Machine dependence and reproducibility for coupled climate simulations: the HadGEM3-GC3.1 CMIP Preindustrial simulation

When the same weather or climate simulation is run on different high-performance computing (HPC) platforms, model outputs may not be identical for a given initial condition. While the role of HPC platforms in delivering better climate projections is to some extent discussed in the literature, attention is mainly focused on scalability and performance rather than on the impact of machine-dependent processes on the numerical solution. Here we investigate the behaviour of the Preindustrial (PI) simulation prepared by the UK Met Office for the forthcoming CMIP6 (Coupled Model Intercomparison Project Phase 6) under different computing environments. Discrepancies between the means of key climate variables were analysed at different timescales, from decadal to centennial. We found that for the two simulations to be statistically indistinguishable, a 200-year averaging period must be used for the analysis of the results. Thus, constant-forcing climate simulations using the HadGEM3-GC3.1 model are reproducible on different HPC platforms provided that a sufficiently long duration of simulation is used. In regions where El Niño–Southern Oscillation (ENSO) teleconnection patterns were detected, we found large sea surface temperature and sea ice concentration differences on centennial timescales. This indicates that a 100-year constant-forcing climate simulation may not be long enough to adequately capture the internal variability of the HadGEM3-GC3.1 model, despite this being the minimum simulation length recommended by CMIP6 protocols for many MIP (Model Intercomparison Project) experiments. On the basis of our findings, we recommend a minimum simulation length of 200 years whenever possible

Net return distributions when metaphylaxis is used to control bovine respiratory disease in high health-risk cattle

This study’s objective was to estimate net returns and return risk for antimicrobial metaphylaxis options to manage bovine respiratory disease (BRD) in high health-risk feedlot cattle. The effectiveness of antimicrobials for metaphylaxis varies by cattle population. How differing antimicrobial effectiveness translates to net return profitability for heterogeneous cattle populations is less understood. Net returns and return risk were assessed using a net return simulation model adapted to allow for heterogeneity in high health-risk cattle placement characteristics and antimicrobial choice to control BRD. The net return model incorporated how antimicrobials modify BRD health and performance outcomes. Health and performance outcomes were calibrated from published literature and proprietary feedlot data. Proprietary data came from 10 Midwestern feedlots representing nearly 6 million animals and 50,000 cohorts. Twelve placement-by-metaphylaxis decision combinations were assessed: high health-risk steer placement demographics were 600 or 800 lb steers placed in Winter (Oct–Mar) or Summer (Apr–Sept) managed with one of three different health programs: “no metaphylaxis,” “Upper Tier” antimicrobial, or “Lower Tier” antimicrobial. Net return distributions were compared between “no metaphylaxis” and a specific antimicrobial tier within specific cattle populations. We found the expected incremental net return of administering an “Upper Tier” (“Lower Tier”) antimicrobial for metaphylaxis compared to “no metaphylaxis” for high health-risk steers was $122.55 per head ($65.72) for 600 lb and $148.65 per head ($79.65) for 800 lb winter placements. The incremental expected net return and risk mitigated by metaphylaxis varied by placement weight, season, and antimicrobial choice. The probability net returns would decline by at least $50 per head was signif-icantly reduced (from approximately 4% to 40%) when any antimicrobial was used on high health-risk steers. Both tiers of antimicrobials used for metaphylaxis increased expected net returns and decreased net return variability relative to no met-aphylaxis. Thus, feedlots were more certain and realize a greater profit on high health-risk pens of steers when metaphylaxis was used. This occurred because the reduction in cattle health and performance outcomes using any antimicrobial was sufficiently large to cover added initial and subsequent antimicrobial costs. Results aid in assessing metaphylaxis strategies in high health-risk cattle

Dietary manipulation and caloric restriction in the development of mouse models relevant to neurological diseases

AbstractManipulation of diet such as increasing the level of fat or inducing insulin resistance has been shown to exacerbate the pathology in several animal models of neurological disease. Caloric restriction, however, has been demonstrated to extend the life span of many organisms. Reduced calorie consumption appears to increase the resistance of neurons to intracellular and extracellular stress and consequently improves the behavioural phenotype in animal models of neurological diseases, such as Alzheimer's disease. We review the evidence from a variety of mouse models that diet is a risk factor that can significantly contribute to the development of neurological diseases

Value of Arrival Metaphylaxis in U.S. Cattle Industry

Although several studies have estimated economic impacts of antimicrobials for growth promotion, little is known about economic impacts of the common animal health management strategy known as metaphylaxis: administering antimicrobials to groups of animals to prevent disease. This article develops a new framework to map animal disease to producer profitability and determine societal economic impacts surrounding metaphylactic use of antimicrobials in beef cattle production. Results indicate the direct net return value of metaphylaxis to the U.S. fed cattle industry is at least $532 million. Beef producer surplus losses of$1.8 billion would be associated with eliminating metaphylaxis

Elemental concentrations in the seed of mutants and natural variants of Arabidopsis thaliana grown under varying soil conditions

Peer reviewedPublisher PD

Approaching Conformality with Ten Flavors

We present first results for lattice simulations, on a single volume, of the low-lying spectrum of an SU(3) Yang-Mills gauge theory with ten light fermions in the fundamental representation. Fits to the fermion mass dependence of various observables are found to be globally consistent with the hypothesis that this theory is within or just outside the strongly-coupled edge of the conformal window, with mass anomalous dimension consistent with 1 over the range of scales simulated. We stress that we cannot rule out the possibility of spontaneous chiral-symmetry breaking at scales well below our infrared cutoff. We discuss important systematic effects, including finite-volume corrections, and consider directions for future improvement.Comment: 7 pages, 3 figures. Submitted to Physical Review Letters. v2: corrected global fits. v3: corrected estimation of confidence interval

The pathogen profile of a honey bee queen does not reflect that of her workers

Throughout a honey bee queen’s lifetime, she is tended to by her worker daughters, who feed and groom her. Such interactions provide possible horizontal transmission routes for pathogens from the workers to the queen, and as such a queen’s pathogen profile may be representative of the workers within a colony. To explore this further, we investigated known honey bee pathogen co-occurrence, as well as pathogen transmission from workers to queens. Queens from 42 colonies were removed from their source hives and exchanged into a second, unrelated foster colony. Worker samples were taken from the source colony on the day of queen exchange and the queens were collected 24 days after introduction. All samples were screened for Nosema spp., Trypanosome spp., acute bee paralysis virus (ABPV), black queen cell virus (BQCV), chronic bee paralysis virus (CBPV), Israeli acute paralysis virus (IAPV), Lake Sinai virus (LSV), and deformed wing virus master variants (DWV-A, B, and C) using RT-qPCR. The data show that LSV, Nosema, and DWV-B were the most abundant pathogens in colonies. All workers (n = 42) were LSV-positive, 88% were Nosema-positive, whilst pathogen loads were low (1 × 106 genome equivalents per pooled worker sample). All queens (n = 39) were negative for both LSV and Nosema. We found no evidence of DWV transmission occurring from worker to queen when comparing queens to foster colonies, despite DWV being present in both queens and workers. Honey bee pathogen presence and diversity in queens cannot be revealed from screening workers, nor were pathogens successfully transmitted to the queen

Day length as a key factor moderating the response of coccolithophore growth to elevated pCO2

The fate of coccolithophores in the future oceans remains uncertain, in part due to key factors having not been standardized across experiments. A potentially moderating role for differences in day length (photoperiod) remains largely unexplored. We therefore cultured four different geographical isolates of the species Emiliania huxleyi, as well as two additional species, Gephyrocapsa oceanica (tropical) and Coccolithus braarudii (temperate), to test for interactive effects of pCO2 with the light : dark (L : D) cycle. We confirmed a general regulatory effect of photoperiod on the pCO2 response, whereby growth and particulate inorganic carbon and particulate organic carbon (PIC : POC) ratios were reduced with elevated pCO2 under 14 : 10 h L : D, but these reductions were dampened under continuous (24 h) light. The dynamics underpinning this pattern generally differed for the temperate vs. tropical isolates. Reductions in PIC : POC with elevated pCO2 for tropical taxa were largely through reduced calcification and enhanced photosynthesis under 14 : 10 h L : D, with differences dampened under continuous light. In contrast, reduced PIC : POC for temperate strains reflected increases of photosynthesis that outpaced increases in calcification rates under 14 : 10 h L : D, with both responses again dampened under continuous light. A multivariate analysis of 35 past studies of E. huxleyi further demonstrated that differences in photoperiod account for as much as 40% (strain B11/92) to 55% (strain NZEH) of the variance in reported pCO2-induced reductions to growth but not PIC : POC. Our study thus highlights a critical role for day length in moderating the effect of ocean acidification on coccolithophore growth and consequently how this response may play out across latitudes and seasons in future oceans