NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature.

Automatically identifying chemical and drug names in scientific publications advances information access for this important class of entities in a variety of biomedical disciplines by enabling improved retrieval and linkage to related concepts. While current methods for tagging chemical entities were developed for the article title and abstract, their performance in the full article text is substantially lower. However, the full text frequently contains more detailed chemical information, such as the properties of chemical compounds, their biological effects and interactions with diseases, genes and other chemicals. We therefore present the NLM-Chem corpus, a full-text resource to support the development and evaluation of automated chemical entity taggers. The NLM-Chem corpus consists of 150 full-text articles, doubly annotated by ten expert NLM indexers, with ~5000 unique chemical name annotations, mapped to ~2000 MeSH identifiers. We also describe a substantially improved chemical entity tagger, with automated annotations for all of PubMed and PMC freely accessible through the PubTator web-based interface and API. The NLM-Chem corpus is freely available.

Draft genome of the European medicinal leech Hirudo medicinalis (Annelida, Clitellata, Hirudiniformes) with emphasis on anticoagulants.

The European medicinal leech has been used for medicinal purposes for millennia, and continues to be used today in modern hospital settings. Its utility is granted by the extremely potent anticoagulation factors that the leech secretes into the incision wound during feeding and, although a handful of studies have targeted certain anticoagulants, the full range of anticoagulation factors expressed by this species remains unknown. Here, we present the first draft genome of the European medicinal leech, Hirudo medicinalis, and estimate that we have sequenced between 79-94% of the full genome. Leveraging these data, we searched for anticoagulation factors across the genome of H. medicinalis. Following orthology determination through a series of BLAST searches, as well as phylogenetic analyses, we estimate that fully 15 different known anticoagulation factors are utilized by the species, and that 17 other proteins that have been linked to antihemostasis are also present in the genome. We underscore the utility of the draft genome for comparative studies of leeches and discuss our results in an evolutionary context.

Clustering a Chemical Inventory for Safety Assessment of Fragrance Ingredients: Identifying Read-Across Analogs to Address Data Gaps.

A valuable approach to chemical safety assessment is the use of read-across chemicals to provide safety data to support the assessment of structurally similar chemicals. An inventory of over 6000 discrete organic chemicals used as fragrance materials in consumer products has been clustered into chemical class-based groups for efficient search of read-across sources. We developed a robust, tiered system for chemical classification based on (1) organic functional group, (2) structural similarity and reactivity features of the hydrocarbon skeletons, (3) predicted or experimentally verified Phase I and Phase II metabolism, and (4) expert pruning to consider these variables in the context of specific toxicity end points. The systematic combination of these data yielded clusters, which may be visualized as a top-down hierarchical clustering tree. In this tree, chemical classes are formed at the highest level according to organic functional groups. Each subsequent subcluster stemming from classes in this hierarchy of the cluster is a chemical cluster defined by common organic functional groups and close similarity in the hydrocarbon skeleton. By examining the available experimental data for a toxicological endpoint within each cluster, users can better identify potential read-across chemicals to support safety assessments.

The amino acid derivative reactivity assay with fluorescence detection and its application to multi-constituent substances.

The Amino acid Derivative Reactivity Assay (ADRA) is an in chemico alternative to animal testing for the prediction of skin sensitization potential. Although co-elution of test chemicals and nucleophilic reagents during HPLC analysis is sometimes problematic when using the Direct Peptide Reactivity Assay (DPRA), it rarely occurs when using ADRA. Nevertheless, the application of either of these tests to multi-constituent substances requires nucleophilic reagents capable of selective detection. With this issue in mind, the authors developed an ADRA fluorescence detection method (ADRA-FL), which utilizes the natural fluorescence of ADRA nucleophilic reagents. In this study, we demonstrate the efficacy of ADRA-FL by testing 82 test chemicals used in the development of both DPRA and the conventional ADRA (ADRA-UV) as well as establish a threshold value for distinguishing sensitizers and non-sensitizers. Our results show that not only are depletion values obtained using ADRA-FL virtually identical to those obtained using ADRA-UV, the threshold value for either test is 4.9%. Additionally, in order to demonstrate the applicability of ADRA-FL to multi-constituent substances, we prepared test samples that consisted of a set of 10 non-sensitizers combined with one of 10 different sensitizers and tested each using ADRA-FL. The test results were concordant with those obtained using ADRA-UV. Also, because ADRA-FL chromatograms showed a significant decrease in multiple peaks as well as extremely stable baselines, we conclude that ADRA-FL is a highly selective and highly accurate mans of quantifying nucleophilic reagents that is applicable to a wide variety of chemical substances.

Rapid Visualization of Chemically Related Compounds Using Kendrick Mass Defect As a Filter in Mass Spectrometry Imaging.

Kendrick mass defect (KMD) analysis is widely used for helping the detection and identification of chemically related compounds based on exact mass measurements. We report here the use of KMD as a criterion for filtering complex mass spectrometry data set. The method allow automated, easy and efficient data processing, enabling the reconstruction of 2D distributions of families of homologous compounds from MSI images. We show that KMD filtering, based on in-house software, is suitable and robust for high resolution (full width at half-maximum, fwhm, at m/z 410 of 20 000) and very high-resolution (fwhm, at m/z 410 of 160 000) MSI data. This method has been successfully applied to two different types of samples, bacteria cocultures, and brain tissue sections.

A novel graph kernel on chemical compound classification.

Considering the classification of compounds as a nonlinear problem, the use of kernel methods is a good choice. Graph kernels provide a nice framework combining machine learning methods with graph theory, whereas the essence of graph kernels is to compare the substructures of two graphs, how to extract the substructures is a question. In this paper, we propose a novel graph kernel based on matrix named the local block kernel, which can compare the similarity of partial substructures that contain any number of vertexes. The paper finally tests the efficacy of this novel graph kernel in comparison with a number of published mainstream methods and results with two datasets: NCI1 and NCI109 for the convenience of comparison.

Growth and production of volatile compounds of yarrow (Achillea millefolium L.) under different irrigation depths.

Yarrow (Achillea millefolium L., Asteraceae) is an important medicinal plant used worldwide for its medicinal properties such as the analgesic, antioxidant and anti-inflammatory ones. The aim of this study was to evaluate the growth and production of photosynthetic pigments and of volatile constituents of Achillea millefolium L. under different irrigation depths. The treatments were the application of 55, 110, 220, 440 and 880 mm of water for a period of 110 days. Data were submitted to polynomial regression analysis at 5% probability, while the volatile constituents were analyzed by standard deviation. Different irrigation depths provided quadratic growth responses being the highest dry matter production at the depth of 440 mm. The contents of chlorophyll a, b, total and carotenoids were higher at the lower depth tested (55 mm). The major volatile compounds identified were sabinene, 1,8-cineol, borneol and ß-caryophyllene. Increased water availability reduced the complexity of the volatile fraction of essential oil. Thus, it is recommended that the species be cultivated at 440 mm irrigation depth to have a higher production of dry matter and lower variation in the volatile profile of the essential oil.

Can the Stockholm convention address the spectrum of chemicals currently under regulatory scrutiny? Advocating a more prominent role for modeling in POP screening assessment.

Frameworks for chemical regulation are based on the science at the time they were written. Today some regulations are being applied to a much broader spectrum of chemicals than we had knowledge of when the regulations were written. This entails a risk that the regulations are being used outside of their chemical application domain. This question is explored using the POP screening assessment in the Stockholm convention, which was developed 20 years ago. Using perfluorinated alkyl acids (PFAAs) as an example, it is shown that the assessment can lead to false negative conclusions. A second case study using octamethylcyclotetrasiloxane (D4) illustrates that there is also a risk of false positives. The risk for false negative classification of PFAAs is due to the inclusion of a screening criterion - bioaccumulation - that is not a requirement for adverse effects of chemicals in remote regions. For D4 the risk of false positive classification stems from the four screening criteria (persistence, bioaccumulation, long-range transport, and adverse effects) applying to different environmental media/compartments. The major lesson is that applying the POP screening procedure to the broad spectrum of chemicals in modern commerce will require that we rely less on the individual screening criteria and more on the comparison of estimated exposure and the thresholds for effects stipulated in Annex D, paragraph 2 of the convention. Models have an important role to play in this context and should become more strongly integrated into the POP screening process.

The impact of exposure route for class-based compounds: a comparative approach of lethal toxicity data in rodent models.

Relationships of toxicities from intravenous (i.v.), intraperitoneal (i.p.), subcutaneous (s.c.) and intragastric (i.g.) exposure routes to mice were investigated. Regression analysis showed that the toxicities from i.v. route is strongly correlated with i.p. and s.c. routes, but poorly with i.g. route. Close toxicities from different routes for some compounds indicate that distribution rate is the determining step and dictates chemical concentration at the target site(s). On the other hand, the absorption rate is the determining step for many compounds, which lead to different toxicities between exposure routes. The classified compounds characterized as having either absorption or distribution rate determining step were based upon the comparison of toxicities from the different routes. We found that some aliphatic acids and benzoic acids have lower toxicity values from i.g. route compared to an i.v. route because of poor absorption. Many compounds show low toxic effects from i.g. route than those from other routes because of the first-pass metabolism in the gastrointestinal tract, resulting in the poor relationship for toxicities between i.g. and i.v. or other routes. Stepwise regression analysis showed that physicochemical properties of a compound, such as molecular volume, polarizability and hydrophobicity, significantly affect adsorption rate, which leads to different toxicities based upon exposure routes. Comparison of the toxicities between mice and rats indicate that toxic effect and the toxicokinetic processes in mice are very similar to that in rats. A universal correlation equation has been developed for the toxicities between rats and mice from different exposure routes, which can be applied to predict toxicities across species.

QSAR modeling of cumulative environmental end-points for the prioritization of hazardous chemicals.

The hazard of chemicals in the environment is inherently related to the molecular structure and derives simultaneously from various chemical properties/activities/reactivities. Models based on Quantitative Structure Activity Relationships (QSARs) are useful to screen, rank and prioritize chemicals that may have an adverse impact on humans and the environment. This paper reviews a selection of QSAR models (based on theoretical molecular descriptors) developed for cumulative multivariate endpoints, which were derived by mathematical combination of multiple effects and properties. The cumulative end-points provide an integrated holistic point of view to address environmentally relevant properties of chemicals.

Derivation of Occupational Thresholds of Toxicological Concern for Systemically Acting Noncarcinogenic Organic Chemicals.

Many substances in workplace do not have occupational exposure limits. The threshold of toxicological concern (TTC) principle is part of the hierarchy of approaches useful in occupational health risk assessment. The aim of this study was to derive occupational TTCs (OTTCs) reflecting the airborne concentrations below which no significant risk to workers would be anticipated. A reference dataset consisting of the 8-h threshold limit values-Time-Weighted Average for 280 organic substances was compiled. Each substance was classified into low (class I), intermediate (class II), or high (class III) hazard categories as per Cramer rules. For each chemical, n-octanol:water partition coefficient and vapor pressure along with the molecular weight were used to predict the blood:air partition coefficient. The blood:air partition coefficient along with data on water solubility and ventilation rate allowed the prediction of pulmonary retention factor and absorbed dose in workers. For each Cramer class, the distribution of the predicted doses was analyzed to identify the various percentile values corresponding to the OTTC. Accordingly, for Cramer classes I-III, the OTTCs derived in this study correspond to 0.15, 0.0085, and 0.006 mmol/d, respectively, at the 10th percentile level, while these values were 1.5, 0.09 and 0.03 mmol/d at the 25th percentile level. The proposed OTTCs are not meant to replace the traditional occupational exposure limits, but can be used in data-poor situations along with exposure estimates to support screening level risk assessment and prioritization.

Ranking REACH registered neutral, ionizable and ionic organic chemicals based on their aquatic persistency and mobility.

The contaminants that have the greatest chances of appearing in drinking water are those that are mobile enough in the aquatic environment to enter drinking water sources and persistent enough to survive treatment processes. Herein a screening procedure to rank neutral, ionizable and ionic organic compounds for being persistent and mobile organic compounds (PMOCs) is presented and applied to the list of industrial substances registered under the EU REACH legislation as of December 2014. This comprised 5155 identifiable, unique organic structures. The minimum cut-off criteria considered for PMOC classification herein are a freshwater half-life >40 days, which is consistent with the REACH definition of freshwater persistency, and a log Doc < 4.5 between pH 4-10 (where Doc is the organic carbon-water distribution coefficient). Experimental data were given the highest priority, followed by data from an array of available quantitative structure-activity relationships (QSARs), and as a third resort, an original Iterative Fragment Selection (IFS) QSAR. In total, 52% of the unique REACH structures made the minimum criteria to be considered a PMOC, and 21% achieved the highest PMOC ranking (half-life > 40 days, log Doc < 1.0 between pH 4-10). Only 9% of neutral substances received the highest PMOC ranking, compared to 30% of ionizable compounds and 44% of ionic compounds. Predicted hydrolysis products for all REACH parents (contributing 5043 additional structures) were found to have higher PMOC rankings than their parents, due to increased mobility but not persistence. The fewest experimental data available were for ionic compounds; therefore, their ranking is more uncertain than neutral and ionizable compounds. The most sensitive parameter for the PMOC ranking was freshwater persistency, which was also the parameter that QSARs performed the most poorly at predicting. Several prioritized drinking water contaminants in the EU and USA, and other contaminants of concern, were identified as PMOCs. This identification and ranking procedure for PMOCs can be part of a strategy to better identify contaminants that pose a threat to drinking water sources.

Devices for the Production of Reference Gas Mixtures.

For many years there has been growing demand for gaseous reference materials, which is connected with development in many fields of science and technology. As a result, new methodological and instrumental solutions appear that can be used for this purpose. Appropriate quality assurance/quality control (QA/QC) must be used to make sure that measurement data are a reliable source of information. Reference materials are a significant element of such systems. In the case of gas samples, such materials are generally called reference gas mixtures. This article presents the application and classification of reference gas mixtures, which are a specific type of reference materials, and the methods for obtaining them are described. Construction solutions of devices for the production of reference gas mixtures are detailed, and a description of a prototype device for dynamic production of reference gas mixtures containing aroma compounds is presented.

Inhalation TTC values: A new integrative grouping approach considering structural, toxicological and mechanistic features.

The present publication describes an integrative grouping concept to derive threshold values for inhalation exposure. The classification scheme starts with differences in toxicological potency and develops criteria to group compounds into two potency classes, namely toxic (T-group) or low toxic (L-group). The TTC concept for inhalation exposure is based on the TTC RepDose data set, consisting of 296 organic compounds with 608 repeated-dose inhalation studies. Initially, 21 structural features (SFs) were identified as being characteristic for compounds of either high or low NOEC values (Schüürmann et al., 2016). In subsequent analyses these SF groups were further refined by taking into account structural homogeneity, type of toxicological effect observed, differences in absorption, metabolism and mechanism of action (MoA), to better define their structural and toxicological boundaries. Differentiation of a local or systemic mode of action did not improve the classification scheme. Finally, 28 groups were discriminated: 19 T-groups and 9 L-groups. Clearly distinct thresholds were derived for the T- and L-toxicity groups, being 2 × 10(-5) ppm (2 µg/person/day) and 0.05 ppm (4260 µg/person/day), respectively. The derived thresholds and the classification are compared to the initial mainly structure driven grouping (Schüürmann et al., 2016) and to the Cramer classification.

Implications for public health demands alternatives to inorganic and synthetic flocculants: bioflocculants as important candidates.

Chemical flocculants are generally used in drinking water and wastewater treatment due to their efficacy and cost effectiveness. However, the question of their toxicity to human health and environmental pollution has been a major concern. In this article, we review the application of some chemical flocculants utilized in water treatment, and bioflocculants as a potential alternative to these chemical flocculants. To the best of our knowledge, there is no report in the literature that provides an up-to-date review of the relevant literature on both chemical flocculants and bioflocculants in one paper. As a result, this review paper comprehensively discussed the various chemical flocculants used in water treatment, including their advantages and disadvantages. It also gave insights into bioflocculants production, challenges, various factors influencing their flocculating efficiency and their industrial applications, as well as future research directions including improvement of bioflocculants yields and flocculating activity, and production of cation-independent bioflocculants. The molecular biology and synthesis of bioflocculants are also discussed.

Discrimination of excess toxicity from narcotic effect: influence of species sensitivity and bioconcentration on the classification of modes of action.

The toxicity data of 2624 chemicals to fish, Daphniamagna, Tetrahymenapyriformis and Vibriofischeri were used to investigate the effects of species sensitivity and bioconcentration on excess toxicity. The results showed that 47 chemical classes were identified as having the same modes of action (MOAs) to all four species, but more than half of the classes were identified as having different MOAs. Difference in chemical MOAs is one of the reasons resulting in the difference in toxic effect to these four species. Other important reasons are the difference in sensitivity and bioconcentration of species. Among the four species, V. fischeri has the most compounds identified as reactive MOA. This may be due to some compounds can be easily absorbed into the bacteria, react with the DNA or proteins, disrupt the normal function of the cell and exhibit significantly greater toxicity to the bacteria. On the other hand, the skin and lipid content of aqueous organisms can strongly inhibit the bio-uptake for some reactive compounds, resulting in a less toxic effect than expected. D. magna is the most sensitive species and T. pyriformis is the least sensitive species of the four species. For a comparison of interspecies toxicity, we need to use the same reference threshold of excess toxicity. However, some reactive compounds may be identified as baseline or less inert compounds for low sensitive species from the threshold developed from high sensitive species. The difference in the discrimination of excess toxicity to different species is not only because of the difference in MOAs for some compounds, but also due to the difference in sensitivity and bioconcentration.

Non-targeted analyses of organic compounds in urban wastewater.

A large number of organic pollutants that cause damage to the ecosystem and threaten human health are transported to wastewater treatment plants (WWTPs). The problems regarding water pollution in Latin America have been well documented, and there is no evidence of substantive efforts to change the situation. In the present work, two methods to study wastewater samples are employed: non-targeted 1D ((13)C and (1)H) and 2D NMR spectroscopic analysis to characterize the largest possible number of compounds from urban wastewater and analysis by HPLC-(UV/MS)-SPE-ASS-NMR to detect non-specific recalcitrant organic compounds in treated wastewater without the use of common standards. The set of data is composed of several compounds with the concentration ranging considerably with treatment and seasonality. An anomalous discharge, the influence of stormwater on the wastewater composition and the presence of recalcitrant compounds (linear alkylbenzene sulfonate surfactant homologs) in the effluent were further identified. The seasonal variations and abnormality in the composition of organic compounds in sewage indicated that the procedure that was employed can be useful in the identification of the pollution source and to enhance the effectiveness of WWTPs in designing preventive action to protect the equipment and preserve the environment.

Risk assessment based prioritization of 200 organic micropollutants in 4 Iberian rivers.

The use of chemicals is continuously growing both in total amount as well as in a number of different substances, among which organic chemicals play a major role. Owing to the growing public awareness on the need of protecting both ecosystems and human health from the risks related to chemical pollution, an increasing attention has been drowned to risk assessment and prioritization of organic pollutants. In this context, the aims of this study were (a) to perform an environmental risk assessment for 200 organic micropollutants including both regulated and emerging contaminants (pesticides, alkylphenols, pharmaceuticals, hormones, personal care products, perflourinated compounds and various industrial organic chemicals) monitored in four rivers located in the Mediterranean side of the Iberian Peninsula, namely, the Ebro, Llobregat, Júcar and Guadalquivir rivers; and (b) to prioritize them for each of the four river basins studied, taking into account their observed concentration levels together with their ecotoxicological potential. For this purpose, a prioritization approach has been developed and a resulting ranking index (RI) associated with each compound. Ranking index is based on the measured concentrations of the chemical in each river and its ecotoxicological potential (EC50 values for algae, Daphnia sp. and fish). Ten compounds were identified as most important for the studied rivers: pesticides chlorpyriphos, chlorfenvinphos, diazinon, dichlofenthion, prochloraz, ethion carbofuran and diuron and the industrial organic chemicals nonylphenol and octylphenol that result from the biodegration of polyethoxylated alkyphenol surfactants. Also, further research into chronic toxicity of emerging contaminants is advocated.

TyPol - a new methodology for organic compounds clustering based on their molecular characteristics and environmental behavior.

Following legislation, the assessment of the environmental risks of 30000-100000 chemical substances is required for their registration dossiers. However, their behavior in the environment and their transfer to environmental components such as water or atmosphere are studied for only a very small proportion of the chemical in laboratory tests or monitoring studies because it is time-consuming and/or cost prohibitive. Therefore, the objective of this work was to develop a new methodology, TyPol, to classify organic compounds, and their degradation products, according to both their behavior in the environment and their molecular properties. The strategy relies on partial least squares analysis and hierarchical clustering. The calculation of molecular descriptors is based on an in silico approach, and the environmental endpoints (i.e. environmental parameters) are extracted from several available databases and literature. The classification of 215 organic compounds inputted in TyPol for this proof-of-concept study showed that the combination of some specific molecular descriptors could be related to a particular behavior in the environment. TyPol also provided an analysis of similarities (or dissimilarities) between organic compounds and their degradation products. Among the 24 degradation products that were inputted, 58% were found in the same cluster as their parents. The robustness of the method was tested and shown to be good. TyPol could help to predict the environmental behavior of a "new" compound (parent compound or degradation product) from its affiliation to one cluster, but also to select representative substances from a large data set in order to answer some specific questions regarding their behavior in the environment.

Annotation of the human serum metabolome by coupling three liquid chromatography methods to high-resolution mass spectrometry.

This work aims at evaluating the relevance and versatility of liquid chromatography coupled to high resolution mass spectrometry (LC/HRMS) for performing a qualitative and comprehensive study of the human serum metabolome. To this end, three different chromatographic systems based on a reversed phase (RP), hydrophilic interaction chromatography (HILIC) and a pentafluorophenylpropyl (PFPP) stationary phase were used, with detection in both positive and negative electrospray modes. LC/HRMS platforms were first assessed for their ability to detect, retain and separate 657 metabolite standards representative of the chemical families occurring in biological fluids. More than 75% were efficiently retained in either one LC-condition and less than 5% were exclusively retained by the RP column. These three LC/HRMS systems were then evaluated for their coverage of serum metabolome. The combination of RP, HILIC and PFPP based LC/HRMS methods resulted in the annotation of about 1328 features in the negative ionization mode, and 1358 in the positive ionization mode on the basis of their accurate mass and precise retention time in at least one chromatographic condition. Less than 12% of these annotations were shared by the three LC systems, which highlights their complementarity. HILIC column ensured the greatest metabolome coverage in the negative ionization mode, whereas PFPP column was the most effective in the positive ionization mode. Altogether, 192 annotations were confirmed using our spectral database and 74 others by performing MS/MS experiments. This resulted in the formal or putative identification of 266 metabolites, among which 59 are reported for the first time in human serum.