Hunter 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.

Full list of authors: Price-Whelan, Adrian M.; Lim, Pey Lian; Earl, Nicholas; Starkman, Nathaniel; Bradley, Larry; Shupe, David L.; Patil, Aarya A.; Corrales, Lia; Brasseur, C. E.; Noethe, Maximilian; Donath, Axel; Tollerud, Erik; Morris, Brett M.; Ginsburg, Adam; Vaher, Eero; Weaver, Benjamin A.; Tocknell, James; Jamieson, William; van Kerkwijk, Marten H.; Robitaille, Thomas P.; Merry, Bruce; Bachetti, Matteo; Gunther, H. Moritz; Aldcroft, Thomas L.; Alvarado-Montes, Jaime A.; Archibald, Anne M.; Bodi, Attila; Bapat, Shreyas; Barentsen, Geert; Bazan, Juanjo; Biswas, Manish; Boquien, Mederic; Burke, D. J.; Cara, Daria; Cara, Mihai; Conroy, Kyle E.; Conseil, Simon; Craig, Matthew W.; Cross, Robert M.; Cruz, Kelle L.; D'Eugenio, Francesco; Dencheva, Nadia; Devillepoix, Hadrien A. R.; Dietrich, Jorg P.; Eigenbrot, Arthur Davis; Erben, Thomas; Ferreira, Leonardo; Foreman-Mackey, Daniel; Fox, Ryan; Freij, Nabil; Garg, Suyog; Geda, Robel; Glattly, Lauren; Gondhalekar, Yash; Gordon, Karl D.; Grant, David; Greenfield, Perry; Groener, Austen M.; Guest, Steve; Gurovich, Sebastian; Handberg, Rasmus; Hart, Akeem; Hatfield-Dodds, Zac; Homeier, Derek; Hosseinzadeh, Griffin; Jenness, Tim; Jones, Craig K.; Joseph, Prajwel; Kalmbach, J. Bryce; Karamehmetoglu, Emir; Kaluszynski, Mikolaj; Kelley, Michael S. P.; Kern, Nicholas; Kerzendorf, Wolfgang E.; Koch, Eric W.; Kulumani, Shankar; Lee, Antony; Ly, Chun; Ma, Zhiyuan; MacBride, Conor; Maljaars, Jakob M.; Muna, Demitri; Murphy, N. A.; Norman, Henrik; O'Steen, Richard; Oman, Kyle A.; Pacifici, Camilla; Pascual, Sergio; Pascual-Granado, J.; Patil, Rohit R.; Perren, Gabriel, I; Pickering, Timothy E.; Rastogi, Tanuj; Roulston, Benjamin R.; Ryan, Daniel F.; Rykoff, Eli S.; Sabater, Jose; Sakurikar, Parikshit; Salgado, Jesus; Sanghi, Aniket; Saunders, Nicholas; Savchenko, Volodymyr; Schwardt, Ludwig; Seifert-Eckert, Michael; Shih, Albert Y.; Jain, Anany Shrey; Shukla, Gyanendra; Sick, Jonathan; Simpson, Chris; Singanamalla, Sudheesh; Singer, Leo P.; Singhal, Jaladh; Sinha, Manodeep; Sipocz, Brigitta M.; Spitler, Lee R.; Stansby, David; Streicher, Ole; Sumak, Jani; Swinbank, John D.; Taranu, Dan S.; Tewary, Nikita; Tremblay, Grant R.; De Val-Borro, Miguel; Vasovic, Zlatan; Van Kooten, Samuel J.; Verma, Shresth; Cardoso, Jose Vinicius de Miranda; Williams, Peter K. G.; Wilson, Tom J.; Winkel, Benjamin; Wood-Vasey, W. M.; Xue, Rui; Yoachim, Peter; Zhang, Chen; Zonca, Andrea; Astropy Project Contributors; TARDIS Collaboration; Astropy Coordination Comm.--This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

A review and tutorial of the fundamental ideas and methods of joint time-frequency distributions is presented. The objective of the field is to describe how the spectral content of a signal changes in time and to develop the physical and mathematical ideas needed to understand what a time-varying spectrum is. The basic gal is to devise a distribution that represents the energy or intensity of a signal simultaneously in time and frequency. Although the basic notions have been developing steadily over the last 40 years, there have recently been significant advances. This review is intended to be understandable to the nonspecialist with emphasis on the diversity of concepts and motivations that have gone into the formation of the field.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Secret sharing is a procedure for splitting a message into several parts so that no subset of parts is sufficient to read the message, but the entire set is. We show how this procedure can be implemented using Greenberger-Horne-Zeilinger (GHZ) states. In the quantum case the presence of an eavesdropper will introduce errors so that his presence can be detected. We also show how GHZ states can be used to split quantum information into two parts so that both parts are necessary to reconstruct the original qubit.

"Weapons of Math Destruction: How Big Data Increases Inequality and Threatens Democracy." The Information Society, 33(5), pp. 301–302

IMPORTANCE: Cancer is among the leading causes of death worldwide. Current estimates of cancer burden in individual countries and regions are necessary to inform local cancer control strategies. OBJECTIVE: To estimate mortality, incidence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs) for 28 cancers in 188 countries by sex from 1990 to 2013. EVIDENCE REVIEW: The general methodology of the Global Burden of Disease (GBD) 2013 study was used. Cancer registries were the source for cancer incidence data as well as mortality incidence (MI) ratios. Sources for cause of death data include vital registration system data, verbal autopsy studies, and other sources. The MI ratios were used to transform incidence data to mortality estimates and cause of death estimates to incidence estimates. Cancer prevalence was estimated using MI ratios as surrogates for survival data; YLDs were calculated by multiplying prevalence estimates with disability weights, which were derived from population-based surveys; YLLs were computed by multiplying the number of estimated cancer deaths at each age with a reference life expectancy; and DALYs were calculated as the sum of YLDs and YLLs. FINDINGS: In 2013 there were 14.9 million incident cancer cases, 8.2 million deaths, and 196.3 million DALYs. Prostate cancer was the leading cause for cancer incidence (1.4 million) for men and breast cancer for women (1.8 million). Tracheal, bronchus, and lung (TBL) cancer was the leading cause for cancer death in men and women, with 1.6 million deaths. For men, TBL cancer was the leading cause of DALYs (24.9 million). For women, breast cancer was the leading cause of DALYs (13.1 million). Age-standardized incidence rates (ASIRs) per 100 000 and age-standardized death rates (ASDRs) per 100 000 for both sexes in 2013 were higher in developing vs developed countries for stomach cancer (ASIR, 17 vs 14; ASDR, 15 vs 11), liver cancer (ASIR, 15 vs 7; ASDR, 16 vs 7), esophageal cancer (ASIR, 9 vs 4; ASDR, 9 vs 4), cervical cancer (ASIR, 8 vs 5; ASDR, 4 vs 2), lip and oral cavity cancer (ASIR, 7 vs 6; ASDR, 2 vs 2), and nasopharyngeal cancer (ASIR, 1.5 vs 0.4; ASDR, 1.2 vs 0.3). Between 1990 and 2013, ASIRs for all cancers combined (except nonmelanoma skin cancer and Kaposi sarcoma) increased by more than 10% in 113 countries and decreased by more than 10% in 12 of 188 countries. CONCLUSIONS AND RELEVANCE: Cancer poses a major threat to public health worldwide, and incidence rates have increased in most countries since 1990. The trend is a particular threat to developing nations with health systems that are ill-equipped to deal with complex and expensive cancer treatments. The annual update on the Global Burden of Cancer will provide all stakeholders with timely estimates to guide policy efforts in cancer prevention, screening, treatment, and palliation.

Journal Article Multiple Regression and Correlation Extensions of the Mantel Test of Matrix Correspondence Get access Peter E. Smouse, Peter E. Smouse 1Department of Human Genetics and Department of Biology, University of MichiganAnn Arbor, Michigan 48109 Search for other works by this author on: Oxford Academic PubMed Google Scholar Jeffrey C. Long, Jeffrey C. Long 2Department of Anthropology, CUNY-Hunter CollegeNew York, New York 10021 Search for other works by this author on: Oxford Academic PubMed Google Scholar Robert R. Sokal Robert R. Sokal 3Department of Ecology and Evolution, State University of New YorkStony Brook, New York 11794 Search for other works by this author on: Oxford Academic PubMed Google Scholar Systematic Biology, Volume 35, Issue 4, December 1986, Pages 627–632, https://doi.org/10.2307/2413122 Published: 01 December 1986 Article history Received: 23 June 1986 Accepted: 23 July 1986 Published: 01 December 1986

We describe a simple method to automate the geometric optimization of molecular orbital calculations of supermolecules on potential surfaces that are corrected for basis set superposition error using the counterpoise (CP) method. This method is applied to the H-bonding complexes HF/HCN, HF/H2O, and HCCH/H2O using the 6-31G(d,p) and D95++(d,p) basis sets at both the Hartree–Fock and second-order Mo/ller–Plesset levels. We report the interaction energies, geometries, and vibrational frequencies of these complexes on the CP-optimized surfaces; and compare them with similar values calculated using traditional methods, including the (more traditional) single point CP correction. Upon optimization on the CP-corrected surface, the interaction energies become more negative (before vibrational corrections) and the H-bonding stretching vibrations decrease in all cases. The extent of the effects vary from extremely small to quite large depending on the complex and the calculational method. The relative magnitudes of the vibrational corrections cannot be predicted from the H-bond stretching frequencies alone.

Emotion regulation has emerged as a popular topic, but there is doubt about its viability as a scientific construct. This article identifies conceptual and methodological challenges in this area of study and describes exemplar studies that provide a substantive basis for inferring emotion regulation. On the basis of those studies, 4 methods are described that provide compelling evidence for emotion regulation: independent measurement of activated emotion and purported regulatory processes; analysis of temporal relations; measurement across contrasting conditions; and multiple, convergent measures. By offering this perspective, this article aims to engage thoughtful debate and critical analysis, with the goal of increasing methodological rigor and advancing an understanding of emotion regulation as a scientific construct.

A novel definition for the hydrogen bond is recommended here. It takes into account the theoretical and experimental knowledge acquired over the past century. This definition insists on some evidence. Six criteria are listed that could be used as evidence for the presence of a hydrogen bond.

Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice.

In this paper we describe a cellular automaton (CA) simulation model developed to predict urban growth as part of a project for estimating the regional and broader impact of urbanization on the San Francisco Bay area's climate. The rules of the model are more complex than those of a typical CA and involve the use of multiple data sources, including topography, road networks, and existing settlement distributions, and their modification over time. In addition, the control parameters of the model are allowed to self-modify: that is, the CA adapts itself to the circumstances it generates, in particular, during periods of rapid growth or stagnation. In addition, the model was written to allow the accumulation of probabilistic estimates based on Monte Carlo methods. Calibration of the model has been accomplished by the use of historical maps to compare model predictions of urbanization, based solely upon the distribution in year 1900, with observed data for years 1940, 1954, 1962, 1974, and 1990. The complexity of this model has made calibration a particularly demanding step. Lessons learned about the methods, measures, and strategies developed to calibrate the model may be of use in other environmental modeling contexts. With the calibration complete, the model is being used to generate a set of future scenarios for the San Francisco Bay area along with their probabilities based on the Monte Carlo version of the model. Animated dynamic mapping of the simulations will be used to allow visualization of the impact of future urban growth.

The research literature on Web-based learning supports the assumption that interaction is important for a successful course, yet questions exist regarding the nature and extent of the interaction and its effects on student performance. Much of the research is based on student perceptions of the quality and quantity of their interactions and how much they have learned in an online course. The purpose of this study is to examine performance in an online course in relationship to student interaction and sense of presence in the course. Data on multiple independent (measures of interaction and presence) and dependent (measures of performance) variables were collected and subjected to analysis. An attempt was made to go beyond typical institutional performance measures such as grades and withdrawal rates and to examine measures specifically related to course objectives.

Gender schemas at work gender begins - and continues - at home learning about gender biology and behaviour biology and cognition schemas that explain behaviour evaluating women and men effects on the self interpreting success and failure women in the professions women in academia professional performance and human values affirmative action and the law remedies.

We analyze the possibility of copying (that is, cloning) arbitrary states of a quantum-mechanical spin-1/2 system. We show that there exists a ``universal quantum-copying machine'' (i.e., transformation) which approximately copies quantum-mechanical states such that the quality of its output does not depend on the input. We also examine a machine which combines a unitary transformation and a selective measurement to produce good copies of states in the neighborhood of a particular state. We discuss the problem of measurement of the output states. \textcopyright{} 1996 The American Physical Society.

In this article, we combine aspects of Critical Race Theory (CRT) and Disability Studies (DS) to propose a new theoretical framework that incorporates a dual analysis of race and ability: Dis/ability Critical Race Studies, or DisCrit. We first examine some connections between the interdependent constructions of race and dis/ability in education and society in the United States and why we find it necessary to add another branch to Critical Race Theory and Disability Studies. Next, we outline the tenets of DisCrit, calling attention to its potential value as well as elucidate some tensions, cautions, and current limitations within DisCrit. Finally, we suggest ways in which DisCrit can be used in relation to moving beyond the contemporary impasse of researching race and dis/ability within education and other fields.

The term “hydrogen bond” has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material scientists, there has been a continual debate about what this term means. This debate has intensified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X – H···Y hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some characteristics that are observed in typical hydrogen-bonding environments.

OBJECTIVE: Sudden hearing loss (SHL) is a frightening symptom that often prompts an urgent or emergent visit to a physician. This guideline provides evidence-based recommendations for the diagnosis, management, and follow-up of patients who present with SHL. The guideline primarily focuses on sudden sensorineural hearing loss (SSNHL) in adult patients (aged 18 and older). Prompt recognition and management of SSNHL may improve hearing recovery and patient quality of life (QOL). Sudden sensorineural hearing loss affects 5 to 20 per 100,000 population, with about 4000 new cases per year in the United States. This guideline is intended for all clinicians who diagnose or manage adult patients who present with SHL. PURPOSE: The purpose of this guideline is to provide clinicians with evidence-based recommendations in evaluating patients with SHL, with particular emphasis on managing SSNHL. The panel recognized that patients enter the health care system with SHL as a nonspecific, primary complaint. Therefore, the initial recommendations of the guideline deal with efficiently distinguishing SSNHL from other causes of SHL at the time of presentation. By focusing on opportunities for quality improvement, the guideline should improve diagnostic accuracy, facilitate prompt intervention, decrease variations in management, reduce unnecessary tests and imaging procedures, and improve hearing and rehabilitative outcomes for affected patients. RESULTS: The panel made strong recommendations that clinicians should (1) distinguish sensorineural hearing loss from conductive hearing loss in a patient presenting with SHL; (2) educate patients with idiopathic sudden sensorineural hearing loss (ISSNHL) about the natural history of the condition, the benefits and risks of medical interventions, and the limitations of existing evidence regarding efficacy; and (3) counsel patients with incomplete recovery of hearing about the possible benefits of amplification and hearing-assistive technology and other supportive measures. The panel made recommendations that clinicians should (1) assess patients with presumptive SSNHL for bilateral SHL, recurrent episodes of SHL, or focal neurologic findings; (2) diagnose presumptive ISSNHL if audiometry confirms a 30-dB hearing loss at 3 consecutive frequencies and an underlying condition cannot be identified by history and physical examination; (3) evaluate patients with ISSNHL for retrocochlear pathology by obtaining magnetic resonance imaging, auditory brainstem response, or audiometric follow-up; (4) offer intratympanic steroid perfusion when patients have incomplete recovery from ISSNHL after failure of initial management; and (5) obtain follow-up audiometric evaluation within 6 months of diagnosis for patients with ISSNHL. The panel offered as options that clinicians may offer (1) corticosteroids as initial therapy to patients with ISSNHL and (2) hyperbaric oxygen therapy within 3 months of diagnosis of ISSNHL. The panel made a recommendation against clinicians routinely prescribing antivirals, thrombolytics, vasodilators, vasoactive substances, or antioxidants to patients with ISSNHL. The panel made strong recommendations against clinicians (1) ordering computerized tomography of the head/brain in the initial evaluation of a patient with presumptive SSNHL and (2) obtaining routine laboratory tests in patients with ISSNHL.

Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome's data content and software can all be freely used and redistributed under open source terms.

This paper introduces urban land teleconnections as a conceptual framework that explicitly links land changes to underlying urbanization dynamics. We illustrate how three key themes that are currently addressed separately in the urban sustainability and land change literatures can lead to incorrect conclusions and misleading results when they are not examined jointly: the traditional system of land classification that is based on discrete categories and reinforces the false idea of a rural-urban dichotomy; the spatial quantification of land change that is based on place-based relationships, ignoring the connections between distant places, especially between urban functions and rural land uses; and the implicit assumptions about path dependency and sequential land changes that underlie current conceptualizations of land transitions. We then examine several environmental "grand challenges" and discuss how urban land teleconnections could help research communities frame scientific inquiries. Finally, we point to existing analytical approaches that can be used to advance development and application of the concept.