Material Legacies and Environmental Constraints Underlie Fire Resilience of a Dominant Boreal Forest Type.

Resilience of plant communities to disturbance is supported by multiple mechanisms, including ecological legacies affecting propagule availability, species' environmental tolerances, and biotic interactions. Understanding the relative importance of these mechanisms for plant community resilience supports predictions of where and how resilience will be altered with disturbance. We tested mechanisms underlying resilience of forests dominated by black spruce (Picea mariana) to fire disturbance across a heterogeneous forest landscape in the Northwest Territories, Canada. We combined surveys of naturally regenerating seedlings at 219 burned plots with experimental manipulations of ecological legacies via seed addition of four tree species and vertebrate exclosures to limit granivory and herbivory at 30 plots varying in moisture and fire severity. Black spruce recovery was greatest where it dominated pre-fire, at wet sites with deep residual soil organic layers, and fire conditions of low soil or canopy combustion and longer return intervals. Experimental addition of seed indicated all species were seed-limited, emphasizing the importance of propagule legacies. Black spruce and birch (Betula papyrifera) recruitment were enhanced with vertebrate exclusion. Our combination of observational and experimental studies demonstrates black spruce is vulnerable to effects of increased fire activity that erode ecological legacies. Moreover, black spruce relies on wet areas with deep soil organic layers where other species are less competitive. However, other species can colonize these areas if enough seed is available or soil moisture is altered by climate change. Testing mechanisms underlying species' resilience to disturbance aids predictions of where vegetation will transform with effects of climate change. Supplementary Information: The online version contains supplementary material available at 10.1007/s10021-022-00772-7.

Carbon and nitrogen cycling dynamics following permafrost thaw in the Northwest Territories, Canada.

Rapid climate warming across northern high latitudes is leading to permafrost thaw and ecosystem carbon release while simultaneously impacting other biogeochemical cycles including nitrogen. We used a two-year laboratory incubation study to quantify concomitant changes in carbon and nitrogen pool quantity and quality as drivers of potential CO2 production in thawed permafrost soils from eight soil cores collected across the southern Northwest Territories (NWT), Canada. These data were contextualized via in situ annual thaw depth measurements from 2015 to 2019 at 40 study sites that varied in burn history. We found with increasing time since experimental thaw the dissolved carbon and nitrogen pool quality significantly declined, indicating sustained microbial processing and selective immobilization across both pools. Piecewise structural equation modeling revealed CO2 trends were predominantly predicted by initial soil carbon content with minimal influence of dissolved phase carbon. Using these results, we provide a first-order estimate of potential near-surface permafrost soil losses of up to 80 g C m-2 over one year in southern NWT, exceeding regional historic mean primary productivity rates in some areas. Taken together, this research provides mechanistic knowledge needed to further constrain the permafrost­carbon feedback and parameterize Earth system models, while building on empirical evidence that permafrost soils are at high risk of becoming weaker carbon sinks or even significant carbon sources under a changing climate.

Discordant diagnostic criteria for pneumonia in COPD trials: a review.

Inhaled corticosteroids (ICS) have a class effect of increasing pneumonia risk in patients with COPD. However, pneumonia incidence varies widely across clinical trials of ICS use in COPD. This review clarifies methodological differences in defining and recording pneumonia events in these trials and discusses factors that could contribute to the varying pneumonia incidence. Literature searches and screening yielded 40 relevant references for inclusion. Methods used to capture pneumonia events in these studies included investigator-reported pneumonia adverse events, standardised list of signs or symptoms, radiographic confirmation of suspected cases and/or confirmation by an independent clinical end-point committee. In general, more stringent pneumonia diagnosis criteria led to lower reported pneumonia incidence rates. In addition, studies varied in design and population characteristics, including exacerbation history and lung function, factors that probably contribute to the varying pneumonia incidence. As such, cross-trial comparisons are problematic. A minimal set of standardised criteria for diagnosis and reporting of pneumonia should be used in COPD studies, as well as reporting of patients' pneumonia history at baseline, to allow comparison of pneumonia rates between trials. Currently, within-trial comparison of ICS-containing versus non-ICS-containing treatments is the appropriate method to assess the influence of ICS on pneumonia incidence.

Increasing fire and the decline of fire adapted black spruce in the boreal forest.

Intensifying wildfire activity and climate change can drive rapid forest compositional shifts. In boreal North America, black spruce shapes forest flammability and depends on fire for regeneration. This relationship has helped black spruce maintain its dominance through much of the Holocene. However, with climate change and more frequent and severe fires, shifts away from black spruce dominance to broadleaf or pine species are emerging, with implications for ecosystem functions including carbon sequestration, water and energy fluxes, and wildlife habitat. Here, we predict that such reductions in black spruce after fire may already be widespread given current trends in climate and fire. To test this, we synthesize data from 1,538 field sites across boreal North America to evaluate compositional changes in tree species following 58 recent fires (1989 to 2014). While black spruce was resilient following most fires (62%), loss of resilience was common, and spruce regeneration failed completely in 18% of 1,140 black spruce sites. In contrast, postfire regeneration never failed in forests dominated by jack pine, which also possesses an aerial seed bank, or broad-leaved trees. More complete combustion of the soil organic layer, which often occurs in better-drained landscape positions and in dryer duff, promoted compositional changes throughout boreal North America. Forests in western North America, however, were more vulnerable to change due to greater long-term climate moisture deficits. While we find considerable remaining resilience in black spruce forests, predicted increases in climate moisture deficits and fire activity will erode this resilience, pushing the system toward a tipping point that has not been crossed in several thousand years.

Measuring change in biological communities: multivariate analysis approaches for temporal datasets with low sample size.

Effective and robust ways to describe, quantify, analyse, and test for change in the structure of biological communities over time are essential if ecological research is to contribute substantively towards understanding and managing responses to ongoing environmental changes. Structural changes reflect population dynamics, changes in biomass and relative abundances of taxa, and colonisation and extinction events observed in samples collected through time. Most previous studies of temporal changes in the multivariate datasets that characterise biological communities are based on short time series that are not amenable to data-hungry methods such as multivariate generalised linear models. Here, we present a roadmap for the analysis of temporal change in short-time-series, multivariate, ecological datasets. We discuss appropriate methods and important considerations for using them such as sample size, assumptions, and statistical power. We illustrate these methods with four case-studies analysed using the R data analysis environment.

Changes in the analysis of temporal community dynamics data: a 29-year literature review.

BACKGROUND: Understanding how biological communities change over time is of increasing importance as Earth moves into the Anthropocene. A wide variety of methods are used for multivariate community analysis and are variously applied to research that aims to characterise temporal dynamics in community composition. Understanding these methods and how they are applied is useful for determining best practice in community ecology. METHODOLOGY: We reviewed the ecological literature from 1990 to 2018 that used multivariate methods to address questions of temporal community dynamics. For each paper that fulfilled our search criteria, we recorded the types of multivariate analysis used to characterise temporal community dynamics in addition to the research aim, habitat type, location, taxon and the experimental design. RESULTS: Most studies had relatively few temporal replicates; the median number was seven time points. Nearly 70% of studies applied more than one analysis method; descriptive methods such as bar graphs and ordination were the most commonly applied methods. Surprisingly, the types of analyses used were only related to the number of temporal replicates, but not to research aim or any other aspects of experimental design such as taxon, or habitat or year of study. CONCLUSIONS: This review reveals that most studies interested in understanding community dynamics use relatively short time series meaning that several, more sophisticated, temporal analyses are not widely applicable. However, newer methods using multivariate dissimilarities are growing in popularity and many can be applied to time series of any length.

Risk of Exacerbation and Pneumonia with Single-Inhaler Triple versus Dual Therapy in IMPACT.

Rationale: In the IMPACT (Informing the Pathway of COPD Treatment) trial, single-inhaler fluticasone furoate/umeclidinium/vilanterol (FF/UMEC/VI) triple therapy reduced exacerbation risk versus FF/VI and UMEC/VI and mortality risk versus UMEC/VI. However, pneumonia incidence was higher in the inhaled corticosteroid (FF)-containing arms, raising questions about the relative benefit of exacerbation reduction compared with the increased risk of pneumonia.Objectives: Determine benefit-risk of the three treatments by evaluating time-to-first and rates of composite exacerbation or pneumonia outcomes.Methods: We evaluated time-to-first (prespecified) and rates (post hoc) of investigator-reported pneumonia, serious pneumonia leading to hospitalization or death, and the composite endpoints of 1) moderate (required antibiotics/corticosteroids)/severe (hospitalized) exacerbation or pneumonia and 2) severe exacerbation or serious (hospitalized) pneumonia. Analyses were repeated for radiographically confirmed pneumonia (post hoc).Results: Moderate/severe exacerbations occurred in 47%, 49%, and 50% of patients randomized to FF/UMEC/VI, FF/VI and UMEC/VI, and pneumonias in 8%, 7%, and 5%, respectively. FF/UMEC/VI reduced the risk of combined moderate/severe exacerbation or pneumonia (time-to-first) versus FF/VI (hazard ratio, 0.87 [95% confidence interval (CI), 0.82-0.92]) and UMEC/VI (0.87 [0.81-0.94]), as well as the risk of combined severe exacerbation or serious pneumonia versus UMEC/VI (0.83 [0.72-0.96]). FF/UMEC/VI reduced the rate of combined moderate/severe exacerbation or pneumonia (rate ratio, 0.78 [0.72-0.84]) and combined severe exacerbation or serious pneumonia (rate ratio, 0.76 [0.65-0.89]) versus UMEC/VI. Results were similar for radiographically confirmed pneumonia endpoints.Conclusions: Despite higher incidence of pneumonia in FF-containing arms, these composite exacerbation/pneumonia outcomes support a favorable benefit-risk profile of FF/UMEC/VI versus FF/VI and UMEC/VI in patients with symptomatic chronic obstructive pulmonary disease and a history of exacerbations.

Single-inhaler triple therapy fluticasone furoate/umeclidinium/vilanterol versus fluticasone furoate/vilanterol and umeclidinium/vilanterol in patients with COPD: results on cardiovascular safety from the IMPACT trial.

BACKGROUND: This analysis of the IMPACT study assessed the cardiovascular (CV) safety of single-inhaler triple therapy with fluticasone furoate/umeclidinium/vilanterol (FF/UMEC/VI) versus FF/VI and UMEC/VI dual therapy. METHODS: IMPACT was a 52-week, randomized, double-blind, multicenter Phase III study comparing the efficacy and safety of FF/UMEC/VI 100/62.5/25 mcg with FF/VI 100/25 mcg or UMEC/VI 62.5/25 mcg in patients ≥40 years of age with symptomatic chronic obstructive pulmonary disease (COPD) and ≥1 moderate/severe exacerbation in the previous year. The inclusion criteria for the study were intentionally designed to permit the enrollment of patients with significant concurrent CV disease/risk. CV safety assessments included proportion of patients with and exposure-adjusted rates of on-treatment CV adverse events of special interest (CVAESI) and major adverse cardiac events (MACE), as well as time-to-first (TTF) CVAESI, and TTF CVAESI resulting in hospitalization/prolonged hospitalization or death. RESULTS: Baseline CV risk factors were similar across treatment groups. Overall, 68% of patients (n = 7012) had ≥1 CV risk factor and 40% (n = 4127) had ≥2. At baseline, 29% of patients reported a current/past cardiac disorder and 58% reported a current/past vascular disorder. The proportion of patients with on-treatment CVAESI was 11% for both FF/UMEC/VI and UMEC/VI, and 10% for FF/VI. There was no statistical difference for FF/UMEC/VI versus FF/VI or UMEC/VI in TTF CVAESI (hazard ratio [HR]: 0.98, 95% confidence interval [CI]: 0.85, 1.11; p = 0.711 and HR: 0.92, 95% CI: 0.78, 1.08; p = 0.317, respectively) nor TTF CVAESI leading to hospitalization/prolonged hospitalization or death (HR: 1.19, 95% CI: 0.93, 1.51; p = 0.167 and HR: 0.96, 95% CI: 0.72, 1.27; p = 0.760, respectively). On-treatment MACE occurred in ≤3% of patients across treatment groups, with similar prevalence and rates between treatments. CONCLUSIONS: In a symptomatic COPD population with a history of exacerbations and a high rate of CV disease/risk, the proportion of patients with CVAESI and MACE was 10-11% and 1-3%, respectively, across treatment arms, and the risk of CVAESI was low and similar across treatment arms. There was no statistically significant increased CV risk associated with the use of FF/UMEC/VI versus FF/VI or UMEC/VI, and UMEC/VI versus FF/VI. TRIAL REGISTRATION: NCT02164513 (GSK study number CTT116855).

Reduction in All-Cause Mortality with Fluticasone Furoate/Umeclidinium/Vilanterol in Patients with Chronic Obstructive Pulmonary Disease.

Rationale: The IMPACT (Informing the Pathway of Chronic Obstructive Pulmonary Disease Treatment) trial demonstrated a significant reduction in all-cause mortality (ACM) risk with fluticasone furoate/umeclidinium/vilanterol (FF/UMEC/VI) versus UMEC/VI in patients with chronic obstructive pulmonary disease (COPD) at risk of future exacerbations. Five hundred seventy-four patients were censored in the original analysis owing to incomplete vital status information.Objectives: Report ACM and impact of stepping down therapy, following collection of additional vital status data.Methods: Patients were randomized 2:2:1 to FF/UMEC/VI 100/62.5/25 µg, FF/VI 100/25 µg, or UMEC/VI 62.5/25 µg following a run-in on their COPD therapies. Time to ACM was prespecified. Additional vital status data collection and subsequent analyses were performed post hoc.Measurements and Main Results: We report vital status data for 99.6% of the intention-to-treat population (n = 10,355), documenting 98 (2.36%) deaths on FF/UMEC/VI, 109 (2.64%) on FF/VI, and 66 (3.19%) on UMEC/VI. For FF/UMEC/VI, the hazard ratio for death was 0.72 (95% confidence interval, 0.53-0.99; P = 0.042) versus UMEC/VI and 0.89 (95% confidence interval, 0.67-1.16; P = 0.387) versus FF/VI. Independent adjudication confirmed lower rates of cardiovascular and respiratory death and death associated with the patient's COPD.Conclusions: In this secondary analysis of an efficacy outcome from the IMPACT trial, once-daily single-inhaler FF/UMEC/VI triple therapy reduced the risk of ACM versus UMEC/VI in patients with symptomatic COPD and a history of exacerbations.

Increasing wildfires threaten historic carbon sink of boreal forest soils.

Boreal forest fires emit large amounts of carbon into the atmosphere primarily through the combustion of soil organic matter1-3. During each fire, a portion of this soil beneath the burned layer can escape combustion, leading to a net accumulation of carbon in forests over multiple fire events4. Climate warming and drying has led to more severe and frequent forest fires5-7, which threaten to shift the carbon balance of the boreal ecosystem from net accumulation to net loss1, resulting in a positive climate feedback8. This feedback will occur if organic-soil carbon that escaped burning in previous fires, termed 'legacy carbon', combusts. Here we use soil radiocarbon dating to quantitatively assess legacy carbon loss in the 2014 wildfires in the Northwest Territories of Canada2. We found no evidence for the combustion of legacy carbon in forests that were older than the historic fire-return interval of northwestern boreal forests9. In forests that were in dry landscapes and less than 60 years old at the time of the fire, legacy carbon that had escaped burning in the previous fire cycle was combusted. We estimate that 0.34 million hectares of young forests (<60 years) that burned in the 2014 fires could have experienced legacy carbon combustion. This implies a shift to a domain of carbon cycling in which these forests become a net source-instead of a sink-of carbon to the atmosphere over consecutive fires. As boreal wildfires continue to increase in size, frequency and intensity7, the area of young forests that experience legacy carbon combustion will probably increase and have a key role in shifting the boreal carbon balance.

Wildfire severity reduces richness and alters composition of soil fungal communities in boreal forests of western Canada.

Wildfire is the dominant disturbance in boreal forests and fire activity is increasing in these regions. Soil fungal communities are important for plant growth and nutrient cycling postfire but there is little understanding of how fires impact fungal communities across landscapes, fire severity gradients, and stand types in boreal forests. Understanding relationships between fungal community composition, particularly mycorrhizas, and understory plant composition is therefore important in predicting how future fire regimes may affect vegetation. We used an extreme wildfire event in boreal forests of Canada's Northwest Territories to test drivers of fungal communities and assess relationships with plant communities. We sampled soils from 39 plots 1 year after fire and 8 unburned plots. High-throughput sequencing (MiSeq, ITS) revealed 2,034 fungal operational taxonomic units. We found soil pH and fire severity (proportion soil organic layer combusted), and interactions between these drivers were important for fungal community structure (composition, richness, diversity, functional groups). Where fire severity was low, samples with low pH had higher total fungal, mycorrhizal, and saprotroph richness compared to where severity was high. Increased fire severity caused declines in richness of total fungi, mycorrhizas, and saprotrophs, and declines in diversity of total fungi and mycorrhizas. The importance of stand age (a surrogate for fire return interval) for fungal composition suggests we could detect long-term successional patterns even after fire. Mycorrhizal and plant community composition, richness, and diversity were weakly but significantly correlated. These weak relationships and the distribution of fungi across plots suggest that the underlying driver of fungal community structure is pH, which is modified by fire severity. This study shows the importance of edaphic factors in determining fungal community structure at large scales, but suggests these patterns are mediated by interactions between fire and forest stand composition.

Cross-scale controls on carbon emissions from boreal forest megafires.

Climate warming and drying is associated with increased wildfire disturbance and the emergence of megafires in North American boreal forests. Changes to the fire regime are expected to strongly increase combustion emissions of carbon (C) which could alter regional C balance and positively feedback to climate warming. In order to accurately estimate C emissions and thereby better predict future climate feedbacks, there is a need to understand the major sources of heterogeneity that impact C emissions at different scales. Here, we examined 211 field plots in boreal forests dominated by black spruce (Picea mariana) or jack pine (Pinus banksiana) of the Northwest Territories (NWT), Canada after an unprecedentedly large area burned in 2014. We assessed both aboveground and soil organic layer (SOL) combustion, with the goal of determining the major drivers in total C emissions, as well as to develop a high spatial resolution model to scale emissions in a relatively understudied region of the boreal forest. On average, 3.35 kg C m-2 was combusted and almost 90% of this was from SOL combustion. Our results indicate that black spruce stands located at landscape positions with intermediate drainage contribute the most to C emissions. Indices associated with fire weather and date of burn did not impact emissions, which we attribute to the extreme fire weather over a short period of time. Using these results, we estimated a total of 94.3 Tg C emitted from 2.85 Mha of burned area across the entire 2014 NWT fire complex, which offsets almost 50% of mean annual net ecosystem production in terrestrial ecosystems of Canada. Our study also highlights the need for fine-scale estimates of burned area that represent small water bodies and regionally specific calibrations of combustion that account for spatial heterogeneity in order to accurately model emissions at the continental scale.

Once-Daily Single-Inhaler Triple versus Dual Therapy in Patients with COPD.

BACKGROUND: The benefits of triple therapy for chronic obstructive pulmonary disease (COPD) with an inhaled glucocorticoid, a long-acting muscarinic antagonist (LAMA), and a long-acting ß2-agonist (LABA), as compared with dual therapy (either inhaled glucocorticoid-LABA or LAMA-LABA), are uncertain. METHODS: In this randomized trial involving 10,355 patients with COPD, we compared 52 weeks of a once-daily combination of fluticasone furoate (an inhaled glucocorticoid) at a dose of 100 µg, umeclidinium (a LAMA) at a dose of 62.5 µg, and vilanterol (a LABA) at a dose of 25 µg (triple therapy) with fluticasone furoate-vilanterol (at doses of 100 µg and 25 µg, respectively) and umeclidinium-vilanterol (at doses of 62.5 µg and 25 µg, respectively). Each regimen was administered in a single Ellipta inhaler. The primary outcome was the annual rate of moderate or severe COPD exacerbations during treatment. RESULTS: The rate of moderate or severe exacerbations in the triple-therapy group was 0.91 per year, as compared with 1.07 per year in the fluticasone furoate-vilanterol group (rate ratio with triple therapy, 0.85; 95% confidence interval [CI], 0.80 to 0.90; 15% difference; P<0.001) and 1.21 per year in the umeclidinium-vilanterol group (rate ratio with triple therapy, 0.75; 95% CI, 0.70 to 0.81; 25% difference; P<0.001). The annual rate of severe exacerbations resulting in hospitalization in the triple-therapy group was 0.13, as compared with 0.19 in the umeclidinium-vilanterol group (rate ratio, 0.66; 95% CI, 0.56 to 0.78; 34% difference; P<0.001). There was a higher incidence of pneumonia in the inhaled-glucocorticoid groups than in the umeclidinium-vilanterol group, and the risk of clinician-diagnosed pneumonia was significantly higher with triple therapy than with umeclidinium-vilanterol, as assessed in a time-to-first-event analysis (hazard ratio, 1.53; 95% CI, 1.22 to 1.92; P<0.001). CONCLUSIONS: Triple therapy with fluticasone furoate, umeclidinium, and vilanterol resulted in a lower rate of moderate or severe COPD exacerbations than fluticasone furoate-vilanterol or umeclidinium-vilanterol in this population. Triple therapy also resulted in a lower rate of hospitalization due to COPD than umeclidinium-vilanterol. (Funded by GlaxoSmithKline; IMPACT ClinicalTrials.gov number, NCT02164513 .).

Inside the root microbiome: bacterial root endophytes and plant growth promotion.

Bacterial root endophytes reside in a vast number of plant species as part of their root microbiome, with some being shown to positively influence plant growth. Endophyte community structure (species diversity: richness and relative abundances) within the plant is dynamic and is influenced by abiotic and biotic factors such as soil conditions, biogeography, plant species, microbe-microbe interactions and plant-microbe interactions, both at local and larger scales. Plant-growth-promoting bacterial endophytes (PGPBEs) have been identified, but the predictive success at positively influencing plant growth in field conditions has been limited. Concurrent to the development of modern molecular techniques, the goal of predicting an organism's ability to promote plant growth can perhaps be realized by more thorough examination of endophyte community dynamics. This paper reviews the drivers of endophyte community structure relating to plant growth promotion, the mechanisms of plant growth promotion, and the current and future use of molecular techniques to study these communities.

Alzheimer's disease biomarker discovery using in silico literature mining and clinical validation.

BACKGROUND: Alzheimer's Disease (AD) is the most widespread form of dementia in the elderly but despite progress made in recent years towards a mechanistic understanding, there is still an urgent need for disease modification therapy and for early diagnostic tests. Substantial international efforts are being made to discover and validate biomarkers for AD using candidate analytes and various data-driven 'omics' approaches. Cerebrospinal fluid is in many ways the tissue of choice for biomarkers of brain disease but is limited by patient and clinician acceptability, and increasing attention is being paid to the search for blood-based biomarkers. The aim of this study was to use a novel in silico approach to discover a set of candidate biomarkers for AD. METHODS: We used an in silico literature mining approach to identify potential biomarkers by creating a summarized set of assertional metadata derived from relevant legacy information. We then assessed the validity of this approach using direct assays of the identified biomarkers in plasma by immunodetection methods. RESULTS: Using this in silico approach, we identified 25 biomarker candidates, at least three of which have subsequently been reported to be altered in blood or CSF from AD patients. Two further candidate biomarkers, indicated from the in silico approach, were choline acetyltransferase and urokinase-type plasminogen activator receptor. Using immunodetection, we showed that, in a large sample set, these markers are either altered in disease or correlate with MRI markers of atrophy. CONCLUSIONS: These data support as a proof of concept the use of data mining and in silico analyses to derive valid biomarker candidates for AD and, by extension, for other disorders.

Cheminformatics analysis of assertions mined from literature that describe drug-induced liver injury in different species.

Drug-induced liver injury is one of the main causes of drug attrition. The ability to predict the liver effects of drug candidates from their chemical structures is critical to help guide experimental drug discovery projects toward safer medicines. In this study, we have compiled a data set of 951 compounds reported to produce a wide range of effects in the liver in different species, comprising humans, rodents, and nonrodents. The liver effects for this data set were obtained as assertional metadata, generated from MEDLINE abstracts using a unique combination of lexical and linguistic methods and ontological rules. We have analyzed this data set using conventional cheminformatics approaches and addressed several questions pertaining to cross-species concordance of liver effects, chemical determinants of liver effects in humans, and the prediction of whether a given compound is likely to cause a liver effect in humans. We found that the concordance of liver effects was relatively low (ca. 39-44%) between different species, raising the possibility that species specificity could depend on specific features of chemical structure. Compounds were clustered by their chemical similarity, and similar compounds were examined for the expected similarity of their species-dependent liver effect profiles. In most cases, similar profiles were observed for members of the same cluster, but some compounds appeared as outliers. The outliers were the subject of focused assertion regeneration from MEDLINE as well as other data sources. In some cases, additional biological assertions were identified, which were in line with expectations based on compounds' chemical similarities. The assertions were further converted to binary annotations of underlying chemicals (i.e., liver effect vs no liver effect), and binary quantitative structure-activity relationship (QSAR) models were generated to predict whether a compound would be expected to produce liver effects in humans. Despite the apparent heterogeneity of data, models have shown good predictive power assessed by external 5-fold cross-validation procedures. The external predictive power of binary QSAR models was further confirmed by their application to compounds that were retrieved or studied after the model was developed. To the best of our knowledge, this is the first study for chemical toxicity prediction that applied QSAR modeling and other cheminformatics techniques to observational data generated by the means of automated text mining with limited manual curation, opening up new opportunities for generating and modeling chemical toxicology data.

Changes in dorsal root ganglion CGRP expression in a chronic inflammatory model of the rat knee joint: differential modulation by rofecoxib and paracetamol.

Neuropeptide-expressing small diameter sensory neurones are thought to be vital in generating inflammatory hyperalgesic responses. Within the dorsal root ganglion (DRG), both the levels of the neuropeptide calcitonin gene-related peptide (CGRP) and the numbers of CGRP-immunoreactive (CGRP-IR) DRG neurones have been shown to increase in a number of acute adjuvant-induced inflammatory pain models. The aim of this study was to look specifically at changes in numbers of CGRP-IR DRG neurones in a chronic model of inflammatory joint pain following complete Freund's adjuvant (CFA) injection into the rat knee. In this model, there were significant increases in the number of ipsilateral CGRP-IR small DRG neurones at days 1, 16 and 35 following intra-articular CFA, compared to saline-injected sham animals. This correlated with the behavioural readouts of hypersensitivity and knee joint inflammation at the same time points. There was also a significant increase in the number of ipsilateral CGRP-IR medium DRG neurones and contralateral CGRP-IR small DRG neurones at day 1. Following dosing of CFA-injected rats with rofecoxib (Vioxx) or paracetamol, there was a significant decrease in the number of ipsilateral CGRP-IR small and medium DRG neurones in rofecoxib- but not paracetamol-treated rats. These data also correlated with behavioural readouts where hypersensitivity and knee joint inflammation were significantly reduced by rofecoxib but not paracetamol treatment. In conclusion, these data show that changes in ipsilateral CGRP expression within small DRG neurones are consistent with behavioural readouts in both time course, rofecoxib and paracetamol studies in this model of chronic inflammatory pain.

Localisation and modulation of prostanoid receptors EP1 and EP4 in the rat chronic constriction injury model of neuropathic pain.

Immunohistochemistry was used to examine the expression of prostaglandin E(2) receptors EP1 and EP4 in sciatic nerves from the rat chronic constriction injury (CCI) model of neuropathic pain. At 21 days post-surgery the CCI rats had developed mechanical hyperalgesia on the operated side, and quantitative image analysis showed a highly significant doubling of the area occupied by EP1- and EP4-positive pixels in sections from CCI nerves when compared to sham-operated controls. Co-localisation studies with the marker ED1 revealed that 73% of the EP1-positive cells and 54% of the EP4-positive cells in the injured nerves represented infiltrating macrophages. Cells negative for ED1 and positive for either EP1 or EP4 were characterised as Schwann cells from their morphology and expression of myelin basic protein and S100 antigens. Similar EP1- and EP4-positive Schwann cell profiles were observed in sections of uninjured control nerves. Low levels of EP receptor expression were found in neurofilament-immunostained axons, but no consistent differences were observed in the levels of axonal EP staining between CCI and control tissue. These data provide further evidence of the importance of prostaglandins in the pathogenesis of neuropathic pain, and suggest that not only infiltrating macrophages but also Schwann cells may be involved in the modulation of these mediators in response to nerve injury.

Prostanoid receptor EP1 and Cox-2 in injured human nerves and a rat model of nerve injury: a time-course study.

BACKGROUND: Recent studies show that inflammatory processes may contribute to neuropathic pain. Cyclooxygenase-2 (Cox-2) is an inducible enzyme responsible for production of prostanoids, which may sensitise sensory neurones via the EP1 receptor. We have recently reported that while macrophages infiltrate injured nerves within days of injury, they express increased Cox-2-immunoreactivity (Cox-2-IR) from 2 to 3 weeks after injury. We have now investigated the time course of EP1 and Cox-2 changes in injured human nerves and dorsal root ganglia (DRG), and the chronic constriction nerve injury (CCI) model in the rat. METHODS: Tissue sections were immunostained with specific antibodies to EP1, Cox-2, CD68 (human macrophage marker) or OX42 (rat microglial marker), and neurofilaments (NF), prior to image analysis, from the following: human brachial plexus nerves (21 to 196 days post-injury), painful neuromas (9 days to 12 years post-injury), avulsion injured DRG, control nerves and DRG, and rat CCI model tissues. EP1 and NF-immunoreactive nerve fibres were quantified by image analysis. RESULTS: EP1:NF ratio was significantly increased in human brachial plexus nerve fibres, both proximal and distal to injury, in comparison with uninjured nerves. Sensory neurones in injured human DRG showed a significant acute increase of EP1-IR intensity. While there was a rapid increase in EP1-fibres and CD-68 positive macrophages, Cox-2 increase was apparent later, but was persistent in human painful neuromas for years. A similar time-course of changes was found in the rat CCI model with the above markers, both in the injured nerves and ipsilateral dorsal spinal cord. CONCLUSION: Different stages of infiltration and activation of macrophages may be observed in the peripheral and central nervous system following peripheral nerve injury. EP1 receptor level increase in sensory neurones, and macrophage infiltration, appears to precede increased Cox-2 expression by macrophages. However, other methods for detecting Cox-2 levels and activity are required. EP1 antagonists may show therapeutic effects in acute and chronic neuropathic pain, in addition to inflammatory pain.