Large-Scale Image Processing with the ROTSE Pipeline for Follow-Up of Gravitational Wave Events

Electromagnetic (EM) observations of gravitational-wave (GW) sources would bring unique insights into a source which are not available from either channel alone. However EM follow-up of GW events presents new challenges. GW events will have large sky error regions, on the order of 10-100 square degrees, which can be made up of many disjoint patches. When searching such large areas there is potential contamination by EM transients unrelated to the GW event. Furthermore, the characteristics of possible EM counterparts to GW events are also uncertain. It is therefore desirable to be able to assess the statistical significance of a candidate EM counterpart, which can only be done by performing background studies of large data sets. Current image processing pipelines such as that used by ROTSE are not usually optimised for large-scale processing. We have automated the ROTSE image analysis, and supplemented it with a post-processing unit for candidate validation and classification. We also propose a simple ad hoc statistic for ranking candidates as more likely to be associated with the GW trigger. We demonstrate the performance of the automated pipeline and ranking statistic using archival ROTSE data. EM candidates from a randomly selected set of images are compared to a background estimated from the analysis of 102 additional sets of archival images. The pipeline's detection efficiency is computed empirically by re-analysis of the images after adding simulated optical transients that follow typical light curves for gamma-ray burst afterglows and kilonovae. We show that the automated pipeline rejects most background events and is sensitive to simulated transients to limiting magnitudes consistent with the limiting magnitude of the images

Incorporating basic needs to reconcile poverty and ecosystem services

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordConservation managers frequently face the challenge of protecting and sustaining biodiversity without producing detrimental outcomes for (often poor) human populations that depend upon ecosystem services for their wellbeing. However, win-win solutions are often elusive and can mask trade-offs and negative outcomes for the wellbeing of particular groups of people. To deal with such trade-offs, approaches are needed to identify both ecological as well as social thresholds to determine the acceptable 'solution space' for conservation. Although human wellbeing as a concept has recently gained prominence among conservationists, they still lack tools to evaluate how their action affects human wellbeing in a given context. This paper presents the Theory of Human Needs in the context of conservation, building on an extensive historical application of needs approaches in international development. We detail an innovative participatory method, to evaluate how human needs are met, using locally relevant thresholds. We then establish the connections between human needs and ecosystem services. An application of this method in coastal East Africa identifies households who are in serious harm through not meeting different basic needs, and uncovers the role of ecosystem services in meeting these. Drawing from the international development and wellbeing literature, we suggest that this methodological approach, can help conservationists and planners balance poverty alleviation and biodiversity protection, ensure that conservation measures do not, at the very least, push individuals into serious harm and as a basis for monitoring the impacts of conservation on multidimensional poverty. This article is protected by copyright. All rights reserved.This paper results from the project Sustainable Poverty Alleviation from Coastal Ecosystem Services (SPACES) project number NE-K010484-1, funded by the Ecosystem Services for Poverty Alleviation (ESPA) programme. The ESPA programme is funded by the Department for International Development (DFID), the Economic and Social Research Council (ESRC), and the Natural Environment Research Council (NERC)

Genetic diversity and low stratification of the population of the United Arab Emirates

© Copyright © 2020 Tay, Henschel, Daw Elbait and Al Safar. With high consanguinity rates on the Arabian Peninsula, it would not have been unexpected if the population of the United Arab Emirates (UAE) was shown to be relatively homogenous. However, this study of 1000 UAE nationals provided a contrasting perspective, one of a relatively heterogeneous population. Located at the apex of Europe, Asia, and Africa, the observed diversity could be explained by a plethora of migration patterns since the first Out-of-Africa movement. A strategy to explore the extent of genetic variation of the population of the UAE is presented. The first step involved a comprehensive population stratification study that was instructive for subsequent whole genome sequencing (WGS) of suitable representatives (which is described elsewhere). When these UAE data were compared to previous smaller studies from the region, the findings were consistent with a population that is a diverse and admixed group of people. However, rather than sharp and distinctive clusters, cluster analysis reveals low levels of stratification throughout the population. UAE emirates exhibit high within-Emirate-distance/among-Emirate distance ratios. Supervised admixture analysis showed a continuous gradient of ancestral populations, suggesting that admixture on the south eastern tip of the Arabian Peninsula occurred gradually. When visualized using a unique technique that combined admixture ratios and principal component analysis (PCA), unappreciated diversity was revealed while mitigating projection bias of conventional PCA. We observe low population stratification in the UAE in terms of homozygosity versus separation cluster coefficients. This holds for the UAE in a global context as well as for isolated cluster analysis of the Emirati birthplaces. However, the subtle clustering observed in the Emirates reflects geographic proximity and historic migration events. The analytical strategy used here highlights the complementary nature of data from genotype array and WGS for anthropological studies. Specifically, genotype array data were instructive to select representative subjects for WGS. Furthermore, from the 2.3 million allele frequencies obtained from genotype arrays, we identified 46,481 loci with allele frequencies that were significantly different with respect to other world populations. This comparison of allele frequencies facilitates variant prioritization in common diseases. In addition, these loci bear great potential as biomarkers in anthropological and forensic studies

A population-specific major allele reference genome from the United Arab Emirates population

The ethnic composition of the population of a country contributes to the uniqueness of each national DNA sequencing project and, ideally, individual reference genomes are required to reduce the confounding nature of ethnic bias. This work represents a representative Whole Genome Sequencing effort of an understudied population. Specifically, high coverage consensus sequences from 120 whole genomes and 33 whole exomes were used to construct the first ever population specific major allele reference genome for the United Arab Emirates (UAE). When this was applied and compared to the archetype hg19 reference, assembly of local Emirati genomes was reduced by ∼19% (i.e., some 1 million fewer calls). In compiling the United Arab Emirates Reference Genome (UAERG), sets of annotated 23,038,090 short (novel: 1,790,171) and 137,713 structural (novel: 8,462) variants; their allele frequencies (AFs) and distribution across the genome were identified. Population-specific genetic characteristics including loss-of-function variants, admixture, and ancestral haplogroup distribution were identified and reported here. We also detect a strong correlation between F and admixture components in the UAE. This baseline study was conceived to establish a high-quality reference genome and a genetic variations resource to enable the development of regional population specific initiatives and thus inform the application of population studies and precision medicine in the UAE. S

Whole genome sequencing of four representatives from the admixed population of the United Arab Emirates

© Copyright © 2020 Daw Elbait, Henschel, Tay and Al Safar. Whole genome sequences (WGS) of four nationals of the United Arab Emirates (UAE) at an average coverage of 33X have been completed and described. The selection of suitable subpopulation representatives was informed by a preceding comprehensive population structure analysis. Representatives were chosen based on their central location within the subpopulation on a principal component analysis (PCA) and the degree to which they were admixed. Novel genomic variations among the different subgroups of the UAE population are reported here. Specifically, the WGS analysis identified 4,161,067–4,798,806 variants in the four individual samples, where approximately 80% were single nucleotide polymorphisms (SNPs) and 20% were insertions or deletions (indels). An average of 2.75% was found to be novel variants according to dbSNP (build 151). This is the first report of structural variants (SV) from WGS data from UAE nationals. There were 15,677–20,339 called SVs, of which around 13.5% were novel. The four samples shared 1,399,178 variants, each with distinct variants as follows: 1,085,524 (for the individual denoted as UAE S011), 1,228,559 (UAE S012), 791,072 (UAE S013), and 906,818 (UAE S014). These results show a previously unappreciated population diversity in the region. The synergy of WGS and genotype array data was demonstrated through variant annotation of the former using 2.3 million allele frequencies for the local population derived from the latter technology platform. This novel approach of combining breadth and depth of array and WGS technologies has guided the choice of population genetic representatives and provides complementary, regionalized allele frequency annotation to new genomes comprising millions of loci

Mean field baryon magnetic moments and sumrules

New developments have spurred interest in magnetic moments ($\mu$-s) of baryons. The measurement of some of the decuplet $\mu$-s and the findings of new sumrules from various methods are partly responsible for this renewed interest. Our model, inspired by large colour approximation, is a relativistic self consistent mean field description with a modified Richardson potential and is used to describe the $\mu$-s and masses of all baryons with up (u), down (d) and strange (s) quarks. We have also checked the validity of the Franklin sumrule (referred to as CGSR in the literature) and sumrules of Luty, March-Russell and White. We found that our result for sumrules matches better with experiment than the non-relativistic quark model prediction. We have also seen that quark magnetic moments depend on the baryon in which they belong while the naive quark model expects them to be constant.Comment: 7 pages, no figure, uses epl.cl

Retrospective model-based inference guides model-free credit assignment

An extensive reinforcement learning literature shows that organisms assign credit efficiently, even under conditions of state uncertainty. However, little is known about credit-assignment when state uncertainty is subsequently resolved. Here, we address this problem within the framework of an interaction between model-free (MF) and model-based (MB) control systems. We present and support experimentally a theory of MB retrospective-inference. Within this framework, a MB system resolves uncertainty that prevailed when actions were taken thus guiding an MF credit-assignment. Using a task in which there was initial uncertainty about the lotteries that were chosen, we found that when participants’ momentary uncertainty about which lottery had generated an outcome was resolved by provision of subsequent information, participants preferentially assigned credit within a MF system to the lottery they retrospectively inferred was responsible for this outcome. These findings extend our knowledge about the range of MB functions and the scope of system interactions

Calculation of Elastic Green's Functions for Lattices with Cavities

In this Brief Report, we present an algorithm for calculating the elastic Lattice Greens Function of a regular lattice, in which defects are created by removing lattice points. The method is computationally efficient, since the required matrix operations are on matrices that scale with the size of the defect subspace, and not with the size of the full lattice. This method allows the treatment of force fields with multi-atom interactions.Comment: 3 pages. RevTeX, using epsfig.sty. One figur

Understanding visual map formation through vortex dynamics of spin Hamiltonian models

The pattern formation in orientation and ocular dominance columns is one of the most investigated problems in the brain. From a known cortical structure, we build spin-like Hamiltonian models with long-range interactions of the Mexican hat type. These Hamiltonian models allow a coherent interpretation of the diverse phenomena in the visual map formation with the help of relaxation dynamics of spin systems. In particular, we explain various phenomena of self-organization in orientation and ocular dominance map formation including the pinwheel annihilation and its dependency on the columnar wave vector and boundary conditions.Comment: 4 pages, 15 figure

Atomistic modelling of large-scale metal film growth fronts

We present simulations of metallization morphologies under ionized sputter deposition conditions, obtained by a new theoretical approach. By means of molecular dynamics simulations using a carefully designed interaction potential, we analyze the surface adsorption, reflection, and etching reactions taking place during Al physical vapor deposition, and calculate their relative probability. These probabilities are then employed in a feature-scale cellular-automaton simulator, which produces calculated film morphologies in excellent agreement with scanning-electron-microscopy data on ionized sputter deposition.Comment: RevTeX 4 pages, 2 figure