Consistent testing for recurrent genomic aberrations: Table 1.

We consider the detection and identification of recurrent departures from stationary behaviour in genomic or similarly arranged data containing measurements at an ordered set of variables. Our primary focus is on departures that occur only at a single variable, or within a small window of contiguous variables, but involve more than one sample. This encompasses the identification of aberrant markers in genome-wide measurements of DNA copy number and DNA methylation, as well as meta-analyses of genome-wide association studies. We propose and analyse a cyclic shift-based procedure for testing recurrent departures from stationarity. Our analysis establishes the consistency of cyclic shift $$p$$-values for datasets with a fixed set of samples as the number of observed variables tends to infinity, under the assumption that each sample is an independent realization of a stationary Markov chain. Our results apply to any test statistic satisfying a simple invariance condition

When to be Discrete: Analyzing Algorithm Performance on Discretized Continuous Problems

The domain of an optimization problem is seen as one of its most important characteristics. In particular, the distinction between continuous and discrete optimization is rather impactful. Based on this, the optimizing algorithm, analyzing method, and more are specified. However, in practice, no problem is ever truly continuous. Whether this is caused by computing limits or more tangible properties of the problem, most variables have a finite resolution. In this work, we use the notion of the resolution of continuous variables to discretize problems from the continuous domain. We explore how the resolution impacts the performance of continuous optimization algorithms. Through a mapping to integer space, we are able to compare these continuous optimizers to discrete algorithms on the exact same problems. We show that the standard $(\mu_W, \lambda)$-CMA-ES fails when discretization is added to the problem

Advection, diffusion and delivery over a network

Many biological, geophysical and technological systems involve the transport of resource over a network. In this paper we present an algorithm for calculating the exact concentration of resource at any point in space or time, given that the resource in the network is lost or delivered out of the network at a given rate, while being subject to advection and diffusion. We consider the implications of advection, diffusion and delivery for simple models of glucose delivery through a vascular network, and conclude that in certain circumstances, increasing the volume of blood and the number of glucose transporters can actually decrease the total rate of glucose delivery. We also consider the case of empirically determined fungal networks, and analyze the distribution of resource that emerges as such networks grow over time. Fungal growth involves the expansion of fluid filled vessels, which necessarily involves the movement of fluid. In three empirically determined fungal networks we found that the minimum currents consistent with the observed growth would effectively transport resource throughout the network over the time-scale of growth. This suggests that in foraging fungi, the active transport mechanisms observed in the growing tips may not be required for long range transport.Comment: 54 pages including appendix, 10 figure

Iso-osmotic regulation of nitrate accumulation in lettuce (Lactuca sativa L.)

Concerns about possible health hazards arising from human consumption of lettuce and other edible vegetable crops with high concentrations of nitrate have generated demands for a greater understanding of processes involved in its uptake and accumulation in order to devise more sustainable strategies for its control. This paper evaluates a proposed iso-osmotic mechanism for the regulation of nitrate accumulation in lettuce (Lactuca sativa L.) heads. This mechanism assumes that changes in the concentrations of nitrate and all other endogenous osmotica (including anions, cations and neutral solutes) are continually adjusted in tandem to minimise differences in osmotic potential of the shoot sap during growth, with these changes occurring independently of any variations in external water potential. The hypothesis was tested using data from six new experiments, each with a single unique treatment comprising a separate combination of light intensity, N source (nitrate with or without ammonium) and nitrate concentration carried out hydroponically in a glasshouse using a butterhead lettuce variety. Repeat measurements of plant weights and estimates of all of the main soluble constituents (nitrate, potassium, calcium, magnesium, organic anions, chloride, phosphate, sulphate and soluble carbohydrates) in the shoot sap were made at intervals from about 2 weeks after transplanting until commercial maturity, and the data used to calculate changes in average osmotic potential in the shoot. Results showed that nitrate concentrations in the sap increased when average light levels were reduced by between 30 and 49 % and (to a lesser extent) when nitrate was supplied at a supra-optimal concentration, and declined with partial replacement of nitrate by ammonium in the external nutrient supply. The associated changes in the proportions of other endogenous osmotica, in combination with the adjustment of shoot water content, maintained the total solute concentrations in shoot sap approximately constant and minimised differences in osmotic potential between treatments at each sampling date. There was, however, a gradual increase in osmotic potential (ie a decline in total solute concentration) over time largely caused by increases in shoot water content associated with the physiological and morphological development of the plants. Regression analysis using normalised data (to correct for these time trends) showed that the results were consistent with a 1:1 exchange between the concentrations of nitrate and the sum of all other endogenous osmotica throughout growth, providing evidence that an iso-osmotic mechanism (incorporating both concentration and volume regulation) was involved in controlling nitrate concentrations in the shoot

Triangulation network of 1929-1944 of the first 1:500 urban map of València

[EN] Triangulation is a surveying method on which earlier maps made were based. Although the origins of the method can be traced back to the 16th century, it is still used today, with minor changes, to adjust networks observed with modern geodetic techniques. In this paper we present the geodetic survey work that was carried out for the primary triangulation network of the first 1:500 urban map of the city of València (Spain). It spanned from 1929 to 1944 and resulted in 421 maps covering about 174 square kilometres. We focus on four key elements to define the geometric framework of a map: (1) the geodetic network, (2) the cartographic projection, (3) the baseline measurements, and (4) the primary triangulation. The paper is based on the interpretation of original documents and field books recovered from the archives of the València City Council. In order to check the accuracy and consistency of the survey work, we recomputed all calculations directly from the field data, following the mathematical procedures of the time. We obtained a set of transformation parameters to convert the coordinates of 1929 to current coordinates based on the European Terrestrial Reference System of 1989 (ETRS89). Results showed that the 1929 primary triangulation angles and coordinates are accurate to 8 s of arc and 35 cm respectively, and that the coordinates transform well into the current reference system with average residuals of 26 cm across nine control points, demonstrating the high quality of the 1929 work.Villar-Cano, M.; Marqués-Mateu, Á.; Jiménez-Martínez, MJ. (2020). Triangulation network of 1929-1944 of the first 1:500 urban map of València. Survey Review (Online). 52(373):317-329. https://doi.org/10.1080/00396265.2018.1564599S31732952373Bitelli, G., Cremonini, S., & Gatta, G. (2014). Cartographic heritage: Toward unconventional methods for quantitative analysis of pre-geodetic maps. Journal of Cultural Heritage, 15(2), 183-195. doi:10.1016/j.culher.2013.04.003Blachut, T. J., Chrzanowski, A., & Saastamoinen, J. H. (1979). Urban Surveying and Mapping. doi:10.1007/978-1-4612-6145-2Brinker, R. C., & Minnick, R. (Eds.). (1987). The Surveying Handbook. doi:10.1007/978-1-4757-1188-2Gatta, G. 2010. Valorizzazione di cartografia storica attraverso moderne tecniche geomatiche: recupero metrico, elaborazione e consultazione in ambiente digitale [Valuation of historic cartography using modern geomatics techniques: metric recovering, making and use in digital environment]. Doctoral thesis. Bologna: Universitá di Bologna. 295 pages. (In Italian).Gorse, C., Johnston, D., & Pritchard, M. (2012). A Dictionary of Construction, Surveying and Civil Engineering. doi:10.1093/acref/9780199534463.001.0001Hotine, M. (1939). THE RE-TRIANGULATION OF GREAT BRITAIN IV—BASE MEASUREMENT. Empire Survey Review, 5(34), 211-225. doi:10.1179/sre.1939.5.34.211Kahmen, H., & Faig, W. (1988). Surveying. doi:10.1515/9783110845716Leick, A., Rapoport, L., & Tatarnikov, D. (2015). GPS Satellite Surveying. doi:10.1002/9781119018612Murdin, P. (2009). Full Meridian of Glory. doi:10.1007/978-0-387-75534-2Schofield, W., & Breach, M. (2007). Engineering Surveying. doi:10.1201/b12847Seeber, G. (2003). Satellite Geodesy. doi:10.1515/9783110200089Snyder, J. P. (1987). Map projections: A working manual. Professional Paper. doi:10.3133/pp139

Environmental regulation of carbon isotope composition and crassulacean acid metabolism in three plant communities along a water availability gradient

Expression of crassulacean acid metabolism (CAM) is characterized by extreme variability within and between taxa and its sensitivity to environmental variation. In this study, we determined seasonal fluctuations in CAM photosynthesis with measurements of nocturnal tissue acidification and carbon isotopic composition (δ13C) of bulk tissue and extracted sugars in three plant communities along a precipitation gradient (500, 700, and 1,000 mm year−1) on the Yucatan Peninsula. We also related the degree of CAM to light habitat and relative abundance of species in the three sites. For all species, the greatest tissue acid accumulation occurred during the rainy season. In the 500 mm site, tissue acidification was greater for the species growing at 30% of daily total photon flux density (PFD) than species growing at 80% PFD. Whereas in the two wetter sites, the species growing at 80% total PFD had greater tissue acidification. All species had values of bulk tissue δ13C less negative than −20‰, indicating strong CAM activity. The bulk tissue δ13C values in plants from the 500 mm site were 2‰ less negative than in plants from the wetter sites, and the only species growing in the three communities, Acanthocereus tetragonus (Cactaceae), showed a significant negative relationship between both bulk tissue and sugar δ13C values and annual rainfall, consistent with greater CO2 assimilation through the CAM pathway with decreasing water availability. Overall, variation in the use of CAM photosynthesis was related to water and light availability and CAM appeared to be more ecologically important in the tropical dry forests than in the coastal dune

Blockade of T-cell activation by dithiocarbamates involves novel mechanisms of inhibition of nuclear factor of activated T cells.

Dithiocarbamates (DTCs) have recently been reported as powerful inhibitors of NF-kappaB activation in a number of cell types. Given the role of this transcription factor in the regulation of gene expression in the inflammatory response, NF-kappaB inhibitors have been suggested as potential therapeutic drugs for inflammatory diseases. We show here that DTCs inhibited both interleukin 2 (IL-2) synthesis and membrane expression of antigens which are induced during T-cell activation. This inhibition, which occurred with a parallel activation of c-Jun transactivating functions and expression, was reflected by transfection experiments at the IL-2 promoter level, and involved not only the inhibition of NF-kappaB-driven reporter activation but also that of nuclear factor of activated T cells (NFAT). Accordingly, electrophoretic mobility shift assays (EMSAs) indicated that pyrrolidine DTC (PDTC) prevented NF-kappaB, and NFAT DNA-binding activity in T cells stimulated with either phorbol myristate acetate plus ionophore or antibodies against the CD3-T-cell receptor complex and simultaneously activated the binding of AP-1. Furthermore, PDTC differentially targeted both NFATp and NFATc family members, inhibiting the transactivation functions of NFATp and mRNA induction of NFATc. Strikingly, Western blotting and immunocytochemical experiments indicated that PDTC promoted a transient and rapid shuttling of NFATp and NFATc, leading to their accelerated export from the nucleus of activated T cells. We propose that the activation of an NFAT kinase by PDTC could be responsible for the rapid shuttling of the NFAT, therefore transiently converting the sustained transactivation of this transcription factor that occurs during lymphocyte activation, and show that c-Jun NH2-terminal kinase (JNK) can act by directly phosphorylating NFATp. In addition, the combined inhibitory effects on NFAT and NF-KB support a potential use of DTCs as immunosuppressants

Binary and Millisecond Pulsars at the New Millennium

We review the properties and applications of binary and millisecond pulsars. Our knowledge of these exciting objects has greatly increased in recent years, mainly due to successful surveys which have brought the known pulsar population to over 1300. There are now 56 binary and millisecond pulsars in the Galactic disk and a further 47 in globular clusters. This review is concerned primarily with the results and spin-offs from these surveys which are of particular interest to the relativity community.Comment: 59 pages, 26 figures, 5 tables. Accepted for publication in Living Reviews in Relativity (http://www.livingreviews.org

Gender and sustainable livelihoods: linking gendered experiences of environment, community and self

In this essay I explore the economic, social, environmental and cultural changes taking place in Bolsena, Italy, where agricultural livelihoods have rapidly diminished in the last two decades. I examine how gender dynamics have shifted with the changing values and livelihoods of Bolsena through three women’s narratives detailing their gendered experiences of environment, community and self. I reflect on these changes with Sabrina, who is engaged in a feminist community-based organization; Anna, who is running an alternative wine bar; and Isabella, a jeweler, who is engaged in ecofeminist practices. My analysis is based on concepts developed by feminist political ecology: specifically, the theory of rooted networks from Dianne Rocheleau, Donna Haraway’s concept of naturecultures (and the work of J. K. Gibson-Graham on new economic imaginaries emerging from the politics of place. I aim to think with, reflect upon and provoke from the ‘‘otherwise’’, taking into account the lived relations entwining nature and gender. My article looks at the interconnections of gender, environment and livelihoods, attentive to the daily needs, embodied interactions and labours of these three women as part of a reappropriation, reconstruction and reinvention of Bolsena’s lifeworld. By listening to the stories of their everyday lives and struggles, I show the dynamic potential of the politics of place and the efforts to build diverse economies and more ethical economic and ecological relationships based on gender-aware subjectivities and values