Coz: Finding Code that Counts with Causal Profiling

Improving performance is a central concern for software developers. To locate optimization opportunities, developers rely on software profilers. However, these profilers only report where programs spent their time: optimizing that code may have no impact on performance. Past profilers thus both waste developer time and make it difficult for them to uncover significant optimization opportunities. This paper introduces causal profiling. Unlike past profiling approaches, causal profiling indicates exactly where programmers should focus their optimization efforts, and quantifies their potential impact. Causal profiling works by running performance experiments during program execution. Each experiment calculates the impact of any potential optimization by virtually speeding up code: inserting pauses that slow down all other code running concurrently. The key insight is that this slowdown has the same relative effect as running that line faster, thus "virtually" speeding it up. We present Coz, a causal profiler, which we evaluate on a range of highly-tuned applications: Memcached, SQLite, and the PARSEC benchmark suite. Coz identifies previously unknown optimization opportunities that are both significant and targeted. Guided by Coz, we improve the performance of Memcached by 9%, SQLite by 25%, and accelerate six PARSEC applications by as much as 68%; in most cases, these optimizations involve modifying under 10 lines of code.Comment: Published at SOSP 2015 (Best Paper Award

Molecular characterization of mesophilic and thermophilic sulfate reducing microbial communities in expanded granular sludge bed (EGSB) reactors

The microbial communities established in mesophilic and thermophilic expanded granular sludge bed reactors operated with sulfate as the electron acceptor were analyzed using 16S rRNA targeted molecular methods, including denaturing gradient gel electrophoresis, cloning, and phylogenetic analysis. Bacterial and archaeal communities were examined over 450 days of operation treating ethanol (thermophilic reactor) or ethanol and later a simulated semiconductor manufacturing wastewater containing citrate, isopropanol, and polyethylene glycol 300 (mesophilic reactor), with and without the addition of copper(II). Analysis, of PCR-amplified 16S rRNA gene fragments using denaturing gradient gel electrophoresis revealed a defined shift in microbial diversity in both reactors following a change in substrate composition (mesophilic reactor) and in temperature of operation from 30 degrees C to 55 degrees C (thermophilic reactor). The addition of copper(II) to the influent of both reactors did not noticeably affect the composition of the bacterial or archaeal communities, which is in agreement with the very low soluble copper concentrations (3-310 microg l(-1)) present in the reactor contents as a consequence of extensive precipitation of copper with biogenic sulfides. Furthermore, clone library analysis confirmed the phylogenetic diversity of sulfate-reducing consortia in mesophilic and thermophilic sulfidogenic reactors operated with simple substrate

How effective is school-based deworming for the community-wide control of soil-transmitted helminths?

Background: The London Declaration on neglected tropical diseases was based in part on a new World Health Organization roadmap to “sustain, expand and extend drug access programmes to ensure the necessary supply of drugs and other interventions to help control by 2020”. Large drug donations from the pharmaceutical industry form the backbone to this aim, especially for soil-transmitted helminths (STHs) raising the question of how best to use these resources. Deworming for STHs is often targeted at school children because they are at greatest risk of morbidity and because it is remarkably cost-effective. However, the impact of school-based deworming on transmission in the wider community remains unclear. Methods: We first estimate the proportion of parasites targeted by school-based deworming using demography, school enrolment, and data from a small number of example settings where age-specific intensity of infection (either worms or eggs) has been measured for all ages. We also use transmission models to investigate the potential impact of this coverage on transmission for different mixing scenarios. Principal Findings: In the example settings <30% of the population are 5 to <15 years old. Combining this demography with the infection age-intensity profile we estimate that in one setting school children output as little as 15% of hookworm eggs, whereas in another setting they harbour up to 50% of Ascaris lumbricoides worms (the highest proportion of parasites for our examples). In addition, it is estimated that from 40–70% of these children are enrolled at school. Conclusions: These estimates suggest that, whilst school-based programmes have many important benefits, the proportion of infective stages targeted by school-based deworming may be limited, particularly where hookworm predominates. We discuss the consequences for transmission for a range of scenarios, including when infective stages deposited by children are more likely to contribute to transmission than those from adults

Examining Seasonal Trends of the Martian Polar Warming with the NASA Ames Mars Global Climate Model

The presented work focuses on polar warming as a diagnostic of the mean circulation to increase our understanding of processes that control the mean meridional circulation and transport in the Mars middle atmosphere. The NASA Ames Mars Global Climate Model is utilized to isolate physical processes to determine their impact on polar warming and its seasonal trends

Understanding the Formation and Evolution of Water Ice Clouds in the Hellas Basin During NH Summer on Mars

Water in the atmosphere of Mars moves between the northern and southern hemispheres seasonally, with north-to-south transport during northern hemisphere (NH) summer and south-to-north transport during southern hemisphere (SH) summer. Understanding the processes that control this seasonal transport of water is critical for understanding the current climate of Mars. Because water ice clouds both track and influence atmospheric circulations on a range of spatial scales, investigations about when and why clouds form enhance our knowledge of the water cycle as a whole. We focus here on a population of clouds that has recently been observed by the MARs Color Imager (MARCI) instrument on the Mars Reconnaissance Orbiter (MRO) to persist in the Hellas Basin throughout the majority of NH summer. Centered at 321 nm, Band 7 of the MARCI instrument is ideally suited for mapping water ice clouds on Mars because water ice is bright in the UV. It is notable that the clouds observed by MARCI in Hellas during NH summer are not as easily observed by the Thermal Emission Spectrometer (TES) on Mars Global Surveyor (MGS), which observes in the IR. We use a Global Climate Model (GCM) to investigate the dynamical mechanisms that control the formation and evolution of Hellas water ice clouds

Falling down a flight of stairs: the impact of age and intoxication on injury pattern and severity

Background Falling down a flight of stairs is a common injury mechanism in major trauma patients, but little research has been undertaken into the impact of age and alcohol intoxication on the injury patterns of these patients. Objectives The objective of this study was to compare the impact of age and alcohol intoxication on injury pattern and severity in patients who fell down a flight of stairs. Methods This was a retrospective observational study of prospectively collected trauma registry data from a major trauma centre in the United Kingdom comparing older and younger adult patients admitted to the Emergency Department following a fall down a flight of stairs between July 2012 and March 2015. Results Older patients were more likely to suffer injuries to all body regions, and sustained more severe injuries to the spine (AIS 2[IQR 2 – 3] vs AIS 2 [IQR 2 – 2] p<0.001). They were also more likely to suffer polytrauma (23.6% vs 10.6%; p<0.001). Intoxicated patients were more likely to suffer injuries to the head and neck (42.9% vs 30.5%; p=0.006) and were significantly younger than sober patients (53 years vs 69 years; p<0.001). Conclusion Older patients who fall down a flight of stairs are significantly different from their younger counterparts, with a different injury pattern and a greater likelihood of polytrauma. In addition, alcohol intoxication also affects injury pattern in people who have fallen down a flight of stairs, increasing the risk of traumatic brain injury. Both age and intoxication should be considered when managing these patients

Upper Boundary Extension of the NASA Ames Mars General Circulation Model

Extending the NASA Ames Mars General Circulation Model (MGCM) upper boundary will expand our understanding of the connection between the lower and upper atmosphere of Mars through the middle atmosphere. The extension's main requirements is incorporation of Non-local thermodynamic equilibrium (NLTE) heating (visible) and cooling (infrared). NLTE occurs when energy is exchanged more rapidly with the radiation field (or other energy sources) rather than collisions with other molecules. Without NLTE above approximately 80km/approximately 60km in Mars' atmosphere the IR/visible heating rates are overestimated. Currently NLTE has been applied successfully into the 1D RT code and is in progress for the 3D application

Coupling the Mars Dust and Water Cycles: Investigating the Role of Clouds in Controlling the Vertical Distribution of Dust During N. H. Summer

The dust cycle is critically important for the current climate of Mars. The radiative effects of dust impact the thermal and dynamical state of the atmosphere (Gierasch and Goody, 1968; Haberle et al., 1982; Zurek et al., 1992). Although dust is present in the Martian atmosphere throughout the year, the level of dustiness varies with season. The atmosphere is generally the dustiest during northern fall and winter and the least dusty during northern spring and summer (Smith, 2004). Dust particles are lifted into the atmosphere by dust storms that range in size from meters to thousands of kilometers across (Cantor et al., 2001). During some years, regional storms combine to produce hemispheric or planet encircling dust clouds that obscure the surface and raise atmospheric temperatures by as much as 40 K (Smith et al., 2002). Key recent observations of the vertical distribution of dust indicate that elevated layers of dust exist in the tropics and sub-tropics throughout much of the year (Heavens et al., 2011). These observations have brought particular focus on the processes that control the vertical distribution of dust in the Martian atmosphere. The goal of this work is to further our understanding of how clouds in particular control the vertical distribution of dust, particularly during N. H. spring and summe

Rotational Evolution During Type I X-Ray Bursts

The rotation rates of six weakly-magnetic neutron stars accreting in low-mass X-ray binaries have most likely been measured by Type I X-ray burst observations with RXTE. The nearly coherent oscillations detected during the few seconds of thermonuclear burning are most simply understood as rotational modulation of brightness asymmetries on the neutron star surface. We show that, as suggested by Strohmayer and colleagues, the frequency changes of 1-2 Hz observed during bursts are consistent with angular momentum conservation as the burning shell hydrostatically expands and contracts. We calculate how vertical heat propagation through the radiative outer layers of the atmosphere and convection affect the coherence of the oscillation. We show that the evolution of the rotational profile depends strongly on whether the burning layers are composed of pure helium or mixed hydrogen/helium. Our results help explain the absence (presence) of oscillations from hydrogen-burning (helium-rich) bursts that was found by Muno and collaborators. We investigate angular momentum transport within the burning layers and the recoupling of the burning layers with the star. We show that the Kelvin-Helmholtz instability is quenched by the strong stratification, and that mixing between the burning fuel and underlying ashes by the baroclinic instability does not occur. However, the baroclinic instability may have time to operate within the differentially rotating burning layer, potentially bringing it into rigid rotation.Comment: To appear in The Astrophysical Journal; minor corrections made to tables and figure