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Objectives Informing research participants of the results of studies in which they took part is viewed as an ethical imperative. However, there is little guidance in the literature about how to do this. The Fluoxetine Or Control Under Supervision trial randomised 3127 patients with a recent acute stroke to 6 months of fluoxetine or placebo and was published in the Lancet on 5 December 2018. The trial team decided to inform the participants of the results at exactly the same time as the Lancet publication, and also whether they had been allocated fluoxetine or placebo. In this report, we describe how we informed participants of the results.Design In the 6-month and 12-month follow-up questionnaires, we invited participants to provide an email address if they wished to be informed of the results of the trial. We re-opened our trial telephone helpline between 5 December 2018 and 31 March 2019.Setting UK stroke services.Participants 3127 participants were randomised. 2847 returned 6-month follow-up forms and 2703 returned 12-month follow-up forms; the remaining participants had died (380), withdrawn consent or did not respond.Results Of those returning follow-up questionnaires, a total of 1845 email addresses were provided and a further 50 people requested results to be sent by post. Results were sent to all email and postal addresses provided; 309 emails were returned unrecognised. Seventeen people replied, of whom three called the helpline and the rest responded by email.Conclusion It is feasible to disseminate results of large trials to research participants, though only around 60% of those randomised wanted to receive the results. The system we developed was efficient and required very little resource, and could be replicated by trialists in the future.Trial registration number ISRCTN83290762; Post-results.

Abstract A significant warming effect on arctic tundra is greening. Although this increase in predominantly woody vegetation has been linked to increases in gross primary productivity, increasing temperatures also stimulate ecosystem respiration. We present a novel analysis from small-scale plot measurements showing that the shape of the temperature- and light-dependent sink-to-source threshold (where net ecosystem exchange (NEE) equals zero) differs between two tussock tundra ecosystems differing in leaf area index (LAI). At the higher LAI site, the threshold is exceeded (i.e the ecosystem becomes a source) at relatively higher temperatures under low light but at lower temperatures under high light. At the lower LAI site, the threshold is exceeded at relatively lower temperatures under low light but at higher temperatures under high light. We confirmed this response at a single site where LAI was experimentally increased. This suggests the carbon balance of the tundra may be sensitive to small increases in temperature under low light, but that this effect may be significantly offset by increases in LAI. Importantly, we found that this LAI effect is reversed under high light, and so in a warming tundra, greater vegetation cover could have a progressively negative effect on net carbon uptake.

Abstract Background Trauma can result in systemic inflammation that leads to organ dysfunction, but the impact on the brain, particularly following extracranial insults, has been largely overlooked. Methods Building upon our prior findings, we aimed to understand the impact of systemic inflammation on neuroinflammatory gene transcripts in eight brain regions in rats exposed to (1) blast overpressure exposure [BOP], (2) cutaneous thermal injury [BU], (3) complex extremity injury, 3 hours (h) of tourniquet-induced ischemia, and hind limb amputation [CEI+tI+HLA], (4) BOP+BU or (5) BOP+CEI and delayed HLA [BOP+CEI+dHLA] at 6, 24, and 168 h post-injury (hpi). Results Globally, the number and magnitude of differentially expressed genes (DEGs) correlated with injury severity, systemic inflammation markers, and end-organ damage, driven by several chemokines/cytokines (Csf3, Cxcr2, Il16, and Tgfb2), neurosteroids/prostaglandins (Cyp19a1, Ptger2, and Ptger3), and markers of neurodegeneration (Gfap, Grin2b, and Homer1). Regional neuroinflammatory activity was least impacted following BOP. Non-blast trauma (in the BU and CEI+tI+HLA groups) contributed to an earlier, robust and diverse neuroinflammatory response across brain regions (up to 2–50-fold greater than that in the BOP group), while combined trauma (in the BOP+CEI+dHLA group) significantly advanced neuroinflammation in all regions except for the cerebellum. In contrast, BOP+BU resulted in differential activity of several critical neuroinflammatory-neurodegenerative markers compared to BU. t-SNE plots of DEGs demonstrated that the onset, extent, and duration of the inflammatory response are brain region dependent. Regardless of injury type, the thalamus and hypothalamus, which are critical for maintaining homeostasis, had the most DEGs. Our results indicate that neuroinflammation in all groups progressively increased or remained at peak levels over the study duration, while markers of end-organ dysfunction decreased or otherwise resolved. Conclusions Collectively, these findings emphasize the brain's sensitivity to mediators of systemic inflammation and provide an example of immune-brain crosstalk. Follow-on molecular and behavioral investigations are warranted to understand the short- to long-term pathophysiological consequences on the brain, particularly the mechanism of blood–brain barrier breakdown, immune cell penetration–activation, and microglial activation.

Summary: Tyrannosauroids are a clade of theropod dinosaur taxa that varied greatly in their body size distribution. We investigated the feeding performance of six tyrannosaur genera of variable body size and skull morphology. We used 3D finite element analysis to test whether skull shape becomes more or less resistant to feeding-induced forces. Cranial and mandibular models were scaled by adult Tyrannosaurus’s surface area to analyze the influence of shape on skull function. It was found that Tyrannosaurus experienced higher absolute stresses compared to small-bodied relatives. When surface area values were equalized across genera to account for the effect of size and test efficiency of skull shape, smaller individuals experience notably greater stresses than larger relatives due to the robust cranial osteology characterized in the allometry of tyrannosaurids. These results may indicate that the wide crania of tyrannosaurids convey a functional advantage that basal tyrannosauroids, juvenile tyrannosauroids, and alioramins lacked.

Silicon photonics is one of the most dynamic fields within photonics, and it has seen huge progress in the last 20 years, addressing applications in data centers, autonomous cars, and sensing. It is mostly focused on the telecommunications wavelength range (1.3 and 1.55 µm), where silicon becomes transparent. In this range, there are excellent light sources and photodetectors, as well as optical fibers operating with extremely low losses and dispersion. It is a technology that hugely benefits from the availability of complementary metal–oxide–semiconductor (CMOS) fabrication infrastructure and techniques used for microelectronics. Silicon and germanium, as another CMOS compatible group IV material, are transparent beyond the wavelength of 2 µm. The mid-IR wavelength range (2–20 µm) is of particular importance as it contains strong absorption signatures of many molecules. Therefore, Si- and Ge-based platforms open up the possibility of small and cost-effective sensing in the fingerprint region for medical and environmental monitoring. In this paper, we discuss the current mid-IR silicon photonics landscape, future directions, and potential applications of the field.

This work introduces the Queen's University Agent-Based Outbreak Outcome Model (QUABOOM). This tool is an agent-based Monte Carlo simulation for modelling epidemics and informing public health policy. We illustrate the use of the model by examining capacity restrictions during a lockdown. We find that public health measures should focus on the few locations where many people interact, such as grocery stores, rather than the many locations where few people interact, such as small businesses. We also discuss a case where the results of the simulation can be scaled to larger population sizes, thereby improving computational efficiency.

Background Enhanced detection of large vessel occlusion (LVO) through machine learning (ML) for acute ischemic stroke appears promising. This systematic review explored the capabilities of ML models compared with prehospital stroke scales for LVO prediction. Methods and Results Six bibliographic databases were searched from inception until October 10, 2023. Meta‐analyses pooled the model performance using area under the curve (AUC), sensitivity, specificity, and summary receiver operating characteristic curve. Of 1544 studies screened, 8 retrospective studies were eligible, including 32 prehospital stroke scales and 21 ML models. Of the 9 prehospital scales meta‐analyzed, the Rapid Arterial Occlusion Evaluation had the highest pooled AUC (0.82 [95% CI, 0.79–0.84]). Support Vector Machine achieved the highest AUC of 9 ML models included (pooled AUC, 0.89 [95% CI, 0.88–0.89]). Six prehospital stroke scales and 10 ML models were eligible for summary receiver operating characteristic analysis. Pooled sensitivity and specificity for any prehospital stroke scale were 0.72 (95% CI, 0.68–0.75) and 0.77 (95% CI, 0.72–0.81), respectively; summary receiver operating characteristic curve AUC was 0.80 (95% CI, 0.76–0.83). Pooled sensitivity for any ML model for LVO was 0.73 (95% CI, 0.64–0.79), specificity was 0.85 (95% CI, 0.80–0.89), and summary receiver operating characteristic curve AUC was 0.87 (95% CI, 0.83–0.89). Conclusions Both prehospital stroke scales and ML models demonstrated varying accuracies in predicting LVO. Despite ML potential for improved LVO detection in the prehospital setting, application remains limited by the absence of prospective external validation, limited sample sizes, and lack of real‐world performance data in a prehospital setting.

Abstract Background Producing animal protein while reducing the animal’s impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible. Results Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet, and time off feed, allowing a clear signal based on methane emissions to be elucidated. Genus-level abundances of rumen microbes showed low-to-moderate heritability and repeatability and were consistent between diets. Conclusions Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. Not accounting for environmental factors may limit the ability to associate the profile with traits of interest. However, these differences can be accounted for by adjusting for Cohort effects, revealing robust biological signals. The abundances of some genera were consistently heritable and repeatable across different environments, suggesting that metagenomic profiles could be used to predict an individual’s future performance, or performance of its offspring, in a range of environments. These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting.

The fossil record of gladius-bearing coleoids is scarce and based only on a few localities with geological horizons particularly favourable to their preservation (the so-called Konservat-Lagerstätten), which naturally leads to strongly limited data on geographical distributions. This emphasizes the importance of every new locality providing gladius-bearing coleoids. Here, we assess for the first time the gladius-bearing coleoid taxonomic diversity within the lower Toarcian “Schistes Cartons” of the Causses Basin (southeastern France). The material includes two fragmentary gladii, identified as Paraplesioteuthis sagittata and ?Loligosepia sp. indet. Just with these two specimens, two (Prototeuthina and Loligosepiina) of the three (Prototeuthina, Loligosepiina and Teudopseina) suborders of Mesozoic gladius-bearing coleoids are represented. Thus, our results hint at a rich early Toarcian gladius-bearing coleoid diversity in the Causses Basin and point out the need for further field investigations in the lower Toarcian “Schistes Cartons” in this area. This new record of Paraplesioteuthis sagittata is only the second one in Europe and the third in the world (western Canada, Germany and now France). Based on these occurrences, we tentatively suggest that P. sagittata originated in the Mediterranean domain and moved to the Arctic realm through the Viking Corridor to eventually move even farther to North America.

Abstract Background Rumen microbes break down complex dietary carbohydrates into energy sources for the host and are increasingly shown to be a key aspect of animal performance. Host genotypes can be combined with microbial DNA sequencing to predict performance traits or traits related to environmental impact, such as enteric methane emissions. Metagenome profiles were generated from 3139 rumen samples, collected from 1200 dual purpose ewes, using restriction enzyme-reduced representation sequencing (RE-RRS). Phenotypes were available for methane (CH4) and carbon dioxide (CO2) emissions, the ratio of CH4 to CH4 plus CO2 (CH4Ratio), feed efficiency (residual feed intake: RFI), liveweight at the time of methane collection (LW), liveweight at 8 months (LW8), fleece weight at 12 months (FW12) and parasite resistance measured by faecal egg count (FEC1). We estimated the proportion of phenotypic variance explained by host genetics and the rumen microbiome, as well as prediction accuracies for each of these traits. Results Incorporating metagenome profiles increased the variance explained and prediction accuracy compared to fitting only genomics for all traits except for CO2 emissions when animals were on a grass diet. Combining the metagenome profile with host genotype from lambs explained more than 70% of the variation in methane emissions and residual feed intake. Predictions were generally more accurate when incorporating metagenome profiles compared to genetics alone, even when considering profiles collected at different ages (lamb vs adult), or on different feeds (grass vs lucerne pellet). A reference-free approach to metagenome profiling performed better than metagenome profiles that were restricted to capturing genera from a reference database. We hypothesise that our reference-free approach is likely to outperform other reference-based approaches such as 16S rRNA gene sequencing for use in prediction of individual animal performance. Conclusions This paper shows the potential of using RE-RRS as a low-cost, high-throughput approach for generating metagenome profiles on thousands of animals for improved prediction of economically and environmentally important traits. A reference-free approach using a microbial relationship matrix from log10 proportions of each tag normalized within cohort (i.e., the group of animals sampled at the same time) is recommended for future predictions using RE-RRS metagenome profiles.

Abstract Objectives This post hoc analysis assessed disease characteristics and response to dupilumab treatment in male and female patients with severe chronic rhinosinusitis with nasal polyps (CRSwNP) (SINUS‐52 study; NCT02898454). Methods Patients received dupilumab 300 mg or placebo every 2 weeks for 52 weeks on background intranasal corticosteroids. Efficacy was assessed through Week 52 using nasal polyp score (NPS), nasal congestion/obstruction score, loss of smell score and University of Pennsylvania Smell Identification Test score. Disease‐specific health‐related quality of life (HRQoL) was assessed using the 22‐item Sino‐Nasal Outcome Test (SNOT‐22). Results The analysis included 192 male and 111 female patients. Female patients had higher mean SNOT‐22 total score (56.6 vs. 49.1, P

IntroductionHeterotopic ossification (HO) is a complex pathology often observed in combat injured casualties who have sustained severe, high energy polytraumatic extremity injuries. Once HO has developed, prophylactic therapies are limited outside of surgical excision. Tourniquet-induced ischemia injury (IR) exacerbates trauma-mediated musculoskeletal tissue injury, inflammation, osteogenic progenitor cell development and HO formation. Others have shown that focal adhesion kinase-2 (FAK2) plays a key role in regulating early inflammatory signaling events. Therefore, we hypothesized that targeting FAK2 prophylactically would mitigate extremity trauma induced IR inflammation and HO formation.MethodsWe tested whether the continuous infusion of a FAK2 inhibitor (Defactinib, PF-573228; 6.94 µg/kg/min for 14 days) can mitigate ectopic bone formation (HO) using an established blast-related extremity injury model involving femoral fracture, quadriceps crush injury, three hours of tourniquet-induced limb ischemia, and hindlimb amputation through the fracture site. Tissue inflammation, infiltrating cells, osteogenic progenitor cell content were assessed at POD-7. Micro-computed tomography imaging was used to quantify mature HO at POD-56.ResultsIn comparison to vehicle control-treated rats, FAK2 administration resulted in no marked wound healing complications or weight loss. FAK2 treatment decreased HO by 43%. At POD-7, marked reductions in tissue proinflammatory gene expression and assayable osteogenic progenitor cells were measured, albeit no significant changes in expression patterns of angiogenic, chondrogenic and osteogenic genes. At the same timepoint, injured tissue from FAK-treated rats had fewer infiltrating cells. Additionally, gene expression analyses of tissue infiltrating cells resulted in a more measurable shift from an M1 inflammatory to an M2 anti-inflammatory macrophage phenotype in the FAK2 inhibitor-treated group.DiscussionOur findings suggest that FAK2 inhibition may be a novel strategy to dampen trauma-induced inflammation and attenuate HO in patients at high risk as a consequence of severe musculoskeletal polytrauma.

Background Dupilumab has been shown to improve clinical outcomes long term while reducing oral corticosteroid (OCS) dose in patients with severe OCS-dependent asthma. This post hoc analysis assesses the impact of OCS dose at baseline (≤10 or >10 mg·day−1) on long-term outcomes of dupilumab treatment. Methods Annualised severe asthma exacerbation rates, forced expiratory volume in 1 s (FEV1), measures of asthma control and quality of life, and OCS dose were evaluated in patients from the phase 3 VENTURE trial with severe OCS-dependent asthma, further categorised by OCS dose ≤10 or >10 mg·day−1 at parent study baseline (PSBL), who enrolled in TRAVERSE. Results Dupilumab reduced the annualised exacerbation rate in VENTURE, and it remained low throughout TRAVERSE (0.202–0.265 (OCS ≤10 mg·day−1 at PSBL) and 0.221–0.366 (OCS >10 mg·day−1 at PSBL)). Improvements in pre-bronchodilator FEV1, asthma control and quality of life observed in VENTURE dupilumab patients were sustained throughout TRAVERSE. Patients on placebo during VENTURE showed rapid improvements in FEV1 upon initiating dupilumab in TRAVERSE, which were sustained to the end of TRAVERSE. Reductions in OCS dose observed in VENTURE were maintained throughout TRAVERSE, with more than two-thirds of patients achieving reductions in OCS doses to ≤5 mg·day−1 by TRAVERSE week 48. Conclusions Improvements in clinical outcomes and reductions in OCS dose with dupilumab observed in VENTURE were maintained throughout TRAVERSE, regardless of baseline disease severity. Patients who switched from placebo in VENTURE to dupilumab in TRAVERSE had improved clinical outcomes and reductions in OCS dose comparable to those given dupilumab in VENTURE.

Abstract Dated, geo‐referenced museum specimens are a rich data source for reconstructing species' distribution and abundance patterns. However, museum records are potentially biased towards over‐representation of rare species, and it is unclear whether museum records can be used to estimate relative abundance in the field. We assembled 17 coupled field and museum datasets to quantitatively compare relative abundance estimates with the Dirichlet distribution. Collectively, these datasets comprise 73,039 museum records and 1,405,316 field observations of 2,240 species. Although museum records of rare species overestimated relative abundance by 1‐fold to over 100‐fold (median study = 9.0), the relative abundance of species estimated from museum occurrence records was strongly correlated with relative abundance estimated from standardized field surveys (r2 range of 0.10–0.91, median study = 0.43). These analyses provide a justification for estimating species relative abundance with carefully curated museum occurrence records, which may allow for the detection of temporal or spatial shifts in the rank ordering of common and rare species.

Background: Safety and efficacy data for dupilumab beyond 1 year are lacking for patients from Japan with moderate-to-severe asthma. Methods: The TRAVERSE open-label extension (OLE) study (NCT02134028) assessed the safety and efficacy of dupilumab 300 mg every 2 weeks up to 96 weeks in 2282 patients who completed a previous dupilumab asthma study. The primary endpoint was incidence of treatment-emergent adverse events (TEAEs). Secondary endpoints included annualized severe exacerbation rate and change from parent study baseline in pre-bronchodilator forced expiratory volume in 1 second (FEV1), asthma control, quality of life, and blood eosinophil levels. Anti-drug antibodies (ADA) were evaluated. We report results in 160 (7.8% of exposed population) patients recruited from Japanese centers with non-oral corticosteroid (OCS)-dependent asthma rolled over from two parent studies, and in subgroups with a type 2 inflammatory phenotype. Results: TEAEs were consistent with the parent studies and the known safety profile of dupilumab. One patient permanently discontinued treatment due to TEAEs. Exacerbation rates remained low and were sustained to Week 96, as were improvements in pre-bronchodilator FEV1. Rapid, sustained improvements were observed in dupilumab-treated patients who previously received placebo in a parent study, while further improvements in exacerbation rates, asthma control, and asthma-related quality of life were observed in those continuing dupilumab. Blood eosinophil levels decreased progressively while on treatment. Treatment-emergent ADA responses were highest in patients who had previously received placebo. Efficacy results were consistent in patients with a type 2 phenotype. Conclusions: Long-term dupilumab treatment was well tolerated and efficacious in patients with non–OCS-dependent, moderate-to-severe asthma recruited from Japan.(Funded by Sanofi and Regeneron Pharmaceuticals, Inc.; ClinicalTrials.gov identifier, NCT02134028)

Abstract We present a convolutional autoencoder to denoise pulses from a p-type point contact high-purity germanium detector similar to those used in several rare event searches. While we focus on training procedures that rely on detailed detector physics simulations, we also present implementations requiring only noisy detector pulses to train the model. We validate our autoencoder on both simulated data and calibration data from an $$^{241}$$ 241 Am source, the latter of which is used to show that the denoised pulses are statistically compatible with data pulses. We demonstrate that our denoising method is able to preserve the underlying shapes of the pulses well, offering improvement over traditional denoising methods. We also show that the shaping time used to calculate energy with a trapezoidal filter can be significantly reduced while maintaining a comparable energy resolution. Under certain circumstances, our denoising method can improve the overall energy resolution. The methods we developed to remove electronic noise are straightforward to extend to other detector technologies. Furthermore, the latent representation from the encoder is also of use in quantifying shape-based characteristics of the signals. Our work has great potential to be used in particle physics experiments and beyond.

A subset of Nucleotide-binding and leucine-rich repeat-containing receptors (NLRs) function to mitigate overzealous pro-inflammatory signaling produced by NF-κB activation. Under normal pathophysiologic conditions, proper signaling by these NLRs protect against potential autoimmune responses. These NLRs associate with several different proteins within both the canonical and noncanonical NF-κB signaling pathways to either prevent activation of the pathway or inhibit signal transduction. Inhibition of the NF-κB pathways ultimately dampens the production of pro-inflammatory cytokines and activation of other downstream pro-inflammatory signaling mechanisms. Dysregulation of these NLRs, including NLRC3, NLRX1, and NLRP12, have been reported in human inflammatory bowel disease (IBD) and colorectal cancer patients, suggesting the potential of these NLRs as biomarkers for disease detection. Mouse models deficient in these NLRs also have increased susceptibility to colitis and colitis-associated colorectal cancer. While current standard of care for IBD patients and FDA-approved therapeutics function to remedy symptoms associated with IBD and chronic inflammation, these negative regulatory NLRs have yet to be explored as potential drug targets. In this review, we describe a comprehensive overview of recent studies that have evaluated the role of NLRC3, NLRX1, and NLRP12 in IBD and colitis-associated colorectal cancer.

Background The phase 3 QUEST (NCT02414854) and TRAVERSE (NCT02134028) studies demonstrated the efficacy of dupilumab 200/300 mg versus placebo every 2 weeks for 52 weeks (QUEST) and dupilumab 300 mg up to an additional 96 weeks (TRAVERSE) in patients ≥12 years of age with uncontrolled, moderate-to-severe asthma. Overall, safety was consistent with the known dupilumab safety profile. This post hoc analysis assessed long-term dupilumab efficacy for up to 3 years by exacerbation history. Patients and methods Unadjusted annualised severe exacerbation rates (AER) and change from parent study baseline (PSBL) in pre-bronchodilator forced expiratory volume in 1 s (FEV1) and 5-item Asthma Control Questionnaire (ACQ-5) score were assessed in patients with PSBL eosinophils ≥150 cells·µL−1 or fractional exhaled nitric oxide ≥20 ppb and 1 (n=624), 2 (n=344), or ≥3 (n=311) exacerbations in the year before enrolment in QUEST. Results In all three groups, dupilumab treatment progressively reduced AER range to 0.17–0.30 during TRAVERSE (Weeks 48–96), increased pre-bronchodilator FEV1 range by 0.28–0.49 L by Week 96 and improved asthma control (reduced ACQ-5 score range by 1.51–2.03 by Week 48). For patients who first received dupilumab upon TRAVERSE enrolment, AER decreased, and lung function and asthma control improved rapidly, as was observed upon initiation of dupilumab in QUEST. Dupilumab was efficacious regardless of exacerbation history. Conclusion For patients with uncontrolled, moderate-to-severe asthma with elevation of at least one type 2 biomarker, dupilumab treatment provides sustained, long-term reduction of exacerbation rates and improvements in lung function and asthma control irrespective of exacerbation history.

Introduction: Lung cancer is the deadliest cancer in the United States and worldwide, and lung adenocarcinoma (LUAD) is the most prevalent histologic subtype in the United States. LUAD exhibits a wide range of aggressiveness and risk of recurrence, but the biological underpinnings of this behavior are poorly understood. Past studies have focused on the biological characteristics of the tumor itself, but the ability of the immune response to contain tumor growth represents an alternative or complementary hypothesis. Emerging technologies enable us to investigate the spatial distribution of specific cell types within the tumor nest and characterize this immune response. This study aimed to investigate the association between immune cell density within the primary tumor and recurrence-free survival (RFS) in stage I and II LUAD. Methods: This study is a prospective collection with retrospective evaluation. A total of 100 patients with surgically resected LUAD and at least 5-year follow-ups, including 69 stage I and 31 stages II tumors, were enrolled. Multiplexed immunohistochemistry panels for immune markers were used for measurement. Results: Cox regression models adjusted for sex and EGFR mutation status revealed that the risk of recurrence was reduced by 50% for the unit of one interquartile range (IQR) change in the tumoral T-cell (adjusted hazard ratio per IQR increase = 0.50, 95% confidence interval: 0.27–0.93) and decreased by 64% in mast cell density (adjusted hazard ratio per IQR increase = 0.36, confidence interval: 0.15–0.84). The analyses were reported without the type I error correction for the multiple types of immune cell testing. Conclusions: Analysis of the density of immune cells within the tumor and surrounding stroma reveals an association between the density of T-cells and RFS and between mast cells and RFS in early-stage LUAD. This preliminary result is a limited study with a small sample size and a lack of an independent validation set.

BackgroundNext-generation sequencing (NGS), including whole genome sequencing (WGS) and whole exome sequencing (WES), is increasingly being used for clinic care. While NGS data have the potential to be repurposed to support clinical pharmacogenomics (PGx), current computational approaches have not been widely validated using clinical data. In this study, we assessed the accuracy of the Aldy computational method to extract PGx genotypes from WGS and WES data for 14 and 13 major pharmacogenes, respectively.MethodsGermline DNA was isolated from whole blood samples collected for 264 patients seen at our institutional molecular solid tumor board. DNA was used for panel-based genotyping within our institutional Clinical Laboratory Improvement Amendments- (CLIA-) certified PGx laboratory. DNA was also sent to other CLIA-certified commercial laboratories for clinical WGS or WES. Aldy v3.3 and v4.4 were used to extract PGx genotypes from these NGS data, and results were compared to the panel-based genotyping reference standard that contained 45 star allele-defining variants within CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DPYD, G6PD, NUDT15, SLCO1B1, TPMT, and VKORC1.ResultsMean WGS read depth was >30x for all variant regions except for G6PD (average read depth was 29 reads), and mean WES read depth was >30x for all variant regions. For 94 patients with WGS, Aldy v3.3 diplotype calls were concordant with those from the genotyping reference standard in 99.5% of cases when excluding diplotypes with additional major star alleles not tested by targeted genotyping, ambiguous phasing, and CYP2D6 hybrid alleles. Aldy v3.3 identified 15 additional clinically actionable star alleles not covered by genotyping within CYP2B6, CYP2C19, DPYD, SLCO1B1, and NUDT15. Within the WGS cohort, Aldy v4.4 diplotype calls were concordant with those from genotyping in 99.7% of cases. When excluding patients with CYP2D6 copy number variation, all Aldy v4.4 diplotype calls except for one CYP3A4 diplotype call were concordant with genotyping for 161 patients in the WES cohort.ConclusionAldy v3.3 and v4.4 called diplotypes for major pharmacogenes from clinical WES and WGS data with >99% accuracy. These findings support the use of Aldy to repurpose clinical NGS data to inform clinical PGx.

Abstract Background The use of rumen microbial community (RMC) profiles to predict methane emissions has driven interest in ruminal DNA preservation and extraction protocols that can be processed cheaply while also maintaining or improving DNA quality for RMC profiling. Our standard approach for preserving rumen samples, as defined in the Global Rumen Census (GRC), requires time-consuming pre-processing steps of freeze drying and grinding prior to international transportation and DNA extraction. This impedes researchers unable to access sufficient funding or infrastructure. To circumvent these pre-processing steps, we investigated three methods of preserving rumen samples for subsequent DNA extraction, based on existing lysis buffers Tris-NaCl-EDTA-SDS (TNx2) and guanidine hydrochloride (GHx2), or 100% ethanol. Results Rumen samples were collected via stomach intubation from 151 sheep at two time-points 2 weeks apart. Each sample was separated into four subsamples and preserved using the three preservation methods and the GRC method (n = 4 × 302). DNA was extracted and sequenced using Restriction Enzyme-Reduced Representation Sequencing to generate RMC profiles. Differences in DNA yield, quality and integrity, and sequencing metrics were observed across the methods (p 0.99) but slightly more variable compared to the GRC method. Relative abundances were moderately to highly correlated (0.68 ± 0.13) between methods for samples collected within a time-point, which was greater than the average correlation (0.17 ± 0.11) between time-points within a preservation method. Conclusions The two modified lysis buffers solutions (TNx2 and GHx2) proposed in this study were shown to be viable alternatives to the GRC method for RMC profiling in sheep. Use of these preservative solutions reduces cost and improves throughput associated with processing and sequencing ruminal samples. This development could significantly advance implementation of RMC profiles as a tool for breeding ruminant livestock.

Abstract Although soft tissues of coleoid cephalopods record key evolutionary adaptations, they are rarely preserved in the fossil record. This prevents meaningful comparative analyses between extant and fossil forms, as well as the development of a relative timescale for morphological innovations. However, unique 3-D soft tissue preservation of Vampyronassa rhodanica (Vampyromorpha) from the Jurassic Lagerstätte of La Voulte-sur-Rhône (Ardèche, France) provides unparalleled opportunities for the observation of these tissues in the oldest likely relative of extant Vampyroteuthis infernalis. Synchrotron X-ray microtomography and reconstruction of V. rhodanica allowed, for the first time, a high-resolution re-examination of external and internal morphology, and comparison with other fossil and extant species, including V. infernalis. The new data obtained demonstrate that some key V. infernalis characters, such as its unique type of sucker attachment, were already present in Jurassic taxa. Nonetheless, compared with the extant form, which is considered to be an opportunistic detritivore and zooplanktivore, many characters in V. rhodanica indicate a pelagic predatory lifestyle. The contrast in trophic niches between the two taxa is consistent with the hypothesis that these forms diversified in continental shelf environments prior to the appearance of adaptations in the Oligocene leading to their modern deep-sea mode of life.

Increasing the efficiency of rumen fermentation is one of the main ways to maximize the production of ruminants. It is therefore important to understand the ruminal microbiome, as well as environmental influences on that community. However, there are no studies that describe the ruminal microbiota in buffaloes in the Amazon. The objective of this study was to characterize the rumen microbiome of the water buffalo (Bubalus bubalis) in the eastern Amazon in the dry and rainy seasons in three grazing ecosystems: Baixo Amazonas (BA), Continente do Pará (CP), Ilha do Marajó (IM), and in a confinement system: Tomé-Açu (TA). Seventy-one crossbred male buffaloes (Murrah × Mediterranean) were used, aged between 24 and 36 months, with an average weight of 432 kg in the rainy season and 409 kg in the dry season, and fed on native or cultivated pastures. In the confinement system, the feed consisted of sorghum silage, soybean meal, wet sorghum premix, and commercial feed. Samples of the diet from each ecosystem were collected for bromatological analysis. The collections of ruminal content were carried out in slaughterhouses, with the rumen completely emptied and homogenized, the solid and liquid fractions separated, and the ruminal pH measured. DNA was extracted from the rumen samples, then sequenced using Restriction Enzyme Reduced Representation Sequencing. The taxonomic composition was largely similar between ecosystems. All 61 genera in the reference database were recognized, including members of the domains Bacteria and Archaea. The abundance of 23 bacterial genera differed significantly (p < 0.01) between the Tomé-Açu confinement and other ecosystems. Bacillus, Ruminococcus, and Bacteroides had lower abundance in samples from the Tomé-Açu system. Among the Archaea, the genus Methanomicrobium was less abundant in Tomé-Açu, while Methanosarcina was more abundant. There was a difference caused by all evaluated factors, but the diet (available or offered) was what most influenced the ruminal microbiota.

IntroductionPseudomonas aeruginosa is known for its ability to form biofilms, which are dependent on the production of exopolysaccharides. During chronic colonization of the airway and biofilm formation, P. aeruginosa converts to a mucoid phenotype, indicating production of the exopolysaccharide alginate. The mucoid phenotype promotes resistance to phagocytic killing, but the mechanism has not been established.Methods and ResultsTo better understand the mechanism of phagocytic evasion conferred by alginate production, Human (THP-1) and murine (MH-S) macrophage cell lines were used to determine the effects of alginate production on macrophage binding, signaling and phagocytosis. Phagocytosis assays using mucoid clinical isolate FRD1 and its non-mucoid algD mutant showed that alginate production inhibited opsonic and non-opsonic phagocytosis, but exogenous alginate was not protective. Alginate caused a decrease in binding to murine macrophages. Blocking antibodies to CD11b and CD14 showed that these receptors were important for phagocytosis and were blocked by alginate. Furthermore, alginate production decreased the activation of signaling pathways required for phagocytosis. Mucoid and non-mucoid bacteria induced similar levels of MIP-2 from murine macrophages.DiscussionThis study demonstrated for the first time that alginate on the bacterial surface inhibits receptor-ligand interactions important for phagocytosis. Our data suggest that there is a selection for alginate conversion that blocks the earliest steps in phagocytosis, leading to persistence during chronic pulmonary infections.

Background Many patients with asthma experience loss of lung function over time, and in certain patients this can lead to progressive obstructive patterns similar to COPD. Patients with severe asthma may experience accelerated lung function decline (LFD). However, characteristics and risk factors for LFD in asthma have not been well described. Dupilumab may prevent or slow the rate of LFD in patients with uncontrolled, moderate-to-severe asthma. ATLAS trial is designed to evaluate the role of dupilumab in preventing/slowing LFD over a period of 3 years versus standard-of-care therapy. Methods ATLAS (clinicaltrials.gov identifier NCT05097287) is a randomised, double-blind, placebo-controlled, multicentre study that will include adult patients with uncontrolled moderate-to-severe asthma. ∼1828 patients will be randomised (2:1) to dupilumab 300 mg or placebo in combination with maintenance therapy every 2 weeks for 3 years. The primary objective is to assess the effect of dupilumab on preventing or slowing LFD by year 1 in the exhaled nitric oxide fraction (FeNO) population (patients with FeNO ≥35 ppb). The effect of dupilumab in slowing the rate of LFD by year 2 and year 3 in both FeNO and total populations, exacerbations, asthma control, quality of life, biomarker changes and utility of FeNO as a biomarker of LFD will also be evaluated. Discussion ATLAS is the first trial assessing the effect of a biologic on LFD, designed to establish the role of dupilumab in prevention of long-term loss of lung function and its potential effect on disease modification, which may provide unique insights into asthma pathophysiology, including predictive and prognostic factors of LFD.

ABSTRACT Lipopolysaccharide (LPS) is an essential component of the outer membrane (OM) of many Gram-negative bacteria, providing a barrier against the entry of toxic molecules. In Escherichia coli, LPS is exported to the cell surface by seven essential proteins (LptA-G) that form a transenvelope complex. At the inner membrane, the ATP-binding cassette (ABC) transporter LptB2FG associates with LptC to power LPS extraction from the membrane and transfer to the periplasmic LptA protein, which is in complex with the OM translocon LptDE. LptC interacts both with LptB2FG and LptADE to mediate the formation of the transenvelope bridge and regulates the ATPase activity of LptB2FG. A genetic screen has previously identified suppressor mutants at a residue (R212) of LptF that are viable in the absence of LptC. Here, we present in vivo evidence that the LptF R212G mutant assembles a six-protein transenvelope complex in which LptA mediates interactions with LptF and LptD in the absence of LptC. Furthermore, we present in vitro evidence that the mutant LptB2FG complexes restore the regulation of ATP hydrolysis as it occurs in the LptB2FGC complex to achieve wild-type efficient coupling of ATP hydrolysis and LPS movement. We also show the suppressor mutations restore the wild-type levels of LPS transport both in vivo and in vitro, but remarkably, without restoring the affinity of the inner membrane complex for LptA. Based on the sensitivity of lptF suppressor mutants to selected stress conditions relative to wild-type cells, we show that there are additional regulatory functions of LptF and LptC that had not been identified. IMPORTANCE The presence of an external LPS layer in the outer membrane makes Gram-negative bacteria intrinsically resistant to many antibiotics. Millions of LPS molecules are transported to the cell surface per generation by the Lpt molecular machine made, in E. coli, by seven essential proteins. LptC is the unconventional regulatory subunit of the LptB2FGC ABC transporter, involved in coordinating energy production and LPS transport. Surprisingly, despite being essential for bacterial growth, LptC can be deleted, provided that a specific residue in the periplasmic domain of LptF is mutated and LptA is overexpressed. Here, we apply biochemical techniques to investigate the suppression mechanism. The data produced in this work disclose an unknown regulatory function of LptF in the transporter that not only expands the knowledge about the Lpt complex but can also be targeted by novel LPS biogenesis inhibitors.

Eosinophilic esophagitis (EoE) is a chronic type 2 inflammatory disease characterized by an eosinophilic inflammatory infiltrate in the esophagus, leading to remodeling, stricture formation, and fibrosis. Triggered by food and aeroallergens, type 2 cytokines interleukin (IL)-4, IL-13, IL-5 produced by CD4+ T helper 2 cells (Th2), eosinophils, mast cells, basophils, and type 2 innate lymphoid cells alter the esophageal epithelial barrier and increase inflammatory cell tissue infiltration. Clustering analysis based on the expression of type 2 inflammatory genes demonstrated the diversity of EoE endotypes. Despite the availability of treatment options for patients with EoE, which include dietary restriction, proton pump inhibitors, swallowed topical steroids, and esophageal dilation, there are still no Food and Drug Administration–approved medications for this disease; as such, there are clear unmet medical needs for these patients. A number of novel biologic therapies currently in clinical trials represent a promising avenue for targeted therapeutic approaches in EoE. This review summarizes our current knowledge on the role of type 2 inflammatory cells and mediators in EoE disease pathogenesis, as well as the future treatment landscape targeting underlying inflammation in EoE.

Introduction. Elevated neutrophil counts in blood, sputum, or lung have been associated with poor clinical outcomes and more severe disease in patients with type 2 asthma. In the phase 3 LIBERTY ASTHMA QUEST (NCT02414854), add-on dupilumab 200 and 300 mg every 2 weeks compared with matched placebo significantly reduced severe asthma exacerbations and improved forced expiratory volume in 1 s (FEV1) in patients with uncontrolled, moderate-to-severe asthma. This post hoc analysis explored the efficacy of dupilumab in patients with type 2 asthma enrolled in QUEST with or without elevated blood neutrophil counts. Methods. Annualized severe exacerbation rates during the 52-week treatment period and least-squares mean change from baseline in FEV1 over time were evaluated for patients with elevated type 2 biomarkers at baseline (blood eosinophils ≥ 150 cells/µL or fractional exhaled nitric oxide (FeNO) ≥ 20 ppb; and eosinophils ≥ 300 cells/µL or FeNO ≥ 50 ppb) and low (

IntroductionDrug-induced prolongation of the heart rate-corrected QT interval (QTc) is associated with increased risk for the potentially fatal arrhythmia torsades de pointes. Due to arrhythmia risk, clinical trials with cancer therapeutics often exclude patients based on thresholds for QTc prolongation. Our objective was to assess associations between prescriptions for QT-prolonging drugs and the odds of meeting cancer trial exclusionary QTc thresholds in a cohort of adults with advanced cancer.MethodsElectronic health records were retrospectively reviewed for 271 patients seen at our institutional molecular solid tumor clinic. Collected data included demographics, QTc measurements, ventricular arrhythmia-related diagnoses, and all inpatient and outpatient prescriptions. Potential associations were assessed between demographic and clinical variables, including prescriptions for QT-prolonging drugs, and QTc measurements.ResultsWomen had longer median QTc measurements than men (p = 0.030) and were prescribed more QT-prolonging drugs during the study (p = 0.010). In all patients, prescriptions for QT-prolonging drugs were associated with longer median and maximum QTc measurements at multiple assessed time points (i.e., for QT-prolonging drugs prescribed within 10, 30, 60, and 90 days of QTc measurements). Similarly, the number of QT-prolonging drugs prescribed was correlated with longer median and maximum QTc measurements at multiple time points. Common QTc-related exclusionary criteria were collected from a review of ClinicalTrials.gov for recent cancer clinical trials. Based on common exclusion criteria, prescriptions for QT-prolonging drugs increased the odds of trial exclusion.ConclusionThis study demonstrates that prescriptions for QT-prolonging drugs were associated with longer QTc measurements and increased odds of being excluded from cancer clinical trials.

Chronic rhinosinusitis with nasal polyps (CRSwNP) is a predominantly type 2 inflammatory disease of the nasal and paranasal sinuses. Dupilumab is a monoclonal antibody that blocks the shared receptor component for interleukin-4 and interleukin-13, which are key and central drivers of type 2 inflammation. In clinical trials, dupilumab significantly improved objective and patient-reported measures of CRSwNP versus placebo and was well tolerated. Dupilumab is approved in the European Union, USA and Japan as add-on maintenance treatment for adults with inadequately controlled CRSwNP. There exists an important evidence gap between efficacy and effectiveness data for dupilumab in severe CRSwNP. In order to bridge this gap, the AROMA prospective global registry (ClinicalTrials.gov: NCT04959448) was established. AROMA will collect long-term data on the utilisation, effectiveness and safety of dupilumab for CRSwNP treatment in real-world clinical practice. AROMA will enrol approximately 1000 adults starting dupilumab for severe CRSwNP across 120 global sites. Baseline data will include patient demographics, medical/surgical history and presence of type 2 comorbidities. Effectiveness outcome assessments will include objective measures of CRSwNP assessed as part of routine clinical care and various patient-reported questionnaires. Treatment patterns, concomitant medications and long-term safety will also be recorded. Results from AROMA, the first prospective, real-world, global registry to characterise patients with severe CRSwNP starting dupilumab, will provide evidence on the real impact of dupilumab in patients with CRSwNP and complement the data from randomised clinical trials. The registry will also provide evidence on disease progression in patients with CRSwNP, including those with coexisting diseases.

Enteric methane emissions from ruminants account for ∼35% of New Zealand’s greenhouse gas emissions. This poses a significant threat to the pastoral sector. Breeding has been shown to successfully lower methane emissions, and genomic prediction for lowered methane emissions has been introduced at the national level. The long-term genetic impacts of including low methane in ruminant breeding programs, however, are unknown. The success of the New Zealand sheep industry is currently heavily reliant on the prolificacy, fecundity and survival of adult ewes. The objective of this study was to determine genetic and phenotypic correlations between adult maternal ewe traits (live weight, body condition score, number of lambs born, litter survival to weaning, pregnancy scanning and fleece weight), faecal and Nematodirus egg counts and measures of methane in respiration chambers. More than 9,000 records for methane from over 2,200 sheep measured in respiration chambers were collected over 10 years. Sheep were fed on a restricted diet calculated as approximately twice the maintenance. Methane measures were converted to absolute daily emissions of methane measured in g per day (CH4/day). Two measures of methane yield were recorded: the ratio of CH4 to dry matter intake (g CH4/kg DMI; CH4/DMI) and the ratio of CH4 to total gas emissions (CH4/(CH4 + CO2)). Ewes were maintained in the flocks for at least two parities. Non-methane trait data from over 8,000 female relatives were collated to estimate genetic correlations. Results suggest that breeding for low CH4/DMI is unlikely to negatively affect faecal egg counts, adult ewe fertility and litter survival traits, with no evidence for significant genetic correlations. Fleece weight was unfavourably (favourably) correlated with CH4/DMI (rg = −0.21 ± 0.09). Live weight (rg = 0.3 ± 0.1) and body condition score (rg = 0.2 ± 0.1) were positively correlated with methane yield. Comparing the two estimates of methane yield, CH4/DMI had lower heritability and repeatability. However, correlations of both measures with adult ewe traits were similar. This suggests that breeding is a suitable mitigation strategy for lowering methane yield, but wool, live weight and fat deposition traits may be affected over time and should be monitored.

Global agreements in place to reduce methane emissions in livestock are a potential threat to food security. Successful but independent breeding strategies for improved production and lower methane are in place. The unanswered questions are whether these strategies can be combined and how they impact one another, physically and economically. The New Zealand economy is largely dependent on pastoral agriculture from grazing ruminants. The sheep industry produces ∼20 million lamb carcasses for export each year primarily from grass. Methane emitted from the fermentation of forage by grazing ruminants accounts for one-third of all New Zealand’s greenhouse gas emissions. Here, we use sheep selection lines bred for divergent methane production and large numbers of their relatives to determine the genetic and phenotypic correlations between enteric methane emissions, carcass yield, and meat quality. The primary objectives were to determine whether previously shown physiological differences between methane selection lines (differing by ∼12% in methane) result in a negative impact on meat production and quality by measuring close relatives. The results show no negative effects of breeding for lowered methane on meat and carcass quality. Gross methane emissions were highly correlated with liveweight and measures of carcass weight and negatively correlated with dressing-out percentage and fat yield (GR). Trends were similar but not significant for methane yield (g CH4/kg DMI). Preliminary evidence, to date, shows that breeding for low methane may result in animals with higher lean yields that are economically favorable even before carbon costs and environmental benefits are taken into account. These benefits were seen in animals measured for methane on fixed intakes and require validation on intakes that are allowed to vary.

There is simultaneous interest in improving the feed efficiency of ruminant livestock and reducing methane (CH4) emissions. The relationship (genetic and phenotypic) between feed efficiency (characterized as residual feed intake: RFI) and greenhouse gases [methane (CH4) and carbon dioxide (CO2)] traits in New Zealand (NZ) maternal sheep has not previously been investigated, nor has their relationship with detailed estimates of body composition. To investigate these relationships in NZ maternal sheep, a feed intake facility was established at AgResearch Invermay, Mosgiel, NZ in 2015, comprising automated feeders that record individual feeding events. Individual measures of feed intake, feeding behavior (length and duration of eating events), and gas emissions (estimated using portable accumulation chambers) were generated on 986 growing maternal ewe lambs sourced from three pedigree recorded flocks registered in the Sheep Improvement Limited database (www.sil.co.nz). Additional data were generated from a subset of 591 animals for body composition (estimated using ultrasound and computed tomography scanning). The heritability estimates for RFI, CH4, and CH4/(CH4+CO2) were 0.42 ± 0.09, 0.32 ± 0.08, and 0.29 ± 0.06, respectively. The heritability estimates for the body composition traits were high for carcass lean and fat traits; for example, the heritability for visceral fat (adjusted for body weight) was 0.93 ± 0.19. The relationship between RFI and CH4 emissions was complex, and although less feed eaten will lead to a lowered absolute amount of CH4 emitted, there was a negative phenotypic and genetic correlation between RFI and CH4/(CH4+CO2) of −0.13 ± 0.03 and −0.41 ± 0.15, respectively. There were also genetic correlations, that were different from zero, between both RFI and CH4 traits with body composition including a negative correlation between the proportion of visceral fat in the body and RFI (−0.52 ± 0.16) and a positive correlation between the proportion of lean in the body and CH4 (0.54 ± 0.12). Together the results provide the first accurate estimates of the genetic correlations between RFI, CH4 emissions, and the body composition (lean and fat) in sheep. These correlations will need to be accounted for in genetic improvement programs.

Finite element analysis (FEA) is a commonly used application in biomechanical studies of both extant and fossil taxa to assess stress and strain in solid structures such as bone. FEA can be performed on 3D structures that are generated using various methods, including computed tomography (CT) scans and surface scans. While previous palaeobiological studies have used both CT scanned models and surface scanned models, little research has evaluated to what degree FE results may vary when CT scans and surface scans of the same object are compared. Surface scans do not preserve the internal geometries of 3D structures, which are typically preserved in CT scans. Here, we created 3D models from CT scans and surface scans of the same specimens (crania and mandibles of a Nile crocodile, a green sea turtle, and a monitor lizard) and performed FEA under identical loading parameters. It was found that once surface scanned models are solidified, they output stress and strain distributions and model deformations comparable to their CT scanned counterparts, though differing by notable stress and strain magnitudes in some cases, depending on morphology of the specimen and the degree of reconstruction applied. Despite similarities in overall mechanical behaviour, surface scanned models can differ in exterior shape compared to CT scanned models due to inaccuracies that can occur during scanning and reconstruction, resulting in local differences in stress distribution. Solid-fill surface scanned models generally output lower stresses compared to CT scanned models due to their compact interiors, which must be accounted for in studies that use both types of scans.

Purpose Endometriosis is a chronic condition where endometrial-like cells proliferate outside the uterus causing pain and disability. Limited treatments are available but symptom management is essential for social and economic participation. The aim was to compare women’s and health professionals’ perceptions of quality of endometriosis health care and opportunities for improvements. Methods Women participated in closed moderated online discussion groups and health professionals in semi-structured telephone interviews. Discussion group text and interview transcripts were thematically analyzed using the Framework Analysis approach. Results Forty-six women, 12 general practitioners (GPs), and 1 gynecologist participated. Endometriosis can have debilitating consequences. However, women reported that healthcare providers may dismiss symptoms, lack essential knowledge and provide inconsistent advice; treatments are seldom successful or without adverse side-effects. Health professionals acknowledged limitations in expertise, persistent myths, and challenges in achieving best practice. Enhancing collaborative care skills, individualized treatment plans, and local referral pathways to multi-disciplinary care may improve satisfaction with endometriosis care-giving and receiving. Conclusions This is the first comparison of patient and practitioner perceptions of endometriosis in primary healthcare. Models of multi-disciplinary, collaborative care need to be developed and evaluated against consumer-informed measures of women’s wellbeing, quality of life and satisfaction with symptom management and health care.

Abstract Background Homonymous visual field defects represent the most frequent type of visual field loss after stroke, affecting nearly 30% of individuals with unilateral post-chiasmal brain damage. This review aimed to gather the available evidence on the biomechanical changes to visual field loss following stroke. Methods A systematic review was conducted inclusive of randomised controlled trials, cohort studies, before-after studies and case-controlled studies. Studies including adult and paediatric participants that investigated eye, head, or body movements in post-stroke visual field loss during visual exploration tasks were included. Search terms included a range of MESH terms as well as alternative terms relating to stroke, visual field loss, hemianopia, visual functions and scanning behaviour. Articles were selected by two authors independently. Data were extracted by one author and verified by a second. All included articles were assessed for risk of bias using checklists appropriate to the study design. Results Thirty-six articles (1123 participants) were included in the overall review (Kappa 0.863) and categorised into simulated or true visual field loss (typically hemianopia). Seven studies identified the biomechanical alterations to simulated hemianopia compared to normal performance. Twenty-nine studies detailed eye, head and body movement parameters in true hemianopia. Hemianopic participants and healthy adults with simulated hemianopia differed significantly from controls in various fixation and saccade parameters as indicated by increased number and duration of fixations, number and duration of saccades and scan path length with shorter mean saccadic amplitude. Under simulated hemianopia, participants were consistently biased towards the sighted visual field while gaze behaviour in true hemianopia was biased in the direction of the blind hemifield. Conclusions There is considerable evidence on the altered eye movements that occur in true hemianopia and in healthy adults with simulated hemianopia. Successful performance in naturalistic tasks of visual exploration appears to be related to compensatory mechanisms of visual exploratory behaviour, namely, an increase in the amplitude and peak velocity of saccades, widening horizontally the distribution of eye movements, and a shift of the overall distribution of saccades into the blind field. This review highlights the lack of studies reporting head and other body movement parameters in hemianopia. Further studies with robust methodology and large sample sizes involving participants with post-stroke visual field loss are needed. Systematic review registration PROSPERO CRD42020194403

Abstract Rodents can influence the succession and assembly of plant communities by preying on and dispersing seeds. Using a seed tray experiment with three common seeds, American beech (Fagus grandifolia), red maple (Acer rubrum), and eastern hemlock (Tsuga canadensis), we assessed factors that influence seed selection and foraging time of three rodents: deer mice (Peromyscus maniculatus), white‐footed mice (Peromyscus leucopus), and southern red‐backed voles (Myodes gapperi). All three rodents preferred beech seeds, likely due to its large size and high lipid content. However, when beech availability was low, secondary seed selection differed by rodent species with P. maniculatus equally selecting hemlock and red maple, P. leucopus preferring hemlock, and M. gapperi preferring red maple. Red maple seeds contained high levels of phenolic compounds, which hinder digestion, and the elongated cecum of M. gapperi may allow for better processing of these compounds relative to Peromyscus. Beech seeds were nearly always removed from trays intact, suggesting rodents could be important dispersers compared to the small‐seeded species, which were generally processed on trays. The influence of environmental factors on seed selection was only notable when beech seed availability was low. Beech seed availability was also the primary factor influencing foraging time on trays, with individuals increasing foraging time as beech availability decreased. Consistent with predator avoidance behaviors, denser shrub cover increased foraging time for P. maniculatus, whereas moon luminosity decreased foraging for all three species. Our findings underscore that seed quality drives seed selection but that preferences are context dependent, varying with seed availability and digestive capacity.

Objectives Reporting of research for stroke-related visual impairment is inconsistent. The aim of this study was to define three core outcome sets (COS) and related core outcome measurements (COM) for central visual impairment, visual field loss and ocular motility disorders in stroke research.Design The consensus process consisted of an online three-round Delphi survey followed by a consensus meeting of key stakeholders.Setting UK-wide survey.Participants Stakeholders included orthoptists, occupational therapists, ophthalmologists, stroke survivors and COS users such as researchers, journal editors and guideline developers.Outcome measures For COS development, a list of potentially relevant visual outcomes was created after review of the literature and further grouped into outcome domains. For COM development, a list of potential instruments was created after review of the literature and quality appraised for reliability and validity.Results COS—119 potential outcomes extracted from published literature. Similar assessment outcomes were grouped into 24 outcome domains. Delphi process included 123 participants in round 1, 65 round 2, 51 round 3. Twelve participants attended the consensus meeting with recommended outcome domains for central visual impairment (visual acuity, functional vision, quality of life), visual field loss (visual fields, functional vision, quality of life) and ocular motility disorders (eye alignment, eye movements, functional vision, quality of life). COM—52 test options extracted from the COS outcomes and grouped into 16 domains. Thirteen participants attended the COM consensus meeting. Recommended instruments for measurement of these outcomes include; Logarithm of the Minimal Angle of Resolution visual acuity, cover test, cardinal position eye movement assessments, peripheral visual field perimetry, Visual Function Questionnaire-25.Conclusions COS and COM are defined for vision research for stroke survivors. Their use has potential to reduce heterogeneity in routine clinical practice and improve standardisation and accuracy of vision assessment. Future research is required to evaluate the use of these COS and COM.

Aims To provide an overview of how the European visual field standards for driving (specified in Commission Directive 2009/113/EC) are applied and determine whether individuals with visual field defects are treated equally across Europe.Methods One ophthalmic expert from each of 32 European countries was invited to participate in an electronic survey. They were presented with threshold and Esterman perimetry results of 15 cases of visual field defects and asked to classify each case as either passed or failed in reference to their national standards. The results were compared with the European Driving Test Group 1 (EDT1), which is a new perimetry algorithm that adheres to the recommendations by the Eyesight Working Group. Fleiss’ kappa was used to determine the inter-rater agreement.Results Twenty-five countries responded. Three of 15 cases were passed by all. Full agreement on a failed case was not reached. Denmark graded most leniently and passed 12 cases. Bulgaria, Romania and Slovakia graded most strictly and passed five cases. The Fleiss’ kappa score was 0.52 (95% CI 0.49 to 0.55). Only Slovenia was in full agreement with the EDT1. Fifteen countries endorsed specific perimetric tests for assessing fitness to drive. Five of these also defined pass/fail criteria.Conclusion The directive fails to establish a uniform approach to the visual field requirements, as evident by moderate pass/fail agreement between the national experts. Because the visual standards for driving are enforced differently, identical visual field loss can result in either revocation or approval of a driving license.

Trauma triggers critical molecular and cellular signaling cascades that drive biological outcomes and recovery. Variations in the gene expression of common endogenous reference housekeeping genes (HKGs) used in data normalization differ between tissue types and pathological states. Systematically, we investigated the gene stability of nine HKGs (Actb, B2m, Gapdh, Hprt1, Pgk1, Rplp0, Rplp2, Tbp, and Tfrc) from tissues prone to remote organ dysfunction (lung, liver, kidney, and muscle) following extremity trauma. Computational algorithms (geNorm, Normfinder, ΔCt, BestKeeper, RefFinder) were applied to estimate the expression stability of each HKG or combinations of them, within and between tissues, under both steady-state and systemic inflammatory conditions. Rplp2 was ranked as the most suitable in the healthy and injured lung, kidney, and skeletal muscle, whereas Rplp2 and either Hprt1 or Pgk1 were the most suitable in the healthy and injured liver, respectively. However, the geometric mean of the three most stable genes was deemed the most stable internal reference control. Actb and Tbp were the least stable in normal tissues, whereas Gapdh and Tbp were the least stable across all tissues post-trauma. Ct values correlated poorly with the translation from mRNA to protein. Our results provide a valuable resource for the accurate normalization of gene expression in trauma-related experiments.

Most tundra carbon flux modeling relies on leaf area index (LAI), generally estimated from measurements of canopy greenness using the normalized difference vegetation index (NDVI), to estimate the direction and magnitude of fluxes. However, due to the relative sparseness and low stature of tundra canopies, such models do not explicitly consider the influence of variation in tundra canopy structure on carbon flux estimates. Structure from motion (SFM), a photogrammetric method for deriving three-dimensional (3D) structure from digital imagery, is a non-destructive method for estimating both fine-scale canopy structure and LAI. To understand how variation in 3D canopy structure affects ecosystem carbon fluxes in Arctic tundra, we adapted an existing NDVI-based tundra carbon flux model to include variation in SFM-derived canopy structure and its interaction with incoming sunlight to cast shadows on canopies. Our study system consisted of replicate plots of dry heath tundra that had been subjected to three herbivore exclosure treatments (an exclosure-free control [CT], large mammals exclosure), and a large and small mammal exclosure [ExLS]), providing the range of 3D canopy structures employed in our study. We found that foliage within the more structurally complex surface of CT canopies received significantly less light over the course of the day than canopies within both exclosure treatments. This was especially during morning and evening hours, and was reflected in modeled rates of net ecosystem exchange (NEE) and gross primary productivity (GPP). We found that in the ExLS treatment, SFM-derived estimates of GPP were significantly lower and NEE significantly higher than those based on LAI alone. Our results demonstrate that the structure of even simple tundra vegetation canopies can have significant impacts on tundra carbon fluxes and thus need to be accounted for.

Objectives In this study, we sought to evaluate the extent of further visual field that could be assessed when using stimulus size V in standard automated perimetry compared with size III in advanced stage glaucoma and whether cut-off values could be determined for when to switch from size III to size V.Design Prospective cross-sectional study.Setting Single-centre outpatient eye clinic in India (New Delhi).Participants Advanced stage glaucoma defined as stages 3–4.Intervention Central static perimetry with Octopus 900 G programme (size III stimulus dynamic strategy) and low vision central programme (size V stimulus dynamic strategy).Primary and secondary outcome measures Visual field assessment for right and left eyes with both sizes III and V were undertaken within one clinic visit.Results We recruited 126 patients (170 eyes). Mean patient age at assessment was 55.86 years (SD 15.15). Means (SD) for size III versus size V, respectively, were 6.94 dB (5.58) and 12.98 dB (7.77) for mean sensitivity, 20.02 dB (5.67) and 19.22 dB (7.74) for mean deviation, 5.89 dB (2.29) and 7.69 dB (2.78) for standard loss variance and 3.32 min (1.07) and 6.40 min (1.43) for test duration. All except mean deviation were significantly different between size III and V tests.Conclusion Useful visual field information was obtained with size V stimuli which allowed continued monitoring of these patients that was not possible with size III. Increased test duration, standard loss variance and mean sensitivity were found with size V, as expected, given that more visual responses were obtained with the increased target size. A switch from size III to V may be considered when mean sensitivity reaches 10 dB and/or mean deviation reaches 18 dB.

Genotypes are often used to assign parentage in agricultural and ecological settings. Sequencing can be used to obtain genotypes but does not provide unambiguous genotype calls, especially when sequencing depth is low in order to reduce costs. In that case, standard parentage analysis methods no longer apply. A strategy for using low-depth sequencing data for parentage assignment is developed here. It entails the use of relatedness estimates along with a metric termed excess mismatch rate which, for parent-offspring pairs or trios, is the difference between the observed mismatch rate and the rate expected under a model of inheritance and allele reads without error. When more than one putative parent has similar statistics, bootstrapping can provide a measure of the relatedness similarity. Putative parent-offspring trios can be further checked for consistency by comparing the offspring’s estimated inbreeding to half the parent relatedness. Suitable thresholds are required for each metric. These methods were applied to a deer breeding operation consisting of two herds of different breeds. Relatedness estimates were more in line with expectation when the herds were analyzed separately than when combined, although this did not alter which parents were the best matches with each offspring. Parentage results were largely consistent with those based on a microsatellite parentage panel with three discordant parent assignments out of 1561. Two models are investigated to allow the parentage metrics to be calculated with non-random selection of alleles. The tools and strategies given here allow parentage to be assigned from low-depth sequencing data.

Abstract Identifying the mechanisms that structure niche breadth and overlap between species is important for determining how species interact and assessing their functional role in an ecosystem. Without manipulative experiments, assessing the role of foraging ecology and interspecific competition in structuring diet is challenging. Systems with regular pulses of resources act as a natural experiment to investigate the factors that influence the dietary niches of consumers. We used natural pulses of mast‐fruiting of American beech (Fagus grandifolia) to test whether optimal foraging or competition structure the dietary niche breadth and overlap between two congener rodent species (Peromyscus leucopus and P. maniculatus), both of which are generalist consumers. We reconstructed diets seasonally over a 2‐year period using stable isotope analysis (δ13C, δ15N) of hair and of potential dietary items and measured niche dynamics using standard ellipse area calculated within a Bayesian framework. Changes in niche breadth were generally consistent with predictions of optimal foraging theory, with both species consuming more beechnuts (a high‐quality food resource) and having a narrower niche breadth during masting seasons compared to nonmasting seasons when dietary niches expanded and more fungi (a low‐quality food source) were consumed. In contrast, changes in dietary niche overlap were consistent with competition theory, with higher diet overlap during masting seasons than during nonmasting seasons. Overall, dietary niche dynamics were closely tied to beech masting, underscoring that food availability influences competition. Diet plasticity and niche partitioning between the two Peromyscus species may reflect differences in foraging strategies, thereby reducing competition when food availability is low. Such dietary shifts may have important implications for changes in ecosystem function, including the dispersal of fungal spores.

Abstract Background Among the available patient-reported outcome measures (PROMs) there is an absence of a PROM with a specific focus on the impact of the wide variety of visual impairments following stroke. Our aim was to develop a patient reported quality of life outcome measure for stroke survivors with visual impairment. Methods Potential items were sourced from a combination of existing PROMs from a systematic review and qualitative in-depth interviews, duplicates were removed and items shortlisted. The initial pilot instrument was created following a ranking exercise of these potential items and consultation with stroke survivors. Version 1 was piloted with 37 stroke survivors at acute and chronic stages. Version 2 was piloted with 243 stroke survivors with visual impairment at acute and chronic stages. This data was analysed using the Rasch measurement model. Simultaneously, items from Version 2 underwent a Delphi process with stroke survivors and stroke clinicians, to assess the importance of each item. Final consensus decisions on item removal were made using the combined analysis from the Rasch measurement model and Delphi process in a nominal group meeting. Results Due to the wide range of rank given to the majority of categories/items, only two items were discarded. Version 1 comprised of 102 items with 5 response categories relating to amount of difficulty. The pilot of Version 1 allowed item reduction based on analysis of floor/ceiling effects and not applicable responses. Version 2 comprised of 62 items. Within the nominal group meeting, the expert panel created a set of rules which aided them with decision making in addition to the Rasch and Delphi analysis data. This resulted in the removal of 43 items and the combination of seven items to create three new items. The expert panel also recommended the rewording of three items. Conclusion The Brain Injury associated Visual Impairment Impact Questionnaire (BIVI-IQ-15), a 15-item instrument with 4 response categories has been developed for capturing vision-related quality of life of stroke survivors with any of the predominant types of visual impairment, in the presence of other impairments and for both inpatients and outpatients.