ALBERT

Description: 〈p〉Publication date: Available online 1 November 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Complexity〈/p〉 〈p〉Author(s): Robert J. Kunsch, Erich Novak, Daniel Rudolf〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We compute the integral of a function or the expectation of a random variable with minimal cost and use, for our new algorithm and for upper bounds of the complexity, i.i.d. samples. Under certain assumptions it is possible to select a sample size based on a variance estimation, or – more generally – based on an estimation of a (central absolute) 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" overflow="scroll" altimg="si1.gif"〉〈mi〉p〈/mi〉〈/math〉-moment. That way one can guarantee a small absolute error with high probability, the problem is thus called solvable. The expected cost of the method depends on the 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" overflow="scroll" altimg="si1.gif"〉〈mi〉p〈/mi〉〈/math〉-moment of the random variable, which can be arbitrarily large. In order to prove the optimality of our algorithm we also provide lower bounds. These bounds apply not only to methods based on i.i.d. samples but also to general randomized algorithms. They show that – up to constants – the cost of the algorithm is optimal in terms of accuracy, confidence level, and norm of the particular input random variable. Since the considered classes of random variables or integrands are very large, the worst case cost would be infinite. Nevertheless one can define adaptive stopping rules such that for each input the expected cost is finite. We contrast these positive results with examples of integration problems that are not solvable.〈/p〉〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Xing-Wei Xiang, Jin-Xing Xiao, Yu-Fang Zhou, Bin Zheng, Zheng-Shun Wen〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The black seabream (〈em〉Sparus macrocephlus〈/em〉) is an economically pivotal aquaculture species cultured in China and Southeast Asian countries. To understand the molecular immune mechanisms underlying the response to 〈em〉Vibrio parahaemolyticus〈/em〉, a comparative gene transcription analysis were performed with utilized fresh livers of 〈em〉V. parahaemolyticus〈/em〉-immunized 〈em〉Sparus macrocephlus〈/em〉 with a control group through RNA-Seq technology. A total of 256663 contigs were obtained after excluded the low-quality sequences and assembly. The average length of contigs collected from this research is 1066.93 bp. Furthermore, blast analysis indicates 30747 contigs were annotated based on homology with matches in the NT, NR, gene, and string databases. A gene ontology analysis was employed to classify 21598 genes according to three major functional categories: molecular function, cellular component, and biological process. A total of 14470 genes were discovered in 303 KEGG pathways. RSEM and EdgeR were introduced to estimate 3841 genes significantly different expressed (False Discovery Rate〈0.001) which includes 4072 up-regulated genes and 3771 down-regulated genes. A significant enrichment analysis of these differentially expressed genes and isogenes were conducted to reveal the major immune-related pathways which refer to the toll-like receptor, complement, coagulation cascades, and chemokine signaling pathways. In addition, 92175 potential simple sequence repeats (SSRs) and 121912 candidate single nucleotide polymorphisms (SNPs) were detected and identified sequencely in the 〈em〉Sparus macrocephlus〈/em〉 liver transcriptome. This research characterized a gene expression pattern for normal and the 〈em〉V. parahaemolyticus〈/em〉 -immunized 〈em〉Sparus macrocephlus〈/em〉 for the first time and not only sheds new light on the molecular mechanisms underlying the host-〈em〉V. parahaemolyticus〈/em〉 interaction but contribute to facilitate future studies on 〈em〉Sparus macrocephlus〈/em〉 gene expression and functional genomics.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Yi-Hong Chen, Jian-Guo He〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The shrimp aquaculture industry is plagued by disease. Due to the lack of deep understanding of the relationship between innate immune mechanism and environmental adaptation mechanism, it is difficult to prevent and control the diseases of shrimp. The shrimp innate immune system has received much recent attention, and the functions of the humoral immune response and the cellular immune response have been preliminarily characterized. The role of environmental stress in shrimp disease has also been investigated recently, attempting to clarify the interactions among the innate immune response, the environmental stress response, and disease. Both the innate immune response and the environmental stress response have a complex relationship with shrimp diseases. Although these systems are important safeguards, allowing shrimp to adapt to adverse environments and resist infection, some pathogens, such as white spot syndrome virus, hijack these host systems. As shrimp lack an adaptive immune system, immunization therapy cannot be used to prevent and control shrimp disease. However, shrimp diseases can be controlled using ecological techniques. These techniques, which are based on the innate immune response and the environmental stress response, significantly reduce the impact of shrimp diseases. The object of this review is to summarize the recent research on shrimp environmental adaptation mechanisms, innate immune response mechanisms, and the relationship between these systems. We also suggest some directions for future research.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Yinnan Mu, Shimin Zhou, Ning Ding, Jingqun Ao, Xinhua Chen〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Chemokines are a superfamily of structurally related chemotactic cytokines exerting significant roles in regulating cell migration and activation. Currently, five subgroups of fish specific CXC chemokines, named CXCL_F1-CXCL_F5, have been identified in teleost fish. However, understanding of the functions of these fish specific CXC chemokines is still limited. Here, a new member of fish specific CXC chemokines, 〈em〉Lc〈/em〉CXCL_F6, was cloned from large yellow croaker 〈em〉Larimichthys crocea〈/em〉. Its open reading frame (ORF) is 369 nucleotides long, encoding a peptide of 122 amino acids (aa). The deduced 〈em〉Lc〈/em〉CXCL_F6 protein contains a 19-aa signal peptide and a 103-aa mature polypeptide, which has four conserved cysteine residues (C〈sup〉28〈/sup〉, C〈sup〉30〈/sup〉, C〈sup〉56〈/sup〉, and C〈sup〉72〈/sup〉), as found in other known CXC chemokines. Phylogenetic analysis showed 〈em〉Lc〈/em〉CXCL_F6 formed a separate clade with sequences from other fish species, tentatively named CXCL_F6, distinct from the clades formed by fish CXCL_F1-5 and mammalian CXC chemokines. The 〈em〉Lc〈/em〉CXCL_F6 transcripts were constitutively expressed in all examined tissues and significantly up-regulated in the spleen and head kidney tissues by poly (I:C) and 〈em〉Vibrio alginolyticus〈/em〉. Its transcripts were also detected in primary head kidney leukocytes (HKLs), peripheral blood leucocytes (PBLs), and large yellow croaker head kidney (LYCK) cell line, and significantly up-regulated by poly(I:C), lipopolysaccharide (LPS), and peptidoglycan (PGN) in HKLs. Recombinant 〈em〉Lc〈/em〉CXCL_F6 protein (r〈em〉Lc〈/em〉CXCL_F6) could not only chemotactically attract monocytes/macrophages and lymphocytes from PBLs, but also enhance NO release and expression of proinflammatory cytokines (TNF-α, IL-1β, and CXCL8) in monocytes/macrophages. These results indicate that 〈em〉Lc〈/em〉CXCL_F6 plays a role in mediating the inflammatory response.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Computers in Industry, Volume 104〈/p〉 〈p〉Author(s): Jacques Bahi, Wiem Elghazel, Christophe Guyeux, Mourad Hakem, Kamal Medjaher, Noureddine Zerhouni〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Monitoring activities in industry may require the use of wireless sensor networks, for instance due to difficult access or hostile environment. But it is well known that this type of networks has various limitations like the amount of disposable energy. Indeed, once a sensor node exhausts its resources, it will be dropped from the network, stopping so to forward information about maybe relevant features towards the sink. This will result in broken links and data loss which impacts the diagnostic accuracy at the sink level. It is therefore important to keep the network's monitoring service as long as possible by preserving the energy held by the nodes. As packet transfer consumes the highest amount of energy comparing to other activities in the network, various topologies are usually implemented in wireless sensor networks to increase the network lifetime. In this paper, we emphasize that it is more difficult to perform a good diagnostic when data are gathered by a wireless sensor network instead of a wired one, due to broken links and data loss on the one hand, and deployed network topologies on the other hand. Three strategies are considered to reduce packet transfers: (1) sensor nodes send directly their data to the sink, (2) nodes are divided by clusters, and the cluster heads send the average of their clusters directly to the sink, and (3) averaged data are sent from cluster heads to cluster heads in a hop-by-hop mode, leading to an avalanche of averages. Their impact on the diagnostic accuracy is then evaluated. We show that the use of random forests is relevant for diagnostics when data are aggregated through the network and when sensors stop to transmit their values when their batteries are emptied. This relevance is discussed qualitatively and evaluated numerically by comparing the random forests performance to state-of-the-art PHM approaches, namely: basic bagging of decision trees, support vector machine, multinomial naive Bayes, AdaBoost, and Gradient Boosting. Finally, a way to couple the two best methods, namely the random forests and the gradient boosting, is proposed by finding the best hyperparameters of the former by using the latter.〈/p〉〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Marine Policy, Volume 99〈/p〉 〈p〉Author(s): Pablo Quero García, Javier García Sanabria, Juan Adolfo Chica Ruiz〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In recent years the European Union has firmly committed itself to energy from oceans as a means of decarbonising the European energy system. Despite a favourable political landscape, the development of offshore renewables still faces economic and technological barriers, which are coupled with the inherent difficulties of an increasingly industrialised marine environment, such as complex evolving regulation, lack of knowledge regarding the possible environmental impact of such an activity, as well as spatial conflicts with other traditional and emerging uses. Most of the coastal Member States have adopted Maritime Spatial Planning (MSP) as a fundamental tool for integrated and sustainable management of human activities in the marine environment. MSP is capable of definitively driving the use of offshore renewable facilities. Its proper application supports decision making, simplifies and accelerates the process of obtaining permits, improves compatibility of uses, integrates stakeholders in planning, prevents environmental deterioration of sensitive areas, enhances the availability of information and promotes cross-border co-operation. This paper aims to evaluate the influence of maritime spatial planning processes on the advance of blue energy within the framework of the European Union. The results show positive relationships between MSP and the development of offshore renewable energy in countries such as Germany, the Netherlands and the United Kingdom.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0308597X1830304X-fx1.jpg" width="477" alt="fx1" title="fx1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Marine Policy, Volume 99〈/p〉 〈p〉Author(s): Bong-Tae Kim, Christopher L. Brown, Do-Hoon Kim〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We assess the vulnerability to climate change of Korean aquaculture based on predicted changes in seawater temperature and salinity in adjacent sea areas of the Korean Peninsula according to representative concentration pathways (RCP) scenarios. Unlike previous studies that have been conducted mostly on a national scale, we classify 14 farming species in major production regions of the Republic of Korea, and assess their vulnerability for each region, using the indicator-based method and the Intergovernmental Panel on Climate Change's definition of vulnerability in order to overcome limitations in developing specific adaptation strategies within a country. First, for each exposure, sensitivity, and adaptive capacity, specific and proper indicators are selected. Subsequently, these indicators are estimated and weighted to analyze vulnerability to climate change. The results show that the absolute level of vulnerability is high in a long-term period of RCP8.5 in which exposure becomes severe, whereas the relative vulnerability is similar among farming species and regions. Specifically, vulnerability is at the highest level in seaweed, such as laver and sea mustard, while fish, shrimp, and abalone are relatively less vulnerable to climate change.〈/p〉〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Soil Biology and Biochemistry, Volume 128〈/p〉 〈p〉Author(s): J.M. Kranabetter〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Forest floor carbon (C) sequestration has been negatively correlated with manganese (Mn) availability, possibly due to reduced efficacy of Mn-peridoxase enzymes produced by Agaricomycete fungi. I examined a soil C and Mn dataset from a podzolization gradient, along with fungal sporocarp Mn concentrations, to potentially corroborate this finding. An inverse power relationship between soil C and soil Mn content across temperate rainforests was confirmed, which provides further evidence of a Mn bottleneck in C turnover. Average Mn concentrations of saprotrophic sporocarps were greater than those of ectomycorrhizal fungi, and displayed a similar inverse correlation with increasing soil C. The absence or limited effectiveness of select saprotrophic fungi across Mn-depleted forest soils may be one mechanism behind impeded turnover of recalcitrant organic matter.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Soil Biology and Biochemistry, Volume 128〈/p〉 〈p〉Author(s): Charles R. Warren〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Phospholipids are isolated from crude lipid extracts by silica solid phase extraction (SPE), but for soils we don't know if phospholipids are the only fatty acid-based lipids present in the polar lipid fraction. Lipids extracted from three soils were fractionated with a silica SPE protocol commonly used for soils, with “neutrals” eluted by chloroform, “glycolipids” eluted by acetone, and “phospholipids” eluted by methanol. Fatty acid-based lipids were identified and quantified by liquid chromatography-mass spectrometry. Phospholipids were recovered in the methanol fraction, but this fraction also included betaine lipids. In two soils the methanol fraction was 3–6% betaine lipid while in one soil betaine lipids accounted for 48% of lipids in the methanol fraction. Clearly the fraction obtained by eluting lipids from silica with methanol is not purely phospholipid but can contain significant amounts of other polar lipids.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 1 March 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Geoderma, Volume 337〈/p〉 〈p〉Author(s): R. Calvelo Pereira, M. Camps Arbestain, F.M. Kelliher, B.K.G. Theng, S.R. McNally, F. Macías, F. Guitián〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We have investigated the effect of supercritical drying (SD) on the porosity and the BET-N〈sub〉2〈/sub〉 specific surface area (SSA) of five allophane-rich and three non-allophanic topsoils. The contribution of organic matter (OM) and short-range ordered (SRO) constituents to the nanoscale porosity (〈100 nm size) and SSA was also evaluated following chemical treatments to oxidise OM and then remove the SRO phase. The average pore volume and SSA of the soils, measured after SD, are greater than the values obtained after air drying. For soils that are rich in SRO constituents, oxidation of OM leads to an increase in SSA. This observation is attributed to the unblocking of pore necks previously covered by OM, while the subsequent removal of SRO constituents causes a sharp decrease in SSA. The SRO constituents containing oxalate-extractable Al, are the major contributors to the SSA of the inorganic fraction. Besides confirming that SD can help preserve the nanoscale porosity of allophane-rich soils, the results highlight the contribution of SRO constituents to the SSA of soils and their ability to accumulate OM.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: March 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Soil and Tillage Research, Volume 186〈/p〉 〈p〉Author(s): Márcio R. Nunes, Eloy A. Pauletto, José E. Denardin, Luis E.A. S. Suzuki, Harold M. van Es〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Tillage and no-tillage result in different soil mechanical responses which in turn may affect crop growth. Better understanding of soil compressive behavior, therefore, is relevant for the assessment of tillage practices in agricultural systems. We studied the change in soil compressive properties and their relationship with soil physical attributes and plant growth through a chisel tillage chronosequence in a Nitisol where soil was untilled after chiseling for 24 months, 18 months, 12 months, 6 months, and zero months, and was under continuous (12-year) NT. The effects were measured for three soil depth layers: 0 to 7-cm, 7 to 17-cm and 20 to 30-cm. Mechanical chiseling was found to reduce both the degree of compactness and the pre-compression pressure compared to continuous NT, but made the soil more susceptible to new compaction. The effects of chisel tillage generally persisted for a period of 12–24 months. The degree of compactness and soil pre-compression pressure were found to be strongly correlated, and were strongly correlated with other soil physical attributes (soil penetration resistance, soil macroporosity, and soil aggregate stability). They were negatively correlated with root length, root density, and root volume, as well as stalk diameter, linking soil structure indicators to plant growth. Our results also showed that soil compressive parameter values can be estimated based on other soil physical properties that influence plant growth. These findings have potential for studies of crop response to soil structure and soil compaction and could be used to aid in choosing optimal soil management practices, in order to reduce the risk of soil compaction, linking soil compressive behavior and soil physical conditions to plant growth.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 379〈/p〉 〈p〉Author(s): Takashi Shiroto, Naofumi Ohnishi, Yasuhiko Sentoku〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉For more than half a century, most of the plasma scientists have encountered a violation of the conservation laws of charge, momentum, and energy whenever they have numerically solved the first-principle equations of kinetic plasmas, such as the relativistic Vlasov–Maxwell system. This fatal problem is brought by the fact that both the Vlasov and Maxwell equations are indirectly associated with the conservation laws by means of some mathematical manipulations. Here we propose a quadratic conservative scheme, which can strictly maintain the conservation laws by discretizing the relativistic Vlasov–Maxwell system. A discrete product rule and summation-by-parts are the key players in the construction of the quadratic conservative scheme. Numerical experiments of the relativistic two-stream instability and relativistic Weibel instability prove the validity of our computational theory, and the proposed strategy will open the doors to the first-principle studies of mesoscopic and macroscopic plasma physics.〈/p〉〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Jinghua Chen, Lu Zhang, Ning Yang, Mengyu Tian, Qiang Fu, Fenghua Tan, Chao Li〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Galectins are a family of galactoside-binding proteins with an affinity for β-galactosides, involved in mediating fundamental processes including development, inflammation, cell migration and apoptosis. Galectin-4 is a member of tendem-repeat galectins, plays vital roles in intestinal epithelial barrier. Here, one galectin-4 gene was captured in turbot (〈em〉Sm〈/em〉Lgals4) contains a 1197 bp open reading frame (ORF). In comparison to other species, 〈em〉Sm〈/em〉Lgals4 showed the highest similarity and identity both to large yellow croaker. The genomic structure analysis showed that 〈em〉Sm〈/em〉Lgals4 had conserved exons in the CRD domains compared to other vertebrate species. The syntenic analysis revealed that galectin-4 had the same neighboring genes across all the selected species, which suggested the synteny encompassing galectin-4 region during vertebrate evolution. Subsequently, 〈em〉Sm〈/em〉Lgals4 was widely expressed in all the examined tissues, with the highest expression level in intestine and the lowest expression level in skin. In addition, 〈em〉Sm〈/em〉Lgals4 was significantly down-regulated in intestine following both Gram-negative bacteria 〈em〉Vibrio anguillarum〈/em〉, and Gram-positive bacteria 〈em〉Streptococcus iniae〈/em〉 immersion challenge. Finally, the 〈em〉rSm〈/em〉Lgals4 showed strong binding ability to all the examined microbial ligands. Taken together, our results suggested 〈em〉Sm〈/em〉Lgals4 plays vital roles in fish intestinal immune responses against infection, but the detailed roles of galectin-4 in teleost are still lacking, further studies are needed to be carried out to characterize whether galectin-4 plays similar roles in teleost intestinal immunity.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Yanxiu Mo, Yunpeng Fan, Wen Fu, Wenting Xu, Shujuan Chen, Yuanhui Wen, Shaojun Liu, Liangyue Peng, Yamei Xiao〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Previous research has indicated that the small compound, SP600125, could induce polyploidy of fish cells, and has established a stable tetraploid cell line from diploid fish cells. In order to explore how fish cells maintain homeostasis under SP600125-stress 〈em〉in vitro〈/em〉, this study investigates impacts of SP600125-stress on intracellular pathways, as well as on regulation of the cellular homeostasis feedback in fish cells. Transcriptomes are obtained from the SP600125-treated cells. Compared with unigenes expressed in control group (crucial carp fin cells), a total of 2670 and 1846 unigenes are significantly upregulated and downregulated in these cells, respectively. Differentially expressed genes are found, which are involved in innate defense, inflammatory pathways and cell adhesion molecules-related pathways. The SP600125-stress enhances cell-mediated immunity, characterized by significantly increasing expression of multiple immune genes. These enhanced immune genes include the pro-inflammatory cytokines (IL-1β, TNF-ɑ, IL-6R), the adaptor signal transducers (STAT, IκBɑ), and the integrins (ɑ2β1, ɑMβ2). Furthermore, mitochondria are contributed to the cellular homeostasis regulation upon the SP600125-stress. The results show that acute inflammation is an adaptive and controlled response to the SP600125-stress, which is beneficial for alleviating toxicity by SP600125. They provide a potential way of breeding fish polyploidy induced by SP600125 in the future research.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Maciej Woźny, Kazimierz Obremski, Piotr Hliwa, Piotr Gomułka, Rafał Różyński, Paweł Wojtacha, Maciej Florczyk, Helmut Segner, Paweł Brzuzan〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉To investigate the effects of feed contamination with zearalenone (ZEN) at the current European Commission (EC) guidance value (2 mg⋅kg〈sup〉−1〈/sup〉 feed) on the growth and health of rainbow trout, we performed a long-term feeding trial under aquaculture conditions. It started with the external feeding of the fish larvae, and continued for 96 weeks, at which point the fish had reached market size. To assess the growth of fish and their feeding efficiency throughout this period, the fish were regularly weighed and measured, and their feed consumption was monitored. Additionally, to investigate potential health effects, after 72 weeks of the exposure to ZEN, the fishes' blood was analyzed for major hematological and biochemical indices, and their head kidney, spleen, and liver were examined for morphological, histopathological, cytological, and molecular changes. Finally, to gain insight into the metabolism and distribution of ZEN in fish, the content of free and glucuronidated forms of ZEN and its major metabolites was measured in the intestine, liver, and muscles of the exposed fish. The feed-borne exposure of rainbow trout to ZEN at a dose of 2 mg⋅kg〈sup〉−1〈/sup〉 feed resulted in higher feeding efficiency and growth rate, most probably due to the anabolic properties of the ZEN metabolite. Importantly for the consumers of fish, despite absorption and metabolism of ZEN in the digestive system of the fish that had been exposed for 72 weeks, the residuals of ZEN were not transferred to the fishes’ muscles, which rules out a potential risk to human health related to the consumption of fish meat. However, the increased growth of fish fed with the contaminated feed may come at some cost, as the exposure to ZEN was associated with modulation of key components of the adaptive and innate immune systems. Moreover, the trunk kidney of ZEN-fed fish showed massive inflammation that was likely caused by pathogen infection. These findings raise concerns about fish health under the current recommended EC guidance values.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Computers & Geosciences, Volume 122〈/p〉 〈p〉Author(s): Hassan Talebi, Ute Mueller, Raimon Tolosana-Delgado〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Ore deposits usually consist of ore materials with different discrete (e.g. rock and alteration types) and continuous (e.g. geochemical and mineral composition) features. Financial feasibility studies are highly dependent on the modelling of these features and their associated joint uncertainties. Few geostatistical techniques have been developed for the joint modelling of high-dimensional mixed data (continuous and categorical) or constrained data, such as compositional data. The compositional nature of the mineral and geochemical data induces several challenges for multivariate geostatistical techniques, because such data carry relative information and are known for spurious statistical and spatial correlation effects. This paper investigates the application of the direct sampling algorithm for joint modelling of compositional and categorical data. In some mining projects the amount of available data may be enormous in some parts of the deposit and if the density of measurements is sufficient, multivariate geospatial patterns can be derived from that data and be simulated (without model inference) at other undersampled areas of the deposit with similar characteristics. In this context, the direct sampling multiple-point simulation method can be implemented for this reconstruction process. The compositional nature of the data is addressed via implementing an isometric log-ratio transformation. The approach is illustrated through two case studies, one synthetic and one real. The accuracy of the results is checked against a set of validation data, revealing the potential of the proposed methodology for joint modelling of compositional and categorical information. The direct sampling technique can be considered as a smart move to assess the future risk and uncertainty of a resource by making use of all the information hidden within the early data.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 1 March 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Geoderma, Volume 337〈/p〉 〈p〉Author(s): Hongfei Liu, Yang Wu, Zemin Ai, Jiaoyang Zhang, Chao Zhang, Sha Xue, Guobin Liu〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉DOM is the most bioavailable organic pool in the soil. The restoration of vegetation on abandoned cropland has a major impact on the concentration and composition of the DOM and thus affects the biodegradability of the soil DOM. Understanding the response of the microbial degradation of the DOM to temperature is important to maintain soil bioavailable organic matter in the field. We conducted a laboratory DOM solution incubation experiment to examine the temporal dynamics of DOM concentrations at temperatures of 4 °C (low), 20 °C (medium), and 35 °C (high) for four types of land uses: sloped cropland, grassland, shrub land, and woodland. Ultraviolet–visible and fluorescence spectroscopy were used to determine the structural complexity of the DOM. The conversion of the sloped cropland to shrub land and woodland significantly increased contents of DOC, DON, and recalcitrant substances in DOM soilution, such as humic-like material and fulvic acid, and stabilised the DOC pool, and reduced the decomposition of the DOC at 20 °C and 35 °C. The conversion of the sloped cropland to woodland dramatically reduced TDN decomposition. The DON loss after 60-day incubation significantly correlated with the initial content of tryptophan-like material. The biodegradability of the DON was higher and more sensitive to temperature than that of the DOC. Rising temperature initially promotes the decomposition of tryptophan-like material, and later promotes the degradation of more recalcitrant substances, such as humic-like material and fulvic acid, which enhanced the decomposition of the DOC and DON. The results suggest that the conversion of sloped cropland to shrubland and woodland not only promoted the accumulation of DOC, TDN, and recalcitrant substances in DOM solution, and decreased their biodegradability but also decreased the temperature sensitivity of the decomposition of the DOC and DON. Therefore, shrubland and woodland were the optimal choices for revegetation in the Loess Plateau of China.〈/p〉〈/div〉 〈/div〉 〈div xml:lang="en"〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0016706117316403-ga1.jpg" width="301" alt="Unlabelled Image" title="Unlabelled Image"〉〈/figure〉〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Agricultural and Forest Meteorology, Volume 264〈/p〉 〈p〉Author(s): Antonio D. del Campo, María González-Sanchis, Alberto García-Prats, Carlos J. Ceacero, Cristina Lull〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Marginal semi-arid forests in areas currently affected by climate change are a challenge to forest management, which has to focus on key functional traits that can effectively contribute to resistance under extreme drought. We studied the effects of thinning in a marginal forest by quantifying functional responses relating to growth, carbon and water fluxes. Two experimental plots were established, one thinned in 2012 and the other one left as a control. The environmental conditions varied substantially during the 4-year study period, although dry years predominated. There were signs of dieback in the control with a decreasing inter-annual trend in LAI, as opposed to the treated plots, where LAI by the end of the study almost reached pre-thinning levels. Sap flow and transpiration were greatly enhanced by the treatment, with thinned trees transpiring 22.4 l tree〈sup〉−1〈/sup〉 day〈sup〉−1〈/sup〉 in the growing season, about twice the control figures. The seasonal patterns of transpiration and soil moisture were uncoupled, indicating a contribution of deep groundwater to the former flux. In the control, limitations to water and carbon dynamics (canopy conductance) occurred at soil moisture values below 16%, whereas in the thinned trees these limitations appeared when soil moisture dropped below 10%. Overall, oaks’ transpiration was enhanced with thinning to the point that stand-water use surpassed that of the control by the second half of the study period, averaging 24% of gross rainfall in both plots. Soil evaporation increased from 12 to 20% of gross rainfall after treatment in the overall period. The treatment had a profound watering effect in this marginal forest, led by fewer trees using the same amount of water as those in the untreated overstocked plot. This research may provide guidelines for ecohydrology-oriented silviculture in stands experiencing tree encroachment and transformation into shrublands that are more prone to global change-induced disturbances.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Agricultural and Forest Meteorology, Volume 264〈/p〉 〈p〉Author(s): Ren Li, Lin Zhao, Tonghua Wu, Qinxue Wang, Yongjian Ding, Jimin Yao, Xiaodong Wu, Guojie Hu, Yao Xiao, Yizhen Du, Xiaofan Zhu, Yanhui Qin, Shuhua Yang, Rui Bai, Erji Du, Guangyue Liu, Defu Zou, Yongping Qiao, Jianzong Shi〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Soil thermal conductivity (〈em〉λ〈/em〉) is one of the essential parameters relating to heat exchange, and it also plays a key role in verifying soil thermal hydrodynamics in permafrost regions. In this paper, the characteristic of in situ 〈em〉λ〈/em〉 was analyzed based on data measured from June 2004 to December 2008 at Tanggula district on the Qinghai–Tibet Plateau. The result showed that diurnal 〈em〉λ〈/em〉 strongly influenced by variation of soil moisture content. The daily 〈em〉λ〈/em〉 exhibited distinct seasonal variation; on average, the largest value of 〈em〉λ〈/em〉 occurred in summer, followed by the autumn and spring season, while the smallest value occurred in winter. As a whole, 〈em〉λ〈/em〉 values in the unfrozen state were larger than those in the frozen state. Unsaturated soil and the huge difference in soil moisture content between the unfrozen state and initial freeze resulted in the lower 〈em〉λ〈/em〉 in the frozen state. For the study area, the critical value of local soil saturation degree was about 0.37, the corresponding critical soil moisture content was about 0.195 m〈sup〉3〈/sup〉 m〈sup〉−3〈/sup〉. And soil moisture content was the main factor controlling in situ 〈em〉λ〈/em〉. Finally, an empirically-derived model was proposed for predicting daily 〈em〉λ〈/em〉, and which showed good performance in the study area.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Agricultural and Forest Meteorology, Volume 264〈/p〉 〈p〉Author(s): Baoqing Zhang, Amir AghaKouchak, Yuting Yang, Jiahua Wei, Guangqian Wang〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Different categories of droughts (e.g., meteorological, agricultural, hydrological), and their multi-scalar features often make description of drought onset, persistence, and termination challenging and often subjective. Here we show that a water-energy balance based indicator, named Standardized Moisture Anomaly Index (SZI), better captures multiple categories of droughts and their multi-scalar features. We globally evaluate and compare the performance of SZI with existing drought indicators that use potential evapotranspiration (PET) as a measure of atmospheric water demand including the Standardized Precipitation Evapotranspiration Index (SPEI) and self-calibrated Palmer Drought Severity Index (scPDSI). We show that while 〈em〉PET〈/em〉 is a good indicator for characterizing the climate aridity, using it as a measure of atmospheric water demand for drought analysis leads to misrepresentation of droughts, especially over water-limited (non-humid) regions where the actual evapotranspiration is primarily dominated by water availability rather than energy (or PET). The main advantage of SZI is that, instead of PET, it uses a variable termed climatically appropriate precipitation for existing conditions (〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si2.gif" overflow="scroll"〉〈mover accent="true"〉〈mi〉P〈/mi〉〈mo〉ˆ〈/mo〉〈/mover〉〈/math〉) as the atmospheric water demand metric. Investigating droughts over 32 large basins across the globe, we show that the SZI can better represent meteorological, hydrological, and agricultural droughts compared to SPEI (especially in non-humid basins; 18 out of 32 basins) and scPDSI at multiple time scales. Given that SZI is physically more reasonable in reflecting surface water-energy balance over both humid and non-humid regions, it enables better characterization of different types of droughts in different climatic regions.〈/p〉〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Xin Cai, Chengbin Gao, Huanhuan Song, Ning Yang, Qiang Fu, Fenghua Tan, Chao Li〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Cathepsin Z (CTSZ) is a lysosomal cysteine protease of the papain superfamily. It participates in the host immune defense via phagocytosis, signal transduction, cell-cell communication, proliferation, and migration of immune cells such as monocytes, macrophages, and dendritic cells. In this study, we reported the identification of 〈em〉Sm〈/em〉CTSZ, a CTSZ homolog from turbot (〈em〉Scophthalmus maximus〈/em〉 L.). 〈em〉Sm〈/em〉CTSZ was 317 residues in length and contains a Pept-C1 domain. In multiple species comparison, 〈em〉Sm〈/em〉CTSZ shared 65–93% overall sequence identities with the CTSZ counterparts from human, rat, and several fish species. In the phylogenetic analysis, 〈em〉Sm〈/em〉CTSZ showed the closest relationship to 〈em〉Cynoglossus semilaevis〈/em〉. The syntenic analysis revealed the similar neighboring genes of CTSZ across all the selected species, which suggested the synteny encompassing CTSZ region during vertebrate evolution. Subsequently, 〈em〉Sm〈/em〉CTSZ was constitutively expressed in various tissues, with the lowest and highest levels in brain and intestine respectively. In addition, 〈em〉Sm〈/em〉CTSZ was significantly up-regulated in intestine following both Gram-negative bacteria 〈em〉Vibrio anguillarum〈/em〉, and Gram-positive bacteria 〈em〉Streptococcus iniae〈/em〉 immersion challenge. Finally, the 〈em〉rSm〈/em〉CTSZ showed strong binding ability to all the examined microbial ligands, and the agglutination effect to different bacteria. Taken together, these results indicated 〈em〉Sm〈/em〉CTSZ could play important roles in mucosal immune response in the event of bacterial infection in teleost. However, the knowledge of CTSZ are still limited in teleost species, further studies should be carried out to better characterize its detailed roles in teleost mucosal immunity.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 14 August 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics〈/p〉 〈p〉Author(s): Mehdi Samiee, Mohsen Zayernouri, Mark M. Meerschaert〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We present the stability and error analysis of the unified Petrov–Galerkin spectral method, developed in [1], for linear fractional partial differential equations with two-sided derivatives and constant coefficients in any (〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.gif" overflow="scroll"〉〈mn〉1〈/mn〉〈mo〉+〈/mo〉〈mi〉d〈/mi〉〈/math〉)-dimensional space-time hypercube, 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si2.gif" overflow="scroll"〉〈mi〉d〈/mi〉〈mo〉=〈/mo〉〈mn〉1〈/mn〉〈mo〉,〈/mo〉〈mn〉2〈/mn〉〈mo〉,〈/mo〉〈mn〉3〈/mn〉〈mo〉,〈/mo〉〈mo〉⋯〈/mo〉〈/math〉, subject to homogeneous Dirichlet initial/boundary conditions. Specifically, we prove the existence and uniqueness of the weak form and perform the corresponding stability and error analysis of the proposed method. Finally, we perform several numerical simulations to compare the theoretical and computational rates of convergence.〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): Giovanni Soligo, Alessio Roccon, Alfredo Soldati〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In this work, we propose and test the validity of a modified Phase Field Method (PFM), which is specifically developed for large scale simulations of turbulent flows with large and deformable surfactant-laden droplets. The time evolution of the phase field, 〈em〉ϕ〈/em〉, and of the surfactant concentration field, 〈em〉ψ〈/em〉, are obtained from two Cahn–Hilliard-like equations together with a two-order-parameter Time-Dependent Ginzburg–Landau (TDGL) free energy functional. The modifications introduced circumvent existing limitations of current approaches based on PFM and improve the well-posedness of the model. The effect of surfactant on surface tension is modeled via an Equation Of State (EOS), further improving the flexibility of the approach. This method can efficiently handle topological changes, i.e. breakup and coalescence, and describe adsorption/desorption of surfactant. The capabilities of the proposed approach are tested in this paper against previous experimental results on the effects of surfactant on the deformation of a single droplet and on the interactions between two droplets. Finally, to appreciate the performances of the model on a large scale complex simulation, a qualitative analysis of the behavior of surfactant-laden droplets in a turbulent channel flow is presented and discussed.〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): Sergii V. Siryk〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We provide a careful Fourier analysis of the Guermond–Pasquetti mass lumping correction technique (Guermond and Pasquetti, 2013 [11]) applied to pure transport and convection–diffusion problems. In particular, it is found that increasing the number of corrections reduces the accuracy for problems with diffusion; however all the corrected schemes are more accurate than the consistent Galerkin formulation in this case. For the pure transport problems the situation is the opposite. We also investigate the differences between two numerical solutions – the consistent solution and the corrected ones, and show that increasing the number of corrections makes solutions of the corrected schemes closer to the consistent solution in all cases.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 377〈/p〉 〈p〉Author(s): Adam S. Jermyn〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Tensors are a natural way to express correlations among many physical variables, but storing tensors in a computer naively requires memory which scales exponentially in the rank of the tensor. This is not optimal, as the required memory is actually set not by the rank but by the mutual information amongst the variables in question. Representations such as the tensor tree perform near-optimally when the tree decomposition is chosen to reflect the correlation structure in question, but making such a choice is non-trivial and good heuristics remain highly context-specific. In this work I present two new algorithms for choosing efficient tree decompositions, independent of the physical context of the tensor. The first is a brute-force algorithm which produces optimal decompositions up to truncation error but is generally impractical for high-rank tensors, as the number of possible choices grows exponentially in rank. The second is a greedy algorithm, and while it is not optimal it performs extremely well in numerical experiments while having runtime which makes it practical even for tensors of very high rank.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 377〈/p〉 〈p〉Author(s): Lam H. Nguyen, Dominik Schillinger〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We describe a local iterative corrector scheme that significantly improves the accuracy of the multiscale finite element method (MsFEM). Our technique is based on the definition of a local corrector problem for each multiscale basis function that is driven by the residual of the previous multiscale solution. Each corrector problem results in a local corrector solution that improves the accuracy of the corresponding multiscale basis function at element interfaces. We cast the strategy of residual-driven correction in an iterative scheme that is straightforward to implement and, due to the locality of corrector problems, well-suited for parallel computing. We show that the iterative scheme converges to the best possible fine-mesh solution. Finally, we illustrate the effectiveness of our approach with multiscale benchmarks characterized by missing scale separation, including the microCT-based stress analysis of a vertebra with trabecular microstructure.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 377〈/p〉 〈p〉Author(s): Brody Bassett, Brian Kiedrowski〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The meshless local Petrov–Galerkin (MLPG) method is applied to the steady-state and 〈em〉k〈/em〉-eigenvalue neutron transport equations, which are discretized in energy using the multigroup approximation and in angle using the discrete ordinates approximation. To prevent oscillations in the neutron flux, the MLPG transport equation is stabilized by the streamline upwind Petrov–Galerkin (SUPG) method. Global neutron conservation is enforced by using moving least squares basis and weight functions and appropriate SUPG parameters. The cross sections in the transport equation are approximated in accordance with global particle balance and without constraint on their spatial dependence or the location of the basis and weight functions. The equations for the strong-form meshless collocation approach are derived for comparison to the MLPG equations. The method of manufactured solutions is used to verify the resulting MLPG method in one, two and three dimensions. Results for realistic problems, including two-dimensional pincells, a reflected ellipsoid and a three-dimensional problem with voids, are verified by comparison to Monte Carlo simulations.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 28 May 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics〈/p〉 〈p〉Author(s): Frederic Gibou, David Hyde, Ron Fedkiw〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We present a review on numerical methods for simulating multiphase and free surface flows. We focus in particular on numerical methods that seek to preserve the discontinuous nature of the solutions across the interface between phases. We provide a discussion on the Ghost-Fluid and Voronoi Interface methods, on the treatment of surface tension forces that avoid stringent time step restrictions, on adaptive grid refinement techniques for improved efficiency and on parallel computing approaches. We present the results of some simulations obtained with these treatments in two and three spatial dimensions. We also provide a discussion of Machine Learning and Deep Learning techniques in the context of multiphase flows and propose several future potential research thrusts for using deep learning to enhance the study and simulation of multiphase flows.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈/p〉〈/div〉 〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0021999118303371-gr001.jpg" width="500" alt="Graphical abstract for this article" title=""〉〈/figure〉

Description: 〈p〉Publication date: Available online 26 October 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics〈/p〉 〈p〉Author(s): Xiaodong Liu, Jiguang Sun〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Inverse scattering has been an active research area for the past thirty years. While very successful in many cases, progress has lagged when only 〈em〉limited-aperture〈/em〉 measurement is available. In this paper, we perform some elementary study to recover data that can not be measured directly. In particular, we aim at recovering the 〈em〉full-aperture〈/em〉 far field data from 〈em〉limited-aperture〈/em〉 measurement. Due to the reciprocity relation, the multi-static response matrix (MSR) has a symmetric structure. Using the Green's formula and single layer potential, we propose two schemes to recover 〈em〉full-aperture〈/em〉 MSR. The recovered data is tested by a recently proposed direct sampling method and the factorization method. Numerical results show that it is possible to, at least, partially recover the missing data and consequently improve the reconstruction of the scatterer.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 377〈/p〉 〈p〉Author(s): D. Reiser, J. Romazanov, Ch. Linsmeier〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The problem of constructing Monte-Carlo solutions of drift-diffusion systems corresponding to Fokker–Planck equations with sources and sinks is revisited. Firstly, a compact formalism is introduced for the specific problem of stationary solutions. This leads to identification of the dwell time as the key quantity to characterize the system and to obtain a proper normalization for statistical analysis of numerical results. Secondly, the question of appropriate track length estimators for drift-diffusion systems is discussed for a 1D model system. It is found that a simple track length estimator can be given only for pure drift motion without diffusion. The stochastic nature of the diffusive part cannot be appropriately described by the path length of simulation particles. Further analysis of the usual situation with inhomogeneous drift and diffusion coefficients leads to an error estimate based on particle trajectories. The result for limits in grid cell size and time step used for the construction of Monte-Carlo trajectories resembles the Courant-Friedrichs-Lewy and von Neumann conditions for explicit methods.〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): Dinshaw S. Balsara, Roger Käppeli〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉The time-dependent equations of computational electrodynamics (CED) are evolved consistent with the divergence constraints on the electric displacement and magnetic induction vector fields. Respecting these constraints has proved to be very useful in the classic finite-difference time-domain (FDTD) schemes. As a result, there has been a recent effort to design finite volume time domain (FVTD) and discontinuous Galerkin time domain (DGTD) schemes that satisfy the same constraints and, nevertheless, draw on recent advances in higher order Godunov methods. This paper catalogues the first step in the design of globally constraint-preserving DGTD schemes. The algorithms presented here are based on a novel DG-like method that is applied to a Yee-type staggering of the electromagnetic field variables in the faces of the mesh. The other two novel building blocks of the method include constraint-preserving reconstruction of the electromagnetic fields and multidimensional Riemann solvers; both of which have been developed in recent years by the first author.〈/p〉 〈p〉The resulting DGTD scheme is linear, at least when limiters are not applied to the DG scheme. As a result, it is possible to carry out a von Neumann stability analysis of the entire suite of DGTD schemes for CED at orders of accuracy ranging from second to fourth. The analysis requires some simplifications in order to make it analytically tractable, however, it proves to be extremely instructive. A von Neumann stability analysis is a necessary precursor to the design of a full DGTD scheme for CED. It gives us the maximal CFL numbers that can be sustained by the DGTD schemes presented here at all orders. It also enables us to understand the wave propagation characteristics of the schemes in various directions on a Cartesian mesh. We find that constraint-preserving DGTD schemes permit CFL numbers that are competitive with conventional DG schemes. However, like conventional DG schemes, the CFL of DGTD schemes decreases with increasing order. To counteract that, we also present constraint-preserving PNPM schemes for CED. We find that the third and fourth order constraint-preserving DGTD and P1PM schemes have some extremely attractive properties when it comes to low-dispersion, low-dissipation propagation of electromagnetic waves in multidimensions. Numerical accuracy tests are also provided to support the von Neumann stability analysis. We expect these methods to play a role in those problems of engineering CED where exceptional precision must be achieved at any cost.〈/p〉 〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 377〈/p〉 〈p〉Author(s): Yinghe Qi, Jiacai Lu, Ruben Scardovelli, Stéphane Zaleski, Grétar Tryggvason〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In spite of considerable progress, computing curvature in Volume of Fluid (VOF) methods continues to be a challenge. The goal is to develop a function or a subroutine that returns the curvature in computational cells containing an interface separating two immiscible fluids, given the volume fraction in the cell and the adjacent cells. Currently, the most accurate approach is to fit a curve (2D), or a surface (3D), matching the volume fractions and finding the curvature by differentiation. Here, a different approach is examined. A synthetic data set, relating curvature to volume fractions, is generated using well-defined shapes where the curvature and volume fractions are easily found and then machine learning is used to fit the data (training). The resulting function is used to find the curvature for shapes not used for the training and implemented into a code to track moving interfaces. The results suggest that using machine learning to generate the relationship is a viable approach that results in reasonably accurate predictions.〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): Mani Razi, Robert M. Kirby, Akil Narayan〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In this paper, we introduce a novel approach for the construction of multi-fidelity surrogate models with “discrete” fidelity levels. The notion of a discrete level of fidelity is in contrast to a mathematical model, for which the notion of refinement towards a high-fidelity model is relevant to sending a discretization parameter toward zero in a continuous way. Our notion of discrete fidelity levels encompasses cases for which there is no notion of convergence in terms of a fidelity parameter that can be sent to zero or infinity. The particular choice of how levels of fidelity are defined in this framework paves the way for using models that may have no apparent physical or mathematical relationship to the target high-fidelity model. However, our approach requires that models can produce results with a common set of parameters in the target model. Hence, fidelity level in this work is not directly representative of the degree of similarity of a low-fidelity model to a target high-fidelity model. In particular, we show that our approach is applicable to competitive ecological systems with different numbers of species, discrete-state Markov chains with a different number of states, polymer networks with a different number of connections, and nano-particle plasmonic arrays with a different number of scatterers. The results of this study demonstrate that our procedure boasts computational efficiency and accuracy for a wide variety of models and engineering systems.〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): Hasan Almanasreh〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In this work we will treat the spurious eigenvalues obstacle that appears in the computation of the radial Dirac eigenvalue problem using numerical methods. The treatment of the spurious solution is based on applying Petrov–Galerkin finite element method. The significance of this work is the employment of just continuous basis functions, thus the need of a continuous function which has a continuous first derivative as a basis, as in [2], [3], is no longer required. The Petrov–Galerkin finite element method for the Dirac eigenvalue problem strongly depends on a stability parameter, 〈em〉τ〈/em〉, that controls the size of the diffusion terms added to the finite element formulation for the problem. The mesh-dependent parameter 〈em〉τ〈/em〉 is derived based on the given problem with the particular basis functions.〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): S.B. Adrian, F.P. Andriulli, T.F. Eibert〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We present a Calderón preconditioner for the electric field integral equation (EFIE), which does not require a barycentric refinement of the mesh and which yields a Hermitian, positive definite (HPD) system matrix allowing for the usage of the conjugate gradient (CG) solver. The resulting discrete equation system is immune to the low-frequency and the dense-discretization breakdown and, in contrast to existing Calderón preconditioners, no second discretization of the EFIE operator with Buffa–Christiansen (BC) functions is necessary. This preconditioner is obtained by leveraging on spectral equivalences between (scalar) integral operators, namely the single layer and the hypersingular operator known from electrostatics, on the one hand, and the Laplace–Beltrami operator on the other hand. Since our approach incorporates Helmholtz projectors, there is no search for global loops necessary and thus our method remains stable on multiply connected geometries. The numerical results demonstrate the effectiveness of this approach for both canonical and realistic (multi-scale) problems.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 21 February 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics〈/p〉 〈p〉Author(s): Mehdi Samiee, Mohsen Zayernouri, Mark M. Meerschaert〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We develop a unified Petrov–Galerkin spectral method for a class of fractional partial differential equations with two-sided derivatives and constant coefficients of the form 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.gif" overflow="scroll"〉〈mmultiscripts〉〈mrow〉〈mi mathvariant="script"〉D〈/mi〉〈/mrow〉〈mrow〉〈mi〉t〈/mi〉〈/mrow〉〈none〉〈/none〉〈none〉〈/none〉〈mrow〉〈mn〉2〈/mn〉〈mi〉τ〈/mi〉〈/mrow〉〈mprescripts〉〈/mprescripts〉〈mrow〉〈mn〉0〈/mn〉〈/mrow〉〈none〉〈/none〉〈/mmultiscripts〉〈mi〉u〈/mi〉〈mo〉+〈/mo〉〈msubsup〉〈mrow〉〈mo〉∑〈/mo〉〈/mrow〉〈mrow〉〈mi〉i〈/mi〉〈mo〉=〈/mo〉〈mn〉1〈/mn〉〈/mrow〉〈mrow〉〈mi〉d〈/mi〉〈/mrow〉〈/msubsup〉〈mo stretchy="false"〉[〈/mo〉〈msub〉〈mrow〉〈msub〉〈mrow〉〈mi〉c〈/mi〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉l〈/mi〉〈/mrow〉〈mrow〉〈mi〉i〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msub〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉a〈/mi〉〈/mrow〉〈mrow〉〈mi〉i〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msub〉〈msubsup〉〈mrow〉〈mi mathvariant="script"〉D〈/mi〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉x〈/mi〉〈/mrow〉〈mrow〉〈mi〉i〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈mrow〉〈mn〉2〈/mn〉〈msub〉〈mrow〉〈mi〉μ〈/mi〉〈/mrow〉〈mrow〉〈mi〉i〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msubsup〉〈mi〉u〈/mi〉〈mo〉+〈/mo〉〈msub〉〈mrow〉〈msub〉〈mrow〉〈mi〉c〈/mi〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉r〈/mi〉〈/mrow〉〈mrow〉〈mi〉i〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msub〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉x〈/mi〉〈/mrow〉〈mrow〉〈mi〉i〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msub〉〈msubsup〉〈mrow〉〈mi mathvariant="script"〉D〈/mi〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉b〈/mi〉〈/mrow〉〈mrow〉〈mi〉i〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈mrow〉〈mn〉2〈/mn〉〈msub〉〈mrow〉〈mi〉μ〈/mi〉〈/mrow〉〈mrow〉〈mi〉i〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msubsup〉〈mi〉u〈/mi〉〈mo stretchy="false"〉]〈/mo〉〈mo〉+〈/mo〉〈mi〉γ〈/mi〉〈mspace width="0.2em"〉〈/mspace〉〈mspace width="0.2em"〉〈/mspace〉〈mi〉u〈/mi〉〈mo〉=〈/mo〉〈msubsup〉〈mrow〉〈mo〉∑〈/mo〉〈/mrow〉〈mrow〉〈mi〉j〈/mi〉〈mo〉=〈/mo〉〈mn〉1〈/mn〉〈/mrow〉〈mrow〉〈mi〉d〈/mi〉〈/mrow〉〈/msubsup〉〈mo stretchy="false"〉[〈/mo〉〈msub〉〈mrow〉〈msub〉〈mrow〉〈mi〉κ〈/mi〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉l〈/mi〉〈/mrow〉〈mrow〉〈mi〉j〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msub〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉a〈/mi〉〈/mrow〉〈mrow〉〈mi〉j〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msub〉〈msubsup〉〈mrow〉〈mi mathvariant="script"〉D〈/mi〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉x〈/mi〉〈/mrow〉〈mrow〉〈mi〉j〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈mrow〉〈mn〉2〈/mn〉〈msub〉〈mrow〉〈mi〉ν〈/mi〉〈/mrow〉〈mrow〉〈mi〉j〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msubsup〉〈mi〉u〈/mi〉〈mo〉+〈/mo〉〈msub〉〈mrow〉〈msub〉〈mrow〉〈mi〉κ〈/mi〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉r〈/mi〉〈/mrow〉〈mrow〉〈mi〉j〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msub〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉x〈/mi〉〈/mrow〉〈mrow〉〈mi〉j〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msub〉〈msubsup〉〈mrow〉〈mi mathvariant="script"〉D〈/mi〉〈/mrow〉〈mrow〉〈msub〉〈mrow〉〈mi〉b〈/mi〉〈/mrow〉〈mrow〉〈mi〉j〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈mrow〉〈mn〉2〈/mn〉〈msub〉〈mrow〉〈mi〉ν〈/mi〉〈/mrow〉〈mrow〉〈mi〉j〈/mi〉〈/mrow〉〈/msub〉〈/mrow〉〈/msubsup〉〈mi〉u〈/mi〉〈mo stretchy="false"〉]〈/mo〉〈mo〉+〈/mo〉〈mi〉f〈/mi〉〈/math〉, where 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si2.gif" overflow="scroll"〉〈mn〉2〈/mn〉〈mi〉τ〈/mi〉〈mo〉∈〈/mo〉〈mo stretchy="false"〉(〈/mo〉〈mn〉0〈/mn〉〈mo〉,〈/mo〉〈mn〉2〈/mn〉〈mo stretchy="false"〉)〈/mo〉〈/math〉, 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si3.gif" overflow="scroll"〉〈mn〉2〈/mn〉〈mi〉τ〈/mi〉〈mo〉≠〈/mo〉〈mn〉1〈/mn〉〈/math〉, 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si4.gif" overflow="scroll"〉〈mn〉2〈/mn〉〈msub〉〈mrow〉〈mi〉μ〈/mi〉〈/mrow〉〈mrow〉〈mi〉i〈/mi〉〈/mrow〉〈/msub〉〈mo〉∈〈/mo〉〈mo stretchy="false"〉(〈/mo〉〈mn〉0〈/mn〉〈mo〉,〈/mo〉〈mn〉1〈/mn〉〈mo stretchy="false"〉)〈/mo〉〈/math〉 and 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si5.gif" overflow="scroll"〉〈mn〉2〈/mn〉〈msub〉〈mrow〉〈mi〉ν〈/mi〉〈/mrow〉〈mrow〉〈mi〉j〈/mi〉〈/mrow〉〈/msub〉〈mo〉∈〈/mo〉〈mo stretchy="false"〉(〈/mo〉〈mn〉1〈/mn〉〈mo〉,〈/mo〉〈mn〉2〈/mn〉〈mo stretchy="false"〉)〈/mo〉〈/math〉, in a (〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si6.gif" overflow="scroll"〉〈mn〉1〈/mn〉〈mo〉+〈/mo〉〈mi〉d〈/mi〉〈/math〉)-dimensional 〈em〉space–time〈/em〉 hypercube, 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si7.gif" overflow="scroll"〉〈mi〉d〈/mi〉〈mo〉=〈/mo〉〈mn〉1〈/mn〉〈mo〉,〈/mo〉〈mn〉2〈/mn〉〈mo〉,〈/mo〉〈mn〉3〈/mn〉〈mo〉,〈/mo〉〈mo〉⋯〈/mo〉〈/math〉, subject to homogeneous Dirichlet initial/boundary conditions. We employ the eigenfunctions of the fractional Sturm–Liouville eigen-problems of the first kind in [1], called 〈em〉Jacobi poly-fractonomial〈/em〉s, as temporal bases, and the eigen-functions of the boundary-value problem of the second kind as temporal test functions. Next, we construct our spatial basis/test functions using Legendre polynomials, yielding mass matrices being independent of the spatial fractional orders (〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si8.gif" overflow="scroll"〉〈msub〉〈mrow〉〈mi〉μ〈/mi〉〈/mrow〉〈mrow〉〈mi〉i〈/mi〉〈/mrow〉〈/msub〉〈mo〉,〈/mo〉〈mspace width="0.2em"〉〈/mspace〉〈msub〉〈mrow〉〈mi〉ν〈/mi〉〈/mrow〉〈mrow〉〈mi〉j〈/mi〉〈/mrow〉〈/msub〉〈mo〉,〈/mo〉〈mspace width="0.2em"〉〈/mspace〉〈mi〉i〈/mi〉〈mo〉,〈/mo〉〈mspace width="0.2em"〉〈/mspace〉〈mi〉j〈/mi〉〈mo〉=〈/mo〉〈mn〉1〈/mn〉〈mo〉,〈/mo〉〈mn〉2〈/mn〉〈mo〉,〈/mo〉〈mo〉⋯〈/mo〉〈mo〉,〈/mo〉〈mi〉d〈/mi〉〈/math〉). Furthermore, we formulate a novel unified fast linear solver for the resulting high-dimensional linear system based on the solution of generalized eigen-problem of spatial mass matrices with respect to the corresponding stiffness matrices, hence, making the complexity of the problem optimal, i.e., 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si9.gif" overflow="scroll"〉〈mi mathvariant="script"〉O〈/mi〉〈mo stretchy="false"〉(〈/mo〉〈msup〉〈mrow〉〈mi〉N〈/mi〉〈/mrow〉〈mrow〉〈mi〉d〈/mi〉〈mo〉+〈/mo〉〈mn〉2〈/mn〉〈/mrow〉〈/msup〉〈mo stretchy="false"〉)〈/mo〉〈/math〉. We carry out several numerical test cases to examine the CPU time and convergence rate of the method. The corresponding stability and error analysis of the Petrov–Galerkin method are carried out in [2].〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): Ruilian Du, Yubin Yan, Zongqi Liang〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉A new high-order finite difference scheme to approximate the Caputo fractional derivative 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.gif" overflow="scroll"〉〈mfrac〉〈mrow〉〈mn〉1〈/mn〉〈/mrow〉〈mrow〉〈mn〉2〈/mn〉〈/mrow〉〈/mfrac〉〈mo stretchy="true" maxsize="2.4ex" minsize="2.4ex"〉(〈/mo〉〈mspace width="0.2em"〉〈/mspace〉〈mmultiscripts〉〈mrow〉〈mi〉D〈/mi〉〈/mrow〉〈mrow〉〈mi〉t〈/mi〉〈/mrow〉〈mrow〉〈mi〉α〈/mi〉〈/mrow〉〈mprescripts〉〈/mprescripts〉〈mrow〉〈mn〉0〈/mn〉〈/mrow〉〈mrow〉〈mi〉C〈/mi〉〈/mrow〉〈/mmultiscripts〉〈mi〉f〈/mi〉〈mo stretchy="false"〉(〈/mo〉〈msub〉〈mrow〉〈mi〉t〈/mi〉〈/mrow〉〈mrow〉〈mi〉k〈/mi〉〈/mrow〉〈/msub〉〈mo stretchy="false"〉)〈/mo〉〈mo〉+〈/mo〉〈mspace width="0.2em"〉〈/mspace〉〈mmultiscripts〉〈mrow〉〈mi〉D〈/mi〉〈/mrow〉〈mrow〉〈mi〉t〈/mi〉〈/mrow〉〈mrow〉〈mi〉α〈/mi〉〈/mrow〉〈mprescripts〉〈/mprescripts〉〈mrow〉〈mn〉0〈/mn〉〈/mrow〉〈mrow〉〈mi〉C〈/mi〉〈/mrow〉〈/mmultiscripts〉〈mi〉f〈/mi〉〈mo stretchy="false"〉(〈/mo〉〈msub〉〈mrow〉〈mi〉t〈/mi〉〈/mrow〉〈mrow〉〈mi〉k〈/mi〉〈mo〉−〈/mo〉〈mn〉1〈/mn〉〈/mrow〉〈/msub〉〈mo stretchy="false"〉)〈/mo〉〈mo stretchy="true" maxsize="2.4ex" minsize="2.4ex"〉)〈/mo〉〈/math〉, 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si2.gif" overflow="scroll"〉〈mi〉k〈/mi〉〈mo〉=〈/mo〉〈mn〉1〈/mn〉〈mo〉,〈/mo〉〈mn〉2〈/mn〉〈mo〉,〈/mo〉〈mo〉…〈/mo〉〈mo〉,〈/mo〉〈mi〉N〈/mi〉〈/math〉, with the convergence order 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si160.gif" overflow="scroll"〉〈mi〉O〈/mi〉〈mo stretchy="false"〉(〈/mo〉〈mi mathvariant="normal"〉Δ〈/mi〉〈msup〉〈mrow〉〈mi〉t〈/mi〉〈/mrow〉〈mrow〉〈mn〉4〈/mn〉〈mo〉−〈/mo〉〈mi〉α〈/mi〉〈/mrow〉〈/msup〉〈mo stretchy="false"〉)〈/mo〉〈/math〉, 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si4.gif" overflow="scroll"〉〈mi〉α〈/mi〉〈mo〉∈〈/mo〉〈mo stretchy="false"〉(〈/mo〉〈mn〉1〈/mn〉〈mo〉,〈/mo〉〈mn〉2〈/mn〉〈mo stretchy="false"〉)〈/mo〉〈/math〉 is obtained when 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si123.gif" overflow="scroll"〉〈msup〉〈mrow〉〈mi〉f〈/mi〉〈/mrow〉〈mrow〉〈mo〉‴〈/mo〉〈/mrow〉〈/msup〉〈mo stretchy="false"〉(〈/mo〉〈msub〉〈mrow〉〈mi〉t〈/mi〉〈/mrow〉〈mrow〉〈mn〉0〈/mn〉〈/mrow〉〈/msub〉〈mo stretchy="false"〉)〈/mo〉〈mo〉=〈/mo〉〈mn〉0〈/mn〉〈/math〉, where Δ〈em〉t〈/em〉 denotes the time step size. Based on this scheme we introduce a finite difference method for solving fractional diffusion wave equation with the convergence order 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si6.gif" overflow="scroll"〉〈mi〉O〈/mi〉〈mo stretchy="false"〉(〈/mo〉〈mi mathvariant="normal"〉Δ〈/mi〉〈msup〉〈mrow〉〈mi〉t〈/mi〉〈/mrow〉〈mrow〉〈mn〉4〈/mn〉〈mo〉−〈/mo〉〈mi〉α〈/mi〉〈/mrow〉〈/msup〉〈mo〉+〈/mo〉〈msup〉〈mrow〉〈mi〉h〈/mi〉〈/mrow〉〈mrow〉〈mn〉2〈/mn〉〈/mrow〉〈/msup〉〈mo stretchy="false"〉)〈/mo〉〈/math〉, where 〈em〉h〈/em〉 denotes the space step size. Numerical examples are given to show that the numerical results are consistent with the theoretical results.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 377〈/p〉 〈p〉Author(s): Jie Du, Yang Yang〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Local discontinuous Galerkin (LDG) methods are popular for convection-diffusion equations. In LDG methods, we introduce an auxiliary variable 〈em〉p〈/em〉 to represent the derivative of the primary variable 〈em〉u〈/em〉, and solve them on the same mesh. It is well known that the maximum-principle-preserving (MPP) LDG method is only available up to second-order accuracy. Recently, we introduced a new algorithm, and solve 〈em〉u〈/em〉 and 〈em〉p〈/em〉 on different meshes, and obtained stability and optimal error estimates. In this paper, we will continue this approach and construct MPP third-order LDG methods for convection-diffusion equations on overlapping meshes. The new algorithm is more flexible and does not increase any computational cost. Numerical evidence will be given to demonstrate the accuracy and good performance of the third-order MPP LDG method.〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): Yunchang Seol, Yu-Hau Tseng, Yongsam Kim, Ming-Chih Lai〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In this paper, a two-dimensional immersed boundary method is developed to simulate the dynamics of Newtonian vesicle in viscoelastic Oldroyd-B fluid under shear flow. The viscoelasticity effect of extra stress is well incorporated into the immersed boundary formulation using the indicator function. Our numerical methodology is first validated in comparison with theoretical results in purely Newtonian fluid, and then a series of numerical experiments is conducted to study the effects of different dimensionless parameters on the vesicle motions. Although the tank-treading (TT) motion of Newtonian vesicle in Oldroyd-B fluid under shear flow can be observed just like in Newtonian fluid, it is surprising to find that the stationary inclination angle can be negative without the transition to tumbling (TB) motion. Moreover, the inertia effect plays a significant role that is able to turn the vesicle back to positive inclination angle through TT-TB-TT transition as the Reynolds number increases. To the best of our knowledge, this is the first numerical work for the detailed investigations of Newtonian vesicle dynamics suspended in viscoelastic Oldroyd-B fluid. We believe that our numerical results can be used to motivate further studies in theory and experiments for such coupling vesicle problems.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Forest Ecology and Management, Volume 433〈/p〉 〈p〉Author(s): Matthew E. Hane, Andrew J. Kroll, Aaron Springford, Jack Giovanini, Mike Rochelle, Edward B. Arnett〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Structural enrichment in commercial tree plantations is a potential tool to increase snag numbers but relatively little information is available about how species, size, and spatial distribution of created snags are associated with longevity of these structures. We created 1197 snags in 31 harvest units from 1997 to 1999 in the Cascade and Coast Ranges, Oregon, USA, by topping live trees with harvesting equipment. We used an experimental design to distribute created snags at three densities and as either single or clumped created snags. We fit Weibull and log-logistic Accelerated Failure Time models and found that the median failure time was insensitive to the choice of distribution. We found a small positive effect of diameter at breast height (DBH) and a slight negative effect of increasing distance between created snags on survival. Assuming Weibull and log-logistic distributions at mean observed values of DBH and distance between snags, median survival times for Douglas-fir (〈em〉Pseudotsuga menziesii〈/em〉) were 21.0 (95% confidence interval: 19.3, 22.8) years and 21.2 (19.7, 22.8) years, respectively. For western hemlock (〈em〉Tsuga heterophylla〈/em〉), median survival times were 13.0 (11.9, 14.2) years and 12.5 (11.4, 13.7) years, respectively. Although the two failure distributions had similar median failure times, the log-logistic implies a higher survival probability over time for snags that remained standing at the end of the study period. Created snags can be a useful supplement for harvest units rotated at ∼45 years and Douglas-fir will be available for longer as standing structures. For example, under the log-logistic model, a predicted 5% of Douglas-fir snags are retained to rotation age, so that 40 snags per hectare would be required at harvest to maintain 2 snags per hectare through stand rotation. Snags created from western hemlock will provide an early rotation pulse but are unlikely to last longer than 20 years. Our results suggest that longevity can be increased by maximizing the snag size within the safety constraints of harvesting equipment. Scattering of snags may have a slightly negative effect on snag survival but this outcome should be weighed against potential ecological benefits of variation in snag distributions.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 15 February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Forest Ecology and Management, Volume 433〈/p〉 〈p〉Author(s): Hilman T. Sukma, Julian Di Stefano, Matthew Swan, Holly Sitters〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Enhanced understanding of relationships between functional diversity (FD) and environmental gradients is crucial given accelerating rates of land-cover change and disturbance worldwide. Functional diversity measures the abundance, range and distribution of traits in a community, and links species diversity with ecosystem function. Several studies have related bird or invertebrate FD to environmental gradients, but information on the responses of mammal FD to vegetation structural diversity at scales of management relevance is scarce. We addressed this knowledge gap by examining responses of ground-dwelling mammal FD to vegetation structural complexity in wet (high-productivity) and dry (low-productivity) eucalypt forest in the Otway Ranges, southeast Australia. In dry forest, we expected a positive relationship between FD and vegetation structural complexity because more resources should enable species with a greater diversity of traits to co-exist. We expected negative correlations in wet forest, where competitive dominance may drive a decrease in FD as structural complexity increases. Ground-dwelling mammals were surveyed using camera traps, and we used five traits to construct four FD indices (richness, evenness, divergence, and dispersion). Six vegetation structure variables were used to calculate two indices of vegetation structure, and we used linear mixed models to relate functional diversity and species richness to vegetation structural complexity (the total abundance of structural attributes) and heterogeneity (the level of contrast or patchiness in structure), in wet and dry forest. Camera traps detected ten native ground-dwelling mammal species. All FD indices were positively correlated with vegetation structural complexity, but only functional dispersion responded to structural heterogeneity. Contrary to expectations, relationships between FD and structural complexity were consistent in both forest types, and we suggest that low levels of functional niche occupancy prevented competitive dominance in wet forest. Species richness did not respond to any predictor variables, and is unlikely to be a useful surrogate of ground-dwelling mammal FD. Our results indicate that forest managers may sustain ecosystem functions performed by ground-dwelling mammals by conserving structurally complex vegetation.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 15 February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Forest Ecology and Management, Volume 433〈/p〉 〈p〉Author(s): Gustavo Mariano Rezende, Daniel Luis Mascia Vieira〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Forest regeneration in abandoned pastures in Amazonia has been well studied, but active restoration of non-resilient pastures has not. In this work, we evaluated large-scale active restoration of intensively used pastures in southern Amazonia, where the highest deforestation rates are observed. With the construction of the Jirau Dam in the Madeira river (state of Rondônia, Brazil), a 3000-ha forest buffer zone has been established. This area was previously covered by African pasture grasses for cattle ranching. Eight mixed-species planting sites with variable grass management and ranging from 6 to 60 months post-planting were measured three times over 2.5 years. We also tested a gradient of restoration intensity in an experimental planting: (i) no intervention (control), (ii) harrowing and herbicides to control grasses, and (iii) harrowing and herbicides plus tree planting. Our goals were to understand the initial trajectory of actively restored sites, the role of harrowing and herbicide application in triggering natural regeneration, and the role of seedling planting on the initial vegetation structure. All tree species ≥30 cm in height were sampled in five circular 10-m-radius plots per site. Plant cover was also monitored using the step-point method. At 18 months, stem density ranged from 2500 to 14,490 ind·ha〈sup〉−1〈/sup〉, demonstrating that density increased suddenly in most sites through colonization, although this was highly variable. Tree cover reached 81% in five years, virtually eliminating grass cover after 36 months. Recruits contributed more to basal area than planted seedlings. Although 17 species, on average, were planted in restoration sites, the number of species at the sites steadily increased over time, at a rate of 7 species·yr〈sup〉−1〈/sup〉 per 1570 m〈sup〉2〈/sup〉. 〈em〉Cecropia〈/em〉 spp. and 〈em〉Trema micrantha〈/em〉 recruits had the highest stem densities and basal areas. Harrowing and grass control were enough to trigger succession in sites where natural regeneration was not taking place, shifting these sites to the highly resilient route of early secondary forest succession in the Amazon. Future restoration efforts should use a combination of methods, first evaluating the potential for natural regeneration and then gradually eliminating barriers.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Agricultural and Forest Meteorology, Volume 264〈/p〉 〈p〉Author(s): Ravshan Eshonkulov, Arne Poyda, Joachim Ingwersen, Alim Pulatov, Thilo Streck〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Turbulent fluxes at the land surface measured by the Eddy Covariance (EC) technique are typically considerably less than the difference between net radiation and ground heat flux. This is known as the energy balance closure (EBC) problem. It is crucial for validating land surface models as it provokes substantial uncertainty to the magnitude and partitioning of energy fluxes. The gap in the energy balance calls for searching for additional energy terms in the soil-plant-atmosphere system. To evaluate the contribution of these minor storage terms to the measured EBC, we conducted an experimental study to evaluate the contribution of these minor storage terms to measured EBC in the Kraichgau region in southwest Germany over two consecutive growing seasons (2015 and 2016). The measured and calculated minor storage terms comprised the enthalpy change in the plant canopy (〈em〉S〈sub〉c〈/sub〉〈/em〉), the air enthalpy change (〈em〉S〈sub〉a〈/sub〉〈/em〉), the energy consumption and release by photosynthesis and respiration (〈em〉S〈sub〉p〈/sub〉〈/em〉), and the atmospheric moisture change (〈em〉S〈sub〉q〈/sub〉〈/em〉). Furthermore, the soil heat storage (〈em〉S〈sub〉g〈/sub〉〈/em〉) was determined at different locations within the EC footprint and compared to the single point measurements of 〈em〉S〈sub〉g〈/sub〉〈/em〉 at the EC station. Calorimetric and harmonic analysis were performed to compute ground heat flux. 〈em〉S〈sub〉p〈/sub〉〈/em〉 had the strongest effect in improving EBC due to the high net CO〈sub〉2〈/sub〉 uptake during the productive phase of plant growth. In 2015, all minor storage terms together increased EBC by 5.0% on average, with a maximum value of 7.4% in May, while the improvement in 2016 was 6.8% on average and 8.4% in May. Ground heat flux computed with the harmonic analysis based on plate data narrowed the EBC by 3% more than the calorimetric method. In summary, a better EBC can be achieved by considering minor storage terms and applying a harmonic analysis to ground heat flux data. Regarding future research, we recommend to focus on year-round measurements of energy terms because energy stored during the growing season might be lost from the system during the rest of the year. Nonetheless, the significant contribution of minor energy terms to EBC indicates that turbulent energy fluxes are most likely overestimated when all the missing energy is assumed to be turbulent–the typical approach when fluxes are corrected by the Bowen ratio post-closure method for instance.〈/p〉〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Computers & Geosciences, Volume 122〈/p〉 〈p〉Author(s): Seth Goodman, Ariel BenYishay, Zhonghui Lv, Daniel Runfola〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Interdisciplinary use of geospatial data requires the integration of data from a breadth of sources, and frequently involves the harmonization of different methods of sampling, measurement, and technical data types. These integrative efforts are often inhibited by fundamental geocomputational challenges, including a lack of memory efficient or parallel processing approaches to traditional methods such as zonal statistics. GeoQuery (〈a href="http://geoquery.org/" target="_blank"〉geoquery.org〈/a〉) is a dynamic web application which utilizes a High Performance Computing cluster and novel parallel geospatial data processing methods to overcome these challenges. Through an online interface, GeoQuery users can request geospatial data - which spans categories including geophysical, environmental and social measurements - to be aggregated to user-selected units of analysis (e.g., subnational administrative boundaries). Once a request has been processed, users are provided with permanent links to access their customized data and documentation. Datasets made available through GeoQuery are reviewed, prepared, and provisioned by geospatial data specialists, with processing routines tailored for each dataset. The code used and steps taken while preparing datasets and processing user requests are publicly available, ensuring transparency and replicability of all data and processes. By mediating the complexities of working with geospatial data, GeoQuery reduces the barriers to entry and the related costs of incorporating geospatial data into research across disciplines. This paper presents the technology and methods used by GeoQuery to process and manage geospatial data and user requests.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Computers & Geosciences, Volume 123〈/p〉 〈p〉Author(s): Pouyan Pirnia, François Duhaime, Yannic Ethier, Jean-Sébastien Dubé〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The thermal, mechanical and hydrodynamic behaviour of porous media in geoscience applications is usually modelled through the finite-element (FEM) or finite-difference methods. These continuum models tend to perform poorly when modelling phenomena that are essentially dependent on behaviour at the particle scale or phenomena that are not accurately described by partial differential equations (PDE), such as internal erosion and filtration. The discrete nature of granular materials can be modelled through the discrete-element method (DEM). However, in some instances, DEM models would benefit from an interface with continuum models to solve coupled PDEs or to model phenomena that occur at a different scale. This paper introduces ICY, an interface between COMSOL Multiphysics, a commercial finite-element engine, and YADE, an open-source discrete-element code. The interface is centred on a JAVA class. It was verified using the simple example of a sphere falling in water according to Stokes’ law. For this example, the drag force was calculated in COMSOL and body forces (gravity, buoyancy and drag) on the sphere were summed in YADE. The paper also presents an application example for the interface based on the modelling of internal erosion tests.〈/p〉〈/div〉 〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0098300417313213-fx1.jpg" width="334" alt="Image 1" title="Image 1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 March 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Geoderma, Volume 337〈/p〉 〈p〉Author(s): Yang Ou, Alain N. Rousseau, Lixia Wang, Baixing Yan, Thiago Gumiere, Hui Zhu〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In China, most riparian wetlands have undergone degradation and shrinkage, due to severe droughts or low hydrological connectivity. There are considerable studies focusing on the impact of water level on wetland vegetation; however, changes in the soil components, such as the microbial community, of wetlands following flooding remains unclear. Here, we verified the effects of an extreme flooding event on the soil physicochemical conditions, enzyme activities and soil microbial composition. Overall, we observed that the flooding event impacted the soil properties and modified the enzyme activities. Also, the flooding affected more the biomass than the composition of the soil microbial community. We observed that after the flooding event, manganese (Mn) replaced total nitrogen (TN) as one of the major governing factors of soil enzyme activities. Soil organic carbon (SOC), and pH were also correlated with soil enzyme activities before and after the flooding event. Soil conductivity (EC), C/N ratio, and iron (Fe) contents had a large influence on microbial communities. Nevertheless, the soil C/N ratio was the dominant governing factor of the microbial structure. Therefore, edaphic factors were remarkably related to microbial organisms as flooding was deemed a key driving factor to the linkage between them. The antecedent long-term drought provoked by human disturbance, and subsequent flooding (i.e., re-inundating) may thus damage the soil dynamics of riparian wetlands, and hence, altering the carbon storage capacity. The results of this study suggest that rehabilitating hydrological connectivity and promoting primary succession of vegetation could become effective practices for improving the soil ecosystem of riparian wetlands.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Agricultural and Forest Meteorology, Volume 264〈/p〉 〈p〉Author(s): Adrià Barbeta, J. Julio Camarero, Gabriel Sangüesa-Barreda, Lena Muffler, Josep Peñuelas〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The performance and persistence of rear-edge tree populations are relevant issues for conserving biodiversity because these stands harbor high intraspecific biodiversity and play a key role during periods of climate change. The occurrence of these populations is associated with the influence of heterogeneous topography, creating suitable refugia with regionally rare environmental conditions. Climate is changing at a global-scale, but little is known about the long-term impact on local climatic singularities and the associated taxa. We analyzed tree-ring growth chronologies of the two species (〈em〉Fagus sylvatica〈/em〉 and 〈em〉Quercus ilex〈/em〉) forming the evergreen-deciduous forest ecotone, constitutive of the rear-edge of 〈em〉F. sylvatica〈/em〉 distribution. The study area is a coastal range with frequent fog immersion, which has been hypothesized to favor the persistence of 〈em〉F. sylvatica〈/em〉 in Mediterranean peninsulas. We analyzed the long-term effect of fog on tree growth along a topographical gradient and the sensitivity of growth to rainfall and temperature. The annual number of foggy days has decreased by 62% over the last four decades, concomitant with increasing temperatures. Fog frequency was a relevant factor determining tree growth; fog during summer had positive effects on 〈em〉F. sylvatica〈/em〉 growth mainly through a temperature buffering effect. The positive effect of fog on the growth of 〈em〉Q. ilex〈/em〉, however, was likely caused by a collinearity with rainfall. 〈em〉Q. ilex〈/em〉 growth was less sensitive to climate than 〈em〉F. sylvatica〈/em〉, but growth of both species was enhanced by a positive early-summer water balance. Our results indicate that a decrease in fog frequency and an increase in temperature may generally benefit 〈em〉Q. ilex〈/em〉 in this forest ecotone. Although future changes in rainfall and temperature matter most for the fate of rear-edge tree populations, local climatic singularities such as fog should also be considered. Those can have complementary effects that can swing the balance in ecotones and rear-edge tree populations such as those studied here.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0168192318303447-ga1.jpg" width="269" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Zhi Zhou, Zhaoqun Liu, Lingui Wang, Jian Luo, Hailang Li〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Giant clams are one of the most important animals in coral reef ecosystem, and its growth and reproduction are being threatened by heat stress due to global warming. In the present study, the symbiont density, the crucial enzyme activities and the transcriptome were investigated in the outer mantle of giant clam 〈em〉Tridacna crocea〈/em〉 after the acute exposure of high temperature. The density of symbiotic zooxanthellae decreased significantly during 12–24 h, with the minimum level (7.75 × 10〈sup〉5〈/sup〉 cell cm〈sup〉−2〈/sup〉, 〈em〉p〈/em〉 〈 0.05) at 12 h after heat stress. The activities of superoxide dismutase in the heat stress group was significantly lower than that in the control group at 24 h after heat stress, while no significant change in the activities of catalase was observed during the entire stress process. The activation level of caspase3 began to increase significantly at 12 h (1.22-fold, 〈em〉p〈/em〉 〈 0.05), and reached the highest level at 24 h (1.38-fold, 〈em〉p〈/em〉 〈 0.05) after heat stress. Six paired-end libraries were sequenced in two groups, including the heat stress and control group at 12 h after heat stress. Through the assembling of 187,116,632 paired-end reads with lengths of 2 × 150 bp, a total of 26,676 genes were obtained which derived from giant clam. Bioinformatics analysis revealed 47 significantly upregulated and 88 significantly downregulated genes at 12 h after the treatment. There were 12 overrepresented GO terms for significantly upregulated genes, mostly related to unfolded protein binding and ATP binding, whereas no GO term was overrepresented for significantly downregulated genes. These results collectively suggest high temperature could induce excessive oxidative stress through the repressed antioxidant ability, the apoptosis activated by the unfolded protein response, and further the collapse of the symbiosis between host and symbiont, which has been threatening the growth and reproduction of the giant clam 〈em〉T. crocea〈/em〉.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Zhi-qiang Du, Yue Wang, Hong-yu Ma, Xiu-li Shen, Kai Wang, Jie Du, Xiao-dong Yu, Wen-hong Fang, Xin-cang Li〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Crustins play important roles in defending against bacteria in the innate immunity system of crustaceans. In present study, we identified a crustin gene in 〈em〉Scylla paramamosain〈/em〉, which was named as 〈em〉SpCrus6〈/em〉. The ORF of 〈em〉Sp〈/em〉Crus6 possessed a signal peptide sequence (SPS) at the N-terminus and a WAP domain at the C-terminus. And there were 5 Proline residues, 5 Glycine and 4 Cysteine residues between SPS and WAP domain in 〈em〉Sp〈/em〉Crus6. These features indicated that 〈em〉Sp〈/em〉Crus6 was a new member of crustin family. The 〈em〉SpCrus6〈/em〉 mRNA transcripts were up-regulated obviously after bacteria or virus challenge. These changes showed that 〈em〉SpCrus6〈/em〉 was involved in the antimicrobial and antiviral responses of 〈em〉Scylla paramamosain〈/em〉. Recombinant 〈em〉Sp〈/em〉Crus6 (r〈em〉Sp〈/em〉Crus6) showed strong inhibitory abilities against Gram-positive bacteria (〈em〉Bacillus megaterium〈/em〉, 〈em〉Staphylococcus aureus〈/em〉, and 〈em〉Bacillus subtilis〈/em〉). But the inhibitory abilities against four Gram-negative bacteria (〈em〉Vibrio parahemolyticus〈/em〉, 〈em〉Vibrio alginolyticus〈/em〉, 〈em〉Vibrio harveyi〈/em〉 and 〈em〉Escherichia coli〈/em〉) and two fungi (〈em〉Pichia pastoris〈/em〉 and 〈em〉Candida albicans〈/em〉) were not strong enough. Besides, r〈em〉Sp〈/em〉Crus6 could strongly bind to two Gram-positive bacteria (〈em〉B〈/em〉. 〈em〉subtilis〈/em〉 and 〈em〉B〈/em〉. 〈em〉megaterium〈/em〉) and three Gram-negative bacteria (〈em〉V〈/em〉. 〈em〉alginolyticus〈/em〉, 〈em〉V〈/em〉. 〈em〉parahemolyticus〈/em〉, and 〈em〉V〈/em〉. 〈em〉harveyi〈/em〉). And the binding levels to 〈em〉S. aureus〈/em〉 and two fungi (〈em〉P〈/em〉. 〈em〉pastoris〈/em〉 and 〈em〉C〈/em〉. 〈em〉albicans〈/em〉) were weak. The polysaccharides binding assays’ results showed r〈em〉Sp〈/em〉Crus6 had superior binding activities to LPS, LTA, PGN and 〈em〉β〈/em〉-glucan. Through agglutinating assays, we found r〈em〉Sp〈/em〉Crus6 could agglutinate well three Gram-positive bacteria (〈em〉S〈/em〉. 〈em〉aureus〈/em〉, 〈em〉B〈/em〉. 〈em〉subtilis〈/em〉 and 〈em〉B〈/em〉. 〈em〉megaterium〈/em〉). And the agglutinating activities to Gram-negative bacteria and fungi were not found. In the aspect of antiviral functions, r〈em〉Sp〈/em〉Crus6 could bind specifically to the recombinant envelop protein 26 (rVP26) of white spot syndrome virus (WSSV) but not to recombinant envelop protein 28 (rVP28), whereas GST protein could not bind to rVP26 or rVP28. Besides, r〈em〉Sp〈/em〉Crus6 could suppress WSSV reproduction to some extent. Taken together, 〈em〉Sp〈/em〉Crus6 was a multifunctional immunity effector in the innate immunity defending response of 〈em〉S〈/em〉. 〈em〉paramamosain〈/em〉.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Yunkun Li, Jiayu Wu, Dong Li, Anqi Huang, Guixian Bu, Fengyan Meng, Fanli Kong, Xiaohan Cao, Xingfa Han, Xiaofu Pan, Wei Fan, Shiyong Yang, Xianyin Zeng, Xiaogang Du〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉〈em〉Schizothorax prenanti〈/em〉 (〈em〉S. prenanti〈/em〉), an important species of economical fish in Southwest China, is susceptible to 〈em〉Aeromonas hydrophila〈/em〉 (Ah). To understand the immune response to Ah, the transcriptome profiling of spleen of 〈em〉S. prenanti〈/em〉 was analyzed after Ah infection. A total of 6, 213 different expression genes (DEGs) were obtained, including 3, 066 up-regulated DEGs and 3, 147 down-regulated DEGs. These DEGs were annotated by KEGG and GO databases, so that the immune-related DEGs (IRDs) can be identified and classified. Then, the interesting IRDs were screened to build heat map, and the reliability of the transcriptome data was validated by qPCR. In order to clarify the mechanism of signal transduction in the anti-bacterial immunity, the signaling pathway initiated by TLRs was predicted. In this pathway, TLR25 and TLR5 mediate the NF-κB and AP-1 signals via MyD88-dependent pathway. Meanwhile, the type I IFN (IFNα/β) induced by IRF1 and IRF3/7 may play an important role in the anti-bacterial immunity. In conclusion, this study preliminarily provides insights into the mechanism of signal transduction after Ah infection in 〈em〉S. prenanti〈/em〉, which contributes to exploring the complex anti-bacterial immunity.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Hongye Jiang, Qing Bian, Weiwei Zeng, Pengli Ren, Hengchang Sun, Zhipeng Lin, Zeli Tang, Xinyi Zhou, Qing Wang, Yingying Wang, Yensheng Wang, Mei X. Wu, Xuerong Li, Xinbing Yu, Yan Huang〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Grass carp (〈em〉Ctenopharyngodon idellus〈/em〉) hemorrhagic disease (GCHD), caused by grass carp reovirus (GCRV), has given rise to an enormous loss in grass carp industry during the past years. Up to date, vaccination remained to be the most effective way to protect grass carp from GCHD. Oral vaccination is of major interest due to its advantages of noninvasive, time-saving, and easily-operated. The introduction of oral vaccination has profound impact on aquaculture industry because of its feasibility of extensive application for fish in various size and age. However, the main challenge in developing oral vaccine is that antigens are easily degraded and are easy to induce tolerance. 〈em〉Bacillus subtilis〈/em〉 (〈em〉B. subtilis〈/em〉) spores would be an ideal oral vaccine delivery system for their robust specialty, gene operability, safety and adjuvant property. VP4 protein is the major outer capsid protein encoded by GCRV segment 6 (S6), which plays an important role in viral invasion and replication. In this study, we used 〈em〉B. subtilis〈/em〉 spores as the oral delivery system and successfully constructed the 〈em〉B. subtilis〈/em〉 CotC-VP4 recombinant spores (CotC-VP4 spores) to evaluate its protective efficacy in grass carp. Grass carp orally immunized with CotC-VP4 spores showed a survival rate of 57% and the relative percent survival (RPS) of 47% after the viral challenge. Further, the specific IgM levels in serum and the specific IgZ levels in intestinal mucus were significantly higher in the CotC-VP4 group than those in the Naive group. The immune-related genes including three innate immune-related genes (IL-4/13A, IL-4/13B, CSF1R), four adaptive immune-related genes (BAFF, CD4L, MHC-II, CD8), three inflammation-related genes (IL-1β, TNF-α, TGF-β) and interferon type I (IFN-I) related signaling pathway genes were significantly up-regulated in the CotC-VP4 group. The study demonstrated that the CotC-VP4 spores produced protection in grass carp against GCRV infection, and triggered both innate and adaptive immunity post oral immunization. This work highlighted that 〈em〉Bacillus subtilis〈/em〉 spores were powerful platforms for oral vaccine delivery, and the combination of 〈em〉Bacillus subtilis〈/em〉 spores with GCRV VP4 protein was a promising oral vaccine.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Marine Policy, Volume 99〈/p〉 〈p〉Author(s): Y.W. Bakker, J. de Koning, J. van Tatenhove〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Between 2010 and 2016, the Orkney Islands Council, Highland Council and Marine Scotland have collaborated to develop a pilot Marine Spatial Plan for the Pentland Firth and Orkney Waters in Scotland. This paper explores the challenges of marine spatial planning processes by looking at the possibilities for fisheries communities to mobilize their social capital – in the form of bonding, bridging or linking – in order to re-position and to empower themselves in these processes. This paper aims to uncover the resilience of local communities that deploy social capital in order to influence MSP processes and safeguard their own interests. For this article ten weeks of qualitative fieldwork in the form of in-depth interviews and participant observation with stakeholders of the pilot marine spatial plan were conducted on the Orkney Islands in Scotland. The strong bonding social capital among fishermen in Orkney has resulted in a resilient community identity which allows for collaboration and self-organization, but also creates a defensive mentality which does not favor linking. Furthermore, a lack of trust in governmental authorities inhibits the mobilization of linking social capital among fishermen, obstructing the ability to access power through cross-scale connections. In response the fisheries community uses bridging social capital outside governance arenas to access networks and mobilize resources to strengthen its socio-economic and political position in support of future linking social capital. Researching this complex interrelation and functioning of social capital uncovers some of the social dimensions and socio-institutional constraints for fisheries engagement with and power in marine spatial planning.〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Agriculture, Ecosystems & Environment, Volumes 270–271〈/p〉 〈p〉Author(s): Camilla Lemming, Astrid Oberson, Jakob Magid, Sander Bruun, Charlotte Scheutz, Emmanuel Frossard, Lars Stoumann Jensen〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Phosphorus (P) accumulated in soil after surplus P applications can potentially serve as a P source for subsequent crop production. This study investigated residual P availability after long-term surplus P application with different organic waste products. Topsoil samples from a long-term field trial treated with different types of organic wastes were subjected to P characterization, including determination of total P, water-soluble P, and isotopically exchangeable P pools. The waste products were applied for 12 years before sampling, at rates according to crop nitrogen demand and thus typically in excess of crop P requirements. Residual waste P in soil was determined based on the difference between total soil P measured in the different specific waste-treated plots and a balanced reference treatment. After 12 years of surplus P balance (inputs – crop offtake) of 79–598 kg P ha〈sup〉−1〈/sup〉 yr〈sup〉−1〈/sup〉 with waste, significant amounts of P (636–4177 kg ha〈sup〉−1〈/sup〉) had accumulated in the soil as residual P. The average fraction of residual waste P which could be recovered as rapidly exchangeable P (within 1 min) followed the order: composted household waste P (2.1%) 〈 sewage sludge P (5.1%) 〈 cattle manure P (10.9%), indicating that type of waste has an impact on residual P availability after long-term surplus P application. Unaccounted P (surplus P balance – residual P, i.e., P potentially lost from the topsoil) followed the same order, so compost P was better retained in the soil, but with a less clear difference between sewage sludge and cattle manure. For the latter two wastes, approximately half the surplus P balance could not be accounted for in the topsoil and was assumed to be transported down the soil profile. Three years after waste application was terminated, the fraction of rapidly exchangeable residual P had not declined significantly, suggesting sustained availability of residual P in the soil after long-term application of organic waste. Overall, the availability and mobility of residual P after applying composted household waste to soil was significantly lower than that of residual P from sewage sludge and cattle manure.〈/p〉〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Guang-hua Wang, Jing-jing Wang, Bin Yue, Xue Du, He-he Du, Min Zhang, Yong-hua Hu〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉High-mobility group box 2 (HMGB2) is a non-histone chromosomal protein that involved diverse functions such as transcriptional regulation and innate immune responses in mammalian. In teleost, very limited studies on HMGB2 proteins have been documented. Black rockfish (〈em〉Sebastes schlegelii〈/em〉) is an economic fish species and cultured worldwide. However, the study of black rockfish about immunology is very scarce. In the present study, a HMGB2 homologue gene (〈em〉SsHMGB2〈/em〉) was identified and characterized in black rockfish. The open reading frame of 〈em〉SsHMGB2〈/em〉 is 648 bp, and the deduced amino acid sequence of 〈em〉SsHMGB2〈/em〉 shares 74.4%–91.2% overall sequence identities with the HMGB2 proteins of several fish species. In silico analysis identified several conserved features, including two basic HMG boxes and an acidic C-terminal tail composed of 24 Asp/Glu residues. Expression of 〈em〉SsHMGB2〈/em〉 occurred in multiple tissues and was upregulated during pathogens infection. Recombinant SsHMGB2 (rSsHMGB2) exhibited apparent binding activities against DNA. 〈em〉In vivo〈/em〉 studies showed that the expressions of multiple immune-related genes in head kidney were significantly enhanced when black rockfish were treated with rSsHMGB2. Furthermore, rSsHMGB2 reduced pathogen dissemination and replication in fish kidney and spleen. Taken together, these results suggest that SsHMGB2 possesses apparent immunoregulatory properties and played a role in fighting bacterial infection.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 1 February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 378〈/p〉 〈p〉Author(s): Oscar P. Bruno, Martín Maas〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This paper introduces a fast algorithm, applicable throughout the electromagnetic spectrum, for the numerical solution of problems of scattering by periodic surfaces in two-dimensional space. The proposed algorithm remains highly accurate and efficient for challenging configurations including randomly rough surfaces, deep corrugations, large periods, near grazing incidences, and, importantly, Wood-anomaly resonant frequencies. The proposed approach is based on use of certain “shifted equivalent sources” which enable FFT acceleration of a Wood-anomaly-capable quasi-periodic Green function introduced recently (Bruno and Delourme (2014) [4]). The Green-function strategy additionally incorporates an exponentially convergent shifted version of the classical 〈em〉spectral〈/em〉 series for the Green function. While the computing-cost asymptotics depend on the asymptotic configuration assumed, the computing costs rise at most linearly with the size of the problem for a number of important rough-surface cases we consider. In practice, single-core runs in computing times ranging from a fraction of a second to a few seconds suffice for the proposed algorithm to produce highly-accurate solutions in some of the most challenging contexts arising in applications.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 379〈/p〉 〈p〉Author(s): Denis S. Grebenkov, Sergey D. Traytak〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The generalized method of separation of variables (GMSV) is applied to solve boundary value problems for the Laplace operator in three-dimensional domains with disconnected spherical boundaries (e.g., an arbitrary configuration of non-overlapping partially reactive spherical sinks or obstacles). We consider both exterior and interior problems and all most common boundary conditions: Dirichlet, Neumann, Robin, and conjugate one. Using the translational addition theorems for solid harmonics to switch between the local spherical coordinates, we obtain a semi-analytical expression of the Green function as a linear combination of partial solutions whose coefficients are fixed by boundary conditions. Although the numerical computation of the coefficients involves series truncation and solution of a system of linear algebraic equations, the use of the solid harmonics as basis functions naturally adapted to the intrinsic symmetries of the problem makes the GMSV particularly efficient, especially for exterior problems. The obtained Green function is the key ingredient to solve boundary value problems and to determine various characteristics of stationary diffusion such as reaction rate, escape probability, harmonic measure, residence time, and mean first passage time, to name but a few. The relevant aspects of the numerical implementation and potential applications in chemical physics, heat transfer, electrostatics, and hydrodynamics are discussed.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 31 October 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Geoderma〈/p〉 〈p〉Author(s): Talita R. Ferreira, Luiz F. Pires, Dorthe Wildenschild, André M. Brinatti, Jaqueline A.R. Borges, André C. Auler, Aline M.H. dos Reis〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The hierarchical organization of aggregates in soil is responsible for the presence of inter and intra-aggregate pores. This research aimed to investigate effects of soil surface liming, considering lime rates of 0, 10 and 15 t ha〈sup〉−1〈/sup〉, on the intra-aggregate porous system of soil aggregates with equivalent diameters of 2–4 and 1–2 mm, from 0 to 10 (A) and 10 to 20 cm (B) soil layers. These aggregates were selected by the wet sieving method carried out for determination of the mean weight diameter. Synchrotron-based computed microtomography (μCT) of aggregates was analyzed in terms of porosity, connectivity, tortuosity, and fractal dimension. Additionally, X-ray fluorescence was used to evaluate the elemental composition of the soil aggregates. All liming effects were concentrated at layer A, where calcium percentage was elevated in aggregates from 1–2 mm class as compared to those from 2–4 mm class. Accordingly, the physical parameters studied were generally more affected in the case of smaller aggregates (1–2 mm). Liming decreased total porosity, increased tortuosity of pores, and decreased fractal dimension for 1–2 mm aggregates, which was in line with the fact that larger pores were replaced by smaller ones in 1–2 mm aggregates, as found 〈em〉via〈/em〉 both quantitative and qualitative analyses. On the other hand, liming did not affect pore connectivity under any of the circumstances.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 377〈/p〉 〈p〉Author(s): Samar Chehade, Audrey Kamta Djakou, Michel Darmon, Gilles Lebeau〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Non Destructive Examination (NDE) of industrial structures requires the modeling of specimen geometry echoes generated by the surfaces (entry, backwall …) of inspected blocks. For that purpose, the study of plane wave diffraction by a wedge is of great interest. The work presented here is preliminary research to model the case of an elastic wave diffracted by a wedge in the future, for which there exist various modeling approaches but the numerical aspects have only been developed for wedge angles lower than 〈em〉π〈/em〉. The spectral functions method has previously been introduced to solve the 2D diffraction problem of an immersed elastic wedge for angles lower than 〈em〉π〈/em〉. As a first step, the spectral functions method has been developed here for the diffraction on an acoustic wave by a stress-free wedge, in 2D and for any wedge angle, before studying the elastic wave diffraction from a wedge. In this method, the solution to the diffraction problem is expressed in terms of two unknown functions called the spectral functions. These functions are computed semi-analytically, meaning that they are the sum of two terms. One of them is determined exactly and the other is approached numerically, using a collocation method. A successful numerical validation of the method for all wedge angles is proposed, by comparison with the GTD (Geometrical Theory of Diffraction) solution derived from the exact Sommerfeld integral.〈/p〉〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Sai-Wei Chen, Chun-Hung Liu, Shao-Yang Hu〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Bacteria-induced diseases are a major cause of mortality in aquaculture. Probiotics have commonly been used to replace antibiotics for prophylactic biocontrol in aquaculture. In the present study, 〈em〉Paenibacillus ehimensis〈/em〉 NPUST1 was isolated from a tilapia culture pond. This probiotic has bacteriocin-like activities against 〈em〉Aeromonas hydrophila〈/em〉 and was characterized by biochemical analysis and 16S rDNA sequencing. The physiochemical properties of a crude extract of the bacteriocin-like substance revealed low pH and high thermal tolerance. The substance exhibited broad-spectrum antimicrobial activity against diverse aquatic pathogens, food spoilage, clinical pathogens, and plant pathogens. The effect of dietary supplementation with 〈em〉P. ehimensis〈/em〉 NPUST1 was evaluated in regard to the growth of Nile tilapia (〈em〉Oreochromis niloticus〈/em〉) and immunity against pathogenic infection. The results showed significantly increased weight gain (WG), feed conversion ratio (FCR), and feed efficiency (FE) in Nile tilapia fed 〈em〉P. ehimensis〈/em〉 NPUST1 for 2 months compared with fish fed a control diet. When challenged with 〈em〉A. hydrophila〈/em〉 and 〈em〉S. iniae,〈/em〉 the fish fed 〈em〉P. ehimensis〈/em〉 NPUST1 also exhibited a higher survival rate than fish fed the control diet. The immune parameters revealed that the 〈em〉P. ehimensis〈/em〉 NPUST1-fed fish had significantly higher phagocytic activity, respiratory burst, and superoxide dismutase (SOD) of the head kidney leukocytes, as well as higher serum lysozyme activity and expression of cytokines TNF-α and IL-1β than the fish fed the control diet. These results indicate that dietary supplementation with 〈em〉P. ehimensis〈/em〉 NPUST1 improved the growth performance, immunity, and disease resistance in Nile tilapia.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Cheng-cai Zheng, Xin-yi Cai, Meng-meng Huang, Idefonce Mkingule, Cong Sun, Shi-Chao Qian, Zhen-ju Wu, Bing-nan Han, Hui Fei〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Japanese eel (〈em〉Anguilla japonica〈/em〉) has become a commercially important fish species all over the world. High-density aquaculture has led to congestion and contributed to bacterial infection outbreaks that have caused high mortality. Therefore a 56-days feeding trial was conducted to determine the effects of dietary 〈em〉Bacillus amyloliquefaciens〈/em〉 (GB-9) and 〈em〉Yarrowia lipolytica〈/em〉 lipase2 (YLL2) on growth performance, digestive enzymes activity, innate immunity and resistance to pathogens of 〈em〉A. japonica〈/em〉. Fish growth performance was significantly affected by dietary YLL2 supplementation but not by GB-9. Fish fed diets with YLL2 at 2.0 g/kg diet in combination of high and low levels of GB-9 (5.0 g/kg and 2.0 g/kg) produced the highest growth. For digestive enzyme, lipase and trypsin activities was promoted by dietary containing YLL2, while amylase activities was increased by dietary containing YLL2, GB-9 single or combination. For innate immunity, the mucus lysozyme activity, leukocytes phagocytosis activity and reactive oxygen species level of skin, peroxidase and lysozyme activity of serum were enhanced in fish fed with GB-9 compared to those in control group (p 〈 0.05). The highest resistance to 〈em〉Vibrio anguillarum〈/em〉 and 〈em〉Aeromonas hydrophila〈/em〉 was determined in fish fed with 5.0 g kg〈sup〉−1〈/sup〉 GB-9 + 2.0 g/kg YLL2. This study demonstrated that GB-9 and YLL2 enhanced non-specific immune defense system of 〈em〉A. japonica〈/em〉, providing them with higher resistance to pathogens. The present results suggested that the combination of these supplements could be considered as potential biological additives for aquaculture farmed fish.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Xianyong Bu, Xuqiu Lian, Yi Wang, Chengzeng Luo, Shengqiang Tao, Yilu Liao, Jiaming Yang, Aijing Chen, Yuhong Yang〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The aim of the present study was to investigate effects of dietary yeast culture on immune response related to TLR2-MyD88-NF-kβ signaling pathway, antioxidant capability and disease resistance against 〈em〉Aeromonas hydrophila〈/em〉 for Ussuri catfish (〈em〉Pseudobagrus ussuriensis〈/em〉). A total of 240 Ussuri catfish (mean weight of 7.39 ± 0.32 g) were randomly distributed into four groups that fed diets containing 0 (Y0), 10 (Y1), 20 (Y2) and 30 (Y3) g kg〈sup〉−1〈/sup〉 yeast culture for 8 weeks. The results indicated that dietary 10 g kg〈sup〉−1〈/sup〉 yeast culture supplementation significantly down-regulated mRNA levels of TLR2, MyD88, NF-kβ p65, IL-1β and IL-8 in the liver tissue compared with the control group (〈em〉P〈/em〉 〈 0.05). Simultaneously, serum lysozyme (LZM) activity, respiratory burst activity (RBA) of phagocytes, plasma alkaline phosphatase (AKP) activity and immunoglobulin M (IgM) content were significantly improved in fish fed Y1 diet (〈em〉P〈/em〉 〈 0.05). Fish fed Y1 diet had significantly higher serum alternative complement pathway activity (ACH50) and plasma complement 3 (C3) content than the Y3 group (〈em〉P〈/em〉 〈 0.05). However, no significant differences were observed in plasma acid phosphatase (ACP) activity and complement 4 (C4) content among the groups (〈em〉P〈/em〉 〉 0.05). Fish cumulative mortality rate (CMR) in the Y1 and Y2 groups were significantly lower than that in Y0 and Y3 groups (〈em〉P〈/em〉 〈 0.05), and the lowest CMR was observed in the Y1 group after challenge by 〈em〉A. hydrophila〈/em〉. The highest hepatic superoxide dismutase and glutathione peroxidase activities, total antioxidant capacity and the lowest malondialdehyde content were found in Y1 group, but no significant difference was found in hepatic catalase activity among the groups (〈em〉P〈/em〉 〉 0.05). These results demonstrate that dietary 10 g kg〈sup〉−1〈/sup〉 yeast culture could effectively improve the immunity, antioxidant capability and disease resistance against 〈em〉A. hydrophila〈/em〉 for Ussuri catfish and could down-regulate the mRNA expression levels of pro-inflammatory cytokines modulated by TLR2-MyD88-NF-kβ signaling pathway.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Tao Wang, Xin Wen, Yadong Hu, Xinyu Zhang, Dan Wang, Shaowu Yin〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Copper nanoparticles (Cu NPs) are a new pollutant in aquaculture, representing a hazard to aquatic organisms. We investigated the effects of Cu NPs exposure on oxidative stress, apoptosis and immune response in an economically important model species, 〈em〉Takifugu fasciatus〈/em〉. The juvenile fish were exposed to control, 20 or 100 μg Cu NPs/L for 30 days. The growth of 〈em〉T. fasciatus〈/em〉 was inhibited after Cu NPs exposure. Copper accumulation in liver increased with increasing Cu NPs dose. Oxidative stress indicators [malondialdehyde (MDA), total superoxide dismutase (T-SOD), catalase (CAT) and glutathione (GSH)], apoptosis index and activities of caspases (caspase-3, caspase-9) were all increased with the increase of Cu NPs concentration in liver. With an increase in Cu NPs dose, the activities of succinate dehydrogenase (SDH) and Na〈sup〉+〈/sup〉-K〈sup〉+〈/sup〉-ATPase as well as cytochrome c (Cyt-c) concentration in mitochondria decreased, accompanied by increased Cyt-c concentration in cytosol. Apoptosis-related gene expressions of 〈em〉p53〈/em〉, 〈em〉caspase-3〈/em〉, 〈em〉caspase-9〈/em〉 and 〈em〉Bax〈/em〉 were increased with the increase of Cu NPs dose. However, the opposite result was found in 〈em〉Bcl2〈/em〉 expression. The physiological indicators of immune response [heat shock protein 70 (HSP70), heat shock protein 90 (HSP90), immunoglobulin M (IgM) and lysozyme (LZM)] as well as the mRNA levels of 〈em〉HSP70〈/em〉, 〈em〉HSP90〈/em〉, 〈em〉IgM〈/em〉 and 〈em〉C-LZM〈/em〉 were all increased after Cu NPs exposure〈em〉.〈/em〉 Our results will be helpful in understanding the mechanism of Cu NPs toxicity in 〈em〉T. fasciatus〈/em〉.〈/p〉〈/div〉 〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S1050464818306867-fx1.jpg" width="278" alt="Image 1" title="Image 1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Forest Ecology and Management, Volume 433〈/p〉 〈p〉Author(s): James M. Dyer, Todd F. Hutchinson〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉When public lands were surveyed in the U.S., “witness trees” were often recorded to facilitate the relocation of property boundaries, and these records provide a snapshot of forest conditions prior to Euro-American settlement and land clearing. This study utilizes witness trees and present-day plot data to explore long-term vegetation changes at a regional scale. Landscape classes for a 5000 km〈sup〉2〈/sup〉 study area in Appalachian Ohio were defined by slope, aspect, topographic position, soil pH, and available water capacity. Cluster analysis and ordination revealed topo-edaphic patterns in the presettlement (c. 1800) and present-day forests, based on 5765 witness trees and 3249 contemporary trees occurring on 547 Forest Inventory and Analysis (FIA) subplots. Mesophication is evident, as the oak-hickory presettlement forest is now dominated by maple-poplar. Size-class analysis suggests the presettlement forest also experienced mesophication following xeric conditions of the preceding centuries. In both presettlement and contemporary forests, ridges form distinctive communities compared to slopes and valleys, although topographic distinctiveness is now more prevalent. Several taxa revealed changes in site affinities over the past two centuries; shifts in their realized niches suggest mesophication acts through diverse individualistic responses to a multiple set of interacting drivers. Specifically, regionally documented changes in land use, drought, N deposition, and fire at the time of the original surveys lead to altered competitive relationships.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 15 February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Forest Ecology and Management, Volume 433〈/p〉 〈p〉Author(s): Paula García-Llamas, Susana Suárez-Seoane, Angela Taboada, Alfonso Fernández-Manso, Carmen Quintano, Víctor Fernández-García, José Manuel Fernández-Guisuraga, Elena Marcos, Leonor Calvo〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The increasing occurrence of large and severe fires in Mediterranean forest ecosystems produces major ecological and socio-economic damage. In this study, we aim to identify the main environmental factors driving fire severity in extreme fire events in 〈em〉Pinus〈/em〉 fire prone ecosystems, providing management recommendations for reducing fire effects. The study case was a megafire (11,891 ha) that occurred in a Mediterranean ecosystem dominated by 〈em〉Pinus pinaster〈/em〉 Aiton in NW Spain. Fire severity was estimated on the basis of the differenced Normalized Burn Ratio from Landsat 7 ETM +, validated by the field Composite Burn Index. Model predictors included pre-fire vegetation greenness (normalized difference vegetation index and normalized difference water index), pre-fire vegetation structure (canopy cover and vertical complexity estimated from LiDAR), weather conditions (spring cumulative rainfall and mean temperature in August), fire history (fire-free interval) and physical variables (topographic complexity, actual evapotranspiration and water deficit). We applied the Random Forest machine learning algorithm to assess the influence of these environmental factors on fire severity. Models explained 42% of the variance using a parsimonious set of five predictors: NDWI, NDVI, time since the last fire, spring cumulative rainfall, and pre-fire vegetation vertical complexity. The results indicated that fire severity was mostly influenced by pre-fire vegetation greenness. Nevertheless, the effect of pre-fire vegetation greenness was strongly dependent on interactions with the pre-fire vertical structural arrangement of vegetation, fire history and weather conditions (i.e. cumulative rainfall over spring season). Models using only physical variables exhibited a notable association with fire severity. However, results suggested that the control exerted by the physical properties may be partially overcome by the availability and structural characteristics of fuel biomass. Furthermore, our findings highlighted the potential of low-density LiDAR for evaluating fuel structure throughout the coefficient of variation of heights. This study provides relevant keys for decision-making on pre-fire management such as fuel treatment, which help to reduce fire severity.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 15 February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Forest Ecology and Management, Volume 433〈/p〉 〈p〉Author(s): Teresa Calvão, Cláudio M. Duarte, Carla S. Pimentel〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉 〈h6〉Context〈/h6〉 〈p〉The pinewood nematode, 〈em〉Bursaphelenchus xylophilus〈/em〉, has been identified as being responsible for the decline of pine forests in Portugal, since its detection in the territory about 20 years ago. Forest decline due to disease and/or pests is a complex phenomenon, and a knowledge of the spatial patterns of tree mortality is important for providing an understanding of forest susceptibility and pest dynamics.〈/p〉 〈/div〉 〈div〉 〈h6〉Objectives〈/h6〉 〈p〉The aim of the present study was to investigate the relationship between the spatial structure of pine mortality and that of different climatic, edaphic and landscape variables in an area of Portugal where 〈em〉B. xylophilus〈/em〉 is known to have spread during the last decade.〈/p〉 〈/div〉 〈div〉 〈h6〉Methods〈/h6〉 〈p〉Pine mortality was assessed in the field, in a large, complex area of Central-North Portugal. An ArcGis database with a range of environmental variables was created for the study area. Spatial autocorrelation of the different variables was investigated by means of Moran’s I and Mantel r analysis. The relationship between pine decline and the different variables was analyzed using bivariate Moran’s I.〈/p〉 〈/div〉 〈div〉 〈h6〉Results〈/h6〉 〈p〉Environmental descriptors exhibit a clear spatial pattern, influenced by an undulating landscape. Pine mortality is spatially aggregated; warm, dry locations with higher evapotranspiration present high values, and in areas of extensive pine occupancy in a diverse landscape mortality decreases.〈/p〉 〈/div〉 〈div〉 〈h6〉Conclusions〈/h6〉 〈p〉Forest mortality attributed to infestation by a non-native forest pathogen cannot be dissociated from the effects of climate and landscape diversity associated with pine forests. The analysis of landscape patterns appears to be crucial for gaining an understanding of forest pathology and decline.〈/p〉 〈/div〉 〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Agricultural and Forest Meteorology, Volume 264〈/p〉 〈p〉Author(s): Nina Pirttioja, Taru Palosuo, Stefan Fronzek, Jouni Räisänen, Reimund P. Rötter, Timothy R. Carter〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉Conventional methods of modelling impacts of future climate change on crop yields often rely on a limited selection of projections for representing uncertainties in future climate. However, large ensembles of climate projections offer an opportunity to estimate yield responses probabilistically. This study demonstrates an approach to probabilistic yield estimation using impact response surfaces (IRSs). These are constructed from a set of sensitivity simulations that explore yield responses to a wide range of changes in temperature and precipitation. Options for adaptation and different levels of future atmospheric carbon dioxide concentration [CO〈sub〉2〈/sub〉] defined by representative concentration pathways (RCP4.5 and RCP8.5) were also considered. Model-based IRSs were combined with probabilistic climate projections to estimate impact likelihoods for yields of spring barley (〈em〉Hordeum vulgare〈/em〉 L.) in Finland during the 21〈sup〉st〈/sup〉 century. Probabilistic projections of climate for the same RCPs were overlaid on IRSs for corresponding [CO〈sub〉2〈/sub〉] levels throughout the century and likelihoods of yield shortfall calculated with respect to a threshold mean yield for the baseline (1981–2010).〈/p〉 〈p〉Results suggest that cultivars combining short pre- and long post-anthesis phases together with earlier sowing dates produce the highest yields and smallest likelihoods of yield shortfall under future scenarios. Higher [CO〈sub〉2〈/sub〉] levels generally compensate for yield losses due to warming under the RCPs. Yet, this does not happen fully under the more moderate warming of RCP4.5 with a weaker rise in [CO〈sub〉2〈/sub〉], where there is a chance of yield shortfall throughout the century. Under the stronger warming but more rapid [CO〈sub〉2〈/sub〉] increase of RCP8.5, the likelihood of yield shortfall drops to zero from mid-century onwards.〈/p〉 〈p〉Whilst the incremental IRS-based approach simplifies the temporal and cross-variable complexities of projected climate, it was found to offer a close approximation of evolving future likelihoods of yield impacts in comparison to a more conventional scenario-based approach. The IRS approach is scenario-neutral and existing plots can be used in combination with any new scenario that falls within the sensitivity range without the need to perform new runs with the impact model. A single crop model is used for demonstration, but an ensemble IRS approach could additionally capture impact model uncertainties.〈/p〉 〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0168192318303241-ga1.jpg" width="355" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Computers & Geosciences, Volume 123〈/p〉 〈p〉Author(s): Timothy J. Naegeli, Jason Laura〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In this paper we present an extension to the Large Crater Clustering (LCC) tool set which places a cone of uncertainty around the trajectories of secondary impact craters to determine potential locations of source craters. The LCC tool set was a first step in the spatial quantification of primary and secondary cratering processes, which allows planetary geologists to accurately estimate the geologic age of a celestial surface. This work builds on the LCC tool set by accounting for the ambiguity of flight path trajectories through a Python script that leverages ArcGIS's ArcPy library. We chronicle the mechanics of the script, which creates geodetically correct cones then counts them within equally sized cells of a vector grid. We describe the process that was used to derive the shape of the cone and provide parameters for the sizes of the cones and the grid. We demonstrate that the cone of uncertainty has the ability to compensate for error in secondary crater trajectories by introducing deviation in the trajectory bearing and comparing the predicted primary crater location. We use two study areas on Mars as well as the entire lunar surface to illustrate the usefulness of the extension as an aid to human interpretation of back-projections.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Junguo Ma, Xi Chen, Guangyuan Xin, Xiaoyu Li〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The present study aimed to determine the chronic toxicity of 1-methyl-3-octylimidazolium bromide ([C〈sub〉8〈/sub〉mim]Br) on the silver carp to further reveal the toxicological mechanisms of ionic liquids. Chronic exposure of silver carp to [C〈sub〉8〈/sub〉mim]Br at concentrations of 1.095 and 4.380 mg/L for 60 d was conducted under laboratory conditions. The results revealed that chronic exposure to [C〈sub〉8〈/sub〉mim]Br inhibited the activity of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) and reduced glutathione (GSH) levels while markedly increasing malondialdehyde (MDA) and protein carbonyl (PC) levels in fish spleen, indicating that [C〈sub〉8〈/sub〉mim]Br treatment induced oxidative stress. Additionally, long-term exposure to [C〈sub〉8〈/sub〉mim]Br markedly upregulated the expressions of nuclear factor-κB (NF-κB), inducible nitric oxide synthase (iNOS), interleukin-1β (IL-1β), IL-6, tumour necrosis factor-α (TNF-α), and interferon-γ (IFN-γ); altered the levels of transforming growth factor-β (TGF-β); and increased the mRNA levels of p38MAPK, c-fos, c-jun, and c-myc, suggesting that long-term exposure to [C〈sub〉8〈/sub〉mim]Br might promote the inflammatory response in fish spleen and that p38MAPK/NF-κB signalling may potentially be involved in this process. Moreover, [C〈sub〉8〈/sub〉mim]Br-exposure altered lysozyme activity and complement 3 (C3) and immunoglobulin M (IgM) content, indicating that chronic [C〈sub〉8〈/sub〉mim]Br exposure also has immunotoxic effects on silver carp. Furthermore, we also found that [C〈sub〉8〈/sub〉mim]Br exposure reduced miR-125b levels, altered miR-143 levels, and upregulated miR-155 and miR-21 levels, suggesting that these miRNAs may be involved in the [C〈sub〉8〈/sub〉mim]Br-induced inflammatory response in fish spleen. In summary, the present study indicates that chronic exposure to [C〈sub〉8〈/sub〉mim]Br induces inflammation in fish spleen and that oxidative stress-mediated p38MAPK/NF-κB signalling and miRNAs may play a key role in this process.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Chaozheng Li, Shaoping Weng, Jianguo He〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉As invertebrates, shrimps rely on multiple innate defense reactions, including humoral immunity and cellular immunity to recognize and eliminate various invaders, such as viruses. White spot syndrome virus (WSSV) causes the most prevalent and devastating viral disease in penaeid shrimps, which are the most widely cultured species in the coastal waters worldwide. In the last couple of decades, studies about WSSV implicate a dual role of the immune system in protecting shrimps against the infection; these studies also explore on the pathogenesis of WSSV infection. Herein, we review our current knowledge of the innate immune responses of shrimps to WSSV, as well as the molecular mechanisms used by this virus to evade host immune responses or actively subvert them for its own benefit. Deciphering the interactions between WSSV and the shrimp host is paramount to understanding the mechanisms that regulate the balance between immune-mediated protection and pathogenesis during viral infection and to the development of a safe and effective WSSV defensive strategy.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 377〈/p〉 〈p〉Author(s): Hong Fang, Yikun Hu, Caihui Yu, Ming Tie, Jie Liu, Chunye Gong〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The mesh deformation method based on radial basis functions (RBF) has many advantages and is widely used. RBF based mesh deformation method mainly has two steps: data reduction and displacement interpolation. The data reduction step includes solving interpolation weight coefficients and searching for the node with the maximum interpolation error. The data reduction schemes based on greedy algorithm is used to select an optimum reduced set of surface mesh nodes. In this paper, a parallel mesh deformation method based on parallel data reduction and displacement interpolation is proposed. The proposed recurrence Choleskey decomposition method (RCDM) can decrease the computational cost of solving interpolation weight coefficients from 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.gif" overflow="scroll"〉〈mi〉O〈/mi〉〈mrow〉〈mo stretchy="true"〉(〈/mo〉〈msubsup〉〈mrow〉〈mi〉N〈/mi〉〈/mrow〉〈mrow〉〈mi〉c〈/mi〉〈/mrow〉〈mrow〉〈mn〉4〈/mn〉〈/mrow〉〈/msubsup〉〈mo stretchy="true"〉)〈/mo〉〈/mrow〉〈/math〉 to 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si2.gif" overflow="scroll"〉〈mi〉O〈/mi〉〈mrow〉〈mo stretchy="true"〉(〈/mo〉〈msubsup〉〈mrow〉〈mi〉N〈/mi〉〈/mrow〉〈mrow〉〈mi〉c〈/mi〉〈/mrow〉〈mrow〉〈mn〉3〈/mn〉〈/mrow〉〈/msubsup〉〈mo stretchy="true"〉)〈/mo〉〈/mrow〉〈/math〉, where 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si3.gif" overflow="scroll"〉〈msub〉〈mrow〉〈mi〉N〈/mi〉〈/mrow〉〈mrow〉〈mi〉c〈/mi〉〈/mrow〉〈/msub〉〈/math〉 denotes the number of support nodes. The technology of parallel computing is used to accelerate the searching for the node with the maximum interpolation error and displacement interpolation. The combination of parallel data reduction and parallel interpolation can greatly improve the efficiency of mesh deformation. Two typical deformation problems of the ONERA M6 and DLR-F6 wing-body-Nacelle-Pylon configuration are taken as the test cases to validate the proposed approach and can get up to 19.57 times performance improvement with the proposed approach. Finally, the aeroelastic response of HIRENASD wing-body configuration is used to verify the efficiency and robustness of the proposed method.〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): Daniil Bochkov, Frederic Gibou〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We present two finite volume schemes to solve a class of Poisson-type equations subject to Robin boundary conditions in irregular domains with 〈em〉piecewise smooth〈/em〉 boundaries. The first scheme results in a symmetric linear system and produces second-order accurate numerical solutions with first-order accurate gradients in the 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.gif" overflow="scroll"〉〈msup〉〈mrow〉〈mi〉L〈/mi〉〈/mrow〉〈mrow〉〈mo〉∞〈/mo〉〈/mrow〉〈/msup〉〈/math〉-norm (for solutions with two bounded derivatives). The second scheme is nonsymmetric but produces second-order accurate numerical solutions as well as second-order accurate gradients in the 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.gif" overflow="scroll"〉〈msup〉〈mrow〉〈mi〉L〈/mi〉〈/mrow〉〈mrow〉〈mo〉∞〈/mo〉〈/mrow〉〈/msup〉〈/math〉-norm (for solutions with three bounded derivatives). Numerical examples are given in two and three spatial dimensions.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 19 October 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics〈/p〉 〈p〉Author(s): Mandeep Deka, Shuvayan Brahmachary, Ramakrishnan Thirumalaisamy, Amaresh Dalal, Ganesh Natarajan〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We describe a new and simple strategy based on the Gauss divergence theorem for obtaining centroidal gradients on unstructured meshes. Unlike the standard Green–Gauss (SGG) reconstruction which requires face values of quantities whose gradients are sought, the proposed approach reconstructs the gradients using the normal derivative(s) at the faces. The new strategy, referred to as the Modified Green–Gauss (MGG) reconstruction results in consistent gradients which are at least first-order accurate on arbitrary polygonal meshes. We show that the MGG reconstruction is linearity preserving independent of the mesh topology and retains the consistent behaviour of gradients even on meshes with large curvature and high aspect ratios. The gradient accuracy in MGG reconstruction depends on the accuracy of discretisation of the normal derivatives at faces and this necessitates an iterative approach for gradient computation on non-orthogonal meshes. Numerical studies on different mesh topologies demonstrate that MGG reconstruction gives accurate and consistent gradients on non-orthogonal meshes, with the number of iterations proportional to the extent of non-orthogonality. The MGG reconstruction is found to be consistent even on meshes with large aspect ratio and curvature with the errors being lesser than those from linear least-squares reconstruction. A non-iterative strategy in conjunction with MGG reconstruction is proposed for gradient computations in finite volume simulations that achieves the accuracy and robustness of MGG reconstruction at a cost equivalent to that of SGG reconstruction. The efficacy of this strategy for fluid flow problems is demonstrated through numerical investigations in both incompressible and compressible regimes. The MGG reconstruction may, therefore, be viewed as a novel and promising blend of least-squares and Green–Gauss based approaches which can be implemented with little effort in open-source finite-volume solvers and legacy codes.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 18 July 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics〈/p〉 〈p〉Author(s): Marvin Bohm, Andrew R. Winters, Gregor J. Gassner, Dominik Derigs, Florian Hindenlang, Joachim Saur〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉The first paper of this series presents a discretely entropy stable discontinuous Galerkin (DG) method for the resistive magnetohydrodynamics (MHD) equations on three-dimensional curvilinear unstructured hexahedral meshes. Compared to other fluid dynamics systems such as the shallow water equations or the compressible Navier–Stokes equations, the resistive MHD equations need special considerations because of the divergence-free constraint on the magnetic field. For instance, it is well known that for the symmetrization of the ideal MHD system as well as the continuous entropy analysis a non-conservative term proportional to the divergence of the magnetic field, typically referred to as the Powell term, must be included. As a consequence, the mimicry of the continuous entropy analysis in the discrete sense demands a suitable DG approximation of the non-conservative terms in addition to the ideal MHD terms.〈/p〉 〈p〉This paper focuses on the 〈em〉resistive〈/em〉 MHD equations: Our first contribution is a proof that the resistive terms are symmetric and positive-definite when formulated in entropy space as gradients of the entropy variables, which enables us to show that the entropy inequality holds for the resistive MHD equations. This continuous analysis is the key for our DG discretization and guides the path for the construction of an approximation that discretely mimics the entropy inequality, typically termed 〈em〉entropy stability〈/em〉. Our second contribution is a detailed derivation and analysis of the discretization on three-dimensional curvilinear meshes. The discrete analysis relies on the summation-by-parts property, which is satisfied by the DG spectral element method (DGSEM) with Legendre–Gauss–Lobatto (LGL) nodes. Although the divergence-free constraint is included in the non-conservative terms, the resulting method has no particular treatment of the magnetic field divergence errors, which might pollute the solution quality. Our final contribution is the extension of the standard resistive MHD equations and our DG approximation with a divergence cleaning mechanism that is based on a generalized Lagrange multiplier (GLM).〈/p〉 〈p〉As a conclusion to the first part of this series, we provide detailed numerical validations of our DGSEM method that underline our theoretical derivations. In addition, we show a numerical example where the entropy stable DGSEM demonstrates increased robustness compared to the standard DGSEM.〈/p〉 〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): James F. Kelly, Harish Sankaranarayanan, Mark M. Meerschaert〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This paper develops appropriate boundary conditions for the two-sided fractional diffusion equation, where the usual second derivative in space is replaced by a weighted average of positive (left) and negative (right) fractional derivatives. Mass preserving, reflecting boundary conditions for two-sided fractional diffusion involve a balance of left and right fractional derivatives at the boundary. Stable, consistent explicit and implicit Euler methods are detailed, and steady state solutions are derived. Steady state solutions for two-sided fractional diffusion equations using both Riemann–Liouville and Caputo flux are computed. For Riemann–Liouville flux and reflecting boundary conditions, the steady-state solution is singular at one or both of the end-points. For Caputo flux and reflecting boundary conditions, the steady-state solution is a constant function. Numerical experiments illustrate the convergence of these numerical methods. Finally, the influence of the reflecting boundary on the steady-state behavior subject to both the Riemann–Liouville and Caputo fluxes is discussed.〈/p〉〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): N. Saini, C. Kleinstreuer〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉All natural and a growing number of manufactured solid particles are non-spherical. Interesting fluid–particle dynamics applications include the transport of granular material, piling of seeds or grains, inhalation of toxic aerosols, use of nanofluids for enhanced cooling or improved lubrication, and optimal drug-targeting of tumors. A popular approach for computer simulations of such scenarios is the multi-sphere (MS) method, where any non-spherical particle is represented by an assemblage of spheres. However, the MS approach may lead to multiple sphere-to-sphere contact points during collision, and subsequently to erroneous particle transport and deposition. In cases where non-spherical particles can be approximated as ellipsoids with arbitrary aspect ratios, a new theory for particle transport, collision and wall interaction is presented which is more accurate computationally and more efficient than the MS method. In general, with the new ellipsoidal particle interaction (EPI) model, contact points and planes of ellipsoids, rather than spheres, are obtained based on a geometric potential algorithm. Then, interaction forces and torques of the colliding particles are determined via inscribed ‘pseudo-spheres’, employing the soft-particle approach. The off-center forces and moments are then transferred to the mass center of the ellipsoids to solve the appropriate translatory and angular equations of motion. Considering ellipses to illustrate the workings and predictive power of the new collision model, turbulent fluid–particle flow with the EPI model in a 2-D channel is simulated and compared with 3-D numerical benchmark results which relied on the MS method. The 2-D concentrations of micron particles with different aspect ratios matched closely with the 3-D cases. However, interesting differences occurred when comparing the particle-velocity profiles for which the 2-D EPI model generated somewhat larger particle velocities due to out-of-plane collisions, slightly higher particle–wall interactions, and two-way coupling effects.〈/p〉〈/div〉

Description: 〈p〉Publication date: January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Fish & Shellfish Immunology, Volume 84〈/p〉 〈p〉Author(s): Xin Zhang, Jialong Shi, Yulong Sun, Yusuf Jibril Habib, Huiping Yang, Ziping Zhang, Yilei Wang〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In recent years, the abalone aquaculture industry has been threatened by the deteriorating environmental conditions, such as hypoxia and thermal stress in the hot summers. It is necessary to investigate the molecular mechanism in response to these environmental challenges, and subsequently understand the immune defense system. In this study, the transcriptome profiles by RNA-seq of hemocytes from the small abalone 〈em〉Haliotis diversicolor〈/em〉 after exposure to hypoxia, thermal stress, and hypoxia plus thermal stress were established. A total of 103,703,074 clean reads were obtained and 99,774 unigenes were assembled. Of the 99,774 unigenes, 47,154 and 20,455 had homologous sequences in the Nr and Swiss-Prot protein databases, while 16,944 and 10,840 unigenes could be classified by COG or KEGG databases, respectively. RNAseq analysis revealed that the differentially expressed genes (DEGs) after challenges of hypoxia, thermal stress, or hypoxia plus thermal stress were 24,189, 29,165 and 23,665, among which more than 3000 genes involved in at least 230 pathways, including several classical immune-related pathways. The genes and pathways that were involved in immune response to hypoxia/thermal challenges were identified by transcriptome analysis and further validated by quantitative real-time PCR and RNAi technology. The findings in this study can provide information on 〈em〉H. diversicolor〈/em〉 innate immunity to improve the abalone aquaculture industry, and the analysis of the potential immune-related genes in innate immunity signaling pathways and the obtained transcriptome data can provide an invaluable genetic resource for the study of the genome and functional genes.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 1 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 376〈/p〉 〈p〉Author(s): Kyongmin Yeo, Igor Melnyk〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We present a deep learning model, DE-LSTM, for the simulation of a stochastic process with an underlying nonlinear dynamics. The deep learning model aims to approximate the probability density function of a stochastic process via numerical discretization and the underlying nonlinear dynamics is modeled by the Long Short-Term Memory (LSTM) network. It is shown that, when the numerical discretization is used, the function estimation problem can be solved by a multi-label classification problem. A penalized maximum log likelihood method is proposed to impose a smoothness condition in the prediction of the probability distribution. We show that the time evolution of the probability distribution can be computed by a high-dimensional integration of the transition probability of the LSTM internal states. A Monte Carlo algorithm to approximate the high-dimensional integration is outlined. The behavior of DE-LSTM is thoroughly investigated by using the Ornstein–Uhlenbeck process and noisy observations of nonlinear dynamical systems; Mackey–Glass time series and forced Van der Pol oscillator. It is shown that DE-LSTM makes a good prediction of the probability distribution without assuming any distributional properties of the stochastic process. For a multiple-step forecast of the Mackey–Glass time series, the prediction uncertainty, denoted by the 95% confidence interval, first grows, then dynamically adjusts following the evolution of the system, while in the simulation of the forced Van der Pol oscillator, the prediction uncertainty does not grow in time even for a 3,000-step forecast.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 February 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 379〈/p〉 〈p〉Author(s): Christopher Eldred, Thomas Dubos, Evaggelos Kritsikis〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The rotating shallow water (RSW) equations are the usual testbed for the development of numerical methods for three-dimensional atmospheric and oceanic models. However, an arguably more useful set of equations are the thermal shallow water equations (TSW), which introduce an additional thermodynamic scalar but retain the single layer, two-dimensional structure of the RSW. As a stepping stone towards a three-dimensional atmospheric dynamical core, this work presents a quasi-Hamiltonian discretization of the thermal shallow water equations using compatible Galerkin methods, building on previous work done for the shallow water equations. Structure-preserving or quasi-Hamiltonian discretizations methods, that discretize the Hamiltonian structure of the equations of motion rather than the equations of motion themselves, have proven to be a powerful tool for the development of models with discrete conservation properties. By combining these ideas with an energy-conserving Poisson time integrator and a careful choice of Galerkin spaces, a large set of desirable properties can be achieved. In particular, for the first time total mass, buoyancy and energy are conserved to machine precision in the fully discrete model.〈/p〉〈/div〉

Description: 〈p〉Publication date: 15 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics, Volume 377〈/p〉 〈p〉Author(s): Fang Qing, Xijun Yu, Zupeng Jia〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The MoF (Moment of Fluid) method is an accurate approach for interface reconstruction in numerical simulation of multi-material fluid flow. So far, most works focus on improving its accuracy and efficiency, such as developing analytic reconstruction method and deducing the iteration schemes based on high order derivatives of the objective function. In this paper, we mainly concern on improving its robustness, especially for severely deformed polygonal meshes, in which case the objective function has multiple minimum value points. By using an efficient method for solving multiple roots of the nonlinear equation in large scope, a new algorithm is developed to enhance robustness of the MoF method. The main idea of this algorithm is as follows. The first derivative of the objective function is continuous, so the minimum value points of the objective function must be the zero points of the first derivative. Instead of finding the zero points of the first derivative directly, we turn to calculating the minimum value points (also zero points) of the square of the first derivative, which is a convex function on a neighborhood of each zero point. Applying the properties of convex function, the neighbor of each extreme minimum point of it can be obtained efficiently. Then each zero point of the square of the first derivative can be obtained using the iterative formula in its neighbor. Finally, by comparing the values of the objective function at these zero points of the first derivative, the global minimum value point of the objective function can be found and is the desired solution. The new algorithm only uses the first derivative of the objective function. It doesn't need an initial guess for the solution, which has to be carefully chosen in previous works. Numerical results are presented to demonstrate the accuracy and robustness of this new algorithm. The results show that it is applicable to severely deformed polygonal mesh, even with concave cells.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 22 March 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Computational Physics〈/p〉 〈p〉Author(s): Savio Poovathingal, Eric C. Stern, Ioannis Nompelis, Thomas E. Schwartzentruber, Graham V. Candler〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Micro scale simulations are performed of flow through porous (pyrolyzing) thermal protection system (TPS) materials using the direct simulation Monte Carlo (DSMC) method. DSMC results for permeability are validated with computational fluid dynamics (CFD) calculations and theory, for simple porous geometries under continuum flow conditions. An artificial fiber-microstructure generation code FiberGen is used to create triangulated surface geometry representative of FiberForm® (FiberForm) material. DSMC results for permeability of FiberForm are validated for a range of pressures (transitional flow conditions) and agree with experimental measurements. Numerical uncertainty is determined to be within 2% if sufficiently large portions of the microstructure are included in the computation. However, small variations in fiber size and angle bias can combine to give 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.gif" overflow="scroll"〉〈mo〉+〈/mo〉〈mn〉30〈/mn〉〈mtext〉%〈/mtext〉〈/math〉 uncertainty when comparing with experimental permeability data. X-ray microtomography scans of FiberForm are used to create microstructure geometry for incorporation within DSMC simulations of coupled oxygen diffusion and gas-surface chemistry in the presence of a blowing pyrolysis gas. In-depth penetration of atomic oxygen is limited to 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si2.gif" overflow="scroll"〉〈mn〉0.2〈/mn〉〈mtext〉–〈/mtext〉〈mn〉0.4〈/mn〉〈/math〉 mm for the range of Knudsen number and pyrolysis gas conditions studied.〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Soil Biology and Biochemistry, Volume 127〈/p〉 〈p〉Author(s): Aikaterini Efthymiou, Birgit Jensen, Iver Jakobsen〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Biochar (BC) application to soil can potentially replace mineral P fertilizers and its effectiveness as fertilizer can be improved by plant inoculation with the phosphate-solubilizing microorganism 〈em〉Penicillium aculeatum〈/em〉 (Pa). Arbuscular mycorrhiza (AM) fungi are important in plant P nutrition and may possibly act synergistically with Pa to improve the uptake of BC-P. Responses in wheat to inoculation with Pa and the AM fungus 〈em〉Rhizophagus irregularis〈/em〉 were studied in a pot experiment at two levels of BC fertilization. Pots contained a mesh-enclosed, root free compartment with 33P-labelled soil for assessment of the AM contribution to P uptake and for studying if Pa would affect P uptake by the AM fungal hyphae. AM application suppressed wheat growth, albeit AM pathway had a major role in total P uptake at the two lowest P levels (nil or 20 mg BC-P kg〈sup〉−1〈/sup〉 soil). Moreover, AM contribution had similar magnitudes in the presence and absence of Pa. Rhizosphere and bulk soil were actively colonized by Pa, both in the presence and absence of AM. The application of Pa or BC at a low rate increased AM-colonized root lengths. Although this was not translated to increased P uptake by wheat, the results suggest that AM and Pa can be combined without showing antagonistic interactions. However, more work is needed to understand how AM and Pa can be combined to increase plant growth.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Beata Klimek, Marcin Chodak, Małgorzata Jaźwa, Hamed Azarbad, Maria Niklińska〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The aim of this study was to assess and to detect factors controlling the temperature sensitivity of soil organic matter (SOM) in boreal forests, constituting an important stock of carbon. Soils were collected under Scots pine, Norway spruce, silver birch and mixed forests (O horizon) in northern Finland and measured for basal respiration rate at five different temperatures (from 4°C to 28°C). Q〈sub〉10〈/sub〉 values were calculated using a Gaussian function and based on temperature-dependent changes. The soils were measured for the a range of physicochemical parameters and functional diversity of soil microbial communities was assessed using the novel MicroResp™ method. Temperature sensitivity of SOM decomposition differed under the studied forest stands, with pine forests exhibiting the highest temperature sensitivity of SOM decomposition at a lower temperature range (0°C – 12°C). In such temperature range we found that Q〈sub〉10〈/sub〉 values were positively correlated with microbial functional diversity index (H’〈sub〉mic〈/sub〉) and soil C-to-P ratio. These suggest that metabolic abilities of soil microbial communities and soil nutrient content are the important controls of temperature sensitivity of taiga soils.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Afsana Praveen, Chandana Pandey, Ehasanullah Khan, Medha Panthri, Meetu Gupta〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Arsenic (As), one of the most harmful toxicant at global level severely affects plant metabolism when taken up. Interestingly, presence of silicon (Si) as fertilizer in As-contaminated soil is an effective strategy to decrease As accumulation in the plants. 〈em〉Brassica juncea〈/em〉 (var. Varuna) were grown hydroponically to investigate the role of Si at biochemical and molecular levels under arsenite [As〈sup〉III〈/sup〉] stress. Seedlings of 〈em〉B. juncea〈/em〉 were exposed to As〈sup〉III〈/sup〉 (150 µM), Si (1.5 mM) and a combination of both the elements. Our data demonstrated that seedlings exposed to As〈sup〉III〈/sup〉 showed an inhibition in shoot length, chlorophyll, carotenoid and protein while co-application of Si improved these growth parameters. Si supplementation has reduced the As accumulation in shoot. Increase/decrease was observed in stress related parameters (cysteine and proline), antioxidant enzymes (SOD, CAT and APX) and oxidative stress markers (MDA and H〈sub〉2〈/sub〉O〈sub〉2〈/sub〉), which were improved on co-application of Si as compared to As〈sup〉III〈/sup〉 treatment. RAPD is a suitable biomarker assay for plants for assessing the genotoxicity. Seven primers used in RAPD produced a total of 39 and 48 bands in the leaves of control and treated seedlings, respectively. RAPD band-profiles and genomic template stability (GTS) were consistent with other growth and physiological parameters. In conclusion, the genotoxic alterations along with the biochemical parameters indicate that the exposure to Si mitigates As〈sup〉III〈/sup〉 induced oxidative stress by improving stress related parameters and antioxidant system in 〈em〉B. juncea.〈/em〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Jun YAN, Xiao Zeng HAN, Wen Feng CHEN, En Tao WANG, Wen Xiu ZOU, Zhi Ming ZHANG〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Aiming to maintain and recover the productivity of Chinese Mollisol, a long-term fertilization experiment has been carried out for 29 years under the wheat-maize-soybean rotation system, including application of ROM (recycled organic manure), chemical fertilizers and their combinations. The effects of different treatments were evaluated by determining the soil physicochemical features, soybean production and soybean rhizobial diversity. The results showed that application of recycled organic manure (ROM)-combined with chemical fertilizer maintained or increased soil fertility, companying by higher production and higher diversity of soybean rhizobia. The negative association of 〈em〉Bradyrhizobium japonicum〈/em〉 with N-fertilizer, positive association of 〈em〉B. diazoefficiens〈/em〉 with soil acidification, and reducing of N-impression on the diversity of 〈em〉Bradyrhizobium〈/em〉 by addition of ROM were recorded as new findings. Therefore, the ROM involved treatments, especially NPK+ROM could be a feasible strategy for maintaining and recovering the fertility of the Chinese Mollisol, while the rhizobial diversity could be an indicator for the soil fertility.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Lin Chen, Xiuli Xin, Jiabao Zhang, Marc Redmile-Gordon, Guangsen Nie〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Modern breeding primarily targets the traits of crop yield and is likely to influence the root-associated microbiomes which play significant roles in plant growth and health. The relative importance of soil and cultivar factors in shaping the root-associated microbiomes of modern maize remains uncertain. We conducted a pot experiment in a controlled environment using three soils (Mollisol, Inceptisol and Ultisol) and four contrasting cultivars which are widely planted in China (Denghai 605, Nonghua 816, Qiaoyu 8 and Zhengdan 958). We applied 16S rRNA gene amplicon sequencing to characterize the bacterial communities in the bulk soil, rhizosphere and endosphere. Our results showed that the four cultivars had different shoot biomass and root exudation levels. The microbiomes in the bulk soil, rhizosphere and endosphere were different. We observed the apparent community divergence between soils rather than cultivars, thereinto, edaphic factors substantially contributed to microbiome variation. Moreover, permutational multivariate analysis of variance corroborated significant contributions of soil type but not cultivar on the root-associated microbiome structure. Differential abundance analysis confirmed that each soil presented a distinct root microbiome, while network analysis indicated different co-occurrence patterns of the root microbiome among the three soils. The core root microbiome members are implicated in plant growth promotion and nutrient acquisition in the roots. In conclusion, the root-associated microbiomes of modern maize are much more controlled by soil characteristics than by cultivar root exudation. Our study is anticipated to help contribute to improved breeding strategies through integrative interactions of soils, cultivars and their associated microbiomes.〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere, Volume 28, Issue 4〈/p〉 〈p〉Author(s): 〈/p〉

Description: 〈p〉Publication date: Available online 1 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Abideen Zainul, Hans-Werner KOYRO, Bernhard HUCHZERMEYER, Bilquees GUL, M. Ajmal KHAN〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Soil water and nutrient status both are of major importance for the plant appearance and its growth performance. The objective of this research was therefore to study the effect of biochar (1.5% BC) and a biochar-compost mixture (1.5% BC + 1.5% Co) on the performance of 〈em〉Phragmites karka〈/em〉 plants grown in a nutrient poor sandy clay (control, 50% sand 30% clay and 20% gravel) soil. The indicators of plant performance such as growth, lignocellulosic biomass, water relations, mineral nutrition status, leaf gas exchange, chlorophyll fluorescence parameters of 〈em〉P. karka〈/em〉, as well as soil respiration activity, were assessed. The sole amendment of BC led to higher growth rate and lignocellulosic biomass production in 〈em〉P. karka〈/em〉 plants compared to the non-treated control. There was also significant increase in soil respiration with biochar treatments that stimulated microbial interaction. The increase in the water holding capacity after BC amendment caused a significant improvement in plant water status (water potential, osmotic potential, leaf turgidity) and plant ion content (K〈sup〉+〈/sup〉, Mg〈sup〉++〈/sup〉 and Ca〈sup〉++〈/sup〉) leading to an increase of net photosynthesis but also a higher energy use efficiency of the Photosystem II. Additionally, the BC plants managed to avoid oxidative stress, improved water use efficiency (WUE) and decreased dark respiration. However, the amendment of a biochar-compost mixture (BC + Co) led to even better improvement of physiological parameters such as growth, leaf turgor, photosynthesis and nutrient content and soil gas exchange of 〈em〉P. karka〈/em〉. Our results suggested that BC and Co promote plant growth with respect to nutrient uptake, water balance, and efficiency of the photosynthetic system. In summary both soil amendments might open an opportunity for 〈em〉P. karka〈/em〉 to sequester CO〈sub〉2〈/sub〉 and to produce higher fodder, bio-active compounds and biomass for bio-energy on nutrient poor degraded soils.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Yuan LIU, Zhong-yi LI, Ren-kou XU〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The manganese(II) [Mn(II)] forms on soybean roots were investigated to determine the main factors affecting the distribution of Mn(II) forms and the relationship with Mn(II) plant toxicity. Fresh roots of soybean obtained from solution culture experiments were reacted with Mn(II) in solutions, and then the Mn(II) adsorbed on soybean roots was differentiated into exchangeable, complexed and precipitated forms through sequentialextraction with KNO〈sub〉3〈/sub〉, EDTAand HCl. Results indicated thatthe exchangeable Mn(II) on soybean roots occupied the largest proportion, followed by the complexed Mn(II) and precipitated Mn(II) occupied the least proportion. Mn(II) toxicity to soybean roots was greater at pH5.5 than at pH4.2 due to the larger amount of exchangeable Mn(II) at higher pH. The cations Al〈sup〉3+〈/sup〉, La〈sup〉3+〈/sup〉, Ca〈sup〉2+〈/sup〉, Mg〈sup〉2+〈/sup〉 and NH〈sub〉4〈/sub〉〈sup〉+〈/sup〉competed with Mn〈sup〉2+〈/sup〉 for cation exchange sites on root surfaces, thus reduced the exchangeable Mn(II) on rootswith the order of Al〈sup〉3+〈/sup〉 and La〈sup〉3+〈/sup〉 〉 Ca〈sup〉2+〈/sup〉 and Mg〈sup〉2+〈/sup〉 〉 NH〈sub〉4〈/sub〉〈sup〉+〈/sup〉. Al〈sup〉3+〈/sup〉 and La〈sup〉3+〈/sup〉 at 100μmol L〈sup〉−1〈/sup〉decreased the exchangeable Mn(II)by 80 and 79%, respectively, and Ca〈sup〉2+〈/sup〉 and Mg〈sup〉2+〈/sup〉at 1mmol L〈sup〉−1〈/sup〉 reduced the exchangeable Mn(II) on soybean roots by 51 and 73%, respectively. Organic anions reduced the concentration of free Mn〈sup〉2+〈/sup〉 in solution through formation of complexes with Mn〈sup〉2+〈/sup〉, and thus efficiently decreased the exchangeable Mn(II) on plant roots. Oxalate, citrate and malate decreased the exchangeable Mn(II) on soybean roots by 30.9, 19.7 and 10.9 %, respectively, which was consistent with thecomplexing abilityof these organic anions with Mn(II).It can be concluded that exchangeable Mn(II) was the dominant form of Mn(II) on soybean roots and was responsible for Mn(II) toxicity to plants. The coexisting cations and organic anions reduced the exchangeableMn(II).〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere, Volume 28, Issue 4〈/p〉 〈p〉Author(s): Qifa ZHOU, Benjamin A. HOUGE, Zhaohui TONG, Bin GAO, Guodong LIU〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Application of biochar to agricultural soils is effective to sequester atmospheric carbon and improve soil quality, but current pyrolysis and transportation costs are high, making biochar too costly to be used at the field scale. This study developed a new 〈em〉in-situ〈/em〉 technique, burning and soil covering (B-SC), which can be used by farmers for production of biochar with crop residue. In this study, the air-dried feedstocks, elephant grass and corn residue, were burnt 〈em〉in situ〈/em〉 for biochar production in the field. After approximately 90% of the leaves were combusted, the burning process was dramatically slowed down by covering the feedstock with soil. The biochar yield averaged 18.0 ± 1.3 (〈em〉n =〈/em〉 15) and 13.7 ± 1.3 (〈em〉n〈/em〉 = 10) kg per 100 kg air-dried feedstock for the elephant grass and corn residue, respectively. The biochar properties were suitable for soil improvement. The inputs for biochar production of the B-SC process only included low labor force, open field, feedstock (〈em〉e.g.,〈/em〉 grass and crop residue), and simple tools. The operation time for processing 10 kg of the corn residue by an individual farmer was 24.4 ± 4.1 min (〈em〉n〈/em〉 = 10). As compared with the conventional field burning process, the B-SC process drastically shortened the time for biomass burning and generated a significantly lower emission of smoke and thermal energy. This simple technique can be particularly practical and effective for farmers to improve the soils of poor quality in China.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Elena OKADA, José Luis COSTA, Francisco BEDMAR〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉Glyphosate is the most used herbicide in Argentina, accounting for 62% of the commercialized pesticides in the market. It is used as a weed controller in no-till systems, and it is also applied in various genetically modified crops (e.g. soybean, corn, cotton). Though it has a high solubility in water, it tends to adsorb and accumulate in agricultural soils. The main objectives of this work were to compare the dissipation of glyphosate and the accumulation of its metabolite aminomethylphosphonic acid (AMPA) over time in three soils from agricultural areas of Argentina, under long-term management of no-till (NT) and conventional tillage (CT) practices. Forty percent of the applied glyphosate was degraded within the first three days in all soils, indicating a fast initial dissipation rate.〈/p〉 〈p〉However, the dissipation rate considerably decreased over time and the degradation kinetics followed a two-compartment kinetic model. No differences were found between tillage practices. Dissipation was not related to the microbial activity measured as soil respiration. The fast decrease in the concentration of glyphosate at the beginning of the dissipation study was not reflected in an increase on the concentration of AMPA. The estimated half-lives for glyphosate ranged between 9 and 38 days. However, glyphosate bioavailability decreases over time as it is strongly adsorbed to the soil matrix. This increases its residence time which may lead to its accumulation in agricultural soils.〈/p〉 〈/div〉

Description: 〈p〉Publication date: December 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere, Volume 28, Issue 6〈/p〉 〈p〉Author(s): Yandong MA, Jingbo ZHAO, Rui LIU, Qi ZHOU, Leipeng YIN〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Permeability and water-bearing space are important hydrological characteristics of the loess strata. In this study a systematic experiment was conducted to measure the magnetic susceptibility, grain size, porosity, and infiltration rate of the loess and palaeosol layers on a loess tableland of the central Chinese Loess Plateau, in order to investigate the differences in hydrological conditions between the loess and palaeosol layers. The magnetic susceptibility of the loess layer was lower than that of the palaeosol layer, but the average quasi-steady infiltration rate was about 0.31 mm min〈sup〉−1〈/sup〉 higher, the coarse silt and very fine sand contents were about 7.1% greater, and the porosity was about 5.7% higher. These differences were mainly due to pedogenesis, which was affected by the Quaternary climate. The pedogenesis differences between the loess and palaeosol layers resulted in hydrological property differences in terms of permeability and water-bearing space. The loess layer had a higher permeability and more water-bearing space than the palaeosol layer, which meant that the loess layer is more likely to form aquifers and the palaeosol layer is more prone to form aquitards. The groundwater in the loess strata had a multilayered characteristic, which depended on the relative impermeability of palaeosol layer and the alternate deposition of loess-palaeosol layers. The hydrological characteristics of the loess strata demonstrated that the Quaternary climate had an important control function on the formation and movement of groundwater. This knowledge provides a reliable theoretical basis for water resource development and utilization on the Chinese Loess Plateau, and this study extends the application of Quaternary climate change theory to hydrological systems in loess deposits.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Ning ZHANG, Dong GUO, Zhu Ye, Xiaomi WANG, Lingjia ZHU, Fang LIU, Ying TENG, Peter Christie, Zhengao LI, Yongming LUO〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉A short-term field experiment (one year) was conducted to explore the potential role of a pentachloronitrobenzene (PCNB)-degrading bacterial isolate, 〈em〉Cupriavidus〈/em〉 sp. YNS-85, in the remediation of a PCNB-contaminated soil in which 〈em〉Panax notoginseng〈/em〉was grown. There were three treatments:(1) control soil without YNS-85 inoculation, (2) soil with 0.15 kg m〈sup〉−2〈/sup〉of solid bacterial inoculum (A), and (3) soil with 0.3 kg m〈sup〉−2〈/sup〉 of solid bacterial inoculum (B). The degradation of soil PCNB during the microbial remediation was monitored using gas chromatography. Soil enzyme activities comprising catalase and fluorescein diacetate (FDA) esterase activities were determined by spectrophotometry. In addition, counts of cultivable bacteria, fungi and actinomycetes were conducted by the plating of serial dilutions, and the microbial biodiversity of the soil was investigated by a BIOLOG analysis. After one year of in-situ remediation, the soil PCNB concentrations decreased significantly by 50.3 and 74.2 %, respectively, in treatments A and B compared with the uninoculated control. Soil catalase activity decreased in the presence of the bacterial isolate. FDA esterase activity decreased in treatment A but increased in treatment B. There was no significant change in plant biomass, the diversity of the soil microbial community, orphysicochemical properties of the soil between the control and isolate-inoculated groups (〈em〉p〈/em〉 〈 0.05). The results indicated that 〈em〉Cupriavidus sp.〈/em〉 YNS-85 was a potential candidate for the remediation of PCNB-contaminated soils using 〈em〉P. notoginseng〈/em〉.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Rim AZOUZI, Abdelkrim CHAREF, Lamia AYED, Samia KHADHAR〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Ni, Cr, Pb, Cd, Cu and Zn Geo-accumulation indexes revealed that industrial activities and used TWW contributed to soil pollution, and water irrigation decreased always this contamination. After long-term use of different water types, high perturbation of metal redistribution have taken. Ground water use changed all metal redistributions in irrigated soil among various soils-solid and soil-solution fractions, compared with non-irrigated soil. Slightly acid water use transferred some metals from different solid phase components into soluble and exchangeable fractions. However, TWW use transformed some Ni, Cr, Cd, Cu and Zn quantities from soluble and exchangeable fractions to the less labile fractions, particularly into organic matter fraction. Reuse of conventional water within the same soil decreased the whole soil redistribution index values indicating tendency to return to the pattern of distribution of groundwater irrigated soil.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Yanqun ZU, Li QIN, Fangdong ZHAN, Jiong WU, Yuan LI, Jianjun CHEN, Jixiu WANG, Wenyou HU〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This paper reports effects of intercropping hyperaccumulator 〈em〉Sonchus asper〈/em〉 with 〈em〉Vicia faba〈/em〉 on plant Cd accumulation and root response in soil from a mining area of Yunnan Province, China. The aim was to evaluate Cd accumulation and mechanisms root-secreted organic acids and root spatial morphology. The pot experiment was conducted with intercropping of 〈em〉S. asper〈/em〉 and 〈em〉V. faba〈/em〉 under increasing soil Cd concentrations (0, 50, 100, 200 mg kg〈sup〉−1〈/sup〉). Biomass and Cd concentrations of plants, and DEPA-extractable Cd in soils, root morphology, and secreted organic acids were determined. Intercropping increased the biomass of 〈em〉S. asper〈/em〉 and 〈em〉V. faba〈/em〉 and increased Cd accumulation and transfer coefficient from roots to shoots of 〈em〉S. asper〈/em〉 and decreased those of 〈em〉V. faba〈/em〉 for the 200 mg kg〈sup〉−1〈/sup〉 Cd treatment. Cd concentrations in intercropped 〈em〉V. faba〈/em〉 roots, shoots and grain were positively correlated with DEPA-extractable Cd content in soil (〈em〉P〈/em〉 〈 0.05). When treated with 50 mg kg〈sup〉−1〈/sup〉 Cd, intercropping decreased citric and malic acids in root secretions of 〈em〉S. asper〈/em〉. Intercropped 〈em〉V. faba〈/em〉 secreted more citric, oxalic, acetic and malic acids. Intercropping led to increased root length and root surface area for 〈em〉S. asper〈/em〉 and 〈em〉V. faba〈/em〉. At 50 mg kg〈sup〉−1〈/sup〉 Cd, root length for 〈em〉S. asper〈/em〉 were higher than the 0 mg kg〈sup〉−1〈/sup〉 Cd, while 〈em〉V. faba〈/em〉 roots had significantly decreased root length and mean diameter. Intercropping of 〈em〉S. asper〈/em〉 and 〈em〉V. faba〈/em〉 is suggested as an 〈em〉in situ〈/em〉 bioremediation strategy of Cd-contaminated soils and may improve the food quality of 〈em〉V. faba〈/em〉.〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere, Volume 28, Issue 4〈/p〉 〈p〉Author(s): Zahir Ur REHMAN, Sardar KHAN, Mohammad Tahir SHAH, Mark L. BRUSSEAU, Said Akbar KHAN, Jon MAINHAGU〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Contamination of the food chain with heavy metals is considered as one of the major environmental pathways of human exposure to metals leading to potential health risks. This study aimed to investigate the concentrations of heavy metals such as copper (Cu), zinc (Zn), chromium (Cr), nickel (Ni), and manganese (Mn) in agricultural soils and food crops (fruit, leaf, and root vegetables), and their associated health risks to the local population in selected southern districts of Khyber Pakhtunkhwa Province, Pakistan. The concentrations of the selected metals in soil varied over a wide range, in the following decreasing order: Mn 〉 Zn 〉 Cr 〉 Ni 〉 Cu. The bioaccumulation of metals in vegetables was within the permissible risk limits, except for Cr which showed higher contamination in all the tested food crops. The trend of metal transfer factors for different vegetables was in the order of Cu 〉 Ni 〉 Cr 〉 Mn 〉 Zn, while the calculated daily intake of metals (DIM) in adults and children through consumption of food crops was in the decreasing order of Mn 〉 Zn 〉 Ni 〉 Cr 〉 Cu. The health risk index (HRI) values for the heavy metals for both adults and children were less than 1. Therefore, no significant health risk is anticipated for the local consumers through ingestion of these food crops.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Xiaoguang ZHANG, Biao HUANG, Feng LIU〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Monitoring the dynamics of soil salinization is of great importance for agricultural production. This study focused on Yucheng County, a typical county on the Huang-Huai-Hai-Plain (HHHP) of China, to evaluate the spatial and temporal variation of soil salinization. Three methods, including principal components analysis (PCA), tasseled cap (TC) transformations, and optimal band combination (OBC), were used to extract information from an early Landsat multispectral scanner (MSS) image from 1984 and their advantages were compared. In addition, OBC was used on a thematic mapper (TM) image from 2009. The tools of an iteratively self-organizing data analysis algorithm and likelihood were used to interpret the MSS and TM images for data classification. Finally, a transfer matrix method was used to assess the spatial and temporal variability of soil salinization, and the driving factors of soil salinization were analyzed. Compared to PCA and OBC, TC transformation was a more effective method to extract soil salinization information from the MSS sensor. The results indicate that an approximately 298 km〈sup〉2〈/sup〉 soil area was affected by salinity in 1984 in Yucheng County, of which 5.40%, 11.96%, and 12.75% soil areas were classified as having slight, moderate, and severe salinization, respectively. In 2009, the salinization area was reduced to only 146 km〈sup〉2〈/sup〉, of which 10.70 % and 3.75% of the soil areas had slight to moderate salinization, and no severe salinization, respectively. The saline land decreased at an average rate of 6km〈sup〉2〈/sup〉 per year, which probably resulted from the lower groundwater depth, increased organic fertilizer or crop straw in soil, changed land use type, and increased vegetation coverage.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2017〈/p〉 〈p〉〈b〉Source:〈/b〉 Pedosphere〈/p〉 〈p〉Author(s): Yan SUN, Hui YE, Zebin WEI, Xuhui KONG, Qi-Tang WU〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉‘Lvbao-701’ is a 〈em〉Brassica parachinensis〈/em〉 cultivar that exhibits low accumulation of cadmium (Cd) and high Cd tolerance. This cultivar was compared with a high-Cd accumulating cultivar, ‘Chixin-4’, to characterize the mechanisms influencing Cd accumulation in 〈em〉B. parachinensis〈/em〉. Root cell walls were isolated by dissolving the cytoplasm with organic solvent, and the root Cd and phytochelatin (PC) contents were subsequently analyzed. Additionally, a PC synthase gene fragment was cloned and expressed under Cd stress conditions. The Cd content and proportion of Cd bound to root cell walls were higher in ‘Lvbao-701’plants (68%–77%) than in ‘Chixin-4’ plants (35%–54%) following exposure to Cd stress. The proportions of Cd bound to root cell walls measured using cell walls isolated with a non-destructive method were higher than those obtained using a conventional method that required grinding and centrifugation steps. Exposure to Cd stress conditions induced the production of PCs, and resulted in higher PC contents in ‘Lvbao-701’ plants than in ‘Chixin-4’ plants. Cloning and expression analysis of a 〈em〉B. parachinensis〈/em〉 PC synthase cDNA fragment indicated that PC synthase gene expression was induced by Cd, and occurred mainly in the roots of both ‘Lvbao-701’ and ‘Chixin-4’ plants. However, the PC synthase gene expression level was higher in the Lvbao-701 roots than in the ‘Chixin-4’ roots. Therefore, a greater abundance of Cd in the root cell walls and up-regulated PC production in the roots are likely the main reasons ‘Lvbao-701’ plants exhibit lower Cd translocation to shoots and greater tolerance to Cd than ‘Chixin-4’ plants.〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2018〈/p〉 〈p〉〈b〉Source:〈/b〉 Journal of Terramechanics, Volume 79〈/p〉 〈p〉Author(s): Congbin Yang, Guang Yang, Zhifeng Liu, Huaxiong Chen, Yongsheng Zhao〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Tracked vehicles assume an important role in engineering and agriculture. Supporting-trafficability is the lifeline of tracked vehicles. The terrain characteristics is concerned with the relationships critical in defining the mobility of tracked vehicles. Conventional terramechanics models cannot accurately describe the relationship between tracks and soil. A major problem is that these models do not account for the water content in the soil and sinkage speed. Water content is an important factor affecting sinkage of vehicles, which in turn affects vehicles’ driving resistance. Increased driving resistance is a barrier to the mobility of an tracked vehicle. Considering sinkage speed is conducive to describe the trafficability of tracked vehicle moving at high speed. In this paper, the terrain characteristics to describe the relationship of the pressure/sinkage of four common soil types in Southwest China were measured using soil bin tests. We discuss characteristics like high sinkage speed, water content variation, and repeated loading, as well as the relationships of these major factors with the deformation of soil. We present a method to deduce the pressure-sinkage relationship for track shoes using the stress-displacement relationship model proposed by Bekker. The described method advances the study and understanding of track-terrain interaction in complex environments.〈/p〉〈/div〉 〈/div〉