The South Asian genome

Genetics of disease Microarrays Variant genotypes Population genetics Sequence alignment AllelesThe genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.Whole genome sequencing to discover genetic variants underlying type-2 diabetes, coronary heart disease and related phenotypes amongst Indian Asians. Imperial College Healthcare NHS Trust cBRC 2011-13 (JS Kooner [PI], JC Chambers)

Accurate calibration of test mass displacement in the LIGO interferometers

We describe three fundamentally different methods we have applied to calibrate the test mass displacement actuators to search for systematic errors in the calibration of the LIGO gravitational-wave detectors. The actuation frequencies tested range from 90 Hz to 1 kHz and the actuation amplitudes range from 1e-6 m to 1e-18 m. For each of the four test mass actuators measured, the weighted mean coefficient over all frequencies for each technique deviates from the average actuation coefficient for all three techniques by less than 4%. This result indicates that systematic errors in the calibration of the responses of the LIGO detectors to differential length variations are within the stated uncertainties.Comment: 10 pages, 6 figures, submitted on 31 October 2009 to Classical and Quantum Gravity for the proceedings of 8th Edoardo Amaldi Conference on Gravitational Wave

Scaling the nexus: towards integrated frameworks for analysing water, energy and food

The emergence of the water-energy-food (WEF) nexus concept following the 2011 Bonn Nexus Conference has resulted in a change to the way we perceive our natural resources. Global pressures such as climate change, and population growth have highlighted the fragility of our WEF systems, necessitating integrated solutions across multiple scales and levels. Whilst a number of frameworks and analytical tools have been developed since 2011, a comprehensive WEF nexus tool remains elusive, hindered in part by our limited data and understanding of the interdependencies and connections across the WEF systems. To achieve this, the community of academics, practitioners and policy-makers invested in WEF nexus research are addressing several critical areas that currently remain as barriers. Firstly, the plurality of scales (e.g., spatial, temporal, institutional, jurisdictional) necessitates a more comprehensive effort to assess interdependencies between water, energy and food, from household to institutional and national levels. Secondly, and closely related to scale, a lack of available data often hinders our ability to quantify physical stocks and flows of resources. In this paper, we elucidate many of the challenges that have arisen across nexus research, including the impact of multiple scales in operation across the nexus, and concomitantly, what impact these scales have on data accessibility. We review some of the critical frameworks and tools that are applied by nexus researchers and discuss some of the steps required to develop from nexus thinking to an operationalizable concept, with a consistent focus on scale and data availability

Search for gravitational-wave bursts in LIGO data from the fourth science run

The fourth science run of the LIGO and GEO 600 gravitational-wave detectors, carried out in early 2005, collected data with significantly lower noise than previous science runs. We report on a search for short-duration gravitational-wave bursts with arbitrary waveform in the 64-1600 Hz frequency range appearing in all three LIGO interferometers. Signal consistency tests, data quality cuts, and auxiliary-channel vetoes are applied to reduce the rate of spurious triggers. No gravitational-wave signals are detected in 15.5 days of live observation time; we set a frequentist upper limit of 0.15 per day (at 90% confidence level) on the rate of bursts with large enough amplitudes to be detected reliably. The amplitude sensitivity of the search, characterized using Monte Carlo simulations, is several times better than that of previous searches. We also provide rough estimates of the distances at which representative supernova and binary black hole merger signals could be detected with 50% efficiency by this analysis.Comment: Corrected amplitude sensitivities (7% change on average); 30 pages, submitted to Classical and Quantum Gravit

Gravitational Waves From Known Pulsars: Results From The Initial Detector Era

We present the results of searches for gravitational waves from a large selection of pulsars using data from the most recent science runs (S6, VSR2 and VSR4) of the initial generation of interferometric gravitational wave detectors LIGO (Laser Interferometric Gravitational-wave Observatory) and Virgo. We do not see evidence for gravitational wave emission from any of the targeted sources but produce upper limits on the emission amplitude. We highlight the results from seven young pulsars with large spin-down luminosities. We reach within a factor of five of the canonical spin-down limit for all seven of these, whilst for the Crab and Vela pulsars we further surpass their spin-down limits. We present new or updated limits for 172 other pulsars (including both young and millisecond pulsars). Now that the detectors are undergoing major upgrades, and, for completeness, we bring together all of the most up-to-date results from all pulsars searched for during the operations of the first-generation LIGO, Virgo and GEO600 detectors. This gives a total of 195 pulsars including the most recent results described in this paper.United States National Science FoundationScience and Technology Facilities Council of the United KingdomMax-Planck-SocietyState of Niedersachsen/GermanyAustralian Research CouncilInternational Science Linkages program of the Commonwealth of AustraliaCouncil of Scientific and Industrial Research of IndiaIstituto Nazionale di Fisica Nucleare of ItalySpanish Ministerio de Economia y CompetitividadConselleria d'Economia Hisenda i Innovacio of the Govern de les Illes BalearsNetherlands Organisation for Scientific ResearchPolish Ministry of Science and Higher EducationFOCUS Programme of Foundation for Polish ScienceRoyal SocietyScottish Funding CouncilScottish Universities Physics AllianceNational Aeronautics and Space AdministrationOTKA of HungaryLyon Institute of Origins (LIO)National Research Foundation of KoreaIndustry CanadaProvince of Ontario through the Ministry of Economic Development and InnovationNational Science and Engineering Research Council CanadaCarnegie TrustLeverhulme TrustDavid and Lucile Packard FoundationResearch CorporationAlfred P. Sloan FoundationAstronom

First joint search for gravitational-wave bursts in LIGO and GEO600 data

We present the results of the first joint search for gravitational-wave bursts by the LIGO and GEO600 detectors. We search for bursts with characteristic central frequencies in the band 768 to 2048 Hz in the data acquired between the 22nd of February and the 23rd of March, 2005 (fourth LSC Science Run - S4). We discuss the inclusion of the GEO600 data in the Waveburst-CorrPower pipeline that first searches for coincident excess power events without taking into account differences in the antenna responses or strain sensitivities of the various detectors. We compare the performance of this pipeline to that of the coherent Waveburst pipeline based on the maximum likelihood statistic. This likelihood statistic is derived from a coherent sum of the detector data streams that takes into account the antenna patterns and sensitivities of the different detectors in the network. We find that the coherentWaveburst pipeline is sensitive to signals of amplitude 30 - 50% smaller than the Waveburst-CorrPower pipeline. We perform a search for gravitational-wave bursts using both pipelines and find no detection candidates in the S4 data set when all four instruments were operating stably.Comment: 30 pages, 8 figure

A Joint Search for Gravitational Wave Bursts with AURIGA and LIGO

The first simultaneous operation of the AURIGA detector and the LIGO observatory was an opportunity to explore real data, joint analysis methods between two very different types of gravitational wave detectors: resonant bars and interferometers. This paper describes a coincident gravitational wave burst search, where data from the LIGO interferometers are cross-correlated at the time of AURIGA candidate events to identify coherent transients. The analysis pipeline is tuned with two thresholds, on the signal-to-noise ratio of AURIGA candidate events and on the significance of the cross-correlation test in LIGO. The false alarm rate is estimated by introducing time shifts between data sets and the network detection efficiency is measured with simulated signals with power in the narrower AURIGA band. In the absence of a detection, we discuss how to set an upper limit on the rate of gravitational waves and to interpret it according to different source models. Due to the short amount of analyzed data and to the high rate of non-Gaussian transients in the detectors noise at the time, the relevance of this study is methodological: this was the first joint search for gravitational wave bursts among detectors with such different spectral sensitivity and the first opportunity for the resonant and interferometric communities to unify languages and techniques in the pursuit of their common goal.Comment: 18 pages, IOP, 12 EPS figure

First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data

Spinning neutron stars asymmetric with respect to their rotation axis are potential sources of continuous gravitational waves for ground-based interferometric detectors. In the case of known pulsars a fully coherent search, based on matched filtering, which uses the position and rotational parameters obtained from electromagnetic observations, can be carried out. Matched filtering maximizes the signalto- noise (SNR) ratio, but a large sensitivity loss is expected in case of even a very small mismatch between the assumed and the true signal parameters. For this reason, narrow-band analysis methods have been developed, allowing a fully coherent search for gravitational waves from known pulsars over a fraction of a hertz and several spin-down values. In this paper we describe a narrow-band search of 11 pulsars using data from Advanced LIGO’s first observing run. Although we have found several initial outliers, further studies show no significant evidence for the presence of a gravitational wave signal. Finally, we have placed upper limits on the signal strain amplitude lower than the spin-down limit for 5 of the 11 targets over the bands searched; in the case of J1813-1749 the spin-down limit has been beaten for the first time. For an additional 3 targets, the median upper limit across the search bands is below the spin-down limit. This is the most sensitive narrow-band search for continuous gravitational waves carried out so far