{"type": "FeatureCollection", "features": [{"id": "10.1007/s00442-009-1516-5", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:14:49Z", "type": "Journal Article", "created": "2009-12-04", "title": "Combined Effects Of Precipitation And Nitrogen Deposition On Native And Invasive Winter Annual Production In California Deserts", "description": "Primary production in deserts is limited by soil moisture and N availability, and thus is likely to be influenced by both anthropogenic N deposition and precipitation regimes altered as a consequence of climate change. Invasive annual grasses are particularly responsive to increases in N and water availabilities, which may result in competition with native forb communities. Additionally, conditions favoring increased invasive grass production in arid and semi-arid regions can increase fire risk, negatively impacting woody vegetation that is not adapted to fire. We conducted a seeded garden experiment and a 5-year field fertilization experiment to investigate how winter annual production is altered by increasing N supply under a range of water availabilities. The greatest production of invasive grasses and native forbs in the garden experiment occurred under the highest soil N (inorganic N after fertilization = 2.99 g m(-2)) and highest watering regime, indicating these species are limited by both water and N. A classification and regression tree (CART) analysis on the multi-year field fertilization study showed that winter annual biomass was primarily limited by November-December precipitation. Biomass exceeded the threshold capable of carrying fire when inorganic soil N availability was at least 3.2 g m(-2) in pi\u00f1on-juniper woodland. Due to water limitation in creosote bush scrub, biomass exceeded the fire threshold only under very wet conditions regardless of soil N status. The CART analyses also revealed that percent cover of invasive grasses and native forbs is primarily dependent on the timing and amount of precipitation and secondarily dependent on soil N and site-specific characteristics. In total, our results indicate that areas of high N deposition will be susceptible to grass invasion, particularly in wet years, potentially reducing native species cover and increasing the risk of fire.", "keywords": ["0106 biological sciences", "Time Factors", "Schismus", "Non-native", "Bromus", "Nitrogen", "Climate Change", "Rain", "Plant Development", "Poaceae", "01 natural sciences", "California", "Fires", "Soil", "Climate change", "Biomass", "Ecology", " Evolution", " Behavior and Systematics", "0105 earth and related environmental sciences", "2. Zero hunger", "Ecology", "Geography", "Ecosystem ecology - Original paper", "Plant Sciences", "Life Sciences", "Water", "Agriculture", "Plants", "15. Life on land", "Fuel load", "6. Clean water", "13. Climate action", "Fertilization", "Regression Analysis", "Seasons", "Desert Climate"], "contacts": [{"organization": "Rao, Leela E., Allen, Edith B.,", "roles": ["creator"]}]}, "links": [{"href": "https://escholarship.org/content/qt8qv4f2kn/qt8qv4f2kn.pdf"}, {"href": "https://doi.org/10.1007/s00442-009-1516-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-009-1516-5", "name": "item", "description": "10.1007/s00442-009-1516-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-009-1516-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-12-05T00:00:00Z"}}, {"id": "10.1007/s00442-011-2133-7", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:14:49Z", "type": "Journal Article", "created": "2011-10-04", "title": "Soil Warming Alters Nitrogen Cycling In A New England Forest: Implications For Ecosystem Function And Structure", "description": "Global climate change is expected to affect terrestrial ecosystems in a variety of ways. Some of the more well-studied effects include the biogeochemical feedbacks to the climate system that can either increase or decrease the atmospheric load of greenhouse gases such as carbon dioxide and nitrous oxide. Less well-studied are the effects of climate change on the linkages between soil and plant processes. Here, we report the effects of soil warming on these linkages observed in a large field manipulation of a deciduous forest in southern New England, USA, where soil was continuously warmed 5\u00b0C above ambient for 7 years. Over this period, we have observed significant changes to the nitrogen cycle that have the potential to affect tree species composition in the long term. Since the start of the experiment, we have documented a 45% average annual increase in net nitrogen mineralization and a three-fold increase in nitrification such that in years 5 through 7, 25% of the nitrogen mineralized is then nitrified. The warming-induced increase of available nitrogen resulted in increases in the foliar nitrogen content and the relative growth rate of trees in the warmed area. Acer rubrum (red maple) trees have responded the most after 7 years of warming, with the greatest increases in both foliar nitrogen content and relative growth rates. Our study suggests that considering species-specific responses to increases in nitrogen availability and changes in nitrogen form is important in predicting future forest composition and feedbacks to the climate system.", "keywords": ["Ecosystem ecology - Original Paper", "0106 biological sciences", "550", "Nitrogen", "Climate Change", "Population Dynamics", "Acer", "04 agricultural and veterinary sciences", "Nitrogen Cycle", "15. Life on land", "Nitrate Reductase", "01 natural sciences", "Trees", "Soil", "Species Specificity", "New England", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Ecology", " Evolution", " Behavior and Systematics", "Ecosystem"]}, "links": [{"href": "https://doi.org/10.1007/s00442-011-2133-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-011-2133-7", "name": "item", "description": "10.1007/s00442-011-2133-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-011-2133-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-10-05T00:00:00Z"}}, {"id": "10.1007/s00894-025-06491-9", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:14:51Z", "type": "Journal Article", "created": "2025-09-13", "title": "Modification of biochar by iron containing adsorption centers as a method to enhance the remediation of perfluorooctanoic (PFOA) and (PFOS) acids from water and soil: a density functional theory study", "description": "Context: Perfluoroalkyl and polyfluoroalkyl substances (PFAS), with over 15,000 types listed in the US EPA\u2019s CompTox database, are found in everyday items like textiles, packaging, firefighting foams, and medical devices. Their widespread use has led to concerning health effects\u2014including cancers, elevated cholesterol, and fertility issues\u2014with detectable levels present in 98% of Americans. While perfluorooctanoic (PFOA) and perfluorooctanesulphonic (PFOS) are among the most studied, their environmental behavior and ecological interactions remain poorly understood. Advances in computer-based methods, including chemoinformatics and quantum modeling, now aid in predicting properties and simulating PFAS dynamics. Biochar (BC), produced via biomass pyrolysis under limited oxygen, is known for its porosity and adsorption capabilities. Magnetic biochar (MBC), enhanced with iron-based compounds, adds the benefit of magnetic separation, making it ideal for water decontamination. This paper explores the use of MBC to remove PFOA and PFOS from the environment, leveraging computational tools to investigate molecular interactions and adsorption properties. Methods: A doubled crystallographic unit of hematite (Fe\u2082\u2084O\u2083\u2086) was constructed and fully optimized using density functional theory (DFT) with the M06-2X functional. Geometry optimization used the 6-31G(d,p) basis set, while single-point energies were calculated with 6\u2013311 + + G(d,p). Antiferromagnetic conditions were ensured by setting the total spin to zero (Sz = 0), and triplet instability analysis was performed to evaluate ferromagnetic potential. To simulate bulk water effects on adsorption, the CPCM solvation model (\u03b5 = 78.3) was applied. Harmonic frequency analysis confirmed structural minima, and Gibbs free energies were calculated using Gaussian 16. PFOA and PFOS, with highly negative pKa values (~ \u20130.1 and <). Quadratic SCF convergence (scf = qc) addressed numerical challenges, and interaction energies were corrected for basis set superposition error using the counterpoise method. Calculated IR spectra and molecular visualizations were generated with Chemcraft, without applying scaling factors.", "keywords": ["Original Paper", "Magnetic biochar", "PFAS remediation", "Density functional theory (DFT)", "Perfluorooctanoic acid", "Perfluorooctanesulphonic acid", "Poly-fluoroalkyl substances"], "contacts": [{"organization": "Gorb, Leonid, Sosnowska, Anita, Bulawska, Natalia, Leszczynska, Danuta, Puzyn, Tomasz, Leszczynski, Jerzy,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/s00894-025-06491-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Molecular%20Modeling", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00894-025-06491-9", "name": "item", "description": "10.1007/s00894-025-06491-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00894-025-06491-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-09-13T00:00:00Z"}}, {"id": "10.1007/s10311-022-01500-2", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:14:56Z", "type": "Journal Article", "created": "2022-10-19", "title": "New separation protocol reveals spray painting as a neglected source of microplastics in soils", "description": "Abstract

Microplastics are recently discovered contaminants, yet knowledge on their sources and analysis is limited. For instance, paint microplastics are poorly known because soil separation protocols using flotation solutions cannot separate paint microplastics due to the higher density of paint microplastic versus common microplastics. Here, we designed a new two-step density separation protocol for paint microplastics, allowing paint microplastics to be separated from the soil without digestion. Paint particles were\uffc2\uffa0separated from soil samples collected around the graffiti wall at the Mauerpark, Berlin, then quantified according to their shape and color characteristic. The presence of polymers as binders in the paint particles was verified by Fourier transform infrared spectroscopy. Results show concentrations from 1.1\uffe2\uff80\uff89\uffc3\uff97\uffe2\uff80\uff89105 to 2.9\uffe2\uff80\uff89\uffc3\uff97\uffe2\uff80\uff89105 microplastics per Kg of dry soil, representing the highest microplastic concentration ever reported in the literature. Particle concentrations decreased and the median size increased with soil depth. Our results provide first evidence that spray painting, a technique with a wide range of applications from industry to art, leaves a legacy of environmental microplastic in soils that has so far gone unnoticed.

", "keywords": ["570", "Original Paper", "13. Climate action", "Paint microplastic", "0211 other engineering and technologies", "500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie", "02 engineering and technology", "Spray paint", "Infrared", "01 natural sciences", "Separation", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s10311-022-01500-2.pdf"}, {"href": "https://doi.org/10.1007/s10311-022-01500-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Chemistry%20Letters", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s10311-022-01500-2", "name": "item", "description": "10.1007/s10311-022-01500-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s10311-022-01500-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-10-19T00:00:00Z"}}, {"id": "10.1007/s11130-020-00799-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:15:23Z", "type": "Journal Article", "created": "2020-02-03", "title": "Profile and Content of Residual Alkaloids in Ten Ecotypes of Lupinus mutabilis Sweet after Aqueous Debittering Process", "description": "Abstract

The evaluation of the level of alkaloids in edible Lupinus species is crucial from a food safety point of view. Debittering of lupin seeds has a long history; however, the control of the level of alkaloids after processing the seeds is typically only evaluated by changes in the bitter taste. The aim of this study was to evaluate the profile and residual levels of quinolizidine alkaloids (QA) in (Lupinus mutabilis Sweet) after aqueous debittering process. Samples from 10 ecotypes from different areas of Peru were analyzed before and after the process. Based on results obtained by gas chromatography and mass spectrometry, from eight alkaloids identified before the debittering process, only small amounts of lupanine (avg. 0.0012\uffc2\uffa0g/100\uffc2\uffa0g DM) and sparteine (avg. 0.0014\uffc2\uffa0g/100\uffc2\uffa0g DM) remained in the seeds after the debittering process, and no other alkaloids were identified. The aqueous debittering process reduced the content of alkaloids to levels far below the maximal level allowed by international regulations (\uffe2\uff89\uffa4 0.2\uffc2\uffa0g/kg DM).

", "keywords": ["0301 basic medicine", "Lupin Seeds", "Sparteine", "Organic chemistry", "Propiedades fisicoqu\u00edmicas", "Plant Science", "Gas Chromatography-Mass Spectrometry", "Evolution and Nutritional Properties of Lupin Seeds", "Agricultural and Biological Sciences", "Food science", "Per\u00fa", "03 medical and health sciences", "Deshidrataci\u00f3n acuosa", "Alkaloids", "Secado", "Tarwi", "https://purl.org/pe-repo/ocde/ford#2.11.01", "Granos", "Composici\u00f3n qu\u00edmica", "ta116", "Biology", "Ecotipos", "Ecology", " Evolution", " Behavior and Systematics", "Ecotype", "2. Zero hunger", "Original Paper", "0303 health sciences", "Rendimiento", "Procesamiento", "Evaluaci\u00f3n", "ta1183", "An\u00e1lisis organol\u00e9ptico", "ta1182", "Botany", "Life Sciences", "Diversity and Applications of Cyperus Species", "Lupinus", "Chocho", "Chemistry", "Contenido proteico", "Evolution and Ecology of Endophyte-Grass Symbiosis", "Taste", "Seeds", "Lupinus mutabilis"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s11130-020-00799-y.pdf"}, {"href": "https://doi.org/10.1007/s11130-020-00799-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Foods%20for%20Human%20Nutrition", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11130-020-00799-y", "name": "item", "description": "10.1007/s11130-020-00799-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11130-020-00799-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-02-03T00:00:00Z"}}, {"id": "10.1007/s11130-016-0583-0", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:15:23Z", "type": "Journal Article", "created": "2016-11-05", "title": "Evaluation of Physicochemical and Glycaemic Properties of Commercial Plant-Based Milk Substitutes", "description": "The market for plant-based dairy-type products is growing as consumers replace bovine milk in their diet, for medical reasons or as a lifestyle choice. A screening of 17 different commercial plant-based milk substitutes based on different cereals, nuts and legumes was performed, including the evaluation of physicochemical and glycaemic properties. Half of the analysed samples had low or no protein contents (<0.5\u00a0%). Only samples based on soya showed considerable high protein contents, matching the value of cow's milk (3.7\u00a0%). An in-vitro method was used to predict the glycaemic index. In general, the glycaemic index values ranged from 47 for bovine milk to 64 (almond-based) and up to 100 for rice-based samples. Most of the plant-based milk substitutes were highly unstable with separation rates up to 54.39\u00a0%/h. This study demonstrated that nutritional and physicochemical properties of plant-based milk substitutes are strongly dependent on the plant source, processing and fortification. Most products showed low nutritional qualities. Therefore, consumer awareness is important when plant-based milk substitutes are used as an alternative to cow's milk in the diet.", "keywords": ["Blood Glucose", "0301 basic medicine", "2. Zero hunger", "Original Paper", "0303 health sciences", "Glycine max", "Plant-based milk substitutes", "Glycaemic index", "Oryza", "Dispersion stability", "03 medical and health sciences", "Chemistry (miscellaneous)", "Humans", "plant-based milk substitutes; protein requirement; glycaemic index; dispersion stability", "Protein requirement", "Milk Substitutes", "Nutritive Value", "Food Science"]}, "links": [{"href": "https://iris.uniroma1.it/bitstream/11573/1660889/1/Jeske_Evaluation-of-physicochemical_2017.pdf"}, {"href": "http://link.springer.com/content/pdf/10.1007/s11130-016-0583-0.pdf"}, {"href": "https://doi.org/10.1007/s11130-016-0583-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Foods%20for%20Human%20Nutrition", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11130-016-0583-0", "name": "item", "description": "10.1007/s11130-016-0583-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11130-016-0583-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-11-05T00:00:00Z"}}, {"id": "10.1016/j.compag.2021.106262", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:16:11Z", "type": "Journal Article", "created": "2021-07-15", "title": "A multifunctional matching algorithm for sample design in agricultural plots", "description": "Collection of accurate and representative data from agricultural fields is required for efficient crop management. Since growers have limited available resources, there is a need for advanced methods to select representative points within a field in order to best satisfy sampling or sensing objectives. The main purpose of this work was to develop a data-driven method for selecting locations across an agricultural field given observations of some covariates at every point in the field. These chosen locations should be representative of the distribution of the covariates in the entire population and represent the spatial variability in the field. They can then be used to sample an unknown target feature whose sampling is expensive and cannot be realistically done at the population scale. An algorithm for determining these optimal sampling locations, namely the multifunctional matching (MFM) criterion, was based on matching of moments (functionals) between sample and population. The selected functionals in this study were standard deviation, mean, and Kendall's tau. An additional algorithm defined the minimal number of observations that could represent the population according to a desired level of accuracy. The MFM was applied to datasets from two agricultural plots: a vineyard and a peach orchard. The data from the plots included measured values of slope, topographic wetness index, normalized difference vegetation index, and apparent soil electrical conductivity. The MFM algorithm selected the number of sampling points according to a representation accuracy of 90% and determined the optimal location of these points. The algorithm was validated against values of vine or tree water status measured as crop water stress index (CWSI). Algorithm performance was then compared to two other sampling methods: the conditioned Latin hypercube sampling (cLHS) model and a uniform random sample with spatial constraints. Comparison among sampling methods was based on measures of similarity between the target variable population distribution and the distribution of the selected sample. MFM represented CWSI distribution better than the cLHS and the uniform random sampling, and the selected locations showed smaller deviations from the mean and standard deviation of the entire population. The MFM functioned better in the vineyard, where spatial variability was larger than in the orchard. In both plots, the spatial pattern of the selected samples captured the spatial variability of CWSI. MFM can be adjusted and applied using other moments/functionals and may be adopted by other disciplines, particularly in cases where small sample sizes are desired.", "keywords": ["2. Zero hunger", "Partially-observed data", "Agricultural sampling", "Representative sampling given covariates", "0207 environmental engineering", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "02 engineering and technology", "15. Life on land", "Two-phase study", "310", "Original Papers", "Spatial autocorrelation"]}, "links": [{"href": "https://doi.org/10.1016/j.compag.2021.106262"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Computers%20and%20Electronics%20in%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.compag.2021.106262", "name": "item", "description": "10.1016/j.compag.2021.106262", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.compag.2021.106262"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-01T00:00:00Z"}}, {"id": "10.1093/bioinformatics/btad407", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:19:03Z", "type": "Journal Article", "created": "2023-06-24", "title": "enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways", "description": "Abstract Motivation

Transformation products (TPs) of man-made chemicals, formed through microbially mediated transformation in the environment, can have serious adverse environmental effects, yet the analytical identification of TPs is challenging. Rule-based prediction tools are successful in predicting TPs, especially in environmental chemistry applications that typically have to rely on small datasets, by imparting the existing knowledge on enzyme-mediated biotransformation reactions. However, the rules extracted from biotransformation reaction databases usually face the issue of being over/under-generalized and are not flexible to be updated with new reactions.

Results

We developed an automatic rule extraction tool called enviRule. It clusters biotransformation reactions into different groups based on the similarities of reaction fingerprints, and then automatically extracts and generalizes rules for each reaction group in SMARTS format. It optimizes the genericity of automatic rules against the downstream TP prediction task. Models trained with automatic rules outperformed the models trained with manually curated rules by 30% in the area under curve (AUC) scores. Moreover, automatic rules can be easily updated with new reactions, highlighting enviRule\uffe2\uff80\uff99s strengths for both automatic extraction of optimized reactions rules and automated updating thereof.

Availability and implementation

enviRule code is freely available at https://github.com/zhangky12/enviRule.

", "keywords": ["10120 Department of Chemistry", "Statistics and Probability", "Original Paper", "1303 Biochemistry", "Computational Biology", "Biochemistry", "Computer Science Applications", "Computational Mathematics", "Computational Theory and Mathematics", "13. Climate action", "540 Chemistry", "1312 Molecular Biology", "1706 Computer Science Applications", "2613 Statistics and Probability", "2605 Computational Mathematics", "Molecular Biology", "Biotransformation", "1703 Computational Theory and Mathematics"]}, "links": [{"href": "https://doi.org/10.1093/bioinformatics/btad407"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/bioinformatics/btad407", "name": "item", "description": "10.1093/bioinformatics/btad407", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/bioinformatics/btad407"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-24T00:00:00Z"}}, {"id": "10.1093/bioinformatics/btz584", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:19:03Z", "type": "Journal Article", "created": "2019-08-19", "title": "MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network", "description": "Abstract Motivation

Analysis of differential expression of genes is often performed to understand how the metabolic activity of an organism is impacted by a perturbation. However, because the system of metabolic regulation is complex and all changes are not directly reflected in the expression levels, interpreting these data can be difficult.

Results

In this work, we present a new algorithm and computational tool that uses a genome-scale metabolic reconstruction to infer metabolic changes from differential expression data. Using the framework of constraint-based analysis, our method produces a qualitative hypothesis of a change in metabolic activity. In other words, each reaction of the network is inferred to have increased, decreased, or remained unchanged in flux. In contrast to similar previous approaches, our method does not require a biological objective function and does not assign on/off activity states to genes. An implementation is provided and it is available online. We apply the method to three published datasets to show that it successfully accomplishes its two main goals: confirming or rejecting metabolic changes suggested by differentially expressed genes based on how well they fit in as parts of a coordinated metabolic change, as well as inferring changes in reactions whose genes did not undergo differential expression.

Availability and implementation

github.com/htpusa/moomin.

Supplementary information

Supplementary data are available at Bioinformatics online.

", "keywords": ["0301 basic medicine", "570", "[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Metabolic networks; omics data", "Genome", "[INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS]", "0206 medical engineering", "610", "Computational Biology", "[INFO.INFO-DS] Computer Science [cs]/Data Structures and Algorithms [cs.DS]", "02 engineering and technology", "[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Original Papers", "Models", " Biological", "03 medical and health sciences", "[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]", "Algorithms", "Metabolic Networks and Pathways", "[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]"]}, "links": [{"href": "https://iris.uniroma1.it/bitstream/11573/1321358/5/Pusa_MOOMIN_2020.pdf"}, {"href": "https://academic.oup.com/bioinformatics/article-pdf/36/2/514/48991611/btz584.pdf"}, {"href": "https://doi.org/10.1093/bioinformatics/btz584"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/bioinformatics/btz584", "name": "item", "description": "10.1093/bioinformatics/btz584", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/bioinformatics/btz584"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-22T00:00:00Z"}}, {"id": "10.26434/chemrxiv.13047818.v1", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:21:29Z", "type": "Journal Article", "created": "2020-12-28", "title": "SoluProt: Prediction of Soluble Protein Expression in Escherichia coli", "description": "AbstractMotivation

Poor protein solubility hinders the production of many therapeutic and industrially useful proteins. Experimental efforts to increase solubility are plagued by low success rates and often reduce biological activity. Computational prediction of protein expressibility and solubility in Escherichia coli using only sequence information could reduce the cost of experimental studies by enabling prioritization of highly soluble proteins.

Results

A new tool for sequence-based prediction of soluble protein expression in E.coli, SoluProt, was created using the gradient boosting machine technique with the TargetTrack database as a training set. When evaluated against a balanced independent test set derived from the NESG database, SoluProt\uffe2\uff80\uff99s accuracy of 58.5% and AUC of 0.62 exceeded those of a suite of alternative solubility prediction tools. There is also evidence that it could significantly increase the success rate of experimental protein studies. SoluProt is freely available as a standalone program and a user-friendly webserver at https://loschmidt.chemi.muni.cz/soluprot/.

Availability and implementation

https://loschmidt.chemi.muni.cz/soluprot/.

Supplementary information

Supplementary data are available at Bioinformatics online.

", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "SOLUBILITY; WEBSERVER; TOPOLOGY; ACCURATE", "Original Papers", "3. Good health"]}, "links": [{"href": "https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75076ee301c0358c7a88e/original/solu-prot-prediction-of-soluble-protein-expression-in-escherichia-coli.pdf"}, {"href": "https://doi.org/10.26434/chemrxiv.13047818.v1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.26434/chemrxiv.13047818.v1", "name": "item", "description": "10.26434/chemrxiv.13047818.v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.26434/chemrxiv.13047818.v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-05T00:00:00Z"}}, {"id": "10261/252976", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:25:50Z", "type": "Journal Article", "created": "2021-07-15", "title": "A multifunctional matching algorithm for sample design in agricultural plots", "description": "Collection of accurate and representative data from agricultural fields is required for efficient crop management. Since growers have limited available resources, there is a need for advanced methods to select representative points within a field in order to best satisfy sampling or sensing objectives. The main purpose of this work was to develop a data-driven method for selecting locations across an agricultural field given observations of some covariates at every point in the field. These chosen locations should be representative of the distribution of the covariates in the entire population and represent the spatial variability in the field. They can then be used to sample an unknown target feature whose sampling is expensive and cannot be realistically done at the population scale. An algorithm for determining these optimal sampling locations, namely the multifunctional matching (MFM) criterion, was based on matching of moments (functionals) between sample and population. The selected functionals in this study were standard deviation, mean, and Kendall's tau. An additional algorithm defined the minimal number of observations that could represent the population according to a desired level of accuracy. The MFM was applied to datasets from two agricultural plots: a vineyard and a peach orchard. The data from the plots included measured values of slope, topographic wetness index, normalized difference vegetation index, and apparent soil electrical conductivity. The MFM algorithm selected the number of sampling points according to a representation accuracy of 90% and determined the optimal location of these points. The algorithm was validated against values of vine or tree water status measured as crop water stress index (CWSI). Algorithm performance was then compared to two other sampling methods: the conditioned Latin hypercube sampling (cLHS) model and a uniform random sample with spatial constraints. Comparison among sampling methods was based on measures of similarity between the target variable population distribution and the distribution of the selected sample. MFM represented CWSI distribution better than the cLHS and the uniform random sampling, and the selected locations showed smaller deviations from the mean and standard deviation of the entire population. The MFM functioned better in the vineyard, where spatial variability was larger than in the orchard. In both plots, the spatial pattern of the selected samples captured the spatial variability of CWSI. MFM can be adjusted and applied using other moments/functionals and may be adopted by other disciplines, particularly in cases where small sample sizes are desired.", "keywords": ["2. Zero hunger", "Partially-observed data", "Agricultural sampling", "Representative sampling given covariates", "0207 environmental engineering", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "02 engineering and technology", "15. Life on land", "Two-phase study", "310", "Original Papers", "Spatial autocorrelation"]}, "links": [{"href": "https://doi.org/10261/252976"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Computers%20and%20Electronics%20in%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10261/252976", "name": "item", "description": "10261/252976", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10261/252976"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-01T00:00:00Z"}}, {"id": "3184389424", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:27:42Z", "type": "Journal Article", "created": "2021-07-15", "title": "A multifunctional matching algorithm for sample design in agricultural plots", "description": "Collection of accurate and representative data from agricultural fields is required for efficient crop management. Since growers have limited available resources, there is a need for advanced methods to select representative points within a field in order to best satisfy sampling or sensing objectives. The main purpose of this work was to develop a data-driven method for selecting locations across an agricultural field given observations of some covariates at every point in the field. These chosen locations should be representative of the distribution of the covariates in the entire population and represent the spatial variability in the field. They can then be used to sample an unknown target feature whose sampling is expensive and cannot be realistically done at the population scale. An algorithm for determining these optimal sampling locations, namely the multifunctional matching (MFM) criterion, was based on matching of moments (functionals) between sample and population. The selected functionals in this study were standard deviation, mean, and Kendall's tau. An additional algorithm defined the minimal number of observations that could represent the population according to a desired level of accuracy. The MFM was applied to datasets from two agricultural plots: a vineyard and a peach orchard. The data from the plots included measured values of slope, topographic wetness index, normalized difference vegetation index, and apparent soil electrical conductivity. The MFM algorithm selected the number of sampling points according to a representation accuracy of 90% and determined the optimal location of these points. The algorithm was validated against values of vine or tree water status measured as crop water stress index (CWSI). Algorithm performance was then compared to two other sampling methods: the conditioned Latin hypercube sampling (cLHS) model and a uniform random sample with spatial constraints. Comparison among sampling methods was based on measures of similarity between the target variable population distribution and the distribution of the selected sample. MFM represented CWSI distribution better than the cLHS and the uniform random sampling, and the selected locations showed smaller deviations from the mean and standard deviation of the entire population. The MFM functioned better in the vineyard, where spatial variability was larger than in the orchard. In both plots, the spatial pattern of the selected samples captured the spatial variability of CWSI. MFM can be adjusted and applied using other moments/functionals and may be adopted by other disciplines, particularly in cases where small sample sizes are desired.", "keywords": ["2. Zero hunger", "Partially-observed data", "Agricultural sampling", "Representative sampling given covariates", "0207 environmental engineering", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "02 engineering and technology", "15. Life on land", "Two-phase study", "310", "Original Papers", "Spatial autocorrelation"]}, "links": [{"href": "https://doi.org/3184389424"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Computers%20and%20Electronics%20in%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3184389424", "name": "item", "description": "3184389424", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3184389424"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-01T00:00:00Z"}}, {"id": "PMC10322654", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:30:17Z", "type": "Journal Article", "created": "2023-06-24", "title": "enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways", "description": "Abstract Motivation

Transformation products (TPs) of man-made chemicals, formed through microbially mediated transformation in the environment, can have serious adverse environmental effects, yet the analytical identification of TPs is challenging. Rule-based prediction tools are successful in predicting TPs, especially in environmental chemistry applications that typically have to rely on small datasets, by imparting the existing knowledge on enzyme-mediated biotransformation reactions. However, the rules extracted from biotransformation reaction databases usually face the issue of being over/under-generalized and are not flexible to be updated with new reactions.

Results

We developed an automatic rule extraction tool called enviRule. It clusters biotransformation reactions into different groups based on the similarities of reaction fingerprints, and then automatically extracts and generalizes rules for each reaction group in SMARTS format. It optimizes the genericity of automatic rules against the downstream TP prediction task. Models trained with automatic rules outperformed the models trained with manually curated rules by 30% in the area under curve (AUC) scores. Moreover, automatic rules can be easily updated with new reactions, highlighting enviRule\uffe2\uff80\uff99s strengths for both automatic extraction of optimized reactions rules and automated updating thereof.

Availability and implementation

enviRule code is freely available at https://github.com/zhangky12/enviRule.

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Climate action", "540 Chemistry", "1312 Molecular Biology", "1706 Computer Science Applications", "2613 Statistics and Probability", "2605 Computational Mathematics", "Molecular Biology", "Biotransformation", "1703 Computational Theory and Mathematics"]}, "links": [{"href": "https://doi.org/PMC10322654"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC10322654", "name": "item", "description": "PMC10322654", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC10322654"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-24T00:00:00Z"}}, {"id": "PMC8329933", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:30:30Z", "type": "Journal Article", "created": "2021-07-15", "title": "A multifunctional matching algorithm for sample design in agricultural plots", "description": "Collection of accurate and representative data from agricultural fields is required for efficient crop management. Since growers have limited available resources, there is a need for advanced methods to select representative points within a field in order to best satisfy sampling or sensing objectives. The main purpose of this work was to develop a data-driven method for selecting locations across an agricultural field given observations of some covariates at every point in the field. These chosen locations should be representative of the distribution of the covariates in the entire population and represent the spatial variability in the field. They can then be used to sample an unknown target feature whose sampling is expensive and cannot be realistically done at the population scale. An algorithm for determining these optimal sampling locations, namely the multifunctional matching (MFM) criterion, was based on matching of moments (functionals) between sample and population. The selected functionals in this study were standard deviation, mean, and Kendall's tau. An additional algorithm defined the minimal number of observations that could represent the population according to a desired level of accuracy. The MFM was applied to datasets from two agricultural plots: a vineyard and a peach orchard. The data from the plots included measured values of slope, topographic wetness index, normalized difference vegetation index, and apparent soil electrical conductivity. The MFM algorithm selected the number of sampling points according to a representation accuracy of 90% and determined the optimal location of these points. The algorithm was validated against values of vine or tree water status measured as crop water stress index (CWSI). Algorithm performance was then compared to two other sampling methods: the conditioned Latin hypercube sampling (cLHS) model and a uniform random sample with spatial constraints. Comparison among sampling methods was based on measures of similarity between the target variable population distribution and the distribution of the selected sample. MFM represented CWSI distribution better than the cLHS and the uniform random sampling, and the selected locations showed smaller deviations from the mean and standard deviation of the entire population. The MFM functioned better in the vineyard, where spatial variability was larger than in the orchard. In both plots, the spatial pattern of the selected samples captured the spatial variability of CWSI. MFM can be adjusted and applied using other moments/functionals and may be adopted by other disciplines, particularly in cases where small sample sizes are desired.", "keywords": ["2. Zero hunger", "Partially-observed data", "Agricultural sampling", "Representative sampling given covariates", "0207 environmental engineering", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "02 engineering and technology", "15. Life on land", "Two-phase study", "310", "Original Papers", "Spatial autocorrelation"]}, "links": [{"href": "https://doi.org/PMC8329933"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Computers%20and%20Electronics%20in%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC8329933", "name": "item", "description": "PMC8329933", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC8329933"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-01T00:00:00Z"}}, {"id": "PMC8391743", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:30:30Z", "type": "Journal Article", "created": "2021-07-06", "title": "The Experience of Key Stakeholders During the Implementation and Use of Trauma Therapy via Digital Health for Military, Veteran, and Public Safety Personnel: Qualitative Thematic Analysis", "description": "Background

Exposure to occupational stressors and potentially psychologically traumatic events experienced by public safety personnel (eg, paramedics, police, fire, and correctional officers), military members, and veterans can lead to the development of posttraumatic stress injuries and other mental health disorders. Providing emergency services during COVID-19 has intensified the challenges. Owing to COVID-19 restrictions, mental health service providers offering support to these populations have had to rapidly pivot to use digital versus in-person methods of service delivery.

Objective

This paper aims to explore the experience of mental health service providers regarding digital health service delivery, including the current state of digital mental health service delivery, barriers to and facilitators of the use of digital health for mental health service delivery experienced during the pandemic, and recommendations for implementing and integrating digital health into regular mental health service delivery.

Methods

This embedded mixed-methods study included questionnaires and focus groups with key stakeholders (N=31) with knowledge and experience in providing mental health services. Data analysis included descriptive, quantitative, and qualitative thematic analyses.

Results

The following three themes emerged: being forced into change, daring to deliver mental health services using digital health, and future possibilities offered by digital health. In each theme, participants\uffe2\uff80\uff99 responses reflected their perceptions of service providers, organizations, and clients. The findings offer considerations regarding for whom and at what point in treatment digital health delivery is appropriate; recommendations for training, support, resources, and guidelines for digitally delivering trauma therapy; and a better understanding of factors influencing mental health service providers\uffe2\uff80\uff99 perceptions and acceptance of digital health for mental health service delivery.

Conclusions

The results indicate the implementation of digital health for mental health service delivery to military members, public safety personnel, and veterans. As the COVID-19 pandemic continues, remote service delivery methods for trauma therapy are urgently needed to support the well-being of those who have served and continue to serve.

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