Lyndon Array Construction during Burrows-Wheeler Inversion

In this paper we present an algorithm to compute the Lyndon array of a string $T$ of length $n$ as a byproduct of the inversion of the Burrows-Wheeler transform of $T$. Our algorithm runs in linear time using only a stack in addition to the data structures used for Burrows-Wheeler inversion. We compare our algorithm with two other linear-time algorithms for Lyndon array construction and show that computing the Burrows-Wheeler transform and then constructing the Lyndon array is competitive compared to the known approaches. We also propose a new balanced parenthesis representation for the Lyndon array that uses $2n+o(n)$ bits of space and supports constant time access. This representation can be built in linear time using $O(n)$ words of space, or in $O(n\log n/\log\log n)$ time using asymptotically the same space as $T$

A degree problem for two algebraic numbers and their sum

For all but one positive integer triplet (a; b; c) with a < b < c and b < 6, we decide whether there are algebraic numbers α,β and γ of degrees a, b and y, respectively, such that α+β+γ = 0. The undecided case (6; 6; 8) will be included in another paper. These results imply, for example, that the sum of two algebraic numbers of degree 6 can be of degree 15 but cannot be of degree 10. We also show that if a positive integer triplet (a; b; c) satisfies a certain triangle-like inequality with respect to every prime number then there exist algebraic numbers α,β γ of degrees a, b, c such that α+β+γ = 0. We also solve a similar problem for all (a; b; c) with a < b < c and b <6 by finding for which a, b, c there exist number fields of degrees a and b such that their compositum has degree c. Further, we have some results on the multiplicative version of the first problem, asking for which triplets (a; b; c) there are algebraic numbers and α, β and γ of degrees a, b and c, respectively, such that αβγ = 1

Detailed time course of the cortisol awakening response in healthy participants

The cortisol awakening response (CAR) can be assessed from saliva samples collected at home, which confers ecological validity but lacks researcher oversight. Participant non-adherence to requested saliva sampling regimes leads to inaccurate CAR estimates. Moderate sampling delays of just 8 (5–15) min between awakening and commencement of saliva sampling are reported to result in over-estimated CAR magnitude and earlier peaking. This has been attributed to an observed ‘latent’ period in which cortisol secretion does not increase for up to 10-min after awakening. Replication of this finding is essential as the findings have considerable implications for CAR research. Healthy participants (n = 26) collected saliva samples at 5-min intervals for 60 min on 2 consecutive typical weekdays. Full electronic monitoring of awakening and sampling enabled exclusion of non-adherent data (i.e., delays of greater than 5 min between awakening and collection of the first sample). In the 0–15 min post awakening segment of the CAR a quadratic effect was observed, with no difference between the awakening and 5 and 10 min samples. Moderate sampling delays will shift assessment of the CAR just sufficiently along the time axis to not impact upon measurement of the first sample but to remove the immediate post-awakening latent period from CAR estimates—whilst retaining later estimates of elevated cortisol secretion. The implication from these results is that accurate CAR measures can only be determined from data with strict adherence to commencement of saliva sampling following awakening

Anxious attachment style predicts an enhanced cortisol response to group psychosocial stress

Insecure attachment style is associated with poor health outcomes. A proposed pathway implicates the hypothalamic pituitary-adrenal axis (HPA-axis), dysregulation of which is associated with a wide range of mental and physical ill-health. However, data on stress reactivity in relation to attachment style is contradictory. This relationship was examined using the novel Trier Social Stress Test for groups (TSST-G): a group based acute psychosocial stressor. Each participant, in the presence of other group members, individually performed public speaking and mental arithmetic tasks. Seventy-eight healthy young females (20.2 ± 3.2 years), in groups of up to six participants completed demographic information and the Vulnerable Attachment Style Questionnaire (VASQ), and were then exposed to the TSST-G. Physiological stress reactivity was assessed using salivary cortisol concentrations, measured on seven occasions at 10-min intervals. Vulnerable attachment predicted greater cortisol reactivity independent of age, smoking status, menstrual phase and body mass index. Supplementary analysis indicated that insecure anxious attachment style (high scores on the insecurity and proximity-seeking sub-scales of the VASQ) showed greater cortisol reactivity than participants with secure attachment style. Avoidant attachment style (high scores for insecurity and low scores for proximity seeking) was not significantly different from the secure attachment style. Attachment style was not associated with the timing of the cortisol peak or post-stress recovery in cortisol concentrations. These findings in healthy young females indicate subtle underlying changes in HPA axis function in relation to attachment style and may be important for future mental health and well-being

Small animal disease surveillance: respiratory disease 2017

This report focuses on surveillance for respiratory disease in companion animals. It begins with an analysis of data from 392 veterinary practices contributing to the Small Animal Veterinary Surveillance Network (SAVSNET) between January and December 2017. The following section describes canine respiratory coronavirus infections in dogs, presenting results from laboratory-confirmed cases across the country between January 2010 and December 2017. This is followed by an update on the temporal trends of three important syndromes in companion animals, namely gastroenteritis, pruritus and respiratory disease, from 2014 to 2017. A fourth section presents a brief update on Streptococcus equi subspecies zooepidemicus in companion animals. The final section summarises some recent developments pertinent to companion animal health, namely eyeworm (Thelazzia callipaeda) infestations in dogs imported to the UK and canine influenza virus in the USA and Canada

Immediate replacement of fishing with dairying by the earliest farmers of the NE Atlantic archipelagos

The appearance of farming, from its inception in the Near East around 12 000 years ago, finally reached the northwestern extremes of Europe by the fourth millennium BC or shortly thereafter. Various models have been invoked to explain the Neolithization of northern Europe; however, resolving these different scenarios has proved problematic due to poor faunal preservation and the lack of specificity achievable for commonly applied proxies. Here, we present new multi-proxy evidence, which qualitatively and quantitatively maps subsistence change in the northeast Atlantic archipelagos from the Late Mesolithic into the Neolithic and beyond. A model involving significant retention of hunter–gatherer–fisher influences was tested against one of the dominant adoptions of farming using a novel suite of lipid biomarkers, including dihydroxy fatty acids, ω-(o-alkylphenyl)alkanoic acids and stable carbon isotope signatures of individual fatty acids preserved in cooking vessels. These new findings, together with archaeozoological and human skeletal collagen bulk stable carbon isotope proxies, unequivocally confirm rejection of marine resources by early farmers coinciding with the adoption of intensive dairy farming. This pattern of Neolithization contrasts markedly to that occurring contemporaneously in the Baltic, suggesting that geographically distinct ecological and cultural influences dictated the evolution of subsistence practices at this critical phase of European prehistory

Relationship between post-awakening salivary cortisol and melatonin secretion in healthy participants

We report the relationship between patterns of post-awakening salivary melatonin and cortisol secretion in healthy participants (n=51; mean age 21.6 ±5.0 years). Saliva samples were collected within the domestic setting, at 0-, 15-, 30-, and 45-min post-awakening on 2 consecutive typical weekdays. Analyses were undertaken on data with electronically verified sample timing accuracy (55-min delay between awakening and the start of saliva sampling). Melatonin secretion declined linearly by an average of 29% within the first 45-min post-awakening. In contrast, there was a marked 112% surge in cortisol, characteristic of the cortisol awakening response. No day differences in melatonin or cortisol secretion were observed but melatonin concentrations were lower with later awakening. Despite contrasting post-awakening changes in these hormones, there was a lack of relationship between overall levels or patterns of melatonin and cortisol during this period

Two-Level Atom in an Optical Parametric Oscillator: Spectra of Transmitted and Fluorescent Fields in the Weak Driving Field Limit

We consider the interaction of a two-level atom inside an optical parametric oscillator. In the weak driving field limit, we essentially have an atom-cavity system driven by the occasional pair of correlated photons, or weakly squeezed light. We find that we may have holes, or dips, in the spectrum of the fluorescent and transmitted light. This occurs even in the strong-coupling limit when we find holes in the vacuum-Rabi doublet. Also, spectra with a sub-natural linewidth may occur. These effects disappear for larger driving fields, unlike the spectral narrowing obtained in resonance fluorescence in a squeezed vacuum; here it is important that the squeezing parameter $N$ tends to zero so that the system interacts with only one correlated pair of photons at a time. We show that a previous explanation for spectral narrowing and spectral holes for incoherent scattering is not applicable in the present case, and propose a new explanation. We attribute these anomalous effects to quantum interference in the two-photon scattering of the system.Comment: 10 pages, 17 figures, submitted to Phys Rev

Final Technical Report for "Collaborative Research: Regional climate-change projections through next-generation empirical and dynamical models"

This project was a continuation of previous work under DOE CCPP funding in which we developed a twin approach of non-homogeneous hidden Markov models (NHMMs) and coupled ocean-atmosphere (O-A) intermediate-complexity models (ICMs) to identify the potentially predictable modes of climate variability, and to investigate their impacts on the regional-scale. We have developed a family of latent-variable NHMMs to simulate historical records of daily rainfall, and used them to downscale seasonal predictions. We have also developed empirical mode reduction (EMR) models for gaining insight into the underlying dynamics in observational data and general circulation model (GCM) simulations. Using coupled O-A ICMs, we have identified a new mechanism of interdecadal climate variability, involving the midlatitude oceans mesoscale eddy field and nonlinear, persistent atmospheric response to the oceanic anomalies. A related decadal mode is also identified, associated with the oceans thermohaline circulation. The goal of the continuation was to build on these ICM results and NHMM/EMR model developments and software to strengthen two key pillars of support for the development and application of climate models for climate change projections on time scales of decades to centuries, namely: (a) dynamical and theoretical understanding of decadal-to-interdecadal oscillations and their predictability; and (b) an interface from climate models to applications, in order to inform societal adaptation strategies to climate change at the regional scale, including model calibration, correction, downscaling and, most importantly, assessment and interpretation of spread and uncertainties in multi-model ensembles. Our main results from the grant consist of extensive further development of the hidden Markov models for rainfall simulation and downscaling specifically within the non-stationary climate change context together with the development of parallelized software; application of NHMMs to downscaling of rainfall projections over India; identification and analysis of decadal climate signals in data and models; and, studies of climate variability in terms of the dynamics of atmospheric flow regimes. Each of these project components is elaborated on below, followed by a list of publications resulting from the grant