Vassar College

Abstract The Astropy Project supports and fosters the development of open-source and openly developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package astropy , which serves as the foundation for more specialized projects and packages. In this article, we provide an overview of the organization of the Astropy project and summarize key features in the core package, as of the recent major release, version 2.0. We then describe the project infrastructure designed to facilitate and support development for a broader ecosystem of interoperable packages. We conclude with a future outlook of planned new features and directions for the broader Astropy Project.

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

With the advent of the Internet, billions of images are now freely available online and constitute a dense sampling of the visual world. Using a variety of non-parametric methods, we explore this world with the aid of a large dataset of 79,302,017 images collected from the Internet. Motivated by psychophysical results showing the remarkable tolerance of the human visual system to degradations in image resolution, the images in the dataset are stored as 32 x 32 color images. Each image is loosely labeled with one of the 75,062 non-abstract nouns in English, as listed in the Wordnet lexical database. Hence the image database gives a comprehensive coverage of all object categories and scenes. The semantic information from Wordnet can be used in conjunction with nearest-neighbor methods to perform object classification over a range of semantic levels minimizing the effects of labeling noise. For certain classes that are particularly prevalent in the dataset, such as people, we are able to demonstrate a recognition performance comparable to class-specific Viola-Jones style detectors.

Abstract Neutron stars are not only of astrophysical interest, but are also of great interest to nuclear physicists because their attributes can be used to determine the properties of the dense matter in their cores. One of the most informative approaches for determining the equation of state (EoS) of this dense matter is to measure both a star’s equatorial circumferential radius R e and its gravitational mass M . Here we report estimates of the mass and radius of the isolated 205.53 Hz millisecond pulsar PSR J0030+0451 obtained using a Bayesian inference approach to analyze its energy-dependent thermal X-ray waveform, which was observed using the Neutron Star Interior Composition Explorer ( NICER ). This approach is thought to be less subject to systematic errors than other approaches for estimating neutron star radii. We explored a variety of emission patterns on the stellar surface. Our best-fit model has three oval, uniform-temperature emitting spots and provides an excellent description of the pulse waveform observed using NICER . The radius and mass estimates given by this model are km and (68%). The independent analysis reported in the companion paper by Riley et al. explores different emitting spot models, but finds spot shapes and locations and estimates of R e and M that are consistent with those found in this work. We show that our measurements of R e and M for PSR J0030+0451 improve the astrophysical constraints on the EoS of cold, catalyzed matter above nuclear saturation density.

For centuries, folk theory has promoted the idea that positive emotions are good for your health. Accumulating empirical evidence is providing support for this anecdotal wisdom. We use the broaden-and-build theory of positive emotions (Fredrickson, 1998; 2001) as a framework to demonstrate that positive emotions contribute to psychological and physical well-being via more effective coping. We argue that the health benefits advanced by positive emotions may be instantiated in certain traits that are characterized by the experience of positive emotion. Towards this end, we examine individual differences in psychological resilience (the ability to bounce back from negative events by using positive emotions to cope) and positive emotional granularity (the tendency to represent experiences of positive emotion with precision and specificity). Individual differences in these traits are examined in two studies, one using psychophysiological evidence, the second using evidence from experience sampling, to demonstrate that positive emotions play a crucial role in enhancing coping resources in the face of negative events. Implications for research on coping and health are discussed.

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.

Abstract This paper provides some new evidence on the behaviour of cross‐country growth rates. We reject the linear model commonly used to study cross‐country growth behaviour in favour of a multiple regime alternative in which different economies obey different linear models when grouped according to initial conditions. Further, the marginal product of capital is shown to vary with the level of economic development. These results are consistent with growth models which exhibit multiple steady states. Our results call into question inferences that have been made in favour of the convergence hypothesis and further suggest that the explanatory power of the Solow growth model may be enhanced with a theory of aggregate production function differences.

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease. This comparative genomics study, comparing the complete human genome sequence with those of 29 placental mammals, including chimpanzees, mice and dogs, identifies 4.2% of the human genome as constrained by evolutionary selection, and ascribes a potential function to about 60% of these constrained bases. A series of evolutionary signatures emerges, providing insights into coding and non-coding functional genomic elements, candidate RNA structural families and aspects of genome organization and evolution. Overlap with disease-associated variants indicates that the findings will be relevant for studies of human disease.

This article addresses the relationship between discourse, textual and social order, and power by means of an examination of the concept of genre. It begins with a critical review of the way genre has been used in linguistic anthropology. A distinction is delineated between approaches that take for granted the status of genre as a tool for classifying and ordering discourse and those that contend with elements of generic ambiguity and dynamism. Proceeding to outline a new approach to genre, the discussion analyzes a wide range of intertextual relations that are deployed in constituting generic links. A series of examples contrasts strategies for minimizing gaps between texts and generic precedents with strategies for maximizing such gaps. A final section points to the ways that investigating generic intertextuality can illuminate questions of ideology, political economy, and power.

Interviews are ubiquitous in modern society, and they play a crucial role in social scientific research. But, as Charles Briggs convincingly argues in this book, received interviewing techniques rest on fundamental misapprehensions about the nature both of the interview as a communicative event, and of the nature of the data that it produces. Furthermore, interviewers rarely examine the compatibility of interviews as a means of acquiring information to one another. These oversights often blind interviewers to ensuing errors of interpretation, as well as to the limitations of the interview as a means of acquiring data. To conflict these problems, Professor Briggs presents an analysis of the 'communicative blunders' that he himself committed in conducting research interviews among Spanish-speakers in northern New Mexico. By focusing on these errors and exploring how they may be avoided, he is able to propose new techniques for designing, implementing, and analyzing interview-based research. These rest on identifying the subjects' resources for conveying information, and the relative compatability of the shared rules and understandings that underlie their strategies with those associated with interviews. Critical of existing paradigms of interviewing, which he sees as deriving from Western 'folk' theories of reality and communication, Briggs shows that the development of more sophisticated interviewing methodologies requires further research into interviewing itself. Briggs's conclusions provide a basis for the reexamination of current uses of interviews in a wide range of contexts - from social science research to job applications, welfare and health care delivery, criminal and legal investigations, journalism and broadcasting, and other areas of everyday life. His book will appeal to linguists, sociologists, anthropologists, historians, psychologists, as well as other readers whose research or professional activities depend on the use of interviews.

Recent interest in the implicit self-esteem construct has led to the creation and use of several new assessment tools whose psychometric properties have not been fully explored. In this article, the authors investigated the reliability and validity of seven implicit self-esteem measures. The different implicit measures did not correlate with each other, and they correlated only weakly with measures of explicit self-esteem. Only some of the implicit measures demonstrated good test-retest reliabilities, and overall, the implicit measures were limited in their ability to predict our criterion variables. Finally, there was some evidence that implicit self-esteem measures are sensitive to context. The implications of these findings for the future of implicit self-esteem research are discussed.

Abstract Mildly-to-moderately depressed and nondepressed subjects were randomly assigned to spend 8 minutes focusing their attention on their current feeling states and personal characteristics (rumination condition) or on descriptions of geographic locations and objects (distraction condition). Depressed subjects in the rumination condition became significantly more depressed, whereas depressed subjects in the distraction condition became significantly less depressed. Rumination and distraction did not affect the moods of nondepressed subjects. These results support the hypothesis that ruminative responses to depressed mood exacerbate and prolong depressed mood. whereas distracting response shorten depressed mood.

Abstract. Recent field and laboratory evidence indicates that the oxidation of isoprene, (2-methyl-1,3-butadiene, C5H8) forms secondary organic aerosol (SOA). Global biogenic emissions of isoprene (600 Tg yr−1) are sufficiently large that the formation of SOA in even small yields results in substantial production of atmospheric particulate matter, likely having implications for air quality and climate. Here we present a review of field measurements, experimental work, and modeling studies aimed at understanding the mechanisms, yield, and atmospheric importance of isoprene-derived SOA. SOA yields depend on a number of factors, including organic aerosol loading (Mo), NOx level (RO2 chemistry), and, because of the importance of multigenerational chemistry, the degree of oxidation. These dependences are not always included in SOA modules used in atmospheric transport models, and instead most yield parameterizations rely on a single set of chamber experiments (carried out over a limited range of conditions); this may lead to very different estimates of the atmospheric importance of isoprene SOA. New yield parameterizations, based on all available laboratory data (Mo=0–50 μg m−3), are presented here, so that SOA formation may be computed as a function of Mo, NOx level, and temperature. Current research needs and future research directions are identified.

Abstract We describe the catalogs assembled and the algorithms used to populate the revised TESS Input Catalog (TIC), based on the incorporation of the Gaia second data release. We also describe a revised ranking system for prioritizing stars for 2 minute cadence observations, and we assemble a revised Candidate Target List (CTL) using that ranking. The TIC is available on the Mikulski Archive for Space Telescopes server, and an enhanced CTL is available through the Filtergraph data visualization portal system at http://filtergraph.vanderbilt.edu/tess_ctl .

Spectral sequences are among the most elegant, most powerful, and most complicated methods of computation in mathematics. This book describes some of the most important examples of spectral sequences and some of their most spectacular applications. The first third of the book treats the algebraic foundations for this sort of homological algebra, starting from informal calculations, to give the novice a familiarity with the range of applications possible. The heart of the book is an exposition of the classical examples from homotopy theory, with chapters on the Leray-Serre spectral sequence, the Eilenberg-Moore spectral sequence, the Adams spectral sequence, and, in this new edition, the Bockstein spectral sequence. The last part of the book treats applications throughout mathematics, including the theory of knots and links, algebraic geometry, differential geometry and algebra. This is an excellent reference for students and researchers in geometry, topology, and algebra.

The major tests of masculinity-femininity (M-F) in adults are reviewed with special attention to the ways in which their construction and use reflect three untested assumptions about the nature of ...

Performance is a critical challenge in mobile image processing. Given a reference imaging pipeline, or even human-adjusted pairs of images, we seek to reproduce the enhancements and enable real-time evaluation. For this, we introduce a new neural network architecture inspired by bilateral grid processing and local affine color transforms. Using pairs of input/output images, we train a convolutional neural network to predict the coefficients of a locally-affine model in bilateral space. Our architecture learns to make local, global, and content-dependent decisions to approximate the desired image transformation. At runtime, the neural network consumes a low-resolution version of the input image, produces a set of affine transformations in bilateral space, upsamples those transformations in an edge-preserving fashion using a new slicing node, and then applies those upsampled transformations to the full-resolution image. Our algorithm processes high-resolution images on a smartphone in milliseconds, provides a real-time viewfinder at 1080p resolution, and matches the quality of state-of-the-art approximation techniques on a large class of image operators. Unlike previous work, our model is trained off-line from data and therefore does not require access to the original operator at runtime. This allows our model to learn complex, scene-dependent transformations for which no reference implementation is available, such as the photographic edits of a human retoucher.

These are the data products for the paper "The Chandra Deep Field North Survey. XIII. 2 Ms Point-Source Catalogs", Alexander D.M., Bauer F.E., Brandt W.N., Schneider D.P., Hornschemeier A.E., Vignali C., et al., 2003, AJ, 126, 539

BACKGROUND: The underlying goal of synthetic biology is to make the process of engineering biological systems easier. Recent work has focused on defining and developing standard biological parts. The technical standard that has gained the most traction in the synthetic biology community is the BioBrick standard for physical composition of genetic parts. Parts that conform to the BioBrick assembly standard are BioBrick standard biological parts. To date, over 2,000 BioBrick parts have been contributed to, and are available from, the Registry of Standard Biological Parts. RESULTS: Here we extended the same advantages of BioBrick standard biological parts to the plasmid-based vectors that are used to provide and propagate BioBrick parts. We developed a process for engineering BioBrick vectors from BioBrick parts. We designed a new set of BioBrick parts that encode many useful vector functions. We combined the new parts to make a BioBrick base vector that facilitates BioBrick vector construction. We demonstrated the utility of the process by constructing seven new BioBrick vectors. We also successfully used the resulting vectors to assemble and propagate other BioBrick standard biological parts. CONCLUSION: We extended the principles of part reuse and standardization to BioBrick vectors. As a result, myriad new BioBrick vectors can be readily produced from all existing and newly designed BioBrick parts. We invite the synthetic biology community to (1) use the process to make and share new BioBrick vectors; (2) expand the current collection of BioBrick vector parts; and (3) characterize and improve the available collection of BioBrick vector parts.

Explosing common misuses of the subsumption relationship and the formal basis for why they are wrong.