The Computer Science Ontology: A Large-Scale Taxonomy of Research Areas

Ontologies of research areas are important tools for characterising, exploring, and analysing the research landscape. Some fields of research are comprehensively described by large-scale taxonomies, e.g., MeSH in Biology and PhySH in Physics. Conversely, current Computer Science taxonomies are coarse-grained and tend to evolve slowly. For instance, the ACM classification scheme contains only about 2K research topics and the last version dates back to 2012. In this paper, we introduce the Computer Science Ontology (CSO), a large-scale, automatically generated ontology of research areas, which includes about 26K topics and 226K semantic relationships. It was created by applying the Klink-2 algorithm on a very large dataset of 16M scientific articles. CSO presents two main advantages over the alternatives: i) it includes a very large number of topics that do not appear in other classifications, and ii) it can be updated automatically by running Klink-2 on recent corpora of publications. CSO powers several tools adopted by the editorial team at Springer Nature and has been used to enable a variety of solutions, such as classifying research publications, detecting research communities, and predicting research trends. To facilitate the uptake of CSO we have developed the CSO Portal, a web application that enables users to download, explore, and provide granular feedback on CSO at different levels. Users can use the portal to rate topics and relationships, suggest missing relationships, and visualise sections of the ontology. The portal will support the publication of and access to regular new releases of CSO, with the aim of providing a comprehensive resource to the various communities engaged with scholarly data

The American Upper Ordovician Standard. XVI, Utility of Clastic-Ratio Values to Distinguish Kope and Fairview Formations, Hamilton County, Ohio

Author Institution: Department of Geological Sciences, University of Southern California, Los Angeles, California 90007The result of a Mann-Whitney U-test indicates that clastic-ratio values for the Kope Formation are stochastically greater than are those for the Fairview Formation in eastern Hamilton County, Ohio. The use of the clastic-ratio as an inferential statistic when applied to these formations is justified

On-lattice agent-based simulation of populations of cells within the open-source chaste framework

Over the years, agent-based models have been developed that combine cell division and reinforced random walks of cells on a regular lattice, reaction-diffusion equations for nutrients and growth factors and ordinary differential equations (ODEs) for the subcellular networks regulating the cell cycle. When linked to a vascular layer, this multiple scale model framework has been applied to tumour growth and therapy. Here we report on the creation of an agent-based multiscale environment amalgamating the characteristics of these models within a Virtual Pysiological Human (VPH) Exemplar Project. This project enables re-use, integration, expansion and sharing of the model and relevant data. The agent-based and reactiondiffusion parts of the multiscale model have been implemented and are available for download as part of the latest public release of Chaste (“Cancer, Heart and Soft Tissue Environment”), (http://www.cs.ox.ac.uk/chaste/) version 3.1, part of the VPH Toolkit (http://toolkit.vph-noe.eu/). The environment functionalities are verified against the original models, in addition to extra validation of all aspects of the code. In this work, we present the details of the implementation of the agent-based environment, including the system description, the conceptual model, the development of the simulation model and the processes of verification and validation of the simulation results. We explore the potential use of the environment by presenting exemplar applications of the “what if” scenarios that can easily be studied in the environment. These examples relate to tumour growth, cellular competition for resources and tumour responses to hypoxia. We conclude our work by summarising the future steps for the expansion of the current system

Colorectal Cancer Through Simulation and Experiment

Colorectal cancer has continued to generate a huge amount of research interest over several decades, forming a canonical example of tumourigenesis since its use in Fearon and Vogelstein’s linear model of genetic mutation. Over time, the field has witnessed a transition from solely experimental work to the inclusion of mathematical biology and computer-based modelling. The fusion of these disciplines has the potential to provide valuable insights into oncologic processes, but also presents the challenge of uniting many diverse perspectives. Furthermore, the cancer cell phenotype defined by the ‘Hallmarks of Cancer’ has been extended in recent times and provides an excellent basis for future research. We present a timely summary of the literature relating to colorectal cancer, addressing the traditional experimental findings, summarising the key mathematical and computational approaches, and emphasising the role of the Hallmarks in current and future developments. We conclude with a discussion of interdisciplinary work, outlining areas of experimental interest which would benefit from the insight that mathematical and computational modelling can provide

Pragmatic Ontology Evolution: Reconciling User Requirements and Application Performance

Increasingly, organizations are adopting ontologies to describe their large catalogues of items. These ontologies need to evolve regularly in response to changes in the domain and the emergence of new requirements. An important step of this process is the selection of candidate concepts to include in the new version of the ontology. This operation needs to take into account a variety of factors and in particular reconcile user requirements and application performance. Current ontology evolution methods focus either on ranking concepts according to their relevance or on preserving compatibility with existing applications. However, they do not take in consideration the impact of the ontology evolution process on the performance of computational tasks – e.g., in this work we focus on instance tagging, similarity computation, generation of recommendations, and data clustering. In this paper, we propose the Pragmatic Ontology Evolution (POE) framework, a novel approach for selecting from a group of candidates a set of concepts able to produce a new version of a given ontology that i) is consistent with the a set of user requirements (e.g., max number of concepts in the ontology), ii) is parametrised with respect to a number of dimensions (e.g., topological considerations), and iii) effectively supports relevant computational tasks. Our approach also supports users in navigating the space of possible solutions by showing how certain choices, such as limiting the number of concepts or privileging trendy concepts rather than historical ones, would reflect on the application performance. An evaluation of POE on the real-world scenario of the evolving Springer Nature taxonomy for editorial classification yielded excellent results, demonstrating a significant improvement over alternative approaches

Civil engineering status report for the ATLAS & CMS worksites

Construction work on the civil engineering contracts at Point 1 and Point 5 started in 1998. The new surface buildings and underground structures are necessary to accommodate the ATLAS and CMS detectors for the LHC Project. The principal underground works at both points consist of two new shafts, two caverns along with a number of small connection tunnels and galleries. At Point 1, the works are 90% complete. Most of the surface buildings as well as the shafts and one of the two new caverns have been completed, and the construction of the second cavern is well underway. At Point 5, the works are 70% complete. Most of the surface buildings as well as the shafts and the pillar have been completed. With excavation of the two large caverns complete, the concreting of the final linings has started. The aim of this paper is to present the status of the civil engineering on these worksites and in particular the challenges encountered constructing the experimental caverns

Resumption of mass accretion in RS Oph

The latest outburst of the recurrent nova RS Oph occurred in 2006 February. Photometric data presented here show evidence of the resumption of optical flickering, indicating re-establishment of accretion by day 241 of the outburst. Magnitude variations of up to 0.32 mag in V band and 0.14 mag in B band on time-scales of 600–7000 s are detected. Over the two-week observational period, we also detect a 0.5 mag decline in the mean brightness, from V≈ 11.4 to 11.9, and record B≈ 12.9 mag. Limits on the mass accretion rate of [inline image] are calculated, which span the range of accretion rates modelled for direct wind accretion and Roche lobe overflow mechanisms. The current accretion rates make it difficult for thermonuclear runaway models to explain the observed recurrence interval, and this implies average accretion rates are typically higher than seen immediately post-outburst

Parenting Practices of Resident Fathers: The Role of Marital and Biological Ties

This paper uses data from the Fragile Families and Child Wellbeing Study to examine differences in the parenting behaviors of resident biological and social fathers on measures of engagement, shared responsibility, and cooperation in parenting. Regression, difference-in-difference, and decomposition techniques are used. Results suggest that biological and social fathers differ significantly on most parenting measures (and in some unexpected ways), but that a considerable portion of these differences can be explained by differences in the background characteristics of the individuals and families in each group. Additionally, the analyses reveal a stronger link between marriage and higher-quality parenting behaviors for social-father families than for biological-father families.