Chapter 39: Transient Event Notification with VOEvent

Events and transients are becoming more and more important in modern astronomy, for example gamma-ray bursts, supernovae, microlensing, and so on. We present the VOEvent infrastructure, for communicating observations of immediate astronomical events with the intention of stimulating rapid and automated follow up from robotic telescopes. The information packet itself will be described, as well as the emerging network that allows authoring, publication, subscription, and global identifiers. VOEvent is a general, standard, flexible, peer-to-peer, robust, secure, scalable solution for this infrastructure: a vision of multiple federated event streams shared by peers and evaluated by decision support

Timekeeping infrastructure for the Catalina Sky Survey

Time domain science forms an increasing fraction of astronomical programs at many facilities. Synoptic and targeted observing modes of transient, varying, and moving sources rely on precise clocks to provide the underlying time tags. Often precision is mistaken for accuracy, or the precise time signals never reach the instrumentation in the first place. We will discuss issues of deploying a stable high-precision GNSS clock on a remote mountaintop, and of conveying the resulting time signals to a computer in a way that permits hardware timestamping of the camera shutter (or equivalent) rather than the arbitrary delays encountered with non-real-time data acquisition software. Strengths and limitations of the Network Time Protocol will be reviewed. Timekeeping infrastructure deployed for the Catalina Sky Survey will serve as an example.Comment: 12 pages, SPIE proceedings, AS107-9

Novel functional roles for \u3cem\u3ePERIANTHIA\u3c/em\u3e and \u3cem\u3eSEUSS\u3c/em\u3e during floral organ identity specification, floral meristem termination, and gynoecial development

The gynoecium is the female reproductive structure of angiosperm flowers. In Arabidopsis thaliana the gynoecium is composed of two carpels that are fused into a tube-like structure. As the gynoecial primordium arises from the floral meristem, a specialized meristematic structure, the carpel margin meristem (CMM), develops from portions of the medial gynoecial domain. The CMM is critical for reproductive competence because it gives rise to the ovules, the precursors of the seeds. Here we report a functional role for the transcription factor PERIANTHIA (PAN) in the development of the gynoecial medial domain and the formation of ovule primordia. This function of PAN is revealed in pan aintegumenta (ant) as well as seuss (seu) pan double mutants that form reduced numbers of ovules. Previously, PAN was identified as a regulator of perianth organ number and as a direct activator of AGAMOUS (AG) expression in floral whorl four. However, the seu pan double mutants display enhanced ectopic AG expression in developing sepals and the partial transformation of sepals to petals indicating a novel role for PAN in the repression of AG in floral whorl one. These results indicate that PAN functions as an activator or repressor of AG expression in a whorl-specific fashion. The seu pan double mutants also display enhanced floral indeterminacy, resulting in the formation of fifth whorl structures and disruption of WUSCHEL (WUS) expression patterns revealing a novel role for SEU in floral meristem termination

Novel functional roles for \u3cem\u3ePERIANTHIA\u3c/em\u3e and \u3cem\u3eSEUSS\u3c/em\u3e during floral organ identity specification, floral meristem termination, and gynoecial development

The gynoecium is the female reproductive structure of angiosperm flowers. In Arabidopsis thaliana the gynoecium is composed of two carpels that are fused into a tube-like structure. As the gynoecial primordium arises from the floral meristem, a specialized meristematic structure, the carpel margin meristem (CMM), develops from portions of the medial gynoecial domain. The CMM is critical for reproductive competence because it gives rise to the ovules, the precursors of the seeds. Here we report a functional role for the transcription factor PERIANTHIA (PAN) in the development of the gynoecial medial domain and the formation of ovule primordia. This function of PAN is revealed in pan aintegumenta (ant) as well as seuss (seu) pan double mutants that form reduced numbers of ovules. Previously, PAN was identified as a regulator of perianth organ number and as a direct activator of AGAMOUS (AG) expression in floral whorl four. However, the seu pan double mutants display enhanced ectopic AG expression in developing sepals and the partial transformation of sepals to petals indicating a novel role for PAN in the repression of AG in floral whorl one. These results indicate that PAN functions as an activator or repressor of AG expression in a whorl-specific fashion. The seu pan double mutants also display enhanced floral indeterminacy, resulting in the formation of fifth whorl structures and disruption of WUSCHEL (WUS) expression patterns revealing a novel role for SEU in floral meristem termination

Training telescope operators and support astronomers at Paranal

The operations model of the Paranal Observatory relies on the work of efficient staff to carry out all the daytime and nighttime tasks. This is highly dependent on adequate training. The Paranal Science Operations department (PSO) has a training group that devises a well-defined and continuously evolving training plan for new staff, in addition to broadening and reinforcing courses for the whole department. This paper presents the training activities for and by PSO, including recent astronomical and quality control training for operators, as well as adaptive optics and interferometry training of all staff. We also present some future plans.Comment: Paper 9910-123 presented at SPIE 201

Improvement and evaluation of the mesoscale meteorological model MM5 for air-quality applications in Southern California and the San Joaquin Valley: Final Report

The objective of the Penn State University (PSU) part of the study was to investigate the MM5's ability to simulate wintertime fog in the San Joaquin Valley (SJV) and summertime sea breeze flows in the South Coast Air Basin (SoCAB). For the SJV work the MM5 was configured with four nested grid and an advanced turbulence sub-model. Applied to the event of 7-12 December 1995, observed during the IMS-95 program, the model's innermost domain used 40 vertical layers and a 4-km mesh. Several experiments were performed to improve the turbulence sub-model for saturated conditions and to provide more accurate initial conditions for soil temperature and moisture. Results showed the MM5 correctly predicted the type of visibility obscuration (fog, haze, status or clear) in 14 out of the 18 events. For depth was estimated by the MM5 with a mean absolute error of only 92 m and a mean error of -41 m. Mean errors for both the surface temperature and dew point were within +1C, while the mean absolute errors were ~1.5-2.0 C. As a consequence, the mean error for dew-point depression is very small. Thus, the MM5 was shown to simulate fog and haze in the SJV with considerable accuracy. Extensions of the turbulence sub-model to include saturation effects and the specification of accurate soil temperature and moisture were important for simulating fog characteristics in the case. Additionally, MM5 was able to simulate the light and variable winds in the Sacramento and San Joaquin Valleys that prevailed during this event. Moreover, the winds responded quite well to the slowly changing synoptic-scale weather, as well, as confirmed by the observations. the objective for the San Jose State University (SJSU) work included use of SCOS97 data and MM5 simulations to understand meteorological factors in the formation of high ozone concentrations during 4-7 August 1997. Meteorological data for the case study included observations at 110 SCOS97 surface sites and upper air measurements from 12 rawinsonde and 26 RWP/RASS profilers. the MM5 version contained the PSU Marine Boundary Layer Initialization (MBLI) scheme, quadruple nested grids (horizontal resolutions of 135, 45, 15, and 5 km), 30 vertical layers, minimum sigma level of 46 m, USGS global land-use, GDAS global gridded model analyses and SSTs, analysis nudging, observational nudging, force-restore surface temperature, 1.5 order TKE, one-way continuous nesting, and a MAPS statistical evaluation. Analysis showed the ozone episode resulting from a unique combination of large-scale upper level synoptic forcings that included a weak local coastal 700 mb anticyclone. Its movement around SoCAB rotated the upper level synoptic background flow from its normal westerly onshore direction to a less common offshore easterly flow during the nighttime period preceding the episode. The resulting easterly upper level synoptic background winds influenced surface flow direction at inland sites, so that a surface frontal convergence zone resulted where the easterly flow met the westerly onshore sea breeze flow. The maximum inland penetration of the convergence zone was about to the San Gabriel Mountain peaks, the location of daytime maximum ozone-episode concentrations. The current MM5 simulations reproduced the main qualitative features of the evolution of the diurnal sea breeze cycle in the SoCAB with reasonable accuracy. The position of the sea breeze front during its daytime inland penetration and nighttime retreat could be determined from the simulated wind fields. the accuracy of predicted MM5 surface winds and temperatures over SoCAB were improved by the modifications of its deep-soil temperatures, interpolation of predicted temperatures and winds to SCOS97 observational levels, use of updated urban land-use patterns, and use of corrected input values for ocean and urban surface roughness parameter values.Prepared for the California Air Resources Board and California Environmental Protection AgencySJSU Foundation Subcontract no. 22-1505-7384Approved for public release; distribution is unlimited

Stepping Beyond the Newtonian Paradigm in Biology. Towards an Integrable Model of Life: Accelerating Discovery in the Biological Foundations of Science

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses

Machine Learning-based Brokers for Real-time Classification of the LSST Alert Stream

The unprecedented volume and rate of transient events that will be discovered by the Large Synoptic Survey Telescope (LSST) demands that the astronomical community update its followup paradigm. Alert-brokers -- automated software system to sift through, characterize, annotate and prioritize events for followup -- will be critical tools for managing alert streams in the LSST era. The Arizona-NOAO Temporal Analysis and Response to Events System (ANTARES) is one such broker. In this work, we develop a machine learning pipeline to characterize and classify variable and transient sources only using the available multiband optical photometry. We describe three illustrative stages of the pipeline, serving the three goals of early, intermediate and retrospective classification of alerts. The first takes the form of variable vs transient categorization, the second, a multi-class typing of the combined variable and transient dataset, and the third, a purity-driven subtyping of a transient class. While several similar algorithms have proven themselves in simulations, we validate their performance on real observations for the first time. We quantitatively evaluate our pipeline on sparse, unevenly sampled, heteroskedastic data from various existing observational campaigns, and demonstrate very competitive classification performance. We describe our progress towards adapting the pipeline developed in this work into a real-time broker working on live alert streams from time-domain surveys.Comment: 33 pages, 14 figures, submitted to ApJ

Signaling and crosstalk by C5a and UDP in macrophages selectively use PLCbeta 3 to regulate intracellular free calcium

Studies in fibroblasts, neurons, and platelets have demonstrated the integration of signals from different G-protein coupled receptors (GPCRs) in raising intracellular free Ca2+. To study signal integration in macrophages, we screened RAW264.7 cells and bone marrow-derived macrophages (BMDM) for their Ca2+ response to GPCR ligands. We found a synergistic response to complement component 5a (C5a) in combination with uridine 5’-diphosphate (UDP), platelet activating factor (PAF) or lysophosphatidic acid (LPA). The C5a response was Gai-dependent, while the UDP, PAF, and LPA responses were Gaqdependent. Synergy between C5a and UDP, mediated by the C5a and P2Y6 receptors, required dual receptor occupancy, and affected the initial release of Ca2+ from intracellular stores as well as sustained Ca2+ levels. C5a and UDP synergized in generating inositol-1,4,5-trisphosphate, suggesting synergy in activating phospholipase C (PLC) ß. Macrophages expressed transcripts for three PLCß isoforms (PLCß2, PLCß3, and PLCß4), but GPCR ligands selectively used these isoforms in Ca2+ signaling. C5a predominantly used PLCß3, while UDP used PLCß3 but also PLCß4. Neither ligand required PLCß2. Synergy between C5a and UDP likewise depended primarily on PLCß3. Importantly, the Ca2+ signaling deficiency observed in PLCß3-deficient BMDM was reversed by reconstitution with PLCß3. Neither PI-3 kinase nor PKC was required for synergy. In contrast to Ca2+, PI3-kinase activation by C5a was inhibited by UDP, as was macropinocytosis, which depends on PI3- kinase. PLCß3 may thus provide a selective target for inhibiting Ca2+ responses to mediators of inflammation, including C5a, UDP, PAF, and LPA