Efficient Markov chain Monte Carlo sampling for hierarchical hidden Markov models

Traditional Markov chain Monte Carlo (MCMC) sampling of hidden Markov models (HMMs) involves latent states underlying an imperfect observation process, and generates posterior samples for top-level parameters concurrently with nuisance latent variables. When potentially many HMMs are embedded within a hierarchical model, this can result in prohibitively long MCMC runtimes. We study combinations of existing methods, which are shown to vastly improve computational efficiency for these hierarchical models while maintaining the modeling flexibility provided by embedded HMMs. The methods include discrete filtering of the HMM likelihood to remove latent states, reduced data representations, and a novel procedure for dynamic block sampling of posterior dimensions. The first two methods have been used in isolation in existing application-specific software, but are not generally available for incorporation in arbitrary model structures. Using the NIMBLE package for R, we develop and test combined computational approaches using three examples from ecological capture–recapture, although our methods are generally applicable to any embedded discrete HMMs. These combinations provide several orders of magnitude improvement in MCMC sampling efficiency, defined as the rate of generating effectively independent posterior samples. In addition to being computationally significant for this class of hierarchical models, this result underscores the potential for vast improvements to MCMC sampling efficiency which can result from combinations of known algorithms.     

联合基于野外的代谢组学和化学分析手段筛选优先关注新兴污染物：在五大湖流域的案例研究

由于毒性评估项目很难与日渐增长的需要测试的污染物保持同步,所以较难将关注点集中在影响水生生态系统的最为生物相关的污染物上。由于评估潜在毒性污染物所造成的生物影响已被证明是有效的,内生性代谢物的研究（代谢组学）对于剔除那些较低可能造成生物影响的污染物或许有一定帮助,从而找出生物重要性最高的污染物。本研究在北美五大湖流域的18个地点针对置于笼中的黑头软口鲦（Pimephales promelas）进行实验。我们测定了水体温度和水样中的污染物浓度（目标污染物132种,检出86种）,并使用1H-NMR谱测量了肝极性提取物中的内生性代谢物。利用偏最小二乘法回归来比对内生性代谢物的相对丰度与污染物浓度和环境温度。结果表明内生性极性代谢物的指标与最多49种污染物存在共同变化。因此我们认为至多52%的检出污染物与内生性代谢物变化的共同变化不显著,表明这些污染物很可能不会在这些地点造成可以检测到的影响。这是通过缩短对于实验地点有着潜在影响的污染物列表从而扫描出检出污染物生物相关性的第一步。类似的信息有助于风险评估者区分不同污染物的重要性并将重点毒性测试放在最为生物相关的污染物上。
精选自Nicol Janecko, Lucie Pokludova, Jana Blahova, Zdenka Svobodova, Ivan Literak. Linking field-based metabolomics and chemical analyses to prioritize contaminants of emerging concern in the Great Lakes basin. Environmental Toxicology and Chemistry: Volume 35, Issue 10, pages 2493–2502, October 2016. DOI: 10.1002/etc.3409
详情请见http://onlinelibrary.wiley.com/doi/10.1002/etc.3409/full
     

Monitoring land use/land cover change impacts on soils in data scarce environments: a case of south-central Ethiopia

To monitor land-use/land-cover (LULC) change and assess its impact on the soil property, the availability of benchmark data is indispensable, which is hardly available in the intensively cultivated regions of developing countries. Our study attempts to solve this problem by generating a benchmark soil data through the development of modified spatial analogue (MSA) method in the context of the Upper Dijo River catchment, south-central Ethiopia. The magnitude and patterns of LULC changes were extracted from air photos and satellite imageries, along with the acquisition of soil samples from the reference and target sites through ground survey. Analysis of digital image processing shows significant LULC changes in a period that spanned three decades. The impact of LULC change on soil quality was assessed by comparing the soil physico-chemical properties sampled from the reference and target sites. The result shows a decline in total nitrogen, organic matter, available potassium and pH levels in soils collected from target sites, which conforms to results reported by studies conducted in data-rich environment. With careful validation, MSA could be useful for monitoring soil property changes in data-scarce environment and generate soil-related parameters for agro-ecological models.     

Moderating effects of empathic concern and personal distress on the emotional reactions of disaster volunteers

This study examines stress and mood outcomes in community volunteers who undertook one week's worth of post‐disaster relief work in L'Aquila, Italy, which had been hit by an earthquake four months earlier. The study team obtained pre‐ and post‐relief work data from 130 volunteers involved in activities such as preparing food for the displaced, cleaning the camps and distributing clean linen. The Perceived Stress Scale, the State‐Trait Anxiety Inventory and the Profile of Mood States were administered at the start and at the end of the aid activities. Psychopathological symptoms and empathy were assessed in the beginning, using the Symptom Checklist 90 Revised and the Interpersonal Reactivity Index, respectively. The results show that, following the assistance work, volunteers displayed decreases in perceived stress, general distress, anxiety and anger, as well as increases in positive emotions. The empathy facets empathic concern and personal distress showed different patterns in modulating the post‐disaster relief work adaptation for some of the mood outcomes.     

Ocean acidification induces budding in larval sea urchins

Ocean acidification (OA), the reduction of ocean pH due to hydration of atmospheric CO₂, is known to affect growth and survival of marine invertebrate larvae. Survival and transport of vulnerable planktonic larval stages play important roles in determining population dynamics and community structures in coastal ecosystems. Here, we show that larvae of the purple urchin, Strongylocentrotus purpuratus, underwent high-frequency budding (release of blastula-like particles) when exposed to elevated pCO₂ level (>700 μatm). Budding was observed in >50 % of the population and was synchronized over short periods of time (~24 h), suggesting this phenomenon may be previously overlooked. Although budding can be a mechanism through which larval echinoids asexually reproduce, here, the released buds did not develop into viable clones. OA-induced budding and the associated reduction in larval size suggest new hypotheses regarding physiological and ecological tradeoffs between short-term benefits (e.g. metabolic savings and predation escape) and long-term costs (e.g. tissue loss and delayed development) in the face of climate change.     

Toxicity of the nerve agent tabun to Daphnia magna,a new experimental species in military toxicology

Daphnia magna, a freshwater microcrustacean, is currently tested as an alternative experimental species in research dealing with nerve agents poisonings treatment. Because of this, the toxicity of the nerve agent tabun (a cyanide-group containing organophosphate) to Daphnia had to be examined by estimating the EC₅₀ values. The immobilization of daphnids was chosen as the end-point. It was found that D. magna is sensitive to small amounts of tabun, even after 15 min exposure, and tabun toxicity increases with time. The estimated EC₅₀ values for 15, 30, 45, and 60 min exposure were as follows: 67.39, 38.10, 26.95, and 21.9 μg l^?1. In addition, the toxicity of media to which tabun was added 24 h before the start of experiments was examined. The results obtained indicate that daphnids can be used in experiments with nerve-agent intoxication treatment.     

Frequency of abnormal heavy metal blood levels in Wegener's granulomatosis

Previous studies suggested environmental exposures, including mercury (Hg) and lead (Pb), may be related to Wegener's granulomatosis. In this study, investigations were extended to include the measurement of heavy metals in blood samples from patients diagnosed with Wegener's. Diagnosis was confirmed by using the 1990 Classification Criteria for Wegener's granulomatosis established by the American College of Rheumatology (ACR). Using commercial lab testing, whole blood heavy metal screenings were obtained from patients, and results were then compared with validated subject self-report questionnaire estimates of exposure. Thirty-eight Wegener's patients were enrolled; 10 of the 38 exhibited abnormal lab values. In those 10 subjects 3 had elevated nickel (Ni), 7 with increased cobalt (Co), 3 with higher manganese, 1 with elevated copper, and 1 with increased Hg. Overall, the questionnaire results did not correlate with the blood heavy metal analysis. Approximately 26% of Wegener's subjects in this study displayed abnormal heavy metal levels. These findings are likely underestimates since blood levels are an insensitive means for assessing total body burden of heavy metals. From these preliminary studies it appears that elevated Co is a common finding in Wegener's patients but Ni and Hg were also found to be increased. The proportion of patients with abnormal heavy metal levels is more than expected by chance alone. In order to yield more definitive results, further analysis is needed with a larger data set, more controls and more sensitive measurements (hair, urine, or nail samples).     

Assessment of community-based initiatives in sustainable management of Indian dry deciduous forests

SUMMARY

This work is devoted to analyzing the pros and cons of the proposed San Ignacio Lagoon (SIL) salt production project in Baja California Sur, México. The analysis of the project was done taking into account the technical data of the main potential effects of the SIL project, and by comparing the SIL proposed actions with the data of Ojo de Liebre Lagoon, where an almost identical salt production project has been operating for more than 44 years. The analysis was done from the following perspectives: biodiversity, biosphere reserve management, and socioeconomic development. The resulting analysis of the pros and cons of the SIL salt production project addresses key aspects of sustainable development in Third World nations. The resulting analysis indicates that the SIL salt production project is compatible with the biodiversity conservation of the zone. The SIL salt production project seems to be one of the best options to attain the sustainable use of natural resources of the most arid and isolated zone of all México.     

An approach to simulate wind fields around an urban environment for wind energy application

This work proposes an approach to simulate wind flow fields around an urban environment with the aim of evaluating the potential impact of buildings on the general wind patterns and power production using the current generation of commercial wind turbines. The simulation process was performed with the aid of accessible computational tools that can potentially render the proposed procedure applicable in other cases of interest. The roughness of the urban environment was defined as the association of roughness map, topography, and an alternative process for obtaining the volumetry of buildings. A case study was conducted in a region located at the district of Boa Viagem (Recife-PE) for assessing the applicability of the approach. Scenarios were designed in order to simulate wind flow patterns and pre-identify sites that have suitable wind energy potential for electric power production by investigating the combination of wind speed magnitude and turbulence intensity. From the results obtained, it was possible to identify zones of potential wind sources that are not detected in classical wind atlas probably due to the influence of the built environment on local wind flow patterns.