Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to improve the reusability of these models and their ability to reproduce virtual experiments becomes critical. Correct and effective model annotation in community-supported and standardised formats is necessary for this improvement. Here, we present recent efforts toward a common framework for annotated, accessible, reproducible and interoperable computational models in biology, and discuss key challenges of the field.

BioModels-15 years of sharing computational models in life science.

Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform allows submission of models encoded in diverse modelling formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication. The curation also involves encoding models in standard formats and annotation with controlled vocabularies following MIRIAM (minimal information required in the annotation of biochemical models) guidelines. BioModels now accepts large-scale submission of auto-generated computational models. With gradual growth in content over 15 years, BioModels currently hosts about 2000 models from the published literature. With about 800 curated models, BioModels has become the world's largest repository of curated models and emerged as the third most used data resource after PubMed and Google Scholar among the scientists who use modelling in their research. Thus, BioModels benefits modellers by providing access to reliable and semantically enriched curated models in standard formats that are easy to share, reproduce and reuse.

SBML Level 3: an extensible format for the exchange and reuse of biological models.

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

The Individualized Addictions Consultation Team Residential Program: A Creative Solution for Integrating Care for Veterans With Substance Use Disorders Too Complex for Other Residential Treatment Programs.

OBJECTIVES: The Veterans Affairs (VA) healthcare system is one of the main providers of substance use treatment within the United States, and many veterans with a substance use disorder (SUD) present with co-occurring diagnoses or other concerns. Though there has been increasing recognition of the need for integration of treatments for SUD and comorbid mental illness, there have been limited studies of such programs, particularly within the VA healthcare system. To address that gap in the literature, this paper examines treatment outcomes in an integrated model of dual diagnosis residential treatment for veterans: the Individualized Addictions Consultation Team (I-ACT) program. Methods: The current paper draws from clinical outcome evaluation data within a residential treatment program at a large Midwestern VA Medical Center (VAMC). The I-ACT program provides residential substance abuse treatment to individuals with a primary SUD and other factors that interfere with the successful completion of a traditional residential rehabilitation program. Between 2017 and 2018, 130 individuals (97.7% men, average age = 60.62 years) entered the I-ACT program. As part of standard measurement-based care, veterans were administered the Brief Addiction Monitor and the Patient Health Questionnaire-9 at admission and discharge. Results: Most individuals (74.6%) who entered I-ACT completed the residential program (average length of stay 34.2 days). Scores on both measures significantly decreased from intake to discharge (p < .001), with the change in depression scores indicating clinically significant improvement. Those with an additional mental health diagnosis achieved similar decreases in substance use symptoms and had lower depression scores at discharge than those with a SUD alone. Conclusions: Our results indicate that even for veterans who may not benefit from traditional SUD treatment programs, a more integrated and personalized residential program can be effective.

Diagnostic Utility of Pathological Investigations in Late Gestation Stillbirth: A Cohort Study.

OBJECTIVE: Near term unexpected stillbirth is a common, complex diagnostic challenge. We review a large cohort of near term to term gestation unexpected fetal deaths to document the common patterns of pathology and evaluate the utility of various standard autopsy procedures. METHODS: A total of 123 perinatal autopsies consisting of 94 intrauterine fetal deaths (IUFDs) and 29 intrapartum deaths (IPDs) were reviewed. Deaths were classified according to the laboratory investigations establishing cause of death. RESULTS: Cause of death was attributable to placental pathology without autopsy in 55.3% of IUFD and 17% of IPD. Correlative findings at autopsy increased the ability to establish cause of death in 86.2% of IUFD and 62% of IPD. Histology was largely corroborative, with the brain, lungs, and heart demonstrating significant changes in 46%, 34.5%, and 13.8%, respectively. Microbiology was corroborative but demonstrated single organism growth in 6 of 29 cases of fatal acute chorioamnionitis. Newborn metabolic screening revealed only elevated thyroid-stimulating hormone levels in 3 cases, of questionable relevance. Aneuploidy was established by screening molecular studies in 5 IUFDs, all of which had external or visceral dysmorphism. Karyotype was established in 69 cases and was not contributory in any of the IPD: 3 IUFDs had changes of unknown significance. Cause of death was not established at autopsy in 9% of IUFD and 10% of IPD. DISCUSSION: This is the largest uniformly investigated cohort of late gestation unexpected fetal deaths studied. We confirm the importance of both placental and fetal autopsy in establishing cause of death. Autopsy histology, microbiology, and cytogenetics provide important but largely corroborative data.

Panoramic view of a superfamily of phosphatases through substrate profiling.

Large-scale activity profiling of enzyme superfamilies provides information about cellular functions as well as the intrinsic binding capabilities of conserved folds. Herein, the functional space of the ubiquitous haloalkanoate dehalogenase superfamily (HADSF) was revealed by screening a customized substrate library against >200 enzymes from representative prokaryotic species, enabling inferred annotation of ∼35% of the HADSF. An extremely high level of substrate ambiguity was revealed, with the majority of HADSF enzymes using more than five substrates. Substrate profiling allowed assignment of function to previously unannotated enzymes with known structure, uncovered potential new pathways, and identified iso-functional orthologs from evolutionarily distant taxonomic groups. Intriguingly, the HADSF subfamily having the least structural elaboration of the Rossmann fold catalytic domain was the most specific, consistent with the concept that domain insertions drive the evolution of new functions and that the broad specificity observed in HADSF may be a relic of this process.

MOCCASIN: converting MATLAB ODE models to SBML.

UNLABELLED: MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging-especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format. AVAILABILITY AND IMPLEMENTATION: MOCCASIN is available under the terms of the LGPL 2.1 license (http://www.gnu.org/licenses/lgpl-2.1.html). Source code, binaries and test cases can be freely obtained from https://github.com/sbmlteam/moccasin CONTACT: : mhucka@caltech.edu SUPPLEMENTARY INFORMATION: More information is available at https://github.com/sbmlteam/moccasin.

BioModels: ten-year anniversary.

BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models of biological processes. A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication. Many models submitted to the database are annotated, cross-referencing its components to external resources such as database records, and terms from controlled vocabularies and ontologies. BioModels comprises two main branches: one is composed of models derived from literature, while the second is generated through automated processes. BioModels currently hosts over 1200 models derived directly from the literature, as well as in excess of 140,000 models automatically generated from pathway resources. This represents an approximate 60-fold growth for literature-based model numbers alone, since BioModels' first release a decade ago. This article describes updates to the resource over this period, which include changes to the user interface, the annotation profiles of models in the curation pipeline, major infrastructure changes, ability to perform online simulations and the availability of model content in Linked Data form. We also outline planned improvements to cope with a diverse array of new challenges.

Placental Pathology in Relation to Uterine Artery Doppler Findings in Pregnancies with Severe Intrauterine Growth Restriction and Abnormal Umbilical Artery Doppler Changes.

Objectives Current guidelines for diagnosis and management of early-onset intrauterine growth restriction (IUGR) rely on umbilical artery Doppler (UAD), without including uterine artery Doppler (UtAD). We hypothesized that IUGR cases with abnormal UAD but normal UtAD has a different spectrum of placental pathology compared with those with abnormal UtAD. Study Design Retrospective review of pregnancies with sonographic evidence of IUGR and abnormal UAD prior to delivery. Cases with ≥ 1 UtAD record(s) after 18+0 weeks' gestation and placental pathology were included. Cases were stratified according to initial UtAD pulsatility index (PI) values (n = 196): normal (n = 19; PI < 95th centile for gestational age/no notching), intermediate (n = 69; PI ≥ 95th centile/no/unilateral notching) and abnormal (n = 108; PI ≥ 95th centile/bilateral notching). Pregnancy outcomes and placental pathology were compared between groups. Results Women in the normal group delivered later than those in the abnormal group (30.1 ± 3.5 vs. 28.0 ± 3.5 weeks; mean ± standard deviation; p = 0.03). Their placentas exhibited higher rates of chronic intervillositis (15.8 vs. 0.9%; p = 0.01), chorangiosis (15.8 vs. 0.9%; p < 0.0001), and massive perivillous fibrin deposition (21.1 vs. 7.4%; p = 0.05), but had lower rates of uteroplacental vascular insufficiency (26.3 vs. 79.6%; p < 0.0001). Conclusion Approximately 10% of pregnancies with early-onset IUGR and abnormal UAD exhibited normal UtAD waveforms. They delivered later, and their placentas exhibited unusual placental pathologies.

The hemodynamics of late-onset intrauterine growth restriction by MRI.

BACKGROUND: Late-onset intrauterine growth restriction (IUGR) results from a failure of the placenta to supply adequate nutrients and oxygen to the rapidly growing late-gestation fetus. Limitations in current monitoring methods present the need for additional techniques for more accurate diagnosis of IUGR in utero. New magnetic resonance imaging (MRI) technology now provides a noninvasive technique for fetal hemodynamic assessment, which could provide additional information over conventional Doppler methods. OBJECTIVE: The objective of the study was to use new MRI techniques to measure hemodynamic parameters and brain growth in late-onset IUGR fetuses. STUDY DESIGN: This was a prospective observational case control study to compare the flow and T2 of blood in the major fetal vessels and brain imaging findings using MRI. Indexed fetal oxygen delivery and consumption were calculated. Middle cerebral artery and umbilical artery pulsatility indexes and cerebroplacental ratio were acquired using ultrasound. A score of ≥ 2 of the 4 following parameters defined IUGR: (1) birthweight the third centile or less or 20% or greater drop in the centile in estimated fetal weight; (2) lowest cerebroplacental ratio after 30 weeks less than the fifth centile; (3) ponderal index < 2.2; and (4) placental histology meets predefined criteria for placental underperfusion. Measurements were compared between the 2 groups (Student t test) and correlations between parameters were analyzed (Pearson's correlation). MRI measurements were compared with Doppler parameters for identifying IUGR defined by postnatal criteria (birthweight, placental histology, ponderal index) using receiver-operating characteristic curves. RESULTS: We studied 14 IUGR and 26 non-IUGR fetuses at 35 weeks' gestation. IUGR fetuses had lower umbilical vein (P = .004) and pulmonary blood flow (P = .01) and higher superior vena caval flow (P < .0001) by MRI. IUGR fetuses had asymmetric growth but smaller brains than normal fetuses (P < .0001). Newborns with IUGR also had smaller brains with otherwise essentially normal findings on MRI. Vessel T2s, oxygen delivery, oxygen consumption, middle cerebral artery pulsatility index, and cerebroplacental ratio were all significantly lower in IUGR fetuses, whereas there was no significant difference in umbilical artery pulsatility index. IUGR score correlated positively with superior vena caval flow and inversely with oxygen delivery, oxygen consumption, umbilical vein T2, and cerebroplacental ratio. Receiver-operating characteristic curves revealed equivalent performance of MRI and Doppler techniques in identifying IUGR that was defined based on postnatal parameters with superior vena caval flow area under the curve of 0.94 (95% confidence interval, 0.87-1.00) vs a cerebroplacental ratio area under the curve of 0.80 (95% confidence interval, 0.64-0.97). CONCLUSION: MRI revealed the expected circulatory redistribution in response to hypoxia in IUGR fetuses. The reduced oxygen delivery in IUGR fetuses indicated impaired placental oxygen transport, whereas reduced oxygen consumption presumably reflected metabolic adaptation to diminished substrate delivery, resulting in slower fetal growth. Despite brain sparing, placental insufficiency limits fetal brain growth. Superior vena caval flow and umbilical vein T2 by MRI may be useful new markers of late-onset IUGR.

Fetal growth restriction and cardiovascular outcome in early human infancy: a prospective longitudinal study.

The association between low birth weight and premature cardiovascular disease has led to the "prenatal origin of adult disease-hypothesis". We postulated that fetal growth restriction is associated with cardiovascular changes detectable at birth and in early infancy. Fifty-two appropriately grown fetuses (AGA) and 60 growth-restricted fetuses (FGR) with (n = 20) or without (n = 40) absent or reversed end-diastolic umbilical artery blood flow were prospectively examined by echocardiography before birth, at 1 week and 6 months of life. The impact of growth restriction on postnatal blood pressure, heart rate, cardiovascular dimensions, and function, as well as on vascular morphology of umbilical cord vessels was studied. FGR fetuses displayed significant blood flow redistribution and were delivered earlier with lower birth weights than AGA fetuses. After adjustment for gender, gestational age, and weight at birth, there were no intergroup differences in blood pressure, heart rate, left ventricular morphology, mass, and performance, and in cord vessel morphology. During the first 6 months of life brachioradial pulse wave velocity increased more in FGR fetuses, while other parameters describing vascular stiffness remained comparable between the groups. Fetal growth restriction had no detectable adverse impact on cardiovascular dimensions and function at birth. Cardiovascular findings also remained comparable during the first 6 months of life between the groups except a higher increase in brachioradial pulse wave velocity in the FGR group. Our observations suggest that abnormalities that link reduced intrauterine growth with premature cardiovascular diseases may commence later in childhood, indicating a potential window for screening and prevention.

MRI Significantly Improves Disease Staging to Direct Surgical Planning for Abnormal Invasive Placentation: A Single Centre Experience.

OBJECTIVE: To describe the role of ultrasound and MRI in defining the extent of disease and guiding perioperative and surgical management of abnormal invasive placentation (AIP). METHODS: We conducted a review of 65 cases of invasive placentation diagnosed antenatally with use of ultrasound and/or MRI in a single tertiary centre between January 2000 and December 2014. Cases were assigned a grade based on the depth of invasion and location of invasion within the uterus as described in ultrasound and MRI reports. These grades were then compared with grades assigned using a combination of pathology and dictated surgical reports. RESULTS: Ultrasound correctly identified the presence of AIP in 91.9% of cases but was accurate in predicting the stage of invasion in only 38.7% of cases. Ultrasound identified only 6.3% of cases with parametrial involvement. MRI correctly identified the presence of AIP in 98.4% of cases and was accurate in predicting the stage of invasion in 61.3% of cases. MRI accurately detected parametrial involvement in 68.8% of cases. CONCLUSIONS: Our results suggest that all women with signs of AIP on ultrasound scanning should be referred for MRI to assess the extent of placental invasion adequately and consequently to allow for adequate perioperative and surgical planning for delivery.

Fetal thrombocytopenia in pregnancies with fetal human parvovirus-B19 infection.

OBJECTIVE: Fetal infection with human parvovirus B19 (hParvo-B19) has been associated mainly with fetal anemia, although data regarding other fetal hematologic effects are limited. Our aim was to assess the rate and consequences of severe fetal thrombocytopenia after fetal hParvo-B19 infection. STUDY DESIGN: We conducted a retrospective study of pregnancies that were complicated by fetal hParvo-B19 infection that underwent fetal blood sampling (FBS). The characteristics and outcomes of fetuses with severe thrombocytopenia (<50 × 10(9)/L) were compared with those of fetuses with a platelet concentration of ≥50 × 10(9)/L (control fetuses). Fetuses in whom 3 FBSs were performed (n = 4) were analyzed to assess the natural history of platelet levels after fetal hParvo-B19 infection. RESULTS: A total of 37 pregnancies that were affected by fetal hParvo-B19 infection were identified. Of the 29 cases that underwent FBS and had information regarding fetal platelets, 11 cases (38%) were complicated by severe fetal thrombocytopenia. Severely thrombocytopenic fetuses were characterized by a lower hemoglobin concentration (2.6 ± 0.9 g/dL vs 5.5 ± 3.6 g/dL; P = .01), lower reticulocyte count (9.1% ± 2.8% vs 17.3% ± 10.6%; P = .02), and lower gestational age at the time of diagnosis (21.4 ± 3.1 wk vs 23.6 ± 2.2 wk; P = .03). Both the fetal death rate within 48 hours of FBS (27.3% vs 0%; P = .02) and the risk of prematurity (100.0% vs 13.3%; P < .001) were higher in fetuses with severe thrombocytopenia. Fetal thrombocytopenia was more common during the second trimester but, in some cases, persisted into the third trimester. Intrauterine transfusion (IUT) of red blood cells resulted in a further mean decrease of 40.1% ± 31.0% in fetal platelet concentration. CONCLUSION: Severe fetal thrombocytopenia is relatively common after fetal hParvo-B19 infection, can be further worsened by IUT, and may be associated with an increased risk of procedure-related fetal loss after either FBS or IUT.

The distribution and frequency of pulmonary neuroendocrine cells in Down syndrome fetal lungs.

The pulmonary neuroendocrine cells (PNEC) are located in the epithelial lining of the airways and consist of solitary neuroendocrine cells (NEC) and NEC clusters, the neuroepithelial bodies (NEB). During fetal life, PNEC are the first to differentiate within the primitive airway epithelium, and bombesin expression favors branching of the respiratory tree. We investigated PNEC in Down syndrome (DS), where the lungs often show enlarged and reduced number of alveoli. Immunohistochemistry for bombesin and synaptophysin, PNEC markers, was evaluated in fetal lungs from 15 cases of DS and 11 age-matched controls from the 17th to 23rd week of gestation. Morphometric analysis assessed PNEC in the mucosal lining of each lung, expressed as number/mm. Nonparametric Mann-Whitney U test showed no statistical difference in frequency of PNEC in DS and controls. Our findings suggest that, at least in late second trimester, the distribution and frequency of PNEC in DS fetuses is not altered.

Broadening the ciliopathy spectrum: motile cilia dyskinesia, and nephronophthisis associated with a previously unreported homozygous mutation in the INVS/NPHP2 gene.

Nephronophthisis associated ciliopathies (NPHP-AC) are a group of phenotypically related conditions that include Joubert syndrome, Meckel syndrome, nephronophthisis (NPHP), and Senior-Loken syndrome. We report on a male fetus with prenatal ultrasound findings at 24 weeks of gestation of anhydramnios, large and echogenic kidneys and situs inversus totalis. Histopathology revealed nephronophthisis and tracheal mucosa electron microscopy revealed ciliary dysgenesis. DNA analysis of the NPHP genes showed a previously unreported homozygous mutation, p.Arg603* (c.1078+1G>A), in the INVS/NPHP2 gene. This mutation is thought to abolish the splice donor site for exon 8, which likely disrupts the normal splicing of the INVS/NPHP2 gene.

Prenatal diagnosis, clinical outcomes, and associated pathology in pregnancies complicated by massive subchorionic thrombohematoma (Breus' mole).

OBJECTIVES: To review the association between ultrasound findings, placental pathology, and prognosis in pregnancies complicated by massive subchorionic thrombohematoma (MTH)/Breus' mole. METHOD: We identified 14 cases of MTH from January 2004 to December 2012. MTH was defined by >1 cm thickness hematoma and extensive (≥50%) involvement of the fetal surface of the placenta. Patient information, details of initial presentation, and perinatal outcome were obtained from the manual and electronic chart records. Ultrasound findings were related to pregnancy outcomes and associated placental pathology. Participants were stratified on the basis of birth outcome into survivors (live births, n = 7) and nonsurvivors (neonatal deaths or intrauterine fetal deaths/termination of pregnancy, n = 7). RESULTS: All 14 cases of MTH were suspected on ultrasound and confirmed by pathology assessment. All cases in the nonsurvivor group had abnormal umbilical artery (UA) Doppler waveforms compared with none in the survivors (p = 0.02). All cases in the nonsurvivor group had extreme preterm deliveries (p = 0.02). Birth weight was significantly reduced in the nonsurvivor group (p = 0.001), and 5/7 cases were diagnosed with severe intrauterine growth restriction, compared with none in the survivor group (p = 0.02). CONCLUSION: Massive subchorionic thrombohematoma/Breus' mole may be diagnosed in the second trimester by ultrasound assessment of the placenta. Normal fetal growth and UA Doppler waveforms are associated with perinatal survival.

Dyssegmental dysplasia, Silverman-Handmaker type: prenatal ultrasound findings and molecular analysis.

OBJECTIVES: The objective of this study is to describe the prenatal sonographic features and the results of DNA analysis on three fetuses with dyssegmental dysplasia, Silverman-Handmaker type (DD-SH). METHODS: A retrospective review of three fetuses with confirmed DD-SH was conducted. The fetal ultrasound findings, the radiological characteristics, and the results of the mutation analysis of the heparan sulphate perlecan gene 2 (HSPG2) were reviewed. RESULTS: There were three cases in two families with DD-SH diagnosed prenatally. The main prenatal ultrasound and the radiological features of DD-SH were severe limb shortening and vertebral segmentation and fusion defects (anisospondyly). The DNA analysis of the HSPG2 gene showed that the two affected fetuses in a nonconsanguineous family had a compound heterozygote for the c.646G > T transversion in exon 7 and a c.5788C > T transition in exon 46. The fetus born to the consanguineous couple had a homozygous mutation c.1356-27_1507 + 59del. CONCLUSION: DD-SH can be diagnosed prenatally using fetal ultrasound as early as 13 weeks. Xrays and DNA analysis of the HSPG2 gene are important for the confirmation of the diagnosis and for the preimplantation and prenatal diagnosis in pregnancies at risk.

Multidisciplinary management of invasive placenta previa.

OBJECTIVE: To assess the effectiveness of a multidisciplinary team approach to reduce severe maternal morbidity in women with invasive placenta previa. METHODS: We conducted a prospective study of 33 women with placenta previa and increta-percreta (diagnosed by ultrasound and/or magnetic resonance imaging) delivering at Mount Sinai Hospital, Toronto, following the introduction in January 2008 of a team-based approach to women with this condition. We included women who delivered by June 2012. We reviewed antenatal outpatient and inpatient records for use of six pre-defined team components by the attending staff obstetrician: (1) antenatal maternal-fetal medicine consultation, (2) surgical gynaecology consultation, (3) antenatal MRI, (4) interventional radiology consultation and preoperative placement of balloon catheters in the anterior divisions of the internal iliac arteries, (5) pre-planned surgical date, and (6) surgery performed by members of the invasive placenta surgical team. Antenatal course, delivery, and postpartum details were recorded to derive a five-point composite severe maternal morbidity score based on the presence or absence of: (1) ICU admission following delivery, (2) transfusion > 2 units of blood, (3) general anaesthesia start or conversion, (4) operating time in highest quartile (> 125 minutes), and (5) significant postoperative complications (readmission, prolonged postpartum stay, and/or pulmonary embolism). RESULTS: All 33 women survived during this time period. Two thirds (22/33) had either five or six of the six components of multidisciplinary care. Increasing use of multidisciplinary team components was associated with a significant reduction in composite morbidity (R2 = 0.228, P = 0.005). CONCLUSION: Team-based assessment and management of women with invasive placenta previa is likely to improve maternal outcomes and should be encouraged on a regional basis.

Objectif : Évaluer l'efficacité d'une approche d'équipe multidisciplinaire visant l'atténuation de la morbidité maternelle grave chez les femmes qui présentent un placenta prævia invasif. Méthodes : Nous avons mené une étude prospective auprès de 33 femmes qui présentaient un placenta prævia et increta-percreta (diagnostiqué par échographie et/ou imagerie par résonance magnétique) et qui accouchaient au Mount Sinai Hospital de Toronto, à la suite du lancement (en janvier 2008) d'une approche d'équipe visant les femmes qui présentaient une telle placentation. Nous avons inclus les accouchements chez les femmes visées jusqu'en juin 2012. Nous avons analysé les dossiers prénataux (services externes et services hospitaliers) en vue d'y repérer l'utilisation par l'obstétricien titulaire de six composantes d'équipe prédéfinies : (1) consultation prénatale en médecine fœto-maternelle; (2) consultation en chirurgie gynécologique; (3) IRM prénatale; (4) consultation en radiologie interventionnelle et mise en place préopératoire de sondes à ballonnet dans les divisions antérieures des artères iliaques internes; (5) planification à l'avance de la date de chirurgie; et (6) chirurgie menée par des membres de l'équipe chirurgicale vouée aux cas de placenta invasif. Les détails de l'évolution prénatale, de l'accouchement et de la période postpartum ont été consignés afin d'établir un score composite de morbidité maternelle grave en cinq points fondé sur la présence ou l'absence de ce qui suit : (1) admission à l'USI à la suite de l'accouchement; (2) transfusion de plus de deux unités de sang; (3) anesthésie générale (administration ou conversion); (4) temps opératoire se situant dans le quartile le plus élevé (> 125 minutes); et (5) complications postopératoires significatives (réhospitalisation, hospitalisation postpartum prolongée et/ou embolie pulmonaire). Résultats : Les 33 participantes ont survécu au cours de cette période. Les deux tiers (22/33) d'entre elles présentaient cinq ou six des six composantes des soins multidisciplinaires. L'utilisation croissante des composantes des soins multidisciplinaires a été associée à une baisse significative de la morbidité composite (R2 = 0,228, P = 0,005). Conclusion : L'évaluation et la prise en charge en équipe des femmes qui présentent un placenta prævia invasif sont susceptibles d'améliorer les issues maternelles et devraient être favorisées sur une base régionale.

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022.

This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2022 special issue presents three updates to the standards: CellML 2.0.1, SBML Level 3 Package: Spatial Processes, Version 1, Release 1, and Synthetic Biology Open Language (SBOL) Version 3.1.0. This document can also be used to identify the latest specifications for all COMBINE standards. In addition, this editorial provides a brief overview of the COMBINE 2022 meeting in Berlin.

Controlled vocabularies and semantics in systems biology.

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments.