The Year in Thoracic Anesthesia: Selected Highlights from 2022.

This article reviews research highlights in the field of thoracic anesthesia. The highlights of this year included new developments in the preoperative assessment and prehabilitation of patients requiring thoracic surgery, updates on the use of devices for one-lung ventilation (OLV) in adults and children, updates on the anesthetic and postoperative management of these patients, including protective OLV ventilation, the use of opioid-sparing techniques and regional anesthesia, and outcomes using enhanced recovery after surgery, as well as the use of expanding indications for extracorporeal membrane oxygenation, specialized anesthetic techniques for airway surgery, and nonintubated video-assisted thoracic surgery.

SOFTLY: Comparison of outcomes of rigid versus soft collar during emergency department investigation for potential cervical spine injury in low-risk blunt trauma patients - A pilot study.

OBJECTIVE: Blunt trauma patients with potential cervical spine injury are traditionally immobilised in rigid collars. Recently, this has been challenged. The present study's objective was comparison of the rate of patient-oriented adverse events in stable, alert, low-risk patients with potential cervical spine injuries immobilised in rigid versus soft collars. METHODS: Unblinded, prospective quasi-randomised clinical trial of neurologically intact, adult, blunt trauma patients assessed as having potential cervical spine injury. Patients were randomised to collar type. All other aspects of care were unchanged. Primary outcome was patient-reported discomfort related to neck immobilisation by collar type. Secondary outcomes included adverse neurological events, agitation and clinically important cervical spine injuries (clinical trial registration number: ACTRN12621000286842). RESULTS: A total of 137 patients were enrolled: 59 patients allocated to a rigid collar and 78 to a soft collar. Most injuries were from a fall <1 m (54%) or a motor vehicle crash (21.9%). Median neck pain score of collar immobilisation was lower in the soft collar group (3.0 [interquartile range 0-6.1] vs 6.0 [interquartile range 3-8.8], P < 0.001). The proportion of patients with clinician-identified agitation was lower in the soft collar group (5% vs 17%, P = 0.04). There were four clinically important cervical spine injuries (two in each group). All were treated conservatively. There were no adverse neurological events. CONCLUSIONS: Use of soft rather than rigid collar immobilisation for low-risk blunt trauma patients with potential cervical spine injury is significantly less painful for patients and results in less agitation. A larger study is needed to determine the safety of this approach or whether collars are required at all.

Outcome of reduction of paediatric forearm fracture by emergency department clinicians.

OBJECTIVES: Paediatric forearm fractures are common. Anecdotally, there is a trend towards ED reduction of selected fractures under procedural sedation. We aimed to determine the rate of subsequent operative intervention for fracture re-displacement. METHODS: Retrospective observational study of children with a forearm/wrist fracture undergoing fracture reduction in ED. Outcome of interest was operative intervention for fracture re-displacement within 6 weeks. RESULTS: Among 176 patients studied, operative intervention occurred in nine patients (5.1%, 95% confidence interval 2.7-9.4%). CONCLUSION: Reduction of paediatric forearm fractures under procedural sedation by ED clinicians is increasingly common and results in a low rate of subsequent operative intervention.

Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus).

Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus).

Although being some of the most valuable and heavily exploited wild organisms, few fisheries species have been studied at the whole-genome level. This is especially the case in New Zealand, where genomics resources are urgently needed to assist fisheries management. Here, we generated 55 Gb of short Illumina reads (92× coverage) and 73 Gb of long Nanopore reads (122×) to produce the first genome assembly of the marine teleost tarakihi [Nemadactylus macropterus (Forster, 1801)], a highly valuable fisheries species in New Zealand. An additional 300 Mb of Iso-Seq reads were obtained to assist in gene annotation. The final genome assembly was 568 Mb long with an N50 of 3.37 Mb. The genome completeness was high, with 97.8% of complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. Heterozygosity values estimated through k-mer counting (1.00%) and bi-allelic SNPs (0.64%) were high compared with the same values reported for other fishes. Iso-Seq analysis recovered 91,313 unique transcripts from 15,515 genes (mean ratio of 5.89 transcripts per gene), and the most common alternative splicing event was intron retention. This highly contiguous genome assembly and the isoform-resolved transcriptome will provide a useful resource to assist the study of population genomics and comparative eco-evolutionary studies in teleosts and related organisms.

Biomarkers of nanomaterials hazard from multi-layer data.

There is an urgent need to apply effective, data-driven approaches to reliably predict engineered nanomaterial (ENM) toxicity. Here we introduce a predictive computational framework based on the molecular and phenotypic effects of a large panel of ENMs across multiple in vitro and in vivo models. Our methodology allows for the grouping of ENMs based on multi-omics approaches combined with robust toxicity tests. Importantly, we identify mRNA-based toxicity markers and extensively replicate them in multiple independent datasets. We find that models based on combinations of omics-derived features and material intrinsic properties display significantly improved predictive accuracy as compared to physicochemical properties alone.

Evaluating new species for aquaculture: A genomic dissection of growth in the New Zealand silver trevally (Pseudocaranx georgianus).

Aquaculture is the fastest-growing food production sector worldwide, yet industry has been slow to implement genomic techniques as routine tools. Applying genomics to new breeding programmes can provide important information about pedigree structure and genetic diversity; key parameters for a successful long-term breeding programme. It can also provide insights on potential gains for commercially important, yet complex, quantitative traits such as growth rate. Here we investigated a population of 1100 captive-bred F1 silver trevally (Pseudocaranx georgianus), a promising new species for New Zealand aquaculture. We used whole-genome information, coupled with image-based phenotypic data collected over two years, to build the pedigree of the population, assess its genetic diversity, describe growth patterns of ten growth traits and estimate their genetic parameters. Successful parentage assignment of 664 F1 individuals showed that the pedigree consisted of a complex mixture of full- and half-sib individuals, with skewed reproductive success among parents, especially in females. Growth patterns showed seasonal fluctuations (average increase across all traits of 27.3% in summer and only 7% in winter) and strong inter-family differences. Heritability values for growth traits ranged from 0.27 to 0.76. Genetic and phenotypic correlations between traits were high and positive, ranging from 0.57 to 0.94 and 0.50 to 1.00 respectively. The implications of these findings are threefold: first, the best on-growing conditions are in warmer months, where highest growth peaks can be achieved; second, size- and family-based selection can be used as early selection criterion if pedigree structure and inbreeding risks are closely monitored; third, selection for body length results in concomitant increases in height and weight, traits of paramount importance for aquaculture. It is concluded that there is substantial potential for genetic improvement of economically important traits, suggesting that silver trevally is a promising species for selective breeding for enhanced growth.

Differential expression analyses reveal extensive transcriptional plasticity induced by temperature in New Zealand silver trevally (Pseudocaranx georgianus).

Ectotherm species, such as marine fishes, depend on environmental temperature to regulate their vital functions. In finfish aquaculture production, being able to predict physiological responses in growth and other economic traits to temperature is crucial to address challenges inherent in the selection of grow-out locations. This will become an even more significant issue under the various predicted future climate change scenarios. In this study, we used the marine teleost silver trevally (Pseudocaranx georgianus), a species currently being explored as a candidate for aquaculture in New Zealand, as a model to study plasticity in gene expression patterns and growth in response to different temperatures. Using a captive study population, temperature conditions were experimentally manipulated for 1 month to mimic seasonal extremes. Phenotypic differences in growth were measured in 400 individuals, and gene expression patterns of pituitary gland and liver were determined in a subset of 100 individuals. Results showed that growth increased 50% in the warmer compared with the colder condition, suggesting that temperature has a large impact on metabolic activities associated with growth. A total of 265,116,678 single-end RNA sequence reads were aligned to the trevally genome, and 28,416 transcript models were developed (27,887 of these had GenBank accessions, and 17,980 unique gene symbols). Further filtering reduced this set to 8597 gene models. 39 and 238 differentially expressed genes (DEGs) were found in the pituitary gland and the liver, respectively (|log2FC| > 0.26, p-value < 0.05). Of these, 6 DEGs showed a common expression pattern between both tissues, all involved in housekeeping functions. Temperature-modulated growth responses were linked to major pathways affecting metabolism, cell regulation and signalling, previously shown to be important for temperature tolerance in other fish species. An interesting finding of this study was that genes linked to the reproductive system were up-regulated in both tissues in the high treatment, indicating the onset of sexual maturation. Few studies have investigated the thermal plasticity of the gene expression in the main organs of the somatotropic axis simultaneously. Our findings indicate that trevally exhibit substantial growth differences and predictable plastic regulatory responses to different temperature conditions. We identified a set of genes that provide a list of candidates for further investigations for selective breeding objectives and how populations may adapt to increasing temperatures.

Unraveling the complex genetic basis of growth in New Zealand silver trevally (Pseudocaranx georgianus).

Growth directly influences production rate and therefore is one of the most important and well-studied traits in animal breeding. However, understanding the genetic basis of growth has been hindered by its typically complex polygenic architecture. Here, we performed quantitative trait locus mapping and genome-wide association studies for 10 growth traits that were observed over 2 years in 1,100 F1 captive-bred trevally (Pseudocaranx georgianus). We constructed the first high-density linkage map for trevally, which included 19,861 single nucleotide polymorphism markers, and discovered 8 quantitative trait loci for height, length, and weight on linkage groups 3, 14, and 18. Using genome-wide association studies, we further identified 113 single nucleotide polymorphism-trait associations, uncovering 10 genetic hot spots involved in growth. Two of the markers found in the genome-wide association studies colocated with the quantitative trait loci previously mentioned, demonstrating that combining quantitative trait locus mapping and genome-wide association studies represents a powerful approach for the identification and validation of loci controlling complex traits. This is the first study of its kind for trevally. Our findings provide important insights into the genetic architecture of growth in this species and supply a basis for fine mapping quantitative trait loci, genomic selection, and further detailed functional analysis of the genes underlying growth in trevally.

Phylogenetic relationships, origin and historical biogeography of the genus Sprattus (Clupeiformes: Clupeidae).

The genus Sprattus comprises five species of marine pelagic fishes distributed worldwide in antitropical, temperate waters. Their distribution suggests an ancient origin during a cold period of the earth's history. In this study, we evaluated this hypothesis and corroborated the non-monophyly of the genus Sprattus, using a phylogenetic approach based on DNA sequences of five mitochondrial genome regions. Sprattus sprattus is more closely related to members of the genus Clupea than to other Sprattus species. We also investigated the historical biogeography of the genus, with the phylogenetic tree showing two well-supported clades corresponding to the species distribution in each hemisphere. Time-calibrated phylogenetic analyses showed that an ancient divergence between Northern and Southern Hemispheres occurred at 55.8 MYBP, followed by a diversification in the Oligocene epoch in the Northern Hemisphere clade (33.8 MYBP) and a more recent diversification in the Southern Hemisphere clade (34.2 MYBP). Historical biogeography analyses indicated that the most recent common ancestor (MRCA) likely inhabited the Atlantic Ocean in the Southern Hemisphere. These results suggest that the ancestral population of the MRCA diverged in two populations, one was dispersed to the Northern Hemisphere and the other across the Southern Hemisphere. Given that the Eocene was the warmest epoch since the Paleogene, the ancestral populations would have crossed the tropics through deeper cooler waters, as proposed by the isothermal submergence hypothesis. The non-monophyly confirmed for the genus Sprattus indicates that its systematics should be re-evaluated.

Description of the growth hormone gene of the Australasian snapper, Chrysophrys auratus, and associated intra- and interspecific genetic variation.

The growth hormone (GH) gene of the marine teleost, the Australasian snapper (Chrysophrys auratus), was identified and characterized from the reference genome showing it was approximately 5577 bp in length and consisted of six exons and five introns. Large polymorphic repeat regions were found in the first and third introns, and putative transcription factor binding sites were identified. Phylogenetic analysis of the GH genes of perciform fish showed largely conserved coding regions and highly variable noncoding regions among species. Despite some exon sequence variation and an amino acid deletion identified between C. auratus and its sister species Chrysophrys/Pagrus major, the amino acid sequences and putative secondary structures were largely conserved across the Sparidae. A population-level assessment of 99 samples caught at five separate coastal locations in New Zealand revealed six variable alleles at the intron 1 site of the C. auratus GH gene. A population genetic analysis suggested that C. auratus from the five sample locations were largely panmictic, with no evidence for departure from the Hardy-Weinberg equilibrium, and have a high level of heterozygosity. Overall these results suggest that the GH gene is largely conserved across the coding regions, but some variability could be detected.

Towards FAIR nanosafety data.

Nanotechnology is a key enabling technology with billions of euros in global investment from public funding, which include large collaborative projects that have investigated environmental and health safety aspects of nanomaterials, but the reuse of accumulated data is clearly lagging behind. Here we summarize challenges and provide recommendations for the efficient reuse of nanosafety data, in line with the recently established FAIR (findable, accessible, interoperable and reusable) guiding principles. We describe the FAIR-aligned Nanosafety Data Interface, with an aggregated findability, accessibility and interoperability across physicochemical, bio-nano interaction, human toxicity, omics, ecotoxicological and exposure data. Overall, we illustrate a much-needed path towards standards for the optimized use of existing data, which avoids duplication of efforts, and provides a multitude of options to promote safe and sustainable nanotechnology.

Exposure to Solar UV During Outdoor Construction Work in Britain.

Excessive exposure to ultraviolet (UV) radiation from the sun in summer can cause skin cancer and in Britain there are around 1500 new cases of non-melanoma skin cancer (NMSC) each year, caused by exposure to solar UV at work. Little is known about the magnitude of UV exposure amongst outdoor construction workers in Britain, although this is one of the main groups at risk. The aim of this paper is to summarise measurements of erythema-weighted UVB radiation amongst construction workers in Scotland and the Southeast of England and interpret the data in terms of the risk of NMSC. The measurements were made as part of an intervention study using short mobile phone text messages to alter worker behaviour to either reduce UV exposure in summer or increase serum vitamin D in winter; the intervention is only briefly reported here. Data were collected from 67 workers from 9 worksites, of whom 41 provided measures of UV exposure for 758 working days. Daily exposure ranged from 0 to 13.47 standard erythema dose (SED), with the mean exposure for outdoor workers being 2.0 SED and the corresponding value for indoor workers being 0.7 SED. These data were obtained from a sensor located on the back of the workers hard hat; others have measured exposure on the wrist or upper arm and these locations probably, on average, have higher levels of UV exposure. It is likely that an outdoor construction worker in Britain could accumulate sufficient solar UV exposure over 30-40 years of work to more than double their risk of NMSC. We argue that employers in Britain should take a more proactive approach to manage sun safety and they should take responsibility for skin health surveillance for their workers.

DNA degradation in fish: Practical solutions and guidelines to improve DNA preservation for genomic research.

The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome-wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25 M EDTA, NaCl saturated solution, and 2. Ethanol >99.5%) under a range of storage conditions over a three-month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. We found that the storage solution has a strong effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hr, making samples unsuitable for next-generation sequencing. Here, we conclude that DESS was the most promising solution when storing samples for genomic applications. We recognize that the best preservation protocol is highly dependent on the organism, tissue type, and study design. We highly recommend performing similar experiments before beginning a study. This study highlights the importance of testing sample preservation protocols and provides both practical and economical advice to improve DNA preservation when sampling for genome-wide applications.

Your Spreadsheets Can Be FAIR: A Tool and FAIRification Workflow for the eNanoMapper Database.

The field of nanoinformatics is rapidly developing and provides data driven solutions in the area of nanomaterials (NM) safety. Safe by Design approaches are encouraged and promoted through regulatory initiatives and multiple scientific projects. Experimental data is at the core of nanoinformatics processing workflows for risk assessment. The nanosafety data is predominantly recorded in Excel spreadsheet files. Although the spreadsheets are quite convenient for the experimentalists, they also pose great challenges for the consequent processing into databases due to variability of the templates used, specific details provided by each laboratory and the need for proper metadata documentation and formatting. In this paper, we present a workflow to facilitate the conversion of spreadsheets into a FAIR (Findable, Accessible, Interoperable, and Reusable) database, with the pivotal aid of the NMDataParser tool, developed to streamline the mapping of the original file layout into the eNanoMapper semantic data model. The NMDataParser is an open source Java library and application, making use of a JSON configuration to define the mapping. We describe the JSON configuration syntax and the approaches applied for parsing different spreadsheet layouts used by the nanosafety community. Examples of using the NMDataParser tool in nanoinformatics workflows are given. Challenging cases are discussed and appropriate solutions are proposed.

External validation of the modified HOPPE score to predict low risk pulmonary embolism suitable for early discharge.

OBJECTIVE: Recently, a novel score for risk stratification of patients with pulmonary embolism (PE)-the HOPPE score-was derived. We aimed to externally validate the HOPPE score in emergency department-diagnosed PE, using SpO2 as a surrogate for PaO2-the modified HOPPE score. METHODS: Retrospective observational study of adult patients with an emergency department diagnosis of PE was performed. Data collected included demographics, co-morbidities, clinical features, electrocardiogram and test results, in-hospital mortality and non-fatal major adverse clinical events (MACE; survived cardiac arrest, cardiogenic shock or thrombolysis administration). The primary outcome of interest was clinical performance of the modified HOPPE score for inhospital mortality and the composite outcome of in-hospital death and MACE. A secondary outcome was comparison of predictive performance between the modified HOPPE score and the simplified Pulmonary Embolism Severity Index score. RESULTS: Two hundred and six patients were studied (median age 61, 55% female). There were no deaths or MACE in patients with a low risk modified HOPPE score of 0 to 6 (0%; 95% confidence interval, 0% to 1.8%). Negative predictive value of a low risk score was 100% (95% confidence interval, 92.2% to 100%) for in-hospital mortality and for the composite of in-hospital mortality or MACE. The modified HOPPE score had similar predictive performance to the simplified Pulmonary Embolism Severity Index score with an area under the curve of 0.88 vs. 0.80 for the composite outcome of in-hospital mortality or MACE (P=0.052). Twenty-eight percent of the patients were classified as low risk and potentially suitable for management as outpatients. CONCLUSION: The modified HOPPE score showed good clinical performance. Prospective validation is warranted.

Does the evidence justify routine transfer of residents of aged care facilities for CT scan after minor head trauma?

BACKGROUND: In 2014, the South Australian coroner recommended that residents of residential aged care facilities (RACF) who had sustained a head injury should be transported to emergency departments (ED) for assessment and a head CT scan, with the view to preventing mortality. The evidence base for the recommendation is unclear. AIMS: To determine the rate of emergent intervention (neurosurgery, transfusion of blood products or reversal of anti-coagulation) in residents transferred to ED with minor head trauma who had their usual cognitive function on ED assessment. METHODS: This was a retrospective cohort study by medical records review at two university-affiliated community ED. Participants were patients from RACF attending ED who had suffered minor head trauma and had their usual cognitive function. Exclusions were altered conscious state, new neurological findings or associated orthopaedic injury requiring hospital admission. The primary outcome was rate of emergent intervention in residents transferred to ED with minor head trauma who had their usual cognitive function on ED assessment. RESULTS: A total of 366 patients was studied; median age 86 years, 45% taking anti-coagulant/anti-platelet medication. Eighty per cent underwent head CT. Six per cent had intracranial haemorrhage (ICH; 95% CI 4-8.9%). No patient underwent neurosurgery. One had emergent intervention, reversal of anti-coagulation (0.3%, 95% CI 0.05-1.5%). CONCLUSION: The rate of emergent intervention for ICH in patients from RACF who sustained a minor head trauma but had their normal cognitive function was <1%. None underwent neurosurgical intervention. The low rate of intervention seriously challenges the appropriateness of routine transfer and CT for this patient group.

Lifetime cumulative exposure to rubber dust, fumes and N-nitrosamines and non-cancer mortality: a 49-year follow-up of UK rubber factory workers.

OBJECTIVES: To examine associations between occupational exposures to rubber dust, rubber fumes and N-nitrosamines and non-cancer mortality. METHODS: A cohort of 36 441 males aged 35+ years employed in British rubber factories was followed-up to 2015 (94% deceased). Competing risk survival analysis was used to assess risks of dying from non-cancer diseases (respiratory, urinary, cerebrovascular, circulatory and digestive diseases). Occupational exposures to rubber dust, rubber fumes, N-nitrosamines were derived based on a population-specific quantitative job-exposure matrix which in-turn was based on measurements in the EU-EXASRUB database. RESULTS: Exposure-response associations of increased risk with increasing exposure were found for N-nitrosomorpholine with mortality from circulatory diseases (subdistribution hazard ratio (SHR) 1.17; 95% CI 1.12 to 1.23), ischaemic heart disease (IHD) (SHR 1.19; 95% CI 1.13 to 1.26), cerebrovascular disease (SHR 1.19; 95% CI 1.07 to 1.32) and exposures to N-nitrosodimethylamine with respiratory disease mortality (SHR 1.41; 95% CI 1.30 to 1.53). Increased risks for mortality from circulatory disease, IHD and digestive diseases were found with higher levels of exposures to rubber dust, rubber fumes and N-nitrosamines sum, without an exposure-dependent manner. No associations were observed between rubber dust, rubber fumes and N-nitrosamines exposures with mortality from asthma, urinary disease, bronchitis, emphysema, liver disease and some digestive diseases. CONCLUSIONS: In a cohort of rubber factory workers with 49 years of follow-up, increased risk for mortality from circulatory, cerebrovascular, respiratory and digestive diseases were found to be associated with cumulative occupational exposures to specific agents.