An Efficient Cell List Implementation for Monte Carlo Simulation on GPUs

Maximizing the performance potential of the modern day GPU architecture requires judicious utilization of available parallel resources. Although dramatic reductions can often be obtained through straightforward mappings, further performance improvements often require algorithmic redesigns to more closely exploit the target architecture. In this paper, we focus on efficient molecular simulations for the GPU and propose a novel cell list algorithm that better utilizes its parallel resources. Our goal is an efficient GPU implementation of large-scale Monte Carlo simulations for the grand canonical ensemble. This is a particularly challenging application because there is inherently less computation and parallelism than in similar applications with molecular dynamics. Consistent with the results of prior researchers, our simulation results show traditional cell list implementations for Monte Carlo simulations of molecular systems offer effectively no performance improvement for small systems [5, 14], even when porting to the GPU. However for larger systems, the cell list implementation offers significant gains in performance. Furthermore, our novel cell list approach results in better performance for all problem sizes when compared with other GPU implementations with or without cell lists.Comment: 30 page

Stable water isotope and surface heat flux simulation using ISOLSM: Evaluation against in-situ measurements

Author's manuscript made available in accordance with the publisher's policy.The stable isotopes of water are useful tracers of water sources and hydrological processes. Stable water isotope-enabled land surface modeling is a relatively new approach for characterizing the hydrological cycle, providing spatial and temporal variability for a number of hydrological processes. At the land surface, the integration of stable water isotopes with other meteorological measurements can assist in constraining surface heat flux estimates and discriminate between evaporation (E) and transpiration (T). However, research in this area has traditionally been limited by a lack of continuous in-situ isotopic observations. Here, the National Centre for Atmospheric Research stable isotope-enabled Land Surface Model (ISOLSM) is used to simulate the water and energy fluxes and stable water isotope variations. The model was run for a period of one month with meteorological data collected from a coastal sub-tropical site near Sydney, Australia. The modeled energy fluxes (latent heat and sensible heat) agreed reasonably well with eddy covariance observations, indicating that ISOLSM has the capacity to reproduce observed flux behavior. Comparison of modeled isotopic compositions of evapotranspiration (ET) against in-situ Fourier Transform Infrared spectroscopy (FTIR) measured bulk water vapor isotopic data (10 m above the ground), however, showed differences in magnitude and temporal patterns. The disparity is due to a small contribution from local ET fluxes to atmospheric boundary layer water vapor (∼1% based on calculations using ideal gas law) relative to that advected from the ocean for this particular site. Using ISOLSM simulation, the ET was partitioned into E and T with 70% being T. We also identified that soil water from different soil layers affected T and E differently based on the simulated soil isotopic patterns, which reflects the internal working of ISOLSM. These results highlighted the capacity of using the isotope-enabled models to discriminate between different hydrological components and add insight into expected hydrological behavior

What do we know about the nexus between culture, age, gender and health literacy? Implications for improving the health and well-being of young Indigenous males

Health literacy, although diversely defined, refers to the abilities, relationships and external environments required for people to successfully promote health. Existing research suggests that health literacy is related to health inequities, including individual and community capacity to navigate health. A diverse range of factors shape health literacy abilities and environments, especially culture, gender and age. However, the nexus between these variables and their cumulative impact on health literacy development remains largely unexplored. Commentary that explores these dynamics among young Indigenous males is particularly scant. In turn, strategies to bridge health equity gaps have been obscured. This article brings together disparate research on health literacy, masculinities, youth studies and men’s health in order to address this oversight. By outlining the collective conceptual contribution of these strands of scholarship, we show that young Indigenous males navigate health literacy through a complex cultural interface that balances both Western and Indigenous understandings of health. Alternative masculine identities, which simultaneously embrace and resist components of hegemonic masculinity, also shape this health literacy lens. We explain that the development of health literacy is important for young people, particularly young Indigenous males, and that this is negotiated in tandem with external support structures, including family and friends. By describing these intersections, we explore the implications for researchers, policymakers and practitioners seeking to achieve the dual goal of improving health literacy and reducing health inequi-ties among this highly marginalised population

Using social media in health literacy research: A promising example involving Facebook with young Aboriginal and Torres Strait Islander males from the top end of the Northern Territory

This brief report describes three key lessons learned during a health literacy research project with young Aboriginal and Torres Strait Islander males from the Top End of the Northern Territory (NT), Australia. More specifically, it is a methodologically focused paper that discusses processes associated with using a combination of yarning sessions and social media content as tools to unpack conceptualisations of health and well‐being among this marginalised population. The lessons discussed include (a) the utility of using social media in providing an authentic window into the lives of a hard‐to‐reach populations; (b) the need to carefully consider ethical implications; and (c) the benefits of using social media content to triangulate data and enhance methodological rigour. To understand the methodological contribution social media can make to equity‐focused health literacy research, it is first useful to understand what is meant by health literacy

Mental health, deprivation, and the neighbourhood social environment: a network analysis

Different aspects of the neighbourhood social environment have been linked with mental ill-health, however the mechanisms underlying these associations remain poorly understood because of the number and complexity of the components involved. We used a novel statistical approach, network analysis, to explore the complex associations between neighbourhood social cohesion, social disorder and mental health symptoms in a sample of 3,670 adults from an economically deprived region of the UK (mean age [SD] = 49.34 years [18.87]; 57% female). Elasso regularised networks were estimated, and network comparisons were conducted by level of deprivation. Mental health symptoms and neighbourhood components formed relatively distinct clusters of items. These domains were linked primarily by paranoia, although only in the most deprived group. Drunken/rowdy behaviour was particularly influential within the neighbourhood cluster, therefore policies aimed at reducing such disruptive behaviour could have positive knock-on effects for social cohesion and mental health

Fire regimes and carbon in Australian vegetation

Fires regularly affect many of the world\u27s terrestrial ecosystems, and, as a result, fires mediate the exchange of greenhouse gases (GHG) between the land and the atmosphere at a global scale and affect the capacity of terrestrial ecosystems to store carbon (Bowman et al. 2009). Variations in fire -regimes can therefore potentially affect the global, regional and local carbon balance and, potentially, climate change itself (Bonan 2008). Here we examine how variation in fire regimes (Gill 1975; Bradstock et al. 2002) will potentially affect carbon in fire-prone Australian ecosystems via interactions with the stocks and transfers of carbon that are inherent to all terrestrial ecosystems. There are two key reasons why an appreciation of fire regimes is needed to comprehend the fate of terrestrial carbon. First, the status of terrestrial carbon over time will be a function of the balance between losses (emissions) from individual fires (of differing type, season and intensity), which occur as a result of immediate combustion as well as mortality and longerterm decomposition of dead biomass, and carbon that accumulates during regeneration in the intervals between fires. The length of the interval between fires will determine the amount of biomass that accumulates. Second, fire regimes influence the composition and structure of ecosystems and key processes such as plant mortality and recruitment. Hence, alternative trajectories of vegetation composition and structure that result from differing fire regimes will affect carbon dynamics. We explore these themes and summarise the dynamic aspects of carbon stocks and transfers in relation to fire, present conceptual models of carbon dynamics and fire regimes, and review how variation in fire regimes may affect overall storage potential as a function of fireinduced losses and post-fire uptake in two widespread Australian vegetation types. We then appraise future trends under global change and the likely potential for managing fire regimes for carbon \u27benefits\u27, especially with respect to emissions

Targeting Medium-Chain Acyl-CoA Dehydrogenase for Glioblastoma

View full abstracthttps://openworks.mdanderson.org/leading-edge/1041/thumbnail.jp

The dpsA Gene of Streptomyces coelicolor: Induction of Expression from a Single Promoter in Response to Environmental Stress or during Development

The DpsA protein plays a dual role in Streptomyces coelicolor, both as part of the stress response and contributing to nucleoid condensation during sporulation. Promoter mapping experiments indicated that dpsA is transcribed from a single, sigB-like dependent promoter. Expression studies implicate SigH and SigB as the sigma factors responsible for dpsA expression while the contribution of other SigB-like factors is indirect by means of controlling sigH expression. The promoter is massively induced in response to osmotic stress, in part due to its sensitivity to changes in DNA supercoiling. In addition, we determined that WhiB is required for dpsA expression, particularly during development. Gel retardation experiments revealed direct interaction between apoWhiB and the dpsA promoter region, providing the first evidence for a direct WhiB target in S. coelicolor

Follicular Dendritic Cell-Specific Prion Protein (PrPc) Expression Alone Is Sufficient to Sustain Prion Infection in the Spleen

Prion diseases are characterised by the accumulation of PrPSc, an abnormally folded isoform of the cellular prion protein (PrPC), in affected tissues. Following peripheral exposure high levels of prion-specific PrPSc accumulate first upon follicular dendritic cells (FDC) in lymphoid tissues before spreading to the CNS. Expression of PrPC is mandatory for cells to sustain prion infection and FDC appear to express high levels. However, whether FDC actively replicate prions or simply acquire them from other infected cells is uncertain. In the attempts to-date to establish the role of FDC in prion pathogenesis it was not possible to dissociate the Prnp expression of FDC from that of the nervous system and all other non-haematopoietic lineages. This is important as FDC may simply acquire prions after synthesis by other infected cells. To establish the role of FDC in prion pathogenesis transgenic mice were created in which PrPC expression was specifically “switched on” or “off” only on FDC. We show that PrPC-expression only on FDC is sufficient to sustain prion replication in the spleen. Furthermore, prion replication is blocked in the spleen when PrPC-expression is specifically ablated only on FDC. These data definitively demonstrate that FDC are the essential sites of prion replication in lymphoid tissues. The demonstration that Prnp-ablation only on FDC blocked splenic prion accumulation without apparent consequences for FDC status represents a novel opportunity to prevent neuroinvasion by modulation of PrPC expression on FDC

Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases

Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises