Using Regular Languages to Explore the Representational Capacity of Recurrent Neural Architectures

The presence of Long Distance Dependencies (LDDs) in sequential data poses significant challenges for computational models. Various recurrent neural architectures have been designed to mitigate this issue. In order to test these state-of-the-art architectures, there is growing need for rich benchmarking datasets. However, one of the drawbacks of existing datasets is the lack of experimental control with regards to the presence and/or degree of LDDs. This lack of control limits the analysis of model performance in relation to the specific challenge posed by LDDs. One way to address this is to use synthetic data having the properties of subregular languages. The degree of LDDs within the generated data can be controlled through the k parameter, length of the generated strings, and by choosing appropriate forbidden strings. In this paper, we explore the capacity of different RNN extensions to model LDDs, by evaluating these models on a sequence of SPk synthesized datasets, where each subsequent dataset exhibits a longer degree of LDD. Even though SPk are simple languages, the presence of LDDs does have significant impact on the performance of recurrent neural architectures, thus making them prime candidate in benchmarking tasks.Comment: International Conference of Artificial Neural Networks (ICANN) 201

A note on the propagation of quantized vortex rings through a quantum turbulence tangle:energy transport or energy dissipation?

We investigate quantum vortex ring dynamics at scales smaller than the inter-vortex spacing in quantum turbulence. Through geometrical arguments and high-resolution numerical simulations, we examine the validity of simple estimates for the mean free path and the structure of vortex rings post-reconnection. We find that a large proportion of vortex rings remain coherent objects where approximately 75% of their energy is preserved. This leads us to consider the effectiveness of energy transport in turbulent tangles. Moreover, we show that in low density tangles, appropriate for the ultra-quantum regime, ring emission cannot be ruled out as an important mechanism for energy dissipation. However at higher vortex line densities, typically associated with the quasi-classical regime, loop emission is expected to make a negligible contribution to energy dissipation, even allowing for the fact that our work shows rings can survive multiple reconnection events. Hence the Kelvin wave cascade seems the most plausible mechanism leading to energy dissipatio

Vascular endothelial growth factor-D over-expressing tumor cells induce differential effects on uterine vasculature in a mouse model of endometrial cancer

BACKGROUND: It has been hypothesised that increased VEGF-D expression may be an independent prognostic factor for endometrial cancer progression and lymph node metastasis; however, the mechanism by which VEGF-D may promote disease progression in women with endometrial cancer has not been investigated. Our aim was to describe the distribution of lymphatic vessels in mouse uterus and to examine the effect of VEGF-D over-expression on these vessels in a model of endometrial cancer. We hypothesised that VEGF-D over-expression would stimulate growth of new lymphatic vessels into the endometrium, thereby contributing to cancer progression. METHODS: We initially described the distribution of lymphatic vessels (Lyve-1, podoplanin, VEGFR-3) and VEGF-D expression in the mouse uterus during the estrous cycle, early pregnancy and in response to estradiol-17beta and progesterone using immunohistochemistry. We also examined the effects of VEGF-D over-expression on uterine vasculature by inoculating uterine horns in NOD SCID mice with control or VEGF-D-expressing 293EBNA tumor cells. RESULTS: Lymphatic vessels positive for the lymphatic endothelial cell markers Lyve-1, podoplanin and VEGFR-3 profiles were largely restricted to the connective tissue between the myometrial circular and longitudinal muscle layers; very few lymphatic vessel profiles were observed in the endometrium. VEGF-D immunostaining was present in all uterine compartments (epithelium, stroma, myometrium), although expression was generally low. VEGF-D immunoexpression was slightly but significantly higher in estrus relative to diestrus; and in estradiol-17beta treated mice relative to vehicle or progesterone treated mice. The presence of VEGF-D over-expressing tumor cells did not induce endometrial lymphangiogenesis, although changes were observed in existing vessel profiles. For myometrial lymphatic and endometrial blood vessels, the percentage of profiles containing proliferating endothelial cells, and the cross sectional area of vessel profiles were significantly increased in response to VEGF-D in comparison to control tumor cells. In contrast, no significant changes were noted in myometrial blood vessels. In addition, examples of invading cells or tumor emboli were observed in mice receiving VEGF-D expressing 293EBNA cells. CONCLUSIONS: These results illustrate that VEGF-D over-expression has differential effects on the uterine vasculature. These effects may facilitate VEGF-D's ability to promote endometrial cancer metastasis and disease progression

Neutrophils from Both Susceptible and Resistant Mice Efficiently Kill Opsonized \u3cem\u3eListeria monocytogenes\u3c/em\u3e

Inbred mouse strains differ in their susceptibility to infection with the facultative intracellular bacterium Listeria monocytogenes, largely due to delayed or deficient innate immune responses. Previous antibody depletion studies suggested that neutrophils (polymorphonuclear leukocytes [PMN]) were particularly important for clearance in the liver, but the ability of PMN from susceptible and resistant mice to directly kill L. monocytogenes has not been examined. In this study, we showed that PMN infiltrated the livers of BALB/c/By/J (BALB/c) and C57BL/6 (B6) mice in similar numbers and that both cell types readily migrated toward leukotriene B4 in an in vitro chemotaxis assay. However, CFU burdens in the liver were significantly higher in BALB/c mice than in other strains, suggesting that PMN in the BALB/c liver might not be able to clear L. monocytogenes as efficiently as B6 PMN. Unprimed PMN harvested from either BALB/c or B6 bone marrow killed L. monocytogenes directly ex vivo, and pretreatment with autologous serum significantly enhanced killing efficiency for both. L. monocytogenes were internalized within 10 min and rapidly triggered intracellular production of reactive oxygen species in a dose-dependent manner. However, PMN from gp91phox-deficient mice also readily killed L. monocytogenes, which suggested that nonoxidative killing mechanisms may be sufficient for bacterial clearance. Together, these results indicate that there is not an intrinsic defect in the ability of PMN from susceptible BALB/c mice to kill L. monocytogenes and further suggest that if PMN function is impaired in BALB/c mice, it is likely due to locally produced modulating factors present in the liver during infection

The California-Kepler survey. X. The radius gap as a function of stellar mass, metallicity, and age

In 2017, the California-Kepler Survey (CKS) published its first data release (DR1) of high-resolution optical spectra of 1305 planet hosts. Refined CKS planet radii revealed that small planets are bifurcated into two distinct populations, super-Earths (smaller than 1.5 R⊕) and sub-Neptunes (between 2.0 and 4.0 R⊕), with few planets in between (the "radius gap"). Several theoretical models of the radius gap predict variation with stellar mass, but testing these predictions is challenging with CKS DR1 due to its limited M⋆ range of 0.8–1.4 M⊙. Here we present CKS DR2 with 411 additional spectra and derived properties focusing on stars of 0.5–0.8 M⊙. We found that the radius gap follows Rp ∝ Pm with m = −0.10 ± 0.03, consistent with predictions of X-ray and ultraviolet- and core-powered mass-loss mechanisms. We found no evidence that m varies with M⋆. We observed a correlation between the average sub-Neptune size and M⋆. Over 0.5–1.4 M⊙, the average sub-Neptune grows from 2.1 to 2.6 R⊕, following ${R}_{p}\propto {M}_{\star }^{\alpha }$ with α = 0.25 ± 0.03. In contrast, there is no detectable change for super-Earths. These M⋆–Rp trends suggest that protoplanetary disks can efficiently produce cores up to a threshold mass of Mc, which grows linearly with stellar mass according to Mc ≈ 10 M⊕(M⋆/M⊙). There is no significant correlation between sub-Neptune size and stellar metallicity (over −0.5 to +0.5 dex), suggesting a weak relationship between planet envelope opacity and stellar metallicity. Finally, there is no significant variation in sub-Neptune size with stellar age (over 1–10 Gyr), which suggests that the majority of envelope contraction concludes after ∼1 Gyr

A rocky planet transiting a nearby low-mass star

M-dwarf stars -- hydrogen-burning stars that are smaller than 60 per cent of the size of the Sun -- are the most common class of star in our Galaxy and outnumber Sun-like stars by a ratio of 12:1. Recent results have shown that M dwarfs host Earth-sized planets in great numbers: the average number of M-dwarf planets that are between 0.5 to 1.5 times the size of Earth is at least 1.4 per star. The nearest such planets known to transit their star are 39 parsecs away, too distant for detailed follow-up observations to measure the planetary masses or to study their atmospheres. Here we report observations of GJ 1132b, a planet with a size of 1.2 Earth radii that is transiting a small star 12 parsecs away. Our Doppler mass measurement of GJ 1132b yields a density consistent with an Earth-like bulk composition, similar to the compositions of the six known exoplanets with masses less than six times that of the Earth and precisely measured densities. Receiving 19 times more stellar radiation than the Earth, the planet is too hot to be habitable but is cool enough to support a substantial atmosphere, one that has probably been considerably depleted of hydrogen. Because the host star is nearby and only 21 per cent the radius of the Sun, existing and upcoming telescopes will be able to observe the composition and dynamics of the planetary atmosphere.Comment: Published in Nature on 12 November 2015, available at http://dx.doi.org/10.1038/nature15762. This is the authors' version of the manuscrip

A Personal Construct Psychology based investigation into a Product Service System for renting pushchairs to consumers

This is the peer-reviewed version of the following article: Maurizio Catulli and Nick Reed, ‘A Personal Construct Psychology Based Investigation Into a Product Service System for Renting Pushchairs to Consumers’, Business Strategy and the Environment, Vol. 26(5): 656-671, February 2017, which has been published in final form at DOI: 10.1002/bse.1944. Under embargo. Embargo end date: 1 February 2019. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.This paper explores how consumers construe a Product Service System (PSS) for the supply of pushchairs. A PSS is a system of products, services, networks of actors and supporting infrastructure designed to be more sustainable than traditional business models. PSS face an implementation challenge in consumer markets and this case based research explores some reasons for this. The study applies Personal Construct Psychology (in particular, Repertory Grid Technique) which has not previously been used in relation to researching PSS. Results suggest that PSS might be difficult to implement in relation to pushchairs. Renting pre-used equipment may meet resistance because of a perceived risk that acquisition by this means might endanger infants. Participants in the study construed buying new products from specialist infant product shops as being the best way of acquiring them. Accordingly PSS providers may, for instance, have to implement certified quality assurance processes in order to reassure consumers.Peer reviewedFinal Accepted Versio

S-COL: A Copernican turn for the development of flexibly reusable collaboration scripts

Collaboration scripts are usually implemented as parts of a particular collaborative-learning platform. Therefore, scripts of demonstrated effectiveness are hardly used with learning platforms at other sites, and replication studies are rare. The approach of a platform-independent description language for scripts that allows for easy implementation of the same script on different platforms has not succeeded yet in making the transfer of scripts feasible. We present an alternative solution that treats the problem as a special case of providing support on top of diverse Web pages: In this case, the challenge is to trigger support based on the recognition of a Web page as belonging to a specific type of functionally equivalent pages such as the search query form or the results page of a search engine. The solution suggested has been implemented by means of a tool called S-COL (Scripting for Collaborative Online Learning) and allows for the sustainable development of scripts and scaffolds that can be used with a broad variety of content and platforms. The tool’s functions are described. In order to demonstrate the feasibility and ease of script reuse with S-COL, we describe the flexible re-implementation of a collaboration script for argumentation in S-COL and its adaptation to different learning platforms. To demonstrate that a collaboration script implemented in S-COL can actually foster learning, an empirical study about the effects of a specific script for collaborative online search on learning activities is presented. The further potentials and the limitations of the S-COL approach are discussed

Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53

Background: The availability of various "omics" datasets creates a prospect of performing the study of genome-wide genetic regulatory networks. However, one of the major challenges of using mathematical models to infer genetic regulation from microarray datasets is the lack of information for protein concentrations and activities. Most of the previous researches were based on an assumption that the mRNA levels of a gene are consistent with its protein activities, though it is not always the case. Therefore, a more sophisticated modelling framework together with the corresponding inference methods is needed to accurately estimate genetic regulation from "omics" datasets. Results: This work developed a novel approach, which is based on a nonlinear mathematical model, to infer genetic regulation from microarray gene expression data. By using the p53 network as a test system, we used the nonlinear model to estimate the activities of transcription factor (TF) p53 from the expression levels of its target genes, and to identify the activation/inhibition status of p53 to its target genes. The predicted top 317 putative p53 target genes were supported by DNA sequence analysis. A comparison between our prediction and the other published predictions of p53 targets suggests that most of putative p53 targets may share a common depleted or enriched sequence signal on their upstream non-coding region. Conclusions: The proposed quantitative model can not only be used to infer the regulatory relationship between TF and its down-stream genes, but also be applied to estimate the protein activities of TF from the expression levels of its target genes

Continuity and change?: Exploring reactions to a guided self-management intervention in a randomised controlled trial for IBS with reference to prior experience of managing a long term condition

Self-care interventions are promoted as effective strategies for improving the quality of life and health outcomes for individuals with long-term health conditions. Outcome measures used in evaluations using Randomised Controlled Trials (RCTs) are not designed to consider patients' prior management strategies and experience of illness. Yet the experience of illness literature suggests that adjusting to living with chronic illness, together with broader contextual influences, are likely to be relevant to understanding responses to self-management initiatives. Using group and individual interview data we attempt to illuminate the transposition of IBS from a condition unsatisfactorily managed by medicine to one successfully managed within the life worlds of individuals. If routine embedding of complex interventions depends on the accomplishment of integration and workability in patients' everyday lives then the design and evaluation of such interventions should view participation as part of a process of continuity as well as change. Responses to formal self-management can be extended beyond psychological and other quantitatively measured outcomes. A useful addendum to trial outcomes for self-management education is an understanding of change as being inextricably linked to people's previous attempts to, and experience of, managing long-term conditions. We suggest that the benefits of understanding the prior experience of managing illness and contact with health services include the acceptability and workability of complex interventions in patients' everyday lives