Whitney Museum of American Art

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene. A description is given of the ENCODE effort to provide a complete catalogue of primary and processed RNAs found either in specific subcellular compartments or throughout the cell, revealing that three-quarters of the human genome can be transcribed, and providing a wealth of information on the range and levels of expression, localization, processing fates and modifications of known and previously unannotated RNAs. These authors describe the ENCODE (Encyclopedia of DNA Elements) effort to provide a complete catalogue of primary and processed RNAs found either in specific sub-cellular compartments or throughout the cell. They show that three-quarters of the human genome can be transcribed, and provide a wealth of information about the range and levels of expression, localization, processing fates and modifications of both known and previously unannotated RNAs. Collectively, these observations suggest that the current concept of a gene should be revisited.

The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.

We present cosmological results from the final galaxy clustering data set of the Baryon Oscillation Spectroscopic Survey, part of the Sloan Digital Sky Survey III. Our combined galaxy sample comprises 1.2 million massive galaxies over an effective area of 9329 deg 2 and volume of 18.7 Gpc 3 , divided into three partially overlapping redshift slices centred at effective redshifts 0.38, 0.51 and 0.61. We measure the angular diameter distance D M and Hubble parameter H from the baryon acoustic oscillation (BAO) method, in combination with a cosmic microwave background prior on the sound horizon scale, after applying reconstruction to reduce non-linear effects on the BAO feature. Using the anisotropic clustering of the

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association. The Structural Variation Analysis Group of The 1000 Genomes Project reports an integrated structural variation map based on discovery and genotyping of eight major structural variation classes in 2,504 unrelated individuals from across 26 populations; structural variation is compared within and between populations and its functional impact is quantified. The Structural Variation Analysis Group of The 1000 Genomes Project reports an integrated structural variation map based on discovery and genotyping of eight major structural variation classes in genomes for 2,504 unrelated individuals from across 26 populations. They characterize structural variation within and between populations and quantify its functional effect. The authors further create a phased reference panel that will be valuable for population genetic and disease association studies.

Citation: Alam, S., Albareti, F. D., Prieto, C. A., Anders, F., Anderson, S. F., Anderton, T., . . . Zhu, G. T. (2015). THE ELEVENTH AND TWELFTH DATA RELEASES OF THE SLOAN DIGITAL SKY SURVEY: FINAL DATA FROM SDSS-III. Astrophysical Journal Supplement Series, 219(1), 27. doi:10.1088/0067-0049/219/1/12

We present a one per cent measurement of the cosmic distance scale from the detections of the baryon acoustic oscillations (BAO) in the clustering of galaxies from the Baryon Oscillation Spectroscopic Survey, which is part of the Sloan Digital Sky Survey III. Our results come from the Data Release 11 (DR11) sample, containing nearly one million galaxies and covering approximately 8500 square degrees and the redshift range 0.2 < z < 0.7. We also compare these results with those from the publicly released DR9 and DR10 samples. Assuming a concordance cold dark matter ( CDM) cosmological model, the DR11 sample covers a volume of 13 Gpc 3 and is the largest region of the Universe ever surveyed at this density. We measure the correlation function and power spectrum, including density-field reconstruction of the BAO feature. The acoustic features are detected at a significance of over 7 in both the correlation function and power spectrum. Fitting for the position of the acoustic features measures the distance relative to the sound horizon at the drag epoch, r d , which has a value of r d,fid = 149.28 Mpc in our fiducial cosmology. We find D V = (1264 25 Mpc)(r d /r d,fid )

Abstract The Apache Point Observatory Galactic Evolution Experiment (APOGEE), one of the programs in the Sloan Digital Sky Survey III (SDSS-III), has now completed its systematic, homogeneous spectroscopic survey sampling all major populations of the Milky Way. After a three-year observing campaign on the Sloan 2.5 m Telescope, APOGEE has collected a half million high-resolution ( R ∼ 22,500), high signal-to-noise ratio (&gt;100), infrared (1.51–1.70 μ m) spectra for 146,000 stars, with time series information via repeat visits to most of these stars. This paper describes the motivations for the survey and its overall design—hardware, field placement, target selection, operations—and gives an overview of these aspects as well as the data reduction, analysis, and products. An index is also given to the complement of technical papers that describe various critical survey components in detail. Finally, we discuss the achieved survey performance and illustrate the variety of potential uses of the data products by way of a number of science demonstrations, which span from time series analysis of stellar spectral variations and radial velocity variations from stellar companions, to spatial maps of kinematics, metallicity, and abundance patterns across the Galaxy and as a function of age, to new views of the interstellar medium, the chemistry of star clusters, and the discovery of rare stellar species. As part of SDSS-III Data Release 12 and later releases, all of the APOGEE data products are publicly available.

We present an overview of a new integral field spectroscopic survey called MaNGA (Mapping Nearby Galaxies at Apache Point Observatory), one of three core programs in the fourth-generation Sloan Digital Sky Survey (SDSS-IV) that began on 2014 July 1. MaNGA will investigate the internal kinematic structure and composition of gas and stars in an unprecedented sample of 10,000 nearby galaxies. We summarize essential characteristics of the instrument and survey design in the context of MaNGA’s key science goals and present prototype observations to demonstrate MaNGA’s scientific potential. MaNGA employs dithered observations with 17 fiber-bundle integral field units that vary in diameter from 12&lt;i&gt;"&lt;/i&gt; (19 fibers) to 32&lt;i&gt;"&lt;/i&gt; (127 fibers). Two dual-channel spectrographs provide simultaneous wavelength coverage over 3600–10300 Å at &lt;i&gt;R&lt;/i&gt;∼2000.With a typical integration time of 3 hr, MaNGA reaches a target &lt;i&gt;r&lt;/i&gt;-band signal-to-noise ratio of 4–8 (Å&lt;sup&gt;−1&lt;/sup&gt; per 2&lt;i&gt;"&lt;/i&gt; fiber) at 23 AB mag arcsec&lt;sup&gt;−2&lt;/sup&gt;, which is typical for the outskirts of MaNGA galaxies. Targets are selected with &lt;i&gt;M&lt;/i&gt;&lt;sub&gt;∗&lt;/sub&gt; ≳ 10&lt;sup&gt;9&lt;/sup&gt; &lt;i&gt;M&lt;/i&gt;&lt;sub&gt;⊙&lt;/sub&gt; using SDSS-I redshifts and &lt;i&gt;i&lt;/i&gt;-band luminosity to achieve uniform radial coverage in terms of the effective radius, an approximately flat distribution in stellar mass, and a sample spanning a wide range of environments. Analysis of our prototype observations demonstrates MaNGA’s ability to probe gas ionization, shed light on recent star formation and quenching, enable dynamical modeling, decompose constituent components, and map the composition of stellar populations. MaNGA’s spatially resolved spectra will enable an unprecedented study of the astrophysics of nearby galaxies in the coming 6 yr.

Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; the ensemble of these binding events forms a regulatory network, constituting the wiring diagram for a cell. To examine the principles of the human transcriptional regulatory network, we determined the genomic binding information of 119 transcription-related factors in over 450 distinct experiments. We found the combinatorial, co-association of transcription factors to be highly context specific: distinct combinations of factors bind at specific genomic locations. In particular, there are significant differences in the binding proximal and distal to genes. We organized all the transcription factor binding into a hierarchy and integrated it with other genomic information (for example, microRNA regulation), forming a dense meta-network. Factors at different levels have different properties; for instance, top-level transcription factors more strongly influence expression and middle-level ones co-regulate targets to mitigate information-flow bottlenecks. Moreover, these co-regulations give rise to many enriched network motifs (for example, noise-buffering feed-forward loops). Finally, more connected network components are under stronger selection and exhibit a greater degree of allele-specific activity (that is, differential binding to the two parental alleles). The regulatory information obtained in this study will be crucial for interpreting personal genome sequences and understanding basic principles of human biology and disease. A description is given of the ENCODE consortium’s efforts to examine the principles of human transcriptional regulatory networks; the results are integrated with other genomic information to form a hierarchical meta-network where different levels have distinct properties. This manuscript describes the effort of the ENCODE (Encyclopedia of DNA Elements) Consortium to examine the principles of human transcriptional regulatory networks, using a subset of 119 transcription factors. The results are integrated with other genomic information to form a multi-level meta-network in which different levels have distinct properties. The findings will aid future interpretations of human genomics and help us to understand the basic principles of human biology and disease.

The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

This paper links the sharp drop in US manufacturing employment after 2000 to a change in US trade policy that eliminated potential tariff increases on Chinese imports. Industries more exposed to the change experience greater employment loss, increased imports from China, and higher entry by US importers and foreign-owned Chinese exporters. At the plant level, shifts toward less labor-intensive production and exposure to the policy via input-output linkages also contribute to the decline in employment. Results are robust to other potential explanations of employment loss, and there is no similar reaction in the European Union, where policy did not change. (JEL D72, E24, F13, F16, L24, L60, P33)

When creating designed experiments, it is not always possible to run the experiment at the exact settings required to maintain orthogonal effects. However, this is not measurement error when precise measurements of the settings can be made once the experiment begins. A comparison is made for a 15-run Box–Behnken design using both the intended design settings and the actual design settings. Variance inflation factors are used to measure the induced collinearity in the effects. Two cutoff values are suggested for use to determine when an effect's variance inflation factor is too large to keep that effect in the model.

The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.

Designing efficient policies to slow global warming requires an approach that combines economic tools with relations from the natural sciences. The dynamic integrated climate-economy (DICE) model presented here, an intertemporal general-equilibrium model of economic growth and climate change, can be used to investigate alternative approaches to slowing climate change. Evaluation of five policies suggests that a modest carbon tax would be an efficient approach to slow global warming, whereas rigid emissions- or climate-stabilization approaches would impose significant net economic costs.

The 3D-HST and CANDELS programs have provided WFC3 and ACS spectroscopy and photometry over 900 arcmin 2 in five fields: AEGIS, COSMOS, GOODS-North, GOODS-South, and the UKIDSS UDS field. All these fields have a wealth of publicly available imaging data sets in addition to the Hubble Space Telescope (HST) data, which makes it possible to construct the spectral energy distributions (SEDs) of objects over a wide wavelength range. In this paper we describe a photometric analysis of the CANDELS and 3D-HST HST imaging and the ancillary imaging data at wavelengths 0.3-8 m. Objects were selected in the WFC3 near-IR bands, and their SEDs were determined by carefully taking the effects of the point-spread function in each observation into account. A total of 147 distinct imaging data sets were used in the analysis. The photometry is made available in the form of six catalogs: one for each field, as well as a master catalog containing all objects in the entire survey. We also provide derived data products: photometric redshifts, determined with the EAZY code, and stellar population parameters determined with the FAST code. We make all the imaging data that were used in the analysis available, including our reductions of the WFC3 imaging in all five fields. 3D-HST is a spectroscopic survey with the WFC3 and ACS grisms, and the photometric catalogs presented here constitute a necessary first step in the analysis of these grism data. All the data presented in this paper are available through the 3D-HST Web site (http://3dhst.research.yale.edu).

This paper makes a short study of Fredholm integral equations related to potential theory and elasticity, with a view to preparing the ground for their exploitation in the numerical solution of difficult boundary-value problems. Attention is drawn to the advantages of Fredholm&amp;apos;s first equation and of Green&amp;apos;s boundary formula. The latter plays a fundamental and hitherto unrecognized role in the integral equation formula of biharmonic problems.

The relation between the partial pressure of atmospheric carbon dioxide (pCO2) and Paleogene climate is poorly resolved. We used stable carbon isotopic values of di-unsaturated alkenones extracted from deep sea cores to reconstruct pCO2 from the middle Eocene to the late Oligocene (approximately 45 to 25 million years ago). Our results demonstrate that pCO2 ranged between 1000 to 1500 parts per million by volume in the middle to late Eocene, then decreased in several steps during the Oligocene, and reached modern levels by the latest Oligocene. The fall in pCO2 likely allowed for a critical expansion of ice sheets on Antarctica and promoted conditions that forced the onset of terrestrial C4 photosynthesis.

We present measurements of galaxy clustering from the Baryon Oscillation Spectroscopic Survey (BOSS), which is part of the Sloan Digital Sky Survey III (SDSS-III). These use the Data Release 9 (DR9) CMASS sample, which contains 264 283 massive galaxies covering 3275 square degrees with an effective redshift z = 0.57 and redshift range 0.43 < z < 0.7. Assuming a concordance CDM cosmological model, this sample covers an effective volume of 2.2 Gpc 3 , and represents the largest sample of the Universe ever surveyed at this density, n 3 10 -4 h -3 Mpc 3 . We measure the angle-averaged galaxy correlation function and power spectrum, including density-field reconstruction of the baryon acoustic oscillation (BAO) feature. The acoustic features are detected at a significance of 5 in both the correlation function and power spectrum. Combining with the SDSS-II luminous red galaxy sample, the detection significance increases to 6.7 . Fitting for the position of the acoustic features measures the distance to z = 0.57 relative to the sound horizon D V /r s = 13.67 0.22 at z = 0.57. Assuming a fiducial sound horizon of 153.19 Mpc, which matches cosmic microwave background constraints, this corresponds to a distance D V (z = 0.57) = 2094 34 Mpc. At 1.7 per cent, this is the most precise distance constraint ever obtained from a galaxy survey. We place this result alongside previous BAO measurements in a cosmological distance ladder and find excellent agreement with the current supernova measurements. We use these distance measurements to constrain various cosmological models, finding continuing support for a flat Universe with a cosmological constant.

The ACC/AHA Task Force on Practice Guidelines makes every effort to avoid any actual or potential conflicts of interest that might arise as a result of an outside relationship or personal interest of a member of the writing panel. Specifically, all members of the writing panel are asked to provide disclosure statements of all such relationships that might be perceived as real or potential conflicts of interest. These statements are reviewed by the parent task force, reported orally to all members of the writing panel at the first meeting, and updated as changes occur. The

Abstract Structured, open-ended interviews were conducted with 30 environmentalists in Kentucky and 26 in Norway (35 men, 21 women) who represented a broad range of issues, from wilderness protection to urban planning, to determine the sources of their environmental commitment. Experiences of natural areas, family influences, organizations, negative experiences, and education were mentioned most often. People were also asked about the period in life when significant experiences occurred, and on this basis, a typical life path of predominant sources of commitment at different ages was constructed. Respondents also recommended strategies for effective environmental action.