Towards an embedding of Graph Transformation in Intuitionistic Linear Logic

Linear logics have been shown to be able to embed both rewriting-based approaches and process calculi in a single, declarative framework. In this paper we are exploring the embedding of double-pushout graph transformations into quantified linear logic, leading to a Curry-Howard style isomorphism between graphs and transformations on one hand, formulas and proof terms on the other. With linear implication representing rules and reachability of graphs, and the tensor modelling parallel composition of graphs and transformations, we obtain a language able to encode graph transformation systems and their computations as well as reason about their properties

DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability

The TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor are important constituents of all eukaryotic initiation complexes. The reason for the emergence and strict requirement of the additional initiation factor Bdp1 in the RNA polymerase (RNAP) III system, however, remained elusive. A poorly studied aspect in this context is the effect of DNA strain arising from DNA compaction and transcriptional activity on initiation complex formation. We made use of a DNA origami-based force clamp to follow the assembly of human initiation complexes in the RNAP II and RNAP III systems at the single-molecule level under piconewton forces. We demonstrate that TBP-DNA complexes are force-sensitive and TFIIB is sufficient to stabilise TBP on a strained promoter. In contrast, Bdp1 is the pivotal component that ensures stable anchoring of initiation factors, and thus the polymerase itself, in the RNAP III system. Thereby, we offer an explanation for the crucial role of Bdp1 for the high transcriptional output of RNAP II

Learning to Learn in Collective Adaptive Systems: Mining Design Patterns for Data-driven Reasoning

Engineering collective adaptive systems (CAS) with learning capabilities is a challenging task due to their multidimensional and complex design space. Data-driven approaches for CAS design could introduce new insights enabling system engineers to manage the CAS complexity more cost-effectively at the design-phase. This paper introduces a systematic approach to reason about design choices and patterns of learning-based CAS. Using data from a systematic literature review, reasoning is performed with a novel application of data-driven methodologies such as clustering, multiple correspondence analysis and decision trees. The reasoning based on past experience as well as supporting novel and innovative design choices are demonstrated

Complementary activation of peripheral natural killer cell immunity in nasopharyngeal carcinoma

NK cells and αβ- and γδ-CTL play important roles in cellular immunity against tumors. We previously demonstrated that NPC patients have a quantitative and qualitative deficit in γδ-CTL and EBV-specific αβ-CTL when compared to normal subjects and NPC long-term survivors. In this study we report further observations of a complementary activation of peripheral NK cells in NPC patients. The NK cells in these patients, compared to those of healthy subjects and NPC survivors, were preferentially activated in response to the stimulation of myeloma cell line XG-7 and expanded in the presence of exogenous IL-2. The production of IFN-γ was lowest in the patient group, whereas IL-12, IL-15 and TNF-α were produced in higher levels in patients than in the donors and survivors. The cytolytic effect of the NK cells against NPC cells in the patient group was also higher than that of the donors and survivors. Furthermore, the patients at later stages of NPC had lower γδ-CTL activity but higher NK cytotoxicity towards NPC targets, with higher production of IL-12, IL-15 and TNF-α but lower production of IFN-γ than in patients at earlier stages. This might be part of a triggered compensatory re-activation of the innate immunity, believed to be mediated through various cytokines and chemokines when adaptive T cell immunity is breached. Together, these data suggest complementary roles of innate and adaptive immune response in tumor immunity where NK cells, γδ- and αβ-CTL compensate for the deficits of one another at different stages of tumor invasion. © 2006 Japanese Cancer Association.published_or_final_versio

Synchronizing inventory and transport within supply chain management

The problem considers synchronized optimization of inventory and transport, and focuses on producer-distributor relations. Particular attention is paid to developing a mathematical model and an optimization problem that can be used to minimize the overall distribution cost by an appropriate placement of warehouses and cross-docking points. Solutions to this problem are explored using genetic algorithms and ideas from graph/network theory. Note: there are three separate reports contained within the uploaded .pdf file

Digital Elevation Models: Terminology and Definitions

Digital elevation models (DEMs) provide fundamental depictions of the three-dimensional shape of the Earth’s surface and are useful to a wide range of disciplines. Ideally, DEMs record the interface between the atmosphere and the lithosphere using a discrete two-dimensional grid, with complexities introduced by the intervening hydrosphere, cryosphere, biosphere, and anthroposphere. The treatment of DEM surfaces, affected by these intervening spheres, depends on their intended use, and the characteristics of the sensors that were used to create them. DEM is a general term, and more specific terms such as digital surface model (DSM) or digital terrain model (DTM) record the treatment of the intermediate surfaces. Several global DEMs generated with optical (visible and near-infrared) sensors and synthetic aperture radar (SAR), as well as single/multi-beam sonars and products of satellite altimetry, share the common characteristic of a georectified, gridded storage structure. Nevertheless, not all DEMs share the same vertical datum, not all use the same convention for the area on the ground represented by each pixel in the DEM, and some of them have variable data spacings depending on the latitude. This paper highlights the importance of knowing, understanding and reflecting on the sensor and DEM characteristics and consolidates terminology and definitions of key concepts to facilitate a common understanding among the growing community of DEM users, who do not necessarily share the same background

The source ambiguity problem: Distinguishing the effects of grammar and processing on acceptability judgments

Judgments of linguistic unacceptability may theoretically arise from either grammatical deviance or significant processing difficulty. Acceptability data are thus naturally ambiguous in theories that explicitly distinguish formal and functional constraints. Here, we consider this source ambiguity problem in the context of Superiority effects: the dispreference for ordering a wh-phrase in front of a syntactically “superior” wh-phrase in multiple wh-questions, e.g., What did who buy? More specifically, we consider the acceptability contrast between such examples and so-called D-linked examples, e.g., Which toys did which parents buy? Evidence from acceptability and self-paced reading experiments demonstrates that (i) judgments and processing times for Superiority violations vary in parallel, as determined by the kind of wh-phrases they contain, (ii) judgments increase with exposure, while processing times decrease, (iii) reading times are highly predictive of acceptability judgments for the same items, and (iv) the effects of the complexity of the wh-phrases combine in both acceptability judgments and reading times. This evidence supports the conclusion that D-linking effects are likely reducible to independently motivated cognitive mechanisms whose effects emerge in a wide range of sentence contexts. This in turn suggests that Superiority effects, in general, may owe their character to differential processing difficulty

A Path Toward the Use of Trail Users’ Tweets to Assess Effectiveness of the Environmental Stewardship Scheme: An Exploratory Analysis of the Pennine Way National Trail

Large and unofficial data sets, for instance those gathered from social media, are increasingly being used in geographical research and explored as decision support tools for policy development. Social media data have the potential to provide new insight into phenomena about which there is little information from conventional sources. Within this context, this paper explores the potential of social media data to evaluate the aesthetic management of landscape. Specifically, this project utilises the perceptions of visitors to the Pennine Way National Trail, which passes through land managed under the Environmental Stewardship Scheme (ESS). The method analyses sentiment in trail users’ public Twitter messages (tweets) with the aim of assessing the extent to which the ESS maintains landscape character within the trail corridor. The method demonstrates the importance of filtering social media data to convert it into useful information. After filtering, the results are based on 161 messages directly related to the trail. Although small, this sample illustrates the potential for social media to be used as a cheap and increasingly abundant source of information. We suggest that social media data in this context should be seen as a resource that can complement, rather than replace, conventional data sources such as questionnaires and interviews. Furthermore, we provide guidance on how social media could be effectively used by conservation bodies, such as Natural England, which are charged with the management of areas of environmental value worldwide