A Comprehensive Python Toolkit for Accessing High‐Throughput Computing to Support Large Hydrologic Modeling Tasks

The National Flood Interoperability Experiment (NFIE) was an undertaking that initiated a transformation in national hydrologic forecasting by providing streamflow forecasts at high spatial resolution over the whole country. This type of large‐scale, high‐resolution hydrologic modeling requires flexible and scalable tools to handle the resulting computational loads. While high‐throughput computing (HTC) and cloud computing provide an ideal resource for large‐scale modeling because they are cost‐effective and highly scalable, nevertheless, using these tools requires specialized training that is not always common for hydrologists and engineers. In an effort to facilitate the use of HTC resources the National Science Foundation (NSF) funded project, CI‐WATER, has developed a set of Python tools that can automate the tasks of provisioning and configuring an HTC environment in the cloud, and creating and submitting jobs to that environment. These tools are packaged into two Python libraries: CondorPy and TethysCluster. Together these libraries provide a comprehensive toolkit for accessing HTC to support hydrologic modeling. Two use cases are described to demonstrate the use of the toolkit, including a web app that was used to support the NFIE national‐scale modeling.     

Use of a food web model to evaluate the factors responsible for high PCB fish concentrations in Lake Ellasjøen, a high Arctic Lake

Background, aim, and scope

Lake Ellasjøen, located in the Norwegian high arctic, contains the highest concentrations of polychlorinated biphenyls (PCBs) ever recorded in fish and sediment from high arctic lakes, and concentrations are more than 10 times greater than in nearby Lake Øyangen. These elevated concentrations in Ellasjøen have been previously attributed, in part, to contaminant loadings from seabirds that use Ellasjøen, but not Øyangen, as a resting area. However, other factors, such as food web structure, organism growth rate, weight, lipid content, lake morphology, and nutrient inputs from the seabird guano, also differ between the two systems. The aim of this study is to evaluate the relative influence of these factors as explanatory variables for the higher PCB fish concentrations in Ellasjøen compared with Øyangen, using both a food web model and empirical data.

Methods

The model is based on previously developed models but parameterized for Lakes Ellasjøen and Øyangen using measured data wherever possible. The model was applied to five representative PCB congeners (PCB 105, 118, 138, 153, and 180) using measured sediment and water concentrations as input data and evaluated with previously collected food web data.

Results

Modeled concentrations are within a factor of two of measured concentrations in 60% and 40% of the cases in Lakes Ellasjøen and Øyangen, respectively, and within a factor of 10 in 100% of the cases in both lakes. In many cases, this is comparable to the variability associated with the data as well as the efficacy of the predictions of other food web model applications.

Discussion

We next used the model to quantify the relative importance of five major differences between Ellasjøen and Øyangen by replacing variables representing each of these factors in the Ellasjøen model with those from Øyangen, in separate simulations. The model predicts that the elevated PCB concentrations in Ellasjøen water and sediment account for 49%–58% of differences in modeled fish PCB concentrations between lakes. These elevated sediment and, to a lesser extent, water concentrations in Ellasjøen are due to PCB loadings from seabird guano. However, sediment–water fugacity ratios of PCBs are consistently greater in Ellasjøen compared with Øyangen, which suggests that internal lake processes also contribute to differences in sediment and water concentrations. We hypothesize that the nutrients associated with guano influence sediment–water fugacity ratios of PCBs by increasing the stock of pelagic algae. As both these algae and the guano settle, their organic carbon content is degraded faster than PCBs, which causes an extra magnification step in Ellasjøen before these detrital particles are consumed by benthic organisms, which are in turn consumed by fish. The model predicts that the remaining ～50% of the differences in PCB concentrations observed between the fish of these lakes are due to other subtle differences in their food web structures.

Conclusions

In conclusion, based on the results of a food web model, we found that the most dominant factors influencing the higher PCB fish concentrations in Lake Ellasjøen compared with Øyangen are the higher sediment and water concentrations in Ellasjøen, caused by seabird guano. Together, sediment and water are predicted to account for 49%–58% of differences in fish concentrations between lakes. Although seabird guano provides a source of nutrients to the lake, in addition to contaminants, empirical data and indirect model results suggest that nutrients are not leading to decreased bioaccumulation, in contrast to what has been observed in temperate, pelagic food webs.

Recommendations and perspectives

The results of this study emphasize the importance of considering even small differences in food web structure when comparing bioaccumulation in two lakes; although the food web structures of Ellasjøen and Øyangen differ only slightly, the model predicts that these differences account for most of the remaining ～50% of the differences in PCB fish concentrations between the two lakes. This study further demonstrates the utility of food web models as we were able to predict and tease apart the influence of various factors responsible for the elevated concentrations in the fish from Lake Ellasjøen, which would have been difficult using the field data alone.     

From food to pest: Conversion factors determine switches between ecosystem services and disservices

Ecosystem research focuses on goods and services, thereby ascribing beneficial values to the ecosystems. Depending on the context, however, outputs from ecosystems can be both positive and negative. We examined how provisioning services of wild animals and plants can switch between being services and disservices. We studied agricultural communities in Laos to illustrate when and why these switches take place. Government restrictions on land use combined with economic and cultural changes have created perceptions of rodents and plants as problem species in some communities. In other communities that are maintaining shifting cultivation practices, the very same taxa were perceived as beneficial. We propose conversion factors that in a given context can determine where an individual taxon is located along a spectrum from ecosystem service to disservice, when, and for whom. We argue that the omission of disservices in ecosystem service accounts may lead governments to direct investments at inappropriate targets.

     

Monitoring the Multi-Year Carbon Balance of a Subarctic Palsa Mire with Micrometeorological Techniques

This article reports a dataset on 8 years of monitoring carbon fluxes in a subarctic palsa mire based on micrometeorological eddy covariance measurements. The mire is a complex with wet minerotrophic areas and elevated dry palsa as well as intermediate sub-ecosystems. The measurements document primarily the emission originating from the wet parts of the mire dominated by a rather homogenous cover of Eriophorum angustifolium. The CO₂/CH₄ flux measurements performed during the years 2001–2008 showed that the areas represented in the measurements were a relatively stable sink of carbon with an average annual rate of uptake amounting to on average ?46 g C m^?2 y^?1 including an equally stable loss through CH₄ emissions (18–22 g CH₄–C m^?2 y^?1). This consistent carbon sink combined with substantial CH₄ emissions is most likely what is to be expected as the permafrost under palsa mires degrades in response to climate warming.     

Life cycle assessment of waste paper management: The importance of technology data and system boundaries in assessing recycling and incineration

The significance of technical data, as well as the significance of system boundary choices, when modelling the environmental impact from recycling and incineration of waste paper has been studied by a life cycle assessment focusing on global warming potentials. The consequence of choosing a specific set of data for the reprocessing technology, the virgin paper manufacturing technology and the incineration technology, as well as the importance of the recycling rate was studied. Furthermore, the system was expanded to include forestry and to include fossil fuel energy substitution from saved biomass, in order to study the importance of the system boundary choices. For recycling, the choice of virgin paper manufacturing data is most important, but the results show that also the impacts from the reprocessing technologies fluctuate greatly. For the overall results the choice of the technology data is of importance when comparing recycling including virgin paper substitution with incineration including energy substitution. Combining an environmentally high or low performing recycling technology with an environmentally high or low performing incineration technology can give quite different results. The modelling showed that recycling of paper, from a life cycle point of view, is environmentally equal or better than incineration with energy recovery only when the recycling technology is at a high environmental performance level. However, the modelling also showed that expanding the system to include substitution of fossil fuel energy by production of energy from the saved biomass associated with recycling will give a completely different result. In this case recycling is always more beneficial than incineration, thus increased recycling is desirable. Expanding the system to include forestry was shown to have a minor effect on the results. As assessments are often performed with a set choice of data and a set recycling rate, it is questionable how useful the results from this kind of LCA are for a policy maker. The high significance of the system boundary choices stresses the importance of scientific discussion on how to best address system analysis of recycling, for paper and other recyclable materials.     

Characterization of organic chemical contaminants in sediments from Jobos Bay, Puerto Rico

Jobos Bay, located on the southeastern coast of Puerto Rico, contains a variety of habitats including mangroves, seagrass meadows, and coral reefs. The watershed surrounding the bay includes a number of towns, agricultural areas, and the Jobos Bay National Estuarine Research Reserve (NERR). Jobos Bay and the surrounding watershed are part of a Conservation Effects Assessment Project (CEAP), involving the Jobos Bay NERR, the US Department of Agriculture, and the National Oceanic and Atmospheric Administration (NOAA) to assess the benefits of agricultural best management practices (BMPs) on the terrestrial and marine environments. As part of the Jobos Bay CEAP, NOAA collected sediment samples in May 2008 to characterize over 130 organic chemical contaminants. This paper presents the results of the organic contaminant analysis. The organic contaminants detected in the sediments included polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls, and the pesticide DDT. PAHs at one site in the inner bay near a boat yard were significantly elevated; however, all organic contaminant classes measured were below NOAA sediment quality guidelines that would have indicated that impacts were likely. The results of this work provide an important baseline assessment of the marine environment that will assist in understanding the benefits of implementing BMPs on water quality in Jobos Bay.     

A possible prenatal evaluation of renal function by amino acid analysis on fetal urine

Intrauterine treatment of 4 fetuses with urethral obstruction was attempted in the third trimester of pregnancy. The fetuses displayed varying sonographic findings including pyelectasis, caliectasis, hydroureter, bladder dilatation, ascites, hydrops, missing kidneys and oligohydramnios. Ultrasonically guided aspiration from the dilated structures was carried out to relieve pressure on the kidney parenchyme and to collect fluid samples for diagnostic purposes. Amino acid concentrations in the fetal urine showed a pattern similar to plasma in 2 fetuses, a pattern almost like urine in 1 fetus and an intermediate pattern in the 4th fetus. Only the fetus with normal amino acid concentrations in the urine survived: the other 3 died in uremia shortly after birth. In 3 cases cells from the aspirated urine were cultured and used for chromosome analysis. The cell cultures grew fast and karyotyping was possible within 1 week. In 2 fetuses an intrauterine catheter was inserted to drain the kidney permanently into the amniotic cavity. In the first case the catheter was displaced to the fetal abdomen after some days of successful drainage. In the second case the catheter tore the placenta, and the child had to be delivered immediately.     

气候变化与紫外线B辐射对北极苔原和极地荒漠生态系统的影响重要发现和扩展总结

引言 北极已成为对当前气候波动和预计的全球变暖增强的影响进行评估的重要地区.原因有以下几个方面:①在过去几十年中北极经历了大幅度的变暖过程(温度平均升高3℃,而在许多地区温度升高了4～5℃);②气候预测表明气候呈现持续变暖趋势,在2080年之前年平均气温升高4～5℃;③近期的气候变暖正在影响北极的环境和经济,这些影响还会加大,并对生活方式、文化及生态系统造成影响;④北极的变化可能会影响到地球上的其它地区.     

Prenatal diagnosis by in situ hybridization on uncultured amniocytes: Reduced sensitivity and potential risk of misdiagnosis in blood-stained samples

Maternal cell contamination was assessed in 18 macroscopically blood-stained amniotic fluid samples from male fetuses. The samples were analysed by double-target fluorescent in situ hybridization (ISH) with Y and X chromosome-specific probes. The only sample with an aberrant karyotype (47, XY, +18) was also analysed by hybridization with a chromosome 18-specific probe. An interpretation of extensive maternal cell contamination was made in two samples, one of which was the sample with trisomy 18. ISH with the chromosome 18-specific probe on this latter sample showed that the sensitivity of the ISH method for chromosome enumeration of uncultured amniotic fluid samples may be reduced in bloodstained samples. It was calculated that by using ISH for chromosome enumeration of the two extensively contaminated samples, a case of trisomy 21 might have been overlooked in both samples, while a case of trisomy 18 might only have been overlooked in one of the samples. It is concluded that ISH should not be used for chromosome enumeration of uncultured amniotic fluid samples that are macroscopically blood-stained without further technical developments.     

气候变化对景观和区域过程的影响及其对气候系统的反馈

北极生态系统的生物和物理过程会在不同的时间、空间尺度上对地球生态系统产生反馈作用,并与之相互影响.气候变化对北极地区的影响及其对全球气候系统的反馈主要存在着四种潜在机制反照率改变、生态系统对温室气体的排放或吸收、甲烷类温室气体的排放、影响海洋暖流淡水量的增长.这些反馈机制在某种程度上是由生态系统的分布和特征,尤其是大规模植被区域变化来控制的.通过少量全年的CO2通量测量表明,目前在地理分布上碳源区要比碳汇区要多.根据目前现有的关于CH4排放源地信息表明,景观规模上的CH4排放量对北极地区的温室效应平衡至关重要.北极地区的能量和水量平衡在变化的气候下,也是一个很重要的反馈机制.植被密度以及分布范围的增加会导致反射率的下降,因而会使地表吸收更多的能量.其效果可能会抵消由于极地沙漠地带向极地苔原带的的转化,或极地苔原带向极地森林带的转化,而造成的植被总净初级生产力碳沉降能力的提高而引起的负反馈.永久冻土带的退化对示踪气体动力学有着很复杂的影响.在不连续的永久冻土带地区,升温将会导致其完全消失.依赖于当地水文条件,温室气体排放可能由于气候环境变的干燥或湿润而使得其通量有所变化.总的来说,影响反馈的各种过程复杂的相互作用,以及这些过程随着时间地点的变化,加之数据的缺乏,又会在陆地生态系统气候变化对气候系统产生反馈作用的净效应估计上,产生许多的不确定性,这种不确定性将会影响到一些反馈的大小和方向.