Sustainable Software Ecosystems: Software Engineers, Domain Scientists, and Engineers Collaborating for Science

The development of scientific software is often a partnership between domain scientists and scientific software engineers. It is especially important to embrace these collaborations when developing advanced scientific software, where sustainability, reproducibility, and extensibility are important. In the ideal case, as discussed in this manuscript, this brings together teams composed of the world's foremost scientific experts in a given field with seasoned software developers experienced in forming highly collaborative teams working on software to further scientific research.Comment: 4 pages, submission for WSSSPE

Neural regulation of cardiovascular response to exercise: role of central command and peripheral afferents

During dynamic exercise, mechanisms controlling the cardiovascular apparatus operate to provide adequate oxygen to fulfill metabolic demand of exercising muscles and to guarantee metabolic end-products washout. Moreover, arterial blood pressure is regulated to maintain adequate perfusion of the vital organs without excessive pressure variations. The autonomic nervous system adjustments are characterized by a parasympathetic withdrawal and a sympathetic activation. In this review, we briefly summarize neural reflexes operating during dynamic exercise. The main focus of the present review will be on the central command, the arterial baroreflex and chemoreflex, and the exercise pressure reflex. The regulation and integration of these reflexes operating during dynamic exercise and their possible role in the pathophysiology of some cardiovascular diseases are also discusse

Hypervelocity Stars from the Andromeda Galaxy

Hypervelocity stars (HVSs) discovered in the Milky Way (MW) halo are thought to be ejected from near the massive black hole (MBH) at the galactic centre. In this paper we investigate the spatial and velocity distributions of the HVSs which are expected to be similarly produced in the Andromeda galaxy (M31). We consider three different HVS production mechanisms: (i) the disruption of stellar binaries by the galactocentric MBH; (ii) the ejection of stars by an in-spiraling intermediate mass black hole; and (iii) the scattering of stars off a cluster of stellar-mass black holes orbiting around the MBH. While the first two mechanisms would produce large numbers of HVSs in M31, we show that the third mechanism would not be effective in M31. We numerically calculate 1.2*10^6 trajectories of HVSs from M31 within a simple model of the Local Group and hence infer the current distribution of these stars. Gravitational focusing of the HVSs by the MW and the diffuse Local Group medium leads to high densities of low mass (~ solar mass) M31 HVSs near the MW. Within the virialized MW halo, we expect there to be of order 1000 HVSs for the first mechanism and a few hundred HVSs for the second mechanism; many of these stars should have distinctively large approach velocities (< -500 km/s). In addition, we predict ~5 hypervelocity RGB stars within the M31 halo which could be identified observationally. Future MW astrometric surveys or searches for distant giants could thus find HVSs from M31.Comment: 14 pages, 6 figures, changed to match version accepted by MNRA

Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts.

Cellular protein-RNA complexes assemble on nascent transcripts, but methods to observe transcription and protein binding in real time and at physiological concentrations are not available. Here, we report a single-molecule approach based on zero-mode waveguides that simultaneously tracks transcription progress and the binding of ribosomal protein S15 to nascent RNA transcripts during early ribosome biogenesis. We observe stable binding of S15 to single RNAs immediately after transcription for the majority of the transcripts at 35 °C but for less than half at 20 °C. The remaining transcripts exhibit either rapid and transient binding or are unable to bind S15, likely due to RNA misfolding. Our work establishes the foundation for studying transcription and its coupled co-transcriptional processes, including RNA folding, ligand binding, and enzymatic activity such as in coupling of transcription to splicing, ribosome assembly or translation

Sustainable Software Ecosystems for Open Science

Sustainable software ecosystems are difficult to build, and require concerted effort, community norms and collaborations. In science it is especially important to establish communities in which faculty, staff, students and open-source professionals work together and treat software as a first-class product of scientific investigation-just as mathematics is treated in the physical sciences. Kitware has a rich history of establishing collaborative projects in the science, engineering and medical research fields, and continues to work on improving that model as new technologies and approaches become available. This approach closely follows and is enhanced by the movement towards practicing open, reproducible research in the sciences where data, source code, methodology and approach are all available so that complex experiments can be independently reproduced and verified.Comment: Workshop on Sustainable Software: Practices and Experiences, 4 pages, 3 figure