A computational model of cellular response to modulated radiation fields

Purpose:
To develop a model to describe the response of cell populations to spatially modulated radiation exposures of relevance to advanced radiotherapies.

Materials and Methods:
A Monte Carlo model of cellular radiation response was developed. This model incorporated damage from both direct radiation and intercellular communication including bystander signaling. The predictions of this model were compared to previously measured survival curves for a normal human fibroblast line (AGO1522) and prostate tumor cells (DU145) exposed to spatially modulated fields.

Results:
The model was found to be able to accurately reproduce cell survival both in populations which were directly exposed to radiation and those which were outside the primary treatment field. The model predicts that the bystander effect makes a significant contribution to cell killing even in uniformly irradiated cells. The bystander effect contribution varies strongly with dose, falling from a high of 80% at low doses to 25% and 50% at 4 Gy for AGO1522 and DU145 cells, respectively. This was verified using the inducible nitric oxide synthase inhibitor aminoguanidine to inhibit the bystander effect in cells exposed to different doses, which showed significantly larger reductions in cell killing at lower doses.

Conclusions:
The model presented in this work accurately reproduces cell survival following modulated radiation exposures, both in and out of the primary treatment field, by incorporating a bystander component. In addition, the model suggests that the bystander effect is responsible for a significant portion of cell killing in uniformly irradiated cells, 50% and 70% at doses of 2 Gy in AGO1522 and DU145 cells, respectively. This description is a significant departure from accepted radiobiological models and may have a significant impact on optimization of treatment planning approaches if proven to be applicable in vivo.

The spark of life:The role of electric fields in regulating cell behaviour using the eye as a model system

Endogenous electric fields (EF) have long been known to influence cell behaviour during development, neural cell tropism, wound healing and cell behaviour generally. The effect is based on short circuiting of electrical potential differences across cell and tissue boundaries generated by ionic segregation. Recent in vitro and in vivo studies have shown that EF regulate not only cell movement but orientation of cells during mitosis, an effect which may underlie shaping of tissues and organs. The molecular basis of this effect is founded on receptor-mediated cell signalling events and alterations in cytoskeletal function as revealed in studies of gene deficient cells. Remarkably, not all cells respond directionally to EF in the same way and this has consequences, for instance, for lens development and vascular remodelling. The physical basis of EF effect may be related to changes induced in 'bound water' at the cell surface, whose organisation in association with trans-membrane proteins (e.g. receptors) is disrupted when EF are generated. Copyright © 2007 S. Karger AG.

Interpretable semantic vectors from a joint model of brain-and text-based meaning

Vector space models (VSMs) represent word meanings as points in a high dimensional space. VSMs are typically created using a large text corpora, and so represent word semantics as observed in text. We present a new algorithm (JNNSE) that can incorporate a measure of semantics not previously used to create VSMs: brain activation data recorded while people read words. The resulting model takes advantage of the complementary strengths and weaknesses of corpus and brain activation data to give a more complete representation of semantics. Evaluations show that the model 1) matches a behavioral measure of semantics more closely, 2) can be used to predict corpus data for unseen words and 3) has predictive power that generalizes across brain imaging technologies and across subjects. We believe that the model is thus a more faithful representation of mental vocabularies.

A Kinetic-Based Model of Radiation-Induced Intercellular Signalling

It is now widely accepted that intercellular communication can cause significant variations in cellular responses to genotoxic stress. The radiation-induced bystander effect is a prime example of this effect, where cells shielded from radiation exposure see a significant reduction in survival when cultured with irradiated cells. However, there is a lack of robust, quantitative models of this effect which are widely applicable. In this work, we present a novel mathematical model of radiation-induced intercellular signalling which incorporates signal production and response kinetics together with the effects of direct irradiation, and test it against published data sets, including modulated field exposures. This model suggests that these so-called "bystander" effects play a significant role in determining cellular survival, even in directly irradiated populations, meaning that the inclusion of intercellular communication may be essential to produce robust models of radio-biological outcomes in clinically relevant in vivo situations.

Soil Moisture Deficit as a predictor of the trend in soil water status of grass fields

Nutrient loss from agricultural land following organic fertilizer spreading can lead to eutrophication and poor water quality. The risk of pollution is partly related to the soil water status during and after spreading. In response to these issues, a decision support system (DSS) for nutrient management has been developed to predict when soil and weather conditions are suitable for slurry spreading. At the core of the DSS, the Hybrid Soil Moisture Deficit (HSMD) model estimates soil water status relative to field capacity (FC) for three soil classes (well, moderately and poorly drained) and has potential to predict the occurrence of a transport vector when the soil is wetter than FC. Three years of field observation of volumetric water content was used to validate HSMD model predictions of water status and to ensure correct use and interpretation of the drainage classes. Point HSMD model predictions were validated with respect to the temporal and spatial variations in volumetric water content and soil strength properties. It was found that the HSMD model predictions were well related to topsoil water content through time, but a new class intermediate between poor and moderate, perhaps ‘imperfectly drained’, was needed. With correct allocations of a field into a drainage class, the HSMD model predictions reflect field scale trends in water status and therefore the model is suitable for use at the core of a DSS.

Judging Time Intevals using a model of perceptuo-motor control

Estimating a time interval and temporally coordinating movements in space are fundamental skills, but the relationships between these different forms of timing, and the neural processes that they incur, are not well understood. While different theories have been proposed to account for time perception, time estimation, and the temporal patterns of coordination, there are no general mechanisms which unify these various timing skills. This study considers whether a model of perceptuo-motor timing, the tau(GUIDE), can also describe how certain judgements of elapsed time are made. To evaluate this, an equation for determining interval estimates was derived from the tau(GUIDE) model and tested in a task where participants had to throw a ball and estimate when it would hit the floor. The results showed that in accordance with the model, very accurate judgements could be made without vision (mean timing error -19.24 msec), and the model was a good predictor of skilled participants' estimate timing. It was concluded that since the tau(GUIDE) principle provides temporal information in a generic form, it could be a unitary process that links different forms of timing.

Neurobiological model of visuo-spatial cognition in young Williams Syndrome children: measures of dorsal-stream and frontal function

We examine hypotheses for the neural basis of the profile of visual cognition in young children with Williams syndrome (WS). These are: (a) that it is a consequence of anomalies in sensory visual processing; (b) that it is a deficit of the dorsal relative to the ventral cortical stream; (c) that it reflects deficit of frontal function, in particular of fronto-parietal interaction; (d) that it is related to impaired function in the right hemisphere relative to the left. The tests reported here are particularly relevant to (b) and (c). They form part of a more extensive programme of investigating visual, visuospatial, and cognitive function in large group of children with WS children, aged 8 months to 15 years. To compare performance across tests, avoiding floor and ceiling effects, we have measured performance in children with WS in terms of the ‘age equivalence’ for typically developing children. In this paper the relation between dorsal and ventral function was tested by motion and form coherence thresholds respectively. We confirm the presence of a subgroup of children with WS who perform particularly poorly on the motion (dorsal) task. However, such performance is also characteristic of normally developingchildren up to 5 years: thus the WS performance may reflect an overall persisting immaturity of visuospatial processing which is particularly evident in the dorsal stream. Looking at the performance on the global coherence tasks of the entire WS group, we find that there is also a subgroup who have both high form and motion coherence thresholds, relative to the performance of children of the same chronological age and verbal age on the BPVS, suggesting a more general global processing deficit. Frontal function was tested by a counterpointing task, ability to retrieve a ball from a ‘detour box’, and the Stroop-like ‘day-night’ task, all of which require inhibition of a familiar response. When considered in relation to overall development as indexed by vocabulary, the day-night task shows little specific impairment, the detour box shows a significant delay relative to controls, and the counterpointing task shows a marked and persistent deficit in many children. We conclude that frontal control processes show most impairment in WS when they are associated with spatially directed responses, reflecting a deficit of fronto-parietal processing. However, children with WS may successfully reduce the effect of this impairment by verbally mediated strategies. On all these tasks we find a range of difficulties across individual children and a small subset of WS who show very good performance, equivalent to chronological age norms of typically developing children. Neurobiological models of visuo-spatial cognition in children with WS p.4 Overall, we conclude that children with WS have specific processing difficulties with tasks involving frontoparietal circuits within the spatial domain. However, some children with WS can achieve similar performance to typically developing children on some tasks involving the dorsal stream, although the strategies and processing may be different in the two groups.

A possible model of benzimidazole binding to beta-tubulin disclosed by invoking an inter-domain movement.

Although it is well established that benzimidazole (BZMs) compounds exert their therapeutic effects through binding to helminth beta-tubulin and thus disrupting microtubule-based processes in the parasites, the precise location of the benzimidazole-binding site on the beta-tubulin molecule has yet to be determined. In the present study, we have used previous experimental data as cues to help identify this site. Firstly, benzimidazole resistance has been correlated with a phenylalanine-to-tyrosine substitution at position 200 of Haemonchus contortus beta-tubulin isotype-I. Secondly, site-directed mutagenesis studies, using fungi, have shown that other residues in this region of the protein can influence the interaction of benzimidazoles with beta-tubulin. However, the atomic structure of the alphabeta-tubulin dimer shows that residue 200 and the other implicated residues are buried within the protein. This poses the question: how might benzimidazoles interact with these apparently inaccessible residues? In the present study, we present a mechanism by which those residues generally believed to interact with benzimidazoles may become accessible to the drugs. Furthermore, by docking albendazole-sulphoxide into a modelled H. contortus beta-tubulin molecule we offer a structural explanation for how the mutation conferring benzimidazole resistance in nematodes may act, as well as a possible explanation for the species-specificity of benzimidazole anthelmintics.

Biofilm formation by bacteria isolated from retrieved failed prosthetic hip implants in an in vitro model of hip arthroplasty antibiotic prophylaxis

Bacterial infection primarily with Staphylococcus spp. and Propionibacterium acnes remains a significant complication following total hip replacement. In this in vitro study, we investigated the efficacy of gentamicin loading of bone cement and pre- and postoperative administration of cefuroxime in the prevention of biofilm formation by clinical isolates. High and low initial inocula, representative of the number of bacteria that may be present at the operative site as a result of overt infection and skin contamination, respectively, were used. When a high initial inoculum was used, gentamicin loading of the cement did not prevent biofilm formation by the 10 Staphylococcus spp. and the 10 P. acnes isolates tested. Similarly, the use of cefuroxime in the fluid phase with gentamicin-loaded cement did not prevent biofilm formation by four Staphylococcus spp. and four P. acnes isolates tested. However, when a low bacterial inoculum was used, a combination of both gentamicin-loaded cement and cefuroxime prevented biofilm formation by these eight isolates. Our results indicate that this antibiotic combination may protect against infection after intra-operative challenge with bacteria present in low numbers as a result of contamination from the skin but would not protect against bacteria present in high numbers as a result of overt infection of an existing implant.