Challenges in Columbia River Fisheries Conservation: A Response to Duda et al.

The salmonid fisheries of the Columbia River Basin (CRB) have enormous socioeconomic, cultural, and ecological importance to numerous diverse stakeholders (eg state, federal, tribal, nonprofit), and there are a wide array of opinions and perspectives on how these fisheries should be managed. Although we appreciate Duda et al.\u27s commentary, it offers only one perspective of many in this context. The objective of our paper (Hand et al. 2018) was to provide justification for “the importance of social–ecological perspectives when communicating conservation values and goals, and the role of independent science in guiding management policy and practice for salmonids in the CRB”. However, we did not intend to strictly advocate for a single course of action, and the available space within our paper\u27s Panel 1 limited us from engaging in a thorough ecological debate

The Atacama Cosmology Telescope: Two-Season ACTPol Lensing Power Spectrum

We report a measurement of the power spectrum of cosmic microwave background (CMB) lensing from two seasons of Atacama Cosmology Telescope Polarimeter (ACTPol) CMB data. The CMB lensing power spectrum is extracted from both temperature and polarization data using quadratic estimators. We obtain results that are consistent with the expectation from the best-fit Planck LCDM model over a range of multipoles L=80-2100, with an amplitude of lensing A_lens = 1.06 +/- 0.15 (stat.) +/- 0.06 (sys.) relative to Planck. Our measurement of the CMB lensing power spectrum gives sigma_8 Omega_m^0.25 = 0.643 +/- 0.054; including baryon acoustic oscillation scale data, we constrain the amplitude of density fluctuations to be sigma_8 = 0.831 +/- 0.053. We also update constraints on the neutrino mass sum. We verify our lensing measurement with a number of null tests and systematic checks, finding no evidence of significant systematic errors. This measurement relies on a small fraction of the ACTPol data already taken; more precise lensing results can therefore be expected from the full ACTPol dataset.Comment: 17 pages, 11 figures, to be submitted to Physical Review

Global data set of long-term summertime vertical temperature profiles in 153 lakes

Climate change and other anthropogenic stressors have led to long-term changes in the thermal structure, including surface temperatures, deepwater temperatures, and vertical thermal gradients, in many lakes around the world. Though many studies highlight warming of surface water temperatures in lakes worldwide, less is known about long-term trends in full vertical thermal structure and deepwater temperatures, which have been changing less consistently in both direction and magnitude. Here, we present a globally-expansive data set of summertime in-situ vertical temperature profiles from 153 lakes, with one time series beginning as early as 1894. We also compiled lake geographic, morphometric, and water quality variables that can influence vertical thermal structure through a variety of potential mechanisms in these lakes. These long-term time series of vertical temperature profiles and corresponding lake characteristics serve as valuable data to help understand changes and drivers of lake thermal structure in a time of rapid global and ecological change

Deeper waters are changing less consistently than surface waters in a global analysis of 102 lakes

Globally, lake surface water temperatures have warmed rapidly relative to air temperatures, but changes in deepwater temperatures and vertical thermal structure are still largely unknown. We have compiled the most comprehensive data set to date of long-term (1970-2009) summertime vertical temperature profiles in lakes across the world to examine trends and drivers of whole-lake vertical thermal structure. We found significant increases in surface water temperatures across lakes at an average rate of +0.37°C decade-1, comparable to changes reported previously for other lakes, and similarly consistent trends of increasing water column stability (+0.08 kg m-3 decade-1). In contrast, however, deepwater temperature trends showed little change on average (+0.06°C decade-1 ), but had high variability across lakes, with trends in individual lakes ranging from -0.68°C decade-1 to +0.65°C decade-1 . The variability in deepwater temperature trends was not explained by trends in either surface water temperatures or thermal stability within lakes, and only 8.4% was explained by lake thermal region or local lake characteristics in a random forest analysis. These findings suggest that external drivers beyond our tested lake characteristics are important in explaining long-term trends in thermal structure, such as local to regional climate patterns or additional external anthropogenic influences.Additional co-authors: Karl Havens, Dag O Hessen, Scott N Higgins, Timo H Huttula, Hannu Huuskonen, Peter D F Isles, Klaus D Joehnk, Wendel Bill Keller, Lesley B Knoll, Johanna Korhonen, Benjamin M Kraemer, Peter R Leavitt, Fabio Lepori, Martin S Luger, Stephen C Maberly, John M Melack, Stephanie J Melles, Döerthe C Müller-Navarra, Don C Pierson, Helen V Pislegina, Pierre-Denis Plisnier, David C Richardson, Alon Rimmer, Michela Rogora, James A Rusak, Steven Sadro, Nico Salmaso, Jasmine E Saros, Émilie Saulnier-Talbot, Daniel E Schindler, Martin Schmid, Svetlana V Shimaraeva, Eugene A Silow, Lewis M Sitoki, Ruben Sommaruga, Dietmar Straile, Kristin E Strock, Wim Thiery, Maxim A Timofeyev, Piet Verburg, Rolf D Vinebrooke, Gesa A Weyhenmeyer, Egor Zaderee

The Atacama Cosmology Telescope: Two-Season ACTPol Spectra and Parameters

We present the temperature and polarization angular power spectra measured by the Atacama Cosmology Telescope Polarimeter (ACTPol). We analyze night-time data collected during 2013-14 using two detector arrays at 149 GHz, from 548 deg$^2$ of sky on the celestial equator. We use these spectra, and the spectra measured with the MBAC camera on ACT from 2008-10, in combination with Planck and WMAP data to estimate cosmological parameters from the temperature, polarization, and temperature-polarization cross-correlations. We find the new ACTPol data to be consistent with the LCDM model. The ACTPol temperature-polarization cross-spectrum now provides stronger constraints on multiple parameters than the ACTPol temperature spectrum, including the baryon density, the acoustic peak angular scale, and the derived Hubble constant. Adding the new data to planck temperature data tightens the limits on damping tail parameters, for example reducing the joint uncertainty on the number of neutrino species and the primordial helium fraction by 20%.Comment: 23 pages, 25 figure

The atacama cosmology telescope: lensing of CMB temperature and polarization derived from cosmic infrared background cross-correlation

We present a measurement of the gravitational lensing of the Cosmic Microwave Background (CMB) temperature and polarization fields obtained by cross-correlating the reconstructed convergence signal from the first season of Atacama Cosmology Telescope Polarimeter data at 146 GHz with Cosmic Infrared Background (CIB) fluctuations measured using the Planck satellite. Using an effective overlap area of 92.7 square degrees, we detect gravitational lensing of the CMB polarization by large-scale structure at a statistical significance of $4.5\sigma$. Combining both CMB temperature and polarization data gives a lensing detection at $9.1\sigma$ significance. A B-mode polarization lensing signal is present with a significance of $3.2\sigma$. We also present the first measurement of CMB lensing–CIB correlation at small scales corresponding to $l\gt 2000$. Null tests and systematic checks show that our results are not significantly biased by astrophysical or instrumental systematic effects, including Galactic dust. Fitting our measurements to the best-fit lensing-CIB cross-power spectrum measured in Planck data, scaled by an amplitude A, gives $A={1.02}_{-0.08}^{+0.12}$(stat.) ± 0.06(syst.), consistent with the Planck results

Identification of PLCL1 Gene for Hip Bone Size Variation in Females in a Genome-Wide Association Study

Osteoporosis, the most prevalent metabolic bone disease among older people, increases risk for low trauma hip fractures (HF) that are associated with high morbidity and mortality. Hip bone size (BS) has been identified as one of the key measurable risk factors for HF. Although hip BS is highly genetically determined, genetic factors underlying the trait are still poorly defined. Here, we performed the first genome-wide association study (GWAS) of hip BS interrogating ∼380,000 SNPs on the Affymetrix platform in 1,000 homogeneous unrelated Caucasian subjects, including 501 females and 499 males. We identified a gene, PLCL1 (phospholipase c-like 1), that had four SNPs associated with hip BS at, or approaching, a genome-wide significance level in our female subjects; the most significant SNP, rs7595412, achieved a p value of 3.72×10−7. The gene's importance to hip BS was replicated using the Illumina genotyping platform in an independent UK cohort containing 1,216 Caucasian females. Two SNPs of the PLCL1 gene, rs892515 and rs9789480, surrounded by the four SNPs identified in our GWAS, achieved p values of 8.62×10−3 and 2.44×10−3, respectively, for association with hip BS. Imputation analyses on our GWAS and the UK samples further confirmed the replication signals; eight SNPs of the gene achieved combined imputed p values<10−5 in the two samples. The PLCL1 gene's relevance to HF was also observed in a Chinese sample containing 403 females, including 266 with HF and 177 control subjects. A SNP of the PLCL1 gene, rs3771362 that is only ∼0.6 kb apart from the most significant SNP detected in our GWAS (rs7595412), achieved a p value of 7.66×10−3 (odds ratio = 0.26) for association with HF. Additional biological support for the role of PLCL1 in BS comes from previous demonstrations that the PLCL1 protein inhibits IP3 (inositol 1,4,5-trisphosphate)-mediated calcium signaling, an important pathway regulating mechanical sensing of bone cells. Our findings suggest that PLCL1 is a novel gene associated with variation in hip BS, and provide new insights into the pathogenesis of HF

Patterns and rates of exonic de novo mutations in autism spectrum disorders

Autism spectrum disorders (ASD) are believed to have genetic and environmental origins, yet in only a modest fraction of individuals can specific causes be identified1,2. To identify further genetic risk factors, we assess the role of de novo mutations in ASD by sequencing the exomes of ASD cases and their parents (n= 175 trios). Fewer than half of the cases (46.3%) carry a missense or nonsense de novo variant and the overall rate of mutation is only modestly higher than the expected rate. In contrast, there is significantly enriched connectivity among the proteins encoded by genes harboring de novo missense or nonsense mutations, and excess connectivity to prior ASD genes of major effect, suggesting a subset of observed events are relevant to ASD risk. The small increase in rate of de novo events, when taken together with the connections among the proteins themselves and to ASD, are consistent with an important but limited role for de novo point mutations, similar to that documented for de novo copy number variants. Genetic models incorporating these data suggest that the majority of observed de novo events are unconnected to ASD, those that do confer risk are distributed across many genes and are incompletely penetrant (i.e., not necessarily causal). Our results support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5 to 20-fold. Despite the challenge posed by such models, results from de novo events and a large parallel case-control study provide strong evidence in favor of CHD8 and KATNAL2 as genuine autism risk factors

The Atacama Cosmology Telescope: CMB Polarization at 200<ℓ<9000200<\ell<9000

We report on measurements of the cosmic microwave background (CMB) and celestial polarization at 146 GHz made with the Atacama Cosmology Telescope Polarimeter (ACTPol) in its first three months of observing. Four regions of sky covering a total of 270 square degrees were mapped with an angular resolution of $1.3'$. The map noise levels in the four regions are between 11 and 17 $\mu$K-arcmin. We present TT, TE, EE, TB, EB, and BB power spectra from three of these regions. The observed E-mode polarization power spectrum, displaying six acoustic peaks in the range $200<\ell<3000$, is an excellent fit to the prediction of the best-fit cosmological models from WMAP9+ACT and Planck data. The polarization power spectrum, which mainly reflects primordial plasma velocity perturbations, provides an independent determination of cosmological parameters consistent with those based on the temperature power spectrum, which results mostly from primordial density perturbations. We find that without masking any point sources in the EE data at $\ell<9000$, the Poisson tail of the EE power spectrum due to polarized point sources has an amplitude less than $2.4$ $\mu$K$^2$ at $\ell = 3000$ at 95\% confidence. Finally, we report that the Crab Nebula, an important polarization calibration source at microwave frequencies, has 8.7\% polarization with an angle of $150.7^\circ \pm 0.6^\circ$ when smoothed with a $5'$ Gaussian beam.Comment: 16 pages, 15 figures, 5 table

The Atacama Cosmology Telescope: A Measurement of the DR6 CMB Lensing Power Spectrum and its Implications for Structure Growth

We present new measurements of cosmic microwave background (CMB) lensing over $9400$ sq. deg. of the sky. These lensing measurements are derived from the Atacama Cosmology Telescope (ACT) Data Release 6 (DR6) CMB dataset, which consists of five seasons of ACT CMB temperature and polarization observations. We determine the amplitude of the CMB lensing power spectrum at $2.3\%$ precision ($43\sigma$ significance) using a novel pipeline that minimizes sensitivity to foregrounds and to noise properties. To ensure our results are robust, we analyze an extensive set of null tests, consistency tests, and systematic error estimates and employ a blinded analysis framework. The baseline spectrum is well fit by a lensing amplitude of $A_{\mathrm{lens}}=1.013\pm0.023$ relative to the Planck 2018 CMB power spectra best-fit $\Lambda$CDM model and $A_{\mathrm{lens}}=1.005\pm0.023$ relative to the $\text{ACT DR4} + \text{WMAP}$ best-fit model. From our lensing power spectrum measurement, we derive constraints on the parameter combination $S^{\mathrm{CMBL}}_8 \equiv \sigma_8 \left({\Omega_m}/{0.3}\right)^{0.25}$ of $S^{\mathrm{CMBL}}_8= 0.818\pm0.022$ from ACT DR6 CMB lensing alone and $S^{\mathrm{CMBL}}_8= 0.813\pm0.018$ when combining ACT DR6 and Planck NPIPE CMB lensing power spectra. These results are in excellent agreement with $\Lambda$CDM model constraints from Planck or $\text{ACT DR4} + \text{WMAP}$ CMB power spectrum measurements. Our lensing measurements from redshifts $z\sim0.5$--$5$ are thus fully consistent with $\Lambda$CDM structure growth predictions based on CMB anisotropies probing primarily $z\sim1100$. We find no evidence for a suppression of the amplitude of cosmic structure at low redshiftsComment: 45+21 pages, 50 figures. Prepared for submission to ApJ. Also see companion papers Madhavacheril et al and MacCrann et a