Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway.

BACKGROUND: Appropriately formulated quantitative computational models can support researchers in understanding the dynamic behaviour of biological pathways and support hypothesis formulation and selection by "in silico" experimentation. An obstacle to widespread adoption of this approach is the requirement to formulate a biological pathway as machine executable computer code. We have recently proposed a novel, biologically intuitive, narrative-style modelling language for biologists to formulate the pathway which is then automatically translated into an executable format and is, thus, usable for analysis via existing simulation techniques. RESULTS: Here we use a high-level narrative language in designing a computational model of the gp130/JAK/STAT signalling pathway and show that the model reproduces the dynamic behaviour of the pathway derived by biological observation. We then "experiment" on the model by simulation and sensitivity analysis to define those parameters which dominate the dynamic behaviour of the pathway. The model predicts that nuclear compartmentalisation and phosphorylation status of STAT are key determinants of the pathway and that alternative mechanisms of signal attenuation exert their influence on different timescales. CONCLUSION: The described narrative model of the gp130/JAK/STAT pathway represents an interesting case study showing how, by using this approach, researchers can model biological systems without explicitly dealing with formal notations and mathematical expressions (typically used for biochemical modelling), nevertheless being able to obtain simulation and analysis results. We present the model and the sensitivity analysis results we have obtained, that allow us to identify the parameters which are most sensitive to perturbations. The results, which are shown to be in agreement with existing mathematical models of the gp130/JAK/STAT pathway, serve us as a form of validation of the model and of the approach itself

Building development and roads: implications for the distribution of stone curlews across the Brecks

Background: Substantial new housing and infrastructure development planned within England has the potential to conflict with the nature conservation interests of protected sites. The Breckland area of eastern England (the Brecks) is designated as a Special Protection Area for a number of bird species, including the stone curlew (for which it holds more than 60% of the UK total population). We explore the effect of buildings and roads on the spatial distribution of stone curlew nests across the Brecks in order to inform strategic development plans to avoid adverse effects on such European protected sites. Methodology: Using data across all years (and subsets of years) over the period 1988 – 2006 but restricted to habitat areas of arable land with suitable soils, we assessed nest density in relation to the distances to nearest settlements and to major roads. Measures of the local density of nearby buildings, roads and traffic levels were assessed using normal kernel distance-weighting functions. Quasi-Poisson generalised linear mixed models allowing for spatial auto-correlation were fitted. Results: Significantly lower densities of stone curlew nests were found at distances up to 1500m from settlements, and distances up to 1000m or more from major (trunk) roads. The best fitting models involved optimally distance-weighted variables for the extent of nearby buildings and the trunk road traffic levels. Significance : The results and predictions from this study of past data suggests there is cause for concern that future housing development and associated road infrastructure within the Breckland area could have negative impacts on the nesting stone curlew population. Given the strict legal protection afforded to the SPA the planning and conservation bodies have subsequently agreed precautionary restrictions on building development within the distances identified and used the modelling predictions to agree mitigation measures for proposed trunk road developments

The influence of landscape features on nest predation rates of grassland-breeding waders

In Europe, lowland wet grasslands have become increasingly fragmented, and populations of waders in these fragments are subject to unsustainably high levels of nest predation. Patches of taller vegetation in these landscapes can support small mammals, which are the main source of prey for many predators. Providing such patches of habitat could potentially reduce levels of nest predation if predators preferentially target small mammals. However, predator attraction to patches of taller vegetation for foraging, shelter, perching and/or nesting could also result in local increases in predation rates, as a consequence of increased predator densities or spill-over foraging into the surrounding area. Here we assess the influence of taller vegetation on wader nest predation rates, and the feasibility of managing vegetation structure to alter predator impacts. Between 2005 and 2011, the nest distribution and hatching success of Northern Lapwings Vanellus vanellus, which nest in the open, and Common Redshanks Tringa totanus, which conceal their nests in vegetation, were measured on a 487-ha area of wet grassland in eastern England that is primarily managed for breeding waders. Predation rates of Lapwing nests increased significantly with distance from patches of taller vegetation, and decreased with increasing area of taller vegetation within 1 km of the nest, whereas neither variable influenced Redshank nest predation probability. These findings suggest that the distribution and activity of nest predators in lowland wet grassland landscapes may be influenced by the presence and distribution of areas of taller vegetation. For Lapwings at least, there may therefore be scope for landscape-scale management of vegetation structure to influence levels of predation in these habitats

Impacts of birds of prey on gamebirds in the UK: a review

The influence of predators on the distribution, density and dynamics of their prey species has long been of interest to ecologists and wildlife managers. Where the prey population is also utilised by humans, conflicts may arise through competition for a limited resource. Because gamebird shooting in the UK provides employment, recreation and income, the impact of birds of prey on gamebird populations has been the subject of intense debate for many years. A variety of approaches has been used to assess the impacts that raptors have on gamebird populations. Here we review the applicability and limitations of the methods used and assess the scientific evidence for population-level and economic impacts of raptors on gamebird populations in the UK. Raptors may, in some situations, take large numbers of gamebirds and may be an important proximate cause of mortality, although few studies have assressed the impacts of raptors on either breeding or pre-shooting densities. Two exceptions are studies of Hen Harrier and Peregrine predation on Red Grouse on moorland in Scotland and Sparrowhawk predation on Grey Partridge on farmland in England. Both these studies suggested that raptors could have population-level impacts when their gamebird prey was already at low density. Studies on predation of captively bred gamebirds suggest that numbers taken by raptors at release pens vary considerably and in a few cases raptors have been documented killing relatively large numbers. On the whole, however, it appears that raptors account for a relatively small proportion of mortality among released birds and the impact on subsequent shooting bags is unknown. We summarise important gaps in current knowledge and recommend specific areas for future research

CD44 targeting reduces tumour growth and prevents post-chemotherapy relapse of human breast cancers xenografts

CD44 is a marker of tumour-initiating cells and is upregulated in invasive breast carcinoma; however, its role in the cancer progression is unknown. Here, we show that antibody-mediated CD44-targeting in human breast cancer xenografts (HBCx) significantly reduces tumour growth and that this effect is associated to induction of growth-inhibiting factors. Moreover, treatment with this antibody prevents tumour relapse after chemotherapy-induced remission in a basal-like HBCx

Exploring the impact of mentoring functions on job satisfaction and organizational commitment of new staff nurses

<p>Abstract</p> <p>Background</p> <p>Although previous studies proved that the implementation of mentoring program is beneficial for enhancing the nursing skills and attitudes, few researchers devoted to exploring the impact of mentoring functions on job satisfaction and organizational commitment of new nurses. In this research we aimed at examining the effects of mentoring functions on the job satisfaction and organizational commitment of new nurses in Taiwan's hospitals.</p> <p>Methods</p> <p>We employed self-administered questionnaires to collect research data and select new nurses from three regional hospitals as samples in Taiwan. In all, 306 nurse samples were obtained. We adopted a multiple regression analysis to test the impact of the mentoring functions.</p> <p>Results</p> <p>Results revealed that career development and role modeling functions have positive effects on the job satisfaction and organizational commitment of new nurses; however, the psychosocial support function was incapable of providing adequate explanation for these work outcomes.</p> <p>Conclusion</p> <p>It is suggested in this study that nurse managers should improve the career development and role modeling functions of mentoring in order to enhance the job satisfaction and organizational commitment of new nurses.</p

Survival-Related Profile, Pathways, and Transcription Factors in Ovarian Cancer

Ate van der Zee and colleagues analyze the gene expression profiles of ovarian cancer samples from 157 patients, and identify an 86-gene expression profile that seems to predict overall survival