A retrospective cohort study evaluating pregnancy outcomes in women with MIDD

AIMS

The most common pathogenic mitochondrial mutation associated with mitochondrial disease is m.3243A>G. Increased obstetric complications, such as spontaneous abortion, gestational diabetes (GDM), preterm delivery, and preeclampsia, have been reported in women carrying this mutation. We aimed to determine the fetal and maternal outcomes in pregnant women with mitochondrial disease.

METHODS

We retrospectively studied the obstetric and perinatal outcomes in 88 pregnancies of 26 women with genetically confirmed mitochondrial disease (m.3243A>G in the MTTL1 gene (n = 25); m.12258C>A in the MT-TS2 gene (n = 1)). Outcomes included pregnancy related complications, mode of delivery, gestational age at delivery and birthweight.

RESULTS

Mean heteroplasmy rate was 18%. The miscarriage rate was higher than background at 25%. 21 pregnancies (24%) were complicated by GDM; 9 pregnancies (13.6%) had a preterm delivery and 2 of them (3%) an extreme premature delivery < 32 weeks. One woman had preeclampsia and one had a postpartum hemorrhage. The caesarean section (CS) rate was 20%. For every unit increase in maternal heteroplasmy levels there was a 26% increased risk of undergoing an assisted operative vaginal delivery (OR 1.26, 95% CI 1.04-1.53, P = 0.002, Bonferroni corrected P = 0.005) and an 18% increased risk of undergoing a CS (OR 1.18, 95% CI 1.01-1.39, P = 0.01, Bonferroni corrected P = 0.03) compared to a spontaneous vaginal delivery. There was a statistical significant correlation between maternal and offspring heteroplasmy levels. Spearman correlation rho = 0.96, 95% CI 0.78-0.99, P = 0.0002.

CONCLUSION

Women with mitochondrial disease appear to have more frequent obstetric complications including miscarriage and GDM. Pre-pregnancy diagnosis of m.3243A>G will enable the counseling of women and increase awareness of possible obstetric complications.

Genome-wide association analysis of plant architecture traits using doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic maize population

Selection in the Iowa Stiff Stalk Synthetic (BSSS) maize population for high yield, grain moisture, and root and stalk lodging has indirectly modified plant architecture traits that are important for adaptation to high plant density. In this study, we developed doubled haploid (DH) lines from the BSSS maize population in the earliest cycle of recurrent selection (BSSS), cycle 17 of reciprocal recurrent selection, [BSSS(R)17] and the cross between the two cycles [BSSS/BSSS(R)C17]. We aimed to determine the phenotypic variation and changes in agronomic traits that have occurred through the recurrent selection program in this population and to identify genes or regions in the genome associated with the plant architecture changes observed in the different cycles of selection. We conducted a per se evaluation of DH lines focusing on high heritability traits important for adaptation to high planting density and grain yield. Trends for reducing flowering time, anthesis-silking interval, ear height, and the number of primary tassel branches in BSSS(R)17 DH lines compared to BSSS and BSSS/BSSS(R)C17 DH lines were observed. Additionally, the BSSS(R)C17 DH lines showed more upright flag leaf angles. Using the entire panel of DH lines increased the number of SNP markers identified within candidate genes associated with plant architecture traits. The genomic regions identified for plant architecture traits in this study may help to elucidate the genetic basis of these traits and facilitate future work about marker-assisted selection or map-based cloning in maize breeding programs.

Posterior stabilised total knee arthroplasty is associated with improved post-operative knee specific function, health related quality of life and greater satisfaction when compared to cruciate retaining protheses

PURPOSE

To assess whether there were differences in knee specific function, health related quality of life (HRQoL), and satisfaction between patients with a cruciate retaining (CR) or a posterior stabilised (PS) total knee arthroplasty (TKA) at 1 and 2 years postoperatively.

METHODS

A retrospective review of TKA (CR and PS) patients from a prospectively collected arthroplasty database. Patient demographics, body mass index and ASA grade, Oxford knee score (OKS) and EuroQol 5-dimension (EQ-5D) 3-level, which was used to assess HRQoL, were collected preoperatively and 1 year and 2 years postoperatively. Regression was used to adjust for confounding factors.

RESULTS

The sample included 3122 TKA, of which 1009 (32.3%) were CR and 2112 (67.7%) were PS. The PS group were more likely to be female (odd ratio (OR) 1.26, p = 0.003) and undergo resurfacing of the patella (OR 6.63, p < 0.001). There was a significantly greater improvement in the 1 year OKS in the PS group (mean difference (MD) 0.9, p = 0.016). The PS TKA was independently associated with a greater 1 year (MD 1.1, 95% CI 0.4 to 1.9, p = 0.001) and 2 years (MD 0.8, p = 0.037) post-operative improvements in OKS. PS TKA was also independently associated with a greater 1 year (MD 0.021, p = 0.024) and 2 years (MD 0.022, p = 0.025) post-operative and change in EQ-5D utility compared to the CR group. The PS group was more likely to be satisfied with their outcome at 1 year (OR 1.75, p < 0.001) and at 2 years (OR 1.38, p = 0.001) when adjusting for confounders.

CONCLUSION

PS TKA was associated with a better knee specific function and HRQoL when compared to CR, but the clinical significance of this is not clear. However, the PS group was more likely to be satisfied with their outcome compared to the CR group.

2020-2021 field seasons of Maize GxE project within the Genomes to Fields Initiative

OBJECTIVES

This release note describes the Maize GxE project datasets within the Genomes to Fields (G2F) Initiative. The Maize GxE project aims to understand genotype by environment (GxE) interactions and use the information collected to improve resource allocation efficiency and increase genotype predictability and stability, particularly in scenarios of variable environmental patterns. Hybrids and inbreds are evaluated across multiple environments and phenotypic, genotypic, environmental, and metadata information are made publicly available.

DATA DESCRIPTION

The datasets include phenotypic data of the hybrids and inbreds evaluated in 30 locations across the US and one location in Germany in 2020 and 2021, soil and climatic measurements and metadata information for all environments (combination of year and location), ReadMe, and description files for each data type. A set of common hybrids is present in each environment to connect with previous evaluations. Each environment had a collaborator responsible for collecting and submitting the data, the GxE coordination team combined all the collected information and removed obvious erroneous data. Collaborators received the combined data to use, verify and declare that the data generated in their own environments was accurate. Combined data is released to the public with minimal filtering to maintain fidelity to the original data.

Molecular characterization of doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic (BSSS) maize population

Molecular characterization of a given set of maize germplasm could be useful for understanding the use of the assembled germplasm for further improvement in a breeding program, such as analyzing genetic diversity, selecting a parental line, assigning heterotic groups, creating a core set of germplasm and/or performing association analysis for traits of interest. In this study, we used single nucleotide polymorphism (SNP) markers to assess the genetic variability in a set of doubled haploid (DH) lines derived from the unselected Iowa Stiff Stalk Synthetic (BSSS) maize population, denoted as C0 (BSSS(R)C0), the seventeenth cycle of reciprocal recurrent selection in BSSS (BSSS(R)C17), denoted as C17 and the cross between BSSS(R)C0 and BSSS(R)C17 denoted as C0/C17. With the aim to explore if we have potentially lost diversity from C0 to C17 derived DH lines and observe whether useful genetic variation in C0 was left behind during the selection process since C0 could be a reservoir of genetic diversity that could be untapped using DH technology. Additionally, we quantify the contribution of the BSSS progenitors in each set of DH lines. The molecular characterization analysis confirmed the apparent separation and the loss of genetic variability from C0 to C17 through the recurrent selection process. Which was observed by the degree of differentiation between the C0_DHL versus C17_DHL groups by Wright's F-statistics (FST). Similarly for the population structure based on principal component analysis (PCA) revealed a clear separation among groups of DH lines. Some of the progenitors had a higher genetic contribution in C0 compared with C0/C17 and C17 derived DH lines. Although genetic drift can explain most of the genetic structure genome-wide, phenotypic data provide evidence that selection has altered favorable allele frequencies in the BSSS maize population through the reciprocal recurrent selection program.

Genomes to Fields 2022 Maize genotype by Environment Prediction Competition

OBJECTIVES

The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize GxE project field trials, leveraging the datasets previously generated by this project and other publicly available data.

DATA DESCRIPTION

This resource used data from the Maize GxE project within the G2F Initiative [1]. The dataset included phenotypic and genotypic data of the hybrids evaluated in 45 locations from 2014 to 2022. Also, soil, weather, environmental covariates data and metadata information for all environments (combination of year and location). Competitors also had access to ReadMe files which described all the files provided. The Maize GxE is a collaborative project and all the data generated becomes publicly available [2]. The dataset used in the 2022 Prediction Competition was curated and lightly filtered for quality and to ensure naming uniformity across years.

2018-2019 field seasons of the Maize Genomes to Fields (G2F) G x E project

OBJECTIVES

This report provides information about the public release of the 2018-2019 Maize G X E project of the Genomes to Fields (G2F) Initiative datasets. G2F is an umbrella initiative that evaluates maize hybrids and inbred lines across multiple environments and makes available phenotypic, genotypic, environmental, and metadata information. The initiative understands the necessity to characterize and deploy public sources of genetic diversity to face the challenges for more sustainable agriculture in the context of variable environmental conditions.

DATA DESCRIPTION

Datasets include phenotypic, climatic, and soil measurements, metadata information, and inbred genotypic information for each combination of location and year. Collaborators in the G2F initiative collected data for each location and year; members of the group responsible for coordination and data processing combined all the collected information and removed obvious erroneous data. The collaborators received the data before the DOI release to verify and declare that the data generated in their own locations was accurate. ReadMe and description files are available for each dataset. Previous years of evaluation are already publicly available, with common hybrids present to connect across all locations and years evaluated since this project's inception.

Yield prediction through integration of genetic, environment, and management data through deep learning

Accurate prediction of the phenotypic outcomes produced by different combinations of genotypes, environments, and management interventions remains a key goal in biology with direct applications to agriculture, research, and conservation. The past decades have seen an expansion of new methods applied toward this goal. Here we predict maize yield using deep neural networks, compare the efficacy of 2 model development methods, and contextualize model performance using conventional linear and machine learning models. We examine the usefulness of incorporating interactions between disparate data types. We find deep learning and best linear unbiased predictor (BLUP) models with interactions had the best overall performance. BLUP models achieved the lowest average error, but deep learning models performed more consistently with similar average error. Optimizing deep neural network submodules for each data type improved model performance relative to optimizing the whole model for all data types at once. Examining the effect of interactions in the best-performing model revealed that including interactions altered the model's sensitivity to weather and management features, including a reduction of the importance scores for timepoints expected to have a limited physiological basis for influencing yield-those at the extreme end of the season, nearly 200 days post planting. Based on these results, deep learning provides a promising avenue for the phenotypic prediction of complex traits in complex environments and a potential mechanism to better understand the influence of environmental and genetic factors.

The Glasgow Microenvironment Score and risk and site of recurrence in TNM I-III colorectal cancer

BACKGROUND

Glasgow Microenvironment Score (GMS) stratifies long-term survival into three groups based on tumour phenotype: peritumoural inflammation (Klintrup-Mäkinen (KM)) and tumour stroma percentage (TSP). However, it is not known if the location of disease recurrence is influenced by the GMS category.

METHODS

Seven hundred and eighty-three TNM I-III colorectal cancers (CRC) were included. GMS (GMS0-high KM; GMS1-low KM, low TSP; GMS2-low KM, high TSP) and cancer-specific survival (CSS), overall survival (OS) and disease recurrence were assessed using Cox regression analysis.

RESULTS

Of the 783 patients, 221 developed CRC recurrence; 65 developed local recurrence + systemic disease. GMS was independent for CSS (HR 1.50, 95% CI 1.17-1.92, p < 0.001) and OS (HR 1.23, 1.05-1.44, p = 0.01). Higher GMS category was associated with T-stage, N-stage, emergency presentation and venous invasion. GMS was independent for local+systemic recurrence (HR 11.53, 95% CI 1.45-91.85, p = 0.04) and distant-only recurrence (HR 3.01, 95% CI 1.59-5.71, p = 0.002). GMS 2 disease did not appear to have statistically better outcomes with adjuvant chemotherapy in high-risk disease.

CONCLUSION

Although confounded by a higher rate of T4 and node-positive disease, GMS 1 and 2 are associated with an increased risk of local and distant recurrence. GMS is an independent poor prognostic indicator for recurrent colorectal cancer. Higher GMS patients may benefit from enhanced postoperative surveillance.

Incisional hernia following colorectal cancer surgery according to suture technique: Hughes Abdominal Repair Randomized Trial (HART)

BACKGROUND

Incisional hernias cause morbidity and may require further surgery. HART (Hughes Abdominal Repair Trial) assessed the effect of an alternative suture method on the incidence of incisional hernia following colorectal cancer surgery.

METHODS

A pragmatic multicentre single-blind RCT allocated patients undergoing midline incision for colorectal cancer to either Hughes closure (double far-near-near-far sutures of 1 nylon suture at 2-cm intervals along the fascia combined with conventional mass closure) or the surgeon's standard closure. The primary outcome was the incidence of incisional hernia at 1 year assessed by clinical examination. An intention-to-treat analysis was performed.

RESULTS

Between August 2014 and February 2018, 802 patients were randomized to either Hughes closure (401) or the standard mass closure group (401). At 1 year after surgery, 672 patients (83.7 per cent) were included in the primary outcome analysis; 50 of 339 patients (14.8 per cent) in the Hughes group and 57 of 333 (17.1 per cent) in the standard closure group had incisional hernia (OR 0.84, 95 per cent c.i. 0.55 to 1.27; P = 0.402). At 2 years, 78 patients (28.7 per cent) in the Hughes repair group and 84 (31.8 per cent) in the standard closure group had incisional hernia (OR 0.86, 0.59 to 1.25; P = 0.429). Adverse events were similar in the two groups, apart from the rate of surgical-site infection, which was higher in the Hughes group (13.2 versus 7.7 per cent; OR 1.82, 1.14 to 2.91; P = 0.011).

CONCLUSION

The incidence of incisional hernia after colorectal cancer surgery is high. There was no statistical difference in incidence between Hughes closure and mass closure at 1 or 2 years.

REGISTRATION NUMBER

ISRCTN25616490 (http://www.controlled-trials.com).

Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study

BACKGROUND

Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications.

METHODS

We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC).

FINDINGS

In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]).

INTERPRETATION

In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required.

FUNDING

British Journal of Surgery Society.

Usefulness of temperate-adapted maize lines developed by doubled haploid and single-seed descent methods

Spontaneous haploid genome doubling is not associated with undesirable linkage drag effects. The presence of spontaneous doubling genes allows maximum exploitation of variability from the temperate-adapted BS39 population Tropical non-elite maize (Zea mays L.) germplasm, such as BS39, provides a unique opportunity for broadening the genetic base of U.S. Corn Belt germplasm. In vivo doubled haploid (DH) technology has been used to efficiently exploit non-elite germplasm. It can help to purge deleterious recessive alleles. The objectives of this study were to determine the usefulness of BS39-derived inbred lines using both SSD and DH methods, to determine the impact of spontaneous as compared with artificial haploid genome doubling on genetic variance among BS39-derived DH lines, and to identify SNP markers associated with agronomic traits among BS39 inbreds monitored at testcross level. We developed two sets of inbred lines directly from BS39 by DH and SSD methods, named BS39_DH and BS39_SSD. Additionally, two sets were derived from a cross between BS39 and A427 (SHGD donor) by DH and SSD methods, named BS39 × A427_DH and BS39 × A427_SSD, respectively. Grain yield, moisture, plant height, ear height, stalk lodging, and root lodging were measured to estimate genetic parameters. For genome-wide association analysis, inbred lines were genotyped using genotype-by-sequencing and Diversity Array Technology Sequencing (DArTSeq). Some BS39-derived inbred lines performed better than elite germplasm inbreds and all sets showed significant genetic variance. The presence of spontaneous haploid genome doubling genes did not affect performance of inbred lines. Five SNPs were significant and three of them located within genes related to plant development or abiotic stresses. These results demonstrate the potential of BS39 to add novel alleles to temperate elite germplasm.

Limited surface impacts of the January 2021 sudden stratospheric warming

Subseasonal weather prediction can reduce economic disruption and loss of life, especially during “windows of opportunity” when noteworthy events in the Earth system are followed by characteristic weather patterns. Sudden stratospheric warmings (SSWs), breakdowns of the winter stratospheric polar vortex, are one such event. They often precede warm temperatures in Northern Canada and cold, stormy weather throughout Europe and the United States - including the most recent SSW on January 5th, 2021. Here we assess the drivers of surface weather in the weeks following the SSW through initial condition “scrambling” experiments using the real-time CESM2(WACCM6) Earth system prediction framework. We find that the SSW itself had a limited impact, and that stratospheric polar vortex stretching and wave reflection had no discernible contribution to the record cold in North America in February. Instead, the tropospheric circulation and bidirectional coupling between the troposphere and stratosphere were dominant contributors to variability.

Experimental forecasts show that a disturbed stratospheric polar vortex was not to blame for the deadly North American cold air outbreak in February 2021 - but it may have acted to sustain weather patterns and increase predictability in early 2021.

Current status of Phytophthora in Australia

Among the most economically relevant and environmentally devastating diseases globally are those caused by Phytophthora species. In Australia, production losses in agriculture and forestry result from several well-known cosmopolitan Phytophthora species and infestation of natural ecosystems by Phytophthora cinnamomi have caused irretrievable loss to biodiversity especially in proteaceous dominated heathlands. For this review, all available records of Phytophthora in Australia were collated and curated, resulting in a database of 7 869 records, of which 2 957 have associated molecular data. Australian databases hold records for 99 species, of which 20 are undescribed. Eight species have no records linked to molecular data, and their presence in Australia is considered doubtful. The 99 species reside in 10 of the 12 clades recognised within the complete phylogeny of Phytophthora. The review includes discussion on each of these species' status and additional information provided for another 29 species of concern. The first species reported in Australia in 1900 was Phytophthora infestans. By 2000, 27 species were known, predominantly from agriculture. The significant increase in species reported in the subsequent 20 years has coincided with extensive surveys in natural ecosystems coupled with molecular taxonomy and the recognition of numerous new phylogenetically distinct but morphologically similar species. Routine and targeted surveys within Australian natural ecosystems have resulted in the description of 27 species since 2009. Due to the new species descriptions over the last 20 years, many older records have been reclassified based on molecular identification. The distribution of records is skewed toward regions with considerable activity in high productivity agriculture, horticulture and forestry, and native vegetation at risk from P. cinnamomi. Native and exotic hosts of different Phytophthora species are found throughout the phylogeny; however, species from clades 1, 7 and 8 are more likely to be associated with exotic hosts. One of the most difficult challenges to overcome when establishing a pest status is a lack of reliable data on the current state of a species in any given country or location. The database compiled here for Australia and the information provided for each species overcomes this challenge. This review will aid federal and state governments in risk assessments and trade negotiations by providing a comprehensive resource on the current status of Phytophthora species in Australia. Citation: Burgess TI, Edwards J, Drenth A, et al. 2021. Current status of Phytophthora in Australia. Persoonia 47: 151-177. https://doi.org/10.3767/persoonia.2021.47.05.

High multidrug resistance in urinary tract infections in a tertiary hospital, Kathmandu, Nepal

SETTING:

Tribhuvan University Teaching Tertiary Care Hospital, Kathmandu, Nepal, May–October 2019.

OBJECTIVE:

1) To describe the bacteriological profile, 2) to identify the antimicrobial resistance (AMR) pattern, and 3) to find the demographic characteristics associated with the presence of bacterial growth and multidrug resistance (MDR) in adult urine samples undergoing culture and drug susceptibility testing.

DESIGN:

This was a hospital-based, cross-sectional study using routine laboratory records.

RESULTS:

Among 11,776 urine samples, 16% (1,865/11,776) were culture-positive, predominantly caused by Escherichia coli (1,159/1,865; 62%). We found a high prevalence of resistance to at least one antibiotic (1,573/1,865; 84%) and MDR (1,000/1,865; 54%). Resistance to commonly used antibiotics for urinary tract infections (UTIs) such as ceftazidime, levofloxacin, cefepime and ampicillin was high. Patients aged ⩾60 years (adjusted prevalence ratio [aPR] 1.6, 95% CI 1.4–1.7) were more likely to have culture positivity. Patients with age ⩾45 years (45–59 years: aPR 1.5, 95% CI 1.3–1.7; ⩾60 years: aPR 1.4, 95% CI 1.2–1.6), male sex (aPR 1.3, 95% CI 1.2–1.5) and from inpatient settings (aPR 1.4, 95% CI 1.2–1.7) had significantly higher prevalence of MDR.

CONCLUSION:

Urine samples from a tertiary hospital showed high prevalence of E. coli and MDR to routinely used antibiotics, especially among inpatients. Regular surveillance and application of updated antibiograms are crucial to monitor the AMR situation in Nepal.

High drug resistance among Gram-negative bacteria in sputum samples from an intensive care unit in Nepal

SETTING

Tribhuvan University Teaching Hospital, Kathmandu, Nepal.

OBJECTIVES

1) To report the number and proportion of Pseudomonas, Acinetobacter, Burkholderia, Stenotrophomonas (PABS) species among intensive care unit (ICU) patients with sputum culture; and 2) to assess antimicrobial resistance patterns, demographic and clinical characteristics associated with resistance to at least one antibiotic and ICU discharge outcomes among those patients with PABS species admitted to hospital between 14 April 2018 and 13 April 2019.

DESIGN

This was a hospital-based, cross-sectional study using secondary data.

RESULTS

Of 166 who underwent sputum culture, 104 (63%) had bacterial growth, of which, 67 (64%) showed PABS species. Of the positive cultures, Pseudomonas, Acinetobacter, Burkholderia and Stenotrophomonas were present in respectively 32 (30.7%), 31 (29.8%), 1 (1%) and 3 (2.8%). Pseudomonas showed a high level of resistance to levofloxacin (61%), cefepime (50%) and amikacin (50%). Acinetobacter was largely resistant to cefepime (95%), imipenem (92%) and levofloxacin (86%). Of the 67 with PABS infection, 32 (48%) died.

CONCLUSION

The study showed a high prevalence of Pseudomonas and Acinetobacter and the emergence of Stenotrophomonas in sputum culture samples of ICU patients. This highlights the need for monitoring PABS and associated resistance patterns to reduce mortality in ICU patients.

Current status of Phytophthora in Australia

Among the most economically relevant and environmentally devastating diseases globally are those caused by Phytophthora species. In Australia, production losses in agriculture and forestry result from several well-known cosmopolitan Phytophthora species and infestation of natural ecosystems by Phytophthora cinnamomi have caused irretrievable loss to biodiversity especially in proteaceous dominated heathlands. For this review, all available records of Phytophthora in Australia were collated and curated, resulting in a database of 7 869 records, of which 2 957 have associated molecular data. Australian databases hold records for 99 species, of which 20 are undescribed. Eight species have no records linked to molecular data, and their presence in Australia is considered doubtful. The 99 species reside in 10 of the 12 clades recognised within the complete phylogeny of Phytophthora. The review includes discussion on each of these species' status and additional information provided for another 29 species of concern. The first species reported in Australia in 1900 was Phytophthora infestans. By 2000, 27 species were known, predominantly from agriculture. The significant increase in species reported in the subsequent 20 years has coincided with extensive surveys in natural ecosystems coupled with molecular taxonomy and the recognition of numerous new phylogenetically distinct but morphologically similar species. Routine and targeted surveys within Australian natural ecosystems have resulted in the description of 27 species since 2009. Due to the new species descriptions over the last 20 years, many older records have been reclassified based on molecular identification. The distribution of records is skewed toward regions with considerable activity in high productivity agriculture, horticulture and forestry, and native vegetation at risk from P. cinnamomi. Native and exotic hosts of different Phytophthora species are found throughout the phylogeny; however, species from clades 1, 7 and 8 are more likely to be associated with exotic hosts. One of the most difficult challenges to overcome when establishing a pest status is a lack of reliable data on the current state of a species in any given country or location. The database compiled here for Australia and the information provided for each species overcomes this challenge. This review will aid federal and state governments in risk assessments and trade negotiations by providing a comprehensive resource on the current status of Phytophthora species in Australia. Citation: Burgess TI, Edwards J, Drenth A, et al. 2021. Current status of Phytophthora in Australia. Persoonia 47: 151-177. https://doi.org/10.3767/persoonia.2021.47.05.

O10 Myocardial tolerance to exsanguination and retrieval using whole blood-selective aortic arch perfusion

Introduction

Exsanguination cardiac arrest is the leading preventable cause of death in trauma. Treatment modalities are limited, and prognosis remains dismal. Selective aortic arch perfusion (SAAP) is an emerging endovascular resuscitation technique consisting of aortic occlusion and perfusion of coronary and cerebral circulation with oxygenated resuscitation fluid. Translational research has demonstrated promising outcomes; however, little is known about the duration of cardiac arrest beyond which the myocardium cannot be resuscitated. The aims of this study are to assess the myocardial tolerance to exsanguination cardiac arrest before successful return of spontaneous circulation (ROSC) following resuscitation with SAAP, and 1-hour survival.

Method

23 male adult swine were anaesthetised and instrumented. Controlled hemorrhage was performed until cardiac arrest defined by MAP &lt;20 mmHg. Animals were randomized into 3 groups: 5, 10 and 15 minutes of cardiac arrest before resuscitation with SAAP. Following ROSC animals were observed for 60 minutes.

Result

Baseline characteristics were similar between groups (P &gt; 0.05). ROSC was 100% (8/8) in the 5 min group, 75% (6/8) and 43% (3/7) in 10- and 15-min groups respectively (P = 0.042). 60 min survival was 75%, 50% and 14% in 5-, 10- and 15-min groups respectively (P = 0.015). 1-hour survivors in the 5 min group required less noradrenaline 23.6 (±7.4) compared to other animals 40.9 (±25.8), (P = 0.008).

Conclusion

Selective aortic arch perfusion is an effective resuscitative tool in eliciting ROSC in a swine model of exsanguination cardiac arrest lasting &gt;5 min. Sustainable resuscitability using SAAP declines after 10 min of exsanguination cardiac arrest.

Take-home Message

SAAP is an emerging resuscitation technique with promising outcomes in exsanguination cardiac arrest and may be a segway to Extracorporeal life support. The time limit for resuscitability of the myocardium lies somewhere between 10 and 15 min after the start of exsanguination cardiac arrest.

The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment

High-dimensional and high-throughput genomic, field performance, and environmental data are becoming increasingly available to crop breeding programs, and their integration can facilitate genomic prediction within and across environments and provide insights into the genetic architecture of complex traits and the nature of genotype-by-environment interactions. To partition trait variation into additive and dominance (main effect) genetic and corresponding genetic-by-environment variances, and to identify specific environmental factors that influence genotype-by-environment interactions, we curated and analyzed genotypic and phenotypic data on 1918 maize (Zea mays L.) hybrids and environmental data from 65 testing environments. For grain yield, dominance variance was similar in magnitude to additive variance, and genetic-by-environment variances were more important than genetic main effect variances. Models involving both additive and dominance relationships best fit the data and modeling unique genetic covariances among all environments provided the best characterization of the genotype-by-environment interaction patterns. Similarity of relative hybrid performance among environments was modeled as a function of underlying weather variables, permitting identification of weather covariates driving correlations of genetic effects across environments. The resulting models can be used for genomic prediction of mean hybrid performance across populations of environments tested or for environment-specific predictions. These results can also guide efforts to incorporate high-throughput environmental data into genomic prediction models and predict values in new environments characterized with the same environmental characteristics.

POS1400 A SYSTEMATIC REVIEW OF INTERNATIONAL GUIDELINES REGARDING THE ROLE OF RADIOGRAPHY IN THE DIAGNOSIS OF OSTEOARTHRITIS

Background:

A substantial proportion of primary care osteoarthritis (OA) consultations are associated with an X-ray request (1,2). Uncertainty exists regarding the ability of radiography to improve a clinical OA diagnosis, and the over-use of radiography may lead to inappropriate referrals due to severe radiographic features that do not correlate with patients’ symptoms. Additionally, there are cost implications of unnecessarily imaging such a prevalent disease. As evidence questions the utility of routine radiography in OA, the extent to which radiography is supported by international guidelines is unknown.

Objectives:

To undertake a systematic review and narrative synthesis of UK and international guideline recommendations on the role of radiography in the diagnosis of OA.

Methods:

A systematic search of eleven electronic databases (including EMBASE, MEDLINE CINAHL, Epistemonikos and Guideline Central) and the websites of nine professional organisations (including NICE, Royal College of Radiologists (RCR), EULAR, and the American College of Radiology (ACR)) identified the most recent evidence-based guidelines produced by professional organisations on the role of imaging in OA. Guidelines not addressing the role of radiography in the diagnosis of OA were excluded, as were non-English and spinal OA guidelines. Each title was screened by one reviewer whilst each abstract and full text underwent dual screening. A single reviewer, using a standard proforma, undertook data extraction. Each guideline was independently appraised by two reviewers using the AGREE II tool. A narrative synthesis of the nature and consistency of OA radiographic recommendations was performed.

Results:

18 evidence-based OA guidelines published between 1998-2019 were included. These guidelines considered OA at any joint (n=8), or at the knee (n=3), hip (n=2), hand (n=2), wrist (n=1), foot (n=1), and ankle (n=1). Seven guidelines were produced by European organisations; four guidelines were produced by EULAR. Guidelines were targeted at general practitioners (n=11), radiologists (n=7), rheumatologist (n=4) and orthopaedic surgeons (n=3). Using the AGREE II tool, the identified guidelines scored highly on rigour of development (mean score 69%) but poorly on applicability (32%). All 18 guidelines recommended X-rays as the first-line modality, where imaging was indicated. A clinical diagnosis of OA without radiographic confirmation was recommended by all eleven guidelines produced by organisations represented general practitioners, with seven guidelines justifying this due to a poor correlation between radiographic features and clinical symptoms. Only three guidelines explicitly discouraged the routine use of radiography for the diagnosis of OA and only two guidelines reassured practitioners of a low probability of missing serious pathology when not routinely requesting radiographs. Guidelines produced by organisations representing radiologists were more supportive of radiography. The ACR recommended radiographic confirmation in patients suspected to have OA at the hand, wrist, hip, knee, ankle, and foot. Conversely, the RCR recommended radiographic confirmation in patients suspected to have OA at the hand, feet, and hip, but not the knee.

Conclusion:

Differences in guideline recommendations on the utility of radiography in OA appear related to country/region, professional organisation, and joint. The use and utility of radiography in OA may need to be reviewed in light of a shift towards remote consultations, a change that has been accelerated by COVID-19 in many countries.

References:

[1]Yu D, Jordan K, Bedson J, Englund M, Blyth F, Turkiewicz A et al. Population trends in the incidence and initial management of osteoarthritis: age-period-cohort analysis of the Clinical Practice Research Datalink, 1992–2013. Rheumatology. 2017;56(11):1902-1917.

[2]Brand C, Harrison C, Tropea J, Hinman R, Britt H, Bennell K. Management of Osteoarthritis in General Practice in Australia. Arthritis Care & Research. 2014;66(4):551-558

Acknowledgements:

JJE is funded by an Academic Clinical Lectureship from the National Institute for Health Research (NIHR) for this research project (CL-2016-10-003). The views expressed in this publication are those of the author(s) and not necessarily those of the NIHR, NHS or the UK Department of Health and Social Care.

Disclosure of Interests:

None declared

O3: EVALUATION OF A 3D PRINTED BIO-ARTIFICIAL MUSCLE-ORGANOID FOR TRAUMA RESEARCH

Introduction

Organoid models serve as a robust platform for investigating injury and disease in vitro. Currently, representative models of injury are lacking to investigate the effects of traumatic damage to organs and tissues. Here we describe a three-dimensional in vitro model of high strain rate loading seen in traumatic blast injury.

Method

3D printing resins were tested for Young's Modulus & Poisson Ratio using a universal testing Organoids were then loaded into a 3D Printed bioreactor for high strain rate loading using a split Hopkinson pressure bar device. machine and digital image. Euler beam theory was used to evaluate post deflection. C2C12 myoblasts were seeded in fibrin hydrogels around 3D printed posts using a custom designed jig. High strain rate loading was applied to constructs, then qPCR & Fluorescent Live/Dead staining was utilised to demonstrate cell alignment and myotube formation.

Result

Young's modulus of Flexible resin was 11.51Mpa. Differentiated C2C12 myoblasts were capable of alignment between posts and expression of key markers of differentiation shown by qPCR & imaging. MYH5, MYH2 & MYH1 all had a &gt; 1.5 old increase in expression compared to undifferentiated controls. Organoids were capable of survival in bioreactor casings for over 24 hours and were intact after application of high strain rate loading.

Conclusion

This work demonstrates the first use of a 3D printed organoid in vitro model to investigate high strain rate loading for trauma research. This organoid is capable of high throughput analysis to facilitate genomic and protein level expression analysis.

Take-home message

This work demonstrates the first use of a 3D printed organoid in vitro model to investigate high strain rate loading for trauma research.

Utility of Climatic Information via Combining Ability Models to Improve Genomic Prediction for Yield Within the Genomes to Fields Maize Project

Genomic prediction provides an efficient alternative to conventional phenotypic selection for developing improved cultivars with desirable characteristics. New and improved methods to genomic prediction are continually being developed that attempt to deal with the integration of data types beyond genomic information. Modern automated weather systems offer the opportunity to capture continuous data on a range of environmental parameters at specific field locations. In principle, this information could characterize training and target environments and enhance predictive ability by incorporating weather characteristics as part of the genotype-by-environment (G×E) interaction component in prediction models. We assessed the usefulness of including weather data variables in genomic prediction models using a naïve environmental kinship model across 30 environments comprising the Genomes to Fields (G2F) initiative in 2014 and 2015. Specifically four different prediction scenarios were evaluated (i) tested genotypes in observed environments; (ii) untested genotypes in observed environments; (iii) tested genotypes in unobserved environments; and (iv) untested genotypes in unobserved environments. A set of 1,481 unique hybrids were evaluated for grain yield. Evaluations were conducted using five different models including main effect of environments; general combining ability (GCA) effects of the maternal and paternal parents modeled using the genomic relationship matrix; specific combining ability (SCA) effects between maternal and paternal parents; interactions between genetic (GCA and SCA) effects and environmental effects; and finally interactions between the genetics effects and environmental covariates. Incorporation of the genotype-by-environment interaction term improved predictive ability across all scenarios. However, predictive ability was not improved through inclusion of naive environmental covariates in G×E models. More research should be conducted to link the observed weather conditions with important physiological aspects in plant development to improve predictive ability through the inclusion of weather data.

Redefining genera of cereal pathogens: Oculimacula, Rhynchosporium and Spermospora

The taxonomy of Oculimacula, Rhynchosporium and Spermospora is re-evaluated, along with that of phylogenetically related genera. Isolates are identified using comparisons of DNA sequences of the internal transcribed spacer ribosomal RNA locus (ITS), partial translation elongation factor 1-alpha (tef1), actin (act), DNA-directed RNA polymerase II largest (rpb1) and second largest subunit (rpb2) genes, and the nuclear ribosomal large subunit (LSU), combined with their morphological characteristics. Oculimacula is restricted to two species, O. acuformis and O. yallundae, with O. aestiva placed in Cyphellophora, and O. anguioides accommodated in a new genus, Helgardiomyces. Rhynchosporium s. str. is restricted to species with 1-septate conidia and hooked apical beaks, while Rhynchobrunnera is introduced for species with 1–3-septate, straight conidia, lacking any apical beak. Rhynchosporium graminicola is proposed to replace the name R. commune applied to the barley scald pathogen based on nomenclatural priority. Spermospora is shown to be paraphyletic, representing Spermospora (type: S. subulata), with three new species, S. arrhenatheri, S. loliiphila and S. zeae, and Neospermospora gen. nov. (type: N. avenae). Ypsilina (type: Y. graminea), is shown to be monophyletic, but appears to be of minor importance on cereals. Finally, Vanderaaea gen. nov. (type: V. ammophilae), is introduced as a new coelomycetous fungus occurring on dead leaves of Ammophila arenaria.

Citation: Crous PW, Braun U, McDonald BA, Lennox CL, Edwards J, Mann RC, Zaveri A, Linde CC, Dyer PS, Groenewald JZ (2020). Redefining genera of cereal pathogens: Oculimacula, Rhynchosporium and Spermospora. Fungal Systematics and Evolution7: 67–98. doi: 10.3114/fuse.2021.07.04

Non-randomized studies should be considered for assessing surgical techniques in rectal prolapse: prospective cohort study

AIM

Randomized trials comparing surgical techniques for rectal prolapse are not always feasible. We assessed whether non-randomized comparisons of those who have had surgery with those still waiting would be confounding baseline health status.

METHOD

This was a prospective cohort study in seven UK hospitals. Participants were ≥ 18 years and listed for surgical interventions of equivalent intensity for rectal prolapse. They were defined as short or long waiters (≤ 18 or > 18 weeks, respectively). Time on the waiting list was compared with baseline comorbidity (Charlson comorbidity index) and change from baseline in health status (EQ-5D-5L) at the time of surgery.

RESULTS

In all, 203 patients were analysed. Median (interquartile range) waiting time was 13.7 weeks (8.1, 20.4) varying across sites. Baseline comorbidity was not an important predictor of waiting time. Median Charlson comorbidity index was 2 (0, 3) for short and 1 (0, 3) for long waiters. A change in waiting time by a week was associated with negligible improvement in the EQ-5D-5L index of 0.001 (95% CI -0.000 to 0.003, P = 0.106).

CONCLUSION

Negligible change in patient reported health status while on the waiting list and lack of effect of comorbidities in influencing waiting time support the use of non-randomized pre-/post-studies to compare the effects of surgical interventions for rectal prolapse.

A packaged intervention to improve viral load monitoring within a deeply rural health district of South Africa

BACKGROUND

The KwaZulu-Natal (KZN) province of South Africa has the highest prevalence of HIV infection in the world. Viral load (VL) testing is a crucial tool for clinical and programmatic monitoring. Within uMkhanyakude district, VL suppression rates were 91% among patients with VL data; however, VL performance rates averaged only 38·7%. The objective of this study was to determine if enhanced clinic processes and community outreach could improve VL monitoring within this district.

METHODS

A packaged intervention was implemented at three rural clinics in the setting of the KZN HIV AIDS Drug Resistance Surveillance Study. This included file hygiene, outreach, a VL register and documentation revisions. Chart audits were used to assess fidelity. Outcome measures included percentage VL performed and suppressed. Each rural clinic was matched with a peri-urban clinic for comparison before and after the start of each phase of the intervention. Monthly sample proportions were modelled using quasi-likelihood regression methods for over-dispersed binomial data.

RESULTS

Mkuze and Jozini clinics increased VL performance overall from 33·9% and 35·3% to 75·8% and 72·4%, respectively which was significantly greater than the increases in the comparison clinics (RR 1·86 and 1·68, p < 0·01). VL suppression rates similarly increased overall by 39·3% and 36·2% (RR 1·84 and 1·70, p < 0·01). The Chart Intervention phase showed significant increases in fidelity 16 months after implementation.

CONCLUSIONS

The packaged intervention improved VL performance and suppression rates overall but was significant in Mkuze and Jozini. Larger sustained efforts will be needed to have a similar impact throughout the province.

Pulmonary Metastasectomy in Colorectal Cancer: updated analysis of 93 randomized patients - control survival is much better than previously assumed

AIM

Lung metastases from colorectal cancer are resected in selected patients in the belief that this confers a significant survival advantage. It is generally assumed that the 5-year survival of these patients would be near zero without metastasectomy. We tested the clinical effectiveness of this practice in Pulmonary Metastasectomy in Colorectal Cancer (PulMiCC), a randomized, controlled noninferiority trial.

METHOD

Multidisciplinary teams in 14 hospitals recruited patients with resectable lung metastases into a two-arm trial. Randomization was remote and stratified according to site, with minimization for age, sex, primary cancer stage, interval since primary resection, prior liver involvement, number of metastases and carcinoembryonic antigen level. The trial management group was blind to patient allocation until after intention-to-treat analysis.

RESULTS

From 2010 to 2016, 93 participants were randomized. These patients were 35-86 years of age and had between one and six lung metastases at a median of 2.7 years after colorectal cancer resection; 29% had prior liver metastasectomy. The patient groups were well matched and the characteristics of these groups were similar to those of observational studies. The median survival after metastasectomy was 3.5 (95% CI: 3.1-6.6) years compared with 3.8 (95% CI: 3.1-4.6) years for controls. The estimated unadjusted hazard ratio for death within 5 years, comparing the metastasectomy group with the control group, was 0.93 (95% CI: 0.56-1.56). Use of chemotherapy or local ablation was infrequent and similar in each group.

CONCLUSION

Patients in the control group (who did not undergo lung metastasectomy) have better survival than is assumed. Survival in the metastasectomy group is comparable with the many single-arm follow-up studies. The groups were well matched with features similar to those reported in case series.

Reducing patient harm following inadvertent endobronchial placecement of nasogastric tubes in patients with SARS-COV-2

Introduction

Methods

Results

Discussion

The effect of postoperative complications on survival and recurrence after surgery for breast cancer: A systematic review and meta-analysis

BACKGROUND

This systematic review investigated the impact of complications on long term outcomes for patients with primary invasive operable breast cancer.

METHODS

A systematic review was performed using appropriate keywords, and meta-analysis using a random effects model completed.

RESULTS

Ten retrospective cohort studies, including 37,657 patients were included. Five studies identified a relationship between wound complications, infection and pyrexia and recurrence or recurrence-free survival. Risk of recurrence, 1-year and 5-year recurrence-free survival and overall survival were related to complications, particularly for patients with poor Nottingham Prognostic Index. Five studies failed to demonstrate a relationship between complications and prognosis. Complication was found to significantly affect 5-year recurrence-free survival (HR 1.48 95 % CI 1.02-2.14, p = 0.04) but not recurrence (HR 2.39, 95 %CI 0.94-6.07, p = 0.07), with a high degree of heterogeneity amongst analysed studies (I2 = 95 %).

DISCUSSION

Further research is needed to quantify the effects of postoperative complication on prognosis following surgery for breast cancer.

New and Interesting Fungi. 3

Seven new genera, 26 new species, 10 new combinations, two epitypes, one new name, and 20 interesting new host and / or geographical records are introduced in this study. New genera are: Italiofungus (based on Italiofungus phillyreae) on leaves of Phillyrea latifolia (Italy); Neolamproconium (based on Neolamproconium silvestre) on branch of Tilia sp. (Ukraine); Neosorocybe (based on Neosorocybe pini) on trunk of Pinus sylvestris (Ukraine); Nothoseptoria (based on Nothoseptoria caraganae) on leaves of Caragana arborescens (Russia); Pruniphilomyces (based on Pruniphilomyces circumscissus) on Prunus cerasus (Russia); Vesiculozygosporium (based on Vesiculozygosporium echinosporum) on leaves of Muntingia calabura (Malaysia); Longiseptatispora (based on Longiseptatispora curvata) on leaves of Lonicera tatarica (Russia). New species are: Barrmaelia serenoae on leaf of Serenoa repens (USA); Chaetopsina gautengina on leaves of unidentified grass (South Africa); Chloridium pini on fallen trunk of Pinus sylvestris (Ukraine); Cadophora fallopiae on stems of Reynoutria sachalinensis (Poland); Coleophoma eucalyptigena on leaf litter of Eucalyptus sp. (Spain); Cylindrium corymbiae on leaves of Corymbia maculata (Australia); Diaporthe tarchonanthi on leaves of Tarchonanthus littoralis (South Africa); Elsinoe eucalyptorum on leaves of Eucalyptus propinqua (Australia); Exophiala quercina on dead wood of Quercus sp., (Germany); Fusarium californicum on cambium of budwood of Prunus dulcis (USA); Hypomyces gamsii on wood of Alnus glutinosa (Ukraine); Kalmusia araucariae on leaves of Araucaria bidwillii (USA); Lectera sambuci on leaves of Sambucus nigra (Russia); Melanomma populicola on fallen twig of Populus canadensis (Netherlands), Neocladosporium syringae on branches of Syringa vulgarishorus (Ukraine); Paraconiothyrium iridis on leaves of Iris pseudacorus (Ukraine); Pararoussoella quercina on branch of Quercus robur (Ukraine); Phialemonium pulveris from bore dust of deathwatch beetle (France); Polyscytalum pinicola on needles of Pinus tecunumanii (Malaysia); Acervuloseptoria fraxini on Fraxinus pennsylvanica (Russia); Roussoella arundinacea on culms of Arundo donax (Spain); Sphaerulina neoaceris on leaves of Acer negundo (Russia); Sphaerulina salicicola on leaves of Salix fragilis (Russia); Trichomerium syzygii on leaves of Syzygium cordatum (South Africa); Uzbekistanica vitis-viniferae on dead stem of Vitis vinifera (Ukraine); Vermiculariopsiella eucalyptigena on leaves of Eucalyptus sp. (Australia).

Age at migration and the risk of psychotic disorders: a systematic review and meta-analysis

OBJECTIVE

To conduct a systematic review and meta-analysis of the existing evidence on the association between age at migration and the risk of psychotic disorders.

METHODS

Observational studies were eligible for inclusion if they presented data on the association between age at migration and the risk of psychotic disorders among first-generation migrant groups. We used two random effects meta-analyses to pool effect estimates for each stratum of age at migration relative to (i) a native-born reference category and (ii) the youngest age stratum (0 to 2 years).

RESULTS

Ten studies met inclusion criteria, and five were included in the meta-analysis. The risk of psychotic disorder among people who migrate prior to age 18 is nearly twice as high as the native-born population, with no evidence of effect modification by age strata. People who migrate during early adulthood (19 to 29 years) have a similar risk of psychotic disorder as the native-born population (IRR = 0.93, 95% CI = 0.60, 1.44) and a lower risk relative to those who migrate during infancy (0 to 2 years) (IRR = 0.58, 95% CI = 0.33, 1.04).

CONCLUSIONS

Migrant status is one of few well-established risk factors for psychotic disorder, yet we have limited understanding of the underlying etiology. The findings of this review advance our understanding of this association and identify high-risk groups to target for intervention.

The design of a line velocity interferometer for any reflector for inertial confinement experiments on the Z-machine

A line VISAR (Velocity Interferometer System for Any Reflector) has been designed and commissioned at the Sandia National Laboratory's Z-machine. The instrument consists of an F/2 collection system, beam transport, and an interferometer table that contains two Mach-Zehnder type interferometers and an eight channel Gated Optical Imaging (GOI) system. The VISAR probe laser operates at the 532 nm wavelength, and the GOI bandpass is 540-600 nm. The output of each interferometer is passed to an optical streak camera with four selectable sweep speeds. The system is designed with three interchangeable optics modules to select a full field of view of 1 mm, 2 mm, or 4 mm. The optical beam transport system connects the target image plane to the interferometers and the gated optical imagers. The target is integrated into a sacrificial final optics assembly that is integral to the transport beamline.