Trematode parasites as indicators of an animal component in the diet of the Water Vole Arvicola amphibius.

The intestinal trematode fauna of the Water Vole Arvicola amphibius, (previously A. terrestris), was investigated to determine whether it might provide evidence of an animal component in the diet of this aquatic herbivorous small mammal. Interrogation of the electronic Host-Parasite Database of the Natural History Museum London revealed the presence of fourteen species of intestinal trematode in water voles, infection with each of which would require the ingestion of tissue from an animal intermediate host. The results obtained using these parasite indicators provide convincing evidence of animal components in the diet of A. amphibius and support anecdotal reports of water voles feeding on animal material in the field.

A markerless motion capture system can reliably determine peak trunk flexion while squatting with and without a weighted vest.

Markerless motion capture has improved physical screening efficiency in sport and occupational settings; however, reliability of kinematic measurements from commercial systems must be established. Further, the impact of torso-borne equipment on these measurements is unclear. The purpose of this study was to evaluate the reliability of HumanTrak, a markerless motion capture system, for estimating peak trunk flexion in squat movements with and without a weighted vest. Eighteen participants completed body weight squats (BWSQ) and overhead squats (OHSQ) to their maximum depth (unrestricted-range) and to a plyometric box (fixed-range) while wearing no body armour (NBA) or 9 kg body armour (BA9). Peak trunk flexion was measured using HumanTrak. Testing was performed in two sessions on one day (intra-day) and one session on a separate day (inter-day) to assess reliability. HumanTrak had a standard error of measurement < 3.74° across all movements and conditions. Reliability was good to excellent (ICC = 0.82-0.96) with very large to nearly perfect Pearson correlations (r > 0.80) for all comparisons except unrestricted-range BWSQ with BA9 (ICC = 0.60-0.71, r = 0.71). HumanTrak was more reliable for intra- than inter-day, but reliability was still excellent for almost all inter-day comparisons (ICC > 0.82). HumanTrak is reliable for detecting differences in peak trunk flexion > 8.5° when body armour is not worn and > 10.5° when body armour is worn. Practitioners can assess meaningful changes in sagittal plane trunk motion when screening squat movements regardless of whether body armour is worn.

Allied health transdisciplinary models of care in hospital settings: A scoping review  .

Improving the productivity of the allied health workforce is a global priority in response to the increasing incidence of chronic disease, associated healthcare costs, and insufficient workforce volume. Team-based healthcare, specifically allied health transdisciplinary teams, might be a solution to improve the utilization of workforce while maintaining high-quality and value-based healthcare. Allied health transdisciplinary teams can be a valuable solution in settings where care is delivered by different allied health professionals. Transdisciplinary teams embrace overlapping skills and blur traditional professional boundaries, allowing one professional to deliver certain aspects of care without eroding the skills and knowledge that each profession offers. The objective of this scoping review is to systematically examine and map the characteristics, outcomes, facilitators, and barriers of contemporary allied health transdisciplinary models of care that have been implemented in hospital settings. The scoping review was guided by the Joanna Briggs Institute methodology and reported in line with the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). Three screening rounds were completed by two independent reviewers. Included sources were synthesized using descriptive and tabular analysis. Nine studies that evaluated hospital-based allied health transdisciplinary teams were included. One study was a randomized controlled trial, five were experimental quantitative studies, two utilized qualitative analyses, and one was a conference abstract. Most studies reported improvements in time-efficiency, quality of care, and positive stakeholder perceptions. One study reported labor and capital cost savings. Barriers and facilitators of transdisciplinary teams were categorized by the authors as person/interpersonal, workflow, organizational or implementation factors. This review presents some evidence that demonstrates the potential of hospital-based allied health transdisciplinary teams, however high-quality evidence is scarce. Further primary research should focus on stakeholder perceptions, and labor and capital cost outcomes.

Assessment of on-treatment platelet reactivity at high and low shear stress and platelet activation status after the addition of dipyridamole to aspirin in the early and late phases after TIA and ischaemic stroke.

BACKGROUND: Data are limited on the ability of dipyridamole to additionally inhibit platelet function/reactivity in ischaemic cerebrovascular disease (CVD) patients on aspirin. AIMS: To assess inhibition of platelet function/reactivity and platelet activation with dipyridamole in CVD. METHODS: This prospective, observational study assessed TIA/ischaemic stroke patients before (baseline; N = 60), at 14 ±7 days (14d, N = 39) and ≥ 90 days (90d, N = 31) after adding dipyridamole to aspirin. Platelet function/reactivity at high shear stress (PFA-100® C-ADP) and low shear stress (VerifyNow® P2Y12 and Multiplate® ADP assays), and platelet activation status (% expression of CD62P, CD63 and leucocyte-platelet complexes on whole blood flow cytometry) were quantified. 'Dipyridamole-high on-treatment platelet reactivity (HTPR)' was defined as failure to inhibit ADP-induced platelet aggregation +/- adhesion compared with the patient's baseline on aspirin monotherapy by more than twice the coefficient-of-variation of the assay after adding dipyridamole to aspirin. RESULTS: Dipyridamole-HTPR was identified in 71.4-75% of patients on PFA-100 C-ADP, 83.9-86.8% of patients on VerifyNow P2Y12, and 81.5-83.3% of patients on Multiplate ADP assays. There were no changes in CD62P/CD63 expression (P ≥ 0.18), or consistent changes in leucocyte-platelet complexes in CVD patients overall at 14d or 90d vs. baseline after commencing dipyridamole. Monocyte-platelet complexes increased in the patient subgroup with dipyridamole-HTPR at 14d and 90d on PFA-100, and at 14d on VerifyNow (P ≤ 0.04), but not in those without dipyridamole-HTPR. DISCUSSION: Additional antiplatelet effects of dipyridamole are detectable under high and low shear stress conditions with user-friendly platelet function/reactivity tests ex vivo. Increasing circulating monocyte-platelet complexes over time are associated with dipyridamole-HTPR.

Protocol of trans-Tasman feasibility randomised controlled trial of the Younger Women's Wellness After Breast Cancer (YWWACP) lifestyle intervention.

BACKGROUND: Younger women (defined as those < 50 years who are likely pre-menopausal at time of diagnosis) with breast cancer often experience persistent treatment-related side effects that adversely affect their physical and psychological wellbeing. The Women's Wellness After Cancer Program (WWACP) was adapted and piloted in Australia to address these outcomes in younger women. The aims of this feasibility study are to determine (1) the potential to translate the Younger WWACP (YWWACP) intervention to a broader population base in Aotearoa/New Zealand and Australia, and (2) the potential for success of a larger, international, phase ΙΙΙ, randomised controlled trial. METHODS: This bi-national, randomised, single-blinded controlled trial involves two main study sites in Aotearoa/New Zealand (Kowhai study) and Australia (EMERALD study). Young women aged 18 to 50 years who completed intensive treatment (surgery, chemotherapy, and/or radiotherapy) for breast cancer in the previous 24 months are eligible. The potential to translate the YWWACP to women in these two populations will be assessed according to several feasibility outcomes. These include examining intervention accessibility, acceptability and uptake; intervention sustainability and adherence; the prevalence components of the intervention in the control group; intervention efficacy; participants' perception of measurement burden; the effectiveness of planned recruitment strategies; and trial methods and procedures. The studies collectively aim to enrol 60 participants in the intervention group and 60 participants in the control group (total = 120 participants). DISCUSSION: Ethical approval has been received from the Southern Health and Disability Ethics Committee (Kowhai ref: 19/STH/215), and UnitingCare Human Research Ethics Committee (EMERALD ref: 202103). This study will provide important data on the feasibility of the refined YWWACP in the trans-Tasman context. This study will account for and harmonise cross-country differences to ensure the success of a proposed international grant application for a phase ΙΙΙ randomised controlled trial of this program to improve outcomes in younger women living with breast cancer. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (ANZCTR): Kowhai ACTRN12620000260921 , registered on 27 February 2020. EMERALD ACTRN12621000447853 , registered on 19 April 2021.

Effects of exercise on vasomotor symptoms in menopausal women: a systematic review and meta-analysis.

The frequency and severity of menopausal vasomotor symptoms negatively impact quality of life. This systematic review evaluates the potential of exercise to relieve the subjective frequency and severity of vasomotor symptoms. We searched four databases to identify randomized controlled trials (RCTs) that evaluated the effect of structured exercise (e.g. aerobic training) on the severity and/or frequency of vasomotor symptoms in menopausal women. Two reviewers independently screened records for eligibility, extracted data and assessed risks of bias and evidence certainty using the Cochrane tool and Grading of Recommendations Assessment, Development and Evaluation (GRADE). When suitable, data were pooled using random-effect meta-analyses. We appraised 21 RCTs involving 2884 participants. Compared to no-treatment control, exercise significantly improved severity of vasomotor symptoms (10 studies, standardized mean difference [SMD] = 0.25; 95% confidence interval [CI]: 0.04 to 0.47, p = 0.02, very low certainty of evidence); the effect size was attenuated when studies with a high risk of bias were excluded (SMD = 0.11, 95% CI: -0.03 to 0.26, p = 0.13). No significant changes in vasomotor frequency were found between exercise and control (SMD = 0.14, 95% CI: -0.03 to 0.31, p = 0.12, high certainty of evidence). In conclusion, exercise might improve vasomotor symptom severity. Future rigorous RCTs addressing the limitations of current review are warranted to explore the optimal exercise prescription principles to target the severity of vasomotor symptoms.

Assessing the factorial validity and the internal reliability of the International Trauma Questionnaire (ITQ); PTSD and complex PTSD among survivors of sexual violence in Ireland.

AIMS: To assess the factorial validity and internal reliability of the International Trauma Questionnaire (ITQ) among a treatment-seeking sample of survivors of sexual violence in Ireland. In addition, to assess the diagnostic rate of post-traumatic stress disorder (PTSD) and complex post-traumatic stress disorder (CPTSD) among the samples. METHODS: Participants were adult survivors of sexual violence (N = 114) in receipt of therapeutic support at the Dublin Rape Crisis Centre. The ITQ was utilised to measure PTSD and CPTSD symptoms and confirmatory factor analysis was employed to assess the factorial validity of the ITQ. Composite reliability was employed to assess the internal reliability of the ITQ scale scores. RESULTS: The confirmatory factor analysis results indicated that a six-factor correlated model and a two-factor higher model were good representations of the latent structure of the ITQ, both models are consistent with the conceptualisation of CPTSD. All ITQ subscales possessed satisfactory internal reliability except for the affective dysregulation subscale. Of the sample, 56.1% met the criteria for CPTSD and 20.2% met the criteria for PTSD. CONCLUSIONS: The ITQ captured a distinction between PTSD and CPTSD symptoms and produced reliable scores within the sample, but replication with a larger sample size is required. In addition, the study findings demonstrated that CPTSD was relatively common among those seeking psychological support following sexual violence.

Anaesthesia management of a child with aromatic L-amino acid decarboxylase deficiency.

Aromatic L-amino acid decarboxylase deficiency is an autosomal recessive disorder that results in a lack of neurotransmitters including serotonin, dopamine, noradrenaline and adrenaline. It is characterised by developmental delay, severe hypotonia and autonomic disturbance. In patients with this condition, catecholamine deficiency and autonomic dysfunction, resulting in haemodynamic instability under anaesthesia is a primary concern. There is increased sensitivity to exogenous catecholamines and indirect acting agents, such as ephedrine, are ineffective. Hypoglycaemia, difficult airway status and drug interactions such as with monoamine oxidase inhibitors are also of concern, and these patients are at risk of dystonic crises peri-operatively. A 6-year-old boy with aromatic L-amino acid decarboxylase deficiency presented for gastrointestinal endoscopy. Following multidisciplinary discussion, we elected to provide general anaesthesia with a propofol target-controlled infusion, which proceeded without incident. In this report, we describe the precautions taken in this case, and discuss the provision of general anaesthesia for children with rare neurometabolic disorders.

Assessment of the adequacy of counselling regarding reproductive-related issues in women of childbearing age on anti-epileptic drugs.

BACKGROUND: The use of anti-epileptic drugs (AEDs) in women of childbearing age (WCBA) necessitates careful counselling regarding reproductive-related issues. AIM: (i) To compare documentation of appropriate counselling regarding reproductive-related issues in WCBA prescribed AEDs for non-epilepsy vs. epilepsy indications, and (ii) to examine whether the frequency of counselling improved after introduction of 'standardized typed advice'. DESIGN: Retrospective audit and quality assessment and improvement programme. METHODS: We analysed medical records of all WCBA prescribed gabapentin, pregabalin, topiramate, valproate or carbamazepine by a general neurology clinical service before (Study period A) and after (Study period B) introduction of standardized typed passages regarding potential teratogenicity ± interactions with hormonal contraception at a university teaching hospital. The χ2 test or the Fisher's exact test was employed, as appropriate. RESULTS: In WCBA prescribed AEDs for non-epilepsy indications, documentation of appropriate counselling regarding potential teratogenicity improved from 49% (17/35 patients) in Period A to 79% (27/34 patients) in Period B (P = 0.008). The frequency of counselling regarding teratogenicity was higher in patients prescribed AEDs for epilepsy compared with non-epilepsy indications in Study period A (100% vs. 49%, P = 0.002), but was no longer significantly different in Study period B (86% vs. 79%, P = 0.64). Documentation of counselling regarding potential interaction of enzyme-inducing AEDs with hormonal contraception did not significantly change between study periods. CONCLUSION: Significant improvements in documentation regarding potential teratogenicity of AEDs prescribed for non-epilepsy indications can be achieved by introducing standardized, typed passages copied to patients. Such a practice change is practical and widely applicable to neurological and non-neurological practice worldwide.

Cancer cachexia: an overview of diagnostic criteria and therapeutic approaches for the accredited practicing dietitian.

BACKGROUND: Cancer cachexia (CC) is a multifactorial syndrome characterised by ongoing skeletal muscle loss that leads to progressive functional impairment driven by reduced food intake and abnormal metabolism. Despite the traditional use of non-volitional weight loss as the primary marker of CC, there is no consensus on how to diagnose and manage CC. METHODS: The aim of this narrative review was to describe and discuss diagnostic criteria and therapeutic approaches for the accredited practicing dietitian with respect to identifying and managing CC. RESULTS: Available diagnostic criteria for cachexia include the cancer-specific (Fearon and Cachexia Score) and general criteria (Evans and Global Leadership Initiative on Malnutrition). These include phenotypic criteria [weight loss, body mass index, (objective) muscle mass assessments, quality of life] and aetiological criteria (disease burden, inflammation, energy expenditure, anorexia and inadequate food intake) and can be incorporated into the nutrition care process (NCP). This informs the nutrition diagnosis of 'chronic disease- or condition-related malnutrition (undernutrition) as related to increased nutrient needs, anorexia or diminished intake due to CC'. Optimal nutrition care and management of CC is multidisciplinary, corrects for increased energy expenditure (via immunonutrition/eicosapentaenoic acid), suboptimal protein/energy intake and poor nutrition quality of life, and includes a physical exercise intervention. Monitoring of intervention efficacy should focus on maintaining or slowing the loss of muscle mass, with weight change as an alternative gross indicator. CONCLUSIONS: Dietitians and the NCP can play an essential role with respect to identifying and managing CC, focusing on aspects of nutrition screening, assessment and intervention.

Longitudinal changes in EEG power, sleep cycles and behaviour in a tau model of neurodegeneration.

BACKGROUND: Disturbed sleep is associated with cognitive decline in neurodegenerative diseases such as Alzheimer's disease (AD) and frontotemporal dementia (FTD). The progressive sequence of how neurodegeneration affects aspects of sleep architecture in conjunction with behavioural changes is not well understood. METHODS: We investigated changes in sleep architecture, spectral power and circadian rhythmicity in the tet-off rTg4510 mouse overexpressing human P301L tau within the same subjects over time. Doxycycline-induced transgene-suppressed rTg4510 mice, tTa carriers and wild-type mice were used as comparators. Spectral power and sleep stages were measured from within the home cage environment using EEG electrodes. In addition, locomotor activity and performance during a T-maze task were measured. RESULTS: Spectral power in the delta and theta bands showed a time-dependent decrease in rTg4510 mice compared to all other groups. After the initial changes in spectral power, wake during the dark period increased whereas NREM and number of REM sleep bouts decreased in rTg4510 compared to wild-type mice. Home cage locomotor activity in the dark phase significantly increased in rTg4510 compared to wild-type mice by 40 weeks of age. Peak-to-peak circadian rhythm amplitude and performance in the T-maze was impaired throughout the experiment independent of time. At 46 weeks, rTG4510 mice had significant degeneration in the hippocampus and cortex whereas doxycycline-treated rTG4510 mice were protected. Pathology significantly correlated with sleep and EEG outcomes, in addition to locomotor and cognitive measures. CONCLUSIONS: We show that reduced EEG spectral power precedes reductions in sleep and home cage locomotor activity in a mouse model of tauopathy. The data shows increasing mutant tau changes sleep architecture, EEG properties, behaviour and cognition, which suggest tau-related effects on sleep architecture in patients with neurodegenerative diseases.

Deciphering the role of Rhodnius prolixus CYP4G genes in straight and methyl-branched hydrocarbon formation and in desiccation tolerance.

Insect cuticle hydrocarbons are involved primarily in waterproofing the cuticle, but also participate in chemical communication and regulate the penetration of insecticides and microorganisms. The last step in insect hydrocarbon biosynthesis is carried out by an insect-specific cytochrome P450 of the 4G subfamily (CYP4G). Two genes (CYP4G106 and CYP4G107) have been reported in the triatomines Rhodnius prolixus and Triatoma infestans. In this work, their molecular and functional characterization is carried out in R. prolixus, and their relevance to insect survival is assessed. Both genes are expressed almost exclusively in the integument and have an expression pattern dependent on the developmental stage and feeding status. CYP4G106 silencing diminished significantly the straight-chain hydrocarbon production while a significant reduction - mostly of methyl-branched chain hydrocarbons - was observed after CYP4G107 silencing. Molecular docking analyses using different aldehydes as hydrocarbon precursors predicted a better fit of straight-chain aldehydes with CYP4G106 and methyl-branched aldehydes with CYP4G107. Survival bioassays exposing the silenced insects to desiccation stress showed that CYP4G107 is determinant for the waterproofing properties of the R. prolixus cuticle. This is the first report on the in vivo specificity of two CYP4Gs to make mostly straight or methyl-branched hydrocarbons, and also on their differential contribution to insect desiccation.

Leptomeningeal Relapse of Embryonal Rhabdomyosarcoma after 15 years.

Aim Rhabdomyosarcoma (RMS) is the most common malignant soft tissue tumour of childhood. We present the case of a late relapse of RMS to the leptomeninges after 15 years. Methods A 20 year old male presented with a 3 week history of headaches and nausea. He previously had RMS of his right ear diagnosed at age 5 years which was treated with concurrent chemoradiotherapy. An MRI Brain and Spine confirmed extensive leptomeningeal disease and CSF analysis confirmed the presence of recurrent embryonal RMS. Results He completed two cycles of cyclophosphamide and topotecan followed by 45Gy/25Fr of craniospinal radiotherapy. Conclusion Late relapses beyond five years can be seen in up to 9% of patients, however very late recurrences (>10 years) are exceedingly rare. Molecular based methods such as gene expression profiling can aid risk stratification and survivorship clinics may become increasingly useful in following patients with high risk features.

Validation of the Seegene RV15 multiplex PCR for the detection of influenza A subtypes and influenza B lineages during national influenza surveillance in hospitalized adults.

Background. The Serious Outcomes Surveillance Network of the Canadian Immunization Research Network (CIRN SOS) has been performing active influenza surveillance since 2009 (ClinicalTrials.gov identifier: NCT01517191). Influenza A and B viruses are identified and characterized using real-time reverse-transcriptase polymerase chain reaction (RT-PCR), and multiplex testing has been performed on a subset of patients to identify other respiratory virus aetiologies. Since both methods can identify influenza A and B, a direct comparison was performed.Methods. Validated real-time RT-PCRs from the World Health Organization (WHO) to identify influenza A and B viruses, characterize influenza A viruses into the H1N1 or H3N2 subtypes and describe influenza B viruses belonging to the Yamagata or Victoria lineages. In a subset of patients, the Seeplex RV15 One-Step ACE Detection assay (RV15) kit was also used for the detection of other respiratory viruses.Results. In total, 1111 nasopharyngeal swabs were tested by RV15 and real-time RT-PCRs for influenza A and B identification and characterization. For influenza A, RV15 showed 98.0 % sensitivity, 100 % specificity and 99.7 % accuracy. The performance characteristics of RV15 were similar for influenza A subtypes H1N1 and H3N2. For influenza B, RV15 had 99.2 % sensitivity, 100 % specificity and 99.8 % accuracy, with similar assay performance being shown for both the Yamagata and Victoria lineages.Conclusions. Overall, the detection of circulating subtypes of influenza A and lineages of influenza B by RV15 was similar to detection by real-time RT-PCR. Multiplex testing with RV15 allows for a more comprehensive respiratory virus surveillance in hospitalized adults, without significantly compromising the reliability of influenza A or B virus detection.

Quality of life and functional outcomes following pelvic exenteration and sacrectomy.

AIM: The aim was to compare postoperative quality of life (QOL) between patients undergoing pelvic exenteration (PE) and pelvic exenteration with sacrectomy (PES), and to investigate the influence of high (L5-S2) vs low (≤ S3) sacrectomy on QOL and functional outcomes. METHOD: Patients undergoing en bloc sacrectomy as part of a PE and PE alone from 2008 to 2015 were identified from a prospectively maintained database. QOL and functional outcomes were assessed using the 36-Item Short Form Survey, the European Organization for Research and Treatment of Cancer Colorectal Cancer questionnaire and Quality of Life questionnaire, the Revised Musculoskeletal Tumour Scale, the Lower Extremity Functional Scale, the Sexual Health Inventory for Men and the Female Sexual Function Index. RESULTS: Of the 344 patients identified, data were available for 116 patients who underwent PE alone and 140 patients who underwent PES. PES patients had significantly poorer physical component scores (P < 0.001) but not mental component scores (P = 0.17). Of the 140 PES patients, 55 were eligible and were invited to participate in a second functional survey, with 30 patients returning the study questionnaire. High sacrectomy patients, compared with low sacrectomy, had significantly worse lower limb motor function (P = 0.03) and poorer physical (P = 0.001) and mental health component scores (P = 0.02). No differences were found in sexual, bladder and bowel function between high and low sacrectomy patients. CONCLUSIONS: Patients undergoing PES had worse physical component scores compared with PE alone, whereas high sacrectomy patients had significantly worse lower limb motor function and physical and mental component scores but comparable bowel, bladder and sexual functional outcomes compared with low sacrectomy patients.

Benchmarking nurse outcomes in Australian Magnet® hospitals: cross-sectional survey.

BACKGROUND: Positive reports of nursing-related outcomes such as quality nursing care, nursing engagement with work and good practice environment are crucial in attaining and maintaining Magnet® designation. The majority of Magnet®-designated organisations (N = 482) are in the USA, with their aggregate nursing outcomes widely published as benchmark data. Australian Magnet® outcomes have not been aggregated or published to date. METHODS: The aims are to benchmark educational preparation, occupational burnout, job satisfaction, intention to leave and working environment of nurses in Australian Magnet®-designated facilities and to determine the reliability of the Practice Environment Scale-Australia.The design is a cross-sectional multisite survey set in all three Australian Magnet®-designated organisations.The demographics included age, gender, level of education, years in practice, level of seniority and position title. Two items measured job satisfaction and intent to stay in current employment. The Maslach Burnout Inventory explored the three domains of nursing engagement: depersonalisation, personal achievement and emotional exhaustion. The Australian version of the Practice Environment Scale interrogated participants' perceptions of their work environments. RESULTS: 2004 nurses participated (response rate 45.9%). Respondents' mean age was 39.2 years (range 20-72). They were predominantly female and had worked in their current facility for more than 5 years. Eighty five percent had a minimum of a Bachelor's degree. Eighty-six percent of respondents were satisfied or very satisfied with their current position. Eighty eight percent had no intention of leaving their current employer within the next 12 months. Participants rated their hospitals highly in all domains of the practice environment. Respondents reported less burnout in the personal accomplishment and depersonalisation domains than in the emotional exhaustion domain, in which they reported average levels of burnout. The internal consistency of the Practice Environment Scale-Australia was confirmed in this sample (Cronbach α's 0.87-0.9 for subscales and 0.89 for composite score). CONCLUSION: In this paper, we present nursing outcome data from all Australian Magnet® hospitals for the first time. This provides a benchmark that facilitates comparison with nursing outcomes published by Australian non-Magnet® hospitals and with international Magnet® organisations.

Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater.

The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.

Colorectal Serrated Neoplasia: An Institutional 12-Year Review Highlights the Impact of a Screening Programme.

BACKGROUND: As the malignant potential of sessile serrated lesions/polyps (SSL/Ps) and traditional serrated adenomas (TSAs) has been clearly demonstrated, it is important that serrated polyps are identified and correctly classified histologically. AIM: Our aim was to characterize the clinicopathological features of a series of SSL/Ps & TSAs, to assess the accuracy of the pathological diagnosis, the incidence, and the rate of dysplasia in SSL/Ps & TSAs. METHODS: We identified all colorectal serrated polyps between 01/01/2004 and 31/05/2016, by searching the laboratory information system for all cases assigned a "serrated adenoma" SNOMED code. All available and suitable slides were reviewed by one pathologist, who was blinded to the original diagnosis and the site of the polyp. Subsequently discordant cases, SSL/Ps with dysplasia, and all TSAs were reviewed by a second pathologist. RESULTS: Over a 149-month period, 759 "serrated adenoma" polyps were identified, with 664 (from 523 patients) available for review. 41.1% were reviewed by both pathologists; 15.1% (100/664) were reclassified, with the majority being changed from SSL/P to hyperplastic polyp (HYP) (66/664; 9.9%). 80.3% of these HYPs were located in the left colon, and the majority exhibited prolapse effect. There were 520 SSL/Ps (92.2%) & 40 TSAs (7.1%). The majority of SSL/Ps were in the right colon (86.7%) and were small (64.5% <1 cm), while most TSAs were in the left colon (85.7%) and were large (73.1%≥1 cm). 6.7% of SSL/Ps exhibited dysplasia, the majority of which were large (66.7%≥1 cm). Following consensus review, 13/520 (2.5%) SSL/Ps were downgraded from SSL/P with dysplasia to SSL/P without dysplasia. Detection of SSL/Ps peaked in the most recent years reviewed (87.5% reported between 2013 and 2016, inclusive), coinciding with the introduction of "BowelScreen" (the Irish FIT-based colorectal cancer screening programme). CONCLUSIONS: Awareness of, and adherence to, diagnostic criteria is essential for accurate classification of colorectal polyps.