A Framework for Megascale Agent Based Model Simulations on Graphics Processing Units

Agent-based modeling is a technique for modeling dynamic systems from the bottom up. Individual elements of the system are represented computationally as agents. The system-level behaviors emerge from the micro-level interactions of the agents. Contemporary state-of-the-art agent-based modeling toolkits are essentially discrete-event simulators designed to execute serially on the Central Processing Unit (CPU). They simulate Agent-Based Models (ABMs) by executing agent actions one at a time. In addition to imposing an un-natural execution order, these toolkits have limited scalability. In this article, we investigate data-parallel computer architectures such as Graphics Processing Units (GPUs) to simulate large scale ABMs. We have developed a series of efficient, data parallel algorithms for handling environment updates, various agent interactions, agent death and replication, and gathering statistics. We present three fundamental innovations that provide unprecedented scalability. The first is a novel stochastic memory allocator which enables parallel agent replication in O(1) average time. The second is a technique for resolving precedence constraints for agent actions in parallel. The third is a method that uses specialized graphics hardware, to gather and process statistical measures. These techniques have been implemented on a modern day GPU resulting in a substantial performance increase. We believe that our system is the first ever completely GPU based agent simulation framework. Although GPUs are the focus of our current implementations, our techniques can easily be adapted to other data-parallel architectures. We have benchmarked our framework against contemporary toolkits using two popular ABMs, namely, SugarScape and StupidModel.GPGPU, Agent Based Modeling, Data Parallel Algorithms, Stochastic Simulations

Endophytic phyllosphere fungi and nutrient cycling in terrestrial ecosystems

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Defoliation and patchy nutrient return drive grazing effects on plant and soil properties in a dairy cow pasture

Large herbivores can influence plant and soil properties in grassland ecosystems, but especially for belowground biota and processes, the mechanisms that explain these effects are not fully understood. Here, we examine the capability of three grazing mechanisms-plant defoliation, dung and urine return, and physical presence of animals (causing trampling and excreta return in patches)-to explain grazing effects in Phleum pratense-Festuca pratensis dairy cow pasture in Finland. Comparison of control plots and plots grazed by cows showed that grazing maintained original plant-community structure, decreased shoot mass and root N and P concentrations, increased shoot N and P concentrations, and had an inconsistent effect on root mass. Among soil fauna, grazing increased the abundance of fungivorous nematodes and Aporrectodea earthworms and decreased the abundance of detritivorous enchytraeids and Lumbricus earthworms. Grazing also increased soil density and pH but did not affect average soil inorganic-N concentration. To reveal the mechanisms behind these effects, we analyzed results from mowed plots and plots that were both mowed and treated with a dung and urine mixture. This comparison revealed that grazing effects on plant attributes were almost entirely explained by defoliation, with only one partly explained by excreta return. Among belowground attributes, however, the mechanisms were more mixed, with effects explained by defoliation, patchy excreta return, and cow trampling. Average soil inorganic-N concentration was not affected by grazing because it was simultaneously decreased by defoliation and increased by cow presence. Presence of cows created great spatial heterogeneity in soil N availability and abundance of fungivorous nematodes. A greenhouse trial revealed a grazing-induced soil feedback on plant growth, which was explained by patchiness in N availability rather than changes in soil biota. Our results show that grazing effects on plant attributes can be satisfactorily predicted using the effects of defoliation, whereas those on soil fauna and soil N availability need understanding of other mechanisms as well. The results indicate that defoliation-induced changes in plant ecophysiology and the great spatial variation in N availability created by grazers are the two key mechanisms through which large herbivores can control grassland ecosystems.Large herbivores can influence plant and soil properties in grassland ecosystems, but especially for belowground biota and processes, the mechanisms that explain these effects are not fully understood. Here, we examine the capability of three grazing mechanisms-plant defoliation, dung and urine return, and physical presence of animals (causing trampling and excreta return in patches)-to explain grazing effects in Phleum pratense-Festuca pratensis dairy cow pasture in Finland. Comparison of control plots and plots grazed by cows showed that grazing maintained original plant-community structure, decreased shoot mass and root N and P concentrations, increased shoot N and P concentrations, and had an inconsistent effect on root mass. Among soil fauna, grazing increased the abundance of fungivorous nematodes and Aporrectodea earthworms and decreased the abundance of detritivorous enchytraeids and Lumbricus earthworms. Grazing also increased soil density and pH but did not affect average soil inorganic-N concentration. To reveal the mechanisms behind these effects, we analyzed results from mowed plots and plots that were both mowed and treated with a dung and urine mixture. This comparison revealed that grazing effects on plant attributes were almost entirely explained by defoliation, with only one partly explained by excreta return. Among belowground attributes, however, the mechanisms were more mixed, with effects explained by defoliation, patchy excreta return, and cow trampling. Average soil inorganic-N concentration was not affected by grazing because it was simultaneously decreased by defoliation and increased by cow presence. Presence of cows created great spatial heterogeneity in soil N availability and abundance of fungivorous nematodes. A greenhouse trial revealed a grazing-induced soil feedback on plant growth, which was explained by patchiness in N availability rather than changes in soil biota. Our results show that grazing effects on plant attributes can be satisfactorily predicted using the effects of defoliation, whereas those on soil fauna and soil N availability need understanding of other mechanisms as well. The results indicate that defoliation-induced changes in plant ecophysiology and the great spatial variation in N availability created by grazers are the two key mechanisms through which large herbivores can control grassland ecosystems.Large herbivores can influence plant and soil properties in grassland ecosystems, but especially for belowground biota and processes, the mechanisms that explain these effects are not fully understood. Here, we examine the capability of three grazing mechanisms-plant defoliation, dung and urine return, and physical presence of animals (causing trampling and excreta return in patches)-to explain grazing effects in Phleum pratense-Festuca pratensis dairy cow pasture in Finland. Comparison of control plots and plots grazed by cows showed that grazing maintained original plant-community structure, decreased shoot mass and root N and P concentrations, increased shoot N and P concentrations, and had an inconsistent effect on root mass. Among soil fauna, grazing increased the abundance of fungivorous nematodes and Aporrectodea earthworms and decreased the abundance of detritivorous enchytraeids and Lumbricus earthworms. Grazing also increased soil density and pH but did not affect average soil inorganic-N concentration. To reveal the mechanisms behind these effects, we analyzed results from mowed plots and plots that were both mowed and treated with a dung and urine mixture. This comparison revealed that grazing effects on plant attributes were almost entirely explained by defoliation, with only one partly explained by excreta return. Among belowground attributes, however, the mechanisms were more mixed, with effects explained by defoliation, patchy excreta return, and cow trampling. Average soil inorganic-N concentration was not affected by grazing because it was simultaneously decreased by defoliation and increased by cow presence. Presence of cows created great spatial heterogeneity in soil N availability and abundance of fungivorous nematodes. A greenhouse trial revealed a grazing-induced soil feedback on plant growth, which was explained by patchiness in N availability rather than changes in soil biota. Our results show that grazing effects on plant attributes can be satisfactorily predicted using the effects of defoliation, whereas those on soil fauna and soil N availability need understanding of other mechanisms as well. The results indicate that defoliation-induced changes in plant ecophysiology and the great spatial variation in N availability created by grazers are the two key mechanisms through which large herbivores can control grassland ecosystems.Peer reviewe

Endophytic phyllosphere fungi and nutrient cycling in terrestrial ecosystems

The importance of phyllosphere fungi to ecosystem functioning via soil processes has aroused increasing interest during the last decade. Here, we briefly review the current knowledge of how the foliar endophytic fungi and nutrient cycling interact. Recent findings suggest that endophytes may affect plant litter quality, organisms that control litter decomposition and the availability of nutrients in plant communities. However, the results obtained so far are highly variable. We attempt to integrate these observations with the knowledge of ecology and life-history strategies of endophytic fungi, and highlight general rules and gaps in our knowledge. Finally, we suggest testable hypotheses for future studies.</p

Transition to adult care in Finnish adolescents with juvenile idiopathic arthritis

Objective The symptoms of juvenile idiopathic arthritis (JIA) and the necessity for continuous treatment may persist in adulthood. Therefore, patients with JIA need to be appropriately transferred to adult care. We aimed to analyse the timing of the patients' transition to adult care, and patients' self-management skills with the process and the quality of the transition. Method This study included 161 Finnish participants of the population-based Nordic JIA cohort who attended a 17 year follow-up appointment. Special attention was paid to the three groups: those referred by the paediatric rheumatology outpatient clinic to primary healthcare (PHC), those who were directly transferred to adult rheumatology care, and those who were later referred. Results A total of 136 patients (84%) were eligible to participate in the study, and 40% of them were directly transferred to an adult rheumatology clinic. Of the patients, 72% eventually ended up being referred to an adult rheumatology outpatient clinic. However, 16% of the patients in the PHC group had active disease during the study appointment and were referred to adult services after the study visit. Conclusion This study reveals the need to improve the transition process from paediatric care to adult care and to find the variables that can indicate the need for immediate transition. Although challenging, it is important to avoid treatment delay in adult patients with JIA who may have active disease but who do not have appropriate access to an adult rheumatological outpatient clinic.Peer reviewe

ANIMAL WELFARE: EUROPEAN STANDARDS AS A BASIS FOR REFORMING NATIONAL LEGISLATION IN UKRAINE

ABSTRACT: Nowadays, Ukraine faces numerous challenges in animal welfare, including ensuring animal welfare, keeping and veterinary care for stray animals, protecting them from cruelty, and preserving endangered species. These areas are important and create the need to improve national legislation and its application. The problem is also becoming more urgent within the framework of Ukraine’s European integration vector, accompanied by the harmonization of national legislation with EU law and the ratification and implementation of European standards in the relevant area. The subject matter of the study necessitated the use of dialectical, systemic, structural-functional and informational approaches. The article aims to study the legal regulation of animal rights protection in Ukraine and analyze the animal treatment standards in foreign countries and international organizations. Keywords: animals; animal protection; international standards; animal cruelty; animal rights.   Bem-estar animal: Padrões europeus como base para reformar a legislação nacional na Ucrânia   RESUMO: Atualmente, a Ucrânia enfrenta inúmeros desafios na área de bem-estar animal, incluindo as garantias e manutenção dos cuidados veterinários de animais perdidos, a proteção da crueldade e preservação de espécies ameaçadas de extinção. Estas áreas são importantes e criam a necessidade de melhorar a legislação nacional e a sua aplicação. O problema também se torna mais urgente no quadro do vetor de integração europeia da Ucrânia, acompanhado pela harmonização da legislação nacional com a legislação da União Européia (EU), e consequentemente, pela ratificação e implementação das normas europeias dessa área relevante, no território nacional. O objeto do estudo exigiu o uso de abordagens dialéticas, sistêmicas, estrutural-funcionais e informacionais. O artigo visa estudar a regulamentação legal da proteção dos direitos dos animais na Ucrânia e analisar os padrões de tratamento animal em países estrangeiros e organizações internacionais da UE. Palavras-chave: animais; proteção animal; padrões internacionais; crueldade animal; direito dos animais.ABSTRACT: Nowadays, Ukraine faces numerous challenges in animal welfare, including ensuring animal welfare, keeping and veterinary care for stray animals, protecting them from cruelty, and preserving endangered species. These areas are important and create the need to improve national legislation and its application. The problem is also becoming more urgent within the framework of Ukraine’s European integration vector, accompanied by the harmonization of national legislation with EU law and the ratification and implementation of European standards in the relevant area. The subject matter of the study necessitated the use of dialectical, systemic, structural-functional and informational approaches. The article aims to study the legal regulation of animal rights protection in Ukraine and analyze the animal treatment standards in foreign countries and international organizations. Keywords: animals; animal protection; international standards; animal cruelty; animal rights.   Bem-estar animal: Padrões europeus como base para reformar a legislação nacional na Ucrânia   RESUMO: Atualmente, a Ucrânia enfrenta inúmeros desafios na área de bem-estar animal, incluindo as garantias e manutenção dos cuidados veterinários de animais perdidos, a proteção da crueldade e preservação de espécies ameaçadas de extinção. Estas áreas são importantes e criam a necessidade de melhorar a legislação nacional e a sua aplicação. O problema também se torna mais urgente no quadro do vetor de integração europeia da Ucrânia, acompanhado pela harmonização da legislação nacional com a legislação da União Européia (EU), e consequentemente, pela ratificação e implementação das normas europeias dessa área relevante, no território nacional. O objeto do estudo exigiu o uso de abordagens dialéticas, sistêmicas, estrutural-funcionais e informacionais. O artigo visa estudar a regulamentação legal da proteção dos direitos dos animais na Ucrânia e analisar os padrões de tratamento animal em países estrangeiros e organizações internacionais da UE. Palavras-chave: animais; proteção animal; padrões internacionais; crueldade animal; direito dos animais

Effects of a glyphosate-based herbicide on soil animal trophic groups and associated ecosystem functioning in a northern agricultural field

Despite an increasing concern of consequences of using vast amounts of glyphosate-based herbicides in agroecosystems, their potential effects on non-target soil organisms and soil functioning are mostly unknown. It has also been argued that fields in northern latitudes should be under special surveillance as the short active period of decomposers may restrict glyphosate degradation. We investigated the effects of a glyphosate- based herbicide, Roundup, on the abundance of enchytraeids and nematodes, both essential groups in decomposer food webs, and plant litter mass loss and soil availability of mineral N in a two-year agricultural field setting in south-west Finland. Our experiment consisted of (1) non-treated weed plots, (2) plots, where weeds were killed by hoeing, and (3) plots treated with both Roundup and hoeing. We found that killing plants by hoeing had drastic effects on soil fauna and functioning, and apparently, distinguishing these effects from direct glyphosate effects is profoundly important when evaluating glyphosate risks in soils. In contrast, the effects of Roundup on soil fauna and functioning were minor and transient and no glyphosate remains were found in the soil at the end of the experiment. These results suggest that side-effects can be minor and glyphosate degradation effective also in soil under northern climatic conditions

Interpreting eddy covariance data from heterogeneous Siberian tundra : land-cover-specific methane fluxes and spatial representativeness

The non-uniform spatial integration, an inherent feature of the eddy covariance (EC) method, creates a challenge for flux data interpretation in a heterogeneous environment, where the contribution of different land cover types varies with flow conditions, potentially resulting in biased estimates in comparison to the areally averaged fluxes and land cover attributes. We modelled flux footprints and characterized the spatial scale of our EC measurements in Tiksi, a tundra site in northern Siberia. We used leaf area index (LAI) and land cover class (LCC) data, derived from very-high-spatial-resolution satellite imagery and field surveys, and quantified the sensor location bias. We found that methane (CH4) fluxes varied strongly with wind direction (-0.09 to 0.59 mu gCH(4)m(-2) s(-1) on average) during summer 2014, reflecting the distribution of different LCCs. Other environmental factors had only a minor effect on short-term flux variations but influenced the seasonal trend. Using footprint weights of grouped LCCs as explanatory variables for the measured CH4 flux, we developed a multiple regression model to estimate LCC group-specific fluxes. This model showed that wet fen and graminoid tundra patches in locations with topography-enhanced wetness acted as strong sources (1.0 mu gCH(4) m(-2) s(-1) during the peak emission period), while mineral soils were significant sinks (-0.13 mu gCH(4) m(-2) s(-1)). To assess the representativeness of measurements, we upscaled the LCC group-specific fluxes to different spatial scales. Despite the landscape heterogeneity and rather poor representativeness of EC data with respect to the areally averaged LAI and coverage of some LCCs, the mean flux was close to the CH4 balance upscaled to an area of 6.3 km(2), with a location bias of 14 %. We recommend that EC site descriptions in a heterogeneous environment should be complemented with footprint-weighted high-resolution data on vegetation and other site characteristics.Peer reviewe

A new method for estimating carbon dioxide emissions from drained peatland forest soils for the greenhouse gas inventory of Finland

Reporting the greenhouse gas (GHG) emissions from the LULUCF sector in the GHG inventory requires sound methods for estimating both the inputs and outputs of carbon (C) in managed ecosystems. Soil CO2 balance of forests consists of the CO2 released from decomposing soil organic matter (SOM) and the C entering the soil through aboveground and belowground plant litter input. Peatlands drained for forestry release soil C as CO2 because the drainage deepens the oxic peat layer prone to SOM decomposition. IPCC Guidelines provide default CO2 emission factors for different climatic zones and the defaults or locally adapted static emission factors are commonly in use in GHG inventory reporting for drained peatlands. In this paper, we describe a new dynamic method to estimate the CO2 balance of drained peatland forest soils in Finland. Contrary to static emission factors, the annual CO2 release from soil is in our method estimated using empirical regression models driven by time series of tree basal area (BA), derived from the national forest inventories in Finland, time series of air temperature and the drained peatland forest site type. Aboveground and belowground litter input is also estimated using empirical models with newly acquired turnover rates for tree fine roots and BA as a dynamic driver. All major components of litter input from ground vegetation and live, harvested and naturally died trees are included. Our method produces an increasing trend of emissions from 1.4 to 7.9 Mt CO2 for drained peatland forest soils in Finland for the period 1990&ndash;2021, with a statistically significant difference between years 1990 and 2021. Across the period 1990&ndash;2021, annual emissions are on average 3.4 Mt and &minus;0.3 Mt in southern and northern parts of Finland, respectively. When combined with data of the CO2 sink created by trees, it appears that in 2021 drained peatland forest ecosystems were a source of 2.3 Mt CO2 in southern Finland and a sink of 2.5 Mt CO2 in northern Finland. We compare the emissions produced by the new method with those produced by the old GHGI method of Finland and discuss the strengths and vulnerabilities of our method in comparison to static emission factors.</p