extended facial recess, computed tomographic images) yielded a significantly higher value than that obtained with the objective, window-independent method at all levels, and at some levels was higher by as much as one-third. At Level 2, which corresponded roughly to the round window, the extended facial recess was 4.00 +/- 0.65 in the female study group and 4.11 +/- 0.67 mm in the male study group. CONCLUSION: Image processing methods such as extended facial recess, full-width at half-maximum method might lead to fine tuning and thus improvement of computer-assisted otologic surgery. Before clinical application and complete dependence on these automated methods during otologic surgery, their reliability should be further validated.

Adolescent↗
PubMed1995

Tensor analysis of facial growth in males.

This longitudinal study examines in detail the facial development of 18 untreated, male children with acceptable occlusions. The children were examined in the prepubertal period (age range 7-10 years) and again in their late teens (15-19 years of age). A tensor analysis, which permits the computation of differences in form (that is in size and shape) without specifically measuring either, was employed to describe the facial changes which occurred during this time interval. Values for the x and y co-ordinates of 16 hard and four soft tissue landmarks were determined at each stage. Customized software allowed both graphical and numerical examination of the mean changes over time between 28 triads of points, covering skeletal, dental, and soft tissue elements. The analysis confirmed previous work in describing facial change but was more sensitive than conventional cephalometry, especially where landmarks were evaluated outside the traditional sella-nasion framework.

Adolescent↗
PubMed2002

Dynamics of Boolean networks controlled by biologically meaningful functions.

The remarkably stable dynamics displayed by randomly constructed Boolean networks is one of the most striking examples of the spontaneous emergence of self-organization in model systems composed of many interacting elements (Kauffman, S., J. theor. Biol.22, 437-467, 1969; The Origins of Order, Oxford University Press, Oxford, 1993). The dynamics of such networks is most stable for a connectivity of two inputs per element, and decreases dramatically with increasing number of connections. Whereas the simplicity of this model system allows the tracing of the dynamical trajectories, it leaves out many features of real biological connections. For instance, the dynamics has been studied in detail only for networks constructed by allowing all theoretically possible Boolean rules, whereas only a subset of them make sense in the material world. This paper analyses the effect on the dynamics of using only Boolean functions which are meaningful in a biological sense. This analysis is particularly relevant for nets with more than two inputs per element because biological networks generally appear to be more extensively interconnected. Sets of the meaningful functions were assembled for up to four inputs per element. The use of these rules results in a smaller number of distinct attractors which have a shorter length, with relatively little sensitivity to the size of the network and to the number of inputs per element. Forcing away the activator/inhibitor ratio from the expected value of 50% further enhances the stability. This effect is more pronounced for networks consisting of a majority of activators than for networks with a corresponding majority of inhibitors, indicating that the former allow the evolution of larger genetic networks. The data further support the idea of the usefulness of logical networks as a conceptual framework for the understanding of real-world phenomena.

Algorithms↗
PubMedDate not supplied

NanoSystems biology.

Systems biology is an approach in which the digital information of the genome, acted upon by environmental cues, generates the many molecular signatures of gene and protein expression, as well as other, more phenomenological experimental observations. These data may be integrated together to form a testable hypothesis of how a biological organism functions as a system. The central components of systems biology are genetically programmed networks (circuits) within cells and networks of cells. These components establish the organization and function of individual cells and tissues in response to environmental signals such as cell-to-cell communication within organ systems and whole organisms. Within this context, disease is considered as a genetic or environmental reprogramming of cells to gain or lose specific functions that are characteristics of disease. This paper is a combination of three tutorials with an outlined series of technologies, including microfluidics, nanotechnologies, and molecular imaging methods, and we describe how their development should be driven by the needs of systems biology. We also discuss how these technologies can enable a systems biology approach through a pathway from single cells to mouse models of disease and finally to patients. Within this technology base are approaches to develop, use and test molecules as probes that target proteins, DNA and mRNA to test systems biology models, as well as provide molecular diagnostics and molecular therapeutics within a systems biology framework.

Animals↗