Expanding Predictive Assessment of Northern Bobwhite Covey Calling Rates to Incorporate Regional Effects

Many surveys based on discrete vocalizations make the invalid assumption that individuals present in the survey area are always available for detection (e.g., calling) during the survey period. Northern bobwhites (Colinus virginianus) are known to exhibit variable calling rates, particularly during autumn covey surveys. Adjustment of density and abundance estimates to account for calling rate may increase reliability of population metrics, and may increase our ability to effectively assess conservation management. Two previous independent studies across 4 regions used logistic regression to evaluate effects of weather, time, and density covariates on calling rates of radio-marked autumn bobwhite coveys. Results from these studies varied and there is uncertainty regarding application without further investigation into regional differences in calling rates. We combined these data sets comprising known calling rates of 279 bobwhite coveys in 4 regions (Florida, Missouri, North Carolina, and Tennessee) from 1998 to 2000. Observed calling rates averaged 69% over all sites, and ranged from 56 to 80% in the Florida and Missouri regions, respectively. We used binomial logistic regression to evaluate effects of region, adjacent calling coveys, weekly period, change in barometric pressure, percent cloud cover, temperature, and wind speed on covey calling rates. The top ranking model suggested strong effects of region and number of adjacent coveys on calling probability (P , 0.0001) with 42% model weight relative to other candidate models. Two competing models suggested inclusion of the 6-hr change in barometric pressure (0100 – 0700 hrs) (18% model weight) or weekly period (17% model weight) might also be appropriate. Validation using the best approximating model (region þ adjacent coveys) suggested calling probability estimates were within 6% of the observed calling rate in one region. This suggests the predictive model may provide a valid estimator of calling rate when applied to covey survey data in the appropriate region. However, there is uncertainty regarding application of region-specific model coefficients to survey data outside of these regions. If effects of region are important predictors of calling rate, managers must be cognizant of these prior to adjusting parameter estimates. Further, there is a research need concerning utility and ubiquity of calling rate predictors, particularly for regions that lack known calling rate data

Electrical lithosphere beneath the Kaapvaal craton, southern Africa

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 116 (2011): B04105, doi:10.1029/2010JB007883.A regional-scale magnetotelluric (MT) experiment across the southern African Kaapvaal craton and surrounding terranes, called the Southern African Magnetotelluric Experiment (SAMTEX), has revealed complex structure in the lithospheric mantle. Large variations in maximum resistivity at depths to 200–250 km relate directly to age and tectonic provenance of surface structures. Within the central portions of the Kaapvaal craton are regions of resistive lithosphere about 230 km thick, in agreement with estimates from xenolith thermobarometry and seismic surface wave tomography, but thinner than inferred from seismic body wave tomography. The MT data are unable to discriminate between a completely dry or slightly “damp” (a few hundred parts per million of water) structure within the transitional region at the base of the lithosphere. However, the structure of the uppermost ∼150 km of lithosphere is consistent with enhanced, but still low, conductivities reported for hydrous olivine and orthopyroxene at levels of water reported for Kaapvaal xenoliths. The electrical lithosphere around the Kimberley and Premier diamond mines is thinner than the maximum craton thickness found between Kimberley and Johannesburg/Pretoria. The mantle beneath the Bushveld Complex is highly conducting at depths around 60 km. Possible explanations for these high conductivities include graphite or sulphide and/or iron metals associated with the Bushveld magmatic event. We suggest that one of these conductive phases (most likely melt-related sulphides) could electrically connect iron-rich garnets in a garnet-rich eclogitic composition associated with a relict subduction slab.In addition to the funding and logistical support provided by SAMTEX consortium members, this work is also supported by research grants from the National Science Foundation (EAR‐0309584 and EAR‐0455242 through the Continental Dynamics Program), the Department of Science and Technology, South Africa, and Science Foundation of Ireland (grant 05/RFP/ GEO001)

Evidence for a companion to BM Gem, a silicate carbon star

Balmer and Paschen continuum emission as well as Balmer series lines of P Cygni-type profile from H_gamma through H_23 are revealed in the violet spectra of BM Gem, a carbon star associated with an oxygen-rich circumstellar shell (`silicate carbon star') observed with the high dispersion spectrograph (HDS) on the Subaru telescope. The blue-shifted absorption in the Balmer lines indicates the presence of an outflow, the line of sight velocity of which is at least 400 km s^-1, which is the highest outflow velocity observed to date in a carbon star. We argue that the observed unusual features in BM Gem are strong evidence for the presence of a companion, which should form an accretion disk that gives rise to both an ionized gas region and a high velocity, variable outflow. The estimated luminosity of ~0.2 (0.03-0.6) L_sun for the ionized gas can be maintained by a mass accretion rate to a dwarf companion of ~10^-8 M_sun yr^-1, while ~10^-10 M_sun yr^-1 is sufficient for accretion to a white dwarf companion. These accretion rates are feasible for some detached binary configurations on the basis of the Bond-Hoyle type accretion process. We concluded that the carbon star BM Gem is in a detached binary system with a companion of low mass and low luminosity. However, we are unable to determine whether this companion object is a dwarf or a white dwarf. The upper limits for binary separation are 210 AU and 930 AU for a dwarf and a white dwarf, respectively. We also note that the observed features of BM Gem mimic those of Mira (omi Cet), which may suggest actual similarities in their binary configurations and circumstellar structures.Comment: 11 pages, 2 figures, 1 table, accepted for publication in Ap

Segmentation of plate coupling, fate of subduction fluids, and modes of arc magmatism in Cascadia, inferred from magnetotelluric resistivity

Author Posting. © American Geophysical Union, 2014. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry, Geophysics, Geosystems 15 (2014): 4230–4253, doi:10.1002/2014GC005509.Five magnetotelluric (MT) profiles have been acquired across the Cascadia subduction system and transformed using 2-D and 3-D nonlinear inversion to yield electrical resistivity cross sections to depths of ∼200 km. Distinct changes in plate coupling, subduction fluid evolution, and modes of arc magmatism along the length of Cascadia are clearly expressed in the resistivity structure. Relatively high resistivities under the coasts of northern and southern Cascadia correlate with elevated degrees of inferred plate locking, and suggest fluid- and sediment-deficient conditions. In contrast, the north-central Oregon coastal structure is quite conductive from the plate interface to shallow depths offshore, correlating with poor plate locking and the possible presence of subducted sediments. Low-resistivity fluidized zones develop at slab depths of 35–40 km starting ∼100 km west of the arc on all profiles, and are interpreted to represent prograde metamorphic fluid release from the subducting slab. The fluids rise to forearc Moho levels, and sometimes shallower, as the arc is approached. The zones begin close to clusters of low-frequency earthquakes, suggesting fluid controls on the transition to steady sliding. Under the northern and southern Cascadia arc segments, low upper mantle resistivities are consistent with flux melting above the slab plus possible deep convective backarc upwelling toward the arc. In central Cascadia, extensional deformation is interpreted to segregate upper mantle melts leading to underplating and low resistivities at Moho to lower crustal levels below the arc and nearby backarc. The low- to high-temperature mantle wedge transition lies slightly trenchward of the arc.Phil Wannamaker and Virginie Maris gratefully acknowledge funding by the U.S. National Science Foundation under grants EAR08–43725 and EAR08–38043 through the Earthscope and Geophysics programs. The 2D inversion capability received development support under U.S. Department of Energy contract DE-PS36-04GO94001. Rob Evans was supported through Earthscope grant EAR08–44041 and Shane McGary through a National Defense Science and Engineering Graduate (NDSEG) fellowship. Fieldwork in Canada was made possible by an NSERC Discovery Grant and a Canadian Foundation for Innovation award to Martyn Unsworth.2015-05-1

Intravital FRAP imaging using an E-cadherin-GFP mouse reveals disease- and drug-dependent dynamic regulation of cell-cell junctions in live tissue

E-cadherin-mediated cell-cell junctions play a prominent role in maintaining the epithelial architecture. The disruption or deregulation of these adhesions in cancer can lead to the collapse of tumor epithelia that precedes invasion and subsequent metastasis. Here we generated an E-cadherin-GFP mouse that enables intravital photobleaching and quantification of E-cadherin mobility in live tissue without affecting normal biology. We demonstrate the broad applications of this mouse by examining E-cadherin regulation in multiple tissues, including mammary, brain, liver, and kidney tissue, while specifically monitoring E-cadherin mobility during disease progression in the pancreas. We assess E-cadherin stability in native pancreatic tissue upon genetic manipulation involving Kras and p53 or in response to anti-invasive drug treatment and gain insights into the dynamic remodeling of E-cadherin during in situ cancer progression. FRAP in the E-cadherin-GFP mouse, therefore, promises to be a valuable tool to fundamentally expand our understanding of E-cadherin-mediated events in native microenvironments

DNA sequence level analyses reveal potential phenotypic modifiers in a large family with psychiatric disorders

Psychiatric disorders are a group of genetically related diseases with highly polygenic architectures. Genome-wide association analyses have made substantial progress towards understanding the genetic architecture of these disorders. More recently, exome- and whole-genome sequencing of cases and families have identified rare, high penetrant variants that provide direct functional insight. There remains, however, a gap in the heritability explained by these complementary approaches. To understand how multiple genetic variants combine to modify both severity and penetrance of a highly penetrant variant, we sequenced 48 whole genomes from a family with a high loading of psychiatric disorder linked to a balanced chromosomal translocation. The (1;11)(q42;q14.3) translocation directly disrupts three genes: DISC1, DISC2, DISC1FP and has been linked to multiple brain imaging and neurocognitive outcomes in the family. Using DNA sequence-level linkage analysis, functional annotation and population-based association, we identified common and rare variants in GRM5 (minor allele frequency (MAF) > 0.05), PDE4D (MAF > 0.2) and CNTN5 (MAF < 0.01) that may help explain the individual differences in phenotypic expression in the family. We suggest that whole-genome sequencing in large families will improve the understanding of the combined effects of the rare and common sequence variation underlying psychiatric phenotypes

The Apache Point Observatory Galactic Evolution Experiment (APOGEE) Spectrographs

We describe the design and performance of the near-infrared (1.51--1.70 micron), fiber-fed, multi-object (300 fibers), high resolution (R = lambda/delta lambda ~ 22,500) spectrograph built for the Apache Point Observatory Galactic Evolution Experiment (APOGEE). APOGEE is a survey of ~ 10^5 red giant stars that systematically sampled all Milky Way populations (bulge, disk, and halo) to study the Galaxy's chemical and kinematical history. It was part of the Sloan Digital Sky Survey III (SDSS-III) from 2011 -- 2014 using the 2.5 m Sloan Foundation Telescope at Apache Point Observatory, New Mexico. The APOGEE-2 survey is now using the spectrograph as part of SDSS-IV, as well as a second spectrograph, a close copy of the first, operating at the 2.5 m du Pont Telescope at Las Campanas Observatory in Chile. Although several fiber-fed, multi-object, high resolution spectrographs have been built for visual wavelength spectroscopy, the APOGEE spectrograph is one of the first such instruments built for observations in the near-infrared. The instrument's successful development was enabled by several key innovations, including a "gang connector" to allow simultaneous connections of 300 fibers; hermetically sealed feedthroughs to allow fibers to pass through the cryostat wall continuously; the first cryogenically deployed mosaic volume phase holographic grating; and a large refractive camera that includes mono-crystalline silicon and fused silica elements with diameters as large as ~ 400 mm. This paper contains a comprehensive description of all aspects of the instrument including the fiber system, optics and opto-mechanics, detector arrays, mechanics and cryogenics, instrument control, calibration system, optical performance and stability, lessons learned, and design changes for the second instrument.Comment: 81 pages, 67 figures, PASP, accepte

New Cancer Immunotherapy Agents in Development: a report from an associated program of the 31

This report is a summary of \u27New Cancer Immunotherapy Agents in Development\u27 program, which took place in association with the 31st Annual Meeting of the Society for Immunotherapy of Cancer (SITC), on November 9, 2016 in National Harbor, Maryland. Presenters gave brief overviews of emerging clinical and pre-clinical immune-based agents and combinations, before participating in an extended panel discussion with multidisciplinary leaders, including members of the FDA, leading academic institutions and industrial drug developers, to consider topics relevant to the future of cancer immunotherapy

BioTIME: A database of biodiversity time series for the Anthropocene.

MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL