The orbit rigidity matrix of a symmetric framework

A number of recent papers have studied when symmetry causes frameworks on a graph to become infinitesimally flexible, or stressed, and when it has no impact. A number of other recent papers have studied special classes of frameworks on generically rigid graphs which are finite mechanisms. Here we introduce a new tool, the orbit matrix, which connects these two areas and provides a matrix representation for fully symmetric infinitesimal flexes, and fully symmetric stresses of symmetric frameworks. The orbit matrix is a true analog of the standard rigidity matrix for general frameworks, and its analysis gives important insights into questions about the flexibility and rigidity of classes of symmetric frameworks, in all dimensions. With this narrower focus on fully symmetric infinitesimal motions, comes the power to predict symmetry-preserving finite mechanisms - giving a simplified analysis which covers a wide range of the known mechanisms, and generalizes the classes of known mechanisms. This initial exploration of the properties of the orbit matrix also opens up a number of new questions and possible extensions of the previous results, including transfer of symmetry based results from Euclidean space to spherical, hyperbolic, and some other metrics with shared symmetry groups and underlying projective geometry.Comment: 41 pages, 12 figure

Assessing wellbeing at school entry using the strengths and difficulties questionnaire: professional perspectives

<p>Background: Emotional and behavioural disorders in early childhood are related to poorer academic attainment and school engagement, and difficulties already evident at the point of starting school can affect a child’s later social and academic development. Successful transfer from pre-school settings to primary education is helped by communication between pre-school staff and primary school teachers. Typically, in Scotland, pre-school establishments prepare individual profiles of children before they start school around the age of five years, highlighting their strengths and development needs, for transfer to primary schools. There is, however, no consistent approach to the identification of potential social, emotional and behavioural problems. In 2010, in one local authority area in Scotland, the Strengths and Difficulties Questionnaire (SDQ) was introduced for children about to start school as a routine, structured, component of the transition process to help teachers plan support arrangements for classes and individual children. The SDQ assesses emotional, conduct, hyperactivity/ inattention and peer-relationship problems as well as pro-social behaviour. In order to be an effective means of communicating social and emotional functioning, the use of instruments such as the SDQ needs to be practicable. Finding out the views of pre-school education staff with experience of assessing children using the SDQ was, therefore, essential to establish its future utility.</p> <p>Aim: The purpose of this study was to explore the views of pre-school education staff about assessing social and emotional wellbeing of children at school entry using the SDQ. The objectives were to examine the opinions of pre-school workers about completing the SDQ and to elicit their thoughts on the value of doing this and their perceptions of the usefulness of the information collected.</p> <p>Method: Pre-school establishments were approached using a purposive sampling strategy in order to achieve a mix of local authority (n=14) and ‘partnership’ establishments (n=8) as well as different socio-economic areas. Semi-structured interviews (n=25) were conducted with pre-school head teachers (n=14) and child development officers (n=11) in order to explore the process of completing the SDQ along with perceptions of its value. The interviews were transcribed verbatim and analysed thematically.</p> <p>Results: In general, staff in pre-school establishments viewed the use of the SDQ positively. It was seen as a chance to highlight the social and emotional development of children rather than just their academic or educational ability. Most felt that the SDQ had not identified anything they did not already know about a child. A minority, nevertheless, suggested that a previously unrecognised potential difficulty was brought to light, most commonly emotional problems. Completing the SDQ was felt to be relatively straightforward even though the staff felt under pressure from competing priorities. Concerns were, however, raised about the potential of labelling a child at an early stage of formal education.</p> <p>Conclusion: The findings from this small scale study suggest that, from the point of view of pre-school education staff, it is feasible to assess children systematically for social and behavioural problems as part of the routine transition process at school entry.</p&gt

An investigation of the influence of extracellular matrix anisotropy and cell-matrix interactions on tissue architecture

Received: 9 September 2014 / Revised: 21 May 2015. Published online: 02 September 2015Mechanical interactions between cells and the fibrous extracellular matrix (ECM) in which they reside play a key role in tissue development. Mechanical cues from the environment (such as stress, strain and fibre orientation) regulate a range of cell behaviours, including proliferation, differentiation and motility. In turn, the ECM structure is affected by cells exerting forces on the matrix which result in deformation and fibre realignment. In this paper we develop a mathematical model to investigate this mechanical feedback between cells and the ECM. We consider a three-phase mixture of collagen, culture medium and cells, and formulate a system of partial differential equations which represents conservation of mass and momentum for each phase. This modelling framework takes into account the anisotropic mechanical properties of the collagen gel arising from its fibrous microstructure. We also propose a cell-collagen interaction force which depends upon fibre orientation and collagen density. We use a combination of numerical and analytical techniques to study the influence of cell-ECM interactions on pattern formation in tissues. Our results illustrate the wide range of structures which may be formed, and how those that emerge depend upon the importance of cell-ECM interactions.R. J. Dyson, J. E. F. Green, J. P. Whiteley, H. M. Byrn

Algorithms for 3D rigidity analysis and a first order percolation transition

A fast computer algorithm, the pebble game, has been used successfully to study rigidity percolation on 2D elastic networks, as well as on a special class of 3D networks, the bond-bending networks. Application of the pebble game approach to general 3D networks has been hindered by the fact that the underlying mathematical theory is, strictly speaking, invalid in this case. We construct an approximate pebble game algorithm for general 3D networks, as well as a slower but exact algorithm, the relaxation algorithm, that we use for testing the new pebble game. Based on the results of these tests and additional considerations, we argue that in the particular case of randomly diluted central-force networks on BCC and FCC lattices, the pebble game is essentially exact. Using the pebble game, we observe an extremely sharp jump in the largest rigid cluster size in bond-diluted central-force networks in 3D, with the percolating cluster appearing and taking up most of the network after a single bond addition. This strongly suggests a first order rigidity percolation transition, which is in contrast to the second order transitions found previously for the 2D central-force and 3D bond-bending networks. While a first order rigidity transition has been observed for Bethe lattices and networks with ``chemical order'', this is the first time it has been seen for a regular randomly diluted network. In the case of site dilution, the transition is also first order for BCC, but results for FCC suggest a second order transition. Even in bond-diluted lattices, while the transition appears massively first order in the order parameter (the percolating cluster size), it is continuous in the elastic moduli. This, and the apparent non-universality, make this phase transition highly unusual.Comment: 28 pages, 19 figure

The reporting quality of natural language processing studies: systematic review of studies of radiology reports.

BACKGROUND: Automated language analysis of radiology reports using natural language processing (NLP) can provide valuable information on patients' health and disease. With its rapid development, NLP studies should have transparent methodology to allow comparison of approaches and reproducibility. This systematic review aims to summarise the characteristics and reporting quality of studies applying NLP to radiology reports. METHODS: We searched Google Scholar for studies published in English that applied NLP to radiology reports of any imaging modality between January 2015 and October 2019. At least two reviewers independently performed screening and completed data extraction. We specified 15 criteria relating to data source, datasets, ground truth, outcomes, and reproducibility for quality assessment. The primary NLP performance measures were precision, recall and F1 score. RESULTS: Of the 4,836 records retrieved, we included 164 studies that used NLP on radiology reports. The commonest clinical applications of NLP were disease information or classification (28%) and diagnostic surveillance (27.4%). Most studies used English radiology reports (86%). Reports from mixed imaging modalities were used in 28% of the studies. Oncology (24%) was the most frequent disease area. Most studies had dataset size > 200 (85.4%) but the proportion of studies that described their annotated, training, validation, and test set were 67.1%, 63.4%, 45.7%, and 67.7% respectively. About half of the studies reported precision (48.8%) and recall (53.7%). Few studies reported external validation performed (10.8%), data availability (8.5%) and code availability (9.1%). There was no pattern of performance associated with the overall reporting quality. CONCLUSIONS: There is a range of potential clinical applications for NLP of radiology reports in health services and research. However, we found suboptimal reporting quality that precludes comparison, reproducibility, and replication. Our results support the need for development of reporting standards specific to clinical NLP studies

Robust Detection of Rare Species Using Environmental DNA: the Importance of Primer Specificity

Environmental DNA (eDNA) is being rapidly adopted as a tool to detect rare animals. Quantitative PCR (qPCR) using probe-based chemistries may represent a particularly powerful tool because of the method\u27s sensitivity, specificity, and potential to quantify target DNA. However, there has been little work understanding the performance of these assays in the presence of closely related, sympatric taxa. If related species cause any cross-amplification or interference, false positives and negatives may be generated. These errors can be disastrous if false positives lead to overestimate the abundance of an endangered species or if false negatives prevent detection of an invasive species. In this study we test factors that influence the specificity and sensitivity of TaqMan MGB assays using co-occurring, closely related brook trout (Salvelinus fontinalis) and bull trout (S. confluentus) as a case study. We found qPCR to be substantially more sensitive than traditional PCR, with a high probability of detection at concentrations as low as 0.5 target copies/ml. We also found that number and placement of base pair mismatches between the Taqman MGB assay and non-target templates was important to target specificity, and that specificity was most influenced by base pair mismatches in the primers, rather than in the probe. We found that insufficient specificity can result in both false positive and false negative results, particularly in the presence of abundant related species. Our results highlight the utility of qPCR as a highly sensitive eDNA tool, and underscore the importance of careful assay design

Chaste: a test-driven approach to software development for biological modelling

Chaste (‘Cancer, heart and soft-tissue environment’) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.\ud \ud Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling

An integrative computational model for intestinal tissue renewal

Objectives\ud \ud The luminal surface of the gut is lined with a monolayer of epithelial cells that acts as a nutrient absorptive engine and protective barrier. To maintain its integrity and functionality, the epithelium is renewed every few days. Theoretical models are powerful tools that can be used to test hypotheses concerning the regulation of this renewal process, to investigate how its dysfunction can lead to loss of homeostasis and neoplasia, and to identify potential therapeutic interventions. Here we propose a new multiscale model for crypt dynamics that links phenomena occurring at the subcellular, cellular and tissue levels of organisation.\ud \ud Methods\ud \ud At the subcellular level, deterministic models characterise molecular networks, such as cell-cycle control and Wnt signalling. The output of these models determines the behaviour of each epithelial cell in response to intra-, inter- and extracellular cues. The modular nature of the model enables us to easily modify individual assumptions and analyse their effects on the system as a whole.\ud \ud Results\ud \ud We perform virtual microdissection and labelling-index experiments, evaluate the impact of various model extensions, obtain new insight into clonal expansion in the crypt, and compare our predictions with recent mitochondrial DNA mutation data. \ud \ud Conclusions\ud \ud We demonstrate that relaxing the assumption that stem-cell positions are fixed enables clonal expansion and niche succession to occur. We also predict that the presence of extracellular factors near the base of the crypt alone suffices to explain the observed spatial variation in nuclear beta-catenin levels along the crypt axis

The future of the global food system

Although food prices in major world markets are at or near a historical low, there is increasing concern about food security—the ability of the world to provide healthy and environmentally sustainable diets for all its peoples. This article is an introduction to a collection of reviews whose authors were asked to explore the major drivers affecting the food system between now and 2050. A first set of papers explores the main factors affecting the demand for food (population growth, changes in consumption patterns, the effects on the food system of urbanization and the importance of understanding income distributions) with a second examining trends in future food supply (crops, livestock, fisheries and aquaculture, and ‘wild food’). A third set explores exogenous factors affecting the food system (climate change, competition for water, energy and land, and how agriculture depends on and provides ecosystem services), while the final set explores cross-cutting themes (food system economics, food wastage and links with health). Two of the clearest conclusions that emerge from the collected papers are that major advances in sustainable food production and availability can be achieved with the concerted application of current technologies (given sufficient political will), and the importance of investing in research sooner rather than later to enable the food system to cope with both known and unknown challenges in the coming decades