Prior-Guided Attribution of Deep Neural Networks for Obstetrics and Gynecology

Obstetrics and gynecology (OB/GYN) are areas of medicine that specialize in the care of women during pregnancy and childbirth and in the diagnosis of diseases of the female reproductive system. Ultrasound scanning has become ubiquitous in these branches of medicine, as breast or fetal ultrasound images can lead the sonographer and guide him through his diagnosis. However, ultrasound scan images require a lot of resources to annotate and are often unavailable for training purposes because of confidentiality reasons, which explains why deep learning methods are still not as commonly used to solve OB/GYN tasks as in other computer vision tasks. In order to tackle this lack of data for training deep neural networks in this context, we propose Prior-Guided Attribution (PGA), a novel method that takes advantage of prior spatial information during training by guiding part of its attribution towards these salient areas. Furthermore, we introduce a novel prior allocation strategy method to take into account several spatial priors at the same time while providing the model enough degrees of liberty to learn relevant features by itself. The proposed method only uses the additional information during training, without needing it during inference. After validating the different elements of the method as well as its genericity on a facial analysis problem, we demonstrate that the proposed PGA method constantly outperforms existing baselines on two ultrasound imaging OB/GYN tasks: breast cancer detection and scan plane detection with segmentation prior maps.

The Human Phenotype Ontology in 2024: phenotypes around the world

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

Prenatal diagnosis of isolated bilateral clubfoot: Is amniocentesis indicated?

INTRODUCTION

The aim of this study is to evaluate the benefit of cytogenetic testing by amniocentesis after an ultrasound diagnosis of isolated bilateral talipes equinovarus.

MATERIAL AND METHODS

This multicenter observational retrospective study includes all prenatally diagnosed cases of isolated bilateral talipes equinovarus in five fetal medicine centers from 2012 through 2021. Ultrasound data, amniocentesis results, biochemical analyses of amniotic fluid and parental blood samples to test neuromuscular diseases, pregnancy outcomes, and postnatal outcomes were collected for each patient.

RESULTS

In all, 214 fetuses with isolated bilateral talipes equinovarus were analyzed. A first-degree family history of talipes equinovarus existed in 9.8% (21/214) of our cohort. Amniocentesis was proposed to 86.0% (184/214) and performed in 70.1% (129/184) of cases. Of the 184 karyotypes performed, two (1.6%) were abnormal (one trisomy 21 and one triple X syndrome). Of the 103 microarrays performed, two (1.9%) revealed a pathogenic copy number variation (one with a de novo 18p deletion and one with a de novo 22q11.2 deletion) (DiGeorge syndrome). Neuromuscular diseases (spinal muscular amyotrophy, myasthenia gravis, and Steinert disease) were tested for in 56 fetuses (27.6%); all were negative. Overall, 97.6% (165/169) of fetuses were live-born, and the diagnosis of isolated bilateral talipes equinovarus was confirmed for 98.6% (139/141). Three medical terminations of pregnancy were performed (for the fetuses diagnosed with Down syndrome, DiGeorge syndrome, and the 18p deletion). Telephone calls (at a mean follow-up age of 4.5 years) were made to all parents to collect medium-term and long-term follow-up information, and 70 (33.0%) families were successfully contacted. Two reported a rare genetic disease diagnosed postnatally (one primary microcephaly and one infantile glycine encephalopathy). Parents did not report any noticeably abnormal psychomotor development among the other children during this data collection.

CONCLUSIONS

Despite the low rate of pathogenic chromosomal abnormalities diagnosed prenatally after this ultrasound diagnosis, the risk of chromosomal aberration exceeds the risks of amniocentesis. These data may be helpful in prenatal counseling situations.

Prenatal diagnosis of pontocerebellar hypoplasia with postnatal follow-up

OBJECTIVE

To describe the MR features enabling prenatal diagnosis of pontocerebellar hypoplasia (PCH).

METHOD

This was a retrospective single monocentre study. The inclusion criteria were decreased cerebellar biometry on dedicated neurosonography and available fetal Magnetic Resonance Imaging (MRI) with PCH diagnosis later confirmed either genetically or clinically on post-natal MRI or by autopsy. The exclusion criteria were non-available MRI and sonographic features suggestive of a known genetic or other pathologic diagnosis. The collected data were biometric or morphological imaging parameters, clinical outcome, termination of pregnancy (TOP), pathological findings and genetic analysis (karyotyping, chromosomal microarray, DNA sequencing targeted or exome). PCH was classified as classic, non-classic, chromosomal, or unknown type.

RESULTS

Forty-two fetuses were diagnosed with PCH, of which 27 were referred for decreased transverse cerebellar diameter at screening ultrasound. Neurosonography and fetal MRI were performed at a mean gestational age of 29 + 4 and 31 + 0 weeks, respectively. Termination of pregnancy occurred. Pregnancy was terminated in 24 cases. Neuropathological examination confirmed the diagnosis in 24 cases and genetic testing identified abnormalities in 29 cases (28 families, 14 chromosomal anomaly). Classic PCH is associated with pontine atrophy and small MR measurements decreasing with advancing gestation.

CONCLUSION

This is the first large series of prenatally diagnosed PCHs. Our study shows the essential contribution of fetal MRI to the prenatal diagnosis of PCH. Classic PCHs are particularly severe and are associated with certain MR features.

[A pragmatic comparison of fetal biometry curves]

INTRODUCTION

The fetal biometrics charts recommended in France for ultrasound screening include measurements of head circumference (HC), biparietal diameter (BIP), abdominal circumference (AC) and femur length (FL). New international growth standards have been recommended since 2022. The aim of this work is to quantitatively describe the differences between these biometric curves.

METHODS

The biometry curves from the French College for Fetal Ultrasound, OMS and INTERGROWTH-21 are pragmatically compared based on their original quantile regression equations (superposition and quantification of differences in millimeters and in proportion) for different percentiles of clinical interest.

RESULTS

Compared with the new charts, CFEF underestimates HC<-3DS and AC<10eP. The proportions of differences between the CFEF and INTERGROWTH-21 or WHO curves always remained <5%. The proportions of difference of the 3rd percentile of HC and FL, 10th and 90th percentile of AC were always lower than 2%, 2%, 5% and 4% respectively, between OMS and INTERGROWTH-21.

CONCLUSION

The switch to prescriptive standards suggests an improvement in the detection of fetuses with AC<10th percentile, an improvement in the detection of prenatal onset microcephaly, with no argument for a decrease in the detection rate of severe constitutional bone disease or modification of obstetrical guidelines.

A Machine Learning Approach for the Prediction of Testicular Sperm Extraction in Nonobstructive Azoospermia: Algorithm Development and Validation Study

BACKGROUND

Testicular sperm extraction (TESE) is an essential therapeutic tool for the management of male infertility. However, it is an invasive procedure with a success rate up to 50%. To date, no model based on clinical and laboratory parameters is sufficiently powerful to accurately predict the success of sperm retrieval in TESE.

OBJECTIVE

The aim of this study is to compare a wide range of predictive models under similar conditions for TESE outcomes in patients with nonobstructive azoospermia (NOA) to identify the correct mathematical approach to apply, most appropriate study size, and relevance of the input biomarkers.

METHODS

We analyzed 201 patients who underwent TESE at Tenon Hospital (Assistance Publique-Hôpitaux de Paris, Sorbonne University, Paris), distributed in a retrospective training cohort of 175 patients (January 2012 to April 2021) and a prospective testing cohort (May 2021 to December 2021) of 26 patients. Preoperative data (according to the French standard exploration of male infertility, 16 variables) including urogenital history, hormonal data, genetic data, and TESE outcomes (representing the target variable) were collected. A TESE was considered positive if we obtained sufficient spermatozoa for intracytoplasmic sperm injection. After preprocessing the raw data, 8 machine learning (ML) models were trained and optimized on the retrospective training cohort data set: The hyperparameter tuning was performed by random search. Finally, the prospective testing cohort data set was used for the model evaluation. The metrics used to evaluate and compare the models were the following: sensitivity, specificity, area under the receiver operating characteristic curve (AUC-ROC), and accuracy. The importance of each variable in the model was assessed using the permutation feature importance technique, and the optimal number of patients to include in the study was assessed using the learning curve.

RESULTS

The ensemble models, based on decision trees, showed the best performance, especially the random forest model, which yielded the following results: AUC=0.90, sensitivity=100%, and specificity=69.2%. Furthermore, a study size of 120 patients seemed sufficient to properly exploit the preoperative data in the modeling process, since increasing the number of patients beyond 120 during model training did not bring any performance improvement. Furthermore, inhibin B and a history of varicoceles exhibited the highest predictive capacity.

CONCLUSIONS

An ML algorithm based on an appropriate approach can predict successful sperm retrieval in men with NOA undergoing TESE, with promising performance. However, although this study is consistent with the first step of this process, a subsequent formal prospective multicentric validation study should be undertaken before any clinical applications. As future work, we consider the use of recent and clinically relevant data sets (including seminal plasma biomarkers, especially noncoding RNAs, as markers of residual spermatogenesis in NOA patients) to improve our results even more.

Imaging factors affecting prenatal counselling in orofacial clefts

INTRODUCTION

we aim to correlate pre-and postnatal data regarding the cleft type and surgical prognostic factors associated to orofacial clefts.

METHODS

retrospective study concerning all cases of orofacial cleft evaluated prenatally (US+/-MRI) between 2015 and 2020 with available postnatal outcome. We compared prenatal imaging (cleft type and surgical prognostic factors) with postnatal findings.

RESULTS

48 fetuses were included. Median gestational age at first US/MRI examination: 29WG+2D and 31WG+6D respectively. The prenatal diagnosis was in accordance with postnatal findings with regard to the cleft type in 88% of the cases (n=42/48) for US and/or MRI, 84% (n=38/45) for US only and 90% (n=37/41) for MRI only. The nasal septum deviation and nostril collapse were underestimated by prenatal US in 48% (n=12/25) and 44% (n=11/25) of cases respectively (Cohen's kappa of 0.22 and 0.32 respectively). Pre-and postnatal examinations were in accordance in 75% of cases (n=8) regarding evaluation of anteroposterior maxillary shift in case of unilateral alveolar cleft and in 90% and 80% of cases (n=10) regarding the degree of protrusion/deviation of the premaxillary protrusion in case of bilateral cleft respectively.

CONCLUSION

Prenatal imaging can accurately assess the type of orofacial cleft and evaluate maxillary shift and deviation of the premaxilla. It underestimates the nose deformity.

Prenatal management of fetal anemia due to pyruvate kinase deficiency: A case report

BACKGROUND

Pyruvate Kinase (PK) deficiency is the most common enzyme defect of glycolysis, leading to congenital hemolytic anemia, which can occur during the neonatal period.

STUDY DESIGN AND METHODS

We report the prenatal management of fetal anemia related to PK deficiency in a family with a severe proband.

RESULTS

The couple had a first child born with hydrops, whose PK deficiency was diagnosed at 18 months of life. He was treated with allogeneic bone marrow transplantation. The second child was free from disease. For the third pregnancy, the amniocentesis revealed a PK deficiency. Weekly ultrasound monitoring of the middle cerebral artery velocity allowed the detection of severe fetal anemia. Two intrauterine red blood cell transfusions (IUTs) were performed, raising the fetal hemoglobin from 6.6 to 14.5 g/dl at 28 weeks' gestation and from 8.9 to 15.3 g/dl at 31 weeks. A hematopoietic stem cell allograft was discussed prenatally but not chosen, as it would not have significantly changed the perinatal prognosis. The patient delivered a 2730 g girl at 37 weeks, with hemoglobin of 13.6 g/dl. The child presented with neonatal jaundice treated with phototherapy and received postnatal transfusions.

DISCUSSION

When a proband is identified in a family, fetal investigation is warranted, to set up third-trimester ultrasound surveillance and perinatal management. In case of fetal severe anemia of unknown etiology, the workup on fetal blood sampling before IUT should comprise the search for erythrocytes enzymopathies, such as PK deficiency. IUTs allow safer full-term delivery in cases with PK deficiency.

Knowledge Representation and Management: Notable Contributions in 2021

OBJECTIVES

To select, present, and summarize the best papers in the field of Knowledge Representation and Management (KRM) published in 2021.

METHODS

Following the International Medical Informatics Association (IMIA) Yearbook guidelines, a comprehensive and standardized review of the biomedical informatics literature was performed to select the best KRM papers published in 2021, based on PubMed queries.

RESULTS

A total of 1,231 publications were retrieved from PubMed. We nominated 15 candidate best papers, and four of them were finally selected as the best papers in the KRM section. The topics covered by these papers include knowledge graph, ontology development, ontology alignment, and the International Classification of Diseases.

CONCLUSION

In the KRM best paper selection for 2021, the candidate best papers covered a wider spectrum of topics compared to the last year's significant focus on ontology curation. In particular, ontology development for specific domains (e.g., Alzheimer's disease, infectious diseases, bioethics) has received the most attention.

P-057 Machine learning-based prediction of testicular sperm extraction: comparison of different preprocessing and models, required sample size and relevance of input biomarkers

Study question

Can advanced machine learning applied to the preoperative assessment predict the testicular sperm extraction outcome in azoospermic context and how many patients are required?

Summary answer

Despite encouraging results (AUC = 92.0%, sensitivity = 83.9% and specificity = 84.2%), integrating new biomarkers would probably be more relevant than enrolling additional patients.

What is known already

Testicular sperm extraction (TESE) is an essential therapeutic tool for the male infertility management and is often the “last hope” before gamete donation for these patients. However, it is an invasive procedure and is successful in up to 50%. Until now, no model is sufficiently powerful to accurately predict the success of sperm retrieval in TESE. Among the few models already developed, the findings are highly disparate despite having common input data (preoperative assessment). Moreover, only few types of machine learning models and procedures have been investigated. Performances were mostly capped despite the inclusion sometimes of more than 1000 patients.

Study design, size, duration

Data of 175 patients who underwent TESE between 2012 and 2021 were retrospectively analyzed. The performances of a wide range of preprocessing methods and machine learning models (state-of-the-art methods in machine learning) we explored, evaluated, and compared. The objective was to predict the presence or absence of spermatozoa, using 17 parameters (clinical, hormonal, genetic, history) from the preoperative assessment. The study protocol was approved by a local ethics committee (IRB CER-2021-041).

Participants/materials, setting, methods

After data preprocessing (standardization…), Machine Learning models (Bayesian Naive Classification, logistic regression, k-nearest neighbor classifier, support vector machine, random forests, GradientBoosting and XGBoost) and Deep Learning models were tested. The validation procedure consisted of splitting the dataset into a training set and test set. Beyond the standard metrics (sensitivity, specificity, AUC-ROC), the identification of the most relevant variables and the learning curve to determine the optimal patient number to be included were performed.

Main results and the role of chance

At least one live spermatozoon was found in the testicular tissue of 104 (59.4%) patients (positive TESE) out of 175. The best performing model (Random Forest with appropriate preprocessing) obtained the following results on the test set: AUC = 92.0%, sensitivity = 83.9% and specificity = 84.2%, leading to an efficient tool, which gives additional and more relevant information than the different variables taken separately. Inhibin B, FSH and history of cryptorchidism were the variables with the most discriminating power. However, a plateau in the model performance was observed (beyond 110 patients), whatever the approach or the preprocessing used. A trend curve shows that beyond 110 patients, no improvement can be observed and cast doubt about the power of the traditional preoperative parameters assessed before TESE. The classic preoperative assessment can probably not fully predict the TESE outcomes. Further work is needed to be enhance with new hypothesis and the use of new biomarkers to be integrated into the models.

Limitations, reasons for caution

The main limitation was the monocentric design and the use of retrospective data.

Wider implications of the findings

Machine learning models can provide the basis for an enhanced decision support system tool in the context of azoospermia. Indefinitely increasing the number of participants is not likely to be the solution: further hypotheses and biomarkers integration into the models will probably be necessary to improve performance.

Trial registration number

not applicable

Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology

Technological advances in both genome sequencing and prenatal imaging are increasing our ability to accurately recognize and diagnose Mendelian conditions prenatally. Phenotype-driven early genetic diagnosis of fetal genetic disease can help to strategize treatment options and clinical preventive measures during the perinatal period, to plan in utero therapies, and to inform parental decision-making. Fetal phenotypes of genetic diseases are often unique and at present are not well understood; more comprehensive knowledge about prenatal phenotypes and computational resources have an enormous potential to improve diagnostics and translational research. The Human Phenotype Ontology (HPO) has been widely used to support diagnostics and translational research in human genetics. To better support prenatal usage, the HPO consortium conducted a series of workshops with a group of domain experts in a variety of medical specialties, diagnostic techniques, as well as diseases and phenotypes related to prenatal medicine, including perinatal pathology, musculoskeletal anomalies, neurology, medical genetics, hydrops fetalis, craniofacial malformations, cardiology, neonatal-perinatal medicine, fetal medicine, placental pathology, prenatal imaging, and bioinformatics. We expanded the representation of prenatal phenotypes in HPO by adding 95 new phenotype terms under the Abnormality of prenatal development or birth (HP:0001197) grouping term, and revised definitions, synonyms, and disease annotations for most of the 152 terms that existed before the beginning of this effort. The expansion of prenatal phenotypes in HPO will support phenotype-driven prenatal exome and genome sequencing for precision genetic diagnostics of rare diseases to support prenatal care.

Pattern-Based Logical Definitions of Prenatal Disorders Grounded on Dispositions

Biomedical ontologies define concepts having biomedical significance and the semantic relations among them. Developing high-quality and reusable ontologies in the biomedical domain is a challenging task. Pattern-based ontology design is considered a promising approach to overcome the challenges. Ontology Design Patterns (ODPs) are reusable modeling solutions to facilitate ontology development. This study relies on ODPs to semantically enrich biomedical ontologies by assigning logical definitions to ontological entities. Specifically, pattern-based logical definitions grounded on dispositions are given to prenatal disorders. The proposed approach is performed under the supervision of fetal domain experts.

Contributions of artificial intelligence reported in Obstetrics and Gynecology journals: a systematic review

Background

The applications of artificial intelligence (AI) processes have grown significantly in all medical disciplines during the last decades. Two main types of AI have been applied in medicine: symbolic AI (eg, knowledge base and ontologies) and nonsymbolic AI (eg, machine learning and artificial neural networks). Consequently, AI has also been applied across most obstetrics and gynecology (OB/GYN) domains, including general obstetrics, gynecology surgery, fetal ultrasound, and assisted reproductive medicine, among others.

Objective

The aim of this study was to provide a systematic review to establish the actual contributions of AI reported in OB/GYN discipline journals.

Methods

The PubMed database was searched for citations indexed with “artificial intelligence” and at least one of the following medical subject heading (MeSH) terms between January 1, 2000, and April 30, 2020: “obstetrics”; “gynecology”; “reproductive techniques, assisted”; or “pregnancy.” All publications in OB/GYN core disciplines journals were considered. The selection of journals was based on disciplines defined in Web of Science. The publications were excluded if no AI process was used in the study. Review, editorial, and commentary articles were also excluded. The study analysis comprised (1) classification of publications into OB/GYN domains, (2) description of AI methods, (3) description of AI algorithms, (4) description of data sets, (5) description of AI contributions, and (6) description of the validation of the AI process.

Results

The PubMed search retrieved 579 citations and 66 publications met the selection criteria. All OB/GYN subdomains were covered: obstetrics (41%, 27/66), gynecology (3%, 2/66), assisted reproductive medicine (33%, 22/66), early pregnancy (2%, 1/66), and fetal medicine (21%, 14/66). Both machine learning methods (39/66) and knowledge base methods (25/66) were represented. Machine learning used imaging, numerical, and clinical data sets. Knowledge base methods used mostly omics data sets. The actual contributions of AI were method/algorithm development (53%, 35/66), hypothesis generation (42%, 28/66), or software development (3%, 2/66). Validation was performed on one data set (86%, 57/66) and no external validation was reported. We observed a general rising trend in publications related to AI in OB/GYN over the last two decades. Most of these publications (82%, 54/66) remain out of the scope of the usual OB/GYN journals.

Conclusions

In OB/GYN discipline journals, mostly preliminary work (eg, proof-of-concept algorithm or method) in AI applied to this discipline is reported and clinical validation remains an unmet prerequisite. Improvement driven by new AI research guidelines is expected. However, these guidelines are covering only a part of AI approaches (nonsymbolic) reported in this review; hence, updates need to be considered.

The Myelic Limited Dorsal Malformation: Prenatal Ultrasonographic Characteristics of an Intermediate Form of Dysraphism

OBJECTIVES

The aim of the study was to report a subtype of dysraphism designated as myelic limited dorsal malformation (MyeLDM) and to describe its characteristics at prenatal ultrasound (US).

METHODS

It was a retrospective study from 2014 to 2020 based on second-line US evaluation of patients referred to our institution for myelomeningocele (MMC). Magnetic resonance imaging and acetylcholine esterase evaluation in the amniotic fluid were also offered. Major and minor criteria for open and closed dysraphism were defined and recorded for each patient. Patients were included as MyeLDM when both criteria of closed and open dysraphism were observed in the same fetus. Correlations were obtained with the postpartum data.

RESULTS

Twenty patients fulfilled the inclusion criteria, some of them being very close to MMC, others very close to limited dorsal myeloschisis (LDM), and others lying in between. There were 13 live-born neonates and 7 terminations of pregnancy. Correlations between prenatal and postpartum data were overall very good.

CONCLUSION

Our series describe the ultrasonographic characteristics of an intermediate type of dysraphism and suggest that there is a continuum between MMC and LDM with numerous possibilities of hybrid forms (MyeLDM) sharing characteristics of both open and closed dysraphisms.

Knowledge Representation and Management: Interest in New Solutions for Ontology Curation

Objective: To select, present and summarize some of the best papers in the field of Knowledge Representation and Management (KRM) published in 2020.

Methods: A comprehensive and standardized review of the medical informatics literature was performed to select the most interesting papers of KRM published in 2020, based on PubMed queries. This review was conducted according to the IMIA Yearbook guidelines.

Results: Four best papers were selected among 1,175 publications. In contrast with the papers selected last year, the four best papers of 2020 demonstrated a significant focus on methods and tools for ontology curation and design. The usual KRM application domains (bioinformatics, machine learning, and electronic health records) were also represented.

Conclusion: In 2020, ontology curation emerges as a significant topic of research interest. Bioinformatics, machine learning, and electronics health records remain significant research areas in the KRM community with various applications. Knowledge representations are key to advance machine learning by providing context and to develop novel bioinformatics metrics. As in 2019, representations serve a great variety of applications across many medical domains, with actionable results and now with growing adhesion to the open science initiative.

Open fetal surgery for myelomeningocele repair in France

INTRODUCTION

Open fetal myelomeningocele (MMC) surgery is currently the standard of care option for prenatal MMC repair. We described the population referred to our center and reviewed outcome after open fetal MMC repair.

MATERIAL AND METHODS

All patients referred to our center for MMC were reviewed from July 2014 to June 2020. For all the patients who underwent fetal MMC repair, surgical details, maternal characteristics and data from the neonatal to the three-years-old evaluations were collected.

RESULTS

Among the 126 patients referred to our center, 49.2% were eligible and 27.4% (n = 17) of them underwent fetal MMC repair. Average gestational age at fetal surgery was 24⁺⁶ weeks. There was no case of fetal complication and the only maternal complication was one case of transfusion. We recorded 70% of premature rupture of membranes and 47% of premature labor. Average gestational age at delivery was 34⁺² weeks and no patient delivered before 30 weeks. There was no case of uterine scar dehiscence or maternal complication during cesarean section. After birth, 59% of the children had a hindbrain herniation reversal. At 1-year-old, 42% were assigned a functional level of one or more better than expected according to the prenatal anatomic level and 25% required a ventriculoperitoneal shunt. At 3-year-old, all the children attended school and 75% were able to walk with orthotics or independently.

CONCLUSION

Open fetal surgery enables anatomical repair of the MMC lesion, a potential benefit on cerebral anomalies and motor function, with a low rate of perinatal and maternal complications.

Effect of intravenous immunoglobulins to postpone the gestational age of first intrauterine transfusion in very severe red blood cell alloimmunization: A case-control study

BACKGROUND

Early intrauterine transfusion (IUT) is associated with a higher risk of fetal loss. Our objective was to evaluate the efficiciency of intravenous immunoglobulins (IVIG) to postpone the gestational age at first IUT beyond 20 weeks of gestation (WG) compared to the previous pregnancy in case of very severe red blood cell (RBC) alloimmunization.

STUDY DESIGN AND METHODS

Very severe RBC alloimmunization was defined by a high titer of antibodies and a previous pregnancy complicated by a first IUT before 24 WG and/or perinatal death directly related to alloimmunization. We performed a single-center case-control study. Cases and controls were patients respectively treated with weekly IVIG infusions started before 13 WG, and without.

RESULTS

Twenty cases and 21 controls were included. Gestational age (GA) at first IUT was postponed after 20 WG in 18/20 (90 %) of patients treated with IVIG and in 15/21 (71 %) in the control group (p = 0.24). Compared to the previous pregnancy, the GA at first IUT was postponed by a median of 22 [+11; +49] days in the IVIG group and occurred in average 2 days earlier [-17 ; +12] in the non-treated group (p = 0.02). There was no difference between number of IUT and need for exchange-transfusion. IVIG treatment was associated with a significant decrease of antibodies' quantitation.

CONCLUSION

In our series, IVIG tends to differ first IUT beyond 20 WG and have a significant effect in postponing the gestational age of the first IUT in patients with very severe RBC alloimmunization.

The impact of optimal dating on the assessment of fetal growth

BACKGROUND

The impact of using the Intergrowth (IG) dating formulae in comparison to the commonly used Robinson dating on the evaluation of biometrics and estimated fetal weight (EFW) has not been evaluated.

METHODS

Nationwide cross-sectional study of routine fetal ultrasound biometry in low-risk pregnant women whose gestational age (GA) had been previously assessed by a first trimester CRL measurement. We compared the CRL-based GA according to the Robinson formula and the IG formula. We evaluated the fetal biometric measurements as well as the EFW taken later in pregnancy depending on the dating formula used. Mean and standard deviation of the Z scores as well as the number and percentage of cases classified as <3rd, < 10th, >90th and > 97th percentile were compared.

RESULTS

Three thousand five hundred twenty-two low-risk women with scans carried out after 18 weeks were included. There were differences of zero, one and 2 days in 642 (18.2%), 2700 (76.7%) and 180 (5%) when GA was estimated based on the Robinson or the IG formula, respectively. The biometry Z scores assessed later in pregnancy were all statistically significantly lower when the Intergrowth-based dating formula was used (p < 10- 4). Likewise, the number and percentage of foetuses classified as <3rd, < 10th, >90th and > 97th percentile demonstrated significant differences. As an example, the proportion of SGA foetuses varied from 3.46 to 4.57% (p = 0.02) and that of LGA foetuses from 17.86 to 13.4% (p < 10- 4).

CONCLUSION

The dating formula used has a quite significant impact on the subsequent evaluation of biometry and EFW. We suggest that the combined and homogeneous use of a recent dating standard, together with prescriptive growth standards established on the same low-risk pregnancies, allows an optimal assessment of fetal growth.

Design and Use of Semantic Resources: Findings from the Section on Knowledge Representation and Management of the 2020 International Medical Informatics Association Yearbook

OBJECTIVE

To select, present, and summarize the best papers in the field of Knowledge Representation and Management (KRM) published in 2019.

METHODS

A comprehensive and standardized review of the biomedical informatics literature was performed to select the most interesting papers of KRM published in 2019, based on PubMed and ISI Web Of Knowledge queries.

RESULTS

Four best papers were selected among 1,189 publications retrieved, following the usual International Medical Informatics Association Yearbook reviewing process. In 2019, research areas covered by pre-selected papers were represented by the design of semantic resources (methods, visualization, curation) and the application of semantic representations for the integration/enrichment of biomedical data. Besides new ontologies and sound methodological guidance to rethink knowledge bases design, we observed large scale applications, promising results for phenotypes characterization, semantic-aware machine learning solutions for biomedical data analysis, and semantic provenance information representations for scientific reproducibility evaluation.

CONCLUSION

In the KRM selection for 2019, research on knowledge representation demonstrated significant contributions both in the design and in the application of semantic resources. Semantic representations serve a great variety of applications across many medical domains, with actionable results.

Cost and outcomes of the ultrasound screening program for birth defects over time: a population-based study in France

OBJECTIVE

To assess trends in the average costs and effectiveness of the French ultrasound screening programme for birth defects.

DESIGN

A population-based study.

SETTING

National Public Health Insurance claim database.

PARTICIPANTS

All pregnant women in the 'Echantillon Généraliste des Bénéficiaires', a permanent representative sample of 1/97 of the individuals covered by the French Health Insurance System.

MAIN OUTCOMES MEASURES

Trends in the costs and in the average cost-effectiveness ratio (ACER) of the screening programme (in € per case detected antenatally), per year, between 2006 and 2014. incremental cost-effectiveness ratio (ICER) from 1 year to another were also estimated. We assessed costs related to the ultrasound screening programme of birth defects excluding the specific screening of Down's syndrome. The outcome for effectiveness was the prenatal detection rate of birth defects, assessed in a previous study. Linear and logistic regressions were used to analyse time trends.

RESULTS

During the study period, there was a slight decrease in prenatal detection rates (from 58.2% in 2006 to 55.2% in 2014; p=0.015). The cost of ultrasound screening increased from €168 in 2006 to €258 per pregnancy in 2014 (p=0.001). We found a 61% increase in the ACER for ultrasound screening during the study period. ACERs increased from €9050 per case detected in 2006 to €14 580 per case detected in 2014 (p=0.001). ICERs had an erratic pattern, with a strong tendency to show that any increment in the cost of screening was highly cost ineffective.

CONCLUSION

Even if the increase in costs may be partly justified, we observed a diminishing returns for costs associated with the prenatal ultrasound screening of birth defects, in France, between 2006 and 2014.

New insights in cerebral findings associated with fetal myelomeningocele: a retrospective cohort study in a single tertiary centre

OBJECTIVE

To investigate cerebral anomalies other than Chiari type 2 malformation in fetuses with myelomeningocele (MMC).

DESIGN

A retrospective cohort study in a single tertiary centre.

SETTING

A review of associated cerebral anomalies in cases with prenatal diagnosis of myelomeningocele.

POPULATION

Seventy cases of fetal myelomeningocele.

METHODS

Ultrasound and MRI images were blindly reviewed. Postnatal imaging and results of the postmortem results were also reviewed. The association between cerebral anomalies and the following ultrasound findings was measured: level of the defect, ventriculomegaly, microcephaly and fetal talipes.

MAIN OUTCOME MEASURES

A microcephaly was observed in 32/70 cases (46%) and a ventriculomegaly was observed in 39/70 cases (56%). Other cerebral anomalies were diagnosed in 47/70 (67%).

RESULTS

Other cerebral anomalies were represented by 42/70 cases with abnormal CC (60%), 8/70 cases with perinodular heterotopia (PNH; 11%), 2/70 cases with abnormal gyration (3%). MRI performed only in fetal surgery cases confirmed the ulltrasound findings in all cases and provided additional findings in two cases (PNH). Risk ratios of fetal cerebral anomalies associated with MMC did not reach significance for microcephaly, ventriculomegaly, talipes or the level of the defect There was an overall good correlation between pre- and postnatal findings with a Kappa value of 0.79 [95% CI 0.57-1] and 82% agreement.

CONCLUSION

Fetal brain anomalies other than Chiari type 2 malformation are frequently observed in fetuses with myelomeningocele, predominantly represented by CC anomalies. Whether these associated cerebral anomalies have an impact on selecting cases eligible for fetal surgery needs further evaluation.

TWEETABLE ABSTRACT

Fetal cerebral anomalies other than Chiari type 2 malformation, microcephaly, and ventriculomegaly may be associated with MMC in up to 67% of the cases.

[Feticide procedures in second and third trimesters terminations of pregnancy]

Performing a feticide as part of termination of late pregnancy is recommended in many countries. Feticide avoids a live birth of a severely affected premature newborn and prevents fetal pain. There are limited data on feticide procedures since only a few countries in the world authorize late termination of pregnancy. The objective of this review was to assess the most appropriate feticide procedure based on published data during the last thirty years. Administration of an initial fetal analgesia followed by a lethal lidocaine injection through the umbilical cord, under ultrasound guidance, appears to be the most effective, safe and ethical way to perform feticide. According to the current knowledge regarding the risk of fetal pain and survival of extremely preterm infants, a feticide should be discussed as early as 20-22 weeks of gestation.

Formal Medical Knowledge Representation Supports Deep Learning Algorithms, Bioinformatics Pipelines, Genomics Data Analysis, and Big Data Processes

OBJECTIVE

To select, present, and summarize the best papers published in 2018 in the field of Knowledge Representation and Management (KRM).

METHODS

A comprehensive and standardized review of the medical informatics literature was performed to select the most interesting papers published in 2018 in KRM, based on PubMed and ISI Web Of Knowledge queries.

RESULTS

Four best papers were selected among the 962 publications retrieved following the Yearbook review process. The research areas in 2018 were mainly related to the ontology-based data integration for phenotype-genotype association mining, the design of ontologies and their application, and the semantic annotation of clinical texts.

CONCLUSION

In the KRM selection for 2018, research on semantic representations demonstrated their added value for enhanced deep learning approaches in text mining and for designing novel bioinformatics pipelines based on graph databases. In addition, the ontology structure can enrich the analyses of whole genome expression data. Finally, semantic representations demonstrated promising results to process phenotypic big data.

[Prenatal diagnosis and postnatal outcome of isolated intra-abdominal calcifications: A 10-year experience from a referral fetal medicine center]

INTRODUCTION

Intra-abdominal calcifications (iAC) detected during fetal ultrasound examinations are characterized by their isolated or associated nature, as well as their location. Our objective was to describe all cases of isolated iAC along with their etiological investigations and neonatal outcome, during a 10-year practice in a referral center.

METHODS

We conducted a retrospective descriptive monocentric study on neonates diagnosed with isolated iAC after antenatal expert ultrasound scan and referred to the Multidisciplinary Center for Prenatal Diagnosis at Trousseau Hospital and born between January 1st, 2008 and June 30th, 2018. The exclusion criteria were: retroperitoneal calcifications, iAC associated with other digestive abnormalities or with congenital malformations.

RESULTS

The 32 isolated iAC cases accounted for 46% of all iAC. Nine cases were excluded for missing neonatal data. Among the 23 remaining isolated iAC cases, we observed 15 intra-hepatic calcifications, 5 peri-hepatic and two peritoneal calcifications. One fetus had both intra- and peri-hepatic calcifications. The majority of iAC remained stable throughout pregnancy. No cases of aneuploidy, fetal infection, or cystic fibrosis were detected. The neonatal outcome was favorable in all cases.

CONCLUSIONS

In case of isolated and stable iAC after expert ultrasound scan, after having ruled out infectious diseases of the fetus and looked for the most frequent mutations of cystic fibrosis in the parents, the prognosis is favorable. Fetal karyotyping is recommended when additional structural anomalies are present.

A Novel Intelligent Scan Assistant System for Early Pregnancy Diagnosis by Ultrasound: Clinical Decision Support System Evaluation Study

Background

Early pregnancy ultrasound scans are usually performed by nonexpert examiners in obstetrics/gynecology (OB/GYN) emergency departments. Establishing the precise diagnosis of pregnancy location is key for appropriate management of early pregnancies, and experts are usually able to locate a pregnancy in the first scan. A decision-support system based on a semantic, expert-validated knowledge base may improve the diagnostic performance of nonexpert examiners for early pregnancy transvaginal ultrasound.

Objective

This study aims to evaluate a novel Intelligent Scan Assistant System for early pregnancy ultrasound to diagnose the pregnancy location and determine the image quality.

Methods

Two trainees performed virtual transvaginal ultrasound examinations of early pregnancy cases with and without the system. The ultrasound images and reports were blindly reviewed by two experts using scoring methods. A diagnosis of pregnancy location and ultrasound image quality were compared between scans performed with and without the system.

Results

Each trainee performed a virtual vaginal examination for all 32 cases with and without use of the system. The analysis of the 128 resulting scans showed higher quality of the images (quality score: +23%; P<.001), less images per scan (4.6 vs 6.3 [without the CDSS]; P<.001), and higher confidence in reporting conclusions (trust score: +20%; P<.001) with use of the system. Further, use of the system cost an additional 8 minutes per scan. We observed a correct diagnosis of pregnancy location in 39 (61%) and 52 (81%) of 64 scans in the nonassisted mode and assisted mode, respectively. Additionally, an exact diagnosis (with precise ectopic location) was made in 30 (47%) and 49 (73%) of the 64 scans without and with use of the system, respectively. These differences in diagnostic performance (+20% for correct location diagnosis and +30% for exact diagnosis) were both statistically significant (P=.002 and P<.001, respectively).

Conclusions

The Intelligent Scan Assistant System is based on an expert-validated knowledge base and demonstrates significant improvement in early pregnancy scanning, both in diagnostic performance (pregnancy location and precise diagnosis) and scan quality (selection of images, confidence, and image quality).

Trends in resource use and effectiveness of ultrasound detection of fetal structural anomalies in France: a multiple registry-based study

OBJECTIVE

To analyse trends in the number of ultrasound examinations in relation to the effectiveness of prenatal detection of birth defects using population-based data in France.

DESIGN

A multiple registry-based study of time trends in resource use (number of ultrasounds) and effectiveness (proportion of cases prenatally diagnosed).

SETTING

Three registries of congenital anomalies and claims data on ultrasounds for all pregnant women in France.

PARTICIPANTS

There were two samples of pregnant women. Effectiveness was assessed using data from three French birth defect registries. Resource use for ultrasound screening was based on the French national healthcare database.

MAIN OUTCOME MEASURES

The main outcome measures were prenatal diagnosis (effectiveness) and the average number of ultrasounds (resource use). Statistical analyses included linear and logistic regression models to assess trends in resource use and effectiveness of prenatal testing, respectively.

RESULTS

The average number of ultrasound examinations per pregnancy significantly increased over the study period, from 2.47 in 2006 to 2.98 in 2014 (p=0.005). However, there was no significant increase in the odds of prenatal diagnosis. The probability of prenatal diagnosis was substantially higher for cases associated with a chromosomal anomaly (91.2%) than those without (51.8%). However, there was no evidence of an increase in prenatal detection of either over time.

CONCLUSIONS

The average number of ultrasound examinations per pregnancy increased over time, whereas the probability of prenatal diagnosis of congenital anomalies did not. Hence, there is a need to implement policies such as high-quality training programmes which can improve the efficiency of ultrasound examinations for prenatal detection of congenital anomalies.

Evaluation of septal insertion of atrioventricular valves in fetuses by postmortem 4.7 Tesla cardiac MRI: A feasibility study

PURPOSE

The purpose of this study was to compare non-invasive high-spatial-resolution postmortem cardiac magnetic resonance imaging (MRI) and autopsy findings for evaluating the septal insertion of atrioventricular valves in fetuses.

MATERIALS AND METHODS

Five fetal heart specimens including two normal hearts, one heart with complete atrioventricular septal defect (AVSD) and two hearts with linear insertion of atrioventricular valves (LIAVV; gestational age 17 to 34 weeks) were studied with cardiac MRI using a 4.7 T MRI scanner without sample preparation. Three (3D) and two-dimensional (2D) turbo-RARE (rapid imaging with refocused echoes) sequences in four-chamber and left-ventricular long-axis planes were obtained with a minimal isotropic/in-plane resolution of 156μm. Nonparametric tests were performed to compare the distance between insertions of medial leaflets of the atrioventricular valves and the inlet/outlet distance ratio between MRI and autopsy findings in normal, complete AVSD and with linear insertion of atrioventricular valves (LIAVV) fetal hearts.

RESULTS

Despite apparent differences between LIAVV/normal hearts, no significant differences were found between differential insertion of medial leaflets and inlet/outlet distance ratios with both techniques. Very good to excellent reliability between both techniques was found for differential insertion (ICC: 87.2%; 95% CI: -21.7%, 99.1%) (P=0.963) and inlet/outlet distance ratio (ICC 98.3%; 95%CI: 85.2%, 99.8%) (P=0.537) measurements.

CONCLUSION

Postmortem cardiac MRI could replace autopsy for assessing normal or abnormal septal insertion of atrioventricular valves in fetuses without requiring specific preparation of the heart.

Pregnancy outcome after first trimester exposure to ionizing radiations

OBJECTIVE

To evaluate the effects of ionizing radiation exposure during the first trimester of pregnancy in usual clinical situations.

STUDY DESIGN

We conducted a prospective observational cohort study using data collected between 1987 and 2014. This database was authorized by the French "Commission Nationale de l'Informatique et des Libertés". The exposed group consisted of 319 pregnant women exposed to sub diaphragmatic ionizing radiations for diagnostic purposes, during the first trimester of pregnancy, and the control group consisted of 319 pregnant women without any exposure or exposed to non-teratogenic agents. Data on maternal history and radiations exposure were collected on first contact, and pregnancy outcomes were documented at follow-up. An univariate analysis was performed to compare both groups for the main outcomes.

RESULTS

Exposure to sub diaphragmatic ionizing radiation for diagnosis purpose (median fetal dose of 3.1 mGy [0.2-130.0]) during the first trimester of pregnancy was not significantly associated with an increased risk of malformations (1.5% vs 1.8%, p = 1.00), miscarriage (7.8% vs 7.2%, p = 0.88), in utero fetal death (0.3% vs 0%, p = 1.00) or fetal growth restriction (5.4% vs 3.5%, p = 0.62).

CONCLUSION

Pregnant women exposed to irradiant diagnostic procedures do not present a higher risk of malformations, miscarriage, in utero fetal death or fetal growth restriction and should be reassured, even if the examination focused on the pelvis.

As Ontologies Reach Maturity, Artificial Intelligence Starts Being Fully Efficient: Findings from the Section on Knowledge Representation and Management for the Yearbook 2018

Objectives:  To select, present, and summarize the best papers published in 2017 in the field of Knowledge Representation and Management (KRM).

Methods:  A comprehensive and standardized review of the medical informatics literature was performed to select the most interesting papers of KRM published in 2017, based on a PubMed query.

Results:  In direct line with the research on data integration presented in the KRM section of the 2017 edition of the International Medical Informatics Association (IMIA) Yearbook, the five best papers for 2018 demonstrate even further the added-value of ontology-based integration approaches for phenotype-genotype association mining. Additionally, among the 15 preselected papers, two aspects of KRM are in the spotlight: the design of knowledge bases and new challenges in using ontologies.

Conclusions:  Ontologies are demonstrating their maturity to integrate medical data and begin to support clinical practices. New challenges have emerged: the query on distributed semantically annotated datasets, the efficiency of semantic annotation processes, the semantic representation of large textual datasets, the control of biases associated with semantic annotations, and the computation of Bayesian indicators on data annotated with ontologies.

Two-Port Fetoscopic Repair of Myelomeningocele in Fetal Lambs

OBJECTIVE

The aim of this study was to assess the feasibility and the effectiveness of a fetoscopic myelomeningocele (MMC) repair with a running single suture using a 2-port access in the sheep model.

METHODS

Eighteen fetuses underwent surgical creation of a MMC defect at day 75. Fetuses were then randomized into 3 groups. Four fetuses remained untreated (control group). In the other 14 fetuses, a prenatal repair was performed at day 90: 7 fetuses had an open repair (oMMC), and 7 fetuses had a fetoscopic repair (fMMC) using a single-layer running suture through a 2-port access. Lambs were sacrificed at term, and histological examinations were performed.

RESULTS

Hindbrain herniation was observed in all live lambs in the control group. A complete closure of the defect was achieved in all the lambs of the fMMC group. A complete healing of the defect and no hindbrain herniation were observed in all live lambs of the oMMC and fMMC groups. The durations of surgeries were not statistically different between the oMMC and the fMMC groups (60 vs. 53 min, p = 0.40), as was the risk of fetal loss (fMMC: 1/7, oMMC: 3/7, p = 0.56).

DISCUSSION

Fetoscopic repair of MMC can be performed using a single-layer running suture through a 2-port access and may be promising to reduce the risk of premature rupture of membranes.

Knowledge Representation and Management, It's Time to Integrate!

Objectives: To select, present, and summarize the best papers published in 2016 in the field of Knowledge Representation and Management (KRM). Methods: A comprehensive and standardized review of the medical informatics literature was performed based on a PubMed query. Results: Among the 1,421 retrieved papers, the review process resulted in the selection of four best papers focused on the integration of heterogeneous data via the development and the alignment of terminological resources. In the first article, the authors provide a curated and standardized version of the publicly available US FDA Adverse Event Reporting System. Such a resource will improve the quality of the underlying data, and enable standardized analyses using common vocabularies. The second article describes a project developed in order to facilitate heterogeneous data integration in the i2b2 framework. The originality is to allow users integrate the data described in different terminologies and to build a new repository, with a unique model able to support the representation of the various data. The third paper is dedicated to model the association between multiple phenotypic traits described within the Human Phenotype Ontology (HPO) and the corresponding genotype in the specific context of rare diseases (rare variants). Finally, the fourth paper presents solutions to annotation-ontology mapping in genome-scale data. Of particular interest in this work is the Experimental Factor Ontology (EFO) and its generic association model, the Ontology of Biomedical AssociatioN (OBAN). Conclusion: Ontologies have started to show their efficiency to integrate medical data for various tasks in medical informatics: electronic health records data management, clinical research, and knowledge-based systems development.

[Ultrasound screening for birth defects: A medico-economic review]

OBJECTIVES

The systematic use of ultrasound during pregnancy aims at birth defect detection. Our objective was to assess the economic efficiency of prenatal ultrasound screening for fetal malformations.

METHODS

We carried out a literature review on Medline via PubMed between 1985 and 2015, from the economic perspective of the prenatal ultrasound screening for fetal malformations.

RESULTS

The literature on this subject was sparse and we selected only twelve articles presenting relevant economic data, of which only eight were proper medico-economic studies. We found arguments for the economic effectiveness of ultrasound screening for fetal malformation detection, which is largely linked to the terminations of pregnancies and to the cost of the handicaps "avoided". However, none of the reviewed articles could reach medico-economic conclusions. Additionally, we highlighted various elements making economic analyses more complex in this field: the choice of the method, the uncertainty around two essential parameters (the efficiency of ultrasound and the costs of procedures) and the difficulties to compare or to generalize results. We also noticed important methodological heterogeneity among the studies and the absence of French study.

CONCLUSIONS

Previously published data are insufficient to assess the economic efficiency of prenatal ultrasound screening for fetal malformations.

Towards ontology-based decision support systems for complex ultrasound diagnosis in obstetrics and gynecology

INTRODUCTION

We have developed a new knowledge base intelligent system for obstetrics and gynecology ultrasound imaging, based on an ontology and a reference image collection. This study evaluates the new system to support accurate annotations of ultrasound images. We have used the early ultrasound diagnosis of ectopic pregnancies as a model clinical issue.

MATERIAL AND METHODS

The ectopic pregnancy ontology was derived from medical texts (4260 ultrasound reports of ectopic pregnancy from a specialist center in the UK and 2795 Pubmed abstracts indexed with the MeSH term "Pregnancy, Ectopic") and the reference image collection was built on a selection from 106 publications. We conducted a retrospective analysis of the signs in 35 scans of ectopic pregnancy by six observers using the new system.

RESULTS

The resulting ectopic pregnancy ontology consisted of 1395 terms, and 80 images were collected for the reference collection. The observers used the knowledge base intelligent system to provide a total of 1486 sign annotations. The precision, recall and F-measure for the annotations were 0.83, 0.62 and 0.71, respectively. The global proportion of agreement was 40.35% 95% CI [38.64-42.05].

DISCUSSION

The ontology-based intelligent system provides accurate annotations of ultrasound images and suggests that it may benefit non-expert operators. The precision rate is appropriate for accurate input of a computer-based clinical decision support and could be used to support medical imaging diagnosis of complex conditions in obstetrics and gynecology.

Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy

Background

Ectopic pregnancy is a frequent early complication of pregnancy associated with significant rates of morbidly and mortality. The positive diagnosis of this condition is established through transvaginal ultrasound scanning. The timing of diagnosis depends on the operator expertise in identifying the signs of ectopic pregnancy, which varies dramatically among medical staff with heterogeneous training. Developing decision support systems in this context is expected to improve the identification of these signs and subsequently improve the quality of care. In this article, we present a new knowledge base for ectopic pregnancy, and we demonstrate its use on the annotation of clinical images.

Results

The knowledge base is supported by an application ontology, which provides the taxonomy, the vocabulary and definitions for 24 types and 81 signs of ectopic pregnancy, 484 anatomical structures and 32 technical elements for image acquisition. The knowledge base provides a sign-centric model of the domain, with the relations of signs to ectopic pregnancy types, anatomical structures and the technical elements. The evaluation of the ontology and knowledge base demonstrated a positive feedback from a panel of 17 medical users. Leveraging these semantic resources, we developed an application for the annotation of ultrasound images. Using this application, 6 operators achieved a precision of 0.83 for the identification of signs in 208 ultrasound images corresponding to 35 clinical cases of ectopic pregnancy.

Conclusions

We developed a new ectopic pregnancy knowledge base for the annotation of ultrasound images. The use of this knowledge base for the annotation of ultrasound images of ectopic pregnancy showed promising results from the perspective of clinical decision support system development. Other gynecological disorders and fetal anomalies may benefit from our approach.

"Hybrid Topics" - Facilitating the Interpretation of Topics Through the Addition of MeSH Descriptors to Bags of Words

Extracting and understanding information, themes and relationships from large collections of documents is an important task for biomedical researchers. Latent Dirichlet Allocation is an unsupervised topic modeling technique using the bag-of-words assumption that has been applied extensively to unveil hidden thematic information within large sets of documents. In this paper, we added MeSH descriptors to the bag-of-words assumption to generate 'hybrid topics', which are mixed vectors of words and descriptors. We evaluated this approach on the quality and interpretability of topics in both a general corpus and a specialized corpus. Our results demonstrated that the coherence of 'hybrid topics' is higher than that of regular bag-of-words topics in the specialized corpus. We also found that the proportion of topics that are not associated with MeSH descriptors is higher in the specialized corpus than in the general corpus.

Trends in Fetal Medicine: A 10-Year Bibliometric Analysis of Prenatal Diagnosis

The objective is to automatically identify trends in Fetal Medicine over the past 10 years through a bibliometric analysis of articles published in Prenatal Diagnosis, using text mining techniques. We processed 2,423 full-text articles published in Prenatal Diagnosis between 2006 and 2015. We extracted salient terms, calculated their frequencies over time, and established evolution profiles for terms, from which we derived falling, stable, and rising trends. We identified 618 terms with a falling trend, 2,142 stable terms, and 839 terms with a rising trend. Terms with increasing frequencies include those related to statistics and medical study design. The most recent of these terms reflect the new opportunities of next-generation sequencing. Many terms related to cytogenetics exhibit a falling trend. A bibliometric analysis based on text mining effectively supports identification of trends over time. This scalable approach is complementary to analyses based on metadata or expert opinion.

[Fetal abdominal cysts at the first trimester scan]

OBJECTIVES

Abdominal cysts are seldom detected at the first trimester scan. The aim of this study is to ascertain their outcome, which is currently not established.

METHODS

The French College of Fetal Ultrasound conducted a prospective observational study of 24months, collecting all cases of abdominal cysts discovered during the first trimester ultrasound. Cases of megacystis were excluded from the study. Ultrasound images, prenatal diagnosis expert reports and pregnancy outcomes were collected by sonographers after patient consent.

RESULTS

Ten cases of abdominal cysts were collected. The cysts had a mean diameter of 15mm. They were anechoic in 5 cases, hyperechoic in 2 cases and mixed in 3 cases. In 6 of 10 cases, complete resolution was observed at 18WG with a good post-natal outcome; the five cases with anechoic images were associated with normal pediatric examination at birth and in the case of the resolved hyperechoic image, an isolated imperforate anus was observed. In the four cases of hyperechoic or mixed images that had not resolved, the outcome was poor with four termination of pregnancies, including two cases of cloacal dysgenesis.

CONCLUSIONS

Abdominal cysts are rare at the first trimester scan. They resolve in two thirds of cases and are then associated with good outcome. When they do not resolve or when they are not strictly anechoic, they require a referral ultrasound examination at 18 and 22WG.

Relation between the quality of the ultrasound image acquisition and the precision of the measurement of the crown-rump length in the late first trimester: what are the consequences?

OBJECTIVE

To assess the extent to which the distribution of crown-rump length (CRL) values may be correlated with different criteria for the quality of the CRL images.

STUDY DESIGN

This is a retrospective analysis of a series of 977 CRL images, by two independent observers, for the presence or the absence of 14 quality hallmarks. Inter-observer agreement for the hallmarks was assessed by the proportion of agreement and Cohen's kappa. The association between the quantiles of the CRL distribution and the presence or absence of the 14 quality hallmarks was modeled using quantile regression.

RESULTS

The overall inter-observer agreement across the 14 hallmarks was 91.7%, kappa=0.81, 95% CI [0.80-0.82]. Distribution of CRL measurements varied considerably as a function of image quality: when the fetus was in extension, the mean CRL was +5.7mm (vs. not in extension, p<0.001), when the fetus was in flexion (vs. not), the mean CRL was -4.7mm (p<0.001) and when the image magnification was <65% (vs. >65%), the mean CRL was -4.2mm (p<0.001). There was a global trend to over-estimate the CRL for the higher deciles and to under-estimate the CRL for the lower deciles when the sagittal quality hallmarks were absent. No significant impact on CRL distribution was observed in association with the precise placement of the calipers nor with the horizontal orientation of the fetus.

CONCLUSION

Distribution of CRL measurements was influenced by the quality of CRL images. In particular, inadequate position of the fetus (flexion/extension) and insufficient image magnification were associated with systematic changes in the values of CRL. Our results show that as the quality of CRL images decreases, the associated variations in the distribution of CRL can have an impact on the chromosomal risk assessment and may lead to inappropriate obstetrical decisions.

Searching for rare diseases in PubMed: a blind comparison of Orphanet expert query and query based on terminological knowledge

BACKGROUND

Despite international initiatives like Orphanet, it remains difficult to find up-to-date information about rare diseases. The aim of this study is to propose an exhaustive set of queries for PubMed based on terminological knowledge and to evaluate it versus the queries based on expertise provided by the most frequently used resource in Europe: Orphanet.

METHODS

Four rare disease terminologies (MeSH, OMIM, HPO and HRDO) were manually mapped to each other permitting the automatic creation of expended terminological queries for rare diseases. For 30 rare diseases, 30 citations retrieved by Orphanet expert query and/or query based on terminological knowledge were assessed for relevance by two independent reviewers unaware of the query's origin. An adjudication procedure was used to resolve any discrepancy. Precision, relative recall and F-measure were all computed.

RESULTS

For each Orphanet rare disease (n = 8982), there was a corresponding terminological query, in contrast with only 2284 queries provided by Orphanet. Only 553 citations were evaluated due to queries with 0 or only a few hits. There were no significant differences between the Orpha query and terminological query in terms of precision, respectively 0.61 vs 0.52 (p = 0.13). Nevertheless, terminological queries retrieved more citations more often than Orpha queries (0.57 vs. 0.33; p = 0.01). Interestingly, Orpha queries seemed to retrieve older citations than terminological queries (p < 0.0001).

CONCLUSION

The terminological queries proposed in this study are now currently available for all rare diseases. They may be a useful tool for both precision or recall oriented literature search.

[How to assess the neutral position of the fetus for the crown-rump length measurement at the nuchal translucency scan]

OBJECTIVES

The objective of this study was to establish a simple and reproducible method for the assessment of the fetal head position when measuring crown-rump length (CRL) at the nuchal translucency scan.

METHODS

Two observers conducted a retrospective analysis of a consecutive series of 570 images of CRL collected by the French College of Fetal Echography (CFEF) national practice assessment program for the first-trimester scan. The images were deemed hyper-flexed if no fluid was visible between the chin and the chest of the fetus. The images were deemed hyper-extended if the angle between the palate and the CRL line was 90° or more. The images were deemed neutral if no hyper-extension nor hyper-flexion was observed.

RESULTS

The proportion of agreement for a non-neutral position of the fetal head was 91.3% (kappa=0.80, 95% CI [0.75 to 0.86]). Images with a non-neutral position corresponded to poor CRL quality images according to the CFEF score (relative risk=4.2, 95% CI [2.9 to 6.1] for one observer and 4.9, 95% CI [3.3 to 7.2] for the other observer). Proportions of agreement for the hyper-flexion and for the hyper-extension were 94.6% (kappa=0.80, 95% CI [0.72 to 0.87]) and 96.8% (kappa=0.81, 95% CI [0.72 to 0.90]), respectively. No additional lines were drawn on the ultrasound images during the evaluation process.

CONCLUSIONS

The proposed method for evaluating the extent to which the fetal head has a non-neutral position at measurement of the CRL appears both simple and reproducible.

Interoperability between phenotypes in research and healthcare terminologies--Investigating partial mappings between HPO and SNOMED CT

Background

Identifying partial mappings between two terminologies is of special importance when one terminology is finer-grained than the other, as is the case for the Human Phenotype Ontology (HPO), mainly used for research purposes, and SNOMED CT, mainly used in healthcare.

Objectives

To investigate and contrast lexical and logical approaches to deriving partial mappings between HPO and SNOMED CT.

Methods

1) Lexical approach—We identify modifiers in HPO terms and attempt to map demodified terms to SNOMED CT through UMLS; 2) Logical approach—We leverage subsumption relations in HPO to infer partial mappings to SNOMED CT; 3) Comparison—We analyze the specific contribution of each approach and evaluate the quality of the partial mappings through manual review.

Results

There are 7358 HPO concepts with no complete mapping to SNOMED CT. We identified partial mappings lexically for 33 % of them and logically for 82 %. We identified partial mappings both lexically and logically for 27 %. The clinical relevance of the partial mappings (for a cohort selection use case) is 49 % for lexical mappings and 67 % for logical mappings.

Conclusions

Through complete and partial mappings, 92 % of the 10,454 HPO concepts can be mapped to SNOMED CT (30 % complete and 62 % partial). Equivalence mappings between HPO and SNOMED CT allow for interoperability between data described using these two systems. However, due to differences in focus and granularity, equivalence is only possible for 30 % of HPO classes. In the remaining cases, partial mappings provide a next-best approach for traversing between the two systems. Both lexical and logical mapping techniques produce mappings that cannot be generated by the other technique, suggesting that the two techniques are complementary to each other. Finally, this work demonstrates interesting properties (both lexical and logical) of HPO and SNOMED CT and illustrates some limitations of mapping through UMLS.

Prenatal ultrasound diagnosis of cystic biliary atresia

Nonvisualization of the gallbladder during the second trimester of pregnancy should prompt concern for biliary atresia. A normal‐sized gallbladder with irregular and crenelated wall associated with a cyst of the extrahepatic tract should raise concern for cystic biliary atresia.