Assessing Landscape Constraints on Species Abundance: Does the Neighborhood Limit Species Response to Local Habitat Conservation Programs?

Landscapes in agricultural systems continue to undergo significant change, and the loss of biodiversity is an ever-increasing threat. Although habitat restoration is beneficial, management actions do not always result in the desired outcome. Managers must understand why management actions fail; yet, past studies have focused on assessing habitat attributes at a single spatial scale, and often fail to consider the importance of ecological mechanisms that act across spatial scales. We located survey sites across southern Nebraska, USA and conducted point counts to estimate Ring-necked Pheasant abundance, an economically important species to the region, while simultaneously quantifying landscape effects using a geographic information system. To identify suitable areas for allocating limited management resources, we assessed land cover relationships to our counts using a Bayesian binomial-Poisson hierarchical model to construct predictive Species Distribution Models of relative abundance. Our results indicated that landscape scale land cover variables severely constrained or, alternatively, facilitated the positive effects of local land management for Ring-necked Pheasants

Cluster vs. Field Elliptical Galaxies and Clues on their Formation

Using new observations for a sample of 931 early-type galaxies we investigate whether the \mg2--\so relation shows any dependence on the local environment. The galaxies have been assigned to three different environments depending on the local overdensity: clusters, groups, and field, having used our completeredshift database to guide the assignment of galaxies. It is found that cluster, group and field early-type galaxies follow almost identical \mg2--\so\ relations, with the largest \mg2 zero-point difference (clusters minus field) being only $0.007\pm 0.002$ mag. No correlation of the residuals is found with the morphological type or the bulge to disk ratio. Using stellar population models in a differential fashion, this small zero-point difference implies a luminosity-weighted age difference of only $\sim 1$ Gyr between the corresponding stellar populations, with field galaxies being younger. The mass-weighted age difference could be significantly smaller, if minor events of late star formation took place preferentially in field galaxies. We combine these results with the existing evidence for the bulk of stars in cluster early-type galaxies having formed at very high redshift, and conclude that the bulk of stars in galactic spheroids had to form at high redshifts (z\gsim 3), no matter whether such spheroids now reside in low or high density regions. The cosmological implications of these findings are briefly discussed.Comment: 16 pages, 2 figures, accepted for publication in the ApJ.

Translating statistical species-habitat models to interactive decision support tools

Understanding species-habitat relationships is vital to successful conservation, but the tools used to communicate species-habitat relationships are often poorly suited to the information needs of conservation practitioners. Here we present a novel method for translating a statistical species-habitat model, a regression analysis relating ring-necked pheasant abundance to landcover, into an interactive online tool. The Pheasant Habitat Simulator combines the analytical power of the R programming environment with the user-friendly Shiny web interface to create an online platform in which wildlife professionals can explore the effects of variation in local landcover on relative pheasant habitat suitability within spatial scales relevant to individual wildlife managers. Our tool allows users to virtually manipulate the landcover composition of a simulated space to explore how changes in landcover may affect pheasant relative habitat suitability, and guides users through the economic tradeoffs of landscape changes. We offer suggestions for development of similar interactive applications and demonstrate their potential as innovative science delivery tools for diverse professional and public audience

Biased Signaling of CCL21 and CCL19 Does Not Rely on N-Terminal Differences, but Markedly on the Chemokine Core Domains and Extracellular Loop 2 of CCR7

Chemokine receptors play important roles in the immune system and are linked to several human diseases. Targeting chemokine receptors have so far shown very little success owing to, to some extent, the promiscuity of the immune system and the high degree of biased signaling within it. CCR7 and its two endogenous ligands display biased signaling and here we investigate the differences between the two ligands, CCL21 and CCL19, with respect to their biased activation of CCR7. We use bystander bioluminescence resonance energy transfer (BRET) based signaling assays and Transwell migration assays to determine (A) how swapping of domains between the two ligands affect their signaling patterns and (B) how receptor mutagenesis impacts signaling. Using chimeric ligands we find that the chemokine core domains are central for determining signaling outcome as the lack of β-arrestin-2 recruitment displayed by CCL21 is linked to its core domain and not N-terminus. Through a mutagenesis screen, we identify the extracellular domains of CCR7 to be important for both ligands and show that the two chemokines interact differentially with extracellular loop 2 (ECL-2). By using in silico modeling, we propose a link between ECL-2 interaction and CCR7 signal transduction. Our mutagenesis study also suggests a lysine in the top of TM3, K1303.26, to be important for G protein signaling, but not β-arrestin-2 recruitment. Taken together, the bias in CCR7 between CCL19 and CCL21 relies on the chemokine core domains, where interactions with ECL-2 seem particularly important. Moreover, TM3 selectively regulates G protein signaling as found for other chemokine receptors.publishe

Hubble Space Telescope Imaging of Brightest Cluster Galaxies

We used the HST WFPC2 to obtain I-band images of the centers of 81 brightest cluster galaxies (BCGs), drawn from a volume-limited sample of nearby BCGs. The images show a rich variety of morphological features, including multiple or double nuclei, dust, stellar disks, point source nuclei, and central surface brightness depressions. High resolution surface brightness profiles could be inferred for 60 galaxies. Of those, 88% have well-resolved cores. Twelve percent of the BCG sample lacks a well-resolved core; all but one of these BCGs have ``power-law'' profiles. Some of these galaxies have higher luminosities than any power-law galaxy identified by Faber et al. (1997), and have physical upper limits on the break radius well below the values observed for core galaxies of the same luminosity. These results support the idea that the central structure of early-type galaxies is bimodal in its physical properties, but also suggest that there exist high luminosity galaxies with power-law profiles (or unusually small cores). The BCGs in the latter category tend to fall at the low end of the BCG luminosity function and tend to have low values of the quantity alpha (the logarithmic slope of the metric luminosity as a function of radius, at 10 kpc). Since theoretical calculations have shown that the luminosities and alpha values of BCGs grow with time as a result of accretion, this suggests a scenario in which elliptical galaxies evolve from power-law profiles to core profiles through accretion and merging. This is consistent with theoretical scenarios that invoke the formation of massive black hole binaries during merger events (Abridged).Comment: Accepted for publication in AJ. Postscript file with high resolution figures (1 and 3) is available at http://spider.ipac.caltech.edu/staff/seppo/bcgfig

The Sloan Digital Sky Survey Quasar Lens Search. III. Constraints on Dark Energy from the Third Data Release Quasar Lens Catalog

We present cosmological results from the statistics of lensed quasars in the Sloan Digital Sky Survey (SDSS) Quasar Lens Search. By taking proper account of the selection function, we compute the expected number of quasars lensed by early-type galaxies and their image separation distribution assuming a flat universe, which is then compared with 7 lenses found in the SDSS Data Release 3 to derive constraints on dark energy under strictly controlled criteria. For a cosmological constant model (w=-1) we obtain \Omega_\Lambda=0.74^{+0.11}_{-0.15}(stat.)^{+0.13}_{-0.06}(syst.). Allowing w to be a free parameter we find \Omega_M=0.26^{+0.07}_{-0.06}(stat.)^{+0.03}_{-0.05}(syst.) and w=-1.1\pm0.6(stat.)^{+0.3}_{-0.5}(syst.) when combined with the constraint from the measurement of baryon acoustic oscillations in the SDSS luminous red galaxy sample. Our results are in good agreement with earlier lensing constraints obtained using radio lenses, and provide additional confirmation of the presence of dark energy consistent with a cosmological constant, derived independently of type Ia supernovae.Comment: 9 pages, 3 figures, 2 tables, accepted for publication in A

A Framework for Multi-Omic Prediction of Treatment Response to Biologic Therapy for Psoriasis.

Biologic therapies have shown high efficacy in psoriasis, but individual response varies and is poorly understood. To inform biomarker discovery in the Psoriasis Stratification to Optimise Relevant Therapy (i.e., PSORT) study, we evaluated a comprehensive array of omics platforms across three time points and multiple tissues in a pilot investigation of 10 patients with severe psoriasis, treated with the tumor necrosis factor (TNF) inhibitor, etanercept. We used RNA sequencing to analyze mRNA and small RNA transcriptome in blood, lesional and nonlesional skin, and the SOMAscan platform to investigate the serum proteome. Using an integrative systems biology approach, we identified signals of treatment response in genes and pathways associated with TNF signaling, psoriasis pathology, and the major histocompatibility complex region. We found association between clinical response and TNF-regulated genes in blood and skin. Using a combination of differential expression testing, upstream regulator analysis, clustering techniques, and predictive modeling, we show that baseline samples are indicative of patient response to biologic therapies, including signals in blood, which have traditionally been considered unreliable for inference in dermatology. In conclusion, our pilot study provides both an analytical framework and empirical basis to estimate power for larger studies, specifically the ongoing PSORT study, which we show as powered for biomarker discovery and patient stratification

The Fifth Data Release of the Sloan Digital Sky Survey

This paper describes the Fifth Data Release (DR5) of the Sloan Digital Sky Survey (SDSS). DR5 includes all survey quality data taken through June 2005 and represents the completion of the SDSS-I project (whose successor, SDSS-II will continue through mid-2008). It includes five-band photometric data for 217 million objects selected over 8000 square degrees, and 1,048,960 spectra of galaxies, quasars, and stars selected from 5713 square degrees of that imaging data. These numbers represent a roughly 20% increment over those of the Fourth Data Release; all the data from previous data releases are included in the present release. In addition to "standard" SDSS observations, DR5 includes repeat scans of the southern equatorial stripe, imaging scans across M31 and the core of the Perseus cluster of galaxies, and the first spectroscopic data from SEGUE, a survey to explore the kinematics and chemical evolution of the Galaxy. The catalog database incorporates several new features, including photometric redshifts of galaxies, tables of matched objects in overlap regions of the imaging survey, and tools that allow precise computations of survey geometry for statistical investigations.Comment: ApJ Supp, in press, October 2007. This paper describes DR5. The SDSS Sixth Data Release (DR6) is now public, available from http://www.sdss.or

Field trial of three different Plasmodium vivax-detecting rapid diagnostic tests with and without evaporative cool box storage in Afghanistan

<p>Abstract</p> <p>Background</p> <p>Accurate parasitological diagnosis of malaria is essential for targeting treatment where more than one species coexist. In this study, three rapid diagnostic tests (RDTs) (AccessBio CareStart (CSPfPan), CareStart PfPv (CSPfPv) and Standard Diagnostics Bioline (SDBPfPv)) were evaluated for their ability to detect natural <it>Plasmodium vivax </it>infections in a basic clinic setting. The potential for locally made evaporative cooling boxes (ECB) to protect the tests from heat damage in high summer temperatures was also investigated.</p> <p>Methods</p> <p>Venous blood was drawn from <it>P. vivax </it>positive patients in Jalalabad, Afghanistan and tested against a panel of six RDTs. The panel comprised two of each test type; one group was stored at room temperature and the other in an ECB. RDT results were evaluated against a consensus gold standard based on two double-read reference slides and PCR. The sensitivity, specificity and a measure of global performance for each test were determined and stratified by parasitaemia level and storage condition.</p> <p>Results</p> <p>In total, 306 patients were recruited, of which 284 were positive for <it>P. vivax</it>, one for <it>Plasmodium malariae </it>and none for <it>Plasmodium falciparum</it>; 21 were negative. All three RDTs were specific for malaria. The sensitivity and global performance index for each test were as follows: CSPfPan [98.6%, 95.1%], CSPfPv [91.9%, 90.5%] and SDBPfPv [96.5%, 82.9%], respectively. CSPfPv was 16% less sensitive to a parasitaemia below 5,000/μL. Room temperature storage of SDBPfPv led to a high proportion of invalid results (17%), which reduced to 10% in the ECB. Throughout the testing period, the ECB maintained ~8°C reduction over ambient temperatures and never exceeded 30°C.</p> <p>Conclusions</p> <p>Of the three RDTs, the CSPfPan test was the most consistent and reliable, rendering it appropriate for this <it>P. vivax </it>predominant region. The CSPfPv test proved unsuitable owing to its reduced sensitivity at a parasitaemia below 5,000/μL (affecting 43% of study samples). Although the SDBPfPv device was more sensitive than the CSPfPv test, its invalid rate was unacceptably high. ECB storage reduced the proportion of invalid results for the SDBPfPv test, but surprisingly had no impact on RDT sensitivity at low parasitaemia.</p