MilkOligoThesaurus, a dataset of mammalian milk oligosaccharide synonyms.

There is a growing interest in milk oligosaccharides (MOs) because of their numerous benefits for newborns' and long-term health. A large number of MO structures have been identified in mammalian milk. Mostly described in human milk, the oligosaccharide richness, although less broad, has also been reported for a wide range of mammalian species. The structure of MOs is particularly difficult to report as it results from the combination of 5 monosaccharides linked by various glycosidic bonds forming structurally diverse and complex matrices of linear and branched oligosaccharides. Exploring the literature and extracting relevant information on MO diversity within or across species appears promising to elucidate structure-function role of MOs. Currently, given the complexity of these molecules, the main issues in exploring literature to extract relevant information on MO diversity within or across species relate to the heterogeneity in the way authors refer to these molecules. Herein, we provide a thesaurus (MilkOligoThesaurus) including the names and synonyms of MOs collected from key selected articles on mammalian milk analyses. MilkOligoThesaurus gathers the names of the MOs with a complete description of their monosaccharide composition and structures. When available, each unique MO molecule is linked to its ID from the NCBI PubChem and ChEBI databases. MilkOligoThesaurus is provided in a tabular format. It gathers 245 unique oligosaccharide structures described by 22 features (columns) including the name of the molecule, its abbreviation, the chemical database IDs if available, the monosaccharide composition, chemical information (molecular formula, monoisotopic mass), synonyms, its formula in condensed form, and in abbreviated condensed form, the abbreviated systematic name, the systematic name, the isomer group, and scientific article sources. MilkOligoThesaurus is also provided in the SKOS (Simple Knowledge Organization System) format. This thesaurus is a valuable resource gathering MO naming variations that are not found elsewhere for (i) Text and Data Mining to enable automatic annotation and rapid extraction of milk oligosaccharide data from scientific papers; (ii) biology researchers aiming to search for or decipher the structure of milk oligosaccharides based on any of their names, abbreviations or monosaccharide compositions and linkages.

Combining different points of view on plant descriptions: mapping agricultural plant roles and biological taxa.

This article describes our study on the alignment of two complementary knowledge graphs useful in agriculture: the thesaurus of cultivated plants in France named French Crop Usage (FCU) and the French national taxonomic repository TAXREF for fauna, flora, and fungi. FCU describes the usages of plants in agriculture: "tomatoes" are crops used for human food, and "grapevines" are crops used for human beverage. TAXREF describes biological taxa and associated scientific names: for example, a tomato species may be "Solanum lycopersicum" or a grapevine species may be "Vitis vinifera". Both knowledge graphs contain vernacular names of plants but those names are ambiguous. Thus, a group of agricultural experts produced some mappings from FCU crops to TAXREF taxa. Moreover, new RDF properties have been defined to declare those new types of mapping relations between plant descriptions. The metadata for the mappings and the mapping set are encoded with the Simple Standard for Sharing Ontological Mappings (SSSOM), a new model which, among other qualities, offers means to report on provenance of particular interest for this study. The produced mappings are available for download in Recherche Data Gouv, the federated national platform for research data in France.

Malat1 deficiency prevents hypoxia-induced lung dysfunction by protecting the access to alveoli.

Hypoxia is common in lung diseases and a potent stimulator of the long non-coding RNA Metastasis-Associated Lung Adenocarcinoma Transcript 1 (MALAT1). Herein, we investigated the impact of Malat1 on hypoxia-induced lung dysfunction in mice. Malat1-deficient mice and their wild-type littermates were tested after 8 days of normoxia or hypoxia (10% oxygen). Hypoxia decreased elastance of the lung by increasing lung volume and caused in vivo hyperresponsiveness to methacholine without altering the contraction of airway smooth muscle. Malat1 deficiency also modestly decreased lung elastance but only when tested at low lung volumes and without altering lung volume and airway smooth muscle contraction. The in vivo responsiveness to methacholine was also attenuated by Malat1 deficiency, at least when elastance, a readout sensitive to small airway closure, was used to assess the response. More impressively, in vivo hyperresponsiveness to methacholine caused by hypoxia was virtually absent in Malat1-deficient mice, especially when hysteresivity, a readout sensitive to small airway narrowing heterogeneity, was used to assess the response. Malat1 deficiency also increased the coefficient of oxygen extraction and decreased ventilation in conscious mice, suggesting improvements in gas exchange and in clinical signs of respiratory distress during natural breathing. Combined with a lower elastance at low lung volumes at baseline, as well as a decreased propensity for small airway closure and narrowing heterogeneity during a methacholine challenge, these findings represent compelling evidence suggesting that the lack of Malat1 protects the access to alveoli for air entering the lung.

Smoking status impacts treatment efficacy in smoke-induced lung inflammation: A pre-clinical study.

Rationale: Smoking status and smoking history remain poorly accounted for as variables that could affect the efficacy of new drugs being tested in chronic obstructive pulmonary disease (COPD) patients. As a proof of concept, we used a pre-clinical model of cigarette smoke (CS) exposure to compare the impact of treatment during active CS exposure or during the cessation period on the anti-inflammatory effects IL-1α signaling blockade. Methods: Mice were exposed to CS for 2 weeks, followed by a 1-week cessation, then acutely re-exposed for 2 days. Mice were treated with an anti-IL-1α antibody either during CS exposure or during cessation and inflammatory outcomes were assessed. Results: We found that mice re-exposed to CS displayed reduced neutrophil counts and cytokine levels in the bronchoalveolar lavage (BAL) compared to mice exposed only acutely. Moreover, we found that treatment with an anti-IL-1α antibody during the initial CS exposure delayed inflammatory processes and interfered with pulmonary adaptation, leading to rebound pulmonary neutrophilia, increased BAL cytokine secretion (CCL2) and upregulated Mmp12 expression. Conversely, administration of anti-IL-1α during cessation had the opposite effect, improving BAL neutrophilia, decreasing CCL2 levels and reducing Mmp12 expression. Discussion: These results suggest that pulmonary adaptation to CS exposure dampens inflammation and blocking IL-1α signaling during CS exposure delays the inflammatory response. More importantly, the same treatment administered during cessation hastens the return to pulmonary inflammatory homeostasis, strongly suggesting that smoking status and treatment timing should be considered when testing new biologics in COPD.

A new semantic resource responding to the principles of Open Science: The meat thesaurus as an IT tool for dialogue between sector actors.

Nowadays, it is important to make the results of scientific research accessible in a simple and understandable way according to the Open Science policy. This movement uses tools to enhance findability and interoperability of data. This paper describes the transformation of the meat dictionary published by the French Meat Academy as a book into a machine actionable and freely accessible terminological resource based on the SKOS standard format. This thesaurus contains 1567 concepts describing the meat production chain. This work was carried out by experts in semantic web, meat biology and meat vocabulary. This thesaurus can be used to index articles, journals and datasets, thus facilitating consultation; it can also be used to facilitate interoperability of the indexed datasets and provide contextual definitions for building ontologies, i.e. formal descriptions of knowledge for reasoning on data. The thesaurus can be useful to enrich other vocabularies with new knowledge, such as French specificities in terms of meat cuts or definitions.

Recombinant human ß-defensin 2 delivery improves smoking-induced lung neutrophilia and bacterial exacerbation.

Treatment of the cigarette smoke-associated lung diseases, such as chronic obstructive pulmonary disease (COPD), has largely focused on broad-spectrum anti-inflammatory therapies. However, these therapies, such as high-dose inhaled corticosteroids, enhance patient susceptibility to lung infection and exacerbation. Our objective was to assess whether the cationic host defense peptide, human ß-defensin 2 (hBD-2), can simultaneously reduce pulmonary inflammation in cigarette smoke-exposed mice while maintaining immune competence during bacterial exacerbation. Mice were exposed to cigarette smoke acutely (4 days) or chronically (5 days/wk for 7 wk) and administered hBD-2 intranasally or by gavage. In a separate model of acute exacerbation, chronically exposed mice treated with hBD-2 were infected with nontypeable Haemophilus influenzae before euthanasia. In the acute exposure model, cigarette smoke-associated pulmonary neutrophilia was significantly blunted by both local and systemic hBD-2 administration. Similarly, chronically exposed mice administered hBD-2 therapeutically exhibited reduced pulmonary neutrophil infiltration and downregulated proinflammatory signaling in the lungs compared with vehicle-treated mice. Finally, in a model of acute bacterial exacerbation, hBD-2 administration effectively limited neutrophil infiltration in the lungs while markedly reducing pulmonary bacterial load. This study shows that hBD-2 treatment can significantly attenuate lung neutrophilia induced by cigarette smoke exposure while preserving immune competence and promoting an appropriate host-defense response to bacterial stimuli.

Glycerol contained in vaping liquids affects the liver and aspects of energy homeostasis in a sex-dependent manner.

Vaping is increasingly popular among the young and adult population. Vaping liquids contained in electronic cigarettes (e-cigarettes) are mainly composed of propylene glycol and glycerol, to which nicotine and flavors are added. Among several biological processes, glycerol is a metabolic substrate used for lipid synthesis in fed state as well as glucose synthesis in fasting state. We aimed to investigate the effects of glycerol e-cigarette aerosol exposure on the aspects of glycerol and glucose homeostasis. Adult and young male and female mice were exposed to e-cigarette aerosols with glycerol as vaping liquid using an established whole-body exposure system. Mice were exposed acutely (single 2-h exposure) or chronically (2 h/day, 5 days/week for 9 weeks). Circulating glycerol and glucose levels were assessed and glycerol as well as glucose tolerance tests were performed. The liver was also investigated to assess changes in the histology, lipid content, inflammation, and stress markers. Lung functions were also assessed as well as hepatic mRNA expression of genes controlling the circadian rhythm. Acute exposure to glycerol aerosols generated by an e-cigarette increased circulating glycerol levels in female mice. Increased hepatic triglyceride and phosphatidylcholine concentrations were observed in female mice with no increase in circulating alanine aminotransferase or evidence of inflammation, fibrosis, or endoplasmic reticulum stress. Chronic exposure to glycerol e-cigarette aerosols mildly impacted glucose tolerance test in young female and male mice. Fasting glycerol, glucose, and insulin remained unchanged. Increased pulmonary resistance was observed in young male mice. Taken together, this study shows that the glycerol contained in vaping liquids can affect the liver as well as the aspects of glucose and glycerol homeostasis. Additional work is required to translate these observations to humans and determine the biological and potential pathological impacts of these findings.

Neutrophils and IL-1α Regulate Surfactant Homeostasis during Cigarette Smoking.

Cigarette smoke exposure induces inflammation marked by rapid and sustained neutrophil infiltration, IL-1α, release and altered surfactant homeostasis. However, the extent to which neutrophils and IL-1α contribute to the maintenance of pulmonary surfactant homeostasis is not well understood. We sought to investigate whether neutrophils play a role in surfactant clearance as well as the effect of neutrophil depletion and IL-1α blockade on the response to cigarette smoke exposure. In vitro and in vivo administration of fluorescently labeled surfactant phosphatidylcholine was used to assess internalization of surfactant by lung neutrophils and macrophages during or following cigarette smoke exposure in mice. We also depleted neutrophils using anti-Ly-6G or anti-Gr-1 Abs, or we neutralized IL-1α using a blocking Ab to determine their respective roles in regulating surfactant homeostasis during cigarette smoke exposure. We observed that neutrophils actively internalize labeled surfactant both in vitro and in vivo and that IL-1α is required for smoke-induced elevation of surfactant protein (SP)-A and SP-D levels. Neutrophil depletion during cigarette smoke exposure led to a further increase in SP-A levels in the bronchoalveolar lavage and increased IL-1α, CCL2, GM-CSF, and G-CSF release. Finally, macrophage expression of Mmp12, a protease linked to emphysema, was increased in neutrophil-depleted groups and decreased following IL-1α blockade. Taken together, our results indicate that neutrophils and IL-1α signaling are actively involved in surfactant homeostasis and that the absence of neutrophils in the lungs during cigarette smoke exposure leads to an IL-1α-dependent exacerbation of the inflammatory response.

Making experimental data tables in the life sciences more FAIR: a pragmatic approach.

Making data compliant with the FAIR Data principles (Findable, Accessible, Interoperable, Reusable) is still a challenge for many researchers, who are not sure which criteria should be met first and how. Illustrated with experimental data tables associated with a Design of Experiments, we propose an approach that can serve as a model for research data management that allows researchers to disseminate their data by satisfying the main FAIR criteria without insurmountable efforts. More importantly, this approach aims to facilitate the FAIR compliance process by providing researchers with tools to improve their data management practices.

Exposure to nicotine-free and flavor-free e-cigarette vapors modifies the pulmonary response to tobacco cigarette smoke in female mice.

Most of electronic cigarette (e-cigarette) users are also smoking tobacco cigarettes. Because of the relative novelty of this habit, very little is known on the impact of vaping on pulmonary health, even less on the potential interactions of dual e-cigarette and tobacco cigarette use. Therefore, we used well-established mouse models to investigate the impact of dual exposure to e-cigarette vapors and tobacco cigarette smoke on lung homeostasis. Groups of female BALB/c mice were exposed to room air, tobacco smoke only, nicotine-free flavor-free e-cigarette vapors only or both tobacco smoke and e-cigarette vapors. Moreover, since tobacco smoke and electronic cigarette vapors both affect circadian processes in the lungs, groups of mice were euthanized at two different time points during the day. We found that dual-exposed mice had altered lung circadian gene expression compared with mice exposed to tobacco smoke alone. Dual-exposed mice also had different frequencies of dendritic cells, macrophages, and neutrophils in the lung tissue compared with mice exposed to tobacco smoke alone, an observation also valid for B-lymphocytes and CD4+ and CD8+ T lymphocytes. Exposure to e-cigarette vapors also impacted the levels of immunoglobulins in the bronchoalveolar lavage and serum. Finally, e-cigarette and dual exposures increased airway resistance compared with mice exposed to room air or tobacco smoke alone, respectively. Taken together, these data suggest that e-cigarette vapors, even without nicotine or flavors, could affect how the lungs react to tobacco cigarette smoke exposure in dual users, potentially altering the pathological course triggered by smoking.

Critical importance of dietary methionine and choline in the maintenance of lung homeostasis during normal and cigarette smoke exposure conditions.

Genetic predispositions and environmental exposures are regarded as the main predictors of respiratory disease development. Although the impact of dietary essential nutrient deficiencies on cardiovascular disease, obesity, and type II diabetes has been widely studied, it remains poorly explored in chronic respiratory diseases. Dietary choline and methionine deficiencies are common in the population, and their impact on pulmonary homeostasis is currently unknown. Mice were fed choline- and/or methionine-deficient diets while being exposed to room-air or cigarette smoke for up to 4 wk. Lung functions were assessed using the FlexiVent. Pulmonary transcriptional activity was assessed using gene expression microarrays and quantitative PCR. Immune cells, cytokines, and phosphatidylcholine were quantified in the bronchoalveolar lavage. In this study, we found that short-term dietary choline and/or methionine deficiencies significantly affect lung function in mice in a reversible manner. It also reduced transcriptional levels of collagens and elastin as well as pulmonary surfactant phosphatidylcholine levels. We also found that dietary choline and/or methionine deficiencies markedly interfered with the pulmonary response to cigarette smoke exposure, modulating lung function and dampening inflammation. These findings clearly show that dietary choline and/or methionine deficiencies can have dramatic pathophysiological effects on the lungs and can also affect the pathobiology of cigarette smoke-induced pulmonary alterations. Expanding our knowledge in the field of "nutri-respiratory research" may reveal a crucial role for essential nutrients in pulmonary health and disease, which may prove to be as relevant as genetic predispositions and environmental exposures.

Pharmacological activation of liver X receptor during cigarette smoke exposure adversely affects alveolar macrophages and pulmonary surfactant homeostasis.

Smoking alters pulmonary reverse lipid transport and leads to intracellular lipid accumulation in alveolar macrophages. We investigated whether stimulating reverse lipid transport with an agonist of the liver X receptor (LXR) would help alveolar macrophages limit lipid accumulation and dampen lung inflammation in response to cigarette smoke. Mice were exposed to cigarette smoke and treated intraperitoneally with the LXR agonist T0901317. Expression of lipid capture and lipid export genes was assessed in lung tissue and alveolar macrophages. Pulmonary inflammation was assessed in the bronchoalveolar lavage (BAL). Finally, cholesterol efflux capacity and pulmonary surfactant levels were determined. In room air-exposed mice, T0901317 increased the expression of lipid export genes in macrophages and the whole lung and increased cholesterol efflux capacity without inducing inflammation or affecting the pulmonary surfactant. However, cigarette smoke-exposed mice treated with T0901317 showed a marked increase in BAL neutrophils, IL-1α, C-C motif chemokine ligand 2, and granulocyte-colony-stimulating factor levels. T0901317 treatment in cigarette smoke-exposed mice failed to increase the ability of alveolar macrophages to export cholesterol and markedly exacerbated IL-1α release. Finally, T0901317 led to pulmonary surfactant depletion only in cigarette smoke-exposed mice. This study shows that hyperactivation of LXR and the associated lipid capture/export mechanisms only have minor pulmonary effects on the normal lung. However, in the context of cigarette smoke exposure, where the pulmonary surfactant is constantly oxidized, hyperactivation of LXR has dramatic adverse effects, once again showing the central role of lipid homeostasis in the pulmonary response to cigarette smoke exposure.

Impact of immunization against OxLDL on the pulmonary response to cigarette smoke exposure in mice.

BACKGROUND: Cigarette smoke exposure can affect pulmonary lipid homeostasis and cause a progressive increase in pulmonary antibodies against oxidized low-density lipoproteins (OxLDL). Similarly, increased anti-OxLDL antibodies are observed in atherosclerosis, a pathology also tightly associated with smoking and lipid homeostasis disruption. Several immunization strategies against oxidized lipid species to help with their clearance have been shown to reduce the formation of atherosclerotic lesions. Since oxidized lipids are generated during cigarette smoke exposure, we investigated the impact of a prophylactic immunization protocol against OxLDL on the pulmonary effects of cigarette smoke exposure in mice. METHODS: Mice were immunized systemically with a mixture of human OxLDL (antigen source) and AddaVax (adjuvant) or PBS alone prior to the initiation of acute (2 week) or sub-chronic (8 weeks) cigarette smoke exposure protocols. Anti-OxLDL antibodies were measured in the bronchoalveolar lavage (BAL) fluid and serum by direct ELISA. Pulmonary impacts of cigarette smoke exposure and OxLDL immunization were assessed by measuring BAL inflammatory cells, lung functions, and changes in lung structure and gene levels of matrix/matrix-related genes. RESULTS: Immunization to OxLDL led to a marked increase in circulating and pulmonary antibodies against OxLDL that persisted during cigarette smoke exposure. OxLDL immunization did not exacerbate or reduce the inflammatory response following acute or sub-chronic exposure to cigarette smoke. OxLDL immunization alone had effects similar to cigarette smoke exposure on lung functions but OxLDL immunization and cigarette smoke exposure had no additive effects on these parameters. No obvious changes in lung histology, airspace or levels of matrix and matrix-related genes were caused by OxLDL immunization compared to vehicle treatment. CONCLUSIONS: Overall, this study shows for the first time that a prophylactic immunization protocol against OxLDL can potentially have detrimental effects lung functions, without having additive effects over cigarette smoke exposure. This work sheds light on a complex dynamic between anti-OxLDL antibodies and the pulmonary response to cigarette smoke exposure.

Exposure to electronic cigarette vapors affects pulmonary and systemic expression of circadian molecular clock genes.

E-cigarette use has exploded in the past years, especially among young adults and smokers desiring to quit. While concerns are mostly based on the presence of nicotine and flavors, pulmonary effects of propylene glycol and glycerol inhalation, the main solvents of e-liquid have not been thoroughly investigated. In this preclinical study, mice were exposed 2 h daily for up to 8 weeks to vapors of propylene glycol and/or glycerol generated by an e-cigarette. Lung transcriptome analysis revealed it affected the expression level of genes of the circadian molecular clock, despite causing no inflammatory response. Periodical sacrifices showed that the rhythmicity of these regulatory genes was indeed altered in the lungs, but also in the liver, kidney, skeletal muscle, and brain. E-cigarette exposure also altered the expression of rhythmic genes (i.e., hspa1a and hspa1b), suggesting that alterations to the 'clock genes' could translate into systemic biological alterations. This study reveals that the major solvents used in e-cigarettes propylene glycol and glycerol, not nicotine or flavors, have unsuspected effects on gene expression of the molecular clock that are to be taken seriously, especially considering the fundamental role of the circadian rhythm in health and disease.

Interplay between cigarette smoking and pulmonary reverse lipid transport.

Reverse lipid transport is critical to maintain homeostasis. Smoking causes lipid accumulation in macrophages, therefore suggesting suboptimal reverse lipid transport mechanisms. In this study, we investigated the interplay between smoking and reverse lipid transport and the consequences on smoking-induced lung and peripheral alterations.To investigate the relationship between smoking and reverse lipid transport, we used a clinical lung gene expression dataset and a mouse model of cigarette smoke exposure. We also used ApoA-1-/- mice, with reduced reverse lipid transport capacity, and a recombinant ApoA-1 Milano/phospholipid complex (MDCO-216) to boost reverse lipid transport. Cellular and functional analyses were performed on the lungs and impact on body composition was also assessed.Smoking affects pulmonary expression of abca1, abcg1, apoe and scarb1 in both mice and humans, key genes involved in reverse lipid transport. In mice, the capacity of bronchoalveolar lavage fluid and serum to stimulate cholesterol efflux in macrophages was increased after a single exposure to cigarette smoke. ApoA-1-/- mice showed increased lung neutrophilia, larger macrophages and greater loss in lean mass in response to smoking, whereas treatment with MDCO-216 reduced the size of macrophages and increased the lean mass of mice exposed to cigarette smoke.Altogether, this study shows a functional interaction between smoking and reverse lipid transport, and opens new avenues for better understanding the link between metabolic and pulmonary diseases related to smoking.

Developing data interoperability using standards: A wheat community use case.

In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. Agreeing on common data formats, metadata, and vocabulary standards is an important step to obtain the required data interoperability level in order to add value by encouraging data sharing, and subsequently facilitate the extraction of new information from existing and new datasets. During a period of more than 18 months, the RDA Wheat Data Interoperability Working Group (WDI-WG) surveyed the wheat research community about the use of data standards, then discussed and selected a set of recommendations based on consensual criteria. The recommendations promote standards for data types identified by the wheat research community as the most important for the coming years: nucleotide sequence variants, genome annotations, phenotypes, germplasm data, gene expression experiments, and physical maps. For each of these data types, the guidelines recommend best practices in terms of use of data formats, metadata standards and ontologies. In addition to the best practices, the guidelines provide examples of tools and implementations that are likely to facilitate the adoption of the recommendations. To maximize the adoption of the recommendations, the WDI-WG used a community-driven approach that involved the wheat research community from the start, took into account their needs and practices, and provided them with a framework to keep the recommendations up to date. We also report this approach's potential to be generalizable to other (agricultural) domains.

Text mining resources for the life sciences.

Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. However, to harness this power the researcher must be well versed in the availability, suitability, adaptability, interoperability and comparative accuracy of current text mining resources. In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work. We categorize the various resources under three sections: Content Discovery looks at where and how to find biomedical publications for text mining; Knowledge Encoding describes the formats used to represent the different levels of information associated with content that enable text mining, including those formats used to carry such information between processes; Tools and Services gives an overview of workflow management systems that can be used to rapidly configure and compare domain- and task-specific processes, via access to a wide range of pre-built tools. We also provide links to relevant repositories in each section to enable the reader to find resources relevant to their own area of interest. Throughout this work we give a special focus to resources that are interoperable-those that have the crucial ability to share information, enabling smooth integration and reusability.

Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches.

BACKGROUND: We study the adaptation of Link Grammar Parser to the biomedical sublanguage with a focus on domain terms not found in a general parser lexicon. Using two biomedical corpora, we implement and evaluate three approaches to addressing unknown words: automatic lexicon expansion, the use of morphological clues, and disambiguation using a part-of-speech tagger. We evaluate each approach separately for its effect on parsing performance and consider combinations of these approaches. RESULTS: In addition to a 45% increase in parsing efficiency, we find that the best approach, incorporating information from a domain part-of-speech tagger, offers a statistically significant 10% relative decrease in error. CONCLUSION: When available, a high-quality domain part-of-speech tagger is the best solution to unknown word issues in the domain adaptation of a general parser. In the absence of such a resource, surface clues can provide remarkably good coverage and performance when tuned to the domain. The adapted parser is available under an open-source license.