Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of seawater in reef environments.

In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (Chaetodon lunulatus) resident to coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater vs gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S and ITS2 sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater based on low levels of taxonomic overlap (3 to 21%) and significant differences between the sampling approaches. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that might include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic.

The complete mitochondrial genome of the invasive cyanobacteriosponge Terpios hoshinota (Demospongiae, Suberitida, Suberitidae).

The cyanobacteriosponge Terpios hoshinota occurs on tropical reefs throughout the Indo-Pacific. The species encrusts live coral, and other benthos, and is considered a pest species that can threaten the health and productivity of locally native benthic communities on coral reefs. Here we assemble a complete mitochondrial genome to aid further research into the range expansion of this species. The circular genome was 20,504 bp in length and encoded 14 protein-coding genes, two ribosomal RNA (rRNA) genes, and 25 transfer RNA (tRNA) genes. A phylogenetic analysis based on the concatenated sequences of 14 protein-coding genes of 12 members of the subclass Heteroscleromorpha including the newly sequenced T. hoshinota, suggests further taxonomic revisions within the order Suberitida may be warranted.

The impact of radiation therapist-led structured peer review meetings on compliance to Radiation Oncology Practice Standards.

INTRODUCTION: Regular tumour-specific peer review meetings (TPRMs) were established by our group during 2016. A dedicated Quality Assurance Radiation Therapist (QART) was employed in 2018 to co-ordinate the meetings and for each patient, complete the Peer Review Audit Tool (PRAT) of the Royal Australian and New Zealand College of Radiologists (RANZCR). The aim of the current quality assurance study was to investigate the impact of the TPRMs and appointment of the QART on compliance to relevant RANZCR Radiation Oncology Practice Standards (ROPS). METHODS: Tumour-specific peer review meetings for eight tumour sites were assessed across our group's three hospitals from January 2017 to December 2019. Data from meetings were collected using the PRAT or from paper-based minutes and assessed against four ROPS (ROPS 3, 4, 8 and 9). Compliance with each of the four standards was measured by presence of the required documentation and presentation at TPRM, as recorded by the PRAT. RESULTS: There was an increase in the overall number of peer review cases audited from 173 in the 2017 calendar year to 469 in 2018 and 619 in 2019, representing 7%, 18% and 22% of all treatment courses started during these years, respectively. Staging was the most incompletely documented item across all years for audited patients. The request for radiation treatment plan modifications increased year-on-year: modifications were requested for 5% of plans in 2017 (8/172), 18% in 2018 (81/452) and 19% (119/619) in 2019. CONCLUSION: This study has shown that an increase in the number of cases for peer-review audit corresponded to the QART-facilitated TPRMs. Application of the PRAT has identified radiation treatment plan modifications that would otherwise go undetected and without opportunity to improve the quality of patients' treatment or avoid harm.

Personal innovative approach in radiation therapy of lung cancer- functional lung avoidance SPECT-guided (ASPECT) radiation therapy: a study protocol for phase II randomised double-blind clinical trial.

BACKGROUND: Radiation therapy (RT) plays a key role in curative-intent treatment for locally advanced lung cancer. Radiation induced pulmonary toxicity can be significant for some patients and becomes a limiting factor for radiation dose, suitability for treatment, as well as post treatment quality of life and suitability for the newly introduced adjuvant immunotherapy. Modern RT techniques aim to minimise the radiation dose to the lungs, without accounting for regional distribution of lung function. Many lung cancer patients have significant regional differences in pulmonary function due to smoking and chronic lung co-morbidity. Even though reduction of dose to functional lung has shown to be feasible, the method of preferential functional lung avoidance has not been investigated in a randomised clinical trial. METHODS: In this study, single photon emission computed tomography (SPECT/CT) imaging technique is used for functional lung definition, in conjunction with advanced radiation dose delivery method in randomised, double-blind trial. The study aims to assess the impact of functional lung avoidance technique on pulmonary toxicity and quality of life in patients receiving chemo-RT for lung cancer. Eligibility criteria are biopsy verified lung cancer, scheduled to receive (chemo)-RT with curative intent. Every patient will undergo a pre-treatment perfusion SPECT/CT to identify functional lung. At radiation dose planning, two plans will be produced for all patients on trial. Standard reference plan, without the use of SPECT imaging data, and functional avoidance plan, will be optimised to reduce the dose to functional lung within the predefined constraints. Both plans will be clinically approved. Patients will then be randomised in a 2:1 ratio to be treated according to either the functional avoidance or the standard plan. This study aims to accrue a total of 200 patients within 3 years. The primary endpoint is symptomatic radiation-induced lung toxicity, measured serially 1-12 months after RT. Secondary endpoints include: a quality of life and patient reported lung symptoms assessment, overall survival, progression-free survival, and loco-regional disease control. DISCUSSION: ASPECT trial will investigate functional avoidance method of radiation delivery in clinical practice, and will establish toxicity outcomes for patients with lung cancer undergoing curative chemo-RT. TRIAL REGISTRATION: Clinicaltrials.gov Identifier: NCT04676828 . Registered 1 December 2020.

Radiation therapist-led telephone follow-up: identifying patients who require post-treatment care.

INTRODUCTION: Radiation therapists implemented telephone follow-up (TFU) in 2015 as an additional point of care post-treatment. The purpose of this study was to determine whether TFU identified patients who required additional post-treatment care before the next scheduled review. METHODS: Between January 2015 and July 2016, all patients who were prescribed curative intent treatment aged 18 years or over were called 10 days post-radiation therapy (RT). Eight questions were developed and included asking patients how they were coping, if their side effects were improving, if they needed to contact the hospital and if more dressings were required. Patients who could not be contacted after two attempts were excluded from the study. Microsoft Excel and Statistical Package for Social Sciences (SPSS) were used to analyse the responses. RESULTS: Data were collected from 850 patients. A total of 28/846 (3%) of patients reported they were not coping after RT, with 26/830 (3%) reporting their side effects were getting worse. A total of 97/826 (12%) of patients felt they needed to contact the hospital because they were unwell. This study identified 104/677 (15%) of patients who responded required more dressings, with 67/104 (65.7%) and 10/104 (9.8%) of this cohort identified in the breast, and head and neck groups, respectively. CONCLUSION: Radiation therapist-led TFU has shown to be beneficial in identifying a small cohort of breast and head and neck cancer patients who required additional care post-radiation treatment.

Draft Genome Sequence of Weissella paramesenteroides STCH-BD1, Isolated from Ensiled Sorghum bicolor.

Weissella paramesenteroides has potential as an industrial biocatalyst due to its ability to produce lactic acid. A novel strain of W. paramesenteroides was isolated from ensiled sorghum. The genome was sequenced using a hybrid assembly of Oxford Nanopore and Illumina data to produce a 2-Mbp genome and 22-kbp plasmid sequence.

Patient-Specific Heart Constraint: A Tool for Optimization and Evaluation of Mean Heart Dose in Breast Cancer Patients.

PURPOSE: Our institution introduced a patient-specific heart constraint (PSHC) and a mean heart dose (MHD) constraint of 4 Gy for all patients receiving breast radiation therapy (RT) with a simultaneous boost (SIB). This was introduced as a method to calculate the predicted MHD before optimizing IMRT fields. We sought to determine whether the introduction of a PSHC reduced MHD, while maintaining optimally dosed treatment plans. MATERIAL/METHODS: Patients were retrospectively divided into 2 groups, pre- and postintroduction of the PSHC. The breast and SIB Planning Target Volumes (PTVs) were prescribed to 50 Gy and 57 Gy, respectively, in 25 fractions. Plans were generated using a hybrid IMRT technique, 30 Gy using an open tangential field arrangement, and 27 Gy using IMRT fields. The PSHC was calculated using MHD of open tangential field × 2. A paired t test compared PTV coverage and heart doses between cohorts (P < .05 significant). RESULTS: A total of 264 patients were included (138 pre-PSHC and 126 post-PSHC) with 137 right-sided and 127 left-sided treatments. MHD was significantly reduced across both right-sided (-0.4 Gy, P < .0001) and left-sided (-1.2 Gy, P < .0001) treatments overall. Left-sided treatments were further examined between free breathing and deep inspiration breath-hold (DIBH). DIBH showed reduction in MHD, although it was not significant (-0.46 Gy, P = .34). Heart V5 Gy showed reduction in right-sided (-1%, P = .002) and left-sided (-9.2%, P < .0001) treatments overall. Left-sided free breathing showed significant reduction (-8.8%, P < .0001), and DIBH also showed significant reduction (-5.1%, P = .0034). Tumor bed doses remained above the 54.15 Gy (95% of 57 Gy) threshold for all plans. CONCLUSION: Introduction of a PSHC can reduce MHD and V5 Gy for patients receiving whole breast RT with SIB while maintaining optimally dosed plans, with the greatest benefit shown for left-sided, free-breathing treatments.

Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia.

Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental DNA (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic 'stygofauna' assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S genes were applied to 159 water and sediment samples collected from 23 caves and springs across the island. Taken together, our assays detected a wide diversity of chordates, cnidarians, porifera, arthropods, molluscs, annelids and bryozoans from 71 families across 60 orders. We report a high level of variation between cave and spring subterranean community compositions which are significantly influenced by varying levels of salinity. Additionally, we show that dissolved oxygen and longitudinal gradients significantly affect biotic assemblages within cave communities. Lastly, we combined eDNA-derived community composition and environmental (water quality) data to predict potential underground interconnectivity across Christmas Island. We identified three cave and spring groups that showed a high degree of biotic and abiotic similarity indicating likely local connectivity. This study demonstrates the applicability of eDNA metabarcoding to detect subterranean eukaryotic communities and explore underground interconnectivity.

Using patient-reported outcomes (PROs) and patient-reported outcome measures (PROMs) in routine head and neck cancer care: What do health professionals perceive as barriers and facilitators?

INTRODUCTION: Patient-reported outcomes (PROs) are direct reports from patients about their health status. Patient-reported outcome measures (PROMs) are validated tools assessing PROs and completed by patients. Though commonly used in research, implementing PROMs into routine clinical care has been challenging. We aimed to examine health professionals' (HPs') perceptions of barriers and facilitators to PRO and PROM use in the routine care of head and neck cancer (HNC) patients. METHODS: A custom survey was created, pilot-tested and disseminated to all HPs involved in the care of HNC patients in Western Sydney Local Health District, Australia. Participants were asked to rate the degree to which they believed the survey items were barriers or facilitators to routine PRO use by answering 'not at all', 'very little', 'quite a bit' and 'very much'. RESULTS: Of 129 HPs, 86% had never routinely used PROs. Key barriers perceived were low workplace awareness of PROs (73%), HPs' lack of knowledge on PRO use (63%) and lack of PROMs in patient preferred languages (63%). Insufficient time, staff and infrastructure to support routine PRO collection and non-integrated PROMs in patient electronic medical records were also highlighted. Top facilitators were time for PRO administration and interpretation (86%), clear definition of staff roles (84%) and automatic scoring and interpretation of PROMs (81%). CONCLUSIONS: This study highlighted key barriers and facilitators to PRO use in routine HNC patient care as perceived by HPs. The findings will be useful in guiding the successful and sustainable implementation of routine PRO collection in clinical settings.

eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem.

Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for cost-effective whole-ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high-resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)-a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.

Radiation-induced oesophagitis in breast cancer: Factors influencing onset and severity for patients receiving supraclavicular nodal irradiation.

AIM: The aim of this study was to determine dosimetric factors, such as mean dose and oesophageal length, which may influence the incidence and severity of oesophagitis in breast cancer patients receiving radiotherapy to the supraclavicular nodes. METHODS: This was a single-arm prospective observational study. Toxicity grading was undertaken twice weekly to determine the onset of grade 2 oesophagitis in consecutive patients prescribed IMRT to the breast or chest wall and supraclavicular fossa (SCF) nodes. Recorded variables included mean and maximum doses to the oesophagus, oesophageal length and pharynx length within the treatment area. Multivariate logistic regression and Fishers' exact test were used with a 0.05 significance level to compare the onset of grade 2 oesophagitis with these variables. RESULTS: A total of 77 patients were included in the study. Twenty-four (31%) patients reported grade 2 oesophagitis. There was a higher incidence of grade 2 oesophagitis in patients receiving a mean oesophageal dose of ≥31 Gy compared to those receiving < 31 Gy (18/24 versus 6/24, respectively, P = 0.025). There was a significant difference in the onset of grade 2 toxicity in patients who had ≥ 1 cm of pharynx included in SCF fields compared with those with <1 cm (15/24 versus 9/24, respectively, P = 0.0116). The odds ratios for developing grade 2 oesophagitis were 3.2 (95% CI = 1.05-9.62, P = 0.04) for a mean dose of ≥31 Gy and 3.4 (95% CI = 1.19-9.5, P = 0.022) for ≥1 cm of pharynx in the SCF field. CONCLUSION: By limiting the mean dose to the irradiated oesophagus to <31 Gy during the planning process and ensuring that <1 cm of pharynx is included in the radiation field, oesophageal toxicity may be minimised.

Collaborative implementation of stereotactic ablative body radiotherapy: A model for the safe implementation of complex radiotherapy techniques in Australia.

INTRODUCTION: Stereotactic ablative radiotherapy (SABR) for lung cancer is a modality of treatment that has improved outcomes for lung cancer patients. However, radiotherapy for lung cancer is underutilized and fewer than half of elderly patients with non-small cell lung cancer (NSCLC) receive active treatment. The purpose of this study is to report on a collaboration in implementing an NSCLC SABR (stereotactic ablative body radiation) program safely, efficiently, and uniformly across several centers, including regional sites. The first aim of this paper is to detail the collaboration and implementation that started in 2013 and is ongoing. The second aim of this paper is to document early toxicities and quality of life outcomes. METHOD: A tripartite approach was used to develop the protocol and networks required for the implementation of SABR across multiple sites in NSW. Departments starting the programmes were supported and physics credentialing with central site submission was required before commencing the treatment. Additional ongoing support was available via an email discussion group involving all members of the collaboration. RESULTS: Between July 22, 2013 and February 22, 2016, 41 patients were enrolled with 34 patients in active follow up. The toxicity profile so far is similar to those of published studies with no appreciable effect on quality of life outcomes. CONCLUSION: The collaboration formed an effective framework in facilitating the implementation of SABR across several sites in NSW and could be used as a model for the safe and uniform implementation of new technologies in Australia.

Referral rates to multidisciplinary team meetings: Is there disparity between tumour streams?

INTRODUCTION: The multidisciplinary team meeting (MDTM) approach is accepted as standard of care to optimise treatment for patients diagnosed with cancer. This retrospective audit reviews the proportion of patients whose care is being discussed at cancer MDTMs within the Sunshine Coast Hospital and Health Service (SCHHS). METHODS: Patients included were those diagnosed with cancer within the SCHHS between 2010 and 2015, and subsequently referred to a public MDTM for discussion. Data were extracted from the Queensland Cancer Control Analysis Team (QCCAT) database regarding the incidence of breast, lung, upper gastrointestinal (GI), colorectal, genitourinary and malignant haematological cancers and the number of patients referred to the corresponding MDTM. RESULTS: Data from 2015 show referral rates to MDTMs as follows: lung 100%, upper gastrointestinal 100%, colorectal 64%, breast 60%, malignant haematology 40% and genitourinary 28%. Of the genitourinary presentations, 70% were prostate cases and 14% bladder cases. Review of genitourinary MDTM outcomes found that, of the patients with prostate cancer discussed, 30% were metastatic, 19% were poor surgical candidates and 15% had biochemical recurrence. CONCLUSION: This audit demonstrates variable utilisation of MDTMs between tumour streams. Our study shows a high and increasing referral rate to all tumour stream MDTMs except for genitourinary. This suggests a possible underutilisation of genitourinary MDTMs to discuss treatment options for patients with genitourinary cancer. Collaborative research is warranted to further investigate whether this is a local or widespread issue.

Functional perfusion image guided radiation treatment planning for locally advanced lung cancer.

BACKGROUND AND PURPOSE: Functional avoidance radiation therapy (RT) aims at sparing functional lung regions. The purpose of this simulation study was to evaluate the feasibility of functional lung avoidance methodology in RT of lung cancer and to characterize the achievable dosimetry of single photon emission computed tomography (SPECT) guided treatment planning. MATERIALS AND METHODS: Fifteen consecutive lung cancer patients were included and planned for definitive RT of 60-66 Gy in 2-Gy fractions. Two plans were optimized: a standard CT-plan, and functional SPECT-plan. The objective was to reduce dose to the highly functional lung subvolumes without compromising tumour coverage, and respecting dose to other organs at risk. For each patient a 3D-conformal, intensity modulated radiation therapy (IMRT) and volumetric modulated arc therapy plans were created for standard and functional avoidance. Standard versus functional dose-volume parameters for functional lung (FL) subvolumes, organs at risk and tumour coverage were compared. RESULTS: The largest dose reduction was achieved with IMRT plans. Functional plans resulted in dose reduction from 9.0 Gy to 6.7 Gy (mean reduction of 2.3 Gy or 26%) to the highest functional subvolume FL80% (95%CI 1.1; 3.5). Dose to FL40% was reduced from 13.3 Gy to 11.6 Gy with functional planning. Dose reduction to FL40% was 1.7 Gy (95%CI 0.9; 2.6). Functional volume of lung receiving over 20 Gy improved by 5% (standard 22%, functional 17%). Dose to organs at risk and tumour coverage were not significantly different between plans. CONCLUSIONS: SPECT/CT-guided planning resulted in improved dose-volumetric outcomes for functional lung. This methodology may lead to potential reduction in radiation-induced lung toxicity.

A randomized trial of fish oil omega-3 fatty acids on arterial health, inflammation, and metabolic syndrome in a young healthy population.

BACKGROUND: Long chain omega-3 fatty acids from fish oils (O3) are known to have beneficial effects on a number of vascular risk factors in at-risk populations. The effects of a highly bioavailable emulsified preparation on an overweight young adult population are less well known. METHODS: Young adults, age 18-30, with body mass indices (BMIs) greater than 23 (average = 28.1) were administered 1.7 g of O3 per day (N = 30) or safflower oil placebo (N = 27) in an emulsified preparation (Coromega, Inc.) for 4 weeks in a double-blind randomized design. Blood was drawn and anthropometric measurements taken before and after dosing. Hemodynamic measures (central pulse wave velocity, augmentation index, and aortic systolic blood pressure), inflammatory cytokines (IL-6, IL-8, IL-10, and tumor necrosis factor-α), red blood cell and plasma phospholipid fatty acid profiles, fasting serum lipids, glucose, and C-reactive protein were measured. RESULTS: Red cell and plasma phospholipid eicosapentaenoic acid and docosahexaenoic acid concentrations increased over the four weeks of dosing in the O3 group. Dosing with O3 did not affect central pulse wave velocity, augmentation index, or aortic systolic blood pressure. None of the five American Heart Association metabolic syndrome components improved over the dosing period. None of the inflammatory cytokines, C-reactive protein, or lipids (total or LDL cholesterol) improved over the dosing period. CONCLUSIONS: No salutary effects of O3 were observed in hemodynamic, metabolic syndrome criteria or inflammatory markers as a result of this relatively short period of administration in this relatively overweight, but healthy young adult cohort.