Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “computational frameworks”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,117 records · Page 62Linked to original sources

Which electron count rules are needed for four-center three-dimensional aromaticity?

A series of charged and neutral four-center n-electron (4c-ne, n = 1-4) molecules based on the adamantane framework, but which include combinations of boron, nitrogen, and phosphorus atoms at bridgehead positions, were studied computationally at the B3LYP/6-31G* level of density functional theory (DFT). The three-dimensional aromaticity, observed earlier for the 1,3,5,7-bisdehydroadamantane dication (1), is found to be general for 4c-2e electron systems. The degree of electron delocalization, evaluated by energetic, geometric, and various magnetic criteria, is quite independent of the molecular symmetry (point groups vary from Td to Cs), the degeneracy of the orbitals, the molecular charges, and the nature of the atoms participating in the delocalized bonding. Although the multiple positive (e.g., in 1 and some of the heteroatom systems) and multiple negative charges are strongly repulsive, the rigid adamantane frameworks help hold the bridgehead atoms within bonding distances with the fewer available electrons. The corresponding 4c-1e doublets are approximately half as aromatic as the 4c-2e singlets based on the same criteria. However, the three-electron systems may either adopt distorted but still four-center delocalized structures, or alternative 3c-2e two-dimensional arrangements in which the fourth bridgehead atom is more distant. There is no need to derive special rules for each point group for 4c-ne systems. Although the three-dimensional stabilization is computed to be quite appreciable, ranging between 10 and 50 kcalmol(-1), this delocalization energy is generally not sufficient to overcome distortion due to strain in higher homologues of 1 and in analogous noncage systems. Among the various 4c-2e homoadamantanedehydro dications studied, only the 1,8-dehydrohomoadamandiyl-3,6-dication forms a three-dimensional aromatic system.

Journal Article↗

Special interest radiology improves the perceived preoperative stage of gastric cancer.

AIM: The aim of this study was to compare the accuracy of spiral computed tomography (CT) performed by a specialist radiologist within a multi disciplinary team (MDT) framework with that of radiologists working outside of this framework. MATERIALS AND METHODS: One hundred and ten patients [median age 70 (35-86)yr, 71m] underwent either a preoperative CT performed by the MDT specialist consultant radiologist (n=60) or a CT performed by one of 13 other consultant radiologists (n=50). The strength of the agreement between the CT stage and the histopathological stage was determined by the weighted Kappa statistic (Kw). RESULTS: Sensitivity for T, N and M stage were 64%, 65% and 25% for MDT specialist CT, compared with 24%, 24% and 5% for control CT. Specificity for T, N and M stage were 68%, 59% and 95% for MDT specialist CT compared with 79%, 94% and 93% for control CT. Kw for T, N and M stage were 0.314, 0.350 and 0.255 for MDT specialist CT compared with 0.088, 0.102 and -0.019 for control CT. Unsuspected metastases were found in 12 patients staged by MDT specialist CT compared with 19 patients staged by control CT (Chi2=4.366, df=1,p =0.037). CONCLUSION: Improved patient selection for surgery should maximize use of limited resource.

Adenocarcinoma↗

Biochemical networks with uncertain parameters.

The modelling of biochemical networks becomes delicate if kinetic parameters are varying, uncertain or unknown. Facing this situation, we quantify uncertain knowledge or beliefs about parameters by probability distributions. We show how parameter distributions can be used to infer probabilistic statements about dynamic network properties, such as steady-state fluxes and concentrations, signal characteristics or control coefficients. The parameter distributions can also serve as priors in Bayesian statistical analysis. We propose a graphical scheme, the 'dependence graph', to bring out known dependencies between parameters, for instance, due to the equilibrium constants. If a parameter distribution is narrow, the resulting distribution of the variables can be computed by expanding them around a set of mean parameter values. We compute the distributions of concentrations, fluxes and probabilities for qualitative variables such as flux directions. The probabilistic framework allows the study of metabolic correlations, and it provides simple measures of variability and stochastic sensitivity. It also shows clearly how the variability of biological systems is related to the metabolic response coefficients.

Animals↗

A biased competition based neurodynamical model of visual neglect.

On the computational basis of a neurodynamical cortical model, we investigate a specific top-down visual cognitive impairment in brain-damaged patients known as visual spatial neglect. The computational cortical model accounts the neurodynamics underlying selective visual attention, is based on the "biased competition hypothesis" and structured in several network modules which can be related with the different areas of the dorsal and ventral path of the visual cortex. Spatial and object attention are accomplished by a multiplicative gain control that emerges dynamically through intercortical mutual biased coupling. By damaging the model in different ways, a variety of dysfunctions associated with visual neglect can be simulated and explained as disruption of specific subsystems. Essentially, the damage destabilizes the underlying intra- and intermodular mutually biased neurodynamical competition that macroscopically yields the functional deficits observed in visual neglect patients. In particular, we are able to explain the asymmetrical effect of spatial cueing on neglect, and the phenomenon of extinction in the framework of visual search.

Animals↗

Does a higher 'quality points' score mean better care in stroke? An audit of general practice medical records.

BACKGROUND: The Royal College of Physicians (RCP) have produced guidelines for stroke management in primary care; this guidance is taken to be the gold standard for the care of people with stroke. UK general practitioners now have a quality-based contract which includes a Quality and Outcomes Framework (QOF). This consists of financially remunerated 'quality points' for specific disease areas, including stroke. Achievement of these quality points is measured by extracting a limited list of computer codes from practice computer systems. OBJECTIVES: To investigate whether a high stroke quality score is associated with adherence to RCP guidelines. DESIGN: Examination of computer and written medical records of all patients with a diagnosis of stroke. SETTING: Two general practices, one in southwest London, one in Surrey, with a combined practice population of over 20 000. Both practices had a similar age-sex profile and prevalence of stroke. RESULTS: One practice scored 93.5% (29/31) of the available stroke quality points. The other practice achieved 73.4% (22.75/31), and only did better in one stroke quality target. However, the practice scoring fewer quality points had much better adherence to RCP guidance: 96% of patients were assessed in secondary care compared with 79% (P=0.001); 64% of stroke patients were seen the same day, compared with 44%; 56% received rehabilitation compared with 37%. CONCLUSIONS: Higher quality points did not reflect better adherence to RCP guidance. This audit highlights a gap between relatively simplistic measures of quality in the QOF, dependent on the recording of a narrow range of computer codes, and the actual standard of care being delivered. Research is needed to see whether this finding is generalisable and how the Quality and Outcomes Framework might be better aligned with delivering best practice.

Adolescent↗

Geometric Clutch model version 3: the role of the inner and outer arm dyneins in the ciliary beat.

The Geometric Clutch model of ciliary and flagellar beating uses the transverse force (t-force) that develops between the outer doublets of the axoneme as the regulator for activating and deactivating the dynein motors and organizing the flagellar beat. The version of the model described here adds detail to the formulations used in the two previous versions as follows: (1) In place of two opposing sets of dyneins, the new model has four sets of dyneins, corresponding to two sets on each side of the axoneme acting in series. (2) The four sets of dyneins are each subdivided into two ranks representing inner and outer arm dyneins. (3) The force produced by each dynein is governed by a force-velocity relationship that is independently specified for the inner and outer arms. Consistent with the original model, the new version of the Geometric Clutch model can simulate both the effective and recovery stroke phases of the ciliary beat using a single uniform algorithm. In addition, the new version can operate with the outer arms disabled. Under this condition, the simulation exhibits a beat pattern similar to the original but the beat frequency is reduced to approximately one third. These results are contingent on using force-velocity relationships for the inner and outer arms similar to those described by Brokaw [1999: Cell Motil. Cytoskeleton 42:134-148], where the inner arms contribute most of the driving force at low shear velocities. This constitutes the first examination of the effects of the force-velocity characteristics of dynein on a cilia-like beat in a theoretical framework.

Algorithms↗

DNA archives and our nearest relative: the trichotomy problem revisited.

Ever since Thomas H. Huxley correctly identified the chimpanzee and the gorilla as the two closest relatives of the human, the problem of the relationship among the three species ("the trichotomy problem") has remained unresolved. Comparative morphology and other classical methods of biological investigation have failed to answer definitively whether the chimpanzee or the gorilla is the closest relative of the human species. DNA sequences, both mitochondrial and nuclear, too, have provided equivocal solutions, depending on the region of the genome analyzed. Random sorting of ancestral allelic lineages, sequence convergence, and sequence exchanges between alleles or duplicated loci have been identified as likely factors confounding the interpretation of the interrelationships among the three species. In the present study most of these difficulties are overcome by identifying evolutionary causes that might potentially provide misleading information. Altogether, 45 loci consisting of 46, 855 bp are analyzed. About 60% of the loci and approximately the same proportion of phylogenetically informative sites support the human-chimpanzee clade. The remaining 40% of loci and sites support the two alternatives equally. It is demonstrated that, while incompatibility between loci can be explained by random sorting of allelic lineages, incompatibility within loci must be attributed largely to the joint effect of recombination and genetic drift. The trichotomy problem can be properly addressed only within this framework.

Alleles↗

The diffusion of virtual communities in health care: concepts and challenges.

OBJECTIVE: This paper providers an overview and discussion of virtual communities in health care. Furthermore, we aim to discuss in this context ethical, legal and technical considerations and the current status of research in this domain. METHODS: We searched medical and social science literature including survey studies, randomized and non-randomized controlled interventions and reviews. RESULTS: The literature indicates that a virtual community in health care as a group of people using telecommunication with the purposes of delivering health care and education, and/or providing support, covers a wide range of clinical specialties, technologies and stakeholders. Examples include peer-to-peer networks, virtual health care delivery and research teams. Ethical challenges including the concepts of identity and deception, privacy and confidentiality and technical issues, such as sociability and usability are discussed. CONCLUSION: Virtual communities may empower patients and enhance coordination of care services; however, there is not sufficient systematic evidence of the effectiveness of virtual communities on clinical outcomes or patient empowerment. Researchers need to address issues, such as sample sizes and experimental design to further the research field in this domain. PRACTICE IMPLICATIONS: When practitioners utilize virtual community tools to communicate with patients or colleagues they have to maximize sociability and usability of this mode of communication, while addressing concerns for privacy and the fear of de-humanizing practice, and the lack of clarity or relevance of current legislative frameworks.

Attitude of Health Personnel↗

Robustness of shape descriptors to incomplete contour representations.

With inspiration from psychophysical researches of the human visual system, we propose a novel aspect and a method for performance evaluation of contour-based shape recognition algorithms regarding their robustness to incompleteness of contours. We use complete contour representations of objects as a reference (training) set. Incomplete contour representations of the same objects are used as a test set. The performance of an algorithm is reported using the recognition rate as a function of the percentage of contour retained. We call this evaluation procedure the ICR test. We consider three types of contour incompleteness, viz. segment-wise contour deletion, occlusion, and random pixel depletion. As an illustration, the robustness of two shape recognition algorithms to contour incompleteness is evaluated. These algorithms use a shape context and a distance multiset as local shape descriptors. Qualitatively, both algorithms mimic human visual perception in the sense that recognition performance monotonously increases with the degree of completeness and that they perform best in the case of random depletion and worst in the case of occluded contours. The distance multiset method performs better than the shape context method in this test framework.

Algorithms↗

Hill coefficient for estimating the magnitude of cooperativity in gating transitions of voltage-dependent ion channels.

A frequently used measure for the extent of cooperativity in ligand binding by an allosteric protein is the Hill coefficient, obtained by fitting data of initial reaction velocity (or fractional binding saturation) as a function of substrate concentration to the Hill equation. Here, it is demonstrated that the simple two-state Boltzmann equation that is widely used to fit voltage-activation data of voltage-dependent ion channels is analogous to the Hill equation. A general empiric definition for a Hill coefficient (n(H)) for channel gating transitions that is analogous to the logarithmic potential sensitivity function of Almers is derived. This definition provides a novel framework for interpreting the meaning of the Hill coefficient. In considering three particular and simple gating schemes for a voltage-activated cation channel, the relation of the Hill coefficient to the magnitude and nature of cooperative interactions along the reaction coordinate of channel gating is demonstrated. A possible functional explanation for the low value of the Hill coefficient for gating transitions of the Shaker voltage-activated K(+) channel is suggested. The analogy between the Hill coefficients for ligand binding and for channel gating transitions further points to a unified conceptual framework in analyzing enzymes and channels behavior.

Computer Simulation↗

Clinical and laboratory considerations for the use of CAD/CAM Y-TZP-based restorations.

Prospective clinical studies are evaluating the long-term success of Y-TZP-based all-ceramic FPDs. Y-TZP-based infrastructures for crowns and FPDs present favorable physical, mechanical, and optical properties. Some Y-TZP-based restorative systems use CAD/CAM technology. Nevertheless, technicians should be able to employ traditional concepts of infrastructure design for both crowns and FPDs when using such materials. The purpose of this article is to review the properties of Y-TZP-based materials as a restorative infrastructure and to review the application of traditional concepts of framework design with CAD/CAM technology.

Computer-Aided Design↗

Zirconium oxide restorations with the DCS precident system.

The DCS Precident system is suitable for the dental practice and enables the processing of different materials and dental structures. The surface is acquired precisely and without contact by means of a semiconductor laser. Easy-to-use software is employed for the three-dimensional design of the restorations. An almost fully automatic milling machine efficiently mills the framework. A clinical case is documented.

Computer-Aided Design↗

CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts.

MOTIVATION: Variant calling for next-generation sequencing (NGS) data relies on a diverse ecosystem of tools and workflows. Large-scale collaborative studies increasingly adopt federated analysis, where each institution processes sensitive data locally using standardized pipelines. Deploying identical pipelines across multiple centers remains challenging because heterogeneous software environments and computing policies can cause workflow divergence and inconsistent results. RESULTS: We developed CBIcall, a workflow backend-flexible, configuration-driven framework that runs standardized variant-calling pipelines from raw FASTQ files to analysis-ready VCFs. Users define each analysis in a single YAML parameters file, which CBIcall resolves against a controlled workflow registry and resource catalog. The execution driver validates parameters and checks compatibility among pipelines, analysis modes, workflow backends, genome builds, tool versions, and resource bundles. CBIcall supports reproducibility auditing by comparing executions using recorded provenance and output fingerprints. CBIcall dispatches validated workflows natively through Bash, Cromwell, Nextflow and Snakemake backends and provides production-ready pipelines for germline WES, WGS (single-sample or cohort joint genotyping following GATK Best Practices), and mitochondrial DNA analysis. We evaluated analytical performance using public benchmark datasets and validated reproducibility across four computing environments. We further deployed CBIcall in the EU HEREDITARY project, where it processed 1102 samples with both WES and mtDNA pipelines on an institutional HPC system, supporting its suitability for reproducible cohort-scale genomic analyses. AVAILABILITY AND IMPLEMENTATION: CBIcall is open source (GPLv3) and distributed with ready-to-run pipelines; full dependency and installation documentation is available at https://github.com/CNAG-Biomedical-Informatics/cbicall.

Journal Article↗

Analysis of a master-slave architecture for distributed evolutionary computations.

This paper introduces a new mathematical model of the master-slave architecture for distributed evolutionary computations (EC). This model is validated using a concrete implementation based on the Distributed BEAGLE C++ framework. Results show that contrary to (current) popular belief, master-slave architectures are able to scale well over local area networks of workstations using off-the-shelf networking equipment. The main properties of the master-slave are also compared with those of the more mainstream island-model.

Artificial Intelligence↗

Bayesian natural selection and the evolution of perceptual systems.

In recent years, there has been much interest in characterizing statistical properties of natural stimuli in order to better understand the design of perceptual systems. A fruitful approach has been to compare the processing of natural stimuli in real perceptual systems with that of ideal observers derived within the framework of Bayesian statistical decision theory. While this form of optimization theory has provided a deeper understanding of the information contained in natural stimuli as well as of the computational principles employed in perceptual systems, it does not directly consider the process of natural selection, which is ultimately responsible for design. Here we propose a formal framework for analysing how the statistics of natural stimuli and the process of natural selection interact to determine the design of perceptual systems. The framework consists of two complementary components. The first is a maximum fitness ideal observer, a standard Bayesian ideal observer with a utility function appropriate for natural selection. The second component is a formal version of natural selection based upon Bayesian statistical decision theory. Maximum fitness ideal observers and Bayesian natural selection are demonstrated in several examples. We suggest that the Bayesian approach is appropriate not only for the study of perceptual systems but also for the study of many other systems in biology.

Alleles↗

An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints.

A novel approach aiding in the prediction of RNA secondary structures is presented. Although phylogenetic methods are the most successful at deriving RNA secondary structures, the are not applicable when the number of sequences or the sequence variability is too low. Methods based on energy minimization are therefore of great interest. However, some of the suboptimal RNA secondary structures computed with classic methods are unsaturated structures, i.e. some structures are included into others. Thus, the incorporation of constraints during the process of folding is not possible, while the incorporation of constraints before the process of folding often introduces a bias into the energy function. This paper describes a new procedure which allows for the incorporation of constraints before and during the process of RNA folding. SAPSSARN is an interactive program which offers a framework, both to specify a secondary structure through a set of folding constraints and to compute all the supoptimal saturated RNA secondary structures which satisfy all the folding constraints. At the start, it relies on the computation of the probabilities of pairing of each base with all others according to McCaskill's algorithm. The constraint satisfaction formulation of the problem deals dynamically with a chosen set of folding constraints and, finally, a search algorithm computes all the suboptimal saturated secondary structures which satisfy those folding constraints. Within such a framework, it is possible to test new ideas about RNA folding and secondary structures, including pseudoknots, can be computed. The program is illustrated with RNA sequences on which we obtained results in agreement with known structures by using a protocol which mimics the hierarchical folding of RNA molecules.

Algorithms↗

Applications of computer modelling for the design of orthopaedic, dental and cardiovascular biomaterials.

Biomaterials do not escape from the general trend present in all contemporary science and technology towards increasing use of computers and information technology. In this paper the use of computer modelling for the design of biomaterials is discussed. The word 'biomaterials' is interpreted in its broadest sense, i.e. referring to any foreign object brought into the body for temporary or permanent use. Computer modelling will first be discussed as a tool to model biological structures (bones, arteries) or to investigate and simulate biological interactions at implant-host interfaces. It will then be illustrated how computer modelling, using insights gained from the modelling of the biological structures themselves, is used in the design process of dental, orthopaedic and cardiovascular prostheses. The area of computer modelling for biomaterials applications has become so vast that an exhaustive overview is impossible in the framework of one paper. Rather, some illustrative case studies will be discussed which are, in the opinion of the authors, representative of general trends in this challenging domain of science on the boundary between engineering and medicine.

Cardiovascular Diseases↗

[The in-vitro study of the marginal fit accuracy of computer-milled titanium crowns. II. A histological-morphometric marginal-gap analysis].

The Digitising Computer System (DCS) can be mechanically programmed to produce computer-milled titanium dentures for veneered ceramic single crowns using three-dimensional computer models. A first analysis by electron scanning microscope of the marginal leakage in titanium framework on 12 extracted teeth showed a marginal accuracy of fit of 68.3 +/- 61.1 microns for the shoulder, and 95.7 +/- 83.2 microns for the chamfered preparation. Owing to limited indicative value of recordings by electron scanning microscopes, the crown edges of the 9 teeth with shoulder preparations were subjected to histological-morphometric measurements. Using this more accurate investigational system, a distinctly higher arithmetic mean of 89.2 +/- 69.1 microns for the marginal accuracy of fit was achieved. It also enabled the marginal leakage of cement (96.5 +/- 85.1 microns), the marginal adaptation (37.4 +/- 93.3 microns) and the shoulder formation (44.4 +/- 58.9 microns) to be judged.

Computer Simulation↗