The place of models and modelling in Digital Humanities: some reflections from a Research Software Engineering perspective

Il presente contributo illustra una posizione sul ruolo dei modelli e della modellizzazione nel contesto del Research Software Engineering (RSE) nelle Digital Humanities (DH). La nostra ipotesi è che all'interno del contesto nel quale opera il King’s Digital Lab, influenzato da fattori storici e di gestione manageriale, la produzione di modelli è di fatto il contributo essenziale dell'RSE all'epistemologia di DH. Tuttavia, riteniamo che quando considerate da una prospettiva di RSE olistica, che include - pur non essendo ad essa limitata – la modellizzazione empirica e predittiva, queste attività di modellizzazione non siano state studiate in modo abbastanza sistematico da supportare a pieno questa posizione. Il nostro contributo può soltanto indicare qualche idea e abbozzare un approccio che meriterebbero ricerche più approfonditeThis paper1 offers a position on the role of models and modelling in the context of Research Software Engineering (RSE) in Digital Humanities (DH). Our hypothesis is that within the context that King’s Digital Lab operates, shaped by historical and management factors, the production of models is arguably the core contribution of RSE to the epistemology of DH. However, we argue that, when analysed from a holistic RSE perspective, encompassing but not limited to empirical and predictive modelling, these modelling activities have not been studied systematically enough to support such a claim in straight-forward ways. Our contribution can only gesture at some ideas and sketch a framework that would need further research

Road distance and travel time for an improved house price Kriging predictor

The paper designs an automated valuation model to predict the price of residential property in Coventry, United Kingdom, and achieves this by means of geostatistical Kriging, a popularly employed distance-based learning method. Unlike traditional applications of distance-based learning, this papers implements non-Euclidean distance metrics by approximating road distance, travel time and a linear combination of both, which this paper hypothesizes to be more related to house prices than straight-line (Euclidean) distance. Given that – to undertake Kriging – a valid variogram must be produced, this paper exploits the conforming properties of the Minkowski distance function to approximate a road distance and travel time metric. A least squares approach is put forth for variogram parameter selection and an ordinary Kriging predictor is implemented for interpolation. The predictor is then validated with 10-fold cross-validation and a spatially aware checkerboard hold out method against the almost exclusively employed, Euclidean metric. Given a comparison of results for each distance metric, this paper witnesses a goodness of fit (r²) result of 0.6901 ± 0.18 SD for real estate price prediction compared to the traditional (Euclidean) approach obtaining a suboptimal r² value of 0.66 ± 0.21 SD

Birds of a Feather Session

Presentation of speakers and topics in a birds of a feather session for the 2013 Digital Frontiers Annual Conference. Topics include: Testing the research usability of finding aids and metadata of primary resources, exploring data curation across disciplines using Google books for academic research, digital collection usage, teaching humanities digitally, and internet politics

Nanoindentation analysis of oriented polypropylene: Influence of elastic properties in tension and compression

YesPolypropylene has been oriented by solid-phase deformation processing to draw ratios up to ∼16, increasing tensile stiffness along the draw direction by factors up to 12. Nanoindentation of these materials showed that moduli obtained for indenter tip motion along the drawing direction (3) into to 1–2 plane (axial indentation) were up to 60% higher than for indenter tip motion along the 2 direction into the 1–3 plane (transverse indentation). In static tests, tensile and compressive determinations of elastic modulus gave results differing by factors up to ∼5 for strain along the draw direction. A material model incorporating both orthotropic elasticity and tension/compression asymmetry was developed for use with Finite Element simulations. Elastic constants for the oriented polypropylene were obtained by combining static testing and published ultrasonic data, and used as input for nanoindentation simulations that were quantitatively successful. The significance of the tension/compression asymmetry was demonstrated by comparing these predictions with those obtained using tensile data only, which gave predictions of indentation modulus higher by up to 70%

Modulation of sirtuins during monolayer chondrocyte culture influences cartilage regeneration upon transfer to a 3D culture environment

This study examined the role of sirtuins in the regenerative potential of articular chondrocytes. Sirtuins (SIRT1-7) play a key role in regulating cartilage homeostasis. By inhibiting pro-inflammatory pathways responsible for cartilage degradation and promoting the expression of key matrix components, sirtuins have the potential to drive a favourable balance between anabolic and catabolic processes critical to regenerative medicine. When subjected to osmolarity and glucose concentrations representative of the in vivo niche, freshly isolated bovine chondrocytes exhibited increases in SIRT1 but not SIRT3 gene expression. Replicating methods adopted for the in vitro monolayer expansion of chondrocytes for cartilage regenerative therapies, we found that SIRT1 gene expression declined during expansion. Manipulation of sirtuin activity during in vitro expansion by supplementation with the SIRT1-specific activator SRT1720, nicotinamide mononucleotide, or the pan-sirtuin inhibitor nicotinamide, significantly influenced cartilage regeneration in subsequent 3D culture. Tissue mass, cellularity and extracellular matrix content were reduced in response to sirtuin inhibition during expansion, whilst sirtuin activation enhanced these measures of cartilage tissue regeneration. Modulation of sirtuin activity during monolayer expansion influenced H3K27me3, a heterochromatin mark with an important role in development and differentiation. Unexpectedly, treatment of primary chondrocytes with sirtuin activators in 3D culture reduced their matrix synthesis. Thus, modulating sirtuin activity during the in vitro monolayer expansion phase may represent a distinct opportunity to enhance the outcome of cartilage regenerative medicine techniques

Early-life nutrition modulates the epigenetic state of specific rDNA genetic variants in mice.

A suboptimal early-life environment, due to poor nutrition or stress during pregnancy, can influence lifelong phenotypes in the progeny. Epigenetic factors are thought to be key mediators of these effects. We show that protein restriction in mice from conception until weaning induces a linear correlation between growth restriction and DNA methylation at ribosomal DNA (rDNA). This epigenetic response remains into adulthood and is restricted to rDNA copies associated with a specific genetic variant within the promoter. Related effects are also found in models of maternal high-fat or obesogenic diets. Our work identifies environmentally induced epigenetic dynamics that are dependent on underlying genetic variation and establishes rDNA as a genomic target of nutritional insults.This work was supported by the following grants and fellowships: Biotechnology and Biological Sciences Research Council, UK (BB/M012494/1) to V.K.R. and (BB/G00711/X/1) to V.K.R. and C.G.; and a Research Council UK Academic Fellowship to M.L.H. R.L. is supported by EU-FP7 BLUEPRINT. S.E.O. is supported by the British Heart Foundation (FS/12/64/30001) and the Medical Research Council (MC_UU_12012/4). This research used Queen Mary’s MidPlus computational facilities, supported by Queen Mary University of London Research-IT and funded by Engineering and Physical Sciences Research Council grant EP/K000128/1. We thank King’s College London FWB Genomics Centre and Barts and The London Genome Centre for performing high-throughput sequencing.This is the author accepted manuscript. The final version is available from the American Association for the Advancement of Science via http://dx.doi.org/10.1126/science.aaf704

Maternal Thyroid Disease, Thyroid Medication Use, and Selected Birth Defects in the National Birth Defects Prevention Study

BACKGROUND: Although thyroid disorders are present in approximately 3% of pregnant women, little is known about the association between maternal thyroid disease and birth defects. METHODS: We assessed the association between maternal thyroid disease, thyroid medication use, and 38 types of birth defects among 14,067 cases and 5875 controls in the National Birth Defects Prevention Study, a multisite, population-based, case-control study. Infants in this study were born between October 1997 and December 2004. Information on exposures including maternal diseases and use of medications was collected by telephone interview. RESULTS: We found statistically significant associations between maternal thyroid disease and left ventricular outflow tract obstruction heart defects (1.5; 95% CI, 1.0-2.3), hydrocephaly (2.9; 95% CI, 1.6-5.2), hypospadias (1.6; 95% CI, 1.0-2.5), and isolated anorectal atresia (2.4; 95% CI, 1.2-4.6). Estimates for the association between periconceptional use of thyroxine and specific types of birth defects were similar to estimates for any thyroid disease. Given that antithyroid medication use was rare, we could not adequately assess risks for their use for most case groups. CONCLUSIONS: Our results are consistent with the positive associations between maternal thyroid disease or thyroid medication use and both hydrocephaly and hypospadias observed in some previous studies. New associations with left ventricular outflow tract obstruction heart defects and anorectal atresia may be chance findings. Birth Defects Research (Part A) 85:621-628, 2009.