P-433 Comparative analysis of serum obtained in early pregnancy using Fourier transform-infrared spectroscopy to predict tubal ectopic pregnancy and miscarriage

Study question

Can Fourier transform-infrared (FT-IR) spectroscopy be used to discriminate adverse early pregnancy outcomes such as tubal ectopic pregnancy and miscarriage from live normally-sited pregnancies?

Summary answer

Biochemical information acquired from serum samples using FT-IR spectroscopy does not discriminate adverse early pregnancy outcomes from live normally-sited pregnancies.

What is known already

Ectopic pregnancy and miscarriage are associated with maternal morbidity and mortality. Current management of pregnancy of unknown location and viability may involve serial blood human chorionic gonadotrophin-beta measurements and several ultrasound scans. Multiple interventions and length of time to diagnosis are costly and have a profound psychological impact on women. Vibrational spectroscopic methods such as Fourier transform-infrared (FT-IR) spectroscopy have been increasingly shown to discriminate disease states such as cancer from controls utilising the ‘metabolomic signature’ of molecules within a biological sample. It is hypothesised that this signature will differ between live normally-sited pregnancies, and tubal ectopic pregnancy and miscarriage.

Study design, size, duration

A total of 380 women were recruited to the prospective cohort study, Ectopic Pregnancy Diagnosis sTudy (ExPeDITe) between November 2018 and November 2021. Inclusion criteria comprised pregnant women ≥18 years presenting with pain and/or bleeding at < 10 weeks of gestation. A sample of blood and demographic data were collected at the time of consent, and a full history was taken. Early pregnancy outcomes were collected and classified according to ESHRE guidance.

Participants/materials, setting, methods

Serum samples prepared from collected blood (n = 340) were diluted 1:4 to prevent oversaturation of spectra and quality controls were created from the pooled diluted serum. Samples were transferred to silicon plates and dried at 37.5 °C. Samples were subjected to FT-IR spectroscopy and spectral data were submitted to baseline correction, smoothing, and vector normalisation prior to multivariate statistical analysis including Principal Component Analysis (PCA) and Partial Least Squares – Discriminant Analysis (PLS-DA).

Main results and the role of chance

Infrared spectral data collected from live normally-sited pregnancies, tubal ectopic pregnancies, pregnancies of unknown location, and miscarriages displayed similar infrared signatures, exhibiting bands associated to vibrational modes related to the main molecular constituents commonly found in most biological samples such as proteins, lipids, nucleic acids, and carbohydrates. Spectral data were used as inputs to PCA and PLS-DA models as clustering algorithms in order to classify the different pregnancy outcomes. The output obtained by the classification model generated with PLS-DA shows two distributions; a ‘real’ and ‘null/random’ model. These models displayed poor correct classification rates, indicating no differences in the infrared signatures between the different pregnancy outcomes. Similar findings were also observed in the PCA results as no clustering pattern indicating correct classification between the experimental groups was observed in the scores plot. Although infrared spectroscopy has been well demonstrated as an analytical tool to discriminate several disorders from healthy/control samples including cancer, diabetes and many others, these findings indicate that the information about the overall biochemistry probed by infrared spectroscopy acquired from serum samples currently lacks accuracy/sensitivity to discriminate different pregnancy outcomes.

Limitations, reasons for caution

Proteins were not removed from samples prior to analysis, which may mask discreet changes in small molecule metabolites. As FT-IR spectra multivariate in nature power calculations are not possible. If this study had shown case-control separation then these findings would have been validated with a second set of samples.

Wider implications of the findings

The findings of this study suggest that FT-IR spectroscopy of serum may not be discriminatory to identify important early pregnancy outcomes, but further analytical techniques should be utilised to confirm if metabolomic analysis of blood or other biofluids would provide a novel diagnostic test.

Trial registration number

REC 17/NW/0646

O-258 Nuclear magnetic resonance profiling of the vaginal metabolome in adverse early pregnancy outcomes

Study question

Is the vaginal metabolome predictive of early pregnancy outcomes?

Summary answer

The vaginal metabolome is moderately predictive of live normally-sited pregnancies when compared to a pregnancy with an adverse outcome.

What is known already

Approximately 15% of all pregnancies are lost in the first trimester and a further 1-2% are ectopic. To date, no non-invasive and clinically useful tests have been developed to differentiate live normally-sited pregnancies from non-viable and ectopic pregnancies. Metabolomics is the comprehensive analysis of small molecules in biological samples used to identify disease biomarkers. The vaginal metabolome has previously been shown to be predictive of later adverse pregnancy outcomes including preterm birth. In this study, we aimed to identify biomarkers of live normally-sited pregnancies when compared to non-viable intrauterine and ectopic pregnancies using NMR metabolomic profiling of vaginal swabs (LVS).

Study design, size, duration

This was a prospective cohort study (EXPEDITE). 222 pregnant women <10 weeks’ gestation with pain and/or bleeding were recruited over a period of 36 months at the Liverpool Women’s Hospital, a tertiary referral centre. Pregnancy outcomes were categorised according to ESHRE guidelines as live normally-sited pregnancy, miscarriage, tubal ectopic pregnancy or pregnancy of unknown location (PUL).

Participants/materials, setting, methods

Participants consented to self-collecting a LVS, which was extracted in acetonitrile and analysis by NMR spectroscopy; 1D 1H and 2D 1H-13C. Spectra were acquired at 25 °C on a 700 MHz spectrometer. Relative metabolite abundances underwent univariate and multivariate statistical analysis using MetaboAnalyst 5.0 and custom-built R scripts (p-value false discovery rate adjusted). Area under receiver operating characteristic curve (AUC) values were used to evaluate predictive models.

Main results and the role of chance

Our cohort of 222 women were categorised in to 100 (45 %) live normally-sited pregnancies, 29 (13 %) tubal ectopic pregnancies, 52 (23 %) miscarriages and 31 (14%) pregnancies of unknown location (PUL). Ten spectra from rare or uncertain pregnancy outcomes (e.g. molar pregnancy) were excluded. Univariate statistical analysis of all four groups identified isoleucine levels as significantly higher (p < 0.05) in live normally-sited pregnancies compared with all groups with adverse pregnancy outcome groups. Multivariate partial least squares discriminant analysis (PLS-DA) models of all groups failed to accurately predict pregnancy outcomes. To enhance the predictive models, miscarriage, tubal ectopic pregnancy and PUL groups were combined and compared to live normally-sited pregnancies. Univariate analysis revealed levels of several metabolites (including isoleucine, tyrosine and maltose) as significantly altered in live normally-sited pregnancies compared with all other outcomes. PLS-DA models demonstrated modest discrimination between live normally-sited pregnancies versus other outcomes (AUC = 0.75). In summary, this study has identified a vaginal metabolite profile and potential biomarkers associated with live normally-sited pregnancy in the first trimester.

Limitations, reasons for caution

The number of tubal ectopic pregnancies and PULs were relatively low compared to other outcomes. Additionally, several factors that may influence the vaginal metabolome, including infection and the vaginal microbiome, were not characterised in this study.

Wider implications of the findings

These findings may be useful in the development of diagnostic tests to confirm an intrauterine pregnancy and exclude potential life-threatening pregnancies. It is well established that the microbiome contributes to the vaginal metabolome. As such, our findings will inform future correlative studies of vaginal microbiome and metabolome in early pregnancy.

Trial registration number

NA

New management unit for conservation of the Endangered green turtle Chelonia mydas at the Xisha (Paracel) Islands, South China Sea

The Qilianyu cluster of the Xisha (Paracel) Islands has one of the few remaining green turtle Chelonia mydas rookeries in the China region. Genetic samples were obtained from dead green turtle embryos and hatchlings salvaged from post-hatched nests at Middle Island (n = 3), North Island (n = 9) and South Sand (n = 1) of the Qilianyu cluster in 2017-2019. The ~800 bp mitochondrial DNA control region was sequenced from the samples, and 5 haplotypes were identified belonging to 2 documented clades (clades III and VIII), including 2 new haplotypes (CmP243.1 and CmP244.1) and 3 previously reported haplotypes (CmP18.1, CmP19.1, CmP20.1). These results were combined with previously published mtDNA data for the Qilianyu cluster and nearby (~93 km) Yongle Islands indicating a lack of differentiation based on truncated 384 bp control region sequences (exact test, p = 0.0997; FST = 0.015, p = 0.2760), to represent a single Xisha Islands rookery. The rookery at the Xisha Islands was significantly differentiated (p < 0.01) from all 19 management units (MUs) documented in the Indo-Pacific and Japan regions, supporting recognition of the Xisha Islands rookery as a new independent MU. The results will help inform national and international conservation action plans by China and the countries around the South China Sea to protect green turtles in the West Pacific Ocean.

Embryo deformities and nesting trends in Kemp’s ridley sea turtles Lepidochelys kempii before and after the Deepwater Horizon oil spill

Kemp’s ridley sea turtles Lepidochelys kempii were disproportionately affected by the Deepwater Horizon (DWH) oil spill, which began on 20 April 2010. Embryo deformities were documented in inviable L. kempii eggs before (2008-2010) and after (2011-2013) the DWH spill in 2 Texas (USA) nesting areas (Upper Texas Coast and Padre Island National Seashore). Additional nesting trends, including clutch size and hatching success, were also investigated. Total and late-stage embryo deformity prevalence were 1.5 times greater after 2010 than before, but low in all nesting seasons (mean ± SD: 0.7 ± 8.5% total; 0.6 ± 8.0% late-stage) and did not differ between locations. Craniofacial and carapace deformities were the most frequently observed deformity types. Documented nests in both areas declined in 2010 relative to previous years, ending an exponential increase observed beginning in 1995. Clutch size remained consistent before and after the spill. Hatching success averaged 87.0 ± 33.3% in all years, but no effects from DWH were determined. Collectively, these data represent useful benchmarks against which to judge impacts of future crude oil spills and other catastrophic events.

Single arm two-stage studies: Improved designs for molecularly targeted agents

Mechanistic understanding of cancers and their potential interactions with molecularly targeted agents is driving the need for stratified medicine to ensure each participant receives the best possible care. This understanding, backed by scientific research, should be used to guide the design of clinical trials for these agents. The mechanism of action of a molecularly targeted agent often suggests that a biomarker can be used as a predictor of activity of the agent on the targeted disease. A biomarker driven trial is needed to confirm that the molecularly targeted agent stratifies the participant population with disease into high and low responder groups. We assume that the biomarker of interest can be dichotomised and propose a balanced parallel two-stage single-arm phase II trial that builds on existing two-stage single-arm designs. A single-arm trial cannot distinguish between a marker being predictive in the population as a whole and the agent causing an increased response in the marker positive group, but it is a first step. We compare this approach to the existing single-arm approaches, sequential enrichment, tandem two-stage, and parallel two-stage designs, and discuss the advantages and disadvantages of each design. We show that our design compares favourably to existing designs in the Bayesian framework, making a more efficient use of collected data. We recommend using the parallel two-stage balanced or sequential enrichment designs when randomisation is not practical in a phase II trial.

Analysis of phase II methodologies for single-arm clinical trials with multiple endpoints in rare cancers: An example in Ewing's sarcoma

Trials run in either rare diseases, such as rare cancers, or rare sub-populations of common diseases are challenging in terms of identifying, recruiting and treating sufficient patients in a sensible period. Treatments for rare diseases are often designed for other disease areas and then later proposed as possible treatments for the rare disease after initial phase I testing is complete. To ensure the trial is in the best interests of the patient participants, frequent interim analyses are needed to force the trial to stop promptly if the treatment is futile or toxic. These non-definitive phase II trials should also be stopped for efficacy to accelerate research progress if the treatment proves to be particularly promising. In this paper, we review frequentist and Bayesian methods that have been adapted to incorporate two binary endpoints and frequent interim analyses. The Eurosarc Trial of Linsitinib in advanced Ewing Sarcoma (LINES) is used as a motivating example and provides a suitable platform to compare these approaches. The Bayesian approach provides greater design flexibility, but does not provide additional value over the frequentist approaches in a single trial setting when the prior is non-informative. However, Bayesian designs are able to borrow from any previous experience, using prior information to improve efficiency.

Acute myocardial infarction in pregnancy following unlicensed use of methylenedioxymethamphetamine (‘ecstasy’)

Acute myocardial infarction is rare in pregnancy; however, the emerging trend towards advanced maternal age and the rising prevalence of obesity and diabetes suggest that more cases of myocardial infarction are likely to be encountered in pregnancy. However, there is scanty evidence on the risk of myocardial infarction with regard to socially misused substances in pregnancy. We describe the management of a case of acute myocardial infarction following unlicensed use of 3,4-methylenedioxymethamphetamine (‘Ecstasy’) in pregnancy. The case highlights a rare but serious risk associated with substance misuse in pregnancy.

Selection of experimental treatments, methods used and evolution of management guidelines for comparing and measuring three grazed farmlet systems

The Cicerone Project was a collaborative effort by livestock producers, researchers and extension specialists, which aimed to explore the profitability and sustainability of grazing enterprises on the Northern Tablelands of New South Wales, Australia. A major part of the Project was the creation of a moderate scale, unreplicated farmlet experiment. The process of selecting the farmlet treatments and the design of the experiment involved considerable negotiation over an extended period in order to achieve ‘ownership’ by all those involved. The farmlets were designed to compare a typical farmlet (B) as the control with a second farmlet (A), which received higher levels of pasture renovation and soil fertility, and a third (C), which employed intensive rotational grazing management with short graze and long rest periods. Management guidelines were developed for all soil, pasture, livestock and grazing management decisions on the three farmlets. Whole-farmlet data are presented for the pastures sown, fertiliser applied, supplement fed, the stocking rates attained and the pattern of graze and rest periods over the experimental period from July 2000 to December 2006. Over the first 4 years of the trial, pastures were renovated on 71% of farmlet A while 8% of each of farmlets B and C were renovated. The rates of fertiliser applied to the three farmlets varied according to soil test values and the different target values for soil phosphorus and sulfur. In the first year of the trial (2000–01), the annual average stocking rates on farmlets A, B and C were 9.5, 7.9 and 9.1 dry sheep eqivalents/ha, respectively, whereas by the fifth year (2005), the stocking rates were 11.2, 7.8 and 7.4 dry sheep equivalents/ha, respectively. This paper provides details of the general methods used in the farmlet trial, of relevance to a series of related papers which explore all aspects of the farmlet experiment and its findings. It also reports on the selection and definition of the farmlet treatments and describes how the guidelines evolved over the duration of the trial in response to the practical realities of conducting this complex, agroecosystem experiment.

Reflections on the concept, conduct and findings of the producer-led Cicerone Project

The Cicerone Project began as a producer-led partnership that sought, over a period of 8 years, to enhance the profitability and sustainability of livestock enterprises by improving the connection between those producers, research and extension. Following a detailed survey, the research and extension needs of livestock producers were identified and several applied investigations were conducted to meet those needs and delivered through a range of extension activities. This final paper of the Cicerone Special Issue reflects on the entire Project from a wide array of perspectives, including livestock producers, researchers, extension specialists and staff employed by the Project, all of whom are authors of this paper. A notable early successful outcome of the Project was the improved precision of footrot diagnosis, which has been of value to the entire sheep industry, and that flowed from a field investigation of benign and virulent footrot combined with detailed genetic investigations, which led to an improved testing regime. This paper also reflects on the findings of an unreplicated agricultural ecosystem research trial, which measured the impact of pasture renovation, increased soil fertility and grazing management on the profitability and sustainability of three different 53-ha farmlets. Valuable findings from this whole-farmlet trial included the need for a high quality feed supply for increasing stocking rate and animal liveweights; the ability and utility of satellite imagery to detect changes in pasture growth, composition and recent grazing pressure; the value of short grazing and long rest periods for controlling Barber’s pole worms of sheep; the impact of increased stocking rates on whole-farm profitability and risk; methods of optimising decisions relating to pasture renovation, fertiliser applications and grazing management; and an integrated analysis of all key measured components of the farmlet management systems. Collectively, these findings were powerful as they were demonstrated at a scale credible to livestock producers using the ‘compare – measure – learn – adopt’ approach, which was the key philosophy adopted by the Cicerone Project. By comparing and measuring different whole-farm systems, and by ensuring that producers had ownership of the trial process, the Project successfully delivered objective findings that producers trusted and which increased our understanding of important drivers of complex grazing enterprises under variable climatic conditions. Some of these drivers included: the influence of soil phosphorus on botanical composition and subsequent livestock production, the role of pasture renovation and soil fertility on herbage supply, herbage quality and stocking rate, and the improved gastrointestinal nematode control delivered by intensive rotational grazing. The beneficiaries of the Project included the 180 farmer members who participated in some 61 field days and workshops; the research and extension collaborators including four postgraduates who completed their research investigations in conjunction with the Project; and some 500 undergraduate and 300 technical students who benefited from coming to understand the applied field comparisons of the three whole-farmlet systems. Having livestock producers play a significant leadership role led to valuable outcomes achieved with research collaborators; this should encourage the development of other learning partnerships which aim to explore complex farming system issues.

Delivering extension and adult learning outcomes from the Cicerone Project by ‘comparing, measuring, learning and adopting'

The Cicerone Project was a partnership between livestock producers, researchers and extension specialists on the Northern Tablelands of New South Wales, Australia that investigated several complex grazing enterprise issues between 1998 and 2006. It was conducted as a Participatory Action Research project, which first surveyed livestock producers to learn of their problems and then carried out investigations according to the Project’s chosen motto of ‘compare – measure – learn – adopt’. The Project included research into footrot diagnosis and an investigation of whole-farmlet livestock and pasture management systems complemented by a multi-faceted extension and education component, which delivered findings to a wide array of stakeholders across the Northern Tablelands and adjacent regions. This paper describes the extension and education methods and outcomes and reflects on how successful the engagement of livestock producers was through a partnership, which focussed on co-learning by all participants. Several different communication approaches were used including the production of 40 newsletters and the delivery of 61 field days. Collaborators also held two symposia, which presented comprehensive overviews of the research results. In the final year of the Project, a roadshow was held to communicate results to a wider audience in neighbouring districts. The results of the two footrot trials, which were conducted as Participatory Action Research projects, led to rapid and substantial changes in the testing regime for virulent footrot, resulting in large savings for livestock producers through more accurate detection of the disease. Other valued extension and industry outcomes were the ability to compare the biophysical and economic performance of different whole farmlets, an appreciation of the value of the whole-farm system approach, the trustworthiness of the results and the stimulation of livestock producers to think more deeply about their management systems, stocking rate and risk. The Project benefited from the research efforts of four postgraduate students and was of benefit to ~300 high school and technical college students and also some 500 university undergraduate students who undertook learning projects in conjunction with Project members and collaborators. This Special Issue of 24 journal papers represents a substantial delivery of the findings from this complex agroecosystem Project, which broke new ground in terms of securing much closer working relationships between livestock producers, scientists and extension specialists. Ultimately, this volume will allow extension of the results of the Cicerone Project to reach a wider audience than has typically been achieved through other Participatory Action Research projects.

Molecular phylogeny for marine turtles based on sequences of the ND4-leucine tRNA and control regions of mitochondrial DNA

Marine turtles are divided into two families, the Dermochelyidae and the Cheloniidae. The majority of species are currently placed within the two tribes of the Cheloniidae, the Chelonini and the Carettini, but debate continues over generic and tribal affinities as well as species boundaries. We used nucleotide sequences (907 bp) from the ND4-LEU tRNA region and the control region (526 bp) of mitochondrial DNA to resolve areas of uncertainty in marine turtle (Chelonioidae) systematics. The ND4-LEU tRNA fragment was more conserved than the fragment from the control region, with sequence divergences ranging from 0.026 to 0.148 and 0.067 to 0.267, respectively. Parsimony analysis based only on the ND4-LEU tRNA data suggests that the hawksbill, Eretmochelys imbricata, lies within the tribe Carettni and is closely related to the genus Caretta, but could not resolve the position of the flatback, Natator depressus. A similar analysis based only on the control region sequence data suggested that N. depressus is affiliated with the Chelonini, but failed to resolve the position of E. imbricata and the loggerhead, Caretta caretta. In contrast to these results, the combination of both data sets with published cytochrome b data produced a phylogeny based on 1924 bp of sequence data which resolves the position of E. imbricata relative to Caretta and Lepidochelys and joins N. depressus as sister to the Carettini. Based on the molecular data, the Chelonini contains the Chelonia species, while the Carettini contains the remaining species of Cheloniidae. The control region sequence divergence between Pacific and Atlantic populations of the leatherback, Dermochelys coriacea, was relatively low (0.0081) when compared with the green turtle, Chelonia mydas (0.071-0.074). Atlantic and Pacific populations of Ch. mydas were found to be paraphyletic with respect to the black turtle, Ch. agassizi, suggesting that the current taxonomic designations within the Pacific Chelonia are questionable. This analysis shows the utility of combining sequence data for different regions of mtDNA that by themselves are insufficient to obtain robust phylogenies.