On the use of Bayesian decision theory for issuing natural hazard warnings

This is the final version of the article. Available from the Royal Society via the DOI in this record.Warnings for natural hazards improve societal resilience and are a good example of decision-making under uncertainty. A warning system is only useful if well defined and thus understood by stakeholders. However, most operational warning systems are heuristic: not formally or transparently defined. Bayesian decision theory provides a framework for issuing warnings under uncertainty but has not been fully exploited. Here, a decision theoretic framework is proposed for hazard warnings. The framework allows any number of warning levels and future states of nature, and a mathematical model for constructing the necessary loss functions for both generic and specific end-users is described. The approach is illustrated using one-day ahead warnings of daily severe precipitation over the UK, and compared to the current decision tool used by the UK Met Office. A probability model is proposed to predict precipitation, given ensemble forecast information, and loss functions are constructed for two generic stakeholders: an end-user and a forecaster. Results show that the Met Office tool issues fewer high-level warnings compared with our system for the generic end-user, suggesting the former may not be suitable for risk averse end-users. In addition, raw ensemble forecasts are shown to be unreliable and result in higher losses from warnings.This work was supported by the Natural Environment Research Council (Consortium on Risk in the Environment: Diagnostics, Integration, Benchmarking, Learning and Elicitation (CREDIBLE); grant no. NE/J017043/1)

Assessing the reliability of probabilistic flood inundation model predictions

An ability to quantify the reliability of probabilistic flood inundation predictions is a requirement not only for guiding model development but also for their successful application. Probabilistic flood inundation predictions are usually produced by choosing a method of weighting the model parameter space, but previous study suggests that this choice leads to clear differences in inundation probabilities. This study aims to address the evaluation of the reliability of these probabilistic predictions. However, a lack of an adequate number of observations of flood inundation for a catchment limits the application of conventional methods of evaluating predictive reliability. Consequently, attempts have been made to assess the reliability of probabilistic predictions using multiple observations from a single flood event. Here, a LISFLOOD-FP hydraulic model of an extreme (>1 in 1000 years) flood event in Cockermouth, UK, is constructed and calibrated using multiple performance measures from both peak flood wrack mark data and aerial photography captured post-peak. These measures are used in weighting the parameter space to produce multiple probabilistic predictions for the event. Two methods of assessing the reliability of these probabilistic predictions using limited observations are utilized; an existing method assessing the binary pattern of flooding, and a method developed in this paper to assess predictions of water surface elevation. This study finds that the water surface elevation method has both a better diagnostic and discriminatory ability, but this result is likely to be sensitive to the unknown uncertainties in the upstream boundary conditio

Detecting Compaction Disequilibrium with Anisotropy of Magnetic Susceptibility

In clay-rich sediment, microstructures and macrostructures influence how sediments deform when under stress. When lithology is fairly constant, anisotropy of magnetic susceptibility (AMS) can be a simple technique for measuring the relative consolidation state of sediment, which reflects the sediment burial history. AMS can reveal areas of high water content and apparent overconsolidation associated with unconformities where sediment overburden has been removed. Many other methods for testing consolidation and water content are destructive and invasive, whereas AMS provides a nondestructive means to focus on areas for additional geotechnical study. In zones where the magnetic minerals are undergoing diagenesis, AMS should not be used for detecting compaction state. By utilizing AMS in the Santa Barbara Basin, we were able to identify one clear unconformity and eight zones of high water content in three cores. With the addition of susceptibility, anhysteretic remanent magnetization, and isothermal remanent magnetization rock magnetic techniques, we excluded 3 out of 11 zones from being compaction disequilibria. The AMS signals for these three zones are the result of diagenesis, coring deformation, and burrows. In addition, using AMS eigenvectors, we are able to accurately show the direction of maximum compression for the accumulation zone of the Gaviota Slide

Branching coral growth and visual health during bleaching and recovery on the central Great Barrier Reef

Coral reefs are under threat from cumulative impacts such as cyclones, crown-of-thorns starfish (COTS) outbreaks and climate-driven coral bleaching events. Branching corals are more severely impacted by these events than other coral morphologies due to their sensitivity to heat stress and weaker skeletons and COTS preferred prey. The central Great Barrier Reef experienced unprecedented back-to-back bleaching events in 2016 and 2017. This study commenced in 2017 at the peak of heat stress and examined the impact of the heatwave on the survival and recovery of corals by assessing the growth, health (based on the visual health index) and physiological parameters (chlorophyll a, zooxanthellae density, lipid and protein content) of two species, Acropora millepora and Pocillopora acuta (N = 60 colonies for each species). It was conducted across a gradient of turbidity at three reefs, Pandora, Orpheus and Rib, that experienced in April 2017, degree heating weeks (DHW) of 9, 8 and 7, respectively. Orpheus experienced the worst bleaching, based on visual health score, followed by Rib and Pandora. Rib experienced the greatest mortality (78% by Nov 2017); however, this was attributed to the presence of actively feeding crown-of-thorns starfish. Growth rates of A. millepora were almost twice the rate of P. acuta. Both species showed significant seasonal variation with growth of A. millepora and P. acuta 35–40% and 23–33% significantly greater in the summer, respectively. Differences in growth rates were best explained by indicators of energy acquisition. For example, the most important predictor variable in determining higher growth rates and visual health score in A. millepora was chlorophyll a content. For P. acuta, visual health score was the best predictor variable for higher growth rates. This study highlights the important role that chlorophyll a and associated symbionts play in growth and survival in these corals during and after a heat stress event

Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci.

BACKGROUND: Genome-wide association studies have identified multiple genetic variants associated with prostate cancer risk which explain a substantial proportion of familial relative risk. These variants can be used to stratify individuals by their risk of prostate cancer. METHODS: We genotyped 25 prostate cancer susceptibility loci in 40,414 individuals and derived a polygenic risk score (PRS). We estimated empirical odds ratios (OR) for prostate cancer associated with different risk strata defined by PRS and derived age-specific absolute risks of developing prostate cancer by PRS stratum and family history. RESULTS: The prostate cancer risk for men in the top 1% of the PRS distribution was 30.6 (95% CI, 16.4-57.3) fold compared with men in the bottom 1%, and 4.2 (95% CI, 3.2-5.5) fold compared with the median risk. The absolute risk of prostate cancer by age of 85 years was 65.8% for a man with family history in the top 1% of the PRS distribution, compared with 3.7% for a man in the bottom 1%. The PRS was only weakly correlated with serum PSA level (correlation = 0.09). CONCLUSIONS: Risk profiling can identify men at substantially increased or reduced risk of prostate cancer. The effect size, measured by OR per unit PRS, was higher in men at younger ages and in men with family history of prostate cancer. Incorporating additional newly identified loci into a PRS should improve the predictive value of risk profiles. IMPACT: We demonstrate that the risk profiling based on SNPs can identify men at substantially increased or reduced risk that could have useful implications for targeted prevention and screening programs.D F. Easton was recipient of the CR-UK grant C1287/A10118. R A. Eeles was recipient of the CR-UK grant C5047/A10692 and B E. Henderson was recipient of the NIH grant 1U19CA148537-01This is the author accepted manuscript. The final version is available via AACR at http://cebp.aacrjournals.org/content/early/2015/04/02/1055-9965.EPI-14-0317.long

CMS physics technical design report : Addendum on high density QCD with heavy ions

Peer reviewe

Effectiveness of short term heat acclimation on intermittent sprint performance with moderately trained females controlling for menstrual cycle phase

YesIntroduction: Investigate the effectiveness of short-term heat acclimation (STHA), over 5-days (permissive dehydration), on an intermittent sprint exercise protocol (HST) with females. Controlling for menstrual cycle phase. Materials and Methods: Ten, moderately trained, females (Mean [SD]; age 22.6 [2.7] y; stature 165.3 [6.2] cm; body mass 61.5 [8.7] kg; VO˙ 2 peak 43.9 [8.6] mL·kg−1 ·min−1 ) participated. The HST (31.0◦C; 50%RH) was 9 × 5 min (45-min) of intermittent exercise, based on exercise intensities of female soccer players, using a motorized treadmill and Wattbike. Participants completed HST1 vs. HST2 as a control (C) trial. Followed by 90 min, STHA (no fluid intake), for five consecutive days in 39.5◦C; 60%RH, using controlled-hyperthermia (∼rectal temperature [Tre] 38.5◦C). The HST3 occurred within 1 week after STHA. The HST2 vs HST3 trials were in the luteal phase, using self-reported menstrual questionnaire and plasma 17β-estradiol. Results: Pre (HST2) vs post (HST3) STHA there was a reduction at 45-min in Tre by 0.20◦C (95%CI −0.30 to −0.10◦C; d = 0.77); Tsk (−0.50; −0.90 to −0.10◦C; d = 0.80); and Tb (−0.25; −0.35 to −0.15◦C; d = 0.92). Cardiac frequency reduced at 45-min (−8; −16 to −1 b·min−1 ; d = 1.11) and %PV increased (7.0; −0.4 to 14.5%: d = 1.27). Mean power output increased across all nine maximal sprints by 56W (−26 to 139W; d = 0.69; n = 9). There was limited difference (P > 0.05) for these measures in HST1 vs HST2 C trial. Discussion: Short-term heat acclimation (5-days) using controlled-hyperthermia, leads to physiological adaptation during intermittent exercise in the heat, in moderately trained females when controlling for menstrual cycle phase

Gammaherpesvirus-Driven Plasma Cell Differentiation Regulates Virus Reactivation from Latently Infected B Lymphocytes

Gammaherpesviruses chronically infect their host and are tightly associated with the development of lymphoproliferative diseases and lymphomas, as well as several other types of cancer. Mechanisms involved in maintaining chronic gammaherpesvirus infections are poorly understood and, in particular, little is known about the mechanisms involved in controlling gammaherpesvirus reactivation from latently infected B cells in vivo. Recent evidence has linked plasma cell differentiation with reactivation of the human gammaherpesviruses EBV and KSHV through induction of the immediate-early viral transcriptional activators by the plasma cell-specific transcription factor XBP-1s. We now extend those findings to document a role for a gammaherpesvirus gene product in regulating plasma cell differentiation and thus virus reactivation. We have previously shown that the murine gammaherpesvirus 68 (MHV68) gene product M2 is dispensable for virus replication in permissive cells, but plays a critical role in virus reactivation from latently infected B cells. Here we show that in mice infected with wild type MHV68, virus infected plasma cells (ca. 8% of virus infected splenocytes at the peak of viral latency) account for the majority of reactivation observed upon explant of splenocytes. In contrast, there is an absence of virus infected plasma cells at the peak of latency in mice infected with a M2 null MHV68. Furthermore, we show that the M2 protein can drive plasma cell differentiation in a B lymphoma cell line in the absence of any other MHV68 gene products. Thus, the role of M2 in MHV68 reactivation can be attributed to its ability to manipulate plasma cell differentiation, providing a novel viral strategy to regulate gammaherpesvirus reactivation from latently infected B cells. We postulate that M2 represents a new class of herpesvirus gene products (reactivation conditioners) that do not directly participate in virus replication, but rather facilitate virus reactivation by manipulating the cellular milieu to provide a reactivation competent environment

Dark Energy from Mass Varying Neutrinos

We show that mass varying neutrinos (MaVaNs) can behave as a negative pressure fluid which could be the origin of the cosmic acceleration. We derive a model independent relation between the neutrino mass and the equation of state parameter of the neutrino dark energy, which is applicable for general theories of mass varying particles. The neutrino mass depends on the local neutrino density and the observed neutrino mass can exceed the cosmological bound on a constant neutrino mass. We discuss microscopic realizations of the MaVaN acceleration scenario, which involve a sterile neutrino. We consider naturalness constraints for mass varying particles, and find that both ev cutoffs and ev mass particles are needed to avoid fine-tuning. These considerations give a (current) mass of order an eV for the sterile neutrino in microscopic realizations, which could be detectable at MiniBooNE. Because the sterile neutrino was much heavier at earlier times, constraints from big bang nucleosynthesis on additional states are not problematic. We consider regions of high neutrino density and find that the most likely place today to find neutrino masses which are significantly different from the neutrino masses in our solar system is in a supernova. The possibility of different neutrino mass in different regions of the galaxy and the local group could be significant for Z-burst models of ultra-high energy cosmic rays. We also consider the cosmology of and the constraints on the ``acceleron'', the scalar field which is responsible for the varying neutrino mass, and briefly discuss neutrino density dependent variations in other constants, such as the fine structure constant.Comment: 26 pages, 3 figures, refs added, typos corrected, comment added about possible matter effect

Vitalism in contemporary chiropractic: a help or a hinderance?

Background: Chiropractic emerged in 1895 and was promoted as a viable health care substitute in direct competition with the medical profession. This was an era when there was a belief that one cause and one cure for all disease would be discovered. The chiropractic version was a theory that most diseases were caused by subluxated (slightly displaced) vertebrae interfering with “nerve vibrations” (a supernatural, vital force) and could be cured by adjusting (repositioning) vertebrae, thereby removing the interference with the body’s inherent capacity to heal. DD Palmer, the originator of chiropractic, established chiropractic based on vitalistic principles. Anecdotally, the authors have observed that many chiropractors who overtly claim to be “vitalists” cannot define the term. Therefore, we sought the origins of vitalism and to examine its effects on chiropractic today. Discussion: Vitalism arose out of human curiosity around the biggest questions: Where do we come from? What is life? For some, life was derived from an unknown and unknowable vital force. For others, a vital force was a placeholder, a piece of knowledge not yet grasped but attainable. Developments in science have demonstrated there is no longer a need to invoke vitalistic entities as either explanations or hypotheses for biological phenomena. Nevertheless, vitalism remains within chiropractic. In this examination of vitalism within chiropractic we explore the history of vitalism, vitalism within chiropractic and whether a vitalistic ideology is compatible with the legal and ethical requirements for registered health care professionals such as chiropractors. Conclusion: Vitalism has had many meanings throughout the centuries of recorded history. Though only vaguely defined by chiropractors, vitalism, as a representation of supernatural force and therefore an untestable hypothesis, sits at the heart of the divisions within chiropractic and acts as an impediment to chiropractic legitimacy, cultural authority and integration into mainstream health care