Towards a set of agrosystem-specific cropland mapping methods to address the global cropland diversity

Accurate cropland information is of paramount importance for crop monitoring. This study compares five existing cropland mapping methodologies over five contrasting Joint Experiment for Crop Assessment and Monitoring (JECAM) sites of medium to large average field size using the time series of 7-day 250 m Moderate Resolution Imaging Spectroradiometer (MODIS) mean composites (red and near-infrared channels). Different strategies were devised to assess the accuracy of the classification methods: confusion matrices and derived accuracy indicators with and without equalizing class proportions, assessing the pairwise difference error rates and accounting for the spatial resolution bias. The robustness of the accuracy with respect to a reduction of the quantity of calibration data available was also assessed by a bootstrap approach in which the amount of training data was systematically reduced. Methods reached overall accuracies ranging from 85% to 95%, which demonstrates the ability of 250 m imagery to resolve fields down to 20 ha. Despite significantly different error rates, the site effect was found to persistently dominate the method effect. This was confirmed even after removing the share of the classification due to the spatial resolution of the satellite data (from 10% to 30%). This underlines the effect of other agrosystems characteristics such as cloudiness, crop diversity, and calendar on the ability to perform accurately. All methods have potential for large area cropland mapping as they provided accurate results with 20% of the calibration data, e.g. 2% of the study area in Ukraine. To better address the global cropland diversity, results advocate movement towards a set of cropland classification methods that could be applied regionally according to their respective performance in specific landscapes.Instituto de Clima y AguaFil: Waldner, François. Université catholique de Louvain. Earth and Life Institute - Environment, Croix du Sud; BelgicaFil: De Abelleyra, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Clima y Agua; ArgentinaFil: Veron, Santiago Ramón. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Clima y Agua; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Métodos Cuantitativos y Sistemas de Información; ArgentinaFil: Zhang, Miao. Chinese Academy of Science. Institute of Remote Sensing and Digital Earth; ChinaFil: Wu, Bingfang. Chinese Academy of Science. Institute of Remote Sensing and Digital Earth; ChinaFil: Plotnikov, Dmitry. Russian Academy of Sciences. Space Research Institute. Terrestrial Ecosystems Monitoring Laboratory; RusiaFil: Bartalev, Sergey. Russian Academy of Sciences. Space Research Institute. Terrestrial Ecosystems Monitoring Laboratory; RusiaFil: Lavreniuk, Mykola. Space Research Institute NAS and SSA. Department of Space Information Technologies; UcraniaFil: Skakun, Sergii. Space Research Institute NAS and SSA. Department of Space Information Technologies; Ucrania. University of Maryland. Department of Geographical Sciences; Estados UnidosFil: Kussul, Nataliia. Space Research Institute NAS and SSA. Department of Space Information Technologies; UcraniaFil: Le Maire, Guerric. UMR Eco&Sols, CIRAD; Francia. Empresa Brasileira de Pesquisa Agropecuária. Meio Ambiante; BrasilFil: Dupuy, Stéphane. Centre de Coopération Internationale en Recherche Agronomique pour le Développement. Territoires, Environnement, Télédétection et Information Spatiale; FranciaFil: Jarvis, Ian. Agriculture and Agri-Food Canada. Science and Technology Branch. Agri-Climate, Geomatics and Earth Observation; CanadáFil: Defourny, Pierre. Université Catholique de Louvain. Earth and Life Institute - Environment, Croix du Sud; Belgic

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. However, even for simple bacteria, whole-cell models will contain thousands of parameters, many of which are poorly characterized or unknown. New algorithms are needed to estimate these parameters and enable researchers to build increasingly comprehensive models. We organized the Dialogue for Reverse Engineering Assessments and Methods (DREAM) 8 Whole-Cell Parameter Estimation Challenge to develop new parameter estimation algorithms for whole-cell models. We asked participants to identify a subset of parameters of a whole-cell model given the model’s structure and in silico “experimental” data. Here we describe the challenge, the best performing methods, and new insights into the identifiability of whole-cell models. We also describe several valuable lessons we learned toward improving future challenges. Going forward, we believe that collaborative efforts supported by inexpensive cloud computing have the potential to solve whole-cell model parameter estimation

PLoS Comput Biol

Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. However, even for simple bacteria, whole-cell models will contain thousands of parameters, many of which are poorly characterized or unknown. New algorithms are needed to estimate these parameters and enable researchers to build increasingly comprehensive models. We organized the Dialogue for Reverse Engineering Assessments and Methods (DREAM) 8 Whole-Cell Parameter Estimation Challenge to develop new parameter estimation algorithms for whole-cell models. We asked participants to identify a subset of parameters of a whole-cell model given the model's structure and in silico "experimental" data. Here we describe the challenge, the best performing methods, and new insights into the identifiability of whole-cell models. We also describe several valuable lessons we learned toward improving future challenges. Going forward, we believe that collaborative efforts supported by inexpensive cloud computing have the potential to solve whole-cell model parameter estimation.5DP1LM01150-05/DP/NCCDPHP CDC HHS/United StatesDP1 LM011510/LM/NLM NIH HHS/United StatesDP1 OD006413/OD/NIH HHS/United States26020786PMC444741

2012 Bacterial Source Tracking - State of the Science Conference Conference Proceedings

The 2012 Bacterial Source Tracking - State of the Science Conference was held February 28-29 at the T Bar M Resort and Conference Center in New Braunfels, Texas. Academia involved in BST analysis; state, federal, and regional agency personnel; elected officials; and other interested persons were targeted through various media outlets. Prior to the conference, the Texas State Soil and Water Conservation Board (TSSWCB) queried state and federal agencies about what their wants and needs in regards to the state of BST science. Staff from the U.S. Environmental Protection Agency (EPA), Texas Parks and Wildlife Department (TPWD), Texas Commission on Environmental Quality (TCEQ) and others were asked to identify questions and issues that should be included in conference presentations and discussion

Cultural re-presentation and translation : Chinese and English anthologies of Tang poetry

Due to its unique prestige, classical Chinese poetry written during the Tang dynasty is often anthologised. These anthologies serve various purposes (e.g. recreational, educational, or both), but they are generally expected to feature works high in aesthetic value, and represent the culture wherein they are produced. While the functions of anthologies are seldom contested, representations of Tang poetry in anthologies have many different manifestations. Using China’s most famous anthology, Tangshi sanbaishou 唐詩三百首, as an opening case study, research shows that within its home culture, the anthologising of Tang poetry has a long history by itself, and anthologists negotiate between ideological agendas, aesthetic judgments, and cultural norms to form representations which suit their purposes best. Complex as the anthologising behaviour in the source culture is, the considerations involved in anthologising translated Tang poetry in the Anglo-American culture are even more complicated, since target-cultural concerns/demands (such as translatability, aesthetic predilection of the target readership, social norms, etc.) are introduced. This study attempts to delineate the differences in various source and target cultural representations of Tang poetry, and explicate the contributing causes engendering such differences. A survey of anthologies of translated classical Chinese literature/poetry reveals that key factors governing anthologising decisions include: the target cultural condition, the intended service to a mostly uninformed, non-native readership, the anthologist-translators’ personal preferences and missions, among others. The canonical landscape of Tang poetry changes often in the West even though the principle of representativeness demands a degree of conformity to the source tradition. The complexity of anthologising is further amplified when the activity of translation takes place. Translation may enhance or discount the aesthetic appeal of poets and poems, thus implicating their claim for canonicity. Besides, questions of form and prosody also shape the target-culture product, and hence the readership’s perception. The representations of Tang poetry and Chinese culture in anthologies are often taken for granted due to the sense of authority attached to anthologies. It is therefore important to take note of and examine how anthologist-translators have shaped literary perceptions by negotiating between source and target cultures

A Survey of Dataset Refinement for Problems in Computer Vision Datasets

Large-scale datasets have played a crucial role in the advancement of computer vision. However, they often suffer from problems such as class imbalance, noisy labels, dataset bias, or high resource costs, which can inhibit model performance and reduce trustworthiness. With the advocacy of data-centric research, various data-centric solutions have been proposed to solve the dataset problems mentioned above. They improve the quality of datasets by re-organizing them, which we call dataset refinement. In this survey, we provide a comprehensive and structured overview of recent advances in dataset refinement for problematic computer vision datasets. Firstly, we summarize and analyze the various problems encountered in large-scale computer vision datasets. Then, we classify the dataset refinement algorithms into three categories based on the refinement process: data sampling, data subset selection, and active learning. In addition, we organize these dataset refinement methods according to the addressed data problems and provide a systematic comparative description. We point out that these three types of dataset refinement have distinct advantages and disadvantages for dataset problems, which informs the choice of the data-centric method appropriate to a particular research objective. Finally, we summarize the current literature and propose potential future research topics.Comment: 33 pages, 10 figures, to be published in ACM Computing Survey

Threats to the Soil Resource Base of Food Security in China and Europe. A report from the Sino-EU Panel on Land and Soil

To secure adequate food supply is the major challenge for humanity in the 21st century. Growing world population and its urbanization put pressure on this basic need, which is further threatened by the constant loss of fertile land. The assessment of sustainability of food supply under increasing pressure on land resources has been selected as one of the most important priority topics of the activities of Sino-EU Panel on Land and Soil (SEPLS). The Panel has performed a number of related researches and discussed the results on a scientific seminar in January 2012 in Nanjing, China. This report is an output of this seminar with a summary of the structured discussions on the below issues. 1. Urban and peri-urban development (soil sealing and loss of land functions) Urbanization and the linked spread of infrastructural development mean sealing of soil surfaces. Soil sealing is the most rapidly growing limitation for soil functions (including biomass production function) both in China and Europe. Soil sealing in China has been taking dramatic degree in the last two decades and the process is estimated to continue in the coming period as well. While urban and peri-urban development is looked as a necessity for social development, its negative effect on natural resources are inevitable. 2. Land degradation Despite the widely recognized importance of land degradation in the unsustainability of economic development and implementation of various policies to halt degradation (e.g. green for grain programme in China; cross-compliance measures in the EU), loss of land productivity by degradation is an ongoing process both in China and the EU. Major forms of soil degradation (erosion, desertification, landslides etc.) are similar in both regions. Assessment of the causes and consequences of soil degradation processes in relation to policy actions is highlighted among the priorities of the SEPLS. 3. Intensive agriculture and multi-function management of land resources Intensification and extensification in agriculture can be considered as the main changes in land use in rural areas in both EU and China. While agricultural intensification is one of the greatest threats to the soil and environment and then hampers the sustainable development of agriculture and food security. To meet this challenge, sustainable management of multi-functionality of land resources is undoubtedly an effective strategy, in which the EU has a good expertise. Bilateral exchange of the experience and knowledge benefits the sustainable management of land resources.JRC.H.5-Land Resources Managemen

3rd Conference on Ecology of Soil Microorganisms

We are pleased to welcome you to the 3rd conference on the Ecology of Soil Microorganisms in Helsinki, Finland. The two previous meetings were organized in Prague in 2011 and 2015 by Petr Baldrian. We are delighted to see that as many participants, 400 are joining us also under the midnight sun. During the meeting, soil science will be linked with traditional microbiology and modern genomic, transcriptomic and proteomic analysis tools, extending from the soil-microbe interphase to their interactions with plants. Indeed, one important goal of the conference is to inspire us to bring forward new dimensions in the characterization of the interplay between soil microbial ecology and larger-scale processes in various ecosystems. In this meeting we will cover not only the role of soil microbiota but also their viruses. We hope that you take a moment to think of recent studies that have begun to unearth relationships found between soil microbes, plant performance and even human health. Sustainability of soils and their role in mitigation of climate change are key challenges for preserving life on Earth. As microbes are living functional components of soils, our focus during the week could not be timelier. The organizers and the host organization Natural Resources Institute Finland wish you a fruitful and invigorating conference. We are excited that you have joined us here in Helsinki to promote state-of-the-art research in soil ecology under the northern midsummer madness!201

Effects of softwood biochars on soil biota in medium-term field experiments in Finland

Biochar soil amendment could be used to sequester carbon, enhance soil fertility and potentially increase crop yields. It can have significant impacts on soil organic carbon levels and physicochemical conditions, which consequently affect soil micro- and macro-biota. It is therefore important to understand how key biological components in the soil such as microbial and earthworm communities response to biochar application in the long-term. This study was conducted in Southern Finland in a fertile Stagnosol and a nutrient deficient Umbrisol, four and five years after biochar amendment, respectively. Biochars were produced from spruce (Picea abies (L.) H.Karst.) and pine (Pinus sylvestris L.), and applied at the rates of 10 and 30 t ha-1, respectively. Earthworms and soil samples for microbial analyses were collected in September 2015. Soil microbial communities were studied by using phospholipid fatty acid profiling and 16S rRNA gene amplicon sequencing. Casts from the sampled earthworms were collected to investigate the consumption of biochar and the potential of earthworm bioturbation to affect biochar distribution. Additionally, greenhouse gas emissions from soil were measured. Biochar and fertilizer treatments or their interaction had no statistically significant effects on the earthworm abundance, community composition or greenhouse gas emissions in either field. Earthworms had ingested biochar as earthworm casts from biochar treated-plots contained significantly more black carbon than those in the control plots, demonstrating that earthworm bioturbation is a potentially important factor in the translocation of applied biochar in the soil profile. Microbial community structure data will be presented in the final presentation.Non peer reviewe