Using dispersion models at microscale to assess long-term air pollution in urban hot spots: A FAIRMODE joint intercomparison exercise for a case study in Antwerp

In the framework of the Forum for Air Quality Modelling in Europe (FAIRMODE), a modelling intercomparison exercise for computing NO2 long-term average concentrations in urban districts with a very high spatial resolution was carried out. This exercise was undertaken for a district of Antwerp (Belgium). Air quality data includes data recorded in air quality monitoring stations and 73 passive samplers deployed during one-month period in 2016. The modelling domain was 800 × 800 m2. Nine modelling teams participated in this exercise providing results from fifteen different modelling applications based on different kinds of model approaches (CFD - Computational Fluid Dynamics-, Lagrangian, Gaussian, and Artificial Intelligence). Some approaches consisted of models running the complete one-month period on an hourly basis, but most others used a scenario approach, which relies on simulations of scenarios representative of wind conditions combined with post-processing to retrieve a one-month average of NO2 concentrations. The objective of this study is to evaluate what type of modelling system is better suited to get a good estimate of long-term averages in complex urban districts. This is very important for air quality assessment under the European ambient air quality directives. The time evolution of NO2 hourly concentrations during a day of relative high pollution was rather well estimated by all models. Relative to high resolution spatial distribution of one-month NO2 averaged concentrations, Gaussian models were not able to give detailed information, unless they include building data and street-canyon parameterizations. The models that account for complex urban geometries (i.e. CFD, Lagrangian, and AI models) appear to provide better estimates of the spatial distribution of one-month NO2 averages concentrations in the urban canopy. Approaches based on steady CFD-RANS (Reynolds Averaged Navier Stokes) model simulations of meteorological scenarios seem to provide good results with similar quality to those obtained with an unsteady one-month period CFD-RANS simulations.

A new winter wheat genetic resource harbors untapped diversity from synthetic hexaploid wheat

KEY MESSAGE

The NIAB_WW_SHW_NAM population, a large nested association mapping panel, is a useful resource for mapping QTL from synthetic hexaploid wheat that can improve modern elite wheat cultivars. The allelic richness harbored in progenitors of hexaploid bread wheat (Triticum aestivum L.) is a useful resource for addressing the genetic diversity bottleneck in modern cultivars. Synthetic hexaploid wheat (SHW) is created through resynthesis of the hybridisation events between the tetraploid (Triticum turgidum subsp. durum Desf.) and diploid (Aegilops tauschii Coss.) bread wheat progenitors. We developed a large and diverse winter wheat nested association mapping (NAM) population (termed the NIAB_WW_SHW_NAM) consisting of 3241 genotypes derived from 54 nested back-cross 1 (BC1) populations, each formed via back-crossing a different primary SHW into the UK winter wheat cultivar 'Robigus'. The primary SHW lines were created using 15 T. durum donors and 47 Ae. tauschii accessions that spanned the lineages and geographical range of the species. Primary SHW parents were typically earlier flowering, taller and showed better resistance to yellow rust infection (Yr) than 'Robigus'. The NIAB_WW_SHW_NAM population was genotyped using a single nucleotide polymorphism (SNP) array and 27 quantitative trait loci (QTLs) were detected for flowering time, plant height and Yr resistance. Across multiple field trials, a QTL for Yr resistance was found on chromosome 4D that corresponded to the Yr28 resistance gene previously reported in other SHW lines. These results demonstrate the value of the NIAB_WW_SHW_NAM population for genetic mapping and provide the first evidence of Yr28 working in current UK environments and genetic backgrounds. These examples, coupled with the evidence of commercial wheat breeders selecting promising genotypes, highlight the potential value of the NIAB_WW_SHW_NAM to variety improvement.

The Dissection of Nitrogen Response Traits Using Drone Phenotyping and Dynamic Phenotypic Analysis to Explore N Responsiveness and Associated Genetic Loci in Wheat

Inefficient nitrogen (N) utilization in agricultural production has led to many negative impacts such as excessive use of N fertilizers, redundant plant growth, greenhouse gases, long-lasting toxicity in ecosystem, and even effect on human health, indicating the importance to optimize N applications in cropping systems. Here, we present a multiseasonal study that focused on measuring phenotypic changes in wheat plants when they were responding to different N treatments under field conditions. Powered by drone-based aerial phenotyping and the AirMeasurer platform, we first quantified 6 N response-related traits as targets using plot-based morphological, spectral, and textural signals collected from 54 winter wheat varieties. Then, we developed dynamic phenotypic analysis using curve fitting to establish profile curves of the traits during the season, which enabled us to compute static phenotypes at key growth stages and dynamic phenotypes (i.e., phenotypic changes) during N response. After that, we combine 12 yield production and N-utilization indices manually measured to produce N efficiency comprehensive scores (NECS), based on which we classified the varieties into 4 N responsiveness (i.e., N-dependent yield increase) groups. The NECS ranking facilitated us to establish a tailored machine learning model for N responsiveness-related varietal classification just using N-response phenotypes with high accuracies. Finally, we employed the Wheat55K SNP Array to map single-nucleotide polymorphisms using N response-related static and dynamic phenotypes, helping us explore genetic components underlying N responsiveness in wheat. In summary, we believe that our work demonstrates valuable advances in N response-related plant research, which could have major implications for improving N sustainability in wheat breeding and production.

A comparison of the efficacy of trastuzumab deruxtecan in advanced HER2-positive breast cancer: active brain metastasis versus progressive extracranial disease alone

BACKGROUND

Trastuzumab deruxtecan (T-DXd) has demonstrated efficacy in patients with brain metastasis (BM), a group historically with poor outcomes. The prevalence of BMs in patients commencing T-DXd is currently unknown. No direct comparisons have been made of the activity of T-DXd in patients with active BM versus those with extracranial progression alone. This real-world study explored the prevalence of BMs in patients commencing T-DXd, the efficacy of T-DXd in active BM versus extracranial progression alone and the safety of T-DXd.

PATIENTS AND METHODS

Patients with human epidermal growth factor receptor 2-positive advanced breast cancer treated with T-DXd between June 2021 and February 2023 at our specialist cancer hospital were identified and notes reviewed. Clinicopathological information, prior treatment, the presence or absence of central nervous system (CNS) disease, outcomes and treatment-emergent adverse events (TEAEs) were recorded.

RESULTS

Twenty-nine female patients, with a median age of 52 years (interquartile range 44-62 years), were identified; the prevalence of BM was 41%. Median number of lines of prior therapy was 2 (range 2-6). At a median follow-up of 13.8 months, median progression-free survival (PFS) for the overall population was 13.9 months [95% confidence interval (CI) 12.4 months-not estimable (NE)], 16.1 months (95% CI 15.1 months-NE) for active BMs and 12.4 months (95% CI 8.3 months-NE) for progressive extracranial disease alone. The 12-month overall survival (OS) rate was 74% (95% CI 59% to 95%) in the overall population, and 83% (95% CI 58% to 100%) and 66% (95% CI 45% to 96%) for active BMs and extracranial disease only, respectively. Most common TEAEs were fatigue, alopecia, and constipation. In nine patients (31%, including two deaths), pneumonitis occurred.

CONCLUSION

In this real-world population, we demonstrate T-DXd to be effective in patients with active BMs and those with progressive extracranial disease alone. PFS and OS were numerically longer in those with active BMs. These data demonstrate that patients with active BM treated with T-DXd have at least comparable outcomes to those with extracranial disease alone. The high rate of pneumonitis warrants further consideration.

Panicle-Cloud: An Open and AI-Powered Cloud Computing Platform for Quantifying Rice Panicles from Drone-Collected Imagery to Enable the Classification of Yield Production in Rice

Rice (Oryza sativa) is an essential stable food for many rice consumption nations in the world and, thus, the importance to improve its yield production under global climate changes. To evaluate different rice varieties' yield performance, key yield-related traits such as panicle number per unit area (PNpM2) are key indicators, which have attracted much attention by many plant research groups. Nevertheless, it is still challenging to conduct large-scale screening of rice panicles to quantify the PNpM2 trait due to complex field conditions, a large variation of rice cultivars, and their panicle morphological features. Here, we present Panicle-Cloud, an open and artificial intelligence (AI)-powered cloud computing platform that is capable of quantifying rice panicles from drone-collected imagery. To facilitate the development of AI-powered detection models, we first established an open diverse rice panicle detection dataset that was annotated by a group of rice specialists; then, we integrated several state-of-the-art deep learning models (including a preferred model called Panicle-AI) into the Panicle-Cloud platform, so that nonexpert users could select a pretrained model to detect rice panicles from their own aerial images. We trialed the AI models with images collected at different attitudes and growth stages, through which the right timing and preferred image resolutions for phenotyping rice panicles in the field were identified. Then, we applied the platform in a 2-season rice breeding trial to valid its biological relevance and classified yield production using the platform-derived PNpM2 trait from hundreds of rice varieties. Through correlation analysis between computational analysis and manual scoring, we found that the platform could quantify the PNpM2 trait reliably, based on which yield production was classified with high accuracy. Hence, we trust that our work demonstrates a valuable advance in phenotyping the PNpM2 trait in rice, which provides a useful toolkit to enable rice breeders to screen and select desired rice varieties under field conditions.

Characterization of 3D organotypic epithelial tissues reveals tonsil-specific differences in tonic interferon signaling

Three-dimensional (3D) culturing techniques can recapitulate the stratified nature of multicellular epithelial tissues. Organotypic 3D epithelial tissue culture methods have several applications, including the study of tissue development and function, drug discovery and toxicity testing, host-pathogen interactions, and the development of tissue-engineered constructs for use in regenerative medicine. We grew 3D organotypic epithelial tissues from foreskin, cervix, and tonsil-derived primary cells and characterized the transcriptome of these in vitro tissue equivalents. Using the same 3D culturing method, all three tissues yielded stratified squamous epithelium, validated histologically using basal and superficial epithelial cell markers. The goal of this study was to use RNA-seq to compare gene expression patterns in these three types of epithelial tissues to gain a better understanding of the molecular mechanisms underlying their function and identify potential therapeutic targets for various diseases. Functional profiling by over-representation and gene set enrichment analysis revealed tissue-specific differences: i.e., cutaneous homeostasis and lipid metabolism in foreskin, extracellular matrix remodeling in cervix, and baseline innate immune differences in tonsil. Specifically, tonsillar epithelia may play an active role in shaping the immune microenvironment of the tonsil balancing inflammation and immune responses in the face of constant exposure to microbial insults. Overall, these data serve as a resource, with gene sets made available for the research community to explore, and as a foundation for understanding the epithelial heterogeneity and how it may impact their in vitro use. An online resource is available to investigate these data (https://viz.datascience.arizona.edu/3DEpiEx/).

Predicting Dental Caries in Young Children in Primary Health Care Settings

Young children need increased access to dental prevention and care. Targeting high caries risk children first helps meet this need. The objective of this study was to develop a parent-completed, easy-to-score, short, accurate caries risk tool for screening in primary health care settings to identify children at increased risk for cavities. A longitudinal, prospective, multisite, cohort study enrolled (primarily through primary health care settings) and followed 985 (out of 1,326) 1-y-old children and their primary caregivers (PCGs) until age 4. The PCG completed a 52-item self-administered questionnaire, and children were examined using the International Caries Detection and Assessment Criteria (ICDAS) at 12 ± 3 mo (baseline), 30 ± 3 mo (80% retention), and 48 ± 3 mo of age (74% retention). Cavitated caries lesion (dmfs = decayed, missing, and filled surfaces; d = ICDAS ≥3) experience at 4 y of age was assessed and tested for associations with questionnaire items using generalized estimating equation models applied to logistic regression. Multivariable analysis used backward model selection, with a limit of 10 items. At age 4, 24% of children had cavitated-level caries experience; 49% were female; 14% were Hispanic, 41% were White, 33% were Black, 2% were other, and 10% were multiracial; 58% enrolled in Medicaid; and 95% lived in urban communities. The age 4 multivariable prediction model, using age 1 responses (area under the receiver operating characteristic curve = 0.73), included the following significant (P < 0.001) variables (odds ratios): child participating in public assistance programs such as Medicaid (1.74), being non-White (1.80-1.96), born premature (1.48), not born by caesarean section (1.28), snacking on sugary snacks (3 or more/d, 2.22; 1-2/d or weekly, 1.55), PCG cleaning the pacifier with juice/soda/honey or sweet drink (2.17), PCG daily sharing/tasting food with child using same spoon/fork/glass (1.32), PCG brushing their teeth less than daily (2.72), PCG's gums bleeding daily when brushing or PCG having no teeth (1.83-2.00), and PCG having cavities/fillings/extractions in past 2 y (1.55). A 10-item caries risk tool at age 1 shows good agreement with cavitated-level caries experience by age 4.

CropQuant-Air: an AI-powered system to enable phenotypic analysis of yield- and performance-related traits using wheat canopy imagery collected by low-cost drones

As one of the most consumed stable foods around the world, wheat plays a crucial role in ensuring global food security. The ability to quantify key yield components under complex field conditions can help breeders and researchers assess wheat's yield performance effectively. Nevertheless, it is still challenging to conduct large-scale phenotyping to analyse canopy-level wheat spikes and relevant performance traits, in the field and in an automated manner. Here, we present CropQuant-Air, an AI-powered software system that combines state-of-the-art deep learning (DL) models and image processing algorithms to enable the detection of wheat spikes and phenotypic analysis using wheat canopy images acquired by low-cost drones. The system includes the YOLACT-Plot model for plot segmentation, an optimised YOLOv7 model for quantifying the spike number per m² (SNpM²) trait, and performance-related trait analysis using spectral and texture features at the canopy level. Besides using our labelled dataset for model training, we also employed the Global Wheat Head Detection dataset to incorporate varietal features into the DL models, facilitating us to perform reliable yield-based analysis from hundreds of varieties selected from main wheat production regions in China. Finally, we employed the SNpM² and performance traits to develop a yield classification model using the Extreme Gradient Boosting (XGBoost) ensemble and obtained significant positive correlations between the computational analysis results and manual scoring, indicating the reliability of CropQuant-Air. To ensure that our work could reach wider researchers, we created a graphical user interface for CropQuant-Air, so that non-expert users could readily use our work. We believe that our work represents valuable advances in yield-based field phenotyping and phenotypic analysis, providing useful and reliable toolkits to enable breeders, researchers, growers, and farmers to assess crop-yield performance in a cost-effective approach.

Evaluation of in Vitro Rat and Human Airway Epithelial Models for Acute Inhalation Toxicity Testing

In vivo models (mostly rodents) are currently accepted by regulatory authorities for assessing acute inhalation toxicity. Considerable efforts have been made in recent years to evaluate in vitro human airway epithelial models (HAEM) as replacements for in vivo testing. In the current work, an organotypic in vitro rat airway epithelial model (RAEM), rat EpiAirway™, was developed and characterized to allow a direct comparison with the available HAEM, human EpiAirway™, in order to address potential interspecies variability in responses to harmful agents. The rat and human models were evaluated in two independent laboratories with 14 reference chemicals, selected to cover a broad range of chemical structures and reactive groups, as well as known acute animal and human toxicity responses, in three replicate rounds of experiments. Toxicity endpoints included changes in tissue viability (MTT assay), epithelial barrier integrity (TEER, transepithelial electrical resistance), and tissue morphology (histopathology). The newly developed rat EpiAirway™ model produced reproducible results across all replicate experiments in both testing laboratories. Furthermore, a high level of concordance was observed between the RAEM and HAEM toxicity responses (determined by IC25) in both laboratories, with R2 = 0.78 and 0.88 when analyzed by TEER; and R2 = 0.92 for both when analyzed by MTT. These results indicate that rat and human airway epithelial tissues respond similarly to acute exposures to chemicals. The new in vitro RAEM will help extrapolate to in vivo rat toxicity responses and support screening as part of a 3Rs program.

Phenomic and genomic prediction of yield on multiple locations in winter wheat

Genomic selection has recently become an established part of breeding strategies in cereals. However, a limitation of linear genomic prediction models for complex traits such as yield is that these are unable to accommodate Genotype by Environment effects, which are commonly observed over trials on multiple locations. In this study, we investigated how this environmental variation can be captured by the collection of a large number of phenomic markers using high-throughput field phenotyping and whether it can increase GS prediction accuracy. For this purpose, 44 winter wheat (Triticum aestivum L.) elite populations, comprising 2,994 lines, were grown on two sites over 2 years, to approximate the size of trials in a practical breeding programme. At various growth stages, remote sensing data from multi- and hyperspectral cameras, as well as traditional ground-based visual crop assessment scores, were collected with approximately 100 different data variables collected per plot. The predictive power for grain yield was tested for the various data types, with or without genome-wide marker data sets. Models using phenomic traits alone had a greater predictive value (R² = 0.39-0.47) than genomic data (approximately R² = 0.1). The average improvement in predictive power by combining trait and marker data was 6%-12% over the best phenomic-only model, and performed best when data from one full location was used to predict the yield on an entire second location. The results suggest that genetic gain in breeding programmes can be increased by utilisation of large numbers of phenotypic variables using remote sensing in field trials, although at what stage of the breeding cycle phenomic selection could be most profitably applied remains to be answered.

Microbial Indicators of Dental Health, Dysbiosis, and Early Childhood Caries

Dental caries lesions are a clinical manifestation of disease, preceded by microbial dysbiosis, which is poorly characterized and thought to be associated with saccharolytic taxa. Here, we assessed the associations between the oral microbiome of children and various caries risk factors such as demographics and behavioral and clinical data across early childhood and characterized over time the salivary and dental plaque microbiome of children before clinical diagnosis of caries lesions. Children (N = 266) were examined clinically at ~1, 2.5, 4, and 6.5 y of age. The microbiome samples were collected at 1, 2.5, and 4 y. Caries groups consisted of children who remained caries free (International Caries Detection and Assessment System [ICDAS] = 0) at all time points (CFAT) (n = 50); children diagnosed with caries (ICDAS ≥ 1) at 6.5 y (C6.5), 4 y (C4), or 2.5 y of age (C2.5); and children with early caries or advanced caries lesions at specific time points. Microbial community analyses were performed on zero-radius operational taxonomic units (zOTUs) obtained from V4 of 16S ribosomal RNA gene amplicon sequences. The oral microbiome of the children was affected by various factors, including antibiotic use, demographics, and dietary habits of the children and their caregivers. At all time points, various risk factors explained more of the variation in the dental plaque microbiome than in saliva. At 1 y, composition of saliva of the C4 group differed from that of the CFAT group, while at 2.5 y, this difference was observed only in plaque. At 4 y, multiple salivary and plaque zOTUs of genera Prevotella and Leptotrichia were significantly higher in samples of the C6.5 group than those of the CFAT group. In conclusion, up to 3 y prior to clinical caries detection, the oral microbial communities were already in a state of dysbiosis that was dominated by proteolytic taxa. Plaque discriminated dysbiotic oral ecosystems from healthy ones better than saliva.

Single cell transcriptomic analysis of HPV16-infected epithelium identifies a keratinocyte subpopulation implicated in cancer

Persistent HPV16 infection is a major cause of the global cancer burden. The viral life cycle is dependent on the differentiation program of stratified squamous epithelium, but the landscape of keratinocyte subpopulations which support distinct phases of the viral life cycle has yet to be elucidated. Here, single cell RNA sequencing of HPV16 infected compared to uninfected organoids identifies twelve distinct keratinocyte populations, with a subset mapped to reconstruct their respective 3D geography in stratified squamous epithelium. Instead of conventional terminally differentiated cells, an HPV-reprogrammed keratinocyte subpopulation (HIDDEN cells) forms the surface compartment and requires overexpression of the ELF3/ESE-1 transcription factor. HIDDEN cells are detected throughout stages of human carcinogenesis including primary human cervical intraepithelial neoplasias and HPV positive head and neck cancers, and a possible role in promoting viral carcinogenesis is supported by TCGA analyses. Single cell transcriptome information on HPV-infected versus uninfected epithelium will enable broader studies of the role of individual keratinocyte subpopulations in tumor virus infection and cancer evolution.

Characterization of 3D organotypic epithelial tissues reveals tonsil-specific differences in tonic interferon signaling

Three-dimensional (3D) culturing techniques can recapitulate the stratified nature of multicellular epithelial tissues. Organotypic 3D epithelial tissue culture methods have several applications, including the study of tissue development and function, drug discovery and toxicity testing, host-pathogen interactions, and the development of tissue-engineered constructs for use in regenerative medicine. We grew 3D organotypic epithelial tissues from foreskin, cervix, and tonsil-derived primary cells and characterized the transcriptome of these in vitro tissue equivalents. Using the same 3D culturing method, all three tissues yielded stratified squamous epithelium, validated histologically using basal and superficial epithelial cell markers. The goal of this study was to use RNA-seq to compare gene expression patterns in these three types of epithelial tissues to gain a better understanding of the molecular mechanisms underlying their function and identify potential therapeutic targets for various diseases. Functional profiling by over-representation and gene set enrichment analysis revealed tissue-specific differences: i.e. , cutaneous homeostasis and lipid metabolism in foreskin, extracellular matrix remodeling in cervix, and baseline innate immune differences in tonsil. Specifically, tonsillar epithelia may play an active role in shaping the immune microenvironment of the tonsil balancing inflammation and immune responses in the face of constant exposure to microbial insults. Overall, these data serve as a resource, with gene sets made available for the research community to explore, and as a foundation for understanding the epithelial heterogeneity and how it may impact their in vitro use. An online resource is available to investigate these data ( https://viz.datascience.arizona.edu/3DEpiEx/ ).

Evaluation of hypoparathyroidism following laryngectomy

BACKGROUND

Hypoparathyroidism is a recognised complication following laryngectomy; it is associated with significant short-and long-term morbidity. This study aimed to further characterise this condition, identify risk factors and describe preventative and management strategies in a large cohort.

MATERIALS AND METHODS

This was a retrospective study at a tertiary referral centre for head and neck cancers. All consecutive patients who had total laryngectomy over an eight-year period were included.

RESULTS

A total of 140 patients were included. Rates of transient and long-term hypoparathyroidism were 14.3% and 10.1%, respectively. The following factors were significantly associated with transient post-surgical hypocalcaemia or hypoparathyroidism: total thyroidectomy (relative risk, RR, 4.33; 95% confidence interval, CI, 1.86-10.10), oesophagectomy (RR 6.05; 95% CI 2.92-12.53) and female sex (RR 3.23; 95% CI 1.45-7.19). In addition, total thyroidectomy (RR 5.89; 95% CI 1.94-17.86), central neck dissection (RR 3.97; 95% CI 1.42-11.10), oesophagectomy (RR 9.38; 95% CI 4.13-21.3), pharyngectomy (RR 7.14; 95% CI 2.08-24.39) and female sex (RR 5.52; 95% CI 1.95-15.63) were risk factors for long-term hypoparathyroidism. There was variability in the use of preventative measures, monitoring and management of hypocalcaemia and hypoparathyroidism following total laryngectomy.

CONCLUSIONS

Transient hypocalcaemia and long-term hypoparathyroidism occur in a significant proportion of patients after laryngectomy. A standard protocol is required to improve care.

1674 The KnifeSavers bleeding control campaign: an evaluation of the public education programme

Aims, Objectives and Background

Penetrating trauma remains a leading cause of mortality in the United Kingdom with major haemorrhage a potentially preventable cause of death.

KnifeSavers, a not-for-profit healthcare professional led organisation based at a regional major trauma centre, launched in 2019 to educate and empower the public how to manage a bleeding wound. There are three pillars of the campaign; an education programme, distribution of bleeding control packs and a public awareness campaign all focused on stopping major bleeding at scene.

The aim of this review is to evaluate the response to the education programme and improvement in confidence and ability of the attendees to control major bleeding.

Method and Design

Adult public members attending KnifeSavers education sessions between July 2021 and March 2022 were recruited to partake in pre and post event surveys.

Utilising a 5-point Likert scale participants willingness and preparedness to manage bleeding knife related wounds were assessed.

The data was comparatively measured, without accounting for attrition, to evaluate a change in response.

Abstract 1674 Figure 1

Comparison of pre and post survey 5-point Likert scale data

Results and Conclusion

There were 137 responses to the pre survey and 74% retention rate for the post session survey (n=101).

Despite a consistently high willingness in participants to intervene (93% pre session and 96% post), only 28% felt prepared to manage a bleeding wound prior to the education session, and 27% felt prepared to use a bleeding control kit.

Following the session an increase to 98% of participants were prepared to deal with a bleeding wound, and 96% prepared use a bleeding control kit.

Of note 97% of attendees stated it was important that training was delivered by health care professionals.

This data suggests that the KnifeSavers education programme is an effective strategy in increasing public preparedness to manage life-threatening bleeding wounds and supports further expansion of the programme.

A further mixed methods qualitative assessment including paired t-test statistical analysis is underway.

Interstitial Duplication on Chromosome 3p14.3p13 in an Adolescent with Dysmorphic Features and Autism, Case Report

Introduction/Objective

The genetic etiology of autism spectrum disorders is only partially understood. Here we describe a 16-year-old male diagnosed with autism at two years of age. He has dysmorphic features, severe cognitive disability, and history of cryptorchidism. A review of systems was significant for slightly coarse features overall, with deep-set eyes, pinched nasal bridge with wide nasal tip, and widely spaced teeth. A large pectus excavatum deformity was also noted. Although the parent’s genetic testing concluded that this likely represents de novo mutation, it is worth mentioning that our patient has a 13-year-old female maternal first cousin with learning difficulties that were said to be less severe. There is no other family history of autism.

Methods/Case Report

Chromosome analysis showed an abnormal karyotype identifying a duplication of the short arm of chromosome 3 from p13 to p14.3, 46,XY,dup(3)(p13p14.3). Additional microarray testing confirmed this duplication and defined the size as 14.9 Mb. Regions of homozygosity of 29.8 Mb were also identified, representing about 1% of the autosomal genome. The duplicated area includes over 70 genes, thirteen of which are known Mendelian disease genes (IL17RD, HESX1, APPL1, FLNB, DNASEIL3, PDHB, ACOX2, ATXN7, SLC25A26, EOGT, LMOD3, MITF, and FOXP1). Duplications of 3p are extremely rare and can be de novo or inherited from a parent with a balanced translocation. Individuals with these better-described chromosome 3p duplications typically present with intellectual and developmental disabilities, such as autism, as 3p duplications typically present with intellectual and developmental disabilities, such as autism and distinctive dysmorphic features. This duplication has never been reported as a known syndrome and has minimal overlap with copy number variants (CNVs) among healthy individuals.

Results (if a Case Study enter NA)

NA

Conclusion

Autism spectrum disorders are largely characterized by speech, communication, and social impairment of varying degrees. Diagnosis is typically made on clinical grounds, but in 14-35% of cases, a genetic basis for the disorder, typically either due to a single gene disorder or a chromosomal deletion/duplication, may be found. This case report describes a rare finding of a 14.9 Mb interstitial duplication on chromosome 3p.

Specialist multidisciplinary input maximises rare disease diagnoses from whole genome sequencing

Diagnostic whole genome sequencing (WGS) is increasingly used in rare diseases. However, standard, semi-automated WGS analysis may overlook diagnoses in complex disorders. Here, we show that specialist multidisciplinary analysis of WGS, following an initial 'no primary findings' (NPF) report, improves diagnostic rates and alters management. We undertook WGS in 102 adults with diagnostically challenging primary mitochondrial disease phenotypes. NPF cases were reviewed by a genomic medicine team, thus enabling bespoke informatic approaches, co-ordinated phenotypic validation, and functional work. We enhanced the diagnostic rate from 16.7% to 31.4%, with management implications for all new diagnoses, and detected strong candidate disease-causing variants in a further 3.9% of patients. This approach presents a standardised model of care that supports mainstream clinicians and enhances diagnostic equity for complex disorders, thereby facilitating access to the potential benefits of genomic healthcare. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project: http://www.genomicsengland.co.uk .

AirMeasurer: open-source software to quantify static and dynamic traits derived from multiseason aerial phenotyping to empower genetic mapping studies in rice

Low-altitude aerial imaging, an approach that can collect large-scale plant imagery, has grown in popularity recently. Amongst many phenotyping approaches, unmanned aerial vehicles (UAVs) possess unique advantages as a consequence of their mobility, flexibility and affordability. Nevertheless, how to extract biologically relevant information effectively has remained challenging. Here, we present AirMeasurer, an open-source and expandable platform that combines automated image analysis, machine learning and original algorithms to perform trait analysis using 2D/3D aerial imagery acquired by low-cost UAVs in rice (Oryza sativa) trials. We applied the platform to study hundreds of rice landraces and recombinant inbred lines at two sites, from 2019 to 2021. A range of static and dynamic traits were quantified, including crop height, canopy coverage, vegetative indices and their growth rates. After verifying the reliability of AirMeasurer-derived traits, we identified genetic variants associated with selected growth-related traits using genome-wide association study and quantitative trait loci mapping. We found that the AirMeasurer-derived traits had led to reliable loci, some matched with published work, and others helped us to explore new candidate genes. Hence, we believe that our work demonstrates valuable advances in aerial phenotyping and automated 2D/3D trait analysis, providing high-quality phenotypic information to empower genetic mapping for crop improvement.

Genome sequencing reveals underdiagnosis of primary ciliary dyskinesia in bronchiectasis

BACKGROUND

Bronchiectasis can result from infectious, genetic, immunological and allergic causes. 60-80% of cases are idiopathic, but a well-recognised genetic cause is the motile ciliopathy, primary ciliary dyskinesia (PCD). Diagnosis of PCD has management implications including addressing comorbidities, implementing genetic and fertility counselling and future access to PCD-specific treatments. Diagnostic testing can be complex; however, PCD genetic testing is moving rapidly from research into clinical diagnostics and would confirm the cause of bronchiectasis.

METHODS

This observational study used genetic data from severe bronchiectasis patients recruited to the UK 100,000 Genomes Project and patients referred for gene panel testing within a tertiary respiratory hospital. Patients referred for genetic testing due to clinical suspicion of PCD were excluded from both analyses. Data were accessed from the British Thoracic Society audit, to investigate whether motile ciliopathies are underdiagnosed in people with bronchiectasis in the UK.

RESULTS

Pathogenic or likely pathogenic variants were identified in motile ciliopathy genes in 17 (12%) out of 142 individuals by whole-genome sequencing. Similarly, in a single centre with access to pathological diagnostic facilities, 5-10% of patients received a PCD diagnosis by gene panel, often linked to normal/inconclusive nasal nitric oxide and cilia functional test results. In 4898 audited patients with bronchiectasis, <2% were tested for PCD and <1% received genetic testing.

CONCLUSIONS

PCD is underdiagnosed as a cause of bronchiectasis. Increased uptake of genetic testing may help to identify bronchiectasis due to motile ciliopathies and ensure appropriate management.

Characterization of changes in the tyrosine pathway by 24-h profiling during nitisinone treatment in alkaptonuria

Background

Although changes in the tyrosine pathway during nitisinone therapy are known, a complete characterization of the induced tyrosinaemia is lacking to improve disease management.

Patients and methods

Our research aims were addressed by 24-h blood sampling. 40 patients with alkaptonuria (AKU), treated with 0, 1, 2, 4 and 8 mg nitisinone daily (n = 8), were studied over four weeks. Serum homogentisic acid (sHGA), tyrosine (sTYR), phenylalanine (sPHE), hydroxyphenylpyruvate (sHPPA), hydroxyphenyllactate (sHPLA) and nitisinone (sNIT) were measured at baseline and after four weeks.

Results

sNIT showed a clear dose-proportional response. sTYR increased markedly but with less clear-cut dose responses after nitisinone. Fasting and average 24-h (C_av) sTYR responses were similar. Individual patient sTYR 24-h profiles showed significant fluctuations during nitisinone therapy. At week 4, sTYR, sHPPA and sHPPL all showed dose-related increases compared to V0, with the greatest difference between 1 and 8 mg nitisinone seen for HPLA, while there was no change from V0 in sPHE. sHGA decreased to values around the lower limit of quantitation.

Discussion

There was sustained tyrosinaemia after four weeks of nitisinone therapy with significant fluctuations over the day in individual patients. Diet and degree of conversion of HPPA to HPLA may determine extent of nitisinone-induced tyrosinaemia.

Conclusion

A fasting blood sample is recommended to monitor sTYR during nitisinone therapy Adaptations in HPPA metabolites as well as the inhibition of tyrosine aminotransferase could be contributing factors generating tyrosinaemia during nitisinone therapy.

•

The tyrosine catabolic pathway is the sole route of disposal of excess dietary phenylalanine and tyrosine

•

Individual patient serum tyrosine 24-h profiles show significant fluctuations especially during nitisinone therapy

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A fasting serum tyrosine measurement is the preferred choice for monitoring tyrosineamia during nitisinone therapy

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Meals are key determinants of tyrosinaemia during nitisinone

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Adaptations in hydroxyphenylpyruvate, hydroxyphenyllactate and tyrosine during nitisinone could determine the extent of tyrosinaemia

Prevalence and Disease Spectrum of Extracoronary Arterial Abnormalities in Spontaneous Coronary Artery Dissection

Question

What is the prevalence of fibromuscular dysplasia, aneurysms, dissection, and tortuosity in extracoronary arteries of patients who developed a spontaneous coronary artery dissection (SCAD)?

Findings

In this case series including 173 patients with SCAD, using magnetic resonance angiography with blinded interpretation of the findings, 32% of the patients had fibromuscular dysplasia, 8% had aneurysms, and 2% had dissections; the prevalence of arterial tortuosity was similar in cases and controls. Extracoronary vascular events over a median 5-year follow-up were rare.

Meaning

The findings of this blinded analysis suggest that, in patients with SCAD, severe multivessel fibromuscular dysplasia, aneurysms, and dissections are infrequent and seldom associated with clinically evident vascular events.

Importance

Spontaneous coronary artery dissection (SCAD) has been associated with fibromuscular dysplasia (FMD) and other extracoronary arterial abnormalities. However, the prevalence, severity, and clinical relevance of these abnormalities remain unclear.

Objective

To assess the prevalence and spectrum of FMD and other extracoronary arterial abnormalities in patients with SCAD vs controls.

Design, Setting, and Participants

This case series included 173 patients with angiographically confirmed SCAD enrolled between January 1, 2015, and December 31, 2019. Imaging of extracoronary arterial beds was performed by magnetic resonance angiography (MRA). Forty-one healthy individuals were recruited to serve as controls for blinded interpretation of MRA findings. Patients were recruited from the UK national SCAD registry, which enrolls throughout the UK by referral from the primary care physician or patient self-referral through an online portal. Participants attended the national SCAD referral center for assessment and MRA.

Exposures

Both patients with SCAD and healthy controls underwent head-to-pelvis MRA (median time between SCAD event and MRA, 1 [IQR, 1-3] year).

Main Outcome and Measures

The diagnosis of FMD, arterial dissections, and aneurysms was established according to the International FMD Consensus. Arterial tortuosity was assessed both qualitatively (presence or absence of an S curve) and quantitatively (number of curves ≥45%; tortuosity index).

Results

Of the 173 patients with SCAD, 167 were women (96.5%); mean (SD) age at diagnosis was 44.5 (7.9) years. The prevalence of FMD was 31.8% (55 patients); 16 patients (29.1% of patients with FMD) had involvement of multiple vascular beds. Thirteen patients (7.5%) had extracoronary aneurysms and 3 patients (1.7%) had dissections. The prevalence and degree of arterial tortuosity were similar in patients and controls. In 43 patients imaged with both computed tomographic angiography and MRA, the identification of clinically significant remote arteriopathies was similar. Over a median 5-year follow-up, there were 2 noncardiovascular-associated deaths and 35 recurrent myocardial infarctions, but there were no primary extracoronary vascular events.

Conclusions and Relevance

In this case series with blinded analysis of patients with SCAD, severe multivessel FMD, aneurysms, and dissections were infrequent. The findings of this study suggest that, although brain-to-pelvis imaging allows detection of remote arteriopathies that may require follow-up, extracoronary vascular events appear to be rare.

Blood phenylalanine reduction reverses gene expression changes observed in a mouse model of phenylketonuria

Phenylketonuria (PKU) is a genetic deficiency of phenylalanine hydroxylase (PAH) in liver resulting in blood phenylalanine (Phe) elevation and neurotoxicity. A pegylated phenylalanine ammonia lyase (PEG-PAL) metabolizing Phe into cinnamic acid was recently approved as treatment for PKU patients. A potentially one-time rAAV-based delivery of PAH gene into liver to convert Phe into tyrosine (Tyr), a normal way of Phe metabolism, has now also entered the clinic. To understand differences between these two Phe lowering strategies, we evaluated PAH and PAL expression in livers of PAHenu2 mice on brain and liver functions. Both lowered brain Phe and increased neurotransmitter levels and corrected animal behavior. However, PAL delivery required dose optimization, did not elevate brain Tyr levels and resulted in an immune response. The effect of hyperphenylalanemia on liver functions in PKU mice was assessed by transcriptome and proteomic analyses. We observed an elevation in Cyp4a10/14 proteins involved in lipid metabolism and upregulation of genes involved in cholesterol biosynthesis. Majority of the gene expression changes were corrected by PAH and PAL delivery though the role of these changes in PKU pathology is currently unclear. Taken together, here we show that blood Phe lowering strategy using PAH or PAL corrects both brain pathology as well as previously unknown lipid metabolism associated pathway changes in liver.

Rectal cancer management during the COVID-19 pandemic (ReCaP): multicentre prospective observational study

Concerns over unacceptable high mortality in patients with rectal cancer undergoing surgery or systemic therapy who contract COVID-19 have led to widespread adoption of alternative treatment strategies.The ReCaP study aimed to study these variations and associated outcomes.

Ethnic variation in implantable cardioverter defibrillator implant trends in New Zealand 2005–2019

Background

Implantable cardioverter defibrillator (ICD) implant rates in New Zealand (NZ) have increased significantly in recent years. Previous studies in NZ have demonstrated that Māori and Pacific patients had higher rates of ischaemic heart disease compared to other ethnicities. Ethnic variation in ICD implant rates have been reported internationally, but whether this trend exists in NZ is unclear.

Purpose

This paper aims to provide the first analysis of new ICD implants by ethnicity over an extended time period.

Methods

All patients who received a new ICD implant were identified for the period of 1st January 2005 to 31st December 2019 using the National Minimum Datasets, which collects information on all public hospital admissions in NZ. Ethnicity prioritisation was performed in the following order: Māori, Pacific, Asian and European. New ICD implant rates were analysed by ethnicity and age-groups.

Results

A total of 5,514 new ICDs were implanted over the study period. New ICD implant rates increased by 137%, from 41.4/million in 2005 to 98.2/million in 2019, at an average of 5.4%/year (p&lt;0.01). Over the study period, the highest age-standardised implant rates were in Māori, followed by Pacific, European and Asian ethnicities. The largest increase was seen in Pacific patients at 8.9%/year (p&lt;0.01), followed by Māori and Asian patients at 4.7%/year (p&lt;0.01) and 4.3%/year (p&lt;0.01), respectively. In European patients, ICD implant rates initially increased by 10.3%/year (p&lt;0.01) between 2005 to 2012, but subsequently plateaued at −0.4%/year (p=0.71) between 2012 to 2019. By 2019, the age-standardised implant rates in Māori, Pacific and European patients were 3 to 4 times higher than Asian patients (Figure 1).

In the age groups of &lt;39, 40–59, 60–69 and 70–79 years, Māori and Pacific patients had higher implant rates through most of the study period. Asian patients consistently had the lowest new ICD implant rates across all age groups. The substantially higher age-specific implant rates in the age groups of 40–59 years and 60–69 years in Māori and Pacific patients resulted in higher overall age-standardised implant rates as compared to Asian and European ethnicities.

Conclusion

There is marked ethnic variation in ICD implant rates in NZ. Implant rates have increased in ethnic minorities but have plateaued in European patients in the past 7 years. The continued difference in implant rates across ethnicities warrants further investigation.

Funding Acknowledgement

Type of funding sources: None.

Activity of the growth hormone-releasing hormone antagonist MIA602 and its underlying mechanisms of action in sarcoidosis-like granuloma

Objectives

Growth hormone-releasing hormone (GHRH) is a potent stimulator of growth hormone (GH) secretion from the pituitary gland. Although GHRH is essential for the growth of immune cells, the regulatory effects of its antagonist in granulomatous disease remain unknown.

Methods

Here, we report expression of GHRH receptor (R) in human tissue with sarcoidosis granuloma and demonstrate the anti-inflammatory effects of MIA602 (a GHRH antagonist) in two in vitro human granuloma models and an in vivo granuloma model using different methods including ELISA, immunohistochemistry, RNA-seq analysis and flow cytometry.

Results

MIA602 decreases the levels of IL-2, IL-2R, IL-7, IL-12, IL-17A and TNF-α in an in vitro granuloma model. Further, we show that the anti-inflammatory effect of MIA602 appears to be mediated by a reduction in CD45⁺CD68⁺ cells in granulomatous tissue and upregulation in PD-1 expression in macrophages. Analysis of the expression of proteins involved in the mitochondrial stage of apoptosis showed that MIA602 increases the levels of caspase-3, BCL-xL/BAK dimer and MCl-1/Bak dimer in the granuloma. These findings indicate that MIA602 may not induce apoptosis.

Conclusions

Our findings further suggest that GHRH-R is potentially a clinical target for the treatment of granulomatous disease and that MIA602 may be used as a novel therapeutic agent for sarcoidosis.

COVID-19 Impact on Acute Ischemic Stroke Treatment at 9 Comprehensive Stroke Centers across Los Angeles

Objective

To describe the impact of COVID-19 on acute cerebrovascular disease care across 9 comprehensive stroke centers throughout Los Angeles County (LAC).

Methods

Volume of emergency stroke code activations, patient characteristics, stroke severity, reperfusion rates, treatment times, and outcomes from February 1 to April 30, 2020, were compared against the same time period in 2019. Demographic data were provided by each participating institution.

Results

There was a 17.3% decrease in stroke code activations across LAC in 2020 compared to 2019 (1,786 vs. 2,159, respectively, χ² goodness of fit test p < 0.0001) across 9 participating comprehensive stroke centers. Patients who did not receive any reperfusion therapy decreased by 16.6% in 2020 (1,527) compared to 2019 (1,832). Patients who received only intravenous thrombolytic (IVT) therapy decreased by 31.8% (107 vs. 157). Patients who received only mechanical thrombectomy (MT) increased by 3% (102 vs. 99). Patients who received both IVT and MT decreased by 31.8% (45 vs. 66). Recanalization treatment times in 2020 were comparable to 2019. CSCs serving a higher proportion of Latinx populations in the eastern parts of LAC experienced a higher incidence of MT in 2020 compared to 2019. Mild increase in stroke severity was seen in 2020 compared to 2019 (8.95 vs. 8.23, p = 0.046). A higher percentage of patients were discharged home in 2020 compared to 2019 (59.5 vs. 56.1%, p = 0.034), a lower percentage of patients were discharged to skilled nursing facility (16.1 vs. 20.7%, p = 0.0004), and a higher percentage of patients expired (8.6 vs. 6.3%, p = 0.008).

Conclusion

LAC saw a decrease in overall stroke code activations in 2020 compared to 2019. Reperfusion treatment times remained comparable to prepandemic metrics. There has been an increase in severe stroke incidence and higher volume of thrombectomy treatments in Latinx communities within LAC during the pandemic of 2020. More patients were discharged home, less patients discharged to skilled nursing facilities, and more patients expired in 2020, compared to the same time frame in 2019.

Risks and benefits of percutaneous coronary intervention in spontaneous coronary artery dissection

OBJECTIVE

To investigate percutaneous coronary intervention (PCI) practice in an international cohort of patients with spontaneous coronary artery dissection (SCAD). To explore factors associated with complications and study angiographic and longer term outcomes.

METHODS

SCAD patients (n=215, 94% female) who underwent PCI from three national cohort studies were investigated and compared with a matched cohort of conservatively managed SCAD patients (n=221).

RESULTS

SCAD-PCI patients were high risk at presentation with only 8.8% undergoing PCI outside the context of ST-elevation myocardial infarction/cardiac arrest, thrombolysis in myocardial infarction (TIMI) 0/1 flow or proximal dissections. PCI complications occurred in 38.6% (83/215), with 13.0% (28/215) serious complications. PCI-related complications were associated with more extensive dissections (multiple vs single American Heart Association coronary segments, OR 1.9 (95% CI: 1.06-3.39),p=0.030), more proximal dissections (proximal diameter per mm, OR 2.25 (1.38-3.67), p=0.001) and dissections with no contrast penetration of the false lumen (Yip-Saw 2 versus 1, OR 2.89 (1.12-7.43), p=0.028). SCAD-PCI involved long lengths of stent (median 46mm, IQR: 29-61mm). Despite these risks, SCAD-PCI led to angiographic improvements in those with reduced TIMI flow in 84.3% (118/140). Worsening TIMI flow was only seen in 7.0% (15/215) of SCAD-PCI patients. Post-PCI major adverse cardiovascular and cerebrovascular events (MACCE) and left ventricular function outcomes were favourable.

CONCLUSION

While a conservative approach to revascularisation is favoured, SCAD cases with higher risk presentations may require PCI. SCAD-PCI is associated with longer stent lengths and a higher risk of complications but leads to overall improvements in coronary flow and good medium-term outcomes in patients.

Ten-Year Outcomes of 1- and 2-Level Cervical Disc Arthroplasty From the Mobi-C Investigational Device Exemption Clinical Trial

BACKGROUND

Short- and mid-term studies have shown the effectiveness of cervical disc arthroplasty (CDA) to treat cervical disc degeneration.

OBJECTIVE

To report the 10-yr outcomes of a multicenter experience with cervical arthroplasty for 1- and 2-level pathology.

METHODS

This was a prospective study of patients treated with CDA at 1 or 2 contiguous levels using the Mobi-C® Cervical Disc (Zimmer Biomet). Following completion of the 7-yr Food and Drug Administration postapproval study, follow-up continued to 10 yr for consenting patients at 9 high-enrolling centers. Clinical and radiographic endpoints were collected out to 10 yr.

RESULTS

At 10 yr, patients continued to have significant improvement over baseline Neck Disability Index (NDI), neck and arm pain, neurologic function, and segmental range of motion (ROM). NDI and pain outcomes at 10 yr were significantly improved from 7 yr. Segmental and global ROM and sagittal alignment also were maintained from 7 to 10 yr. Clinically relevant adjacent segment pathology was not significantly different between 7 and 10 yr. The incidence of motion restricting heterotopic ossification at 10 yr was not significantly different from 7 yr for 1-level (30.7% vs 29.6%) or 2-level (41.7% vs 39.2%) patients. Only 2 subsequent surgeries were reported after 7 yr.

CONCLUSION

Our results through 10 yr were comparable to 7-yr outcomes, demonstrating that CDA with Mobi-C continues to be a safe and effective surgical treatment for patients with 1- or 2-level cervical degenerative disc disease.

In vitro elution characteristics of gentamicin- and teicoplanin-loaded CMW1 and Palacos R bone cement

Purpose

To compare the in vitro elution characteristics of CMW1 and Palacos R bone cement loaded with gentamicin, teicoplanin, or in combination.

Methods

Four bone cement discs were prepared for each cement type. Disc 1 contained no antibiotics; disc 2 contained 0.5 g gentamicin; disc 3 contained 2 g teicoplanin; disc 4 contained 0.5 g gentamicin and 2 g teicoplanin. Elution studies were conducted using a fluorescence polarisation immunoassay technique and performed at intervals of 6 weeks.

Results

For CMW1, gentamicin and teicoplanin elution levels in combination discs were higher than those in the single antibiotic discs (p < 0.001 & p < 0.06). For Palacos R, gentamicin elution levels in combination discs were higher than those in the single antibiotic discs (p < 0.001), but teicoplanin elution levels in combination discs were lesser than that from the single antibiotic discs (p < 0.02). In single and combination discs, gentamicin elution levels in Palacos R were higher than those in CMW1 (p < 0.001 & p < 0.001). Palacos R eluted more teicoplanin than CMW1, except in combined disc with gentamicin, when less teicoplanin was eluted.

Conclusion

Antibiotic elution is higher in Palacos R than CMW1. Antibiotic combination in both cement types has the synergistic effect of increasing antibiotic elution, except for teicoplanin from Palacos R. When high elution of gentamicin is required, Palacos R is preferable. When high elution of teicoplanin is required, Palacos R with only teicoplanin is superior to CMW1.

Sublethal Impacts of Novaluron on Tarnished Plant Bug (Hemiptera: Miridae) Adults

Tarnished plant bug, Lygus lineolaris Palisot de Beauvois (Hemiptera: Miridae), has become a primary pest of cotton in the Midsouthern United States. Insect growth regulators such as novaluron are an important part of L. lineolaris management. While novaluron is lethal to nymphs, it does not kill adults, so it has been used when nymphs are the primary stage present. However, cotton yield protection was observed from an application of novaluron when adults were the predominant stage present. To explain this, a series of studies were conducted to examine sublethal impacts of novaluron to L. lineolaris adults. Novaluron ingestion by adults reduced hatch rate and sometimes reduced oviposition rate. Ingestion by either males or females reduced hatch rates, but the reduction was greater from female exposure. Contact exposure of adults with novaluron residues within 1 d of application reduced hatch rate by about 50%, but the impact on oviposition was inconsistent. A field study showed reduced hatch rate from contact exposure to mixed-age natural populations, but the overall net reproductive rate was not reduced. Surface exposure of eggs to novaluron did not reduce hatch rate. Overall, exposure of tarnished plant bug adults to novaluron, regardless of adult age or exposure route, reduced egg viability. However, the impact on oviposition rate and net reproductive rate varied with adult age and exposure route. This understanding of sublethal impacts of novaluron, in addition to lethal impacts on nymphs, should be considered when choosing application times to maximize effects on L. lineolaris populations.

CRISPR/Cas9 generated knockout mice lacking phenylalanine hydroxylase protein as a novel preclinical model for human phenylketonuria

Phenylketonuria (PKU) is an autosomal recessive inborn error of L-phenylalanine (Phe) metabolism. It is caused by a partial or complete deficiency of the enzyme phenylalanine hydroxylase (PAH), which is necessary for conversion of Phe to tyrosine (Tyr). This metabolic error results in buildup of Phe and reduction of Tyr concentration in blood and in the brain, leading to neurological disease and intellectual deficits. Patients exhibit retarded body growth, hypopigmentation, hypocholesterolemia and low levels of neurotransmitters. Here we report first attempt at creating a homozygous Pah knock-out (KO) (Hom) mouse model, which was developed in the C57BL/6 J strain using CRISPR/Cas9 where codon 7 (GAG) in Pah gene was changed to a stop codon TAG. We investigated 2 to 6-month-old, male, Hom mice using comprehensive behavioral and biochemical assays, MRI and histopathology. Age and sex-matched heterozygous Pah-KO (Het) mice were used as control mice, as they exhibit enough PAH enzyme activity to provide Phe and Tyr levels comparable to the wild-type mice. Overall, our findings demonstrate that 6-month-old, male Hom mice completely lack PAH enzyme, exhibit significantly higher blood and brain Phe levels, lower levels of brain Tyr and neurotransmitters along with lower myelin content and have significant behavioral deficit. These mice exhibit phenotypes that closely resemble PKU patients such as retarded body growth, cutaneous hypopigmentation, and hypocholesterolemia when compared to the age- and sex-matched Het mice. Altogether, biochemical, behavioral, and pathologic features of this novel mouse model suggest that it can be used as a reliable translational tool for PKU preclinical research and drug development.

Abstract P13: Faster Treatment Speed is Not Associated With Bleeds: Intravenous Alteplase Treatment in the Ultra-Early Time Window is Safe

Previous studies have shown that faster Door to Needle (DTN) treatment times are associated with better outcomes for acute ischemic stroke patients. With the continued push for faster times, we aimed to determine if DTN treatment times in the 30- vs 45-minute time window yielded statistically significant differences in outcomes or complications.

Data obtained from a multi-state stroke registry included acute ischemic stroke patients ≥18 years of age discharged between January 2017 and April 2020, and treated with IV alteplase with DTN times between 25-30 or 40-45 minutes. Outcomes were 90-day Modified Rankin Score (mRS) (0-2 vs 3-6), discharge disposition [home or inpatient rehabilitation facility (IRF) vs other location], complications (any treatment-related complication vs none), and hospital length of stay (LOS). Patients with a documented reason for delay or who received thrombectomy were excluded. Outcomes of patients with 25- to 30-minute DTN times were compared to those with 40- to 45-minute DTN times using generalized linear models and multiple linear regression, adjusting for admission NIHSS, age, gender, race/ethnicity, and medical history.

Compared to the 20-25 minute group, patients treated in the 40-45 minute window had higher odds of a documented 90-day mRS of 3 or more (Adjusted Odds Ratio (AOR)=1.19, p=0.253, n=201 ) and treatment-related complication (AOR=1.35, p=0.569) and lower odds of discharge to home or IRF (AOR=0.846, p=0.359). There was little difference in LOS (β=-0.008, p=0.847). None of the outcomes reached statistical significance.

Administering alteplase in the 25- to 30-minute window is safe and did not result in an increase in bleeding complications. Although faster treatment times trended toward better outcomes, there was no statistically significant difference between the 25-30 and 40-45 minute DTN treatment times.

Hartmann's procedure versus intersphincteric abdominoperineal excision (HiP Study): a multicentre prospective cohort study

AIM

In patients with low rectal cancer it is occasionally necessary to avoid a low coloanal anastomosis due to patient frailty or poor function. In such situations there are two alternative approaches: Hartmann's procedure (HP) or intersphincteric abdominoperineal excision (IAPE). There are few data to guide surgeons as to which of these two procedures is the safest. The aim of this study was to determine the surgical complication rates associated with each procedure.

METHOD

This was a multicentre, nonrandomized prospective cohort study of patients undergoing either HP or IAPE. The primary objective was to determine surgical complication rates. Secondary objectives included length of stay, time to adjuvant therapy and quality of life at 90 days.

RESULTS

One hundred and seventy nine patients were recruited between April 2016 and June 2019; approximately two thirds of patients underwent HP and one third IAPE. The overall complication rate was high in both groups (54% for the HP group and 52% for the IAPE group). Surgery-specific complication rates were also high, but not significantly different: 43% for HP and 48% for IAPE. The pelvic abscess rate in HP was 11% and was significantly higher in patients with a palpable staple line (15% vs 2%). There was a higher incidence of serious medical complications following IAPE (16% vs 5%), along with a reduction in 90-day quality of life scores.

CONCLUSION

This is the largest prospective study to compare HP and IAPE in patients undergoing rectal cancer surgery where primary anastomosis is not deemed appropriate. With similar complication rates, these data support the ongoing use of either HP or IAPE in this patient group.

3D Oral and Cervical Tissue Models for Studying Papillomavirus Host-Pathogen Interactions

Human papillomavirus (HPV) infection occurs in differentiating epithelial tissues. Cancers caused by high-risk types (e.g., HPV16 and HPV18) typically occur at oropharyngeal and anogenital anatomical sites. The HPV life cycle is differentiation-dependent, requiring tissue culture methodology that is able to recapitulate the three-dimensional (3D) stratified epithelium. Here we report two distinct and complementary methods for growing differentiating epithelial tissues that mimic many critical morphological and biochemical aspects of in vivo tissue. The first approach involves growing primary human epithelial cells on top of a dermal equivalent consisting of collagen fibers and living fibroblast cells. When these cells are grown at the liquid-air interface, differentiation occurs and allows for epithelial stratification. The second approach uses a rotating wall vessel bioreactor. The low-fluid-shear microgravity environment inside the bioreactor allows the cells to use collagen-coated microbeads as a growth scaffold and self-assemble into 3D cellular aggregates. These approaches are applied to epithelial cells derived from HPV-positive and HPV-negative oral and cervical tissues. The second part of the article introduces potential downstream applications for these 3D tissue models. We describe methods that will allow readers to start successfully culturing 3D tissues from oral and cervical cells. These tissues have been used for microscopic visualization, scanning electron microscopy, and large omics-based studies to gain insights into epithelial biology, the HPV life cycle, and host-pathogen interactions. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Establishing human primary cell-derived 3D organotypic raft cultures Support Protocol 1: Isolation of epithelial cells from patient-derived tissues Support Protocol 2: Growth and maintenance of primary human epithelial cells in monolayer culture Support Protocol 3: PCR-based HPV screening of primary cell cultures Basic Protocol 2: Establishing human 3D cervical tissues using the rotating wall vessel bioreactor Support Protocol 4: Growth and maintenance of human A2EN cells in monolayer culture Support Protocol 5: Preparation of the slow-turning lateral vessel bioreactor Support Protocol 6: Preparation of Cytodex-3 microcarrier beads Basic Protocol 3: Histological assessment of 3D organotypic raft tissues Basic Protocol 4: Spatial analysis of protein expression in 3D organotypic raft cultures Basic Protocol 5: Immunofluorescence imaging of RWV-derived 3D tissues Basic Protocol 6: Ultrastructural visualization and imaging of RWV-derived 3D tissues Basic Protocol 7: Characterization of gene expression by RT-qPCR.

Vesicular trafficking permits evasion of cGAS/STING surveillance during initial human papillomavirus infection

Oncogenic human papillomaviruses (HPVs) replicate in differentiating epithelium, causing 5% of cancers worldwide. Like most other DNA viruses, HPV infection initiates after trafficking viral genome (vDNA) to host cell nuclei. Cells possess innate surveillance pathways to detect microbial components or physiological stresses often associated with microbial infections. One of these pathways, cGAS/STING, induces IRF3-dependent antiviral interferon (IFN) responses upon detection of cytosolic DNA. Virion-associated vDNA can activate cGAS/STING during initial viral entry and uncoating/trafficking, and thus cGAS/STING is an obstacle to many DNA viruses. HPV has a unique vesicular trafficking pathway compared to many other DNA viruses. As the capsid uncoats within acidic endosomal compartments, minor capsid protein L2 protrudes across vesicular membranes to facilitate transport of vDNA to the Golgi. L2/vDNA resides within the Golgi lumen until G2/M, whereupon vesicular L2/vDNA traffics along spindle microtubules, tethering to chromosomes to access daughter cell nuclei. L2/vDNA-containing vesicles likely remain intact until G1, following nuclear envelope reformation. We hypothesize that this unique vesicular trafficking protects HPV from cGAS/STING surveillance. Here, we investigate cGAS/STING responses to HPV infection. DNA transfection resulted in acute cGAS/STING activation and downstream IFN responses. In contrast, HPV infection elicited minimal cGAS/STING and IFN responses. To determine the role of vesicular trafficking in cGAS/STING evasion, we forced premature viral penetration of vesicular membranes with membrane-perturbing cationic lipids. Such treatment renders a non-infectious trafficking-defective mutant HPV infectious, yet susceptible to cGAS/STING detection. Overall, HPV evades cGAS/STING by its unique subcellular trafficking, a property that may contribute to establishment of infection.

Persistent infection is the main risk factor for all HPV-associated cancers. However, cellular innate immune pathways exist to detect and limit viral infections. The cGAS/STING pathway senses cytosolic DNA to initiate antiviral IFN responses. Such responses would likely be detrimental towards the establishment of persistent HPV infections. We therefore hypothesize that HPV evades cGAS/STING detection via its unique vesicular trafficking mechanism. Here, we show that indeed HPV is a stealthy virus, capable of infecting keratinocytes with minimal activation of the cGAS/STING pathway. Such evasion is dependent on HPV’s vesicular trafficking, as perturbation of vesicular integrity during infection results in sensing of virions.

Additive manufacturing techniques for smart prosthetic liners

Elastomeric liners are commonly worn between the prosthetic socket and the limb. A number of improvements to the state of the art of liner technology are required to address outstanding problems. A liner that conforms to the residuum more accurately, may improve the skin health at the stump-socket interface. Previous work has shown that for effective thermal management of the socket environment, an active heat removal system is required, yet this is not available. Volume tracking of the stump could be used as a diagnostic tool for looking at the changes that occur across the day for all users, which depend on activity level, position, and the interaction forces of the prosthetic socket with the limb. We believe that it would be advantageous to embed these devices into a smart liner, which could be replaced and repaired more easily than the highly costly and labour-intensive custom-made socket. This paper presents the work to develop these capabilities in soft material technology, with: the development of a printable nanocomposite stretch sensor system; a low-cost digital method for casting bespoke prosthetic liners; a liner with an embedded stretch sensor for growth / volume tracking; a model liner with an embedded active cooling system.

Spontaneous coronary artery dissection: insights from intravascular ultrasound

Introduction

Spontaneous Coronary Artery Dissection (SCAD) may be at the origin of up to 25% of acute coronary events in women &lt;50 yo with no or few risk factors. The diagnosis of SCAD is challenging and in some cases it may be ascertained only by intracoronary imaging such as intravascular ultrasound (IVUS) or optical coherence tomography (OCT). IVUS is widely available and has a better depth penetration compared to OCT, showing the extent of the false lumen and the aspect of the adventitia but its lower resolution does not always allow the visualization of smaller structures such as fenestrations. In a previous study we investigated the role of OCT in understanding the pathophysiology of SCAD and we reported a number of OCT complications. It is not known if these also apply to IVUS but since IVUS does not require additional contrast injection, the risk of false lumen (FL) propagation should be lower.

Aim of the study

To analyze the value of IVUS in the assessment of key features of SCAD and to explore the feasibility of three-dimensional (3D) reconstruction using IVUS imaging.

Methods

We collated the imaging findings of 15 cases of SCAD for which IVUS was used as part of routine clinical care. Images were assessed to determine the visualisation of the true lumen, the false lumen extent and its contents, the intima-media membrane, the presence of fenestrations, the external elastic lamina and underlying adventitia. Furthermore, we performed a 3D reconstruction of a type 2a dissection of the right coronary artery. The IVUS images were exported in DICOM format. The segmentation of the true and false lumens in the regions of interest was manually done using the ImageJ software. Subsequent images were processed using 3D Slicer and Paraview in order to obtain the 3D reconstruction of the dissected segment.

Results

The false lumen was entirely visible in 13/15 cases (87%) and the external elastic lamina in 12/15 cases (80%). In 3/15 cases (20%) the dissection was circumferential. The false lumen content had lower echogenicity compared to the surrounding tissue in all 15 cases. There was no visible fenestration. The 3D reconstruction (Figure 1) showed that the false lumen was larger than the true lumen. The general cross-sectional appearance was that of a “horseshoe” dissection but there was also a short segment of circumferential dissection and the intima-media membrane looked thickened.

Conclusion

Despite its resolution being lower than OCT, IVUS has a deep penetration and provides adequate imaging of the key features of SCAD.

Perspectives

We plan to further expand these findings in a larger series, intending to better characterize the false lumen and the adventitia in SCAD.

IVUS findings in SCAD, 3D reconstruction

Funding Acknowledgement

Type of funding source: None

Occupational groups and ischaemic heart disease in New Zealand – a longitudinal linkage study

Background/Introduction

Occupation is a poorly characterised risk factor for cardiovascular disease (CVD), with females and minority populations particularly under-represented in research. There is also a lack of longitudinal studies using detailed health data that does not rely on self-reports.

Purpose

This study aimed to address these gaps by assessing the association between a range of occupational groups and ischaemic heart disease (IHD) in New Zealand (NZ), through linkage of population-based occupational surveys to routinely collected health data. Half of the study population were females and 40% were indigenous Māori (who comprise 15% of the total 4.8 million NZ population), which enabled sex and ethnicity-specific aspects of the relationship between occupation and IHD to be assessed.

Methods

Two probability-based sample surveys of the NZ adult population (New Zealand Workforce Survey (NZWS); 2004–2006; n=3003) and of the Māori population (NZWS Māori; 2009–2010; n=2107), for which detailed occupational histories and lifestyle factors were collected, were linked with routinely collected health data available through Statistics NZ. Cox regression was used to calculate hazard ratios (HR) for “ever-worked” in any one of nine major occupational groups, with “never worked” in that occupational group defined as the reference group. Analyses were controlled for age, deprivation and smoking, and stratified by sex and ethnicity.

Results

The strongest associations were found for “plant/machine operators and assemblers” and “elementary workers”, particularly among female Māori (HR 2.19, 95% CI 1.16–4.13 and HR 2.03, 1.07–3.82 respectively). In contrast, inverse associations with IHD across all groups were observed for “technicians and associate professionals”, which was significant for NZWS males (HR 0.52, 0.32–0.84). There were some sex and ethnic differences, particularly for “clerks”, where a positive association was found for NZWS males (HR 1.81, 1.19–2.74), whilst an inverse association was observed for Māori females (HR 0.42, 0.22–0.82). Duration analyses (≤2 years, 2–10 years and 10+ years) showed significant dose-response trends for “clerks” in NZWS males, and “plant/machine operators and assemblers” and “elementary workers” in Māori females. Further adjustments for other potential confounders such diabetes mellitus, hypertension and high cholesterol did not affect the results.

Conclusion

Associations between occupation and IHD differed significantly across occupational groups and between sexes and ethnicities, even within the same occupational groups. This suggests that results may not be generalised across these groups and occupational interventions to reduce IHD risk may therefore need different approaches depending on the population and specific groups of interest.

Funding Acknowledgement

Type of funding source: Other. Main funding source(s): Health Research Council (HRC) of New Zealand

Combined endovascular and surgical approaches to treat intralobar pulmonary sequestration: a case report

Pulmonary sequestration is a congenital abnormality of a non-functional pulmonary mass with anomalous systemic arterial supply. Surgical resection is the gold standard treatment, but it carries a risk of life-threatening haemorrhage from accidental injury of the anomalous artery. Endovascular embolisation has been introduced as a safe alternative, but does not eliminate the possibility of symptom recurrence. We report a case of a 61-year old woman with intralobar pulmonary sequestration treated with a combination of endovascular coil embolisation and surgical resection.

An evaluation of continuous subcutaneous infusions across seven NHS acute hospitals: is there potential for 48-hour infusions?

BACKGROUND

Continuous subcutaneous infusions (CSCIs) are commonly used in the United Kingdom as a way of administering medication to patients requiring symptom control when the oral route is compromised. These infusions are typically administered over 24 h due to currently available safety data. The ability to deliver prescribed medication by CSCI over 48 h may have numerous benefits in both patient care and health service resource utilisation. This service evaluation aims to identify the frequency at which CSCI prescriptions are altered at NHS Acute Hospitals.

METHODS

Pharmacists or members of palliative care teams at seven acute NHS hospitals recorded anonymised prescription data relating to the drug combination(s), doses, diluent and compatibility of CSCIs containing two or more drugs on a daily basis for a minimum of 2 days, to a maximum of 7 days.

RESULTS

A total of 1301 prescriptions from 288 patients were recorded across the seven sites, yielding 584 discrete drug combinations. Of the 584 combinations, 91% (n = 533) included an opioid. The 10 most-common CSCI drug combinations represented 37% of the combinations recorded. Median duration of an unchanged CSCI prescription across all sites was 2 days.

CONCLUSION

Data suggests medication delivered by CSCI over 48 h may be a viable option. Before a clinical feasibility study can be undertaken, a pharmacoeconomic assessment and robust chemical and microbiological stability data will be required, as will the assessment of the perceptions from clinical staff, patients and their families on the acceptability of such a change in practice.

Pathogen-Host Analysis Tool (PHAT): an integrative platform to analyze next-generation sequencing data

SUMMARY

The Pathogen-Host Analysis Tool (PHAT) is an application for processing and analyzing next-generation sequencing (NGS) data as it relates to relationships between pathogens and their hosts. Unlike custom scripts and tedious pipeline programming, PHAT provides an integrative platform encompassing raw and aligned sequence and reference file input, quality control (QC) reporting, alignment and variant calling, linear and circular alignment viewing, and graphical and tabular output. This novel tool aims to be user-friendly for life scientists studying diverse pathogen-host relationships.

AVAILABILITY AND IMPLEMENTATION

The project is available on GitHub (https://github.com/chgibb/PHAT) and includes convenient installers, as well as portable and source versions, for both Windows and Linux (Debian and RedHat). Up-to-date documentation for PHAT, including user guides and development notes, can be found at https://chgibb.github.io/PHATDocs/. We encourage users and developers to provide feedback (error reporting, suggestions and comments).

Anti-inflammatory effects of α-MSH through p-CREB expression in sarcoidosis like granuloma model

Lung inflammation due to sarcoidosis is characterized by a complex cascade of immunopathologic events, including leukocyte recruitment and granuloma formation. α-melanocyte stimulating hormone (α-MSH) is a melanocortin signaling peptide with anti-inflammatory properties. We aimed to evaluate the effects of α-MSH in a novel in vitro sarcoidosis model. An in vitro sarcoidosis-like granuloma model was developed by challenging peripheral blood mononuclear cells (PBMCs) derived from patients with confirmed treatment-naïve sarcoidosis with microparticles generated from Mycobacterium abscessus cell walls. Unchallenged PBMCsand developed granulomas were treated daily with 10 μM α-MSH or saline as control. Cytokine concentrations in supernatants of culture and in cell extracts were measured using Illumina multiplex Elisa and western blot, respectively. Gene expression was analyzed using RNA-Seq and RT-PCR. Protein secretion and gene expression of IL-7, IL-7R, IFN-γ, MC1R, NF-κB, phosphorylated NF-κB (p-NF-κB), MARCO, and p-CREB were measured with western blot and RNAseq. A significant increase in IL-7, IL-7R, and IFN-γ protein expression was found in developed granulomas comparing to microparticle unchallenged PBMCs. IL-7, IL-7R, and IFN-γ protein expression was significantly reduced in developed granulomas after exposure to α-MSH compared with saline treated granulomas. Compared with microparticle unchallenged PBMCs, total NF-κB and p-NF-κB were significantly increased in developed granulomas, while expression of p-CREB was not changed. Treatment with α-MSH promoted a significantly higher concentration of p-CREB in granulomas. The anti-inflammatory effects of α-MSH were blocked by specific p-CREB inhibition. α-MSH has anti-inflammatory properties in this in vitro granuloma model, which is an effect mediated by induction of phosphorylation of CREB.