Function, Role, and Disposition in Basic Formal Ontology

Numerous research groups are now utilizing Basic Formal Ontology (BFO) as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three BFO categories of function, role, and disposition, and considers two proposed sub-categories of artifactual function and bio-logical function. The motivation is to help advance the coherent treatment of functions, roles, and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO’s general structure and use

Life and the Homeostatic Organization View of Biological Phenomena

In this paper, I argue that starting with the organelles that constitute a cell – and continuing up the hierarchy of components in processes and subsystems of an organism – there are clear instances of emergent biological phenomena that can be considered "living” entities. These components and their attending processes are living emergent phenomena because of the way in which the components are organized to maintain homeostasis of the organism at the various levels in the hierarchy. I call this view the homeostatic organization view (HOV) of biological phenomena and, as is shown, it comports well with the standard philosophical accounts of nomological (metaphysical) emergence and representational (epistemological) emergence. To proffer HOV, I describe properties of biological entities that include internal-hierarchical data exchange, data selectivity, informational integration, and environmental-organismic information exchange. Further, a distinction is drawn between particularized homeostasis and generalized homeostasis, and I argue that because the various processes and subsystems of an organism are functioning properly in their internal environments (particularized homeostasis), the organism is able to exist as a hierarchically-organized entity in some environment external to it (generalized homeostasis). Stated simply: that components of biological phenomena are organized to perform some function resulting in homeostasis marks them out to be living emergent entities distinguishable, in description and in reality, from the very physico-chemical processes of which they are composed

The Philosophy of J. J. Abrams

American auteur Jeffrey Jacob “J. J.” Abrams’s genius for creating densely plotted scripts has won him broad commercial and critical success in TV shows such as Felicity (1998–2002), Emmy-nominated Alias (2001–2006), Emmy and Golden Globe-winning Lost (2004–2010), and the critically acclaimed Fringe (2008–2013). In addition, his direction in films such as Cloverfield (2008), Super 8 (2011), and the new Mission Impossible and Star Trek films has left fans eagerly awaiting his revival of the Star Wars franchise. As a writer, director, producer, and composer, Abrams seamlessly combines geek appeal with blockbuster intuition, leaving a distinctive stamp on all of his work and establishing him as one of Tinsel Town’s most influential visionaries. In The Philosophy of J.J. Abrams, editors Patricia L. Brace and Robert Arp assemble the first collection of essays to highlight the philosophical insights of the Hollywood giant’s successful career. The filmmaker addresses a diverse range of themes in his onscreen pursuits, including such issues as personal identity in an increasingly impersonal digitized world, the morality of terrorism, bioethics, friendship, family obligation, and free will. Utilizing Abrams’s scope of work as a touchstone, this comprehensive volume is a guide for fans as well as students of film, media, and culture. The Philosophy of J.J. Abrams is a significant contribution to popular culture scholarship, drawing attention to the mind behind some of the most provocative television and movie plots of our day. Patricia L. Brace is professor of art history at Southwest Minnesota State University. She has contributed to many philosophy and popular culture volumes, including Lost and Philosophy: The Island Has its Reasons, The Philosophy of Joss Whedon, and The Philosophy of David Lynch. Robert Arp is the editor of a number of books, including The Philosophy of Ang Lee and South Park and Philosophy: You Know, I Learned Something Today, and coeditor of Philosophy of Biology: An Anthology. “This work is a significant contribution to pop culture scholarship that draws attention to the mind behind some of the most provocative television and movie plots of our day.” – Sharon Kaye, author of Philosophy, A Complete Introduction “This well designed book opens up the works of J.J. Abrams like a Lamborghini on beautiful boundless freeway. With essays ranging from the metaphysics of time and self, to emerging issues in ethics as technology advances, this book is great for any class in Introductory Philosophy. Students will encounter essays that focus on everything from existential dread in the vast infinity of Star Trek space (Piven & Stephenson) to the nature of love in Super 8 (Auxier). Abrams forces us to shift our understanding out of automatic when we view his many creative works; he drives us in many philosophical directions. This book is a V6 thrill-ride that makes thinking in high gear fun.”-- Sara Waller, Associate Professor of Philosophy, Montana State Universityhttps://uknowledge.uky.edu/upk_american_popular_culture/1016/thumbnail.jp

Arp 302: Non-starburst Luminous Infrared Galaxies

Arp 302, a luminous infrared source (L_{IR} = 4.2x10^{11} Lsun), consisting of two spiral galaxies (VV340A and VV340B) with nuclear separation of 40'', has the highest CO luminosity known. Observations with the BIMA array at 5'' X 7'' resolution reveal that the CO emission is extended over 23.0 kpc in the edge-on spiral galaxy, VV340A, corresponding to 6.7x10^{10} Msun of H_2. In the companion face-on galaxy, VV340B, the CO emission is extended over ~10.0 kpc, with 1.1x10^{10} Msun of H_2. The large CO extent is in strong contrast to starburst systems, such as Arp 220, in which the CO extent is typically $\le$ 1 kpc. Furthermore, $L_{IR}/M$(H_2) is found to be $\le$ 6.0 Lsun/Msun throughout both galaxies. Thus the high IR luminosity of Arp 302 is apparently not due to starbursts in the nuclear regions, but is due to its unusually large amount of molecular gas forming stars at a rate similar to giant molecular clouds in the Milky Way disk. Arp 302 consists of a pair of very gas-rich spiral galaxies that may be interacting and in a phase before a likely onset of starbursts.Comment: AAS Latex plus two postscript figures. ApJ Letters (accepted

Standard Operating Procedure and Workplan for the Terrestrial Environmental Observation Network (TEON) – Arctic Landscape Conservation Cooperative: Kuparuk River Basin and Adjacent Catchments

TABLE OF CONTENTS ................................................................................................................. i DISCLAIMER ................................................................................................................................ ii CONVERSION FACTORS, UNITS, WATER QUALITY UNITS, VERTICAL AND HORIZONTAL DATUM, ABBREVIATIONS AND SYMBOLS .............................................. iii 1 INTRODUCTION .................................................................................................................. 1 2 STATION HISTORY ............................................................................................................. 5 3 DATA COLLECTION METHODS ....................................................................................... 8 3.1 Air Temperature and Relative Humidity ........................................................................ 12 3.2 Wind Speed and Direction ............................................................................................. 14 3.3 Radiation ........................................................................................................................ 15 3.3.1 Net Radiation .......................................................................................................... 15 3.3.2 Shortwave Radiation ............................................................................................... 16 3.3.3 Longwave Radiation ............................................................................................... 17 3.4 Summer Precipitation ..................................................................................................... 18 3.5 Snow Depth .................................................................................................................... 18 3.6 Field Snow Survey ......................................................................................................... 20 3.7 Water Levels .................................................................................................................. 21 3.8 Discharge Measurements ............................................................................................... 23 3.8.1 Acoustic Doppler Current Profiler .......................................................................... 25 4 STATION TELEMETRY ..................................................................................................... 28 5 DATALOGGER PROGRAM .............................................................................................. 30 6 METADATA ........................................................................................................................ 31 7 QUALITY CONTROL AND DATA PROCESSING .......................................................... 32 8 DATA REPORTING AND ARCHIVING ........................................................................... 33 9 REFERENCES ..................................................................................................................... 36 10 APPENDIX LIST ................................................................................................................. 3

Lopsided Galaxies, Weak Interactions and Boosting the Star Formation Rate

To investigate the link between weak tidal interactions in disk galaxies and the boosting of their recent star formation, we obtain images and spatially integrated spectra (3615A < lambda < 5315A) for 40 late-type spiral galaxies (Sab-Sbc) with varying degrees of lopsidedness (a dynamical indicator of weak interactions). We quantify lopsidedness as the amplitude of the m=1 Fourier component of the azimuthal surface brightness distribution, averaged over a range of radii. We compare the young stellar content, quantified by EW(H\delta_abs) and the strength of the 4000 Angstrom break (D_4000), with lopsidedness and find a 3-4 sigma correlation between the two. We also find a 3.2 sigma correlation between EW(H\beta_emission) and lopsidedness. Using the evolutionary population synthesis code of Bruzual & Charlot we model the spectra as an ``underlying population'' and a superimposed ``boost population'' with the aim of constraining the fractional boost in the SFR averaged over the past 0.5 Gyr (the characteristic lifetime of lopsidedness). From the difference in both EW(H\delta_abs) and D_4000 between the most and least symmetric thirds of our sample, we infer that ~ 1x10^9 M_solar of stars are formed over the duration of a lopsided event in addition to the ``underlying'' SFH (assuming a final galactic stellar mass of 10^10 M_solar). This corresponds to a factor of 8 increase in the SFR over the past 5x10^8 years. For the nuclear spectra, all of the above correlations except D_4000 vs. are weaker than for the disk, indicating that in lopsided galaxies, the SF boost is not dominated by the nucleus.Comment: 35 pages, including 10 figures, to appear in the Astrophysical Journal, abridged abstrac

Building Ontologies with Basic Formal Ontology

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies

It Takes a Village: Open Source Software Sustainability

This Guidebook is designed to serve as a practical reference source to help open source software programs serving cultural and scientific heritage organizations plan for long-term sustainability, ensuring that commitment and resources will be available at levels sufficient for the software to remain viable and effective as long as it is needed. One of the most significant themes of this Guidebook is that sustainability is not a linear process, with set beginning and end points. Program sustainability shifts and evolves over time across a number of phases and facets. The phases speak to where a program is in its lifecycle: getting started, growing, or stable but not static. The facets describe the different components of sustainability, each of which is critical to overall program health, but may have different timelines, goals, and resource needs. The facets deemed most critical by the Guidebook’s authors and contributors are: Governance, Technology, Resources (Financial and Human), and Community Engagement. Sections of the Guidebook will: define the phases and facets of sustainability; identify goals, characteristics, and common roadblocks for each phase in each facet; provide guidance for moving an OSS program to the next phase in a given facet, with the understanding that the same program may be in different phases along different facets of sustainability; and highlight case studies and additional resources to help a program’s research and decision-making process. The Guidebook is intended for a broad audience. While certain paths may be of more interest than others, we would recommend reading through each of the facets before returning to the one that aligns most closely with a specific role, e.g., governance for a program manager, technology for a technical lead, engagement for a community manager, or resources for an administrator. The worksheet in Appendix A can help identify the specific phase a program is in along each facet. The open source landscape is wide and varied. Bringing open source programs serving cultural and scientific heritage together under one shared umbrella can provide us all with the power to better advocate for our needs, develop shared sustainability strategies, and provide our communities with the information needed to assess and contribute to the sustainability of the programs they depend on

Male fertility in Arabidopsis requires active DNA demethylation of genes that control pollen tube function.

Active DNA demethylation is required for sexual reproduction in plants but the molecular determinants underlying this epigenetic control are not known. Here, we show in Arabidopsis thaliana that the DNA glycosylases DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1) act semi-redundantly in the vegetative cell of pollen to demethylate DNA and ensure proper pollen tube progression. Moreover, we identify six pollen-specific genes with increased DNA methylation as well as reduced expression in dme and dme;ros1. We further show that for four of these genes, reinstalling their expression individually in mutant pollen is sufficient to improve male fertility. Our findings demonstrate an essential role of active DNA demethylation in regulating genes involved in pollen function