Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes

Background: Untranslated regions (UTRs) are important mediators of post-transcriptional regulation. The length of UTRs and the composition of regulatory elements within them are known to vary substantially across genes, but little is known about the reasons for this variation in humans. Here, we set out to determine whether this variation, specifically in 5’UTRs, correlates with gene dosage sensitivity. Results: We investigate 5’UTR length, the number of alternative transcription start sites, the potential for alternative splicing, the number and type of upstream open reading frames (uORFs) and the propensity of 5’UTRs to form secondary structures. We explore how these elements vary by gene tolerance to loss-of-function (LoF; using the LOEUF metric), and in genes where changes in dosage are known to cause disease. We show that LOEUF correlates with 5’UTR length and complexity. Genes that are most intolerant to LoF have longer 5’UTRs, greater TSS diversity, and more upstream regulatory elements than their LoF tolerant counterparts. We show that these differences are evident in disease gene-sets, but not in recessive developmental disorder genes where LoF of a single allele is tolerated. Conclusions: Our results confirm the importance of post-transcriptional regulation through 5'UTRs in tight regulation of mRNA and protein levels, particularly for genes where changes in dosage are deleterious and lead to disease. Finally, to support gene-based investigation we release a web-based browser tool, VuTR, that supports exploration of the composition of individual 5'UTRs and the impact of genetic variation within them

Universal Ecological Patterns in College Basketball Communities

The rank abundance of common and rare species within ecological communities is remarkably consistent from the tropics to the tundra. This invariant patterning provides one of ecology's most enduring and unified tenets: most species rare and a few very common. Increasingly, attention is focused upon elucidating biological mechanisms that explain these species abundance distributions (SADs), but these evaluations remain controversial. We show that college basketball wins generate SADs just like those observed in ecological communities. Whereas college basketball wins are structured by competitive interactions, the result produces a SAD pattern indistinguishable from random wins. We also show that species abundance data for tropical trees exhibits a significant-digit pattern consistent with data derived from complex structuring forces. These results cast doubt upon the ability of SAD analysis to resolve ecological mechanism, and their patterning may reflect statistical artifact as much as biological processes

Ecological distribution and population physiology defined by proteomics in a natural microbial community

Community proteomics applied to natural microbial biofilms resolves how the physiology of different populations from a model ecosystem change with measured environmental factors in situ.The initial colonists, Leptospirillum Group II bacteria, persist throughout ecological succession and dominate all communities, a pattern that resembles community assembly patterns in some macroecological systems.Interspecies interactions, and not abiotic environmental factors, demonstrate the strongest correlation to physiological changes of Leptospirillum Group II.Environmental niches of subdominant populations seem to be determined by combinations of specific sets of abiotic environmental factors

Hyper Suprime-Cam Year 3 Results: Cosmology from Cosmic Shear Two-point Correlation Functions

We perform a blinded cosmology analysis with cosmic shear two-point correlation functions (2PCFs) measured from more than 25 million galaxies in the Hyper Suprime-Cam three-year shear catalog in four tomographic redshift bins ranging from 0.3 to 1.5. After conservative masking and galaxy selection, the survey covers 416 deg$^2$ of the northern sky with an effective galaxy number density of 15 arcmin$^{-2}$ over the four redshift bins. The 2PCFs adopted for cosmology analysis are measured in the angular range: $7.1 < \theta/{\rm arcmin} < 56.6$ for $\xi_+$ and $31.2 <\theta/{\rm arcmin} < 248$ for $\xi_-$, with a total signal-to-noise ratio of 26.6. We apply a conservative, wide, flat prior on the photometric redshift errors on the last two tomographic bins, and the relative magnitudes of the cosmic shear amplitude across four redshift bins allow us to calibrate the photometric redshift errors. With this flat prior on redshift errors, we find $\Omega_{\rm m}=0.256_{-0.044}^{+0.056}$ and $S_8\equiv \sigma_8 \sqrt{\Omega_{\rm m}/0.3}=0.769_{-0.034}^{+0.031}$ (both 68\% CI) for a flat $\Lambda$ cold dark matter cosmology. We find, after unblinding, that our constraint on $S_8$ is consistent with the Fourier space cosmic shear and the 3$\times$2pt analyses on the same HSC dataset. We carefully study the potential systematics from astrophysical and systematic model uncertainties in our fiducial analysis using synthetic data, and report no biases (including projection bias in the posterior space) greater than $0.5\sigma$ in the estimation of $S_8$. Our analysis hints that the mean redshifts of the two highest tomographic bins are higher than initially estimated. In addition, a number of consistency tests are conducted to assess the robustness of our analysis. Comparing our result with Planck-2018 cosmic microwave background observations, we find a ~$2\sigma$ tension for the $\Lambda$CDM model.Comment: 38 pages, 32 figures, 4 tables (PRD in press.

Hyper Suprime-Cam Year 3 results: Cosmology from cosmic shear two-point correlation functions

We perform a blinded cosmology analysis with cosmic shear two-point correlation functions measured from more than 25 million galaxies in the Hyper Suprime-Cam three-year shear catalog in four tomographic redshift bins ranging from 0.3 to 1.5. After conservative masking and galaxy selection, the survey covers 416 deg2 of the northern sky with an effective galaxy number density of 15 arcmin-2 over the four redshift bins. The 2PCFs adopted for cosmology analysis are measured in the angular range; 7.1&lt;θ/arcmin&lt;56.6 for ζ+ and 31.2&lt;θ/arcmin&lt;248 for ζ-, with a total signal-to-noise ratio of 26.6. We apply a conservative, wide, flat prior on the photometric redshift errors on the last two tomographic bins, and the relative magnitudes of the cosmic shear amplitude across four redshift bins allow us to calibrate the photometric redshift errors. With this flat prior on redshift errors, we find ωm=0.256-0.044+0.056 and S8σ8ωm/0.3=0.769-0.034+0.031 (both 68% C.I.) for a flat Λ cold dark matter cosmology. We find, after unblinding, that our constraint on S8 is consistent with the Fourier space cosmic shear and the 3×2 pt analyses on the same HSC dataset. We carefully study the potential systematics from astrophysical and systematic model uncertainties in our fiducial analysis using synthetic data, and report no biases (including projection bias in the posterior space) greater than 0.5σ in the estimation of S8. Our analysis hints that the mean redshifts of the two highest tomographic bins are higher than initially estimated. In addition, a number of consistency tests are conducted to assess the robustness of our analysis. Comparing our result with Planck-2018 cosmic microwave background observations, we find a ∼2σ tension for the ΛCDM model

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie

Hyper Suprime-Cam Year 3 results: cosmology from cosmic shear power spectra

We measure weak lensing cosmic shear power spectra from the 3-year galaxy shear catalog of the Hyper Suprime-Cam (HSC) Subaru Strategic Program imaging survey. The shear catalog covers 416  deg2 of the northern sky, with a mean i-band seeing of 0.59 arcsec and an effective galaxy number density of 15  arcmin−2 within our adopted redshift range. With an i-band magnitude limit of 24.5 mag, and four tomographic redshift bins spanning 0.3≤zph≤1.5 based on photometric redshifts, we obtain a high-significance measurement of the cosmic shear power spectra, with a signal-to-noise ratio of approximately 26.4 in the multipole range 300<ℓ<1800. The accuracy of our power spectrum measurement is tested against realistic mock shear catalogs, and we use these catalogs to get a reliable measurement of the covariance of the power spectrum measurements. We use a robust blinding procedure to avoid confirmation bias, and model various uncertainties and sources of bias in our analysis, including point spread function systematics, redshift distribution uncertainties, the intrinsic alignment of galaxies and the modeling of the matter power spectrum. For a flat ΛCDM model, we find S8≡σ8(Ωm/0.3)0.5=0.776+0.032−0.033, which is in excellent agreement with the constraints from the other HSC Year 3 cosmology analyses, as well as those from a number of other cosmic shear experiments. This result implies a ∼2σ-level tension with the Planck 2018 cosmology. We study the effect that various systematic errors and modeling choices could have on this value, and find that they can shift the best-fit value of S8 by no more than ∼0.5σ, indicating that our result is robust to such systematics

Gravitational Waves From Known Pulsars: Results From The Initial Detector Era

We present the results of searches for gravitational waves from a large selection of pulsars using data from the most recent science runs (S6, VSR2 and VSR4) of the initial generation of interferometric gravitational wave detectors LIGO (Laser Interferometric Gravitational-wave Observatory) and Virgo. We do not see evidence for gravitational wave emission from any of the targeted sources but produce upper limits on the emission amplitude. We highlight the results from seven young pulsars with large spin-down luminosities. We reach within a factor of five of the canonical spin-down limit for all seven of these, whilst for the Crab and Vela pulsars we further surpass their spin-down limits. We present new or updated limits for 172 other pulsars (including both young and millisecond pulsars). Now that the detectors are undergoing major upgrades, and, for completeness, we bring together all of the most up-to-date results from all pulsars searched for during the operations of the first-generation LIGO, Virgo and GEO600 detectors. This gives a total of 195 pulsars including the most recent results described in this paper.United States National Science FoundationScience and Technology Facilities Council of the United KingdomMax-Planck-SocietyState of Niedersachsen/GermanyAustralian Research CouncilInternational Science Linkages program of the Commonwealth of AustraliaCouncil of Scientific and Industrial Research of IndiaIstituto Nazionale di Fisica Nucleare of ItalySpanish Ministerio de Economia y CompetitividadConselleria d'Economia Hisenda i Innovacio of the Govern de les Illes BalearsNetherlands Organisation for Scientific ResearchPolish Ministry of Science and Higher EducationFOCUS Programme of Foundation for Polish ScienceRoyal SocietyScottish Funding CouncilScottish Universities Physics AllianceNational Aeronautics and Space AdministrationOTKA of HungaryLyon Institute of Origins (LIO)National Research Foundation of KoreaIndustry CanadaProvince of Ontario through the Ministry of Economic Development and InnovationNational Science and Engineering Research Council CanadaCarnegie TrustLeverhulme TrustDavid and Lucile Packard FoundationResearch CorporationAlfred P. Sloan FoundationAstronom