Modeling the Effects of Introducing Low Impact Development in a Tropical City: a Case Study from Joinville, Brazil

In tropical countries like Brazil, fast and uncontrolled urbanization, together with high rainfall intensities, makes flooding a frequent event. The implementation of decentralized stormwater controls is a promising strategy aiming to reduce surface runoff and pollution through retention, infiltration, filtration, and evapotranspiration of stormwater. Although the application of such controls has increased in the past years in developed countries, they are still not a common approach in developing countries, such as Brazil. In this paper we evaluate to what extend different low impact development (LID) techniques are able to reduce the flood risk in an area of high rainfall intensities in a coastal region of South Brazil. Feasible scenarios of placing LID units throughout the catchment were developed, analyzed with a hydrodynamic solver, and compared against the baseline scenario to evaluate the potential of flood mitigation. Results show that the performance improvements of different LID scenarios are highly dependent on the rainfall events. On average, a total flood volume reduction between 30% and 75% could be achieved for seven LID scenarios. For this case study the best results were obtained when using a combination of central and decentral LID units, namely detention ponds, infiltration trenches, and rain gardens.(VLID)2512613Version of recor

Tautomerism in large databases

We have used the Chemical Structure DataBase (CSDB) of the NCI CADD Group, an aggregated collection of over 150 small-molecule databases totaling 103.5 million structure records, to conduct tautomerism analyses on one of the largest currently existing sets of real (i.e. not computer-generated) compounds. This analysis was carried out using calculable chemical structure identifiers developed by the NCI CADD Group, based on hash codes available in the chemoinformatics toolkit CACTVS and a newly developed scoring scheme to define a canonical tautomer for any encountered structure. CACTVS’s tautomerism definition, a set of 21 transform rules expressed in SMIRKS line notation, was used, which takes a comprehensive stance as to the possible types of tautomeric interconversion included. Tautomerism was found to be possible for more than 2/3 of the unique structures in the CSDB. A total of 680 million tautomers were calculated from, and including, the original structure records. Tautomerism overlap within the same individual database (i.e. at least one other entry was present that was really only a different tautomeric representation of the same compound) was found at an average rate of 0.3% of the original structure records, with values as high as nearly 2% for some of the databases in CSDB. Projected onto the set of unique structures (by FICuS identifier), this still occurred in about 1.5% of the cases. Tautomeric overlap across all constituent databases in CSDB was found for nearly 10% of the records in the collection

Identification of regulatory variants associated with genetic susceptibility to meningococcal disease.

Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA - a NF-kB subunit, master regulator of the response to infection - under bacterial stimuli in nasopharyngeal epithelial cells. We designed a custom panel to cover these RELA binding sites and used it for targeted sequencing in cases and controls. Variant calling and association analysis were performed followed by validation of candidate polymorphisms by genotyping in three independent cohorts. We identified two new polymorphisms, rs4823231 and rs11913168, showing signs of association with meningococcal disease susceptibility. In addition, using our genomic data as well as publicly available resources, we found evidences for these SNPs to have potential regulatory effects on ATXN10 and LIF genes respectively. The variants and related candidate genes are relevant for infectious diseases and may have important contribution for meningococcal disease pathology. Finally, we described a novel genetic association approach that could be applied to other phenotypes

chembience/chembience: Version 0.2.10

Update to RDKit 2019.03 + Postgres 11.2 with RDKit 2019.03 database cartridg

Mapping Between Databases of Compounds and Protein Targets

<p>Databases that provide links between bioactive compounds and their protein targets are increasingly important in drug discovery and chemical biology. They join the expanding universes of cheminformatics via chemical structures on the one hand and bioinformatics via sequences on the other. However, it is difficult to assess the relative utility of databases without the explicit comparison of content. We have exemplified an approach to this by comparing resources that each has a different focus on bioactive chemistry (ChEMBL, DrugBank, Human Metabolome Database, and Therapeutic Target Database) both at the chemical structure and protein levels. We compared the compound sets at different representational stringencies using NCI/CADD Structure Identifiers. The overlap and uniqueness in chemical content can be broadly interpreted in the context of different data capture strategies. However, we recorded apparent anomalies, such as many compounds-in-common between the metabolite and drug databases. We also compared the content of sequences mapped to the compounds via their UniProt protein identifiers. While these were also generally interpretable in the context of individual databases we discerned differences in coverage and the types of supporting data used. For example, the target concept is applied differently between DrugBank and the Therapeutic Target Database. In ChEMBL it encompasses a broader range of mappings from chemical biology and species orthologue cross-screening in addition to drug targets per se. Our analysis should assist users not only in exploiting the synergies between these four high-value resources but also in assessing the utility of other databases at the interface of chemistry and biology.</p

Enumeration of Ring–Chain Tautomers Based on SMIRKS Rules

A compound exhibits (prototropic) tautomerism if it can be represented by two or more structures that are related by a formal intramolecular movement of a hydrogen atom from one heavy atom position to another. When the movement of the proton is accompanied by the opening or closing of a ring it is called ring–chain tautomerism. This type of tautomerism is well observed in carbohydrates, but it also occurs in other molecules such as warfarin. In this work, we present an approach that allows for the generation of all ring–chain tautomers of a given chemical structure. Based on Baldwin’s Rules estimating the likelihood of ring closure reactions to occur, we have defined a set of transform rules covering the majority of ring–chain tautomerism cases. The rules automatically detect substructures in a given compound that can undergo a ring–chain tautomeric transformation. Each transformation is encoded in SMIRKS line notation. All work was implemented in the chemoinformatics toolkit CACTVS. We report on the application of our ring–chain tautomerism rules to a large database of commercially available screening samples in order to identify ring–chain tautomers

Impact of hybridwater supply on the centralised water system

Traditional (technical) concepts to ensure a reliable water supply, a safe handling of wastewater and flood protection are increasingly criticised as outdated and unsustainable. These so-called centralised urban water systems are further maladapted to upcoming challenges because of their long lifespan in combination with their short-sighted planning and design. A combination of (existing) centralised and decentralised infrastructure is expected to be more reliable and sustainable. However, the impact of increasing implementation of decentralised technologies on the local technical performance in sewer or water supply networks and the interaction with the urban form has rarely been addressed in the literature. In this work, an approach which couples the UrbanBEATS model for the planning of decentralised strategies together with a water supply modelling approach is developed and applied to a demonstration case. With this novel approach, critical but also favourable areas for such implementations can be identified. For example, low density areas, which have high potential for rainwater harvesting, can result in local water quality problems in the supply network when further reducing usually low pipe velocities in these areas. On the contrary, in high demand areas (e.g., high density urban forms) there is less effect of rainwater harvesting due to the limited available space. In these high density areas, water efficiency measures result in the highest savings in water volume, but do not cause significant problems in the technical performance of the potable water supply network. For a more generalised and case-independent conclusion, further analyses are performed for semi-virtual benchmark networks to answer the question of an appropriate representation of the water distribution system in a computational model for such an analysis. Inappropriate hydraulic model assumptions and characteristics were identified for the stated problem, which have more impact on the assessments than the decentralised measures

Industrielle Energieflexibilität im Energiesystem

Energy from renewable resources is not always readily available. Depending on the season and the weather, the power made available by solar parks or wind turbines varies, for example. Due to the continuous expansion of renewable energies, the volatility in the energy system will become more and more pronounced in the future. Preparing and adapting the industry to the changing supply structures is a major challenge for the next few decades. In the future, companies must be able to design their processes and operational organization in such a way that energy consumption can at least partially adapt flexibly to the volatile energy supply. In addition to developing technologies, Concepts and measures to make industrial processes more energetic, a second focus of future work is the development of a consistent IT infrastructure with which companies and energy providers can provide and exchange information from the production machine to the energy markets in the future. This leads to a paradigm shift in the operation of industrial processes - away from continuous and purely demand-driven energy consumption towards the adaptable, energy-flexible operation of industrial plants. This reference work presents the most important results of the research in the context of the Kopernikus project Synergy and clarifies trend-setting findings for further developments in the still young field of industrial energy flexibility