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42 results for “transformation products”
S38 | SOLNSLMCTPS | SOLUTIONS Predicted Transformation Products by LMC
<p>This is the collection associated with list S38 SOLNSLMCTPS on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p>S38 | SOLNSLMCTPS | <strong>SOLUTIONS Predicted Transformation Products by LMC</strong></p> <p>Predicted Transformation Products calculated by LMC during the SOLUTIONS project, interactive table available <a href="https://www.normandata.eu/solutions/modelsTransformationProducts.php">here</a>.</p> <p>14/11/19 update: added CSV version. 9/7/2025: fixed several corrupt SMILES and added InChIKeys to XLSX/CSV. Note that the author had to be changed to the University to satisfy Zenodo upload requirements, the original authors were listed as <a href="https://oasis-lmc.org/about/contacts.aspx">LMC</a>. </p>
S66 | EAWAGTPS | Parent-Transformation Product Pairs from Eawag
<p>This is the collection associated with list S66 EAWAGTPS - Parent-Transformation Product Pairs from Eawag on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p>Parent-Transformation Product Pairs of various micropollutants from Eawag: Swiss Federal Institute for Aquatic Science and Technology (<a href="https://www.eawag.ch/en/">https://www.eawag.ch/en/</a>), described in Schollee et al 2017 DOI:<a href="http://doi.org/10.1007/s13361-017-1797-6">10.1007/s13361-017-1797-6</a> . Dataset DOI: 10.5281/zenodo.3754448</p> <p>Update 23/04/2020: fixed names, added synonym columns and classification information.<br>Update 15/05/2020: adjusted classification information following feedback from Juliane.<br>Update 13/01/2023: adjusted <a href="https://gitlab.lcsb.uni.lu/eci/pubchem/-/commit/447d9a7eabe3660732a80ad261cf80b7491cc027" target="_blank" rel="noopener">selected BT entries</a> based on feedback from Emma Palm.<br>Update 07/02/2023: adjusted <a href="https://gitlab.lcsb.uni.lu/eci/pubchem/-/commit/6b56bd345b1598081062607d458927dd99bd64d2" target="_blank" rel="noopener">selected BT entries</a> to fix 4-Me-BT issues. </p>
Research data: Continuity Amid Transformation: An Analysis of Pottery Production from the Late La Tène to Early Roman Periods in Eastern Bohemia
<p>Data used in the research presented in the article titled "Continuity Amid Transformation: An Analysis of Pottery Production from the Late La Tène to Early Roman Periods in Eastern Bohemia".</p> <p><strong>Abstract of the article:</strong></p> <p>At the end of the La Tène period and the beginning of the Roman period in the first century BC, society in Central Europe underwent a significant transformation, which included notable changes in pottery production. This transformation is often attributed to the collapse of the social structures of the La Tène period and the arrival of a new population. Pottery production, in particular, is generally considered to have undergone a complete transformation.</p> <p>However, previous studies on this transition have primarily focused on the stylistic analysis of shapes and decorations, as illustrated by the pottery assemblage from Slepotice (Eastern Bohemia). In order to obtain additional data on the transitional period, this study of pottery from Slepotice incorporates analyses of the materials used and the manufacturing process through macroscopic observation, X-ray fluorescence analysis, and thin-section analysis. These analyses provide new insights into the differences in pottery production and distribution during the first century BC.</p> <p>Our research indicates that while the transformation included the collapse of the La Tène socioeconomic network, it did not result in a complete break in the pottery production process.</p> <p>Link to the article: <a href="https://doi.org/10.1016/j.jasrep.2025.105073">https://doi.org/10.1016/j.jasrep.2025.105073</a></p> <p> </p> <p><strong>List of the files:</strong></p> <p>Supplementary Material 1<br>Settlement structure in the vicinity of Slepotice during the La Tène and Roman periods: 1 – Slepotice, 2 – České Lhotice, 3 – Brčekoly, 4 – Chrudim</p> <p>Supplementary Material 2<br>Values of pottery attributes (Mat, InMn, InVar, In, traces left from the shaping process, Po, Vy, and morphological groups) classified based on macroscopic observation</p> <p>Supplementary material 3<br>Schematic classification of rim attributes, illustrating different variants of rim direction (Op), thickening of the upper part of the rim (Oz), and trimming of the lip (Os)</p> <p>Supplementary material 4<br>Attributes of the 30 samples selected for XRF analysis based on macroscopic observation. These attributes include fabric properties, surface treatment, morphological features, and technological traces</p> <p>Supplementary material 5<br>Figures of ceramic samples (with corresponding IDs) from feature 144/1998 showing preserved rims and bases</p> <p>Supplementary material 6<br>Figures of ceramic samples (with corresponding IDs) from feature 355/2001 showing preserved rims</p> <p>Supplementary Material 7<br>Chemical composition of 30 selected samples according to XRF analysis (main oxides in wt%, and elements in ppm)</p> <p>Supplementary Material 8<br>Principal Component Analysis (PCA) results: The scree plot (top left) visualises the proportion of variance explained by each principal component. The biplots (top right and bottom right) illustrate the distribution of samples, with arrows indicating the contribution of specific elements to the observed variance. The dendrogram (bottom left) shows hierarchical clustering of the samples, aiding in the selection of representative samples for thin-section petrographic analysis</p> <p>Supplementary Material 9<br>Relationships between the dating and other attributes of pottery classified based on macroscopic observation. These attributes include fabric properties, surface treatment, morphological features, and technological traces</p> <p>Supplementary Material 10<br>Relationships between the chemical groups (determined by XRF analysis) and pottery attributes classified based on macroscopic observation. These attributes include fabric properties, surface treatment, morphological features, and technological traces</p> <p>Supplementary Material 11<br>Petrography of fabric groups and subgroups, focusing on their properties. The evaluation begins with a general assessment of each fabric group as a whole, followed by a detailed examination of its subgroups</p> <p>Supplementary Material 12<br>Petrographic characterization of ceramics using a semiquantitative scale, simplified for statistical analysis (0.1 – trace, 0.5 – rare, 1 – occasional, 2 – common, 3 – frequent, 4 – abundant, 5 – dominant)</p> <p>Supplementary Material 13<br>Thin-section samples: Description of the ceramic matrix, natural inclusions, and added tempers</p> <p>Supplementary material 14<br>Variations in chemical composition among different fabric groups</p>
S68 | HSDBTPS | Transformation Products Extracted from HSDB Content in PubChem
<p>This is the collection associated with list S68 HSDBTPS Transformation Products Extracted from HSDB Content in PubChem on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p>HSDBTPS is a list of metabolites / transformation products extracted from the "Metabolites/Metabolism" section from HSDB (Hazardous Substance Data Bank) in PubChem (<a href="https://pubchem.ncbi.nlm.nih.gov/source/11933">https://pubchem.ncbi.nlm.nih.gov/source/11933</a>). Dataset DOI: <a href="https://doi.org/10.5281/zenodo.3827487">10.5281/zenodo.3827487</a>.</p> <p>Entries automatically extracted from HSDB are manually validated to remove mismatching CIDs, and add additional CIDs not captured using the descriptions provided. Files are created with a default to not import any data until this has been checked. Please report any mismatches, despite best efforts it is possible that errors are present, all files are under version control so that entries can be corrected/updated/enhanced over time and recommitted.</p> <p>Recent uploads (2022 and later) are handled with ShinyTPs (<a href="https://gitlab.lcsb.uni.lu/eci/shinytps">code</a> + article from Palm et al 2023 DOI:<a href="https://doi.org/10.1021/acs.estlett.3c00537">10.1021/acs.estlett.3c00537</a>). The original code associated with this deposit is located <a href="https://gitlab.lcsb.uni.lu/eci/pubchem/-/tree/master/annotations/tps/">here</a>. </p> <p>Updates:</p> <p>16 May 2020: Added the source file (extract of all HSDB Metabolites/Metabolism entries as is from JSON file), plus an updated S68_HSDBTPS_StructInfoOnly.csv with one new structure and renamed to include S68, plus the first draft of the Transformations table. 28 May 2020: added InChIKey and DIXSID files. 11 June 2020: added updated Transformations and Structure files to contain new CIDs and resulting reactions from new PubChem registrations. Dec 23, 2022: first dataset from Emma Palm added, using her TP curation app. DTXSID file dropped. 23 Mar 2023: added Biosystem and Enzyme columns, filling in biosystem where appropriate. 24 Mar 2023: new azo dye reactions from Emma Palm added. 1 Apr 2023: more azo dye reactions from Emma Palm. 4 Apr 2023: added new CIDs. 27 June 2023: added many new substances, including new CIDs. 28 June 2023 added transformations, 30 June 2023 added new CIDs. 11 July added missing CIDs to transformations table. 18 Nov 2023: added new reactions from Jolly Komolo (no new CIDs). 1 Dec 2023: new reactions from Marie, incl. two new CIDs. 19 Dec 2023: new reactions from Marie, incl. 1 new CID, updated CIDs from Dec 1. 29 April 2024: new reactions from Marie, CID updated. 16 July 2024: added reactions from Olga. 26 July 2024: added BPA=>MBP. 6 Aug 2024: adjusted many triazine names, added one new reaction. 27 Nov 2024: added Griseofulvin reactions. 8 Feb 2025: added Sertraline TP. 14 Mar 2025: added missing CID for O-Demethyl phosphamidon.</p>
S74 | REFTPS | Transformation Products and Reactions from Literature
<p>This is the collection associated with list S74 REFTPS Transformation Products and Reactions from Literature on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p>This dataset is designed to provide an entry point for users to contribute transformation products and reactions documented in the literature for addition to the NORMAN SLE, SusDat and the PubChem Transformations section.</p> <p>Change logs and version tracking at the <a href="https://gitlab.com/uniluxembourg/lcsb/eci/pubchem/-/tree/master/annotations/tps/REFTPS">ECI GitLab site</a>.</p> <p>Change log: v0.0.2 added InChIKey file. v0.1.0 added new reactions from Anca Baesu and DTXSIDs. v0.2.0 added PFAS TPs from Parviel Chirsir. v0.2.1 more PFAS TPs from Parviel. v0.3.0 Emma added HMMM TPs; v0.3.1 updated references and added new CIDs; added new MS/MS file. v0.4.0 new PFAS TPs plus MS/MS and NMR. v0.4.1 new CID added, plus CID 67543 updated to 14571268. v0.5.0 new 8:2 FT TPs plus annotation data; new structures. v0.5.1 added new CIDs. v0.5.2 added 2:2 to 6:2 FT TPs, updated ref for Bugsel. v0.5.3: added new CIDs. v0.6.0 added new structures. v0.7.0 added more new structures. v 0.7.1: updated CIDs in substances, fixed PFHpA mapping in transformations (some were mismapped to CID 67819). v 0.7.2: updated Biosystem description for many records. v0.8.0: updated CID 163201609 => 166001338, adjusted last 4 MS/MS, added Barisci AOP transformations. v0.9.0 added new structures. v0.9.1 updated CIDs and added radical structures from deposition. v0.10.0 added new irgarol reaction; v0.10.1 added new CID. v0.11.0 added Avendano and Mabury transformations from Parviel. v0.12.0 added Washington MS/MS and Marjanovic MS/MS and reactions. v0.13.0 added Galaxolide transformation. v0.14.0 added Zweigle PFAS TPs with MSMS. v0.14.1 added new CIDs. v0.15.0 added antibiotic TPs from Paul Löffler, SLU, incl. entries with no CID. v0.15.1 added new CIDs. v0.16.0 added benzothiazole reactions. v0.17.0 added TooCOLD TPs from Rick. v0.18.0 added new TFA reactions. v0.19.0 added pak choi reactions, several with no CID. v0.19.1 added new CIDs. v0.20.0 added dimers from Li Ji. v0.20.1 added new CIDs. v0.21.0 added the EJ Weber PFAS libraries "EnvLib" and "MetaLib", curation by Parviel and Emma. Some new CIDs to come. v0.21.1: fixed char issues in substance & transformation files. v0.21.2 added new CIDs. v0.22.0 added "Class_parent" column to the substance deposition file to aid annotation. v0.23.0: added Parviel's zebrafish entries</p>
Predicted Transformation Products of 321 Pesticides
<p>This dataset contains transformation products predicted for 321 pesticides detected in European and Australian surface and ground waters. All predictions were done using the environmental microbial degradation module of BioTransformer3.0 version 2023-05-23. Five generations of transformation products were predicted.</p> <p><br>The files in this deposition include:<br><strong>pesticides_compounds.sql</strong> contains the all unique compounds and their identifiers (including both precursors and transformation products).<br><strong>pesticides_dead_end_tps.sql</strong> contains the IDs of all transformation products for which no further transformation products could be predicted as well as the original precursors.<br><strong>pesticides_input_pesticides.sql</strong> contains the IDs of the 321 original pesticides.<br><strong>pesticides_reaction_types.sql</strong> contains the unique enzyme biosystem and transformation rules.<br><strong>pesticides_reactions.sql</strong> contains the unique combinations of precursor IDs and transformation product IDs.<br><strong>pesticides_routines.sql </strong>contains query functions to obtain TPs and precursors as well as full transformation pathways.<br><strong>pesticides.sql</strong> is a self-contained file containing all the other files.</p> <p> </p>
Basic tools for deriving photolysis endpoints for soil photo-transformation products in groundwater
<p>This spreadsheet has been designed to determine input parameters for consideration of the photolysis pathway in FOCUS-PELMO 5.5.3 and subsequent versions. It should be used alongside the EFSA scientific guidance on “Soil phototransformation products in groundwater – consideration, parameterisation and simulation in the exposure assessment of plant protection products”.</p> <p>The tools in the spreadsheet allow to identify the relevant grid points in the solar database 'AGRI4CAST', to retrieve irradiance values for the relevant grid points and for the period of the study from the 'AGRI4CAST' database via a spatial interpolation of the irradiance values (this can also be used for other solar databases besides 'AGRI4CAST'). Furthermore, the tools enable to convert the irradiance from kWh/m², kJ/m² or J/cm² into W/m², to perform a time-step normalisation for field studies, and to compare the normalised k<sub>fast</sub> values from different field studies.</p>
Reuse of Model Transformations for Propagating Variability Annotations in Annotative Software Product Lines - Evaluation Data
<p>This package contains all data that was produced for and used in the doctoral thesis for evaluating commutativity of propagating annotations in model-driven product lines.<br> This includes the implementation that conducts the evaluation, the measured results, and the input subjects.</p>
The effects of nitrogen and warming on inorganic nitrogen pool and production rates in arctic and boreal ecosystems: inorganic nitrogen transformation during a 3-month laboratory incubation
We incubated (2006) northern Alaskan soils (boreal and tundra) at two temperatures (5 degC and 15 degC) and two levels of nitrogen addition (with and without) to directly test for nitrogen limitation of inorganic nitrogen production rate and explore the interaction between temperature and nitrogen limitation. Over the 3-month laboratory incubation, we measured initial extratable inorganic nitrogen and inorganic nitrogen production rates from organic and mineral soils from four different ecosystem types (boreal burned, boreal unburned, moist acidic, moist non-acidic). To charactarize the soils, we also measured total C, total N, microbial biomass, isotopes values (delta 13, delta14), total free amino acid, and total soluble protein.
Sulfamethoxazole transformation products in anaerobic batch assays
<p>The document contains the ion spectra and sulfamethoxazole’s extracted ion chromatogram (XIC). The antibiotic was spiked in anaerobic batch assays containing graphene oxide at different levels. Two transformation products were detected, and the proposed biotransformation pathway is described in the last figure.</p>
Supplementary material "Designing robust transformation toward a sustainable circular battery production"
<p>Supplementary material for the publication " Designing robust transformation toward a sustainable circular battery production" in Procedia CIRP. The paper is available at <a href="https://doi.org/10.1016/j.procir.2023.02.069">https://doi.org/10.1016/j.procir.2023.02.069</a>.</p> <p> </p> <p>The underlying research of this publication was funded by the German Federal Ministry of Education and Research within the Competence Cluster Recycling & Green Battery (greenBatt) (03XP0302A) and the research project EffizientNutzen (033R240C). The authors are responsible for the content of this publication.</p> <p><em>Accepted for publication</em></p>
Interview Transcriptions related to PhD Thesis "Degrowth at a Global Scale? Geographies of Chile's Fruit Production and Export between Extractivism and Socio-Ecological Transformation"
<p>The material is composed of transcriptions of interviews conducted for the empirical work of this PhD Thesis.</p> <p>Not all conducted interviews are included (which can be seen from the accompanying table); those not included are not available mostly due to lack of consent of interviewees or because certain interviews were not registered and only hand-written notes were taken.</p>
Data from: Nitrogen transformations differentially affect nutrient-limited primary production in lakes of varying trophic state
The concept of lakes "evolving" phosphorus (P) limitation has persisted in limnology despite limited direct evidence. Here, we developed a simple model to broadly characterize nitrogen (N) surpluses and deficits relative to P in lakes, and compared the magnitude of this imbalance to estimates of N gains and losses through biological N transformations. The model suggested that approximately half of oligotrophic lakes in the US had a stoichiometric N deficit, but almost 90% of the most productive lakes had a similar N deficit. Although reactive N appeared to accumulate in the most oligotrophic lakes, net denitrification perpetuated the N deficit in more productive lakes. Productive lakes tended to export reactive N via biological N transformations regardless of their N deficit. The lack of N accumulation through N fixation has important implications for our understanding of lake biogeochemistry, ecology, and eutrophication management.
Suspect and Nontarget Screening Reveal the Underestimated Risks of Antibiotic Transformation Products in Wastewater Treatment Plant Effluents
<p>This repository is supplementary to the manuscript "Suspect and Nontarget Screening Reveal the Underestimated Risks of Antibiotic Transformation Products in Wastewater Treatment Plant Effluents" (DOI: 10.1021/acs.est.3c05008). This repository contains scripts of TPs collection and QSRR model as well the generated data set.</p><p>We compiled a suspect list of antibiotics containing 663 compounds. Corresponding suspect TPs were collected in silico with BioTransformer 3.0 and through a library search from PubChem data, which were both performed in batch mode using the patRoon 2.0 package. After merging results and removing duplicates, 88,823 TPs remained for suspect screening. Quantitative-structure retention relationship (QSRR) models were developed for the suspect antibiotics and TPs using target compounds to predict their retention times with the Retip package.</p>
16S rRNA gene data for aerobic BTEX-degrading enrichments exposed to sulfonamide polyfluorinated substances in fire-fighting foams and transformation products
<p>Per- and polyfluoroalkyl substances (PFASs) from aqueous film forming foams (AFFFs) can hinder bioremediation of co-contaminants, such as trichloroethene (TCE) and benzene, toluene, ethylbenzene, and xylene (BTEX). Anaerobic dechlorination can require bioaugmentation of <em>Dehalococcoides</em> and for BTEX, oxygen is often sparged to stimulate in-situ aerobic biodegradation. We tested PFAS inhibition to TCE and BTEX bioremediation by exposing an anaerobic TCE-dechlorinating co-culture, an aerobic BTEX-degrading enrichment culture, and an anaerobic toluene-degrading enrichment culture to n-dimethyl perfluorohexane sulfonamido amine (AmPr-FHxSA), perfluorohexane sulfonamide (FHxSA), perfluorohexane sulfonic acid (PFHxS), or non-fluorinated surfactant sodium dodecyl sulfate (SDS). The anaerobic TCE-dechlorinating co-culture was resistant to individual PFASs exposures but was inhibited by >1,000x diluted AFFF. FHxSA and AmPr-FHxSA inhibited the aerobic BTEX-degrading enrichment. The anaerobic toluene-degrading enrichment was not inhibited by AFFF or individual PFASs. Increases in amino acids in the anaerobic TCE-dechlorinating co-culture compared to the control indicated stress response, while the BTEX culture exhibited lower concentrations of all amino acids upon exposure to most surfactants (both fluorinated and non-fluorinated) compared to the control. These data suggest the main mechanisms of microbial toxicity are related to interactions with cell membrane synthesis as well as protein stress signaling.</p>
Fig. 7 in Lichen-associated bacteria transform antibacterial usnic acid to products of lower antibiotic activity
Fig. 7. Molecular networking results from GNPS visualized with Cytoscape. Inset: cluster of UA and derivatives with close fragmentation pathway (m/z 357.12: compound K, m/z 389.104: compound L) and self-loop of compound H (at m/z 386.139).
Fig. 4 in Lichen-associated bacteria transform antibacterial usnic acid to products of lower antibiotic activity
Fig. 4. HPLC chromatograms of S. cyaneofuscatus cultures with or without UA: A) At the beginning of the stationary phase of bacterial growth; B) After 7 days of stationary phase. Circled in blue: compounds inhibited in the presence of UA, circled in orange: compounds more concentrated in the presence of UA, circled in red: UA. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Lichen-associated bacteria transform antibacterial usnic acid to products of lower antibiotic activity
Fig. 1. Monitoring of the bacterial growth over 15 days (D0 to D15) by measuring optical density (log OD (optical density), gray curve) and cell viability (%) using MTT assay (blue curve) compared to untreated culture (orange curve). A) Nocardia sp., B) S. cyaneofuscatus, C) M. ruber. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Lichen-associated bacteria transform antibacterial usnic acid to products of lower antibiotic activity
Fig. 3. HPLC chromatograms of Nocardia sp. culture with or without UA. A) At the beginning of the stationary phase of the bacterial growth; B) After 7 days of stationary phase. Compounds circled in red appear only in the culture with UA. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Lichen-associated bacteria transform antibacterial usnic acid to products of lower antibiotic activity
Fig. 2. HPLC chromatograms of M. ruber cultures with or without UA. A) At the beginning of the stationary phase of bacterial growth; B) After 7 days of stationary phase. Compounds circled in red appear only in the culture with UA. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
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