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Shape Expressions Editor based on Javascript and CodeMirror
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Version 0.2.4 Changelog Trying to create molecules with segids > 4 characters now produces a warning. Updates to correct issues in doc strings for some classes. Known issues: Structure does not respect fixed atom coordinates.
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Object-oriented interface for NetCDF4 in Fortran, like h5fortran (HDF5)
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Introduces "partners" - direct many-to-many relationships. These can be used in filters and rendering in a similar manner to "number of children".
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  • Software/Code
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Lateral movements of materials and energy in coastal wetlands, due mainly to tidal activities, have been recognized as key processes in understanding the biogeochemical cycles of ecosystems. However, our understanding of the roles of lateral movement in shaping ecosystem functions remains limited. Here, we quantified the effects of lateral sediment transport on total carbon (C, inorganic + organic) and nitrogen (N) pools in plants and soils in two dominant wetland types: invasive Spartina alterniflora (Spartina) marshes and native Phragmites australis (Phragmites) marshes in coastal Shanghai of the Yangtze Estuary. We found that the accreted sediments across the water-marsh gradients caused by lateral movement resulted in contrasting C and N contents between the two communities. The sediment load and C and N pools in the plants and soils of the Spartina marshes were significantly higher than those in the adjacent Phragmites marshes. The shifts in species composition and community structure not only altered the C and N balance but also enhanced the ecosystem net primary productivity (NPP). Our findings highlight the importance of lateral transport in altering ecosystem structure after Spartina invasion. The ecosystem C and N pools were significantly higher in the invaded ecosystems than in the native community. Our study also reveals that the plant density and structures can alter tidal hydrodynamics and the lateral transportations of sediments, which in turn influence ecosystem C and N cycle. The C accumulation processes of the native and invaded marshes were further complicated by the contrasting productivities of the ecosystems.
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Fluence map optimization for intensity-modulated radiation therapy planning can be formulated as a large-scale inverse problem with multi-objectives on the tumors and organs-at-risk. Unfortunately, clinically relevant dose–volume constraints are nonconvex, so convex formulations and algorithms cannot be directly applied to the problem. We propose a novel approach to handle dose–volume constraints while preserving their nonconvexity, as opposed to previous efforts which focused on convex approximations. The proposed method is amenable to efficient algorithms based on partial minimization and naturally adapts to handle maximum-dose constraints and cases of infeasibility. We demonstrate our approach using the CORT dataset, and show that it is easily adaptable to radiation treatment planning with dose–volume constraints for multiple tumors and organs-at-risk.
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This repository contains genome annotation files for the genome assembly reported in Kapheim et al. 2020.
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  • Sequencing Data
  • Tabular Data
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various fixes
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SimThyr is a numeric simulator of pituitary-thyroid feedback control (aka thyrotropic feedback control, hypothalamus-pituitary-thyroid axis or thyroid homeostasis), based on a non-linear MiMe-NoCoDI model of the information processing structure. Its intended main use is in education and in silico research.
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  • Software/Code
  • Document
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This dataset contains the monitoring results of veterinary medicinal product residues and other substances measured in live animals and animal products analysed by the national competent authority of Estonia. The presence of unauthorised substances, residues of veterinary medicinal products or chemical contaminants in food may pose a risk factor for public health. For this reason and in order to ensure a high level of consumer protection, a comprehensive legislative framework has been established in the European Union (EU) which defines maximum limits permitted in food and monitoring programmes for the control of the presence of these substances in the food chain. Regulation (EU) No 37/2010 establishes maximum limits for residues of veterinary medicinal products in food-producing animals and animal products. Maximum residue levels for pesticides in or on food and feed of plant and animal origin are laid down in Regulation (EC) No 396/2005. Commission Regulation (EC) 1881/2006 lays down the maximum limits for the presence of certain contaminants in animal products. Council Directive 96/23/EC lays down measures to monitor certain substances and residues thereof, mainly veterinary medicinal products, in live animals and animal products. Additionally, Commission Decision 97/747/EC lays down levels and frequencies of sampling for certain animal products. The dataset contains the results of laboratory tests from samples taken from bovines, pigs, sheep, goats, horses, poultry, rabbits, farmed game, wild game aquaculture, milk, eggs and honey. Targeted samples are taken with the aim of detecting illegal treatment or controlling compliance with the maximum levels laid down in the relevant legislation. This means that, in their national plans Member States target the groups of animals (species, gender, age) where the probability of finding residues is the highest. Suspect samples are taken as a consequence of i) non-compliant results on samples taken in accordance with the monitoring plan, ii) possession or presence of prohibited substances at any point during manufacture, storage, distribution or sale through the food and feed production chain, or iii) suspicion or evidence of illegal treatment or non-compliance with the withdrawal period for an authorised medicinal veterinary product. Residues of pharmacologically active substances mean active substances, excipients or degradation products and their metabolites, which remain in food. Unauthorised substances or products mean substances or products prohibited under European Union legislation. Non-compliant sample is a sample that has been analysed for the presence of one or more substances and failed to comply with the legal provisions for at least one substance. Thus, a sample can be non-compliant for one or more substances. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: VMPR_2018 – Veterinary and Food Board VMPR_2017 – Veterinary and Food Board
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