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At least 1,135 records · Page 63Linked to original sources
PubMed2006

IT-adoption and the interaction of task, technology and individuals: a fit framework and a case study.

BACKGROUND: Factors of IT adoption have largely been discussed in the literature. However, existing frameworks (such as TAM or TTF) are failing to include one important aspect, the interaction between user and task. METHOD: Based on a literature study and a case study, we developed the FITT framework to help analyse the socio-organisational-technical factors that influence IT adoption in a health care setting. RESULTS: Our FITT framework ("Fit between Individuals, Task and Technology") is based on the idea that IT adoption in a clinical environment depends on the fit between the attributes of the individual users (e.g. computer anxiety, motivation), attributes of the technology (e.g. usability, functionality, performance), and attributes of the clinical tasks and processes (e.g. organisation, task complexity). We used this framework in the retrospective analysis of a three-year case study, describing the adoption of a nursing documentation system in various departments in a German University Hospital. We will show how the FITT framework helped analyzing the process of IT adoption during an IT implementation: we were able to describe every found IT adoption problem with regard to the three fit dimensions, and any intervention on the fit can be described with regard to the three objects of the FITT framework (individual, task, technology). We also derive facilitators and barriers to IT adoption of clinical information systems. CONCLUSION: This work should support a better understanding of the reasons for IT adoption failures and therefore enable better prepared and more successful IT introduction projects. We will discuss, however, that from a more epistemological point of view, it may be difficult or even impossible to analyse the complex and interacting factors that predict success or failure of IT projects in a socio-technical environment.

Anxiety↗
PubMed2026

MegaPlantTF: a machine learning framework for comprehensive identification and classification of plant transcription factors.

MOTIVATION: Understanding the role of transcription factors (TFs) in plants is essential for the study of gene regulation and various biological processes. However, both TF detection and classification remain challenging due to the great diversity and complexity of these proteins. Conventional approaches, such as BLAST, often suffer from high computational complexity and limited performance on less common TF families. RESULTS: We introduce MegaPlantTF, the first comprehensive machine learning and deep learning framework for the prediction (TF versus non-TF) and classification (family-level) of plant TFs. Our method employs k-mer-based protein representations and a two-stage architecture combining a deep feed-forward neural network with a stacking ensemble classifier. To ensure robust performance assessment, we report micro-, macro-, and weighted-average performance metrics, providing a holistic evaluation of both frequent and underrepresented TF families. Additionally, we employ threshold-based evaluation to calibrate confidence in TF detection. The results show that MegaPlantTF achieves strong accuracy and precision, particularly with a k-mer size of 3 and a classification threshold of 0.5, and maintains stable performance even under stringent thresholds. In addition to the standard cross-validation tests, a use case study on Sorghum bicolor confirms that our method performs strongly in the genome-wide analysis, making it highly suitable for large-scale TF identification and classification tasks. MegaPlantTF represents a novel contribution by integrating k-mer encoding, binary family-specific classifiers, and a two-stage stacking ensemble into a unified, reproducible framework for large-scale plant TF identification and classification. AVAILABILITY AND IMPLEMENTATION: MegaPlantTF is freely accessible through a public web server available at https://bioinformatics.um6p.ma/MegaPlantTF. The complete source code, including pretrained models and example datasets, is available at https://github.com/Bioinformatics-UM6P/MegaPlantTF.

Transcription Factors↗
PubMed2005

Generalized mosaicing: polarization panorama.

We present an approach to image the polarization state of object points in a wide field of view, while enhancing the radiometric dynamic range of maging systems by generalizing image mosaicing. The approach is biologically-inspired, as it emulates spatially varying polarization sensitivity of some animals. In our method, a spatially varying polarization and attenuation filter is rigidly attached to a camera. As the system moves, it senses each scene point multiple times, each time filtering it through a different filter polarizing angle, polarizance, and transmittance. Polarization is an additional dimension of the generalized mosaicing paradigm, which has recently yielded high dynamic range images and multispectral images in a wide field of view using other kinds of filters. The image acquisition is as easy as in traditional image mosaics. The computational algorithm can easily handle nonideal polarization filters (partial polarizers), variable exposures, and saturation in a single framework. The resulting mosaic represents the polarization state at each scene point. Using data acquired by this method, we demonstrate attenuation and enhancement of specular reflections and semireflection separation in an image mosaic.

Algorithms↗
PubMed2006

Multipole electrostatic potential derived atomic charges in NDDO-methods with spd-basis sets.

The recently introduced multipole approach for computing the molecular electrostatic potential (MEP) within the semiempirical neglect of diatomic differential overlap (NDDO) framework [Horn AHC, Lin Jr-H., Clark T (2005) Theor Chem Acc 114:159-168] has been used to obtain atomic charges of nearly ab initio quality by scaling the semiempirical MEP. The parameterization set comprised a total of 797 compounds and included not only the newly parameterized AM1* elements Al, Si, P, S, Cl, Ti, Zr, and Mo but also the standard AM1 elements H, C, N, O and F. For comparison, the ZDO-approximated MEP was also calculated analytically in the spd-basis. For the AM1*-optimized structures, single-point calculations at the B3LYP, HF and MP2 levels with the 6-31G(d) and LanL2DZP basis sets were performed to obtain the MEP. The regression analysis of all 12 combinations of semiempirical and ab initio MEP data yielded correlation coefficients of at least 0.99 in all cases. Scaling the analytical and multipole-derived semiempirical MEP by the regression coefficients yielded mean unsigned errors below 2.6 and 1.9 kcal mol(-1), respectively. Subsequently, for 22 drug molecules from the World Drug Index, atomic charges were computed according to the RESP procedure using XX/6-31G(d) (XX=B3LYP, HF, MP2) and scaled AM1* multipole MEP; the correlation coefficients obtained are 0.83, 0.85 and 0.83, respectively.

Models, Chemical↗
PubMed1998

Marginal adaptation of implant-supported metal-ceramic crowns fabricated with gold cylinders.

PURPOSE: The purpose of this investigation was to determine the mean marginal discrepancy of metal-ceramic crowns fabricated with gold cylinders and cemented on implant abutments. These discrepancies were then compared with those measured previously for implant-supported ceramic crowns. MATERIALS AND METHODS: Fifteen Nobel BioCare CeraOne abutments were connected to implant fixtures embedded in acrylic resin blocks. Marginal discrepancies were determined for gold cylinders, gold cylinders plus ceramic alloy (metal frameworks), completed metal-ceramic crowns, and cemented metal-ceramic crowns using a stereomicroscope equipped with a video camera linked to a computer. A Hotelling's T2 test (p < or = .05) was used to evaluate potential differences in mean marginal discrepancies among groups. RESULTS: The mean marginal discrepancies were: 1) gold cylinders, 7.56 +/- 2.73 microns; 2) metal frameworks, 6.21 +/- 1.34 microns; 3) metal-ceramic crowns, 11.06 +/- 3.21 microns; and 4) zinc-phosphate cemented crowns, 31.47 +/- 6.65 microns. No significant difference between gold cylinders and metal frameworks was found. Mean marginal discrepancies for metal-ceramic crowns were significantly greater than discrepancies for cast gold cylinders. Cemented-crown mean marginal discrepancy was significantly greater than all other means. CONCLUSIONS: Cemented metal-ceramic crowns fabricated using proprietary gold cylinders exhibited well-fitting margins (31.47 microns).

Cementation↗
PubMed2026

Partial enumeration of extreme rays in metabolic networks using bit pattern trees.

Extreme ray analysis of metabolic networks, even though very powerful, is currently limited to smaller metabolic networks. Some approaches to generating partial sets of extreme rays exist, but the computational efficiency of the so-called double-description method is yet to be exploited. Previous work highlighted the possibility of sampling within its iterations, enabling partial enumeration for double-description based methods. However, these approaches severely lack computational efficiency to be a suitable alternative. In this work, the highly efficient bit pattern trees are used within the sampling framework to significantly enhance its output and speed. Combined with the recent revision of the Canonical Basis Approach (CBA), our approach outperforms the other tested methods under the reported benchmark conditions even for a full enumeration study, requiring only half the computation time. In addition, a filter setting allows the memory demand to be scaled down while retaining high efficiency. However, some issues with the combinatorial explosion of candidates still persist and are further investigated. This study therefore puts forward a novel, double description-based alternative to partial enumeration of extreme rays. Further improvements in memory efficiency would allow this promising approach to scale powerful extreme ray-based analyses to genome-scale metabolic networks.

constraint-based modelling↗
PubMed1997

An Internet service for manipulating 3D models of human organs reconstructed from computer tomography and magnetic resonance imaging.

Our paper describes an integrated methodology addressing the development of an Internet service for medical professionals, medical students and generally, people interested in medicine. The service (currently developed in the framework of IAEVA, a Telematics Application Programme project of the European Union), incorporates a mechanism for retrieving from a relational database (reference library) 3D volumetric models of human organs reconstructed from computer tomography (CT) and/or magnetic resonance imaging (MRI). Retrieval is implemented in a way transparent to the actual physical location of the database. Prospective users are provided with a Solid Object Viewer that offers them manipulation (rotation, zooming, dissection etc.) of 3D volumetric models. The service constitutes an excellent foundation of understanding for medical professionals/students and a mechanism for broad and rapid dissemination of information related to particular pathological conditions; although pathological conditions of the knee and skin are supported currently, our methodology allows easy service extension into other human organs ultimately covering the entire human body. The service accepts most Internet browsers and supports MS-Windows 32 platforms; no graphics accelerators or any specialised hardware are necessary, thereby allowing service availability to the widest possible audience. Nevertheless, the service operates in near real-time not only over high speed expensive network lines but also over low/medium network connections.

Computer Communication Networks↗
PubMed1993

A simple network model simulates hippocampal place fields: parametric analyses and physiological predictions.

Hippocampal place cells may be the computational units of a neuronal cognitive mapping system. A network model trained to compute locations from distal cues simulated the defining properties of hippocampal place cells (i.e., place-specific activation). The model produced units with detailed properties of place cells, including multiple subfields, "silent" and "noisy" cells, fields that persisted after cue removal, and groups of simulated fields that overlapped in multiple clusters. Quantitative variants of the model showed that different properties of the fields were influenced by the complexity of the visual input (the number of spatial cues), the available computational resources (the number of hidden units), and the output encoding used to represent location. The simulations provide a framework for testing relationships between place field properties, variations in spatial environments, and the integrity of the hippocampal system.

Animals↗
PubMed2003

A comparison of two methods for the estimation of precision with incomplete longitudinal data, jointly modelled with a time-to-event outcome.

Several methods for the estimation and comparison of rates of change in longitudinal studies with staggered entry and informative drop-outs have been recently proposed. For multivariate normal linear models, REML estimation is used. There are various approaches to maximizing the corresponding log-likelihood; in this paper we use a restricted iterative generalized least squares method (RIGLS) combined with a nested EM algorithm. An important statistical problem in such approaches is the estimation of the standard errors adjusted for the missing data (observed data information matrix). Louis has provided a general technique for computing the observed data information in terms of completed data quantities within the EM framework. The multiple imputation (MI) method for obtaining variances can be regarded as an alternative to this. The aim of this paper is to develop, apply and compare the Louis and a modified MI method in the setting of longitudinal studies where the source of missing data is either death or disease progression (informative) or end of the study (assumed non-informative). Longitudinal data are simultaneously modelled with the missingness process. The methods are illustrated by modelling CD4 count data from an HIV-1 clinical trial and evaluated through simulation studies. Both methods, Louis and MI, are used with Monte Carlo simulations of the missing data using the appropriate conditional distributions, the former with 100 simulations, the latter with 5 and 10. It is seen that naive SEs based on the completed data likelihood can be seriously biased. This bias was largely corrected by Louis and modified MI methods, which gave broadly similar estimates. Given the relative simplicity of the modified MI method, it may be preferable.

Algorithms↗
PubMed2001

Separating processes in object perception.

In this article, I consider research by Needham and colleagues examining the role of object knowledge on infant's segregation of scenes into objects. I suggest that research in this area would benefit from closer connections to computational, psychophysical, and neurophysiological research on adult perceptual segmentation and grouping. I sketch a framework for understanding the components of object perception and apply it to the paradigm and displays used by Needham. This analysis suggests two ideas. First, it would be valuable to demonstrate the role of object knowledge in cases that are less impoverished in terms of perceptual information for segregation and more typical of object arrangements in ordinary scenes. Second, some method is needed to distinguish whether infants' object knowledge affects perceptual organization of new scenes or produces specific beliefs, inferences, or expectations about particular objects and scenes. As a specific example of the benefits of connecting developmental and adult research, some recent research in adult perception is described. The research indicates that in adult object segregation, two types of processes may be distinguished: basic perceptual processes of object segregation and more cognitive processes involving recognition. I suggest that Needham's research may be revealing the developmental origins of the latter processes.

Child Development↗
PubMed2000

Condition number as a measure of noise performance of diffusion tensor data acquisition schemes with MRI.

Diffusion tensor mapping with MRI can noninvasively track neural connectivity and has great potential for neural scientific research and clinical applications. For each diffusion tensor imaging (DTI) data acquisition scheme, the diffusion tensor is related to the measured apparent diffusion coefficients (ADC) by a transformation matrix. With theoretical analysis we demonstrate that the noise performance of a DTI scheme is dependent on the condition number of the transformation matrix. To test the theoretical framework, we compared the noise performances of different DTI schemes using Monte-Carlo computer simulations and experimental DTI measurements. Both the simulation and the experimental results confirmed that the noise performances of different DTI schemes are significantly correlated with the condition number of the associated transformation matrices. We therefore applied numerical algorithms to optimize a DTI scheme by minimizing the condition number, hence improving the robustness to experimental noise. In the determination of anisotropic diffusion tensors with different orientations, MRI data acquisitions using a single optimum b value based on the mean diffusivity can produce ADC maps with regional differences in noise level. This will give rise to rotational variances of eigenvalues and anisotropy when diffusion tensor mapping is performed using a DTI scheme with a limited number of diffusion-weighting gradient directions. To reduce this type of artifact, a DTI scheme with not only a small condition number but also a large number of evenly distributed diffusion-weighting gradients in 3D is preferable.

Algorithms↗
PubMed2003

A unified variational approach to denoising and bias correction in MR.

We propose a novel bias correction method for magnetic resonance (MR) imaging that uses complementary body coil and surface coil images. The former are spatially homogeneous but have low signal intensity; the latter provide excellent signal response but have large bias fields. We present a variational framework where we optimize an energy functional to estimate the bias field and the underlying image using both observed images. The energy functional contains smoothness-enforcing regularization for both the image and the bias field. We present extensions of our basic framework to a variety of imaging protocols. We solve the optimization problem using a computationally efficient numerical algorithm based on coordinate descent, preconditioned conjugate gradient, half-quadratic regularization, and multigrid techniques. We show qualitative and quantitative results demonstrating the effectiveness of the proposed method in producing debiased and denoised MR images.

Algorithms↗
PubMed2003

ASTRO-FOLD: a combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence.

The field of computational biology has been revolutionized by recent advances in genomics. The completion of a number of genome projects, including that of the human genome, has paved the way toward a variety of challenges and opportunities in bioinformatics and biological systems engineering. One of the first challenges has been the determination of the structures of proteins encoded by the individual genes. This problem, which represents the progression from sequence to structure (genomics to structural genomics), has been widely known as the structure-prediction-in-protein-folding problem. We present the development and application of ASTRO-FOLD, a novel and complete approach for the ab initio prediction of protein structures given only the amino acid sequences of the proteins. The approach exhibits many novel components and the merits of its application are examined for a suite of protein systems, including a number of targets from several critical-assessment-of-structure-prediction experiments.

Algorithms↗
PubMed1981

Lexical meaning: a case report, some striking phenomena, theoretical implications.

A case of global aphasia is reported. In spite of severe impairments in auditory comprehension, as testified by failure in matching spoken words to pictured objects, the patient performed significantly higher than chance level in sorting out the odd item from a spoken list of semantically related words. This preserved ability to achieve the semantic processing of "non-understood" spoken words in the given task is compared to similar experimental data from the study of written word comprehension in dyslexic patients or normal subjects. Taken together, these data call for a procedural approach of the lexicon. In this theoretical framework, lexical meaning should not only be stored and retrieved but it should be computed at each word occurrence.

Adult↗
PubMed1994

Models of activity-dependent neural development.

What makes a useful model of neural development? One important contribution of modeling is to demonstrate that proposed biological mechanisms can be sufficient to account for experimental results. The Von der Malsburg model is a classic example. But such demonstrations alone do not provide tools to experimentally distinguish one mechanism from another. To draw such distinctions, the connection between measurable biological quantities and developmental outcomes must be established. Perhaps the most important task for the future of developmental modeling is to deepen the connection between theory and experiment. Experimentally, this requires detailed and difficult measurements or experimental perturbations of the correlations among inputs and the intracortical connectivity existing during development. Simultaneous measurement of the maps of spatial phase and orientation of mature simple cells will provide important information for the understanding of orientation column development. Theoretically, the number of open problems is enormous. How will inclusion of additional plasticity mechanisms, such as sprouting and retraction of synapses or plasticity of intracortical connections, alter the analytical understanding thus far achieved? What precisely determines the width of orientation columns in the model presented here? Can the relationship between ocular dominance and orientation columns be understood from developmental rules in a testable way? The existing framework may be extended to a three-dimensional cortex and to more complex models of intracortical connectivity. It may also be applied to other developmental phenomena including the development of lamination in the LGN (Shatz and Stryker, 1988; Hahm et al., 1991), the formation of visual maps in experimentally altered auditory cortex (Roe et al., 1990, 1992), and the mapping of visual and auditory maps in the optic tectum (Knudsen and Brainard, 1991; Brainard and Knudsen, 1993). For each system the goal is to develop testable predictions as to the patterns of activity and connectivity that could or could not lead to the results observed given a proposed mechanism of plasticity. Incorporation of deeper levels of biophysical realism will extend, deepen, and perhaps fundamentally alter the framework presented here. An important goal for the future will be to understand the computational and functional significance of developmental rules. Activity-dependent, competitive mechanisms of synaptic plasticity appear to play an important role in many processes of late neural development, where an initially rough connectivity pattern refines to a precise, mature pattern. A prominent example is the formation of ocular dominance columns in the visual cortex of many mammals. These processes may be modeled at several levels.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2002

Estimation of the partial volume effect in MRI.

The partial volume effect (PVE) arises in volumetric images when more than one tissue type occurs in a voxel. In such cases, the voxel intensity depends not only on the imaging sequence and tissue properties, but also on the proportions of each tissue type present in the voxel. We have demonstrated in previous work that ignoring this effect by establishing binary voxel-based segmentations introduces significant errors in quantitative measurements, such as estimations of the volumes of brain structures. In this paper, we provide a statistical estimation framework to quantify PVE and to propagate voxel-based estimates in order to compute global magnitudes, such as volume, with associated estimates of uncertainty. Validation is performed on ground truth synthetic images and MRI phantoms, and a clinical study is reported. Results show that the method allows for robust morphometric studies and provides resolution unattainable to date.

Brain↗
PubMed2006

Calculating multidimensional discrete variable representations from cubature formulas.

Finding multidimensional nondirect product discrete variable representations (DVRs) of Hamiltonian operators is one of the long standing challenges in computational quantum mechanics. The concept of a "DVR set" was introduced as a general framework for treating this problem by R. G. Littlejohn, M. Cargo, T. Carrington, Jr., K. A. Mitchell, and B. Poirier (J. Chem. Phys. 2002, 116, 8691). We present a general solution of the problem of calculating multidimensional DVR sets whose points are those of a known cubature formula. As an illustration, we calculate several new nondirect product cubature DVRs on the plane and on the sphere with up to 110 points. We also discuss simple and potentially very useful finite basis representations (FBRs), based on general (nonproduct) cubatures. Connections are drawn to a novel view on cubature presented by I. Degani, J. Schiff, and D. J. Tannor (Num. Math. 2005, 101, 479), in which commuting extensions of coordinate matrices play a central role. Our construction of DVR sets answers a problem left unresolved in the latter paper, namely, the problem of interpreting as function spaces the vector spaces on which commuting extensions act.

Journal Article↗
PubMed2006

Theoretical insight into the spectroscopy and photochemistry of isoalloxazine, the flavin core ring.

The electronic singlet-singlet and singlet-triplet electronic transitions of the isoalloxazine ring of the flavin core are studied using second-order perturbation theory within the framework of the CASPT2//CASSCF protocol. The main features of the absorption spectrum are computed at 3.09, 4.28, 4.69, 5.00, and 5.37 eV. The lowest singlet (S1) and triplet (T1) excited states are found to be both of pi character with a singlet-triplet splitting of 0.57 eV. On the basis of the analysis of the computed spin-orbit couplings and the potential energy hypersurfaces built for the relevant excited states, the intrinsic mechanism for photoinduced population of T1 is discussed. Upon light absorption, evolution of the lowest singlet excited state along the relaxation pathway leads ultimately to the population of the lowest triplet state, which is mediated by a singlet-triplet crossing with a state of npi* type. Subsequently a radiationless decay toward T1 through a conical intersection takes place. The intersystem crossing mechanism and the internal conversion processes documented here provide a plausible route to access the lowest triplet state, which has a key role in the photochemistry of the flavin core ring and is mainly responsible for the reactivity of the system.

Flavins↗