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PubMed2002

Steady state and dynamic modelling of nitrogen in the River Kennet: impacts of land use change since the 1930s.

Steady state and dynamic models have been developed and applied to the River Kennet system. Annual nitrogen exports from the land surface to the river have been estimated based on land use from the 1930s and the 1990s. Long term modelled trends indicate that there has been a large increase in nitrogen transport into the river system driven by increased fertiliser application associated with increased cereal production, increased population and increased livestock levels. The dynamic model INCA (Integrated Nitrogen in Catchments) has been applied to simulate the day-to-day transport of N from the terrestrial ecosystem to the riverine environment. This process-based model generates spatial and temporal data and reproduces the observed instream concentrations. Applying the model to current land use and 1930s land use indicates that there has been a major shift in the short term dynamics since the 1930s, with increased river and groundwater concentrations caused by both non-point source pollution from agriculture and point source discharges.

Agriculture↗

PubMed2002

Development of quantitative structure-property relationship models for pseudoternary microemulsions formulated with nonionic surfactants and cosurfactants: application of data mining and molecular modeling.

Data mining, computer-aided molecular modeling, descriptor calculation and multiple linear regression techniques were utilized to produce statistically significant and predictive models for O/W and W/O microemulsions. The literature was scanned over the last 20 years, subsequently, 68 phase diagrams from eight different references were collected. Molecular modeling techniques were then applied on the components of the microemulsion systems to generate plausible 3-D structures. Subsequently, various physicochemical descriptors were calculated based on the resulting 3-D structures. The generated descriptors were correlated with microemulsion existence areas utilizing multiple linear regression analysis (MLR). The generated models were statistically cross-validated and were found to be of significant predictive power. Furthermore, the resulting models allowed better understanding of the process of microemulsion formation.

Drug Compounding↗

PubMed2006

Pairwise linkage disequilibrium under disease models.

Many genetic studies of disease association rely heavily on linkage disequilibrium (LD) patterns between pairs of markers to detect susceptibility markers. This is true of large-scale positional mapping approaches as well as haplotype construction, selection of tagging single-nucleotide polymorphisms and population genetic analyses. Whereas the distribution of different LD measures has been investigated for randomly selected chromosomes from populations undergoing a variety of demographic effects, little is known about LD within disease-affected samples, and how various disease models influence the difference in LD between patients and the general population. As whole-genome efforts are now underway to characterize and utilize LD patterns in randomly sampled individuals, knowledge about the extent that LD differs between patients and the general population becomes crucial. Such information will allow investigators to design improved mapping experiments and better understand haplotype information arising from such experiments. In this paper, we explore two-site LD measures in the context of single gene disease models. Analytic expressions are presented for infinite populations and properties of sampling densities are reported for different disease models. Interestingly, results indicate that 'underdominant', some dominant, recessive and 'protective' disease models generate weaker LD levels in patients compared to the general population, whereas other models produce stronger LD among affected individuals. Analytic results are also presented for the ratio of LD in patients to the LD in the general population as a function of recombination fraction using a Haldane model. In addition, we explore the impact of various allele frequency combinations on LD differences.

Genetic Predisposition to Disease↗

PubMed1995

Mate finding via a trail sex pheromone by a parasitoid wasp.

In field observations and laboratory experiments, we found that virgin females of the solitary parasitoid Aphelinus asychis did not emit a volatile sex pheromone to attract males, contrary to what has been reported in many other parasitoid species. Instead, we found that virgin females deposited a sex pheromone on the substrate to which males responded by intensively searching on and near the marked area. Males did not respond to leaves exposed to mated females or to other males. In patches of 64 wheat leaves, males were dispersed from a central release point, and more males were subsequently observed on leaves exposed to virgin females than on unexposed leaves. The pheromone faded to inactivity in less than 24 h. To examine whether the trail pheromone would be sufficient for mate finding by males in the field, we modeled random movement of males among plant stems where the trail pheromone was the only cue males used to find females. The probability that females encountered at least one male in their lifetime increased with male density and time after female emergence. Given the range of densities of A. asychis in barley and wheat fields near Montpellier, France, the model generated an encounter probability sufficient to explain the survival of established populations. The model also suggested that difficulty in finding mates at low density might be a problem for invading populations.

Animals↗

PubMed1993

Schizophrenic delusions: a phenomenological approach.

The issue of specificity of delusions in schizophrenia is still a matter of debate. The authors analyze the delusion formation in schizophrenia from a prototypical, phenomenological point of view, focusing on the subject's experience. This perspective links delusion formation to the autistic predisposition, which is considered here as the elementary phenotypic expression of the vulnerability to schizophrenia. Autism is viewed as a defective preconceptual (i.e., before language) attunement to the world. It impedes the individual's sharing of "common sense" with others and impairs the ability to project into the future. The development of delusions is illustrated, in part, by Klaus Conrad's work on the onset of paranoid schizophrenia. Delusions are viewed as transformations of the structure of experiencing. When threatened in future ability to be, the autistic, vulnerable person looks for the clues to becoming by attributing significance to disparate elements of the environment, which become self-referential. The link established between these disparate elements is based on universal characteristics that give the schizophrenic delusion a metaphysical quality. The transitivistic experience in delusions of control and omnipotence points to a specific way of crossing the border between "mine" and "yours" (disturbances of the experiencing "I"). What strikes a clinician in these delusions is that the normally tacit link between the sense of being and the sense of acting becomes quite apparent. The authors also propose a specificity in the themes of schizophrenic delusions. Delusions acquire a schizophrenic quality when ontological (i.e., universal) elements of the discourse between the locutor and the Other dominate at the expense of the worldly elements. It is emphasized that delusional content and form are dialectically related and hardly distinguishable. The authors consider the delusion formation as a phenomenon of emergence, a situation in which a new qualitative order arises from the reorganization of essentially unchanged elements. To consider schizophrenia as an emergent, particular way of experiencing, related to the autistic defect, has important consequences for research and for treatment. A dialectic exchange is needed between prototypical models generated by phenomenological inquiry and empirical, operational validation of testable aspects of such models.

Activities of Daily Living↗

PubMed1996

The role of cardiac imaging and biochemical markers in patients with acute chest pain.

Acute chest pain syndromes are common, with over 6 million patients in the United States presenting to emergency departments with suggestive symptoms. This review concentrates on the previous models and new diagnostic testing procedures. The different modalities emphasized are computer-generated models, serum markers, echocardiography, and nuclear imaging in the emergency department. The use of new markers and imaging may help to risk-stratify patients earlier for potential treatment and triage decisions.

Biomarkers↗

PubMed1991

Conserved amino acid sequences among plant proteins sorted to protein bodies and plant vacuoles. Can they play a role in protein sorting?

Amino acid sequence comparisons were made between the soybean alpha subunit of beta-conglycinin and 34 members of different plant protein families targeted to seed protein bodies or vacuoles. A number of short conserved amino acid sequences were identified in seed storage proteins, plant protease inhibitors and lectins, and the probable functions of these sequences are discussed. For proteins of known tertiary structure, these sequences map to the surface of the respective molecules. It is postulated that these regions produce a common secondary structure which could interact with other molecules involved in the sorting process. One of these regions, region A, is similar to the yeast carboxypeptidase Y (CPY) vacuolar targeting signal, and is present in both storage proteins and lectins. Computer modeling based upon the tertiary structure of concanavalin A (ConA) was used to generate models representing the structure of two highly related lectins from Dolichos biflorus, one of which is targeted to protein bodies and the other secreted. A different glycosylation pattern together with amino acid sequences upstream of the identified conserved amino acid sequences are predicted to modulate the presentation of the sorting domains in the lectins and be the determinant in the sorting of these lectins.

Amino Acid Sequence↗

PubMed2004

The PAS fold. A redefinition of the PAS domain based upon structural prediction.

In the postgenomic era it is essential that protein sequences are annotated correctly in order to help in the assignment of their putative functions. Over 1300 proteins in current protein sequence databases are predicted to contain a PAS domain based upon amino acid sequence alignments. One of the problems with the current annotation of the PAS domain is that this domain exhibits limited similarity at the amino acid sequence level. It is therefore essential, when using proteins with low-sequence similarities, to apply profile hidden Markov model searches for the PAS domain-containing proteins, as for the PFAM database. From recent 3D X-ray and NMR structures, however, PAS domains appear to have a conserved 3D fold as shown here by structural alignment of the six representative 3D-structures from the PDB database. Large-scale modelling of the PAS sequences from the PFAM database against the 3D-structures of these six structural prototypes was performed. All 3D models generated (> 5700) were evaluated using prosaii. We conclude from our large-scale modelling studies that the PAS and PAC motifs (which are separately defined in the PFAM database) are directly linked and that these two motifs form the PAS fold. The existing subdivision in PAS and PAC motifs, as used by the PFAM and SMART databases, appears to be caused by major differences in sequences in the region connecting these two motifs. This region, as has been shown by Gardner and coworkers for human PAS kinase (Amezcua, C.A., Harper, S.M., Rutter, J. & Gardner, K.H. (2002) Structure 10, 1349-1361, [1]), is very flexible and adopts different conformations depending on the bound ligand. Some PAS sequences present in the PFAM database did not produce a good structural model, even after realignment using a structure-based alignment method, suggesting that these representatives are unlikely to have a fold resembling any of the structural prototypes of the PAS domain superfamily.

Amino Acid Sequence↗

PubMed2000

How can the incidence of negative specimens resulting from large loop excision of the cervical transformation zone (LLETZ) be reduced? An analysis of negative LLETZ specimens and development of a predictive model.

OBJECTIVE: To analyse biopsies of large loop excision of the transformation zone of the cervix; to identify factors associated with negative histology; and to develop predictive models in order to reduce the number of negative loop excisions. DESIGN: Retrospective analysis of patient notes and audit database. SETTING: Colposcopy clinic of a large district general hospital in North Staffordshire. POPULATION: Four hundred and fifty-two women who underwent a large loop excision of the transformation zone (LLETZ) procedure for suspected cervical intraepithelial neoplasia. METHODS: Women who underwent a LLETZ procedure were placed in two different groups, one positive for cervical intra epithelial neoplasia and the other negative for cervical intra epithelial neoplasia. Information was obtained on a number of clinical and colposcopic variables. Analysis was undertaken to determine if there were any differences between the two groups. These factors were then identified and three predictive models generated. Receiver-operator characteristic curves were used to assess and test these models. MAIN OUTCOMES MEASURES: To identify factors associated with negative histology on a LLETZ specimen. To predict how to reduce the number of negative LLETZ specimens. RESULTS: Four hundred and fifty-two women underwent a LLETZ procedure, 88 were negative (19%) and 364 were positive (81%). In women who were treated at their first visit, 56/316 (18%) had negative histology. There were significant associations between negative histology in the LLETZ and negative or low grade cytological atypia, negative colposcopic findings and years of age > 50 in both bivariate analysis and stepwise logistic regression. In the predictive models, the sensitivity ranged between 72% and 80%, the specificity 59%-72%, and the area under the receiver-operator characteristic was 0.75-0.77. If we had used the predictor models and managed women with negative or low grade cervical atypia and negative colposcopy findings conservatively, we would have reduced the negative biopsy rate from 19% to 14%, but five cases of high grade disease and 25 cases of low grade disease would have been missed. If we had also included women aged > 50 years in this model, the negative biopsy rate would have dropped from 19% to 15%, with only one case of high grade disease and 11 cases of low grade disease missed. All these women would require continued cytological and colposcopic surveillance. Importantly, no cases of invasion would have been missed. CONCLUSION: Using a predictive model can reduce the number of negative LLETZ specimens, but at the expense of continued cytological and colposcopic surveillance and cannot be recommended in normal practice. This raises the question whether current standards for negative histology in LLETZ specimens are set unrealistically high.

Adolescent↗

PubMed1994

Three-dimensional models for head and neck tumor treatment planning.

The authors have evaluated two types of practical maxillofacial model systems useful to the head and neck surgeon:1. plastic mandibular model generated by three-dimensional computerized tomography (CT) reconstruction, and 2. dental impression model of the maxilla. The first model is expensive and technology intensive; the second is simple but limited. Both three-dimensional models offer several advantages: 1. they provide segmental mandibular relationships that are not known because of oncologic restrictions or previous surgery; 2. they allow preoperative reconstructive planning including prosthesis fabrication and visualization of tumor extent not obvious by two dimensional imaging; and 3. they provide a permanent record for future needs or reconstructions. The disadvantages include cost, time, and possible inaccuracies secondary to image artifacts. We find both models to be of significant practical value in selected head and neck tumor patients.

Adenocarcinoma↗

PubMed2001

Two-dimensional model of biofilm detachment caused by internal stress from liquid flow.

A two-dimensional model for biofilm growth and detachment was used to evaluate the effect of detachment on biofilm structures. The detachment process is considered to be due to internal stress created by moving liquid past the biofilm. This model generated a variety of realistic biofilm-formation patterns. It was possible to model in a unified way two different biofilm detachment processes, erosion (small-particle loss), and sloughing (large-biomass-particle removal). The distribution of the fraction from total biomass detached as a function of detached particle mass, gives indications about which of the two mechanisms is dominant. Model simulations indicate that erosion makes the biofilm surface smoother. Sloughing, in contrast, leads to an increased biofilm-surface roughness. Faster growing biofilms have a faster detachment rate than slow-growing biofilms, under similar hydrodynamic conditions and biofilm strength. This is in perfect accordance with the experimental evidence showing that detachment is dependent on both shear- and microbial-growth rates. High growth rates trigger instability in biofilm accumulation and abrupt biomass loss (sloughing). Massive sloughing can be avoided by high liquid shear, combined with low biomass growth rates. As the modeling results show, the causes for sloughing must be sought not only in the biofilm strength, but also in its shape. Several "mushroom-like" biofilm structures like those repeatedly reported in the literature occurred, due to a combined effect of nutrient depletion and breaking at the colony base. A rough carrier surface promotes biofilm development in hydrodynamic conditions in which the biofilm on a flat surface would not form. Although biofilm patches filled completely the cavity in which they started to grow, they were unable to spill over the carrier peaks and to fully colonize the substratum.

Algorithms↗

PubMedDate not supplied

Fluid dynamic characteristics of monopivot magnetic suspension blood pumps.

A monopivot magnetic suspension blood pump is a centrifugal pump under development with a magnetic suspension and a ceramic pivot to support the impeller with minimum contact. The pump size has been reduced by implementing a direct impeller drive mechanism in place of a magnetic coupling and motor. Flow visualization studies revealed that high shear, which seems to be closely related to hemolysis, concentrates in boundary layers near the walls. This implies that fluid dynamic shear can be reduced not by widening the gap, but by reducing the impeller velocity. Therefore, compared with the results of the previous semi-open curved vane impeller model, impeller velocity was reduced by 30% with a closed impeller having radial straight vanes, and smaller impeller/housing gaps. The volute shape around the impeller tip was also changed such that the outflow from the impeller enters along the center plane of the volute. To examine the effect of the improvements, hemolysis testing was conducted and found that the newly developed closed impeller model generated a lower level of hemolysis than the previous semi-open impeller model.

Animals↗

PubMed2000

Learning chaotic attractors by neural networks.

An algorithm is introduced that trains a neural network to identify chaotic dynamics from a single measured time series. During training, the algorithm learns to short-term predict the time series. At the same time a criterion, developed by Diks, van Zwet, Takens, and de Goede (1996) is monitored that tests the hypothesis that the reconstructed attractors of model-generated and measured data are the same. Training is stopped when the prediction error is low and the model passes this test. Two other features of the algorithm are (1) the way the state of the system, consisting of delays from the time series, has its dimension reduced by weighted principal component analysis data reduction, and (2) the user-adjustable prediction horizon obtained by "error propagation"-partially propagating prediction errors to the next time step. The algorithm is first applied to data from an experimental-driven chaotic pendulum, of which two of the three state variables are known. This is a comprehensive example that shows how well the Diks test can distinguish between slightly different attractors. Second, the algorithm is applied to the same problem, but now one of the two known state variables is ignored. Finally, we present a model for the laser data from the Santa Fe time-series competition (set A). It is the first model for these data that is not only useful for short-term predictions but also generates time series with similar chaotic characteristics as the measured data.

Algorithms↗

PubMed1994

Thalamic mediodorsal and intralaminar nuclear lesions disrupt the generation of experimentally induced generalized absence-like seizures in rats.

The effect of bilateral electrolytic lesions of various thalamic sites on the generation of bilaterally synchronous spike and wave discharges (SWD) was studied in two experimental rat models of absence-like seizures. SWD induced by both pentylenetetrazole (20 mg/kg, i.p.) and gamma-hydroxybutyric acid (gamma-butyrolactone, 100 mg/kg, i.p.) were recorded simultaneously from the thalamus and cortex. In both models generation of SWD from the mediodorsal, intralaminar (central lateral and paracentral), ventroposterolateral (VPL) and the reticular thalamic (RT) nucleus was synchronous with that of frontoparietal cortex. Bilateral lesions in mediodorsal and intralaminar thalamic nuclei abolished SWD from both cortex and thalamus in both models. Similar lesions in VPL did not abolish, but attenuated the duration of pentylenetetrazole- and gamma-hydroxybutyric acid-induced SWD, more significantly from the thalamus than from the cortex. RT lesions were associated with more pronounced suppression of pentylenetetrazole-, but not gamma-hydroxybutyric acid-induced SWD in the thalamus. These findings suggest a potential role for mediodorsal and intralaminar thalamic nuclei in the generation of experimental absence-like seizures in rats.

Animals↗

PubMed2003

Random Boolean network models and the yeast transcriptional network.

The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean networks. We find that, for ensembles of generated models, those with canalyzing Boolean rules are remarkably stable, whereas those with random Boolean rules are only marginally stable. Furthermore, substantial parts of the generated networks are frozen, in the sense that they reach the same state, regardless of initial state. Thus, our ensemble approach suggests that the yeast network shows highly ordered dynamics.

Computational Biology↗

PubMed1998

Evaluation of segmentation algorithms for generation of patient models in radiofrequency hyperthermia.

Time-efficient and easy-to-use segmentation algorithms (contour generation) are a precondition for various applications in radiation oncology, especially for planning purposes in hyperthermia. We have developed the three following algorithms for contour generation and implemented them in an editor of the HyperPlan hyperthermia planning system. Firstly, a manual contour input with numerous correction and editing options. Secondly, a volume growing algorithm with adjustable threshold range and minimal region size. Thirdly, a watershed transformation in two and three dimensions. In addition, the region input function of the Helax commercial radiation therapy planning system was available for comparison. All four approaches were applied under routine conditions to two-dimensional computed tomographic slices of the superior thoracic aperture, mid-chest, upper abdomen, mid-abdomen, pelvis and thigh; they were also applied to a 3D CT sequence of 72 slices using the three-dimensional extension of the algorithms. Time to generate the contours and their quality with respect to a reference model were determined. Manual input for a complete patient model required approximately 5 to 6 h for 72 CT slices (4.5 min/slice). If slight irregularities at object boundaries are accepted, this time can be reduced to 3.5 min/slice using the volume growing algorithm. However, generating a tetrahedron mesh from such a contour sequence for hyperthermia planning (the basis for finite-element algorithms) requires a significant amount of postediting. With the watershed algorithm extended to three dimensions, processing time can be further reduced to 3 min/slice while achieving satisfactory contour quality. Therefore, this method is currently regarded as offering some potential for efficient automated model generation in hyperthermia. In summary, the 3D volume growing algorithm and watershed transformation are both suitable for segmentation of even low-contrast objects. However, they are not always superior to user-friendly manual programs for contour generation. When the volume growing algorithm is used, the contours have to be postprocessed with suitable filters. The watershed transformation has a large potential if appropriately developed to 3D sequences and 3D interaction features. After all, the practicality and feasibility of every segmentation method critically depend on various details of the user software as pointed out in this article.

Algorithms↗

PubMed1998

The power ratio and the interval map: spiking models and extracellular recordings.

We describe a new, computationally simple method for analyzing the dynamics of neuronal spike trains driven by external stimuli. The goal of our method is to test the predictions of simple spike-generating models against extracellularly recorded neuronal responses. Through a new statistic called the power ratio, we distinguish between two broad classes of responses: (1) responses that can be completely characterized by a variable firing rate, (for example, modulated Poisson and gamma spike trains); and (2) responses for which firing rate variations alone are not sufficient to characterize response dynamics (for example, leaky integrate-and-fire spike trains as well as Poisson spike trains with long absolute refractory periods). We show that the responses of many visual neurons in the cat retinal ganglion, cat lateral geniculate nucleus, and macaque primary visual cortex fall into the second class, which implies that the pattern of spike times can carry significant information about visual stimuli. Our results also suggest that spike trains of X-type retinal ganglion cells, in particular, are very similar to spike trains generated by a leaky integrate-and-fire model with additive, stimulus-independent noise that could represent background synaptic activity.

Action Potentials↗

PubMed1991

Finite limb dimensions and finite muscle length in a model for the generation of electromyographic signals.

A volume conductor model is presented in which the aspects of finite volume conductor dimensions and finite muscle fiber length are combined. The effects of these aspects on single muscle fiber action potentials (SFAPs) and on motor unit action potentials (MUAPs) are shown and verified with surface recorded motor unit action potentials. It is demonstrated that the influence of the fiber length being finite is enhanced significantly by the finite limb dimensions of the volume conductor model, for single fiber action potentials as well as for motor unit action potentials. The model described is found to be capable of generating surface MUAPs which show a very good resemblance with measured surface MUAPs. Recorded MUAPs illustrate clearly the effects caused by finite muscle fiber length. The effect of finite limb dimensions in simulated intramuscular MUAPs was evidently less dominant than in simulated surface MUAPs.

Action Potentials↗