DESI Commissioning Instrument Metrology

The Dark Energy Spectroscopic Instrument (DESI) is under construction to measure the expansion history of the Universe using the Baryon Acoustic Oscillation technique. The spectra of 35 million galaxies and quasars over 14000 sq deg will be measured during the life of the experiment. A new prime focus corrector for the KPNO Mayall telescope will deliver light to 5000 fiber optic positioners. The fibers in turn feed ten broad-band spectrographs. We will describe the methods and results for the commissioning instrument metrology program. The primary goals of this program are to calculate the transformations and further develop the systems that will place fibers within 5um RMS of the target positions. We will use the commissioning instrument metrology program to measure the absolute three axis Cartesian coordinates of the five CCDs and 22 illuminated fiducials on the commissioning instrument

Invest to Save: Report and Recommendations of the NSF-DELOS Working Group on Digital Archiving and Preservation

Digital archiving and preservation are important areas for research and development, but there is no agreed upon set of priorities or coherent plan for research in this area. Research projects in this area tend to be small and driven by particular institutional problems or concerns. As a consequence, proposed solutions from experimental projects and prototypes tend not to scale to millions of digital objects, nor do the results from disparate projects readily build on each other. It is also unclear whether it is worthwhile to seek general solutions or whether different strategies are needed for different types of digital objects and collections. The lack of coordination in both research and development means that there are some areas where researchers are reinventing the wheel while other areas are neglected. Digital archiving and preservation is an area that will benefit from an exercise in analysis, priority setting, and planning for future research. The WG aims to survey current research activities, identify gaps, and develop a white paper proposing future research directions in the area of digital preservation. Some of the potential areas for research include repository architectures and inter-operability among digital archives; automated tools for capture, ingest, and normalization of digital objects; and harmonization of preservation formats and metadata. There can also be opportunities for development of commercial products in the areas of mass storage systems, repositories and repository management systems, and data management software and tools.

Demographic characteristics of exploited tropical lutjanids: a comparative analysis

Demographic parameters from seven exploited coral reef lutjanid species were compared as a case study of the implications of intrafamily variation in life histories for multispecies harvest management. Modal lengths varied by 4 cm among four species (Lutjanus fulviflamma, L. vitta, L. carponotatus, L. adetii), which were at least 6 cm smaller than the modal lengths of the largest species (L. gibbus, Symphorus nematophorus, Aprion virescens). Modal ages, indicating ages of full selection to fishing gear, were 10 years or less for all species, but maximum ages ranged from 12 (L. gibbus) to 36 years (S. nematophorus). Each species had a unique growth pattern, with differences in length-at-age and mean asymptotic fork length (L∞), but smaller species generally grew fast during the first 1–2 years of life and larger species grew more slowly over a longer period. Total mortality rates varied among species; L. gibbus had the highest mortality and L. fulviflamma, the lowest mortality. The variability in life history strategies of these tropical lutjanids makes generalizations about lutjanid life histories difficult, but the fact that all seven had characteristics that would make them particularly vulnerable to fishing indicates that harvest of tropical lutjanids should be managed with caution

Large-scale analysis of the SDSS-III DR8 photometric luminous galaxies angular correlation function

We analyse the large-scale angular correlation function (ACF) of the CMASS luminous galaxies (LGs), a photometric-redshift catalogue based on the Data Release 8 (DR8) of the Sloan Digital Sky Survey-III. This catalogue contains over $600 \, \, 000$ LGs in the range $0.45 \leq z \leq 0.65$, which was split into four redshift shells of constant width. First, we estimate the constraints on the redshift-space distortion (RSD) parameters $b\sigma_8$ and $f\sigma_8$, where $b$ is the galaxy bias, $f$ the growth rate and $\sigma_8$ is the normalization of the perturbations, finding that they vary appreciably among different redshift shells, in agreement with previous results using DR7 data. When assuming constant RSD parameters over the survey redshift range, we obtain $f\sigma_8 = 0.69 \pm 0.21$, which agrees at the $1.5\sigma$ level with Baryon Oscillation Spectroscopic Survey DR9 spectroscopic results. Next, we performed two cosmological analyses, where relevant parameters not fitted were kept fixed at their fiducial values. In the first analysis, we extracted the baryon acoustic oscillation peak position for the four redshift shells, and combined with the sound horizon scale from 7-year \textit{Wilkinson Microwave Anisotropy Probe} $(WMAP7)$ to produce the constraints $\Omega_{m}=0.249 \pm 0.031$ and $w=-0.885 \pm 0.145$. In the second analysis, we used the ACF full shape information to constrain cosmology using real data for the first time, finding $\Omega_{m} = 0.280 \pm 0.022$ and $f_b = \Omega_b/\Omega_m = 0.211 \pm 0.026$. These results are in good agreement with $WMAP7$ findings, showing that the ACF can be efficiently applied to constrain cosmology in future photometric galaxy surveys.Comment: MNRAS accepted. Minor corrections to match publish versio

Networks and the epidemiology of infectious disease

The science of networks has revolutionised research into the dynamics of interacting elements. It could be argued that epidemiology in particular has embraced the potential of network theory more than any other discipline. Here we review the growing body of research concerning the spread of infectious diseases on networks, focusing on the interplay between network theory and epidemiology. The review is split into four main sections, which examine: the types of network relevant to epidemiology; the multitude of ways these networks can be characterised; the statistical methods that can be applied to infer the epidemiological parameters on a realised network; and finally simulation and analytical methods to determine epidemic dynamics on a given network. Given the breadth of areas covered and the ever-expanding number of publications, a comprehensive review of all work is impossible. Instead, we provide a personalised overview into the areas of network epidemiology that have seen the greatest progress in recent years or have the greatest potential to provide novel insights. As such, considerable importance is placed on analytical approaches and statistical methods which are both rapidly expanding fields. Throughout this review we restrict our attention to epidemiological issues

Multi-tracer extension of the halo model:probing quenching and conformity in eBOSS

We develop a new Multi-Tracer Halo Occupation Distribution (\texttt{MTHOD}) framework for the galaxy distribution and apply it to the extended Baryon Oscillation Spectroscopic Survey (eBOSS) final data between $z=0.7-1.1$. We obtain a best fit \mthod\, for each tracer and describe the host halo properties of these galaxies. The mean halo masses for LRGs, ELGs and QSOs are found to be 1.9 \times 10^{13} \msolaroh, 1.1 \times 10^{12} \msolaroh and 5 \times 10^{12} \msolaroh respectively in the eBOSS data. We use the \texttt{MTHOD} framework to create mock galaxy catalogues and predict auto- and cross-correlation functions for all the tracers. Comparing these results with data, we investigate galactic conformity, the phenomenon whereby the properties of neighbouring galaxies are mutually correlated in a manner that is not captured by the basic halo model. We detect \textsl{1-halo} conformity at more than 3$\sigma$ statistical significance, while obtaining upper limit on \textsl{2-halo} conformity. We also look at the environmental dependence of the galaxy quenching efficiency and find that halo mass driven quenching successfully explains the behaviour in high density regions, but it fails to describe the quenching efficiency in low density regions. In particular, we show that the quenching efficiency in low density filaments is higher in the observed data, as compared to the prediction of the \mthod\ with halo mass driven quenching. The mock galaxy catalogue constructed in this paper is publicly available on https://www.roe.ac.uk/~salam/MTHOD/ .Comment: 17 pages, 12 figures, the software and mock catalogue should be made available through: https://www.roe.ac.uk/~salam/MTHOD/ , Accepted for publication in MNRA

Quasars at intermediate redshift are not special; but they are often satellites

Understanding the links between the activity of supermassive black holes (SMBH) at the centres of galaxies and their host dark matter haloes is a key question in modern astrophysics. The final data release of the SDSS-IV eBOSS provides the largest contemporary spectroscopic sample of galaxies and QSOs. Using this sample and covering the redshift interval $z=0.7-1.1$, we have measured the clustering properties of the eBOSS QSOs, Emission Line Galaxies (ELGs) and Luminous Red Galaxies (LRGs). We have also measured the fraction of QSOs as a function of the overdensity defined by the galaxy population. Using these measurements, we investigate how QSOs populate and sample the galaxy population, and how the host dark-matter haloes of QSOs sample the underlying halo distribution. We find that the probability of a galaxy hosting a QSO is independent of the host dark matter halo mass of the galaxy. We also find that about 60\% of eBOSS QSOs are hosted by LRGs and about 20-40\% of QSOs are hosted by satellite galaxies. We find a slight preference for QSOs to populate satellite galaxies over central galaxies. This is connected to the host halo mass distribution of different types of galaxies. Based on our analysis, QSOs should be hosted by a very broad distribution of haloes, and their occurrence should be modulated only by the efficiency of galaxy formation processes.Comment: 15 pages, 6 Figures, Data and code from this analysis is available at https://www.roe.ac.uk/~salam/GQOD/ , submitted to MNRAS, comments and suggestions are welcom

Transition between terrestrial-submerged walking and swimming revealed by Early Permian amphibian trackways and a new proposal for the nomenclature of compound trace fossils

Exceptionally preserved Early Permian tetrapod trackways from the Orobic Basin (Central-Western Southern Alps) offer a unique opportunity to investigate in detail locomotion in fossil vertebrates that lived on continental European landmasses. Herein are reported the results of a study on several tetrapod trackways that display a large variety of behavioral, gait and substrate related extramorphologies. They clearly document the transition from terrestrial-underwater walking to swimming and are assigned to the compound ichnotaxon Batrachichnus C Lunichnium. The use of the "C" symbol is here introduced for the first time as nomenclatural indication of a Compound trace. Producers were probably small-sized temnospondyl or lepospondyl (microsaurs) amphibians. Comparisons with living urodelan anatomy and mechanics provide evidence for conservatism of locomotor mechanics in evolutionary history among amphibians. The derived model for locomotor kinematics in Early Permian amphibians provides a reference for interpreting transitional land-to-water trackways. The shift from walking to swimming behavior in early tetrapods, as in extant urodelan amphibians, is described as a complex balance between different dynamics

Limitations in the Use of Archived Vent Mussel Samples to Assess Genetic Connectivity Among Seafloor Massive Sulfide Deposits: A Case Study with Implications for Environmental Management

Genetic connectivity studies can inform the design of mitigation strategies used in environmental management. However, the expense of developing species-specific molecular markers and collecting samples at appropriate spatial and temporal scales can be prohibitive. Using archived material and existing molecular markers may provide a cost-effective way to assess population connectivity. Genetic connectivity studies are increasingly in demand in the deep sea in response to mounting anthropogenic pressures, including seafloor massive sulfide (SMS) mining. The feasibility of using archived material was assessed using the New Zealand-endemic vent mussel Gigantidas gladius, which inhabits areas licensed for the prospecting phase of SMS mining. Four molecular markers were tested, but only one (mitochondrial COI) provided suitable sequences. Of 942 specimens, only 150 individuals were informative, largely due to poor tissue quality of archived samples. Seven populations spanning the distributional range of G. gladius were assessed. The results indicate that G. gladius has high levels of gene flow among sites 10s to 100s km apart and limited genetic structure. Haplotypic diversity was not equally distributed among populations, with lower diversity for the Macauley Volcano population at the northern extent of the species distribution and greater diversity within central populations. Migrant exchange was also greatest between central populations, with one population at Rumble V Seamount appearing important in terms of maintaining genetic diversity within the Kermadec Volcanic Arc region. However, interpretation of the results should be viewed with caution as small sample sizes may have limited the ability to detect genetic structure. Despite these limitations, mitigation strategies that protect areas of seabed from mining activities should consider the genetic vulnerability of the population at the northern edge of the species’ distribution and the significance of certain central populations