GIS-based G × E modeling of maize hybrids through enviromic markers engineering.

Through enviromics, precision breeding leverages innovative geotechnologies to customize crop varieties to specific environments, potentially improving both crop yield and genetic selection gains. In Brazil's four southernmost states, data from 183 distinct geographic field trials (also accounting for 2017-2021) covered information on 164 genotypes: 79 phenotyped maize hybrid genotypes for grain yield and their 85 nonphenotyped parents. Additionally, 1342 envirotypic covariates from weather, soil, sensor-based, and satellite sources were collected to engineer 10 K synthetic enviromic markers via machine learning. Soil, radiation light, and surface temperature variations remarkably affect differential genotype yield, hinting at ecophysiological adjustments including evapotranspiration and photosynthesis. The enviromic ensemble-based random regression model showcases superior predictive performance and efficiency compared to the baseline and kernel models, matching the best genotypes to specific geographic coordinates. Clustering analysis has identified regions that minimize genotype-environment (G × E) interactions. These findings underscore the potential of enviromics in crafting specific parental combinations to breed new, higher-yielding hybrid crops. The adequate use of envirotypic information can enhance the precision and efficiency of maize breeding by providing important inputs about the environmental factors that affect the average crop performance. Generating enviromic markers associated with grain yield can enable a better selection of hybrids for specific environments.

High Glass Transition Temperature Fluorinated Polymers Based on Transfer Learning with Small Experimental Data.

Machine learning can be used to predict the properties of polymers and explore vast chemical spaces. However, the limited number of available experimental datasets hinders the enhancement of the predictive performance of a model. This study proposes a machine learning approach that leverages transfer learning and ensemble modeling to efficiently predict the glass transition temperature (Tg) of fluorinated polymers and guide the design of high Tg copolymers. Initially, the quantum machine 9 (QM9) dataset is employed for model pretraining, thus providing robust molecular representations for the subsequent fine-tuning of a specialized copolymer dataset. Ensemble modeling is used to further enhance prediction robustness and reliability, effectively addressing the problems owing to the limited and unevenly distributed nature of the copolymer dataset. Finally, a fine-tuned ensemble model is used to navigate a vast chemical space comprising 61 monomers and identify promising candidates for high Tg fluorinated polymers. The model predicts 247 entries capable of achieving a Tg over 390 K, of which 14 are experimentally validated. This study demonstrates the potential of machine learning in material design and discovery, highlighting the effectiveness of transfer learning and ensemble modeling strategies for overcoming the challenges posed by small datasets in complex copolymer systems.

A dynamic kinetic model captures cell-free metabolism for improved butanol production.

Cell-free systems are useful tools for prototyping metabolic pathways and optimizing the production of various bioproducts. Mechanistically-based kinetic models are uniquely suited to analyze dynamic experimental data collected from cell-free systems and provide vital qualitative insight. However, to date, dynamic kinetic models have not been applied with rigorous biological constraints or trained on adequate experimental data to the degree that they would give high confidence in predictions and broadly demonstrate the potential for widespread use of such kinetic models. In this work, we construct a large-scale dynamic model of cell-free metabolism with the goal of understanding and optimizing butanol production in a cell-free system. Using a combination of parameterization methods, the resultant model captures experimental metabolite measurements across two experimental conditions for nine metabolites at timepoints between 0 and 24 h. We present analysis of the model predictions, provide recommendations for butanol optimization, and identify the aldehyde/alcohol dehydrogenase as the primary bottleneck in butanol production. Sensitivity analysis further reveals the extent to which various parameters are constrained, and our approach for probing valid parameter ranges can be applied to other modeling efforts.

A new malaria vector in Africa: Predicting the expansion range of Anopheles stephensi and identifying the urban populations at risk.

In 2012, an unusual outbreak of urban malaria was reported from Djibouti City in the Horn of Africa and increasingly severe outbreaks have been reported annually ever since. Subsequent investigations discovered the presence of an Asian mosquito species; Anopheles stephensi, a species known to thrive in urban environments. Since that first report, An. stephensi has been identified in Ethiopia and Sudan, and this worrying development has prompted the World Health Organization (WHO) to publish a vector alert calling for active mosquito surveillance in the region. Using an up-to-date database of published locational records for An. stephensi across its full range (Asia, Arabian Peninsula, Horn of Africa) and a set of spatial models that identify the environmental conditions that characterize a species' preferred habitat, we provide evidence-based maps predicting the possible locations across Africa where An. stephensi could establish if allowed to spread unchecked. Unsurprisingly, due to this species' close association with man-made habitats, our maps predict a high probability of presence within many urban cities across Africa where our estimates suggest that over 126 million people reside. Our results strongly support the WHO's call for surveillance and targeted vector control and provide a basis for the prioritization of surveillance.

Improving groundwater nitrate concentration prediction using local ensemble of machine learning models.

Groundwater is one of the most important water resources around the world, which is increasingly exposed to contamination. As nitrate is a common pollutant of groundwater and has negative effects on human health, predicting its concentration is of particular importance. Ensemble machine learning (ML) algorithms have been widely employed for nitrate concentration prediction in groundwater. However, existing ensemble models often overlook spatial variation by combining ML models with conventional methods like averaging. The objective of this study is to enhance the spatial accuracy of groundwater nitrate concentration prediction by integrating the outputs of ML models using a local approach that accounts for spatial variation. Initially, three widely used ML models including random forest regression (RFR), k-nearest neighbor (KNN), and support vector regression (SVR) were employed to predict groundwater nitrate concentration of Qom aquifer in Iran. Subsequently, the output of these models were integrated using geographically weighted regression (GWR) as a local model. The findings demonstrated that the ensemble of ML models using GWR resulted in the highest performance (R2 = 0.75 and RMSE = 9.38 mg/l) compared to an ensemble model using averaging (R2 = 0.68 and RMSE = 10.56 mg/l), as well as individual models such as RFR (R2 = 0.70 and RMSE = 10.16 mg/l), SVR (R2 = 0.59 and RMSE = 11.95 mg/l), and KNN (R2 = 0.57 and RMSE = 12.19 mg/l). The resulting prediction map revealed that groundwater nitrate contamination is predominantly concentrated in urban areas located in the northwestern regions of the study area. The insights gained from this study have practical implications for managers, assisting them in preventing nitrate pollution in groundwater and formulating strategies to improve water quality.

Online learning-empowered smart management for A2O process in sewage treatment processes.

Using artificial intelligence method to describe general working process is a more meaningful and widely used idea in various practical projects. At the same time, it is also an important way to realize intelligent management. Water pollution is serious all over the world, also the intelligent management of sewage treatment has always been one of the urgent problems to be solved. For this, an intelligent management system is designed in this study to realize automatic monitoring and intelligent decision-making of sewage treatment. However, the existing technology usually trains artificial intelligence models based on historical data, and such models have some limitations in describing nonlinear and complex wastewater treatment processes. Offline machine learning lacks dynamic adaptive characteristics to scene changes. Considering this, this paper designs an online learning-empowered smart management for A2/O process in sewage treatment processes (OL-AP). Online learning is based on the new data generated by the scene transformation, so that the model can learn again and give better results. In this study, relevant simulation experiments are carried out on the sewage treatment data of a sewage treatment plant in Chongqing. Firstly, automatic data collection is realized based on the sensor network of the IoT. Then, according to the preprocessed data, the designed prediction model is trained and a set of parameters with better evaluation indexes is obtained. Finally, online learning uses the latest data samples based on the online feedback of real scenes to optimize the model by retraining and adjusting parameters.

Spatial ensemble modeling for predicting the potential distribution of Lymantria dispar asiatica (Lepidoptera: Erebidae: Lymantriinae) in South Korea.

The spongy moth, Lymantria dispar, is a pest that damages various tree species throughout North America and Eurasia, has recently emerged in South Korea, threatening local forests and landscapes. The establishment of effective countermeasures against this species' outbreak requires predicting its potential distribution with climate change. In this study, we used species distribution models (CLIMEX and MaxEnt) to predict the potential distribution of the spongy moth and identify areas at risk of exposure to a sustained occurrence of the pest by constructing an ensemble map that simultaneously projected the outcomes of the two models. The results showed that the spongy moth could be distributed over the entire country under the current climate, but the number of suitable areas would decrease under a climate change scenario. This study is expected to provide basic data that can predict areas requiring intensive control and monitoring in advance with methodologically improved modeling technique.

Using ensemble modeling to predict the impacts of assisted migration on recipient ecosystems.

Assisted migration is a controversial conservation measure that aims to protect threatened species by moving part of their population outside its natural range. Although this could save species from extinction, it also introduces a range of risks. The magnitude of the threat to recipient ecosystems has not been investigated quantitatively, despite being the most common criticism leveled at the action. We used an ensemble modeling framework to estimate the risks of assisted migration to existing species within ecosystems. With this approach, we calculated the consequences of an assisted migration project across a very large combination of translocated species and recipient ecosystems. We predicted the probability of a successful assisted migration and the number of local extinctions would result from establishment of the translocated species. Using an ensemble of 1.5×106 simulated 15-species recipient ecosystems, we estimated that translocated species will successfully establish in 83% of cases if introduced to stable, high-quality habitats. However, assisted migration projects were estimated to cause an average of 0.6 extinctions and 5% of successful translocations triggered 4 or more local extinctions. Quantifying the impacts to species within recipient ecosystems is critical to help managers weigh the benefits and negative consequences of assisted migration.

Modelación en Conjunto para Predecir los Impactos de la Migración Asistida sobre los Ecosistemas Receptores Resumen La migración asistida es una medida controversial de conservación que busca proteger a las especies amenazadas mediante la mudanza de parte de su población fuera de su extensión natural. Este método podría salvar a las especies de la extinción, pero también implica una gama de riesgos. La magnitud de la amenaza para el ecosistema receptor no ha sido investigada cuantitativamente a pesar de ser la crítica más común para esta acción. Usamos un marco de trabajo de modelación en conjunto para estimar los riesgos de la migración asistida para las especies existentes dentro de los ecosistemas. Mediante este enfoque calculamos las consecuencias de un proyecto de migración asistida en una combinación de especies reubicadas y ecosistemas receptores. Pronosticamos la probabilidad de una migración asistida exitosa y el número local de extinciones que resultarían de la introducción de especies reubicadas. Con un conjunto simulado de 1.5×106 ecosistemas receptores con 15 especies, estimamos que las especies reubicadas se establecerán exitosamente en 83% de los casos si son introducidas a hábitats estables y de alta calidad. Sin embargo, se estimó que los proyectos de migración asistida causarían un promedio de 0.6 extinciones y el 5% de las reubicaciones exitosas generaron cuatro o más extinciones locales. La cuantificación de los impactos para las especies dentro de los ecosistemas receptores es crítica para ayudar a los manejadores a sopesar los beneficios y las consecuencias negativas de la migración asistida.

Examining PM2.5 concentrations and exposure using multiple models.

Epidemiologic studies have found associations between fine particulate matter (PM2.5) exposure and adverse health effects using exposure models that incorporate monitoring data and other relevant information. Here, we use nine PM2.5 concentration models (i.e., exposure models) that span a wide range of methods to investigate i) PM2.5 concentrations in 2011, ii) potential changes in PM2.5 concentrations between 2011 and 2028 due to on-the-books regulations, and iii) PM2.5 exposure for the U.S. population and four racial/ethnic groups. The exposure models included two geophysical chemical transport models (CTMs), two interpolation methods, a satellite-derived aerosol optical depth-based method, a Bayesian statistical regression model, and three data-rich machine learning methods. We focused on annual predictions that were regridded to 12-km resolution over the conterminous U.S., but also considered 1-km predictions in sensitivity analyses. The exposure models predicted broadly consistent PM2.5 concentrations, with relatively high concentrations on average over the eastern U.S. and greater variability in the western U.S. However, differences in national concentration distributions (median standard deviation: 1.00 µg m-3) and spatial distributions over urban areas were evident. Further exploration of these differences and their implications for specific applications would be valuable. PM2.5 concentrations were estimated to decrease by about 1 µg m-3 on average due to modeled emission changes between 2011 and 2028, with decreases of more than 3 µg m-3 in areas with relatively high 2011 concentrations that were projected to experience relatively large emission reductions. Agreement among models was closer for population-weighted than uniformly weighted averages across the domain. About 50% of the population was estimated to experience PM2.5 concentrations less than 10 µg m-3 in 2011 and PM2.5 improvements of about 2 µg m-3 due to modeled emission changes between 2011 and 2028. Two inequality metrics were used to characterize differences in exposure among the four racial/ethnic groups. The metrics generally yielded consistent information and suggest that the modeled emission reductions between 2011 and 2028 would reduce absolute exposure inequality on average.

A novel approach for estimation of aboveground biomass of a carbon-rich mangrove site in India.

Mangroves can play a crucial part in climate change mitigation policies due to their high carbon-storing capacity. However, the carbon sequestration potential of Indian mangroves generally remained unexplored to date. In this study, multi-temporal Sentinel-1 and 2 data-derived variables were used to estimate the AGB of a tropical carbon-rich mangrove forest of India. Ensemble prediction of multiple machine learning algorithms, including Random Forest (RF), Gradient Boosted Model (GBM), and Extreme Gradient Boosting (XGB), were used for AGB prediction. The multi-temporal dataset was used in two different ways to find the most suitable method of using them. The results of the analysis showed that the modeling field measured AGB with individual date data values results in estimates with root mean square errors (RMSE) ranging from 149.242 t/ha for XGB to 151.149 t/ha for the RF. Modeling AGB with the average and percentile metrics of the multi-temporal image stack improves the prediction accuracy of AGB, with RMSE ranging from 81.882 t/ha for the XGB to 74.493 t/ha for the RF. The AGB modeling using ensemble prediction showed further improvement in accuracy with an RMSE of 72.864 t/ha and normalized RMSE of 11.38%. In this study, the intra-seasonal variation of Sentinel-1 and 2 data for mangrove ecosystems was explored for the first time. The variations in remotely sensed variables could be attributed mainly to soil moisture availability and rainfall in the mangrove ecosystem. The efficiency of Sentinel-1 and 2 data-derived variables and ensemble prediction of machine learning models for Indian mangroves were also explored for the first time. The methodologies established in this study can be used in the future for accurate prediction and repeated monitoring of AGB for mangrove ecosystems.

Ensemble evaluation of the potential risk areas of yellow-legged hornet distribution.

Invasion of alien species facilitated by climate change and human assistant is one of global threats that cause irreversible damages on the local flora and fauna. One of these issued species, Vespa velutina nigrithorax du Buysson, 1905 (Hymenoptera:Vespidae), is a significant threat to entomofauna, including honeybees, in the introduced regions. This wasp is still expanding its habitats, prioritizing the development of a reliable species distribution model based on recently updated occurrence data. Therefore, the aim of this study was to evaluate the potential areas that are climatically exposed to V. v. nigrithorax invasion globally and in South Korea, where the wasp has caused severe damage to local ecosystems and apiculture after its recent introduction. We developed a new global scale ensemble model based on CLIMEX and Maxent models and applied it to South Korea using field survey data. As a result, risky areas were predicted to be temperate and subtropical climate regions, including the eastern USA, western Europe, Far East Asia, and small areas in South America and Australia. In particular, South Korea has a high potential risk throughout the country. We expect that this study would provide fundamental data for monitoring the environmental risks caused by V. v. nigrithorax using advanced species distribution modeling.

Evaluation of CME Arrival Prediction Using Ensemble Modeling Based on Heliospheric Imaging Observations.

In this study, we evaluate a coronal mass ejection (CME) arrival prediction tool that utilizes the wide-angle observations made by STEREO's heliospheric imagers (HI). The unsurpassable advantage of these imagers is the possibility to observe the evolution and propagation of a CME from close to the Sun out to 1 AU and beyond. We believe that by exploiting this capability, instead of relying on coronagraph observations only, it is possible to improve today's CME arrival time predictions. The ELlipse Evolution model based on HI observations (ELEvoHI) assumes that the CME frontal shape within the ecliptic plane is an ellipse and allows the CME to adjust to the ambient solar wind speed; that is, it is drag based. ELEvoHI is used to perform ensemble simulations by varying the CME frontal shape within given boundary conditions that are consistent with the observations made by HI. In this work, we evaluate different setups of the model by performing hindcasts for 15 well-defined isolated CMEs that occurred when STEREO was near L4/5, between the end of 2008 and the beginning of 2011. In this way, we find a mean absolute error of between 6.2 ± 7.9 and 9.9 ± 13 hr depending on the model setup used. ELEvoHI is specified for using data from future space weather missions carrying HIs located at L5 or L1. It can also be used with near-real-time STEREO-A HI beacon data to provide CME arrival predictions during the next ∼7 years when STEREO-A is observing the Sun-Earth space.

TopoFilter: a MATLAB package for mechanistic model identification in systems biology.

BACKGROUND: To develop mechanistic dynamic models in systems biology, one often needs to identify all (or minimal) representations of the biological processes that are consistent with experimental data, out of a potentially large set of hypothetical mechanisms. However, a simple enumeration of all alternatives becomes quickly intractable when the number of model parameters grows. Selecting appropriate dynamic models out of a large ensemble of models, taking the uncertainty in our biological knowledge and in the experimental data into account, is therefore a key current problem in systems biology. RESULTS: The TopoFilter package addresses this problem in a heuristic and automated fashion by implementing the previously described topological filtering method for Bayesian model selection. It includes a core heuristic for searching the space of submodels of a parametrized model, coupled with a sampling-based exploration of the parameter space. Recent developments of the method allow to balance exhaustiveness and speed of the model space search, to efficiently re-sample parameters, to parallelize the search, and to use custom scoring functions. We use a theoretical example to motivate these features and then demonstrate TopoFilter's applicability for a yeast signaling network with more than 250'000 possible model structures. CONCLUSIONS: TopoFilter is a flexible software framework that makes Bayesian model selection and reduction efficient and scalable to network models of a complexity that represents contemporary problems in, for example, cell signaling. TopoFilter is open-source, available under the GPL-3.0 license at https://gitlab.com/csb.ethz/TopoFilter. It includes installation instructions, a quickstart guide, a description of all package options, and multiple examples.

Ensemble modeling informs hypoxia management in the northern Gulf of Mexico.

A large region of low-dissolved-oxygen bottom waters (hypoxia) forms nearly every summer in the northern Gulf of Mexico because of nutrient inputs from the Mississippi River Basin and water column stratification. Policymakers developed goals to reduce the area of hypoxic extent because of its ecological, economic, and commercial fisheries impacts. However, the goals remain elusive after 30 y of research and monitoring and 15 y of goal-setting and assessment because there has been little change in river nitrogen concentrations. An intergovernmental Task Force recently extended to 2035 the deadline for achieving the goal of a 5,000-km2 5-y average hypoxic zone and set an interim load target of a 20% reduction of the spring nitrogen loading from the Mississippi River by 2025 as part of their adaptive management process. The Task Force has asked modelers to reassess the loading reduction required to achieve the 2035 goal and to determine the effect of the 20% interim load reduction. Here, we address both questions using a probabilistic ensemble of four substantially different hypoxia models. Our results indicate that, under typical weather conditions, a 59% reduction in Mississippi River nitrogen load is required to reduce hypoxic area to 5,000 km2 The interim goal of a 20% load reduction is expected to produce an 18% reduction in hypoxic area over the long term. However, due to substantial interannual variability, a 25% load reduction is required before there is 95% certainty of observing any hypoxic area reduction between consecutive 5-y assessment periods.

Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism.

In silico kinetic modeling is an essential tool for rationally designing metabolically engineered organisms based on a system-level understanding of their regulatory mechanisms. However, an estimation of enzyme parameters has been a bottleneck in the computer simulation of metabolic dynamics. In this study, the ensemble-modeling approach was integrated with the transomics data to construct kinetic models. Kinetic metabolic models of a photosynthetic bacterium, Synechocystis sp. PCC 6803, were constructed to identify engineering targets for improving ethanol production based on an understanding of metabolic regulatory systems. A kinetic model ensemble was constructed by randomly sampling parameters, and the best 100 models were selected by comparing predicted metabolic state with a measured dataset, including metabolic flux, metabolite concentrations, and protein abundance data. Metabolic control analysis using the model ensemble revealed that a large pool size of 3-phosphoglycerate could be a metabolic buffer responsible for the stability of the Calvin-Benson cycle, and also identified that phosphoglycerate kinase (PGK) is a promising engineering target to improve a pyruvate supply such as for ethanol production. Overexpression of PGK in the metabolically engineered PCC 6803 strain showed that the specific ethanol production rate and ethanol titers at 48 h were 1.23- and 1.37-fold greater than that of the control strain. PGK is useful for future metabolic engineering since pyruvate is a common precursor for the biosynthesis of various chemicals.

Twenty-first-century climate change impacts on marine animal biomass and ecosystem structure across ocean basins.

Climate change effects on marine ecosystems include impacts on primary production, ocean temperature, species distributions, and abundance at local to global scales. These changes will significantly alter marine ecosystem structure and function with associated socio-economic impacts on ecosystem services, marine fisheries, and fishery-dependent societies. Yet how these changes may play out among ocean basins over the 21st century remains unclear, with most projections coming from single ecosystem models that do not adequately capture the range of model uncertainty. We address this by using six marine ecosystem models within the Fisheries and Marine Ecosystem Model Intercomparison Project (Fish-MIP) to analyze responses of marine animal biomass in all major ocean basins to contrasting climate change scenarios. Under a high emissions scenario (RCP8.5), total marine animal biomass declined by an ensemble mean of 15%-30% (±12%-17%) in the North and South Atlantic and Pacific, and the Indian Ocean by 2100, whereas polar ocean basins experienced a 20%-80% (±35%-200%) increase. Uncertainty and model disagreement were greatest in the Arctic and smallest in the South Pacific Ocean. Projected changes were reduced under a low (RCP2.6) emissions scenario. Under RCP2.6 and RCP8.5, biomass projections were highly correlated with changes in net primary production and negatively correlated with projected sea surface temperature increases across all ocean basins except the polar oceans. Ecosystem structure was projected to shift as animal biomass concentrated in different size-classes across ocean basins and emissions scenarios. We highlight that climate change mitigation measures could moderate the impacts on marine animal biomass by reducing biomass declines in the Pacific, Atlantic, and Indian Ocean basins. The range of individual model projections emphasizes the importance of using an ensemble approach in assessing uncertainty of future change.

Ensemble outlier detection and gene selection in triple-negative breast cancer data.

BACKGROUND: Learning accurate models from 'omics data is bringing many challenges due to their inherent high-dimensionality, e.g. the number of gene expression variables, and comparatively lower sample sizes, which leads to ill-posed inverse problems. Furthermore, the presence of outliers, either experimental errors or interesting abnormal clinical cases, may severely hamper a correct classification of patients and the identification of reliable biomarkers for a particular disease. We propose to address this problem through an ensemble classification setting based on distinct feature selection and modeling strategies, including logistic regression with elastic net regularization, Sparse Partial Least Squares - Discriminant Analysis (SPLS-DA) and Sparse Generalized PLS (SGPLS), coupled with an evaluation of the individuals' outlierness based on the Cook's distance. The consensus is achieved with the Rank Product statistics corrected for multiple testing, which gives a final list of sorted observations by their outlierness level. RESULTS: We applied this strategy for the classification of Triple-Negative Breast Cancer (TNBC) RNA-Seq and clinical data from the Cancer Genome Atlas (TCGA). The detected 24 outliers were identified as putative mislabeled samples, corresponding to individuals with discrepant clinical labels for the HER2 receptor, but also individuals with abnormal expression values of ER, PR and HER2, contradictory with the corresponding clinical labels, which may invalidate the initial TNBC label. Moreover, the model consensus approach leads to the selection of a set of genes that may be linked to the disease. These results are robust to a resampling approach, either by selecting a subset of patients or a subset of genes, with a significant overlap of the outlier patients identified. CONCLUSIONS: The proposed ensemble outlier detection approach constitutes a robust procedure to identify abnormal cases and consensus covariates, which may improve biomarker selection for precision medicine applications. The method can also be easily extended to other regression models and datasets.

Investigating energy-based pool structure selection in the structure ensemble modeling with experimental distance constraints: The example from a multidomain protein Pub1.

The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates.

Ensemble Prediction of a Halo Coronal Mass Ejection Using Heliospheric Imagers.

The Solar TErrestrial RElations Observatory (STEREO) and its heliospheric imagers (HIs) have provided us the possibility to enhance our understanding of the interplanetary propagation of coronal mass ejections (CMEs). HI-based methods are able to forecast arrival times and speeds at any target and use the advantage of tracing a CME's path of propagation up to 1 AU and beyond. In our study, we use the ELEvoHI model for CME arrival prediction together with an ensemble approach to derive uncertainties in the modeled arrival time and impact speed. The CME from 3 November 2010 is analyzed by performing 339 model runs that are compared to in situ measurements from lined-up spacecraft MErcury Surface, Space ENvironment, GEochemistry, and Ranging and STEREO-B. Remote data from STEREO-B showed the CME as halo event, which is comparable to an HI observer situated at L1 and observing an Earth-directed CME. A promising and easy approach is found by using the frequency distributions of four ELEvoHI output parameters, drag parameter, background solar wind speed, initial distance, and speed. In this case study, the most frequent values of these outputs lead to the predictions with the smallest errors. Restricting the ensemble to those runs, we are able to reduce the mean absolute arrival time error from 3.5 ± 2.6 to 1.6 ± 1.1 hr at 1 AU. Our study suggests that L1 may provide a sufficient vantage point for an Earth-directed CME, when observed by HI, and that ensemble modeling could be a feasible approach to use ELEvoHI operationally.

Integrating subsistence practice and species distribution modeling: assessing invasive elodea's potential impact on Native Alaskan subsistence of Chinook salmon and whitefish.

Alaska has one of the most rapidly changing climates on earth and is experiencing an accelerated rate of human disturbance, including resource extraction and transportation infrastructure development. Combined, these factors increase the state's vulnerability to biological invasion, which can have acute negative impacts on ecological integrity and subsistence practices. Of growing concern is the spread of Alaska's first documented freshwater aquatic invasive plant Elodea spp. (elodea). In this study, we modeled the suitable habitat of elodea using global and state-specific species occurrence records and environmental variables, in concert with an ensemble of model algorithms. Furthermore, we sought to incorporate local subsistence concerns by using Native Alaskan knowledge and available statewide subsistence harvest data to assess the potential threat posed by elodea to Chinook salmon (Oncorhynchus tshawytscha) and whitefish (Coregonus nelsonii) subsistence. State models were applied to future climate (2040-2059) using five general circulation models best suited for Alaska. Model evaluations indicated that our results had moderate to strong predictability, with area under the receiver-operating characteristic curve values above 0.80 and classification accuracies ranging from 66 to 89 %. State models provided a more robust assessment of elodea habitat suitability. These ensembles revealed different levels of management concern statewide, based on the interaction of fish subsistence patterns, known spawning and rearing sites, and elodea habitat suitability, thus highlighting regions with additional need for targeted monitoring. Our results suggest that this approach can hold great utility for invasion risk assessments and better facilitate the inclusion of local stakeholder concerns in conservation planning and management.