Reply to ‘Pseudoreplication and greenhouse-gas emissions from rivers'

Tiegs et al.1 highlight the significance and relevance of the findings of Comer-Warner et al.2 on greenhouse-gas emissions from streambed sediments but raise questions about some aspects of the experimental design. We support their call for more detailed field and laboratory-based studies on this subject. However, we believe that their concerns relate to uncertainties and limitations in the experimental design that were discussed explicitly in the original paper (and accompanying transparent peer review process—available online), or represent criticisms related to highly improbable minor anomalies that may unnecessarily dismiss experimental results as discussed below

Weak lensing power spectra for precision cosmology: Multiple-deflection, reduced shear and lensing bias corrections

It is usually assumed that the ellipticity power spectrum measured in weak lensing observations can be expressed as an integral over the underlying matter power spectrum. This is true at second order in the gravitational potential. We extend the standard calculation, constructing all corrections to fourth order in the gravitational potential. There are four types of corrections: corrections to the lensing shear due to multiple-deflections; corrections due to the fact that shape distortions probe the reduced shear $\gamma/(1-\kappa)$ rather than the shear itself; corrections associated with the non-linear conversion of reduced shear to mean ellipticity; and corrections due to the fact that observational galaxy selection and shear measurement is based on galaxy brightnesses and sizes which have been (de)magnified by lensing. We show how the previously considered corrections to the shear power spectrum correspond to terms in our analysis, and highlight new terms that were not previously identified. All correction terms are given explicitly as integrals over the matter power spectrum, bispectrum, and trispectrum, and are numerically evaluated for the case of sources at z=1. We find agreement with previous works for the ${\mathcal O}(\Phi^3)$ terms. We find that for ambitious future surveys, the ${\mathcal O}(\Phi^4)$ terms affect the power spectrum at the ~ 1-5 $\sigma$ level; they will thus need to be accounted for, but are unlikely to represent a serious difficulty for weak lensing as a cosmological probe.Comment: 14 pages, 3 figures; matches A & A accepted versio

Assessing Change in Social Support During Late Life

The purpose of this study is to evaluate change in 14 measures of social support with data provided by a nationwide longitudinal study of older adults. The findings reveal that fairly substantial change took place during the three-year follow-up period. More important, the data indicate that change is not uniform or systematic across the entire study sample. Instead, there appears to be considerable individual-level change taking place. The implications of these findings for the development of conceptual models as well as support-based interventions are discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68866/2/10.1177_0164027599214002.pd

The emission by dust and stars of nearby galaxies in the Herschel KINGFISH survey

Using new far-infrared imaging from the Herschel Space Observatory with ancillary data from ultraviolet (UV) to submillimeter wavelengths, we estimate the total emission from dust and stars of 62 nearby galaxies in the KINGFISH survey in a way that is as empirical and model independent as possible. We collect and exploit these data in order to measure from the spectral energy distributions (SEDs) precisely how much stellar radiation is intercepted and re-radiated by dust, and how this quantity varies with galaxy properties. By including SPIRE data, we are more sensitive to emission from cold dust grains than previous analyses at shorter wavelengths, allowing for more accurate estimates of dust temperatures and masses. The dust/stellar flux ratio, which we measure by integrating the SEDs, has a range of nearly three decades (from 10(-2.2) to 10(0.5)). The inclusion of SPIRE data shows that estimates based on data not reaching these far-IR wavelengths are biased low by 17% on average. We find that the dust/stellar flux ratio varies with morphology and total infrared (IR) luminosity, with dwarf galaxies having faint luminosities, spirals having relatively high dust/stellar ratios and IR luminosities, and some early types having low dust/stellar ratios. We also find that dust/stellar flux ratios are related to gas-phase metallicity ((log(f(dust)/f(*)) over bar) = -0.66 +/- 0.08 and -0.22 +/- 0.12 for metal-poor and intermediate-metallicity galaxies, respectively), while the dust/stellar mass ratios are less so (differing by approximate to 0.2 dex); the more metal-rich galaxies span a much wider range of the flux ratios. In addition, the substantial scatter between dust/stellar flux and dust/stellar mass indicates that the former is a poor proxy of the latter. Comparing the dust/stellar flux ratios and dust temperatures, we also show that early types tend to have slightly warmer temperatures (by up to 5 K) than spiral galaxies, which may be due to more intense interstellar radiation fields, or possibly to different dust grain compositions. Finally, we show that early types and early-type spirals have a strong correlation between the dust/stellar flux ratio and specific star formation rate, which suggests that the relatively bright far-IR emission of some of these galaxies is due to ongoing (if limited) star formation as well as to the radiation field from older stars, which is heating the dust grains

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.

MotivationElectronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.ResultsWe present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.Availability and implementationPatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.Supplementary informationSupplementary data are available at Bioinformatics online

Thermal sensitivity of CO2 and CH4 emissions varies with streambed sediment properties

Globally, rivers and streams are important sources of carbon dioxide and methane, with small rivers contributing disproportionately relative to their size. Previous research on greenhouse gas (GHG) emissions from surface water lacks mechanistic understanding of contributions from streambed sediments. We hypothesise that streambeds, as known biogeochemical hotspots, significantly contribute to the production of GHGs. With global climate change, there is a pressing need to understand how increasing streambed temperatures will affect current and future GHG production. Current global estimates assume linear relationships between temperature and GHG emissions from surface water. Here we show non-linearity and threshold responses of streambed GHG production to warming. We reveal that temperature sensitivity varies with substrate (of variable grain size), organic matter (OM) content and geological origin. Our results confirm that streambeds, with their non-linear response to projected warming, are integral to estimating freshwater ecosystem contributions to current and future global GHG emissions

Gregariousness Does Not Vary with Geography, Developmental Stage, or Group Relatedness in Feeding Redheaded Pine Sawfly Larvae

Aggregations are widespread across the animal kingdom, yet the underlying proximate and ultimate causes are still largely unknown. An ideal system to investigate this simple, social behavior is the pine sawfly genus Neodiprion, which is experimentally tractable and exhibits interspecific variation in larval gregariousness. To assess intraspecific variation in this trait, we characterized aggregative tendency within a single widespread species, the redheaded pine sawfly (N. lecontei). To do so, we developed a quantitative assay in which we measured interindividual distances over a 90-min video. This assay revealed minimal behavioral differences: (1) between early-feeding and late-feeding larval instars, (2) among larvae derived from different latitudes, and (3) between groups composed of kin and those composed of nonkin. Together, these results suggest that, during the larval feeding period, the benefits individuals derive from aggregating outweigh the costs and that this cost-to-benefit ratio does not vary dramatically across space (geography) or ontogeny (developmental stage). In contrast to the feeding larvae, our assay revealed a striking reduction in gregariousness following the final larval molt in N. lecontei. We also found some intriguing interspecific variation: While N. lecontei and N. maurus feeding larvae exhibit significant aggregative tendencies, feeding N. compar larvae do not aggregate at all. These results set the stage for future work investigating the proximate and ultimate mechanisms underlying developmental and interspecific variation in larval gregariousness across Neodiprion

Science Impacts of the SPHEREx All-Sky Optical to Near-Infrared Spectral Survey: Report of a Community Workshop Examining Extragalactic, Galactic, Stellar and Planetary Science

SPHEREx is a proposed SMEX mission selected for Phase A. SPHEREx will carry out the first all-sky spectral survey and provide for every 6.2" pixel a spectra between 0.75 and 4.18 $\mu$m [with R$\sim$41.4] and 4.18 and 5.00 $\mu$m [with R$\sim$135]. The SPHEREx team has proposed three specific science investigations to be carried out with this unique data set: cosmic inflation, interstellar and circumstellar ices, and the extra-galactic background light. It is readily apparent, however, that many other questions in astrophysics and planetary sciences could be addressed with the SPHEREx data. The SPHEREx team convened a community workshop in February 2016, with the intent of enlisting the aid of a larger group of scientists in defining these questions. This paper summarizes the rich and varied menu of investigations that was laid out. It includes studies of the composition of main belt and Trojan/Greek asteroids; mapping the zodiacal light with unprecedented spatial and spectral resolution; identifying and studying very low-metallicity stars; improving stellar parameters in order to better characterize transiting exoplanets; studying aliphatic and aromatic carbon-bearing molecules in the interstellar medium; mapping star formation rates in nearby galaxies; determining the redshift of clusters of galaxies; identifying high redshift quasars over the full sky; and providing a NIR spectrum for most eROSITA X-ray sources. All of these investigations, and others not listed here, can be carried out with the nominal all-sky spectra to be produced by SPHEREx. In addition, the workshop defined enhanced data products and user tools which would facilitate some of these scientific studies. Finally, the workshop noted the high degrees of synergy between SPHEREx and a number of other current or forthcoming programs, including JWST, WFIRST, Euclid, GAIA, K2/Kepler, TESS, eROSITA and LSST.Comment: Report of the First SPHEREx Community Workshop, http://spherex.caltech.edu/Workshop.html , 84 pages, 28 figure

Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA

Aneuploidies, and in particular, trisomies represent the most common genetic aberrations observed in human genetics today. To explore the presence of trisomies in historic and prehistoric populations we screen nearly 10,000 ancient human individuals for the presence of three copies of any of the target autosomes. We find clear genetic evidence for six cases of trisomy 21 (Down syndrome) and one case of trisomy 18 (Edwards syndrome), and all cases are present in infant or perinatal burials. We perform comparative osteological examinations of the skeletal remains and find overlapping skeletal markers, many of which are consistent with these syndromes. Interestingly, three cases of trisomy 21, and the case of trisomy 18 were detected in two contemporaneous sites in early Iron Age Spain (800-400 BCE), potentially suggesting a higher frequency of burials of trisomy carriers in those societies. Notably, the care with which the burials were conducted, and the items found with these individuals indicate that ancient societies likely acknowledged these individuals with trisomy 18 and 21 as members of their communities, from the perspective of burial practice