Showing papers by "University of California, Santa Cruz published in 2018"

The Complete Light-curve Sample of Spectroscopically Confirmed SNe Ia from Pan-STARRS1 and Cosmological Constraints from the Combined Pantheon Sample

Abstract: Author(s): Scolnic, DM; Jones, DO; Rest, A; Pan, YC; Chornock, R; Foley, RJ; Huber, ME; Kessler, R; Narayan, G; Riess, AG; Rodney, S; Berger, E; Brout, DJ; Challis, PJ; Drout, M; Finkbeiner, D; Lunnan, R; Kirshner, RP; Sanders, NE; Schlafly, E; Smartt, S; Stubbs, CW; Tonry, J; Wood-Vasey, WM; Foley, M; Hand, J; Johnson, E; Burgett, WS; Chambers, KC; Draper, PW; Hodapp, KW; Kaiser, N; Kudritzki, RP; Magnier, EA; Metcalfe, N; Bresolin, F; Gall, E; Kotak, R; McCrum, M; Smith, KW | Abstract: We present optical light curves, redshifts, and classifications for 365 spectroscopically confirmed Type Ia supernovae (SNe Ia) discovered by the Pan-STARRS1 (PS1) Medium Deep Survey. We detail improvements to the PS1 SN photometry, astrometry, and calibration that reduce the systematic uncertainties in the PS1 SN Ia distances. We combine the subset of 279 PS1 SNe Ia (0.03 l z l 0.68) with useful distance estimates of SNe Ia from the Sloan Digital Sky Survey (SDSS), SNLS, and various low-z and Hubble Space Telescope samples to form the largest combined sample of SNe Ia, consisting of a total of 1048 SNe Ia in the range of 0.01 l z l 2.3, which we call the Pantheon Sample. When combining Planck 2015 cosmic microwave background (CMB) measurements with the Pantheon SN sample, we find Wm = 0.307 ± 0.012 and w = -1.026 ± 0.041 for the wCDM model. When the SN and CMB constraints are combined with constraints from BAO and local H0 measurements, the analysis yields the most precise measurement of dark energy to date: w0 = -1.007 ± 0.089 and wa = -0.222 ± 0.407 for the w0waCDM model. Tension with a cosmological constant previously seen in an analysis of PS1 and low-z SNe has diminished after an increase of 2× in the statistics of the PS1 sample, improved calibration and photometry, and stricter light-curve quality cuts. We find that the systematic uncertainties in our measurements of dark energy are almost as large as the statistical uncertainties, primarily due to limitations of modeling the low-redshift sample. This must be addressed for future progress in using SNe Ia to measure dark energy.

Nanopore sequencing and assembly of a human genome with ultra-long reads

Abstract: We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ∼3 Mb). We developed a protocol to generate ultra-long reads (N50 > 100 kb, read lengths up to 882 kb). Incorporating an additional 5× coverage of these ultra-long reads more than doubled the assembly contiguity (NG50 ∼6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4-Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length, and closure of gaps in the reference human genome assembly GRCh38.

NanoPack: visualizing and processing long-read sequencing data.

Abstract: Summary Here we describe NanoPack, a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Availability and implementation The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools. Supplementary information Supplementary data are available at Bioinformatics online.

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

Abstract: The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.

CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens.

Abstract: CRISPOR.org is a web tool for genome editing experiments with the CRISPR-Cas9 system. It finds guide RNAs in an input sequence and ranks them according to different scores that evaluate potential off-targets in the genome of interest and predict on-target activity. The list of genomes is continuously expanded, with more 150 genomes added in the last two years. CRISPOR tries to provide a comprehensive solution from selection, cloning and expression of guide RNA as well as providing primers needed for testing guide activity and potential off-targets. Recent developments include batch design for genome-wide CRISPR and saturation screens, creating custom oligonucleotides for guide cloning and the design of next generation sequencing primers to test for off-target mutations. CRISPOR is available from http://crispor.org, including the full source code of the website and a stand-alone, command-line version.

Modules for Experiments in Stellar Astrophysics (MESA) : Convective Boundaries, Element Diffusion, and Massive Star Explosions

Abstract: We update the capabilities of the software instrument Modules for Experiments in Stellar Astrophysics (MESA) and enhance its ease of use and availability. Our new approach to locating convective boundaries is consistent with the physics of convection, and yields reliable values of the convective-core mass during both hydrogen- and helium-burning phases. Stars with become white dwarfs and cool to the point where the electrons are degenerate and the ions are strongly coupled, a realm now available to study with MESA due to improved treatments of element diffusion, latent heat release, and blending of equations of state. Studies of the final fates of massive stars are extended in MESA by our addition of an approximate Riemann solver that captures shocks and conserves energy to high accuracy during dynamic epochs. We also introduce a 1D capability for modeling the effects of Rayleigh–Taylor instabilities that, in combination with the coupling to a public version of the radiation transfer instrument, creates new avenues for exploring Type II supernova properties. These capabilities are exhibited with exploratory models of pair-instability supernovae, pulsational pair-instability supernovae, and the formation of stellar-mass black holes. The applicability of MESA is now widened by the capability to import multidimensional hydrodynamic models into MESA. We close by introducing software modules for handling floating point exceptions and stellar model optimization, as well as four new software tools— , -Docker, , and mesastar.org—to enhance MESA's education and research impact.

The chromatin accessibility landscape of primary human cancers

Abstract: INTRODUCTION Cancer is one of the leading causes of death worldwide. Although the 2% of the human genome that encodes proteins has been extensively studied, much remains to be learned about the noncoding genome and gene regulation in cancer. Genes are turned on and off in the proper cell types and cell states by transcription factor (TF) proteins acting on DNA regulatory elements that are scattered over the vast noncoding genome and exert long-range influences. The Cancer Genome Atlas (TCGA) is a global consortium that aims to accelerate the understanding of the molecular basis of cancer. TCGA has systematically collected DNA mutation, methylation, RNA expression, and other comprehensive datasets from primary human cancer tissue. TCGA has served as an invaluable resource for the identification of genomic aberrations, altered transcriptional networks, and cancer subtypes. Nonetheless, the gene regulatory landscapes of these tumors have largely been inferred through indirect means. RATIONALE A hallmark of active DNA regulatory elements is chromatin accessibility. Eukaryotic genomes are compacted in chromatin, a complex of DNA and proteins, and only the active regulatory elements are accessible by the cell’s machinery such as TFs. The assay for transposase-accessible chromatin using sequencing (ATAC-seq) quantifies DNA accessibility through the use of transposase enzymes that insert sequencing adapters at these accessible chromatin sites. ATAC-seq enables the genome-wide profiling of TF binding events that orchestrate gene expression programs and give a cell its identity. RESULTS We generated high-quality ATAC-seq data in 410 tumor samples from TCGA, identifying diverse regulatory landscapes across 23 cancer types. These chromatin accessibility profiles identify cancer- and tissue-specific DNA regulatory elements that enable classification of tumor subtypes with newly recognized prognostic importance. We identify distinct TF activities in cancer based on differences in the inferred patterns of TF-DNA interaction and gene expression. Genome-wide correlation of gene expression and chromatin accessibility predicts tens of thousands of putative interactions between distal regulatory elements and gene promoters, including key oncogenes and targets in cancer immunotherapy, such as MYC , SRC , BCL2 , and PDL1 . Moreover, these regulatory interactions inform known genetic risk loci linked to cancer predisposition, nominating biochemical mechanisms and target genes for many cancer-linked genetic variants. Lastly, integration with mutation profiling by whole-genome sequencing identifies cancer-relevant noncoding mutations that are associated with altered gene expression. A single-base mutation located 12 kilobases upstream of the FGD4 gene, a regulator of the actin cytoskeleton, generates a putative de novo binding site for an NKX TF and is associated with an increase in chromatin accessibility and a concomitant increase in FGD4 gene expression. CONCLUSION The accessible genome of primary human cancers provides a wealth of information on the susceptibility, mechanisms, prognosis, and potential therapeutic strategies of diverse cancer types. Prediction of interactions between DNA regulatory elements and gene promoters sets the stage for future integrative gene regulatory network analyses. The discovery of hundreds of noncoding somatic mutations that exhibit allele-specific regulatory effects suggests a pervasive mechanism for cancer cells to manipulate gene expression and increase cellular fitness. These data may serve as a foundational resource for the cancer research community.

The waning of the WIMP? A review of models, searches, and constraints

Abstract: Weakly Interacting Massive Particles (WIMPs) are among the best-motivated dark matter candidates. No conclusive signal, despite an extensive search program that combines, often in a complementary way, direct, indirect, and collider probes, has been detected so far. This situation might change in near future due to the advent of one/multi-TON Direct Detection experiments. We thus, find it timely to provide a review of the WIMP paradigm with focus on a few models which can be probed at best by these facilities. Collider and Indirect Detection, nevertheless, will not be neglected when they represent a complementary probe.

First results from the IllustrisTNG simulations: a tale of two elements - chemical evolution of magnesium and europium

Abstract: The distribution of elements in galaxies provides a wealth of information about their production sites and their subsequent mixing into the interstellar medium. Here we investigate the distribution of elements within stars in the IllustrisTNG simulations. In particular, we analyze the abundance ratios of magnesium and europium in Milky Way-like galaxies from the TNG100 simulation (stellar masses ${\log} (M_\star / {\rm M}_\odot) \sim 9.7 - 11.2$). As abundances of magnesium and europium for individual stars in the Milky Way are observed across a variety of spatial locations and metallicities, comparison with the stellar abundances in our more than $850$ Milky Way-like galaxies provides stringent constraints on our chemical evolutionary methods. To this end we use the magnesium to iron ratio as a proxy for the effects of our SNII and SNIa metal return prescription, and a means to compare our simulated abundances to a wide variety of galactic observations. The europium to iron ratio tracks the rare ejecta from neutron star -- neutron star mergers, the assumed primary site of europium production in our models, which in turn is a sensitive probe of the effects of metal diffusion within the gas in our simulations. We find that europium abundances in Milky Way-like galaxies show no correlation with assembly history, present day galactic properties, and average galactic stellar population age. In general, we reproduce the europium to iron spread at low metallicities observed in the Milky Way, with the level of enhancement being sensitive to gas properties during redshifts $z \approx 2-4$. We show that while the overall normalization of [Eu/Fe] is susceptible to resolution and post-processing assumptions, the relatively large spread of [Eu/Fe] at low [Fe/H] when compared to that at high [Fe/H] is very robust.

Moving in the Anthropocene : global reductions in terrestrial mammalian movements

Abstract: Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral changes of individual animals and to the exclusion of species with long-range movements from areas with higher human impact. Global loss of vagility alters a key ecological trait of animals that affects not only population persistence but also ecosystem processes such as predator-prey interactions, nutrient cycling, and disease transmission.

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics.

Abstract: Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression to compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy and general robustness to misspecified reference sets. We apply this framework to 44 GTEx tissues and 100+ phenotypes from GWAS and meta-analysis studies, creating a growing public catalog of associations that seeks to capture the effects of gene expression variation on human phenotypes. Replication in an independent cohort is shown. Most of the associations are tissue specific, suggesting context specificity of the trait etiology. Colocalized significant associations in unexpected tissues underscore the need for an agnostic scanning of multiple contexts to improve our ability to detect causal regulatory mechanisms. Monogenic disease genes are enriched among significant associations for related traits, suggesting that smaller alterations of these genes may cause a spectrum of milder phenotypes.

Efficient hydrogen peroxide generation using reduced graphene oxide-based oxygen reduction electrocatalysts

Abstract: Electrochemical oxygen reduction has garnered attention as an emerging alternative to the traditional anthraquinone oxidation process to enable the distributed production of hydrogen peroxide. Here, we demonstrate a selective and efficient non-precious electrocatalyst, prepared through an easily scalable mild thermal reduction of graphene oxide, to form hydrogen peroxide from oxygen. During oxygen reduction, certain variants of the mildly reduced graphene oxide electrocatalyst exhibit highly selective and stable peroxide formation activity at low overpotentials (<10 mV) under basic conditions, exceeding the performance of current state-of-the-art alkaline catalysts. Spectroscopic structural characterization and in situ Raman spectroelectrochemistry provide strong evidence that sp2-hybridized carbon near-ring ether defects along sheet edges are the most active sites for peroxide production, providing new insight into the electrocatalytic design of carbon-based materials for effective peroxide production. Electrochemical routes for the production of hydrogen peroxide would reduce the waste inherent in the current anthraquinone process, and also make distributed and on-site production more feasible. Here, inexpensive reduced graphene oxide is proven to be a stable and selective catalyst for oxygen reduction at remarkably low overpotentials.

The global flood protection savings provided by coral reefs

Abstract: Coral reefs can provide significant coastal protection benefits to people and property. Here we show that the annual expected damages from flooding would double, and costs from frequent storms would triple without reefs. For 100-year storm events, flood damages would increase by 91% to $US 272 billion without reefs. The countries with the most to gain from reef management are Indonesia, Philippines, Malaysia, Mexico, and Cuba; annual expected flood savings exceed $400 M for each of these nations. Sea-level rise will increase flood risk, but substantial impacts could happen from reef loss alone without better near-term management. We provide a global, process-based valuation of an ecosystem service across an entire marine biome at (sub)national levels. These spatially explicit benefits inform critical risk and environmental management decisions, and the expected benefits can be directly considered by governments (e.g., national accounts, recovery plans) and businesses (e.g., insurance). Coral reefs provide significant coastal protection from storms but they have experienced significant losses. Here the authors show that the annual damages from flooding would double globally without reefs and they quantify where reefs provide the most protection to people and property.

The ecological importance of intraspecific variation

Abstract: Human activity is causing wild populations to experience rapid trait change and local extirpation. The resulting effects on intraspecific variation could have substantial consequences for ecological processes and ecosystem services. Although researchers have long acknowledged that variation among species influences the surrounding environment, only recently has evidence accumulated for the ecological importance of variation within species. We conducted a meta-analysis comparing the ecological effects of variation within a species (intraspecific effects) with the effects of replacement or removal of that species (species effects). We evaluated direct and indirect ecological responses, including changes in abundance (or biomass), rates of ecological processes and changes in community composition. Our results show that intraspecific effects are often comparable to, and sometimes stronger than, species effects. Species effects tend to be larger for direct ecological responses (for example, through consumption), whereas intraspecific effects and species effects tend to be similar for indirect responses (for example, through trophic cascades). Intraspecific effects are especially strong when indirect interactions alter community composition. Our results summarize data from the first generation of studies examining the relative ecological effects of intraspecific variation. Our conclusions can help inform the design of future experiments and the formulation of strategies to quantify and conserve biodiversity.

The dark energy survey data release 1

Abstract: We describe the first public data release of the Dark Energy Survey, DES DR1, consisting of reduced single-epoch images, co-added images, co-added source catalogs, and associated products and services assembled over the first 3 yr of DES science operations. DES DR1 is based on optical/near-infrared imaging from 345 distinct nights (2013 August to 2016 February) by the Dark Energy Camera mounted on the 4 m Blanco telescope at the Cerro Tololo InterAmerican Observatory in Chile. We release data from the DES wide-area survey covering similar to 5000 deg(2) of the southern Galactic cap in five broad photometric bands, grizY. DES DR1 has a median delivered point-spread function of g = 1.12, r = 0.96, i = 0.88, z = 0.84, and Y = 0.'' 90 FWHM, a photometric precision of <1% in all bands, and an astrometric precision of 151 mas. The median co-added catalog depth for a 1.'' 95 diameter aperture at signal-to-noise ratio (S/N) = 10 is g = 24.33, r = 24.08, i = 23.44, z = 22.69, and Y = 21.44 mag. DES DR1 includes nearly 400 million distinct astronomical objects detected in similar to 10,000 co-add tiles of size 0.534 deg(2) produced from similar to 39,000 individual exposures. Benchmark galaxy and stellar samples contain similar to 310 million and similar to 80 million objects, respectively, following a basic object quality selection. These data are accessible through a range of interfaces, including query web clients, image cutout servers, jupyter notebooks, and an interactive co-add image visualization tool. DES DR1 constitutes the largest photometric data set to date at the achieved depth and photometric precision.

Carbon-Supported Single Atom Catalysts for Electrochemical Energy Conversion and Storage.

Abstract: Single atoms of select transition metals supported on carbon substrates have emerged as a unique system for electrocatalysis because of maximal atom utilization (≈100%) and high efficiency for a range of reactions involved in electrochemical energy conversion and storage, such as the oxygen reduction, oxygen evolution, hydrogen evolution, and CO2 reduction reactions. Herein, the leading strategies for the preparation of single atom catalysts are summarized, and the electrocatalytic performance of the resulting samples for the various reactions is discussed. In general, the carbon substrate not only provides a stabilizing matrix for the metal atoms, but also impacts the electronic density of the metal atoms due to strong interfacial interactions, which may lead to the formation of additional active sites by the adjacent carbon atoms and hence enhanced electrocatalytic activity. This necessitates a detailed understanding of the material structures at the atomic level, a critical step in the construction of a relevant structural model for theoretical simulations and calculations. Finally, a perspective is included highlighting the promises and challenges for the future development of carbon-supported single atom catalysts in electrocatalysis.

Reversible Mn 2+ /Mn 4+ double redox in lithium-excess cathode materials

Abstract: There is an urgent need for low-cost, resource-friendly, high-energy-density cathode materials for lithium-ion batteries to satisfy the rapidly increasing need for electrical energy storage. To replace the nickel and cobalt, which are limited resources and are associated with safety problems, in current lithium-ion batteries, high-capacity cathodes based on manganese would be particularly desirable owing to the low cost and high abundance of the metal, and the intrinsic stability of the Mn4+ oxidation state. Here we present a strategy of combining high-valent cations and the partial substitution of fluorine for oxygen in a disordered-rocksalt structure to incorporate the reversible Mn2+/Mn4+ double redox couple into lithium-excess cathode materials. The lithium-rich cathodes thus produced have high capacity and energy density. The use of the Mn2+/Mn4+ redox reduces oxygen redox activity, thereby stabilizing the materials, and opens up new opportunities for the design of high-performance manganese-rich cathodes for advanced lithium-ion batteries.

The Hyper Suprime-Cam software pipeline

Abstract: In this paper, we describe the optical imaging data processing pipeline developed for the Subaru Telescope's Hyper Suprime-Cam (HSC) instrument. The HSC Pipeline builds on the prototype pipeline being developed by the Large Synoptic Survey Telescope's Data Management system, adding customizations for HSC, large-scale processing capabilities, and novel algorithms that have since been reincorporated into the LSST codebase. While designed primarily to reduce HSC Subaru Strategic Program (SSP) data, it is also the recommended pipeline for reducing general-observer HSC data. The HSC pipeline includes high level processing steps that generate coadded images and science-ready catalogs as well as low-level detrending and image characterizations.

The UCSC Genome Browser database: 2018 update.

Abstract: The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.

Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study

Abstract: Purpose The prevalence and features of treatment-emergent small-cell neuroendocrine prostate cancer (t-SCNC) are not well characterized in the era of modern androgen receptor (AR)-targeting therapy. We sought to characterize the clinical and genomic features of t-SCNC in a multi-institutional prospective study. Methods Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy and were followed for survival. Metastatic biopsy specimens underwent independent, blinded pathology review along with RNA/DNA sequencing. Results A total of 202 consecutive patients were enrolled. One hundred forty-eight (73%) had prior disease progression on abiraterone and/or enzalutamide. The biopsy evaluable rate was 79%. The overall incidence of t-SCNC detection was 17%. AR amplification and protein expression were present in 67% and 75%, respectively, of t-SCNC biopsy specimens. t-SCNC was detected at similar proportions in bone, node, and visceral organ biopsy specimens. Genomic alterations in the DNA repair pathway were nearly mutually exclusive with t-SCNC differentiation ( P = .035). Detection of t-SCNC was associated with shortened overall survival among patients with prior AR-targeting therapy for mCRPC (hazard ratio, 2.02; 95% CI, 1.07 to 3.82). Unsupervised hierarchical clustering of the transcriptome identified a small-cell-like cluster that further enriched for adverse survival outcomes (hazard ratio, 3.00; 95% CI, 1.25 to 7.19). A t-SCNC transcriptional signature was developed and validated in multiple external data sets with > 90% accuracy. Multiple transcriptional regulators of t-SCNC were identified, including the pancreatic neuroendocrine marker PDX1. Conclusion t-SCNC is present in nearly one fifth of patients with mCRPC and is associated with shortened survival. The near-mutual exclusivity with DNA repair alterations suggests t-SCNC may be a distinct subset of mCRPC. Transcriptional profiling facilitates the identification of t-SCNC and novel therapeutic targets.

Looking Beyond the Surface: A Challenge Set for Reading Comprehension over Multiple Sentences

Abstract: We present a reading comprehension challenge in which questions can only be answered by taking into account information from multiple sentences. We solicit and verify questions and answers for this challenge through a 4-step crowdsourcing experiment. Our challenge dataset contains 6,500+ questions for 1000+ paragraphs across 7 different domains (elementary school science, news, travel guides, fiction stories, etc) bringing in linguistic diversity to the texts and to the questions wordings. On a subset of our dataset, we found human solvers to achieve an F1-score of 88.1%. We analyze a range of baselines, including a recent state-of-art reading comprehension system, and demonstrate the difficulty of this challenge, despite a high human performance. The dataset is the first to study multi-sentence inference at scale, with an open-ended set of question types that requires reasoning skills.

Variation graph toolkit improves read mapping by representing genetic variation in the reference.

Abstract: Reference genomes guide our interpretation of DNA sequence data. However, conventional linear references represent only one version of each locus, ignoring variation in the population. Poor representation of an individual's genome sequence impacts read mapping and introduces bias. Variation graphs are bidirected DNA sequence graphs that compactly represent genetic variation across a population, including large-scale structural variation such as inversions and duplications. Previous graph genome software implementations have been limited by scalability or topological constraints. Here we present vg, a toolkit of computational methods for creating, manipulating, and using these structures as references at the scale of the human genome. vg provides an efficient approach to mapping reads onto arbitrary variation graphs using generalized compressed suffix arrays, with improved accuracy over alignment to a linear reference, and effectively removing reference bias. These capabilities make using variation graphs as references for DNA sequencing practical at a gigabase scale, or at the topological complexity of de novo assemblies.

Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

Abstract: The idea that noncrop habitat enhances pest control and represents a win-win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win-win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies.

The Hyper Suprime-Cam SSP Survey: Overview and survey design

Abstract: Hyper Suprime-Cam (HSC) is a wide-field imaging camera on the prime focus of the 8.2m Subaru telescope on the summit of Maunakea. A team of scientists from Japan, Taiwan and Princeton University is using HSC to carry out a 300-night multi-band imaging survey of the high-latitude sky. The survey includes three layers: the Wide layer will cover 1400 deg$^2$ in five broad bands ($grizy$), with a $5\,\sigma$ point-source depth of $r \approx 26$. The Deep layer covers a total of 26~deg$^2$ in four fields, going roughly a magnitude fainter, while the UltraDeep layer goes almost a magnitude fainter still in two pointings of HSC (a total of 3.5 deg$^2$). Here we describe the instrument, the science goals of the survey, and the survey strategy and data processing. This paper serves as an introduction to a special issue of the Publications of the Astronomical Society of Japan, which includes a large number of technical and scientific papers describing results from the early phases of this survey.

Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Abstract: Malignant pleural mesothelioma (MPM) is a highly lethal cancer of the lining of the chest cavity. To expand our understanding of MPM, we conducted a comprehensive integrated genomic study, including the most detailed analysis of BAP1 alterations to date. We identified histology-independent molecular prognostic subsets, and defined a novel genomic subtype with TP53 and SETDB1 mutations and extensive loss of heterozygosity. We also report strong expression of the immune checkpoint gene VISTA in epithelioid MPM, strikingly higher than in other solid cancers, with implications for the immune response to MPM and for its immunotherapy. Our findings highlight new avenues for further investigation of MPM biology and novel therapeutic options.

Soft Somatosensitive Actuators via Embedded 3D Printing.

Abstract: Humans possess manual dexterity, motor skills, and other physical abilities that rely on feedback provided by the somatosensory system. Herein, a method is reported for creating soft somatosensitive actuators (SSAs) via embedded 3D printing, which are innervated with multiple conductive features that simultaneously enable haptic, proprioceptive, and thermoceptive sensing. This novel manufacturing approach enables the seamless integration of multiple ionically conductive and fluidic features within elastomeric matrices to produce SSAs with the desired bioinspired sensing and actuation capabilities. Each printed sensor is composed of an ionically conductive gel that exhibits both long-term stability and hysteresis-free performance. As an exemplar, multiple SSAs are combined into a soft robotic gripper that provides proprioceptive and haptic feedback via embedded curvature, inflation, and contact sensors, including deep and fine touch contact sensors. The multimaterial manufacturing platform enables complex sensing motifs to be easily integrated into soft actuating systems, which is a necessary step toward closed-loop feedback control of soft robots, machines, and haptic devices.