scholarly journals Holistic Evaluation of Biodegradation Pathway Prediction: Assessing Multi-Step Reactions and Intermediate Products

2021 ◽  
Author(s):  
Jason Tam ◽  
Tim Lorsbach ◽  
Sebastian Schmidt ◽  
Jörg Wicker
Keyword(s):  
Reference Data ◽  
Life Sciences ◽  
Transformation Products ◽  
Biodegradation Pathway ◽  
Intermediate Products ◽  
Transformation Rules ◽  
Low Concentrations ◽  
Pathway Prediction ◽  
Prediction Systems ◽  
Transient Intermediates

The prediction of metabolism and biotransformation pathways of xenobiotics is a highly desired tool in environmental and life sciences. There are several systems that currently predict single transformation steps or complete pathways as series of parallel and subsequent steps. Their accuracy is often evaluated on the level of a single transformation step. Such an approach cannot account for some specific challenges that are related to the nature of the biotransformation experiments. This is particularly true for missing transformation products in the reference data that occur only in low concentrations, e.g. transient intermediates or higher-generation metabolites. Furthermore, some rulebased prediction systems evaluate accuracy only based on the defined set of transformation rules. Therefore, the performance of different models cannot be directly compared.

scholarly journals Holistic Evaluation of Biodegradation Pathway Prediction: Assessing Multi-Step Reactions and Intermediate Products

2021 ◽  
Author(s):  
Jason Tam ◽  
Tim Lorsbach ◽  
Sebastian Schmidt ◽  
Jörg Wicker
Keyword(s):  
Reference Data ◽  
Life Sciences ◽  
Transformation Products ◽  
Biodegradation Pathway ◽  
Intermediate Products ◽  
Transformation Rules ◽  
Low Concentrations ◽  
Pathway Prediction ◽  
Prediction Systems ◽  
Transient Intermediates

The prediction of metabolism and biotransformation pathways of xenobiotics is a highly desired tool in environmental and life sciences. There are several systems that currently predict single transformation steps or complete pathways as series of parallel and subsequent steps. Their accuracy is often evaluated on the level of a single transformation step. Such an approach cannot account for some specific challenges that are related to the nature of the biotransformation experiments. This is particularly true for missing transformation products in the reference data that occur only in low concentrations, e.g. transient intermediates or higher-generation metabolites. Furthermore, some rulebased prediction systems evaluate accuracy only based on the defined set of transformation rules. Therefore, the performance of different models cannot be directly compared.

scholarly journals Holistic Evaluation of Biodegradation Pathway Prediction: Assessing Multi-Step Reactions and Intermediate Products

2021 ◽  
Author(s):  
Jason Tam ◽  
Tim Lorsbach ◽  
Sebastian Schmidt ◽  
Jörg Wicker
Keyword(s):  
Reference Data ◽  
Life Sciences ◽  
Transformation Products ◽  
Biodegradation Pathway ◽  
Intermediate Products ◽  
Transformation Rules ◽  
Low Concentrations ◽  
Pathway Prediction ◽  
Prediction Systems ◽  
Transient Intermediates

The prediction of metabolism and biotransformation pathways of xenobiotics is a highly desired tool in environmental and life sciences. There are several systems that currently predict single transformation steps or complete pathways as series of parallel and subsequent steps. Their accuracy is often evaluated on the level of a single transformation step. Such an approach cannot account for some specific challenges that are related to the nature of the biotransformation experiments. This is particularly true for missing transformation products in the reference data that occur only in low concentrations, e.g. transient intermediates or higher-generation metabolites. Furthermore, some rulebased prediction systems evaluate accuracy only based on the defined set of transformation rules. Therefore, the performance of different models cannot be directly compared.

scholarly journals Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Jason Y. C. Tam ◽  
Tim Lorsbach ◽  
Sebastian Schmidt ◽  
Jörg S. Wicker
Keyword(s):  
Performance Metrics ◽  
Reference Data ◽  
Transformation Products ◽  
Evaluation Framework ◽  
Transformation Rules ◽  
Low Concentrations ◽  
Pathway Prediction ◽  
Prediction Systems ◽  
Transient Intermediates

AbstractThe prediction of metabolism and biotransformation pathways of xenobiotics is a highly desired tool in environmental sciences, drug discovery, and (eco)toxicology. Several systems predict single transformation steps or complete pathways as series of parallel and subsequent steps. Their performance is commonly evaluated on the level of a single transformation step. Such an approach cannot account for some specific challenges that are caused by specific properties of biotransformation experiments. That is, missing transformation products in the reference data that occur only in low concentrations, e.g. transient intermediates or higher-generation metabolites. Furthermore, some rule-based prediction systems evaluate the performance only based on the defined set of transformation rules. Therefore, the performance of these models cannot be directly compared. In this paper, we introduce a new evaluation framework that extends the evaluation of biotransformation prediction from single transformations to whole pathways, taking into account multiple generations of metabolites. We introduce a procedure to address transient intermediates and propose a weighted scoring system that acknowledges the uncertainty of higher-generation metabolites. We implemented this framework in enviPath and demonstrate its strict performance metrics on predictions of in vitro biotransformation and degradation of xenobiotics in soil. Our approach is model-agnostic and can be transferred to other prediction systems. It is also capable of revealing knowledge gaps in terms of incompletely defined sets of transformation rules.

scholarly journals Analysis of ice phenomena hazard on the middle Odra river

2017 ◽  
Vol 49 (4) ◽  
pp. 301-314 ◽  
Author(s):  
Krzysztof Wolski ◽  
Tomasz Tymiński ◽  
Beata Głuchowska
Keyword(s):  
Water Management ◽  
Cross Sections ◽  
Reference Data ◽  
Life Sciences ◽  
Ice Cover ◽  
Frazil Ice ◽  
Ice Jam ◽  
Odra River ◽  
Regional Water ◽  
Ice Phenomena

Abstract The paper contains analysis of ice phenomena occurrence in the light of recent observations conducted on middle Odra river from Krapkowice (ca. km 125+000) to Krosno Odrzańskie (ca. km 530+000). In detail the research embraced time of occurrence and intensity of individual ice phenomena in years 2006–2017 together with reference and comparison of data to previous data from period 1957–2005. In characteristic cross-sections there is a reference to occurrence of all observed forms of ice phenomena (frazil ice, border ice, ice cover, floe and ice-jam). In the study a reference data of Regional Water Management Authority in Wrocław were used together with results of previous research conducted at the Wrocław University of Environmental and Life Sciences. The results legitimized, that the occurrence of ice phenomena on middle Odra river has time of its appearance, duration and intensity and is not stable in every year. Occurrence of ice phenomena on middle Odra river varies in time, being observed as manifold forms of icing – most frequently border ice and frazil ice. During the last 12 years greater than the average number of days with ice phenomena occurrence can be observed, but these phenomena have definitely “milder” character (border ice).

scholarly journals Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction

2008 ◽  
Vol 24 (18) ◽  
pp. 2079-2085 ◽  
Author(s):  
Kathrin Fenner ◽  
Junfeng Gao ◽  
Stefan Kramer ◽  
Lynda Ellis ◽  
Larry Wackett
Keyword(s):  
Data Driven ◽  
Combinatorial Explosion ◽  
Biodegradation Pathway ◽  
Pathway Prediction

scholarly journals Evaluation of field calibration methods and performance of AQMesh, a low-cost air quality monitor

2021 ◽  
Vol 193 (5) ◽  
Author(s):  
Dan Wahlborg ◽  
Mikael Björling ◽  
Magnus Mattsson
Keyword(s):  
Air Quality ◽  
Environmental Quality ◽  
Reference Data ◽  
Multivariate Calibration ◽  
Limit Of Detection ◽  
Reference Station ◽  
Raw Data ◽  
Low Concentrations ◽  
Calibration Methods ◽  
Data Points

AbstractField calibrations of NO2, NO, and PM10 from AQMesh Air Quality Monitors (AQMs) were conducted during a summer and an autumn period in a busy street in a midsize Swedish city. All the three linear calibration procedures studied (postscaled, bisquare, and orthogonal data) significantly reduced the ranges and magnitudes of the performance indicators to yield more reliable results than the raw data. The improvements were sufficient to satisfy the European Union (EU) Data Quality Objective (DQO) for indicative measurements as compared to reference data only for NO2 (above 50 µg m−3) and NO (above 30 µg m−3) during the autumn calibration period. The relatively simple bisquare procedure had the best performance overall. The bisquare procedure improved the root mean square error by the same amount as other studies using complex multivariate calibration methods. Low concentrations of pollutants were measured, far below the EU Environmental Quality Standard thresholds and even satisfying the future goals for the Environmental Quality Objectives. Cleaning the raw data by removing data points in the reference data that were below the reference station limit of detections (and the synchronous data points in the AQM prescaled data) was found to improve the performances of the calibration procedures appreciably. Many NO2 and almost all PM10 data points in this study fell below the AQM limit of detection. These low concentrations will probably be a common problem in many field studies, at least in areas with relatively low air pollution. However, the relative errors were sufficiently low for these data points that they could be interpreted as accurately representing low concentrations and did not need to be removed from the datasets. For the NO2 measurements, a slight periodic error correlated with sunlight and increased ambient temperature was noted. NO measurements correlated strongly with increased traffic.

Transformation, products, and pathways of chlorophenols via electro-enzymatic catalysis: How to control toxic intermediate products

Chemosphere ◽  
2016 ◽  
Vol 144 ◽  
pp. 1674-1681 ◽  
Author(s):  
Penghui Du ◽  
He Zhao ◽  
Haitao Li ◽  
Di Zhang ◽  
Ching-Hua Huang ◽  
...  
Keyword(s):  
Enzymatic Catalysis ◽  
Transformation Products ◽  
Intermediate Products

Modelling the transfer of pesticide transformation products from agricultural fields to the aquatic environment – state of knowledge and future challenges

2020 ◽  
Author(s):  
Matthias Gassmann
Keyword(s):  
Aquatic Environment ◽  
Prediction Models ◽  
Environmental Fate ◽  
Transformation Products ◽  
Model Complexity ◽  
Agricultural Fields ◽  
Catchment Scale ◽  
Pathway Prediction ◽  
Scale Models ◽  
Leaching Models

<p>Transformation products (TP) of pesticides are found everywhere in the aquatic environment. Their dynamic formation and subsequent transport from agricultural fields to adjacent water bodies can be estimated by using environmental fate models, which is done e.g. in the registration process for plant protection products in the European Union. In this study, an overview of models, transformation simulation concepts and model applications for TP estimation including leaching and catchment scale models is given. The review is restricted to models which were tested against field data in peer-reviewed publications. The models included in this review are GLEAMS, MACRO, RZWQM(2), PEARL, PRZM, Pelmo, LEACHM, HYDRUS 1-D, ZIN-AgriTra and the Field Release Model (FRM).</p><p>Investigating model structures revealed, that six transformation schemes, i.e. possible transformation pathways, are implemented in the models. Only one of the reviewed models, PELMO, uses a completely flexible scheme. In all other models, pathways are restricted. An assessment of model complexity, including hydrological processes and transformation-affecting processes, resulted in PELMO having the highest transformation but the least hydrological complexity among leaching models. RZWQM is the leaching model with the highest hydrological complexity and ranks second in transformation processes. Among the three catchment scale models, ZIN-AgriTra ranks highest in both, hydrological and transformation complexity.</p><p>Even though the number of publications of TP model applications is rather low, the number of leaching models is adequate (eight models). At the catchment scale, however, only two models with proven applications exist in the literature. A spatio-temporal analysis of all models revealed a gap in catchment and regional-scale models with a daily or lower temporal resolution. Thus, well-developed and applied catchment-scale models should be extended by a TP module. This would enable scientists and authorities to estimate TP concentrations or to analyse the environmental fate of TPs at the larger catchment scale. At the same time, the fate processes in models should be updated to reflect the current state of knowledge, especially more flexible transformation schemes and the formation of TPs in different compartments (i.e. plant, soil, water). The integration of pathway prediction models such as the University of Minnesota Pathway Prediction System could enhance the assessment of the large number of pesticide TPs in the aquatic environment.</p>

scholarly journals The Dark Side of Platinum Based Cytostatic Drugs: From Detection to Removal

Processes ◽  
2021 ◽  
Vol 9 (11) ◽  
pp. 1873
Author(s):  
Yessica Roque-Diaz ◽  
Martina Sanadar ◽  
Dong Han ◽  
Montserrat López-Mesas ◽  
Manuel Valiente ◽  
...  
Keyword(s):  
Adverse Effects ◽  
Transformation Products ◽  
Dark Side ◽  
Pharmaceutical Drugs ◽  
Cytostatic Drugs ◽  
Low Concentrations ◽  
Cytostatic Compounds ◽  
Living Organisms ◽  
A Minor ◽  
The Impact

The uncontrolled release of pharmaceutical drugs into the environment raised serious concerns in the last decades as they can potentially exert adverse effects on living organisms even at the low concentrations at which they are typically found. Among them, platinum based cytostatic drugs (Pt CDs) are among the most used drugs in cancer treatments which are administered via intravenous infusion and released partially intact or as transformation products. In this review, the studies on environmental occurrence, transformation, potential ecotoxicity, and possible treatment for the removal of platinum cytostatic compounds are revised. The analysis of the literature highlighted the generally low total platinum concentration values (from a few tens of ng L−1 to a few hundred μg L−1) found in hospital effluents. Additionally, several studies highlighted how hospitals are sources of a minor fraction of the total Pt CDs found in the environment due to the slow excretion rate which is longer than the usual treatment durations. Only some data about the impact of the exposure to low levels of Pt CDs on the health of flora and fauna are present in literature. In some cases, adverse effects have been shown to occur in living organisms, even at low concentrations. Further ecotoxicity data are needed to support or exclude their chronic effects on the ecosystem. Finally, fundamental understanding is required on the platinum drugs removal by MBR, AOPs, technologies, and adsorption.

Synergistic health effects between chemical pollutants and electromagnetic fields

2015 ◽  
Vol 30 (4) ◽  
Author(s):  
Gérard Ledoigt ◽  
Chaima Sta ◽  
Eric Goujon ◽  
Dalila Souguir ◽  
Ezzeddine El Ferjani
Keyword(s):  
Electromagnetic Fields ◽  
Transformation Products ◽  
Parent Molecule ◽  
Photochemical Process ◽  
Chemical Risk Assessment ◽  
Low Concentrations ◽  
Metal Trace Elements ◽  
Living Organisms ◽  
The Impact ◽  
By Products

AbstractHumans and ecosystems are exposed to highly variable and unknown cocktail of chemicals and radiations. Although individual chemicals are typically present at low concentrations, they can interact with each other resulting in additive or potentially synergistic mixture effects. This was also observed with products obtained by radiation actions such as sunlight or electromagnetic fields that can change the effects of chemicals, such as pesticides, and metal trace elements on health. Concomitant presence of various pesticides and their transformation products adds further complexity to chemical risk assessment since chronic inflammation is a key step for cancer promotion. Degradation of a parent molecule can produce several by-products which can trigger various toxic effects with different impacts on health and environment. For instance, the cocktail of sunlight irradiated sulcotrione pesticide has a greater cytotoxicity and genotoxicity than parent molecule, sulcotrione, and questions about the impact of photochemical process on environment. Adjuvants were shown to modify the biological features of pesticides. Addition of other elements, metals or biological products, can differently enhance cell toxicity of pesticides or electromagnetic radiations suggesting a synergy in living organisms. Electromagnetic fields spreading, pesticide by-products and mixtures monitoring become greater for environmental contamination evaluations.

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