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Because of the pervasiveness, persistence, and toxicity of per- and polyfluoroalkyl substances (PFAS), there is growing concern over PFAS contamination, exposures, and health effects. The diversity of potential PFAS is astounding, with nearly 10,000 PFAS catalogued in databases to date (and growing). The ability to detect the thousands of known PFAS, and discover previously uncatalogued PFAS, is necessary to understand the scope of PFAS contamination and to identify appropriate remediation and regulatory solutions. Current non-targeted methods for PFAS analysis require manual curation and are time-consuming, prone to error, and not comprehensive. FluoroMatch Flow 2.0 is the first software to cover all steps of data processing for PFAS discovery in liquid chromatography–high-resolution tandem mass spectrometry samples. These steps include feature detection, feature blank filtering, exact mass matching to catalogued PFAS, mass defect filtering, homologous series detection, retention time pattern analysis, class-based MS/MS screening, fragment screening, and predicted MS/MS from SMILES structures. In addition, a comprehensive confidence level criterion is implemented to help users understand annotation certainty and integrate various layers of evidence to reduce overreporting. Applying the software to aqueous film forming foam analysis, we discovered over one thousand likely PFAS including previously unreported species. Furthermore, we were able to filter out 96% of features which were likely not PFAS. FluoroMatch Flow 2 increased coverage of likely PFAS by over tenfold compared to the previous release. This software will enable researchers to better characterize PFAS in the environment and in biological systems.

There are thousands of different per- and polyfluoroalkyl substances (PFAS) in everyday products and in the environment. Discerning the abundance and diversity of PFAS is essential for understanding sources, fate, exposure routes, and the associated health impacts of PFAS. While comprehensive detection of PFAS requires the use of nontargeted mass spectrometry, data processing is time intensive and prone to error. While automated approaches can compile all mass spectrometric evidence (e.g., retention time, isotopic pattern, fragmentation, and accurate mass) and provide ranking or scoring metrics for annotations, confident assignment of structure often still requires extensive manual review of the data. To aid this process, we present FluoroMatch Visualizer, an open-source free software which was developed to provide interactive visualizations which include normalized mass defect plots, retention time versus accurate mass plots, MS/MS fragmentation spectra, and tables of annotations and metadata. All graphs and tables are interactive and have cross-filtering such that when a user selects a feature, all other visuals highlight the feature of interest. Several filtering options have been integrated into this novel data visualization tool, specifically with the capability to filter by PFAS chemical series, fragment(s), assignment confidence, and MS/MS file(s). FluoroMatch Visualizer is part of FluoroMatch Suite, which consists of FluoroMatch Modular, FluoroMatch Flow, and FluoroMatch Generator. FluoroMatch Visualizer enables annotations to be extensively validated, increasing annotation confidence. The resulting visualizations and datasets can be shared online in an interactive format for community-based PFAS discovery. FluoroMatch visualizer holds potential to promote harmonization of nontargeted data processing and interpretation throughout the PFAS scientific community.

Grasslands provide fundamental ecosystem services in many arid and semi-arid regions of the world, but are experiencing rapid increases in fire activity making them highly susceptible to post-fire accelerated soil erosion by wind. A quantitative assessment that integrates fire-wind erosion feedbacks is therefore needed to account for vegetation change, soil biogeochemical cycling, air quality, and landscape evolution. We investigated the applicability of a novel tracer technique – the use of multiple rare earth elements (REE) - to quantify aeolian soil erosion and to identify sources and sinks of wind-blown sediments in a burned and unburned shrub-grass transition zone in the Chihuahuan desert, NM, USA. Results indicate that the horizontal mass flux of wind-borne sediment increased approximately three times following the fire. The REE-tracer analysis of aeolian sediments shows that an average 88% of the horizontal mass flux in the control area was derived from bare microsites, whereas at the burned site it was derived from shrub and bare microsites, 42% and 39% respectively. The vegetated microsites, which were predominantly sinks of aeolian sediments in the unburned areas, became sediment sources following the fire. The burned areas exhibited a spatial homogenization of sediment tracers, highlighting a potential negative feedback on landscape heterogeneity induced by shrub encroachment into grasslands. Though fires are known to increase aeolian sediment transport, accompanying changes in the sources and sinks of wind-borne sediments likely influence biogeochemical cycling and land degradation dynamics. Our experiment demonstrated that REEs can be used as reliable tracers for field-scale aeolian studies.

Up to 70% of patients with primary biliary cholangitis develop pruritus (itch) during the course of their disease. Treatment of pruritus in primary biliary cholangitis is challenging and novel therapies are needed. Ursodeoxycholic acid, the standard first-line treatment for primary biliary cholangitis, is largely ineffective for pruritus. We investigated the efficacy and safety of GSK2330672, a selective inhibitor of human ileal bile acid transporter (IBAT), in patients with primary biliary cholangitis with pruritus. We conducted this phase 2a, double-blind, randomised, placebo-controlled, crossover trial in two UK medical centres. Following 2 weeks of open placebo run-in, patients were randomly assigned in a 1:1 ratio with a block size of 4 to receive GSK2330672 or placebo twice daily during two consecutive 14-day treatment periods in a crossover sequence. The treatment periods were followed by a 14-day single-blinded placebo follow-up period. The primary endpoints were safety of GSK2330672, assessed using clinical and laboratory parameters, and tolerability as rated by the Gastrointestinal Symptom Rating Scale. The secondary endpoints were changes in pruritus scores measured using the 0 to 10 numerical rating scale (NRS), primary biliary cholangitis-40 (PBC-40) itch domain score and 5-D itch scale, changes in serum total bile acids and 7 alpha hydroxy-4-cholesten-3-one (C4), and changes in the pharmacokinetic parameters of ursodeoxycholic acid and its conjugates. The trial was registered with ClinicalTrials.gov, number NCT01899703. Between March 10, 2014, and Oct 7, 2015, we enrolled 22 patients. 11 patients were assigned to receive intervention followed by placebo (sequence 1), and 11 patients were assigned to receive placebo followed by intervention (sequence 2). One patient assigned to sequence 2 withdrew consent prior to receiving randomised therapy. One patient did not attend the placebo follow-up period, but was included in the final analysis. GSK2330672 treatment for 14 days was safe with no serious adverse events reported. Diarrhoea was the most frequent adverse event during treatment with GSK2330672 (seven with GSK2330672 vs one with placebo) and headache was the most frequent adverse event during treatment with placebo (seven with placebo vs six with GSK2330672). After GSK2330672 treatment, the percentage changes from baseline itch scores were −57% (95% CI −73 to −42, p<0·0001) in the NRS, −31% (−42 to −20, p<0·0001) in the PBC-40 itch domain and −35% (−45 to −25, p<0·0001) in the 5-D itch scale. GSK2330672 produced significantly greater reduction from baseline than the double-blind placebo in the NRS (−23%, 95% CI −45 to −1; p=0·037), PBC-40 itch domain, (−14%, −26 to −1; p=0·034), and 5-D itch scale (−20%, −34 to −7; p=0·0045). After GSK2330672 treatment, serum total bile acid concentrations declined by 50% (95% CI −37 to −61, p<0·0001) from 30 to 15 μM, with a significant 3·1-times increase (95% CI 2·4 to 4·0, p<0·0001) in serum C4 concentrations from 7·9 to 24·7ng/mL. In patients with primary biliary cholangitis with pruritus, 14 days of ileal bile acid transporter inhibition by GSK2330672 was generally well tolerated without serious adverse events, and demonstrated efficacy in reducing pruritus severity. GSK2330672 has the potential to be a significant and novel advance for the treatment of pruritus in primary biliary cholangitis. Diarrhoea, the most common adverse event associated with GSK2330672 treatment, might limit the long-term use of this drug. GlaxoSmithKline and National Institute for Health Research.

Neoantigens derived from somatic mutations are specific to cancer cells and are ideal targets for cancer immunotherapy. KRAS is the most frequently mutated oncogene and drives the pathogenesis of several cancers. Here we show the identification and development of an affinity-enhanced T cell receptor (TCR) that recognizes a peptide derived from the most common KRAS mutant, KRAS G12D , presented in the context of HLA-A*11:01. The affinity of the engineered TCR is increased by over one million-fold yet fully able to distinguish KRAS G12D over KRAS WT . While crystal structures reveal few discernible differences in TCR interactions with KRAS WT versus KRAS G12D , thermodynamic analysis and molecular dynamics simulations reveal that TCR specificity is driven by differences in indirect electrostatic interactions. The affinity enhanced TCR, fused to a humanized anti-CD3 scFv, enables selective killing of cancer cells expressing KRAS G12D . Our work thus reveals a molecular mechanism that drives TCR selectivity and describes a soluble bispecific molecule with therapeutic potential against cancers harboring a common shared neoantigen. Cancers often harbor mutations in genes encoding important regulatory proteins, but therapeutic targeting of these molecules proves difficult due to their high structural similarity to their non-mutated counterpart. Here authors show the engineering of T cell engaging bispecific protein able to selectively target cancer cells with a high-frequency mutation in the KRAS oncogene.

1. Recent debates about the role of biotic resistance in controlling invasion success have focused on effects of species richness. However, functional composition could be a stronger control: species already in the community with similar functional traits to those of the invaders should have the greatest competitive effect on invaders. Still, experiments assessing effects of functional similarity have found contradictory results. 2. We used experimental communities in a serpentine grassland in California, USA, to assess the extent to which functional composition and functional diversity influenced success of two different types of invading plants: early season annuals (E) and late-season annuals (L) that have been previously shown to differ in patterns of resource acquisition. 3. We seeded known quantities of seed of six different species (three in each functional group) into experimental plots containing established communities differing in functional composition and functional diversity. The experimental communities contained different combinations of E, L, perennial bunchgrass (P) and nitrogen-fixer (N) functional groups, with functional diversity ranging from 0 to 4 groups. Each invading species was seeded into a separate quadrat within each plot to minimize competitive effects of invaders on each other. We measured both seedling and adult success of invaders for two full growing seasons to further understand mechanisms underlying biotic resistance. 4. More functionally diverse communities were less invaded overall, as measured by the average success of individual invaders. However, assessment of invaders by functional groups was more informative: Es in the extant community suppressed E invaders the most, and Ls in the extant community suppressed L invaders the most. 5. We observed a variety of interactions among extant functional groups in reducing invader success, including synergism, complementarity and 'basement' effects, where two or more groups negatively affected invaders, but combinations of groups were no more suppressive than single groups. The extant community influenced invaders more strongly through suppression of adult plant growth than through effects on seedling establishment. 6.Synthesis. Contrary to predictions from neutral theory, these results indicate that niche overlap was an important component of biotic resistance in these experimental plant communities and summed up to significant effects of species richness.

Building on the affectivism approach, we expand on Binz et al.'s meta-learning research program by highlighting that emotion and other affective phenomena should be key to the modeling of human learning. We illustrate the added value of affective processes for models of learning across multiple domains with a focus on reinforcement learning, knowledge acquisition, and social learning.

Abstract Background Studies describing the clinical progression of animals with reverse patent ductus arteriosus (PDA) are lacking. Objectives To describe the signalment, presenting signs, echocardiographic features, and survival in a group of dogs and cats with bidirectional and continuous right-to-left PDA. Animals Forty-six client-owned animals included, comprising 43 dogs and 3 cats with bidirectional or continuous right-to-left PDA. Methods Retrospective multicenter study. Medical records and echocardiographic findings reviewed from animals diagnosed with bidirectional or continuous right-to-left PDA. Impact of ductal morphology, spectral Doppler flow profile, PCV, sildenafil treatment at presentation, sildenafil dose, severity of pulmonary hypertension, general anesthesia with or without surgery and the presence of right-sided congestive heart failure (R-CHF) on crude mortality rate were evaluated via Mantel-Cox log rank comparison of Kaplan-Meier survival curves. Univariable and multivariable Cox proportional hazards analysis was performed, and hazard ratio (HR) (95% confidence intervals [CI]) was presented. Results Hindlimb collapse was the most common presenting sign in dogs (n = 16). Clinical signs in cats were variable. Median survival time was 626 days in dogs (range 1-3628 days). Dogs with R-CHF had a shorter median survival time (58 days vs 1839 days, P = .03). Dogs treated with sildenafil at initial presentation survived longer (1839 days vs 302 days, P = .03), which was the only independent predictor of survival (HR 0.35, CI 0.15-0.86, P = 0.021). Conclusions and Clinical Importance Dogs and cats with reverse PDA have a variable clinical presentation and prognosis. Survival time was longer in animals prescribed sildenafil at diagnosis. Dogs with R-CHF at presentation have a worse overall outcome.

Tumor genomic instability and selective treatment pressures result in clonal disease evolution; molecular stratification for molecularly targeted drug administration requires repeated access to tumor DNA. We hypothesized that circulating plasma DNA (cpDNA) in advanced cancer patients is largely derived from tumor, has prognostic utility, and can be utilized for multiplex tumor mutation sequencing when repeat biopsy is not feasible. We utilized the Sequenom MassArray System and OncoCarta panel for somatic mutation profiling. Matched samples, acquired from the same patient but at different time points were evaluated; these comprised formalin-fixed paraffin-embedded (FFPE) archival tumor tissue (primary and/or metastatic) and cpDNA. The feasibility, sensitivity, and specificity of this high-throughput, multiplex mutation detection approach was tested utilizing specimens acquired from 105 patients with solid tumors referred for participation in Phase I trials of molecularly targeted drugs. The median cpDNA concentration was 17 ng/ml (range: 0.5-1600); this was 3-fold higher than in healthy volunteers. Moreover, higher cpDNA concentrations associated with worse overall survival; there was an overall survival (OS) hazard ratio of 2.4 (95% CI 1.4, 4.2) for each 10-fold increase in cpDNA concentration and in multivariate analyses, cpDNA concentration, albumin, and performance status remained independent predictors of OS. These data suggest that plasma DNA in these cancer patients is largely derived from tumor. We also observed high detection concordance for critical 'hot-spot' mutations (KRAS, BRAF, PIK3CA) in matched cpDNA and archival tumor tissue, and important differences between archival tumor and cpDNA. This multiplex sequencing assay can be utilized to detect somatic mutations from plasma in advanced cancer patients, when safe repeat tumor biopsy is not feasible and genomic analysis of archival tumor is deemed insufficient. Overall, circulating nucleic acid biomarker studies have clinically important multi-purpose utility in advanced cancer patients and further studies to pursue their incorporation into the standard of care are warranted.

This article discusses how the affectivism framework and the componential approach to emotion may serve the future of affective sciences. A particular aim of the article is to show that an appraisal-based componential approach to emotion can help reconcile opposing theories. It begins by contextualizing the evolution of emotion science within the framework of affectivism, acknowledging that the significant epistemological differences between various theories have paradoxically spurred interest in studying emotion across various perspectives and disciplines. If affectivism is regarded as the pursuit of a deeper understanding of not only emotions and other affective processes but also cognitive and behavioral processes, then its success can be partly attributed to the existence of multiple approaches, allowing each discipline and perspective to advance using the most suitable theory and methodology. We contend that a componential approach reveals that the five principal theories of emotion have each focused on one of five components of emotion. Overall, based on the analysis of several articles published in the special issue on the future of affective science, we argue that affective scientists are well equipped not only to build a future in which conceptual and methodological tools will be used to test diverging hypotheses between competing theories but also to acknowledge and celebrate where such theories converge.