Seeking arrangements: cell contact as a cleavage-stage biomarker.

RESEARCH QUESTION: What can three-dimensional cell contact networks tell us about the developmental potential of cleavage-stage human embryos? DESIGN: This pilot study was a retrospective analysis of two Embryoscope imaging datasets from two clinics. An artificial intelligence system was used to reconstruct the three-dimensional structure of embryos from 11-plane focal stacks. Networks of cell contacts were extracted from the resulting embryo three-dimensional models and each embryo's mean contacts per cell was computed. Unpaired t-tests and receiver operating characteristic curve analysis were used to statistically analyse mean cell contact outcomes. Cell contact networks from different embryos were compared with identical embryos with similar cell arrangements. RESULTS: At t4, a higher mean number of contacts per cell was associated with greater rates of blastulation and blastocyst quality. No associations were found with biochemical pregnancy, live birth, miscarriage or ploidy. At t8, a higher mean number of contacts was associated with increased blastocyst quality, biochemical pregnancy and live birth. No associations were found with miscarriage or aneuploidy. Mean contacts at t4 weakly correlated with those at t8. Four-cell embryos fell into nine distinct cell arrangements; the five most common accounted for 97% of embryos. Eight-cell embryos, however, displayed a greater degree of variation with 59 distinct cell arrangements. CONCLUSIONS: Evidence is provided for the clinical relevance of cleavage-stage cell arrangement in the human preimplantation embryo beyond the four-cell stage, which may improve selection techniques for day-3 transfers. This pilot study provides a strong case for further investigation into spatial biomarkers and three-dimensional morphokinetics.

Predicting the number of oocytes retrieved from controlled ovarian hyperstimulation with machine learning.

STUDY QUESTION: Can machine learning predict the number of oocytes retrieved from controlled ovarian hyperstimulation (COH)? SUMMARY ANSWER: Three machine-learning models were successfully trained to predict the number of oocytes retrieved from COH. WHAT IS KNOWN ALREADY: A number of previous studies have identified and built predictive models on factors that influence the number of oocytes retrieved during COH. Many of these studies are, however, limited in the fact that they only consider a small number of variables in isolation. STUDY DESIGN, SIZE, DURATION: This study was a retrospective analysis of a dataset of 11,286 cycles performed at a single centre in France between 2009 and 2020 with the aim of building a predictive model for the number of oocytes retrieved from ovarian stimulation. The analysis was carried out by a data analysis team external to the centre using the Substra framework. The Substra framework enabled the data analysis team to send computer code to run securely on the centre's on-premises server. In this way, a high level of data security was achieved as the data analysis team did not have direct access to the data, nor did the data leave the centre at any point during the study. PARTICIPANTS/MATERIALS, SETTING, METHODS: The Light Gradient Boosting Machine algorithm was used to produce three predictive models: one that directly predicted the number of oocytes retrieved and two that predicted which of a set of bins provided by two clinicians the number of oocytes retrieved fell into. The resulting models were evaluated on a held-out test set and compared to linear and logistic regression baselines. In addition, the models themselves were analysed to identify the parameters that had the biggest impact on their predictions. MAIN RESULTS AND THE ROLE OF CHANCE: On average, the model that directly predicted the number of oocytes retrieved deviated from the ground truth by 4.21 oocytes. The model that predicted the first clinician's bins deviated by 0.73 bins whereas the model for the second clinician deviated by 0.62 bins. For all models, performance was best within the first and third quartiles of the target variable, with the model underpredicting extreme values of the target variable (no oocytes and large numbers of oocytes retrieved). Nevertheless, the erroneous predictions made for these extreme cases were still within the vicinity of the true value. Overall, all three models agreed on the importance of each feature which was estimated using Shapley Additive Explanation (SHAP) values. The feature with the highest mean absolute SHAP value (and thus the highest importance) was the antral follicle count, followed by basal AMH and FSH. Of the other hormonal features, basal TSH, LH, and testosterone levels were similarly important and baseline LH was the least important. The treatment characteristic with the highest SHAP value was the initial dose of gonadotropins. LIMITATIONS, REASONS FOR CAUTION: The models produced in this study were trained on a cohort from a single centre. They should thus not be used in clinical practice until trained and evaluated on a larger cohort more representative of the general population. WIDER IMPLICATIONS OF FINDINGS: These predictive models for the number of oocytes retrieved from COH may be useful in clinical practice, assisting clinicians in optimizing COH protocols for individual patients. Our work also demonstrates the promise of using the Substra framework for allowing external researchers to provide clinically relevant insights on sensitive fertility data in a fully secure, trustworthy manner and opens a number of exciting avenues for accelerating future research. STUDY FUNDING/COMPETING INTEREST(S): This study was funded by the French Public Bank of Investment as part of the Healthchain Consortium. T.Fe., C.He., J.C., C.J., C.-A.P., and C.Hi. are employed by Apricity. C.Hi. has received consulting fees and honoraria from Vitrolife, Merck Serono, Ferring, Cooper Surgical, Dibimed, Apricity, and Fairtility and travel support from Fairtility and Vitrolife, participates on an advisory board for Merck Serono, was the founder and organizer of the AI Fertility conference, has stock in Aria Fertility, TMRW, Fairtility, Apricity, and IVF Professionals, and received free equipment from Planar in exchange for first user feedback. C.J. has received a grant from BPI. J.C. has also received a grant from BPI, is a member of the Merck AI advisory board, and is a board member of Labelia Labs. C.He has a contract for medical writing of this manuscript by CHU Nantes and has received travel support from Apricity. A.R. haș received honoraria from Ferring and Organon. T.Fe. has received a grant from BPI. TRIAL REGISTRATION NUMBER: N/A.

Machine learning for prediction of euploidy in human embryos: in search of the best-performing model and predictive features.

OBJECTIVE: To assess the best-performing machine learning (ML) model and features to predict euploidy in human embryos. DESIGN: Retrospective cohort analysis. SETTING: Department for reproductive medicine in a university hospital. PATIENT(S): One hundred twenty-eight infertile couples treated between January 2016 and December 2019. Demographic and clinical data and embryonic developmental and morphokinetic data from 539 embryos (45% euploid, 55% aneuploid) were analyzed. INTERVENTION(S): Random forest classifier (RFC), scikit-learn gradient boosting classifier, support vector machine, multivariate logistic regression, and naïve Bayes ML models were trained and used in 9 databases containing either 26 morphokinetic features (as absolute [A1] or interim [A2] times or combined [A3]) alone or plus 19 standard development features [B1, B2, and B3] with and without 40 demographic and clinical characteristics [C1, C2, and C3]. Feature selection and model retraining were executed for the best-performing combination of model and dataset. MAIN OUTCOME MEASURE(S): The main outcome measures were overall accuracy, precision, recall or sensitivity, F1 score (the weighted average of precision and recall), and area under the receiver operating characteristic curve (AUC) of ML models for each dataset. The secondary outcome measure was ranking of feature importance for the best-performing combination of model and dataset. RESULT(S): The RFC model had the highest accuracy (71%) and AUC (0.75) when trained and used on dataset C1. The precision, recall or sensitivity, F1 score, and AUC were 66%, 86%, 75%, and 0.75, respectively. The accuracy, recall or sensitivity, and F1 score increased to 72%, 88%, and 76%, respectively, after feature selection and retraining. Morphokinetic features had the highest relative predictive weight. CONCLUSION(S): The RFC model can predict euploidy with an acceptable accuracy (>70%) using a dataset including embryos' morphokinetics and standard embryonic development and subjects' demographic and clinical features.

Data sharing: using blockchain and decentralized data technologies to unlock the potential of artificial intelligence: What can assisted reproduction learn from other areas of medicine?

The extension of blockchain use for nonfinancial domains has revealed opportunities to the health care sector that answer the need for efficient and effective data and information exchanges in a secure and transparent manner. Blockchain is relatively novel in health care and particularly for data analytics, although there are examples of improvements achieved. We provide a systematic review of blockchain uses within the health care industry, with a particular focus on the in vitro fertilization (IVF) field. Blockchain technology in the fertility sector, including data sharing collaborations compliant with ethical data handling within confines of international law, allows for large-scale prospective cohort studies to proceed at an international scale. Other opportunities include gamete donation and matching, consent sharing, and shared resources between different clinics.

Predictive modeling in reproductive medicine: Where will the future of artificial intelligence research take us?

Artificial intelligence (AI) systems have been proposed for reproductive medicine since 1997. Although AI is the main driver of emergent technologies in reproduction, such as robotics, Big Data, and internet of things, it will continue to be the engine for technological innovation for the foreseeable future. What does the future of AI research look like?

Use of Staby(®) technology for development and production of DNA vaccines free of antibiotic resistance gene.

The appearance of new viruses and the cost of developing certain vaccines require that new vaccination strategies now have to be developed. DNA vaccination seems to be a particularly promising method. For this application, plasmid DNA is injected into the subject (man or animal). This plasmid DNA encodes an antigen that will be expressed by the cells of the subject. In addition to the antigen, the plasmid also encodes a resistance to an antibiotic, which is used during the construction and production steps of the plasmid. However, regulatory agencies (FDA, USDA and EMA) recommend to avoid the use of antibiotics resistance genes. Delphi Genetics developed the Staby(®) technology to replace the antibiotic-resistance gene by a selection system that relies on two bacterial genes. These genes are small in size (approximately 200 to 300 bases each) and consequently encode two small proteins. They are naturally present in the genomes of bacteria and on plasmids. The technology is already used successfully for production of recombinant proteins to achieve higher yields and without the need of antibiotics. In the field of DNA vaccines, we have now the first data validating the innocuousness of this Staby(®) technology for eukaryotic cells and the feasibility of an industrial production of an antibiotic-free DNA vaccine. Moreover, as a proof of concept, mice have been successfully vaccinated with our antibiotic-free DNA vaccine against a deadly disease, pseudorabies (induced by Suid herpesvirus-1).

Measurement by magnetic resonance imaging of the peritoneal membrane in contact with dialysate in rats.

To be optimal, a peritoneal dialysis prescription should consider the peritoneal surface area recruitment. In fact, as shown by computed tomography imaging, only a fraction of the available anatomic peritoneum is in contact with the dialysate (PDF). Various factors may dynamically affect the recruitment of the wetted membrane: posture, fill volume, PDF composition (biocompatibility), and pharmacologic agents (phospholipids). To precisely determine the peritoneal membrane recruitment capacity, we developed an animal model. In 5/6 bi-nephrectomized rats on peritoneal dialysis, between week 6 and week 8 post surgery, we used MRI to assess the contact area, with the dialysate acting as the contrast medium (fill volume: 10 mL per 100-g rat body weight). The MRI protocol consisted of axially oriented, turbo spin-echo, 3-mm slice, T2 weighted sequences. The contact area was measured using an adapted three-dimensional MRI reconstruction software based on DICOM (digital imaging and communications in medicine) images. The MRI studies (n=10) were successful. They showed that only a fraction of the presumed anatomic area (30% - 40%) was in contact with the PDF Peritoneal MRI in rats is a method that shows potential for assessing peritoneal contact area and its variation under experimental conditions.

Identification and subcellular distribution of endogenous Ins(1,4,5)P(3) 3-kinase B in mouse tissues.

Inositol 1,4,5-trisphosphate 3-kinase (IP(3)-3K) catalyses the phosphorylation of inositol 1,4,5-trisphosphate to inositol 1,3,4,5-tetrakisphosphate. cDNAs encoding three mammalian isoforms have been reported and referred to as IP(3)-3KA, IP(3)-3KB, and IP(3)-3KC. IP(3)-3KB is particularly sensitive to proteolysis at the N-terminus, a mechanism known to generate active fragments of lower molecular mass. Endogenous IP(3)-3KB has therefore not been formally identified in tissues. We have probed a series of murine tissues with an antibody directed against the C-terminus of IP(3)-3KB and used IP(3)-3KB deficient mouse tissues as negative controls. IP(3)-3KB was shown to be particularly well expressed in brain, lung, and thymus with molecular masses of 110-120kDa. The identification of the native IP(3)-3KB by Western blotting for the first time will facilitate further studies of regulation of its activity by specific proteases and/or phosphorylation.