Archeological Significance Testing at 41BX17/271, the Granberg Site: A Multi-Component Site along the Salado Creek in Bexar County, Texas

The Center for Archaeological Research (CAR) of The University of Texas at San Antonio conducted archeological significance testing at 41BX17, the Granberg Site, from January to March 2006. The testing was conducted for the Texas Department of Transportation, Environmental Affairs Division (TxDOT-ENV). The Granberg Site sits on the eastern flood terrace of the Salado Creek south of Loop 410 in San Antonio, Bexar County, Texas. Planned road improvements including installation of a storm sewer line and a water main prompted the need to assess whether (1) cultural deposits including human remains still exist after previous testing and (2) if the deposits contribute to the site’s National Register of Historic Places eligibility. The archeological work was conducted under Texas Antiquities Permit No. 4010. Steve A. Tomka served as Principal Investigator and Jennifer Thompson served as Project Archeologist. Fieldwork included mechanical auger boring and backhoe trenching to determine the horizontal extent of the site boundaries within the median of Loop 410 eastbound. Sixteen 1-x-1-m units were excavated to determine the distribution and integrity of the cultural deposits and to locate any possible burials that may still exist at the site. Materials recovered included burned rock features, chipped stone artifacts, animal bone, snail and mussel shell and charred plant remains. The distribution of the artifacts, the geomorphic investigations, the radiocarbon assays, and temporally diagnostic artifacts indicate the presence of Middle and Late Archaic archeological materials with good stratigraphic integrity. The Granberg Site was determined to be ineligible for the National Register of Historic Places. Following the completion of eligibility testing efforts, the TxDOT directed the CAR to develop a research design linking the data recovered from the various excavations at the Granberg Site with research goals. The CAR developed the research design (Munoz et al. 2007) under Work Authorization No. 57513SA005 with Cynthia M. Munoz serving as Project Archeologist. At roughly the time of the research design implementation, the CAR was the recipient of a donation of a collection of commingled human skeletal remains recovered from the Granberg Site. These remains were recovered from 41BX17/271 in 1962 by Harvey Kohnitz, an avocational archeologist, without knowledge or permission from the Texas Highway Department. The remains were stored at the Kohnitz home until his son, Mark Kohnitz, donated them to the CAR in 2007. An osteological analysis was conducted at the CAR laboratory during February 2008 for TxDOT, under Work Authorization No. 57513SA005 Supplemental Work Authorization No. 4. The results of this analysis are reported in Appendix H of this report. The commingled remains will be curated the CAR and all required documents, including an inventory, will be submitted to the National Park Service National NAGPRA Program to fulfill all obligations pertaining to the NAGPRA laws. All artifacts collected during this project and all project-associated documentation are permanently curated at the CAR according to Texas Historical Commission guidelines

In-situ characterization of the Hamamatsu R5912-HQE photomultiplier tubes used in the DEAP-3600 experiment

The Hamamatsu R5912-HQE photomultiplier-tube (PMT) is a novel high-quantum efficiency PMT. It is currently used in the DEAP-3600 dark matter detector and is of significant interest for future dark matter and neutrino experiments where high signal yields are needed. We report on the methods developed for in-situ characterization and monitoring of DEAP's 255 R5912-HQE PMTs. This includes a detailed discussion of typical measured single-photoelectron charge distributions, correlated noise (afterpulsing), dark noise, double, and late pulsing characteristics. The characterization is performed during the detector commissioning phase using laser light injected through a light diffusing sphere and during normal detector operation using LED light injected through optical fibres

Measurement of the scintillation time spectra and pulse-shape discrimination of low-energy beta and nuclear recoils in liquid argon with DEAP-1

The DEAP-1 low-background liquid argon detector was used to measure scintillation pulse shapes of electron and nuclear recoil events and to demonstrate the feasibility of pulse-shape discrimination (PSD) down to an electron-equivalent energy of 20 keV. In the surface dataset using a triple-coincidence tag we found the fraction of beta events that are misidentified as nuclear recoils to be $<1.4\times 10^{-7}$ (90% C.L.) for energies between 43-86 keVee and for a nuclear recoil acceptance of at least 90%, with 4% systematic uncertainty on the absolute energy scale. The discrimination measurement on surface was limited by nuclear recoils induced by cosmic-ray generated neutrons. This was improved by moving the detector to the SNOLAB underground laboratory, where the reduced background rate allowed the same measurement with only a double-coincidence tag. The combined data set contains $1.23\times10^8$ events. One of those, in the underground data set, is in the nuclear-recoil region of interest. Taking into account the expected background of 0.48 events coming from random pileup, the resulting upper limit on the electronic recoil contamination is $<2.7\times10^{-8}$ (90% C.L.) between 44-89 keVee and for a nuclear recoil acceptance of at least 90%, with 6% systematic uncertainty on the absolute energy scale. We developed a general mathematical framework to describe PSD parameter distributions and used it to build an analytical model of the distributions observed in DEAP-1. Using this model, we project a misidentification fraction of approx. $10^{-10}$ for an electron-equivalent energy threshold of 15 keV for a detector with 8 PE/keVee light yield. This reduction enables a search for spin-independent scattering of WIMPs from 1000 kg of liquid argon with a WIMP-nucleon cross-section sensitivity of $10^{-46}$ cm$^2$, assuming negligible contribution from nuclear recoil backgrounds.Comment: Accepted for publication in Astroparticle Physic

Radon backgrounds in the DEAP-1 liquid-argon-based Dark Matter detector

The DEAP-1 \SI{7}{kg} single phase liquid argon scintillation detector was operated underground at SNOLAB in order to test the techniques and measure the backgrounds inherent to single phase detection, in support of the \mbox{DEAP-3600} Dark Matter detector. Backgrounds in DEAP are controlled through material selection, construction techniques, pulse shape discrimination and event reconstruction. This report details the analysis of background events observed in three iterations of the DEAP-1 detector, and the measures taken to reduce them. The $^{222}$Rn decay rate in the liquid argon was measured to be between 16 and \SI{26}{\micro\becquerel\per\kilogram}. We found that the background spectrum near the region of interest for Dark Matter detection in the DEAP-1 detector can be described considering events from three sources: radon daughters decaying on the surface of the active volume, the expected rate of electromagnetic events misidentified as nuclear recoils due to inefficiencies in the pulse shape discrimination, and leakage of events from outside the fiducial volume due to imperfect position reconstruction. These backgrounds statistically account for all observed events, and they will be strongly reduced in the DEAP-3600 detector due to its higher light yield and simpler geometry

Are quantitative trait-dependent sampling designs cost-effective for analysis of rare and common variants?

Use of trait-dependent sampling designs in whole-genome association studies of sequence data can reduce total sequencing costs with modest losses of statistical efficiency. In a quantitative trait (QT) analysis of data from the Genetic Analysis Workshop 17 mini-exome for unrelated individuals in the Asian subpopulation, we investigate alternative designs that sequence only 50% of the entire cohort. In addition to a simple random sampling design, we consider extreme-phenotype designs that are of increasing interest in genetic association analysis of QTs, especially in studies concerned with the detection of rare genetic variants. We also evaluate a novel sampling design in which all individuals have a nonzero probability of being selected into the sample but in which individuals with extreme phenotypes have a proportionately larger probability. We take differential sampling of individuals with informative trait values into account by inverse probability weighting using standard survey methods which thus generalizes to the source population. In replicate 1 data, we applied the designs in association analysis of Q1 with both rare and common variants in the FLT1 gene, based on knowledge of the generating model. Using all 200 replicate data sets, we similarly analyzed Q1 and Q4 (which is known to be free of association with FLT1) to evaluate relative efficiency, type I error, and power. Simulation study results suggest that the QT-dependent selection designs generally yield greater than 50% relative efficiency compared to using the entire cohort, implying cost-effectiveness of 50% sample selection and worthwhile reduction of sequencing costs

Search for dark matter with a 231-day exposure of liquid argon using DEAP-3600 at SNOLAB

DEAP-3600 is a single-phase liquid argon (LAr) direct-detection dark matter experiment, operating 2 km underground at SNOLAB (Sudbury, Canada). The detector consists of 3279 kg of LAr contained in a spherical acrylic vessel. This paper reports on the analysis of a 758  tonne⋅day exposure taken over a period of 231 live-days during the first year of operation. No candidate signal events are observed in the WIMP-search region of interest, which results in the leading limit on the WIMP-nucleon spin-independent cross section on a LAr target of 3.9×10−45  cm2 (1.5×10−44  cm2) for a 100  GeV/c2 (1  TeV/c2) WIMP mass at 90% C.L. In addition to a detailed background model, this analysis demonstrates the best pulse-shape discrimination in LAr at threshold, employs a Bayesian photoelectron-counting technique to improve the energy resolution and discrimination efficiency, and utilizes two position reconstruction algorithms based on the charge and photon detection time distributions observed in each photomultiplier tube

Identification of multiple rare variants associated with a disease

Identifying rare variants that are responsible for complex disease has been promoted by advances in sequencing technologies. However, statistical methods that can handle the vast amount of data generated and that can interpret the complicated relationship between disease and these variants have lagged. We apply a zero-inflated Poisson regression model to take into account the excess of zeros caused by the extremely low frequency of the 24,487 exonic variants in the Genetic Analysis Workshop 17 data. We grouped the 697 subjects in the data set as Europeans, Asians, and Africans based on principal components analysis and found the total number of rare variants per gene for each individual. We then analyzed these collapsed variants based on the assumption that rare variants are enriched in a group of people affected by a disease compared to a group of unaffected people. We also tested the hypothesis with quantitative traits Q1, Q2, and Q4. Analyses performed on the combined 697 individuals and on each ethnic group yielded different results. For the combined population analysis, we found that UGT1A1, which was not part of the simulation model, was associated with disease liability and that FLT1, which was a causal locus in the simulation model, was associated with Q1. Of the causal loci in the simulation models, FLT1 and KDR were associated with Q1 and VNN1 was correlated with Q2. No significant genes were associated with Q4. These results show the feasibility and capability of our new statistical model to detect multiple rare variants influencing disease risk

The Dopamine D3 Receptor Knockout Mouse Mimics Aging-Related Changes in Autonomic Function and Cardiac Fibrosis

Blood pressure increases with age, and dysfunction of the dopamine D3 receptor has been implicated in the pathogenesis of hypertension. To evaluate the role of the D3 receptor in aging-related hypertension, we assessed cardiac structure and function in differently aged (2 mo, 1 yr, 2 yr) wild type (WT) and young (2 mo) D3 receptor knockout mice (D3KO). In WT, systolic and diastolic blood pressures and rate-pressure product (RPP) significantly increased with age, while heart rate significantly decreased. Blood pressure values, heart rate and RPP of young D3KO were significantly elevated over age-matched WT, but similar to those of the 2 yr old WT. Echocardiography revealed that the functional measurements of ejection fraction and fractional shortening decreased significantly with age in WT and that they were significantly smaller in D3KO compared to young WT. Despite this functional change however, cardiac morphology remained similar between the age-matched WT and D3KO. Additional morphometric analyses confirmed an aging-related increase in left ventricle (LV) and myocyte cross-sectional areas in WT, but found no difference between age-matched young WT and D3KO. In contrast, interstitial fibrosis, which increased with age in WT, was significantly elevated in the D3KO over age-matched WT, and similar to 2 yr old WT. Western analyses of myocardial homogenates revealed significantly increased levels of pro- and mature collagen type I in young D3KO. Column zymography revealed that activities of myocardial MMP-2 and MMP-9 increased with age in WTs, but in D3KO, only MMP-9 activity was significantly increased over age-matched WTs. Our data provide evidence that the dopamine D3 receptor has a critical role in the emergence of aging-related cardiac fibrosis, remodeling, and dysfunction