Scientific Computing Meets Big Data Technology: An Astronomy Use Case

Scientific analyses commonly compose multiple single-process programs into a dataflow. An end-to-end dataflow of single-process programs is known as a many-task application. Typically, tools from the HPC software stack are used to parallelize these analyses. In this work, we investigate an alternate approach that uses Apache Spark -- a modern big data platform -- to parallelize many-task applications. We present Kira, a flexible and distributed astronomy image processing toolkit using Apache Spark. We then use the Kira toolkit to implement a Source Extractor application for astronomy images, called Kira SE. With Kira SE as the use case, we study the programming flexibility, dataflow richness, scheduling capacity and performance of Apache Spark running on the EC2 cloud. By exploiting data locality, Kira SE achieves a 2.5x speedup over an equivalent C program when analyzing a 1TB dataset using 512 cores on the Amazon EC2 cloud. Furthermore, we show that by leveraging software originally designed for big data infrastructure, Kira SE achieves competitive performance to the C implementation running on the NERSC Edison supercomputer. Our experience with Kira indicates that emerging Big Data platforms such as Apache Spark are a performant alternative for many-task scientific applications

Panoramic optical and near-infrared SETI instrument: prototype design and testing

The Pulsed All-sky Near-infrared Optical Search for ExtraTerrestrial Intelligence (PANOSETI) is an instrument program that aims to search for fast transient signals (nano-second to seconds) of artificial or astrophysical origin. The PANOSETI instrument objective is to sample the entire observable sky during all observable time at optical and near-infrared wavelengths over 300 - 1650 nm$^1$. The PANOSETI instrument is designed with a number of modular telescope units using Fresnel lenses ($\sim$0.5m) arranged on two geodesic domes in order to maximize sky coverage$^2$. We present the prototype design and tests of these modular Fresnel telescope units. This consists of the design of mechanical components such as the lens mounting and module frame. One of the most important goals of the modules is to maintain the characteristics of the Fresnel lens under a variety of operating conditions. We discuss how we account for a range of operating temperatures, humidity, and module orientations in our design in order to minimize undesirable changes to our focal length or angular resolution.Comment: 12 pages, 8 figures, 1 tabl

Elevating the impact of conservation physiology by building a community devoted to excellence, transparency, ethics, integrity and mutual respect

[Extract] Ten years ago, the journal Conservation Physiology was launched jointly by the Society for Experimental Biology and Oxford University Press. Much has been accomplished since 2012 including publishing over 600 papers in the journal and helping to build a sense of place for aspiring and practicing conservation physiologists (Cooke et al., 2020). Yet, more work is needed to further elevate the impact of conservation physiology as a discipline and community. Here, we summarize what is needed to build and strengthen a community devoted to not only excellence, transparency, ethics, integrity and mutual respect, but also courage to tackle some of the overarching challenges humanity faces. As active voices in the conservation physiology community we hope that this paper will help shape the future of our discipline while also guiding the activities and priorities of the journal and editorial team. Since the term ‘conservation physiology’ was coined by Wikelski and Cooke (2006) it has emerged as an essential component of conservation science and practice. Conservation physiology is about the use of physiological tools, knowledge and concepts to understand and solve conservation problems across diverse taxa (Cooke et al., 2013). It is regarded as being particularly effective at understanding mechanisms, generating cause–effect relationships (e.g. threat X does Y to organism Z), creating predictive tools and testing conservation interventions (Cooke and O’Connor, 2010). Issues relevant to conservation physiology range from very local, focused on recovery of an imperilled population (Birnie-Gauvin et al., 2017), to global-scale issues such as tackling the UN Sustainable Development Goals (Cooke et al., 2020) and the climate crisis (Madliger et al., 2021c). The discipline is now supported by a conceptual framework (Coristine et al., 2014), a journal (https://academic.oup.com/conphys) and a reference book (Madliger et al. 2021a). There is also a growing community of researchers who engage in conservation physiology and even define themselves as conservation physiologists (Madliger et al., 2021b). Moreover, in conservation physiology there are success stories that demonstrate the potential of conservation physiology (Madliger et al., 2016)

Isospin splitting in heavy baryons and mesons

A recent general analysis of light-baryon isospin splittings is updated and extended to charmed baryons. The measured $\Sigma_c$ and $\Xi_c$ splittings stand out as being difficult to understand in terms of two-body forces alone. We also discuss heavy-light mesons; though the framework here is necessarily less general, we nevertheless obtain some predictions that are not strongly model-dependent.Comment: 12 pages REVTEX 3, plus 4 uuencoded ps figures, CMU-HEP93-

Corticospinal excitability is facilitated by combined action observation and motor imagery of a basketball free throw

Objectives This experiment aimed to establish the extent to which independent action observation, independent motor imagery and combined action observation and motor imagery of a sport-related motor skill would elicit activity within the motor system. Design and method Eighteen, right-handed, male participants engaged in four conditions following a repeated measures design. The experimental conditions involved action observation, motor imagery, or combined action observation and motor imagery of a basketball free throw, whilst the control condition involved observation of a static image of a basketball player holding a basketball. In all conditions, single pulse transcranial magnetic stimulation was delivered to the forearm representation of the left motor cortex. The amplitude of the resulting motor evoked potentials were recorded from the flexor carpi ulnaris and extensor carpi ulnaris muscles of the right forearm and used as a marker of corticospinal excitability. Results Corticospinal excitability was facilitated significantly by combined action observation and motor imagery of the basketball free throw, in comparison to both the action observation and control conditions. In contrast, the independent use of either action observation or motor imagery did not facilitate corticospinal excitability compared to the control condition. Conclusions The findings have implications for the design and delivery of action observation and motor imagery interventions in sport. As corticospinal excitability was facilitated by the use of combined action observation and motor imagery, researchers should seek to establish the efficacy of implementing combined action observation and motor imagery interventions for improving motor skill performance and learning in applied sporting settings

Effects of cooling on the propagation of magnetized jets

We present multidimensional simulations of magnetized radiative jets appropriate to young stellar objects (YSOs). Magnetized jets subject to collisionally excited radiative losses have not, as yet, received extensive scrutiny. The purpose of this Letter is to articulate the propagation dynamics of radiative MHD jets in the context of the extensive jet literature. Most importantly, we look for morphological and kinematic diagnostics that may distinguish hydrodynamic protostellar jets from their magnetically dominated cousins. Our simulations are axisymmetric (2.5 dimensions). A toroidal (B-phi) field geometry is used. Our models have high sonic Mach numbers (M-f approximate to 10) but lower fast-mode Mach number (M-f approximate to 5). This is approximately the case for jets formed via disk-wind or X-wind models-currently the consensus choice for launching and collimating YSO jets. Time-dependent radiative losses are included via a coronal cooling curve. Our results demonstrate that the morphology and propagation characteristics of strongly magnetized radiative jets can differ significantly from jets with weak fields. In particular, the formation of nose cones via postshock hoop stresses leads to narrow bow shocks and enhanced bow shock speeds. In addition, the hoop stresses produce strong shocks in the jet beam, which contrasts with the relatively unperturbed beam in radiative hydrodynamic jets. Our simulations show that pinch modes produced by magnetic tension can strongly affect magnetized protostellar jets. These differences may be useful in observational studies designed to distinguish between competing jet collimation scenariosopen515

School Programs and Characteristics and Their Influence on Student BMI: Findings from Healthy Passages

Background: Little is known about the contribution of school contextual factors to individual student body mass index (BMI). We set out to determine if school characteristics/resources: (1) are associated with student BMI; (2) explain racial/ethnic disparities in student BMI; and (3) explain school-level differences in student BMI. Methods: Using gender-stratified multi-level modeling strategies we examined the association of school characteristics/resources and individual BMI in 4,387 5th graders in the Healthy Passages Longitudinal Study of Adolescent Health. Additionally, we examined the association of race/ethnicity and individual BMI as well as the between-school variance in BMI before and after adding individual and school characteristics to test for attenuation. Results: The school-level median household income, but not physical activity or nutrition resources, was inversely associated with female BMI (β = −0.12, CI: −0.21,−0.02). Neither school demographics nor physical activity/nutrition resources were predictive of individual BMI in males. In Black females, school characteristics attenuated the association of race/ethnicity and BMI. Individual student characteristics—not school characteristics/resources-reduced the between-school variation in BMI in males by nearly one-third and eliminated it in females. Conclusions: In this cohort of 5th graders, school SES was inversely associated with female BMI while school characteristics and resources largely explained Black/White disparities in female weight status. Between-school differences in average student weight status were largely explained by the composition of the student body not by school characteristics or programming

Panoramic SETI: overall focal plane electronics and timing and network protocols

The PANOSETI experiment is an all-sky, all-the-time visible search for nanosecond to millisecond time-scale transients. The experiment will deploy observatory domes at several sites, each dome containing ~45 telescopes and covering ~4,440 square degrees. Here we describe the focal-plane electronics for the visible wavelength telescopes, each of which contains a Mother Board and four Quadrant Boards. On each quadrant board, 256 silicon photomultiplier (SiPM) photon detectors are arranged to measure pulse heights to search for nanosecond time-scale pulses. To simultaneously examine pulse widths over a large range of time scales (nanoseconds to milliseconds), the instrument implements both a Continuous Imaging Mode (CI-Mode) and a Pulse Height Mode (PH-Mode). Precise timing is implemented in the gateware with the White Rabbit protocol