The ODD protocol for describing agent-based and other simulation models: A second update to improve clarity, replication, and structural realism

© 2020, University of Surrey. All rights reserved. The Overview, Design concepts and Details (ODD) protocol for describing Individual-and Agent-Based Models (ABMs) is now widely accepted and used to document such models in journal articles. As a standardized document for providing a consistent, logical and readable account of the structure and dynamics of ABMs, some research groups also find it useful as a workflow for model design. Even so, there are still limitations to ODD that obstruct its more widespread adoption. Such limitations are discussed and addressed in this paper: the limited availability of guidance on how to use ODD; the length of ODD documents; limitations of ODD for highly complex models; lack of sufficient details of many ODDs to enable reimplementation without access to the model code; and the lack of provision for sections in the document structure covering model design ratio-nale, the model’s underlying narrative, and the means by which the model’s fitness for purpose is evaluated. We document the steps we have taken to provide better guidance on: structuring complex ODDs and an ODD summary for inclusion in a journal article (with full details in supplementary material; Table 1); using ODD to point readers to relevant sections of the model code; update the document structure to include sections on model rationale and evaluation. We also further advocate the need for standard descriptions of simulation experiments and argue that ODD can in principle be used for any type of simulation model. Thereby ODD would provide a lingua franca for simulation modelling

Phoma stem canker disease on oilseed rape (Brassica napus) in China is caused by Leptosphaeria biglobosa ‘brassicae’

This document is the Accepted Manuscript version of the following article: Ze Liu, Akinwunmi O. Latunde-Dada, Avice M. Hall, Bruce D. L. Fitt, ‘Phoma stem canker disease on oilseed rape (Brassica napus) in China is caused by Leptosphaeria biglobosa ‘brassicae’’, European Journal of Plant Pathology, Vol. 140(4): 841-857, December 2014. The final publication is available at Springer via: http://dx.doi.org/10.1007/s10658-014-0513-7 © Koninklijke Nederlandse Planteziektenkundige Vereniging 2014Phoma stem canker of oilseed rape (Brassica napus) is a globally important disease that is caused by the sibling ascomycete species Leptosphaeria maculans and L. biglobosa. Sixty fungal isolates obtained from oilseed rape stems with phoma stem canker disease symptoms collected from four provinces in China in 1999, 2005 and 2006 were all identified as Leptosphaeria biglobosa, not L. maculans, by PCR diagnostics based on species-specific primers. There were no differences in cultural characteristics (e.g. pigmentation and in vitro growth) between these L. biglobosa isolates from China and those of 37 proven L. biglobosa isolates from Europe or Canada. In studies using amplified fragment length polymorphism (AFLP) markers, Chinese L. biglobosa populations were genetically more similar to European L. biglobosa populations than to the more diverse Canadian L. biglobosa populations. Sequencing of gene fragments of β-tubulin, actin and the internal transcribed spacer (ITS) region of rDNA from L. biglobosa isolates from China, Europe, Australia and Canada showed a closer taxonomic similarity of Chinese L. biglobosa to the European L. biglobosa ‘brassicae’ than to Canadian L. biglobosa ‘canadensis’ or to the Australian L. biglobosa ‘occiaustralensis’ or ‘australensis’ subclades. These results suggest that the Chinese L. biglobosa population in this study is in the same subclade as European L. biglobosa ‘brassicae’ populationsPeer reviewe

Low-intensity continuous ultrasound triggers effective bisphosphonate anticancer activity in breast cancer

Ultrasound (US) is a non-ionizing pressure wave that can produce mechanical and thermal effects. Bisphosphonates have demonstrated clinical utility in bone metastases treatment. Preclinical studies suggest that bisphosphonates have anticancer activity. However, bisphosphonates exhibit a high affinity for bone mineral, which reduces their bioavailability for tumor cells. Ultrasound has been shown to be effective for drug delivery but in interaction with gas bubbles or encapsulated drugs. We examined the effects of a clinically relevant dose of bisphosphonate zoledronate (ZOL) in combination with US. In a bone metastasis model, mice treated with ZOL+US had osteolytic lesions that were 58% smaller than those of ZOL-treated animals as well as a reduced skeletal tumor burden. In a model of primary tumors, ZOL+US treatment reduced by 42% the tumor volume, compared with ZOL-treated animals. Using a fluorescent bisphosphonate, we demonstrated that US forced the release of bisphosphonate from the bone surface, enabling a continuous impregnation of the bone marrow. Additionally, US forced the penetration of ZOL within tumors, as demonstrated by the intratumoral accumulation of unprenylated Rap1A, a surrogate marker of ZOL antitumor activity. Our findings made US a promising modality to trigger bisphosphonate anticancer activity in bone metastases and in primary tumors

Connecting environmental, genetic and geographic distances: A case study of maritime pine (Pinus pinaster Ait.).

International audienc

Adaptive variation, environmental gradients and demography in maritime pine: from genes to phenotypes and niches

International audienc