Comparison of trends in butterfly populations between monitoring schemes

Butterflies are an important indicator of the impacts of environmental change. Butterfly monitoring schemes (BMS) have provided national and Europe-wide trends in their abundance and been widely used for research. Most schemes sample sites that are self-selected by contributors and therefore tend to cover locations that are rich in butterflies. To provide a more representative assessment of butterfly populations, the wider countryside butterfly survey (WCBS) was developed with a stratified-random sample of survey sites across the UK. We compare butterfly trends from the WCBS locations against those measured from traditional butterfly transects which are typically located in areas of good quality semi-natural habitats. Across the 26 species analysed, there was a significant positive relationship between trends measured from the two schemes between 2009 and 2013, the period when both schemes were operating fully. There was a tendency (17 out of 26 species analysed) for these changes to be greater within WCBS compared to traditional BMS transects, although this effect was not consistent across comparisons between pairs of consecutive years. When assessing these individual year-to-year changes, there was however a significant correlation between the two schemes in all cases. Over relatively short time periods, weather patterns are likely to dominate butterfly population fluctuations and lead to comparable trends across monitoring schemes. Over longer time periods, differences in land management may affect habitat condition differently for protected areas versus the wider countryside and it is therefore important to maintain comprehensive butterfly monitoring programmes to detect and interpret such effects

Investigating the topology of interacting networks - Theory and application to coupled climate subnetworks

Network theory provides various tools for investigating the structural or functional topology of many complex systems found in nature, technology and society. Nevertheless, it has recently been realised that a considerable number of systems of interest should be treated, more appropriately, as interacting networks or networks of networks. Here we introduce a novel graph-theoretical framework for studying the interaction structure between subnetworks embedded within a complex network of networks. This framework allows us to quantify the structural role of single vertices or whole subnetworks with respect to the interaction of a pair of subnetworks on local, mesoscopic and global topological scales. Climate networks have recently been shown to be a powerful tool for the analysis of climatological data. Applying the general framework for studying interacting networks, we introduce coupled climate subnetworks to represent and investigate the topology of statistical relationships between the fields of distinct climatological variables. Using coupled climate subnetworks to investigate the terrestrial atmosphere's three-dimensional geopotential height field uncovers known as well as interesting novel features of the atmosphere's vertical stratification and general circulation. Specifically, the new measure "cross-betweenness" identifies regions which are particularly important for mediating vertical wind field interactions. The promising results obtained by following the coupled climate subnetwork approach present a first step towards an improved understanding of the Earth system and its complex interacting components from a network perspective

Asteroseismology of red giants & galactic archaeology

Red-giant stars are low- to intermediate-mass ($M \lesssim 10$~M$_{\odot}$) stars that have exhausted hydrogen in the core. These extended, cool and hence red stars are key targets for stellar evolution studies as well as galactic studies for several reasons: a) many stars go through a red-giant phase; b) red giants are intrinsically bright; c) large stellar internal structure changes as well as changes in surface chemical abundances take place over relatively short time; d) red-giant stars exhibit global intrinsic oscillations. Due to their large number and intrinsic brightness it is possible to observe many of these stars up to large distances. Furthermore, the global intrinsic oscillations provide a means to discern red-giant stars in the pre-helium core burning from the ones in the helium core burning phase and provide an estimate of stellar ages, a key ingredient for galactic studies. In this lecture I will first discuss some physical phenomena that play a role in red-giant stars and several phases of red-giant evolution. Then, I will provide some details about asteroseismology -- the study of the internal structure of stars through their intrinsic oscillations -- of red-giant stars. I will conclude by discussing galactic archaeology -- the study of the formation and evolution of the Milky Way by reconstructing its past from its current constituents -- and the role red-giant stars can play in that.Comment: Lecture presented at the IVth Azores International Advanced School in Space Sciences on "Asteroseismology and Exoplanets: Listening to the Stars and Searching for New Worlds" (arXiv:1709.00645), which took place in Horta, Azores Islands, Portugal in July 201

Efficient computation of the outer hull of a discrete path

We present here a linear time and space algorithm for computing the outer hull of any discrete path encoded by its Freeman chain code. The basic data structure uses an enriched version of the data structure introduced by Brlek, Koskas and Provençal: using quadtrees for representing points in the discrete plane ℤ×ℤ with neighborhood links, deciding path intersection is achievable in linear time and space. By combining the well-known wall follower algorithm for traversing mazes, we obtain the desired result with two passes resulting in a global linear time and space algorithm. As a byproduct, the convex hull is obtained as well

Somatic alteration burden involving non-cancer genes predicts prognosis in early-stage non-small cell lung cancer

The burden of somatic mutations and neoantigens has been associated with improved survival in cancer treated with immunotherapies, especially non-small cell lung cancer (NSCLC). However, there is uncertainty about their effect on outcome in early-stage untreated cases. We posited that the burden of mutations in a specific set of genes may also contribute to the prognosis of early NSCLC patients. From a small cohort of 36 NSCLC cases, we were able to identify somatic mutations and copy number alterations in 865 genes that contributed to patient overall survival. Simply, the number of altered genes (NAG) among these 865 genes was associated with longer disease-free survival (hazard ratio (HR) = 0.153, p = 1.48 × 10−4). The gene expression signature distinguishing patients with high/low NAG was also prognostic in three independent datasets. Patients with a high NAG could be further stratified based on the presence of immunogenic mutations, revealing a further subgroup of stage I NSCLC with even better prognosis (85% with >5 years survival), and associated with cytotoxic T-cell expression. Importantly, 95% of the highly-altered genes lacked direct relation to cancer, but were implicated in pathways regulating cell proliferation, motility and immune response

A secreted PD-L1 splice variant that covalently dimerizes and mediates immunosuppression

Targeting immune checkpoint pathways, such as programmed death ligand-1 (PD-L1, also known as CD274 or B7-H1) or its receptor programmed cell death-1 (PD-1) has shown improved survival for patients with numerous types of cancers, not limited to lung cancer, melanoma, renal cell carcinoma, and Hodgkin lymphoma. PD-L1 is a co-inhibitory molecule whose expression on the surface of tumor cells is associated with worse prognosis in many tumors. Here we describe a splice variant (secPD-L1) that does not splice into the transmembrane domain, but instead produces a secreted form of PD-L1 that has a unique 18 amino acid tail containing a cysteine that allows it to homodimerize and more effectively inhibit lymphocyte function than monomeric soluble PD-L1. We show that recombinant secPD-L1 can dimerize and inhibit T-cell proliferation and IFN-gamma production in vitro. The secPD-L1 variant is expressed by malignant cells in vitro that also express high levels of full-length PD-L1. Transcriptomic analysis of gene expression across The Cancer Genome Atlas found the strongest association of secPD-L1 with full-length PD-L1, but also with subsets of immunologic genes, such as in myeloid-derived suppressor cells. Moreover, the splice variant is also expressed in normal tissues and within normal peripheral blood cells it is preferentially expressed in activated myeloid cells. This is the first report of a form of secreted PD-L1 that homodimerizes and is functionally active. SecPD-L1 may function as a paracrine negative immune regulator within the tumor, since secPD-L1 does not require a cell-to-cell interaction to mediate its inhibitory effect