The Power of Non-Determinism in Higher-Order Implicit Complexity

We investigate the power of non-determinism in purely functional programming languages with higher-order types. Specifically, we consider cons-free programs of varying data orders, equipped with explicit non-deterministic choice. Cons-freeness roughly means that data constructors cannot occur in function bodies and all manipulation of storage space thus has to happen indirectly using the call stack. While cons-free programs have previously been used by several authors to characterise complexity classes, the work on non-deterministic programs has almost exclusively considered programs of data order 0. Previous work has shown that adding explicit non-determinism to cons-free programs taking data of order 0 does not increase expressivity; we prove that this - dramatically - is not the case for higher data orders: adding non-determinism to programs with data order at least 1 allows for a characterisation of the entire class of elementary-time decidable sets. Finally we show how, even with non-deterministic choice, the original hierarchy of characterisations is restored by imposing different restrictions.Comment: pre-edition version of a paper accepted for publication at ESOP'1

On the use of blow up to study regularizations of singularities of piecewise smooth dynamical systems in R3\mathbb{R}^3

In this paper we use the blow up method of Dumortier and Roussarie \cite{dumortier_1991,dumortier_1993,dumortier_1996}, in the formulation due to Krupa and Szmolyan \cite{krupa_extending_2001}, to study the regularization of singularities of piecewise smooth dynamical systems \cite{filippov1988differential} in $\mathbb R^3$. Using the regularization method of Sotomayor and Teixeira \cite{Sotomayor96}, first we demonstrate the power of our approach by considering the case of a fold line. We quickly recover a main result of Bonet and Seara \cite{reves_regularization_2014} in a simple manner. Then, for the two-fold singularity, we show that the regularized system only fully retains the features of the singular canards in the piecewise smooth system in the cases when the sliding region does not include a full sector of singular canards. In particular, we show that every locally unique primary singular canard persists the regularizing perturbation. For the case of a sector of primary singular canards, we show that the regularized system contains a canard, provided a certain non-resonance condition holds. Finally, we provide numerical evidence for the existence of secondary canards near resonance.Comment: To appear in SIAM Journal of Applied Dynamical System

Capturing quantitative zooplankton information in the sea : Performance test of laser optical plankton counter and video plankton recorder in Calanus finmarchicus dominated summer situation

Author's accepted version (post-print).NOTICE: this is the author’s version of a work that was accepted for publication in Progress in Oceanography (2012). Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Progress in Oceanography (2012), 108. doi: http://dx.doi.org/10.1016/j.pocean.2012.10.005.We compared two optical plankton counters, the Laser Optical Plankton Counter (LOPC) and the Video Plankton Recorder (VPR) for their abundance estimates of Calanus finmarchicus during an early summer situation (June 2008) in two North Norwegian fjords. The LOPC was mounted on the VPR frame in order to sample the same body of water. The combined system of LOPC and VPR was operated by vertical profiling from the surface to 100 m of depth in several locations of the fjords representing different blooming conditions and zooplankton community structures. Data from the two instruments, as well as from CTD-F, were logged concurrently and retrieved on deck after about 15 depth profiles. Primary data were analysed according to standard routines, and choices made during sampling and analyses (sampling volume, selection of size range, transparency of particles, statistics) are discussed. Data were averaged for every 5, 10 and 15 m depth bins. The vertical profiles of C. finmarchicus CIV–CVI abundance that were obtained by LOPC and VPR, respectively, showed a striking similarity. No significant differences between profiles sampled by these two instruments were observed when data were binned into 15 m bins. At low abundances (<100 Calanus sp. L−1) profiles were significantly different when data were binned into 5- or 10-m bins. This is attributed to the small sampling volumes of the LOPC and the VPR, and to very patchy distributions of copepods, resulting in a high standard deviation between consecutive profiles. Based on the results we conclude that the time is mature for a more extensive use of optical instruments to estimate zooplankton abundances and distributions in the sea

EPIC 219217635: A Doubly Eclipsing Quadruple System Containing an Evolved Binary

We have discovered a doubly eclipsing, bound, quadruple star system in the field of K2 Campaign 7. EPIC 219217635 is a stellar image with $Kp = 12.7$ that contains an eclipsing binary (`EB') with $P_A = 3.59470$ d and a second EB with $P_B = 0.61825$ d. We have obtained followup radial-velocity (`RV') spectroscopy observations, adaptive optics imaging, as well as ground-based photometric observations. From our analysis of all the observations, we derive good estimates for a number of the system parameters. We conclude that (1) both binaries are bound in a quadruple star system; (2) a linear trend to the RV curve of binary A is found over a 2-year interval, corresponding to an acceleration, $\dot \gamma = 0.0024 \pm 0.0007$ cm s$^{-2}$; (3) small irregular variations are seen in the eclipse-timing variations (`ETVs') detected over the same interval; (4) the orbital separation of the quadruple system is probably in the range of 8-25 AU; and (5) the orbital planes of the two binaries must be inclined with respect to each other by at least 25$^\circ$. In addition, we find that binary B is evolved, and the cooler and currently less massive star has transferred much of its envelope to the currently more massive star. We have also demonstrated that the system is sufficiently bright that the eclipses can be followed using small ground-based telescopes, and that this system may be profitably studied over the next decade when the outer orbit of the quadruple is expected to manifest itself in the ETV and/or RV curves.Comment: Accepted for publication in MNRA

Quantitative real-time RT-PCR of CD24 mRNA in the detection of prostate cancer

BACKGROUND: Gene expression profiling has recently shown that the mRNA for CD24 is overexpressed in prostate carcinomas (Pca) compared to benign or normal prostate epithelial tissues. Immunohistochemical studies have reported the usefulness of anti-CD24 for detecting prostate cancer over the full range of prostate specimens encountered in surgical pathology, e.g. needle biopsies, transurethral resection of prostate chips, or prostatectomies. It is a small mucin-like cell surface protein and thus promises to become at least a standard adjunctive stain for atypical prostate biopsies. We tested the usefulness of real-time RT-PCR for specific and sensitive detection of CD24 transcripts as a supplementary measure for discriminating between malignant and benign lesions in prostatic tissues. METHODS: Total RNA was isolated from snap-frozen chips in 55 cases of benign prostatic hyperplasia (BPH) and from frozen sections in 59 prostatectomy cases. The latter contain at least 50% malignant epithelia. Relative quantification of CD24 transcripts was performed on the LightCycler instrument using hybridization probes for detection and porphobilinogen deaminase transcripts (PBGD) for normalization. RESULTS: Normalized CD24 transcript levels showed an average 2.69-fold increase in 59 Pca-cases (mean 0.21) when compared to 55 cases of BPH (mean 0.08). This difference was highly significant (p < 0.0001). The method has a moderate specificity (47.3%) but a high sensitivity (86.4%) if the cutoff is set at 0.0498. CD24 expression levels among Pca cases were not statistically associated with the tumor and lymph-node stage, the grading (WHO), the surgical margins, or the Gleason score. CONCLUSION: The present study demonstrates the feasibility of quantitative CD24 RNA transcript detection in prostatic tissues even without previous laser microdissection

K2 Variable Catalogue II: Machine Learning Classification of Variable Stars and Eclipsing Binaries in K2 Fields 0-4

We are entering an era of unprecedented quantities of data from current and planned survey telescopes. To maximise the potential of such surveys, automated data analysis techniques are required. Here we implement a new methodology for variable star classification, through the combination of Kohonen Self Organising Maps (SOM, an unsupervised machine learning algorithm) and the more common Random Forest (RF) supervised machine learning technique. We apply this method to data from the K2 mission fields 0-4, finding 154 ab-type RR Lyraes (10 newly discovered), 377 Delta Scuti pulsators, 133 Gamma Doradus pulsators, 183 detached eclipsing binaries, 290 semi-detached or contact eclipsing binaries and 9399 other periodic (mostly spot-modulated) sources, once class significance cuts are taken into account. We present lightcurve features for all K2 stellar targets, including their three strongest detected frequencies, which can be used to study stellar rotation periods where the observed variability arises from spot modulation. The resulting catalogue of variable stars, classes, and associated data features are made available online. We publish our SOM code in Python as part of the open source PyMVPA package, which in combination with already available RF modules can be easily used to recreate the method.Comment: Accepted for publication in MNRAS, 16 pages, 13 figures. Updated with proof corrections. Full catalogue tables available at https://www2.warwick.ac.uk/fac/sci/physics/research/astro/people/armstrong/ or at the CD

Dynamical Dark Energy model parameters with or without massive neutrinos

We use WMAP5 and other cosmological data to constrain model parameters in quintessence cosmologies, focusing also on their shift when we allow for non-vanishing neutrino masses. The Ratra-Peebles (RP) and SUGRA potentials are used here, as examples of slowly or fastly varying state parameter w(a). Both potentials depend on an energy scale \Lambda. Here we confirm the results of previous analysis with WMAP3 data on the upper limits on \Lambda, which turn out to be rather small (down to ~10^{-9} in RP cosmologies and ~10^{-5} for SUGRA). Our constraints on \Lambda are not heavily affected by the inclusion of neutrino mass as a free parameter. On the contrary, when the neutrino mass degree of freedom is opened, significant shifts in the best-fit values of other parameters occur.Comment: 9 pages, 3 figures, submitted to JCA

MDM2 facilitates adipocyte differentiation through CRTC-mediated activation of STAT3

The ubiquitin ligase MDM2 is best known for balancing the activity of the tumor suppressor p53. We have previously shown that MDM2 is vital for adipocyte conversion through controlling Cebpd expression in a p53-independent manner. Here, we show that the proadipogenic effect of MDM2 relies on activation of the STAT family of transcription factors. Their activation was required for the cAMP-mediated induction of target genes. Interestingly, rather than influencing all cAMP-stimulated genes, inhibition of the kinases directly responsible for STAT activation, namely JAKs, or ablation of MDM2, each resulted in abolished induction of a subset of cAMP-stimulated genes, with Cebpd being among the most affected. Moreover, STATs were able to interact with the transcriptional cofactors CRTC2 and CRTC3, hitherto only reported to associate with the cAMP-responsive transcription factor CREB. Last but not least, the binding of CRTC2 to a transcriptional enhancer that interacts with the Cebpd promoter was dramatically decreased upon JAK inhibition. Our data reveal the existence of an unusual functional interplay between STATs and CREB at the onset of adipogenesis through shared CRTC cofactors

Neutrinos in Non-linear Structure Formation - a Simple SPH Approach

We present a novel method for implementing massive neutrinos in N-body simulations. Instead of sampling the neutrino velocity distribution by individual point particles we take neutrino free-streaming into account by treating it as an effective redshift dependent sound speed in a perfect isothermal fluid, and assume a relation between the sound speed and velocity dispersion of the neutrinos. Although the method fails to accurately model the true neutrino power spectrum, it is able to calculate the total matter power spectrum to the same accuracy as more complex hybrid neutrino methods, except on very small scales. We also present an easy way to update the publicly available Gadget-2 version with this neutrino approximation.Comment: 13 pages, 7 figure