Overview of data preprocessing for machine learning applications in human microbiome research

Although metagenomic sequencing is now the preferred technique to study microbiome-host interactions, analyzing and interpreting microbiome sequencing data presents challenges primarily attributed to the statistical specificities of the data (e.g., sparse, over-dispersed, compositional, inter-variable dependency). This mini review explores preprocessing and transformation methods applied in recent human microbiome studies to address microbiome data analysis challenges. Our results indicate a limited adoption of transformation methods targeting the statistical characteristics of microbiome sequencing data. Instead, there is a prevalent usage of relative and normalization-based transformations that do not specifically account for the specific attributes of microbiome data. The information on preprocessing and transformations applied to the data before analysis was incomplete or missing in many publications, leading to reproducibility concerns, comparability issues, and questionable results. We hope this mini review will provide researchers and newcomers to the field of human microbiome research with an up-to-date point of reference for various data transformation tools and assist them in choosing the most suitable transformation method based on their research questions, objectives, and data characteristics.

Comparison of different prognostic scores in estimating short- and long-term mortality in COVID-19 patients above 60 years old in a university hospital in Belgium

BACKGROUND AND OBJECTIVES

Multiple scoring systems were used for risk stratification in COVID-19 patients. The objective was to determine among 6 scores which performed the best in predicting short-and long-term mortality in hospitalized COVID-19 patients ≥ 60 years.

METHODS

An observational, retrospective cohort study conducted between 21/10/2020 and 20/01/2021. 6 scores were calculated (Clinical Frailty Scale (CFS), Charlson Comorbidity Index (CCI), 4C Mortality Score (4CMS), NEWS score (NEWS), quick-SOFA score (qSOFA), and Quick COVID-19 Severity Index (qCSI)). We included unvaccinated hospitalized patients with COVID-19 ≥ 60 years old in Brugmann hospital, detected by PCR and/or suggestive CT thorax images. Old and nosocomial infections, and patients admitted immediately at the intensive care unit were excluded.

RESULTS

199 patients were included, mean age was 76.2 years (60-99). 47.2% were female. 56 patients (28%) died within 1 year after the first day of hospitalization. The 4CMS predicted the best intrahospital, 30 days and 6 months mortality, with area under the ROC curve (AUROC) 0.695 (0.58-0.81), 0.76 (0.65-0.86) and 0.72 (0.63-0.82) respectively. The CCI came right after with respectively AUROC of 0.69 (0.59-0.79), 0.74 (0.65-0.83) and 0.71 (0.64-0.8). To predict mortality at 12 months after hospitalization, the CCI had the highest AUROC with 0.77 (0.69-0.85), before the 4CMS with 0.69 (0.60-0.79).

DISCUSSION

Among 6 scores, the 4CMS was the best to predict intrahospital, 30-day and 6-month mortality. To predict mortality at 12 months, CCI had the best performance before 4CMS. This reflects the importance of considering comorbidities for short- and long-term mortality after COVID 19.

REGISTRATION

This study was approved by the ethical committee of Brugmann University Hospital (reference CE 2020/228).

Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action

The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory 'omics' features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices.

Machine learning approaches in microbiome research: challenges and best practices

Microbiome data predictive analysis within a machine learning (ML) workflow presents numerous domain-specific challenges involving preprocessing, feature selection, predictive modeling, performance estimation, model interpretation, and the extraction of biological information from the results. To assist decision-making, we offer a set of recommendations on algorithm selection, pipeline creation and evaluation, stemming from the COST Action ML4Microbiome. We compared the suggested approaches on a multi-cohort shotgun metagenomics dataset of colorectal cancer patients, focusing on their performance in disease diagnosis and biomarker discovery. It is demonstrated that the use of compositional transformations and filtering methods as part of data preprocessing does not always improve the predictive performance of a model. In contrast, the multivariate feature selection, such as the Statistically Equivalent Signatures algorithm, was effective in reducing the classification error. When validated on a separate test dataset, this algorithm in combination with random forest modeling, provided the most accurate performance estimates. Lastly, we showed how linear modeling by logistic regression coupled with visualization techniques such as Individual Conditional Expectation (ICE) plots can yield interpretable results and offer biological insights. These findings are significant for clinicians and non-experts alike in translational applications.

Both Disease Activity and HLA-B27 Status Are Associated With Gut Microbiome Dysbiosis in Spondyloarthritis Patients

OBJECTIVE

Gut microbiome dysbiosis has previously been reported in spondyloarthritis (SpA) patients and could be critically involved in the pathogenesis of this disorder. The objectives of this study were to further characterize the microbiota structure in SpA patients and to investigate the relationship between dysbiosis and disease activity in light of the putative influence of the genetic background.

METHODS

Shotgun sequencing was performed on fecal DNA isolated from stool samples from 2 groups of adult volunteers: SpA patients (n = 102) and healthy controls (n = 63). A subset of the healthy controls comprised the age-matched siblings of patients whose HLA-B27 status was known. Changes in gut microbiota composition were assessed based on species diversity, enterotypes, and taxonomic and functional differences.

RESULTS

Dysbiosis was confirmed in SpA patients as compared to healthy controls. The restriction of microbiota diversity was detected in patients with the most active disease, and the abundance of several bacterial species was correlated with Bath Ankylosing Spondylitis Disease Activity Index score. Among healthy controls, significant differences in microbiota composition were also detected between the HLA-B27-positive and the HLA-B27-negative siblings of SpA patients. We highlighted a decreased abundance of several species of bacteria in SpA patients, especially those bacteria belonging to the Clostridiales order. Among the few species of bacteria showing increased abundance, Ruminococcus gnavus was one of the top differentiating species.

CONCLUSION

These findings reveal that genetic background and level of disease activity are likely to influence the composition of the gut microbiota of patients with SpA. It may be appropriate for further research on chronic arthritis to focus on these key parameters.

Gestational Age, Socioeconomic Context and Infection-Related Hospital Admissions of Infants Born With Gestational Age Less Than 33 Weeks

Using data from a regional medical follow-up network database of preterm infants born with gestational age (GA) <33 weeks, we found that low GA and deprived socioeconomic neighborhoods increased incidence of infection-related hospitalization during the first year of life. Respiratory tract infections rates were higher in extremely preterm infants.

A combined test for feature selection on sparse metaproteomics data-an alternative to missing value imputation

One of the difficulties encountered in the statistical analysis of metaproteomics data is the high proportion of missing values, which are usually treated by imputation. Nevertheless, imputation methods are based on restrictive assumptions regarding missingness mechanisms, namely "at random" or "not at random". To circumvent these limitations in the context of feature selection in a multi-class comparison, we propose a univariate selection method that combines a test of association between missingness and classes, and a test for difference of observed intensities between classes. This approach implicitly handles both missingness mechanisms. We performed a quantitative and qualitative comparison of our procedure with imputation-based feature selection methods on two experimental data sets, as well as simulated data with various scenarios regarding the missingness mechanisms and the nature of the difference of expression (differential intensity or differential presence). Whereas we observed similar performances in terms of prediction on the experimental data set, the feature ranking and selection from various imputation-based methods were strongly divergent. We showed that the combined test reaches a compromise by correlating reasonably with other methods, and remains efficient in all simulated scenarios unlike imputation-based feature selection methods.

Diet Supplementation with NUTRIOSE, a Resistant Dextrin, Increases the Abundance of Parabacteroides distasonis in the Human Gut

SCOPE

An imbalance of the gut microbiota ("dysbiosis") is associated with numerous chronic diseases, and its modulation is a promising novel therapeutic approach. Dietary supplementation with soluble fiber is one of several proposed modulation strategies. This study aims at confirming the impact of the resistant dextrin NUTRIOSE (RD), a soluble fiber with demonstrated beneficial health effects, on the gut microbiota of healthy individuals.

METHODS AND RESULTS

Fifty healthy women are enrolled and supplemented daily with either RD (n = 24) or a control product (n = 26) during 6 weeks. Characterization of the fecal metagenome with shotgun sequencing reveals that RD intake dramatically increases the abundance of the commensal bacterium Parabacteroides distasonis. Furthermore, presence in metagenomes of accessory genes from P. distasonis, coding for susCD (a starch-binding membrane protein complex) is associated with a greater increase of the species. This suggests that response to RD might be strain-dependent.

CONCLUSION

Supplementation with RD can be used to specifically increase P. distasonis in gut microbiota of healthy women. The magnitude of the response may be associated with fiber-metabolizing capabilities of strains carried by subjects. Further research will seek to confirm that P. distasonis directly modulates the clinical effects observed in other studies.

Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers—Example of Crohn’s Disease and Ulcerative Colitis Flare-Ups

Thanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis. This is illustrated here, for the still highly challenging diagnosis of intestinal bowel diseases (IBDs). Using bottom-up proteomics, we analyzed the gut metaproteomes of the same twenty faecal specimens processed either fresh or after a two-month freezing period. We focused on metaproteomes of microbial cell envelopes since it is an outstanding way of capturing host and host–microbe interaction signals. The protein profiles of pairs of fresh and frozen-thawed samples were closely related, making feasible deferred analysis in a distant diagnosis centre. The taxonomic and functional landscape of microbes in diverse IBD phenotypes—active ulcerative colitis, or active Crohn’s disease either with ileo-colonic or exclusive colonic localization—differed from each other and from the controls. Based on their specific peptides, we could identify proteins that were either strictly overrepresented or underrepresented in all samples of one clinical group compared to all samples of another group, paving the road for promising additional diagnostic tool for IBDs.

StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs

Current studies are shifting from the use of single linear references to representation of multiple genomes organised in pangenome graphs or variation graphs. Meanwhile, in metagenomic samples, resolving strain-level abundances is a major step in microbiome studies, as associations between strain variants and phenotype are of great interest for diagnostic and therapeutic purposes. We developed StrainFLAIR with the aim of showing the feasibility of using variation graphs for indexing highly similar genomic sequences up to the strain level, and for characterizing a set of unknown sequenced genomes by querying this graph. On simulated data composed of mixtures of strains from the same bacterial species Escherichia coli, results show that StrainFLAIR was able to distinguish and estimate the abundances of close strains, as well as to highlight the presence of a new strain close to a referenced one and to estimate its abundance. On a real dataset composed of a mix of several bacterial species and several strains for the same species, results show that in a more complex configuration StrainFLAIR correctly estimates the abundance of each strain. Hence, results demonstrated how graph representation of multiple close genomes can be used as a reference to characterize a sample at the strain level.

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

The number of microbiome-related studies has notably increased the availability of data on human microbiome composition and function. These studies provide the essential material to deeply explore host-microbiome associations and their relation to the development and progression of various complex diseases. Improved data-analytical tools are needed to exploit all information from these biological datasets, taking into account the peculiarities of microbiome data, i.e., compositional, heterogeneous and sparse nature of these datasets. The possibility of predicting host-phenotypes based on taxonomy-informed feature selection to establish an association between microbiome and predict disease states is beneficial for personalized medicine. In this regard, machine learning (ML) provides new insights into the development of models that can be used to predict outputs, such as classification and prediction in microbiology, infer host phenotypes to predict diseases and use microbial communities to stratify patients by their characterization of state-specific microbial signatures. Here we review the state-of-the-art ML methods and respective software applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on the application of ML in microbiome studies related to association and clinical use for diagnostics, prognostics, and therapeutics. Although the data presented here is more related to the bacterial community, many algorithms could be applied in general, regardless of the feature type. This literature and software review covering this broad topic is aligned with the scoping review methodology. The manual identification of data sources has been complemented with: (1) automated publication search through digital libraries of the three major publishers using natural language processing (NLP) Toolkit, and (2) an automated identification of relevant software repositories on GitHub and ranking of the related research papers relying on learning to rank approach.

Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets

The gut microbiota are increasingly considered as a main partner of human health. Metaproteomics enables us to move from the functional potential revealed by metagenomics to the functions actually operating in the microbiome. However, metaproteome deciphering remains challenging. In particular, confident interpretation of a myriad of MS/MS spectra can only be pursued with smart database searches. Here, we compare the interpretation of MS/MS data sets from 48 individual human gut microbiomes using three interrogation strategies of the dedicated Integrated nonredundant Gene Catalog (IGC 9.9 million genes from 1267 individual fecal samples) together with the Homo sapiens database: the classical single-step interrogation strategy and two iterative strategies (in either two or three steps) aimed at preselecting a reduced-sized, more targeted search space for the final peptide spectrum matching. Both iterative searches outperformed the single-step classical search in terms of the number of peptides and protein clusters identified and the depth of taxonomic and functional knowledge, and this was the most convincing with the three-step approach. However, iterative searches do not help in reducing variability of repeated analyses, which is inherent to the traditional data-dependent acquisition mode, but this variability did not affect the hierarchical relationship between replicates and all other samples.

Alterations in Gut Microbiome in Cirrhosis as Assessed by Quantitative Metagenomics: Relationship With Acute-on-Chronic Liver Failure and Prognosis

BACKGROUND AND AIMS

Cirrhosis is associated with changes in gut microbiome composition. Although acute-on-chronic liver failure (ACLF) is the most severe clinical stage of cirrhosis, there is lack of information about gut microbiome alterations in ACLF using quantitative metagenomics. We investigated the gut microbiome in patients with cirrhosis encompassing the whole spectrum of disease (compensated, acutely decompensated without ACLF, and ACLF). A group of healthy subjects was used as control subjects.

METHODS

Stool samples were collected prospectively in 182 patients with cirrhosis. DNA library construction and sequencing were performed using the Ion Proton Sequencer (ThermoFisher Scientific, Waltham, MA). Microbial genes were grouped into clusters, denoted as metagenomic species.

RESULTS

Cirrhosis was associated with a remarkable reduction in gene and metagenomic species richness compared with healthy subjects. This loss of richness correlated with disease stages and was particularly marked in patients with ACLF and persisted after adjustment for antibiotic therapy. ACLF was associated with a significant increase of Enterococcus and Peptostreptococcus sp and a reduction of some autochthonous bacteria. Gut microbiome alterations correlated with model for end-stage liver disease and Child-Pugh scores and organ failure and was associated with some complications, particularly hepatic encephalopathy and infections. Interestingly, gut microbiome predicted 3-month survival with good stable predictors. Functional analysis showed that patients with cirrhosis had enriched pathways related to ethanol production, γ-aminobutyric acid metabolism, and endotoxin biosynthesis, among others.

CONCLUSIONS

Cirrhosis is characterized by marked alterations in gut microbiome that parallel disease stages with maximal changes in ACLF. Altered gut microbiome was associated with complications of cirrhosis and survival. Gut microbiome may contribute to disease progression and poor prognosis. These results should be confirmed in future studies.

Converting bulk sugars into prebiotics: semi-rational design of a transglucosylase with controlled selectivity

Bad sugars in, good sugar out: an engineered sucrose phosphorylase for the production of kojibiose from sucrose and glucose.

107 DETECTION OF BIOTINYLATED-OVULATION-INDUCING FACTOR (OIF) IN CEREBROSPINAL FLUID AND ITS ABILITY TO INDUCE OVULATION

Ovulation-inducing factor (OIF) is a protein in the seminal plasma of llamas that induces a preovulatory LH surge by acting directly or indirectly on the hypothalamic GnRH neurons (Silva et al. 2011 Reprod. Biol. Endocr. 9, 74). We hypothesize that OIF crosses the blood–brain barrier and reaches the hypothalamus via secretion into the cerebro-spinal fluid (CSF) through the choroid plexus. Two experiments were designed to determine whether biotinylation of OIF (as a tracer) alters its bioactivity in a llama model (Experiment 1) and whether it crosses the blood–brain barrier in a rabbit model (Experiment 2). In Experiment 1, llamas with a follicle ≥8 mm in diameter that had grown for 3 consecutive days were assigned randomly to 5 groups (n = 2/group) and given an IV dose of 1) 800 µg of OIF, 2) 800 µg of OIF biotinylated at the amino end; 3) 1600 µg of OIF biotinylated at the amino end, 4) 800 µg of OIF biotinylated at the carboxyl end, or 5) phosphate buffered saline (control). The ovaries were examined daily by transrectal ultrasonography on Day 3 and 8 after treatment (Day 0 = treatment) to detect ovulation and corpus luteum formation. In Experiment 2, adult female rabbits were assigned randomly to 3 groups and given an IV dose of (1) 250 µg of OIF, (2) 250 µg of OIF biotinylated at the amino end, or (3) 250 µg of OIF biotinylated at the carboxyl end. A 50-µL sample of CSF was collected from the cisterna magna under general anesthesia before (0 min) and 10, 20, 30, and 45 min after treatment. The presence of biotinylated OIF in CSF samples was determined by dot blot, using streptavidin-peroxidase and diaminobenzidine. In Experiment 1, the diameter of the follicle at the time of the treatment did not differ among groups (9.7 ± 0.2, 9.4 ± 0.0, 10.5 ± 1.0, 10.1 ± 0.2, 10.3 ± 0.4). Ovulation was detected in all llamas except one llama treated with 800 µg OIF biotinylated at the carboxyl end and both llamas given PBS. The diameter of the corpus luteum did not differ among OIF-treated groups. In Experiment 2, OIF biotinylated at both amino and carboxyl ends was detected in CSF samples at 10, 20, 30, and 45 min after IV administration. No signal was recorded before IV administration (0 min) or in samples from rabbits that were given nonbiotinylated OIF. We conclude that the biotinylation process did not affect OIF bioactivity, and OIF crosses the blood–brain barrier and reaches the CSF in rabbits. Research supported by FONDECYT 1120518, the Natural Sciences and Engineering Research Council of Canada, and the Alpaca Research Foundation.

[Perinatal transfers: survey to evaluate the satisfaction degree of obstetricians and pediatricians with the Rhône-Alpes regional hotline center]

OBJECTIVE

In 2006, the Ministry of Health issued a legal text relating to organization of maternal transports: "By the end of the year 2008, transfers of women and new-born babies will have to be treated in a centralized way", have to provide a 24 hours service and can take several forms such as a regional transfer center, working for several perinatal network or a simple hotline within the level 3 maternity hospital of the perinatal network and would be managed by efficiently trained professionals. In order to help professionals to choose between various types of organizations, we considered to evaluate their degree of satisfaction with the Rhône-Alpes regional hotline center.

PATIENTS AND METHODS

A postal survey was carried out 15 months after the creation of the regional hotline center to the 146 obstetricians and neonatologists of the perinatal network. Eight questions dealt with the following points: organization of in utero transfers and retransfers for obstetricians on the one hand, and the organization of neonatal transfers and retransfers for pediatricians on the other hand.Moreover, several questions relating to the communication quality and the global transport organization were asked to all of these professionals. Finally, practitioners were asked whether the regional hotline center should carry on its activity or not.

RESULTS

The response rate was 51%. Seventy-two percent of practitioners considered the regional hotline center improved the communication between professionals. 66,7% thought that it improved the organization of transport. Obstetricians get benefits in 91,7% of in utero transfers and in 63,8% of retransfers. Neonatologists get benefits in 92,3% of new born babies' transfers and in 53,8% of retransfers. Finally, 85,3% of the doctors felt that the regional hotline center was time saving and 96% of them felt that this structure should carry on its activity.

DISCUSSION AND CONCLUSION

In the French Rhône-Alpes region, most obstetricians and pediatricians are satisfied by a regional hotline center dedicated to in utero as well as neonate transfer.

[Patterns physicians use to screen for gestational diabetes: descriptive analysis in a cohort of 701 women]

OBJECTIVE

To study the way physicians screen for gestational diabetes.

PATIENTS AND METHODS

Descriptive analysis of the pattern of screening used by physicians for 701 women who gave birth in a public or private maternity in the Rhône district in France.

RESULTS

Overall, a screening test was used in 17.7% of the women (95%CI 14.9-20.7). A 50 g glucose tolerance test was performed in 60% of the screening prescriptions and was positive in 37.3%. One-third of the screening tests were achieved after the 28th gestational week. About half of the women were at risk for gestational diabetes. Among them, 24.6% had had a screening test. Factors associated with prescription of a screening test were gestational diabetes or macrosomia in a previous pregnancy, diabetes in relatives, high body mass index, weight gain of more than 15 kg, African origin, and follow-up in a public maternity. The diagnosis of gestational diabetes was made in 9 women. The prevalence of gestational diabetes was 1.28% (95%CI 0.59%-2.42%).

CONCLUSION

Guidelines from the national colleges of obstetricians and endocrinologists for systematic screening for gestational diabetes are not properly applied. Questions concerning the implementation, results, and feasibility of these guidelines are raised.

[Systematic screening of deafness at a maternity ward using evoked otoacoustic emissions: practical aspects and parental attitudes]

OBJECTIVE

Evaluation of the feasibility and parental attitudes towards a hearing screening programme using evoked otoacoustic emissions, implemented in a maternity ward in France.

METHODS

A hearing screening test using transiently evoked otoacoustic emissions (TEOAE) was proposed to each baby, and an anonymous questionnaire was given to parents to assess their attitudes towards the screening procedure.

RESULTS

Although the refusal of the test reached 16% (mainly during the first two weeks of the program), more than 92% of parents judged the test as being useful, and 65% wished it to be systematically done. However, nearly 35% of parents admitted to have a low level anxiety about being unnecessarily worried by the test results. One hundred and twenty-four babies were screened. Fifty three per cent of the tests have been performed in less than ten minutes, with an average of 12.2 minutes. This duration does not include delays due to programme and babies management. False positive rate (uni or bilateral fail) was 10.5% at the first stage. Repeating the test before discharge decreased the false positive rate to 6.5%.

CONCLUSION

Although limited in time, this study shows that a systematic hearing screening programme using TEOAE is possible and should be done in France. False positive rate was below 7%, and the test was considered as useful by more than 90% of parents, although knowledge about deafness in childhood and its consequences were clearly insufficient.

Binocular competition does not regulate retinogeniculate arbor size in fetal monkey

Binocular interactions play a prominent role in shaping the axonal arbors of geniculocortical fibers and the arbors of Y cells in the retinogeniculate pathway of the fetal cat. Fiber interactions between the two eyes have also been suggested to regulate the formation of retinal projections to the dorsal lateral geniculate nucleus (dlgn) of the fetal monkey, but whether this reflects structural refinements of retinal arbors has not been established. To address this issue, we quantified the morphologic properties of individual fibers in two macaque monkeys at embryonic day (E) 110 and E121 that had an eye removed at E69 and E61, respectively. Fibers were labeled by DiI crystals into the fixed optic tract and were visualized by confocal microscopy. Three measurements were made: the number of branch points within the axon terminal arbor, the total arborization length, and the incidence of axonal side branches on the preterminal axon within the confines of the geniculate. There were no significant differences with respect to these parameters between the prenatal enucleates and normal monkeys of comparable age. This was the case for retinal fibers innervating the magnocellular and the parvocellular segments of the dlgn. The arbors stemming from the remaining eye were widely distributed in the dlgn, with some terminating in territories normally innervated by the other (enucleated) eye. These results lend support to the hypothesis that the expanded projection from the remaining eye to the lateral geniculate nucleus of the prenatally enucleated monkey is due to the maintenance of a contingent of retinal fibers normally eliminated by ganglion cell death.

Prenatal development of retinogeniculate axons in the macaque monkey during segregation of binocular inputs

In the fetal monkey the projections from the two eyes are initially completely intermingled within the dorsal lateral geniculate nucleus (DLGN) before separating into eye-specific layers (). To assess the cellular basis of this developmental process, we examined the morphological properties of individual retinogeniculate axons in prenatal monkeys of known gestational ages. The period studied spanned the time from when binocular overlap has been reported to be maximum, circa embryonic (E) day 77 through E112, when the segregation process is already largely completed in the caudal portion of the nucleus. Retinogeniculate fibers were labeled by making small deposits of DiI crystals into the fixed optic tract. After adequate time was allowed for diffusion of the tracer, fibers were visualized by confocal microscopy, and morphometric measures were made from photomontages. This revealed that retinogeniculate fibers in the embryonic monkey undergo continuous growth and elaboration during binocular overlap and subsequent segregation. Importantly, very few side-branches were found along the preterminal axon throughout the developmental period studied. Thus, restructuring of retinogeniculate fibers does not underlie the formation of eye-restricted projections in the primate. Rather, the results support the hypothesis that binocular segregation in the embryonic monkey is caused by the loss of retinal fibers that initially innervate inappropriate territories ().

[Prevention of prematurity by psychotherapeutic management]

The establishment of the mother-baby relationship is often disturbed in case of preterm birth. Clinical observations and epidemiological studies have highlighted the existence of a relationship between psychological factors and preterm birth. Therefore, a psychological support may have a beneficial effect in order to prevent preterm delivery. The aim of this study was to assess the effectiveness of psychological support in pregnant women with symptoms of preterm labor, which is considered as a somatic expression of psychological difficulty related to pregnancy. The study, which involved two cohorts of women, hospitalized or not, identified during two successive periods in the same maternity ward, included 309 women in the experimental group and 323 in the control group. The women in the control group were followed up according to the usual therapeutic procedures, whereas additional psychological support was offered to the experimental group. 92% of the women who met the psychologist accepted the psychological support. The analysis, conducted "in intent to treat", showed a significant decrease in the preterm birth rate in the experimental group (12%) compared with the control group (26%). This study confirms the feasibility of this kind of intervention and the effectiveness of psychological support on the risk of preterm delivery. The interviews help the women regain confidence in their own capacity to fulfil their pregnancy.

Prevention of preterm birth in patients with symptoms of preterm labor--the benefits of psychologic support

OBJECTIVE

The aim of this study was to assess the effectiveness of psychologic support against preterm delivery in pregnant women with symptoms of preterm labor.

STUDY DESIGN

The study, which involved two cohorts of women identified during two successive periods in the same maternity ward, included 309 women in the experimental group and 323 in the control group. The women in the control group were followed up according to the usual therapeutic procedures, whereas additional psychologic support was offered to the experimental group. The analysis, conducted "in intent to treat," was based on the estimation of the relative risk by a multivariate logistic regression adjusting for confounding factors.

RESULTS

A significant decrease in the preterm birth rate was observed in the experimental group (12.3%) compared with the control group (25.7%), with an adjusted relative risk of 0.37 (95% confidence interval 0.30 to 0.47).

CONCLUSION

This study confirms the feasibility of this kind of intervention and the effectiveness of psychologic support on the risk of preterm delivery.

[Pregnancy and perinatality: biological follow-up]

Blood and urinary tests which are necessary for pregnancy diagnosis and follow-up, for newborn and mother medical supervision, during the month following birthday, are today described in reglementary texts, laws, and recommendations such as advised medical references (RMO). These documents specify the nature of obligatory tests, the checking rhythm and the list of useless tests. hCG research remains necessary for pregnancy diagnosis, but hCG dosage is essential only in case of programmed medical assistance or pathological pregnancy (extrauterine pregnancy, hydatiform mole, choriocarcinoma). The obligatory follow-up of a pregnant woman includes determination of blood groups, research of infectious agents responsible for diseases (toxoplasmosis, rubeola, hepatitis B, syphilis), proteinuria and glycosuria research and blood count according to a given calendar. When the mother's condition is bad and reminiscent of a pathological pregnancy, when a genetic risk exists for the fetus or when fetal growth is abnormal as indicated by echographic control (intra-uterine growth retardation), laboratory tests are used to follow the maternal pathological course (arterial hypertension, diabetes mellitus, anemia, bacterial, viral or parasitic disease), to verify the existence of a genetic disease, to know about the fetal functional state (by amniocentesis or cordocentesis), to identify an erythrocyte fetomaternal incompatibility. Since last trimester pregnancy accidents are able to endanger mother's and fetus lives, the feto-maternal follow-up must be adjusted to pathological diagnosis types and requires a particular supervision of the delivery. Finally mother and child must undergo a post-natal follow-up during the four weeks after birthday (perinatality control).

Phenotypic characterisation of respecified visual cortex subsequent to prenatal enucleation in the monkey: development of acetylcholinesterase and cytochrome oxidase patterns

Prenatal bilateral enucleation induces cortex, which normally would have become striate cortex, to follow a default developmental pathway and to take on the cytoarchitectonic appearance of extrastriate cortex (default extrastriate cortex, Dehay et al. [1996] J. Comp. Neurol. 367:70-89). We have investigated if this manipulation influences the cortical expression of acetylcholinesterase (AChE) and cytochrome oxidase (CO). Early enucleation (before embryonic day 81; E81) had only minor effects on the distribution of AChE and CO in the striate cortex. In animals that underwent operation, the striate cortex CO blobs were significantly more closely spaced on the operculum compared with the calcarine. After early enucleation, there was a periodic distribution of CO dense patches in default extrastriate cortex. These CO patches had a center-to-center spacing that was considerably smaller than that of CO stripes in normal area V2, but was somewhat larger than that of the CO blobs in striate cortex. Although the CO stripes characteristic of normal area V2 could not be detected, there were some high-frequency CO patches, similar to those found in default extrastriate cortex. Early enucleation caused a failure to form the transient AChE bands running perpendicular to the striate border, which are normally present in the fetus and early neonate. Late enucleation did not alter AChE expression in extrastriate cortex. The relatively minor effects of early enucleation in the reduced striate cortex contrast with the changes in expression of these enzymes in extrastriate cortex, which accompany large shifts in the location of the striate border. This suggests a massive reorganisation of cortical phenotype in extrastriate cortex.

Role of directed growth and target selection in the formation of cortical pathways: prenatal development of the projection of area V2 to area V4 in the monkey

In experiments combining retrograde tracers and histochemistry, we have looked at the prenatal development of the cortical pathway linking areas V2 and V4. Transient expression of acetylcholinesterase in fetal area V2 reveals the separate compartments that project to V4 (temporal directed pathway) and V5 (parietal directed pathway). During early stages of pathway formation, V2 neurons projecting to area V4 are clustered in the appropriate compartments. During the phase of rapid axonal growth, there is a selective increase of connections originating from the appropriate compartments leading to a strongly clustered organization at the peak of connectivity. During this phase, injections involving the white matter also showed clustering, but this was somewhat reduced in comparison to that of gray matter injections. The growth phase is followed by an elimination phase during which there is a tendency for a preferential loss of intercluster connections, which may sharpen the early formed pattern. These results demonstrate the primary role of axonal guidance and target recognition mechanisms followed by a limited extent of selective elimination during the formation of functional cortical pathways in the primate isocortex. Compared to previous findings, these results suggest that the developmental restriction of callosal connections is not a universal model of cortical development. In the present report, the directed growth and early specification of feed-forward connections contrast with the prolonged remodelling of monkey feedback projections, suggesting two distinct developmental strategies of pathway formation in the monkey.

Contribution of thalamic input to the specification of cytoarchitectonic cortical fields in the primate: effects of bilateral enucleation in the fetal monkey on the boundaries, dimensions, and gyrification of striate and extrastriate cortex

Bilateral enucleation was performed at different fetal ages during corticogenesis, and the brains were prepared for histological examination. Early-enucleated fetuses (operated prior to embryonic day 77) showed morphological changes at the level of the thalamus and the cortex. In the thalamus, there was a loss of lamination and a decrease in size of the lateral geniculate nucleus. There was a decrease in the size of the inferior pulvinar, but there was no change in the lateral pulvinar. The border of striate cortex was as sharp in the enucleates as it was in the normal monkeys. In three of the four early enucleates, we observed an interdigitation of striate and extrastriate cortex. In three of the early enucleates, we observed a small island of nonstriate cortex near the striate border that was surrounded entirely by striate cortex. Enucleation led to an age-related reduction of striate cortex. This reduction was greater in the operculum than in the calcarine fissure. The reduction of striate cortex was accompanied by an increase in the dimensions of extrastriate visual cortex, so that the overall dimensions of the neocortex remained invariant. The extrastriate cortex in the enucleated animals presented a uniform cytoarchitecture and was indistinguishable from area 18 in the normal animal. There were changes in the gyral pattern that were restricted mainly to the cortex on the operculum. A deepening of minor dimples as well as the induction of a variable number of supplementary sulci led to an increase in the convolution of the occipital lobe. These results are discussed with respect to the specification of cortical areas. They demonstrate that the reduction in striate cortex was not accompanied by an equivalent reduction in the neocortex; rather, there was a border shift, and a large volume of cortex that was destined to become striate cortex appears to be cytoarchitectonically normal extrastriate cortex.

Developmental remodeling of primate visual cortical pathways

The pre- and postnatal developmental changes of the cortical afferents to area 17 were studied in the macaque monkey. Paired injections of the retrograde tracers fast blue and diamidino yellow were made in area 17. Quantitative techniques were used to examine the spatial patterns of labeling in three distinct locations of the extrastriate cortex that correspond to known visual areas. In the adult, each cortical region has a characteristic laminar distribution. In the fetus the proportion of supragranular layer neurons in all cortical regions was much higher than in the adult. The present study shows that despite the very high levels of labeled supragranular layer neurons, there is some early areal specialization so that the adult configuration does not emerge from a uniform distribution. The developmental decline in the proportion of labeled supragranular neurons is complete by 1 month after birth. Each injection of tracer gave rise in each cortical area to dense labeling in a restricted region (projection zone). Areal measurements of projection zones in the supra- and infragranular layers showed that the developmental decrease in the proportion of labeled supragranular layer neurons is accompanied by a relative change of the dimensions of supra- and infragranular projection zones: the supragranular projection zone in the fetus is larger than the infragranular projection zone and vice versa in the adult. In the fetus, the two projection zones corresponding to each of the two tracers overlap in the supragranular layers whereas they are largely separated in the infragranular layers. During development there is a progressive decrease in the overlap of the supragranular projection zones and an increase in the overlap in the infragranular layers. Again, the adult configuration is achieved 1 month after birth. This developmental inversion of the areal dimensions of the projection zones in supra- and infragranular layers is accompanied by a drastic decrease in the proportion of double-labeled neurons located in supragranular layers. These results clearly show that early in development, axonal projections to area V1 are modified in very different ways according to whether they originate from supra- or infragranular layers. This developmental process lasts for about 80 d. These findings show that in the primate there is a prolonged remodeling of axonal projections that is a highly characteristic feature of this species.

Developmental changes in the distribution of acetylcholinesterase in the extrastriate visual cortex of the monkey

In the fetal and neonatal monkey, periodically organized regions of high activity of acetylcholinesterase were found in the visual cortical area V2 (Area 18). The acetylcholinesterase bands, like the thin and thick stripes of cytochrome oxidase, were found to run orthogonal to the area 17/18 border. During neonatal development these bands progressively narrow and finally disappear shortly after four months of age.

In vitro fertilization and development of llama () oocytes using epididymal spermatozoa and oviductal cell co-culture

A study was designed to determine the feasibility of developing in vitro maturation, fertilization and culture systems utilizing follicular oocytes and epididymal spermatozoa collected from llamas at slaughter. From a total of 1324 cumulus oocyte complexes (COCs) recovered, 972 were cultured in 50-ul drops of TCM-199 medium with 10% heat inactivated steer serum (DBS) and hormones for 30 h. After maturation, the oocytes were randomly allocated into 4 groups in a 2x2 factorial design: cumulus-enclosed oocytes, 2 ug/ml heparin (Group 1); cumulus-enclosed oocytes, 5 ug/ml heparin (Group 2); denuded oocytes, 2 ug/ml heparin (Group 3); and denuded oocytes, 5 ug/ml heparin (Group 4). Denuded oocytes were obtained for groups 3 and 4 by vortexing. Epididymides were also collected at slaugther and fresh spermatozoa (for each replicate) were obtained by mincing the cauda epididymis with a scalpel blade. A total of 721 oocytes were inseminated with 2-3 x 10(6) epididymal spermatozoa/ml in a 50-ul drop of FERT-TALP medium. After 18 h of in vitro insemination, 234 oocytes were placed in a llama oviductal epithelial cell (LLOEC) co-culture in TCM-199 for 9 d. All cultures were done at 38.5 degrees C under 5% CO(2) in air with high humidity. The rate of fertilization, initial cleavage and development in co-culture were evaluated and compared. Of 192 oocytes examined for signs of fertilization, 56 (29.2%) were penetrated by spermatozoa with 57.1% (32 56 ) of the penetrated oocytes having a male and female pronucleus. There were no differences among treatment groups in total fertilization. However, the frequency of oocytes fertilized normally tended to be higher in the denuded oocytes 67.7% (21 31 ) than the oocytes inseminated with cumulus cells 44.0% (11 25 ) independent of heparin concentration (P<0.06). The total embryo development rate to the 2 cells to blastocyst stage was 32.1% (75 234 ). There was no difference in development rate between groups. From the 234 oocytes co-cultured in LLOEC for 9 d, 15.8% developed into 2 to 16 cells, 5.6% into morulae, 6.0% into early/expanded blastocysts and 4.7% into hatching/hatched blastocysts. The results indicate that an in vitro fertilization system is possible in the llama utilizing slaughterhouse material and that llama oocytes can be fertilized in the presence of heparin and epididymal spermatozoa.

Modulation of the cell cycle contributes to the parcellation of the primate visual cortex

An as-yet unresolved issue in developmental neurobiology is whether the discrete areas that form the mammalian cortex emerge from a uniform cortical plate or whether they are already specified in the germinal zone. A feature of the primate striate cortex is that the number of neurons per unit area is twice that of anywhere else in the cerebral cortex. Here we take advantage of this unique structural feature to investigate whether the extra striate cortical cells are due to increased neuron production during neurogenesis. We labelled precursors undergoing terminal cell division with 3H-thymidine and allowed them to migrate to the cortical plate. Cell counts revealed that their rate of production in the germinal zone of striate cortex is higher than in that given rise to extrastriate cortex. Also, we used 3H-thymidine pulse injections to investigate cell cycle dynamics and found that this phase of increased production of striate cortical cells is associated with changes in the parameters of the cell cycle. These results show that cortical area identity is at least partially determined at the level of the ventricular zone.

Home uterine activity monitoring in France: a randomized, controlled trial

OBJECTIVES

We assessed the effectiveness of ambulatory tocodynamometry in reducing the preterm delivery rate in women at risk of preterm delivery such as women with risk factors and women previously hospitalized and discharged.

STUDY DESIGN

In four public maternity units these women were randomly allocated to two groups: 84 had home uterine activity monitoring and daily midwife contact and 84 were given the standard care for high-risk women, which generally includes home visits by community midwives.

RESULTS

The proportion of deliveries before 37 weeks' gestation was slightly higher in the monitored group than in the control group (32% vs 22%). The corresponding odds ratio was 1.7 (95% confidence interval: 0.9 to 3.5).

CONCLUSION

Although the sample was small, these results suggest that home uterine activity monitoring was probably not beneficial to the population studied, or at least that any benefit would have been too small to justify extending this monitoring in this high-risk population.

[Genital herpes and childbirth]

Neonatal herpes is a serious infection due to the risk of diffusion and damage to the central nervous system. Depending on the author, the incidence of herpetic infection reported ranges from 1/7,500 to 1/1,000,000 neonates. type II herpes virus is responsible for three quarters of infections. The risk or in-utero damage is low, and does not exceed 5 percent of cases. Contamination usually occurs during delivery or during the immediate post-partum period. The clinical forms of neonatal infection consist essentially of diffuse forms, located in the central nervous system, and localized forms in the integuments and the eye. The prognosis for diffused forms and for damage to the central nervous system was particularly serious (two thirds mortality and a high risk of sequelae amongst survivors); but these results involve children who received anti-viral treatment too late. Primary maternal herpetic infection during the month preceding birth is the most serious risk for the neonate due to the high level of virus in the lesions and the absence of neutralizing antibodies. In this situation, the risk of neonate infection appears to be 75 percent. Fortunately, this situation is unusual. Recurrent infection is accompanied by a lower viral titer, viral elimination is rapid and the patient has neutralizing antibodies. The risk of neonatal involvement in the case of recurrence at the time of childbirth is thought to be less than 5 percent. In cases with a history of genital herpes in the mother or her partner, the risk of neonatal contamination is reported to be 1/1,000.(ABSTRACT TRUNCATED AT 250 WORDS)

Segregation of callosal and association pathways during development in the visual cortex of the primate

The segregation of callosal and association pathways in the developing visual cortex of the monkey was studied using the retrograde tracers fast blue and diamidino yellow. Quantitative analysis of the laminar distribution of labeled callosal and association neurons made it possible to reveal the shifting pattern of connections that characterizes the development of these two pathways. In the adult, callosal neurons are restricted to supragranular layers, where they are concentrated at the bottom of layer 3. Association neurons are located both in infra- and supragranular layers. Supragranular layer association neurons are concentrated in layer 2, with limited spread into layer 3 so that there is little overlap with callosal neurons. In the immature brain, callosal neurons are characterized by a tangential distribution that is more widespread than in the adult, while their laminar distribution undergoes little developmental change. Association neurons show two types of changes in their laminar distribution: (1) in the early fetus, there is a large excess of association neurons in supragranular layers, the adult distribution being achieved some time after birth; and (2) during maturation there is a selective elimination of at least 50% of the projections originating from the lower part of layers 2/3. Hence, the adult radial segregation of association and callosal pathways is achieved in part by regressive phenomena. The developmental reduction of bihemispheric projections is largely independent of changes in the organization of association neurons. Quantitative analysis of the morphology and spatial location of neurons sending axon collaterals to both hemispheres suggests that they constitute a subset of callosal neurons and that their frequency is determined by factors that regulate directly this population. These results are discussed with respect to the specification of visual cortical pathways during ontogenesis.

The effects of bilateral enucleation in the primate fetus on the parcellation of visual cortex

Bilateral enucleation in the macaque fetus causes an areal reduction of an otherwise normal striate cortex. Here we show that in early operated animals this reduction is accompanied by a separation of striate and prostriate cortices which are normally contiguous. However this induced separation does not correspond to the areal reduction of striate cortex, indicating that extrinsic signals regulate either the proliferation and/or survival of striate cortical neurons.

[The significance of the level of C-reactive protein in gynecologic infections]

C-reactive protein, synthesized by the liver, belongs to the group of proteins in the acute stage of inflammation. It has a very short half life of 6 to 8 hours with rapid evolution kinetics. The CRP level has been measured 959 times by the immuno-turbidimetric method in 500 in-patients of the Gynaecology Department of Claude Bernard Hospital. It was measured every 48 hours. The CRP level increases in the immediate post-operative period, reaches its maximum on D3 and falls back to normal between D5 and D7. The CRP level seems to be the most reliable parameter for the diagnosis of pelvic infections (namely salpingitis). It represents the best criterium to assess the effectiveness of the treatments administered to the infected patients (adnexitis, post-operative complications).

Incidence of visual cortical neurons which have axon collaterals projecting to both cerebral hemispheres during prenatal primate development

Fast blue was injected massively in extrastriate cortex of one hemisphere Diamidino yellow in area 17 of the other hemisphere, in adult and prenatal cynomolgus monkeys. After a suitable survival period the brains were processed for fluorescent dyes. Counts were made of the total number of labeled neurons and of those neurons which were labeled by both dyes and which project therefore to both hemispheres by means of bifurcating axon collaterals. At 122 and 135 days after conception (E122 and E135), shortly after cortico-cortical pathways are established, double-labeled neurons constituted 0.45% and 0.46% of the total population of labeled neurons in area V2. In V2 in the adult the range of values of double-labeled neurons was 0.03-0.08%.

Maturation and connectivity of the visual cortex in monkey is altered by prenatal removal of retinal input

In several species, the peripheral input from the eyes partly determines the pattern of interconnections between the visual areas of the two cerebral hemispheres through the fibre tract termed the corpus callosum. In the macaque monkey, the neurons projecting through the callosum are largely restricted to area 18 throughout ontogeny, whereas area 17 is characterized by few or no callosal projections. Here, we show that suppressing the peripheral input by prenatal removal of the eyes leads to a marked reduction in the extent of area 17, resulting in a large shift in the position of the histologically identifiable boundary between the two areas. Even so, the boundary continues to separate an area rich with callosal connections (area 18) from one poor in such projections (area 17), indicating there is no effect on the callosal connectivity of area 17. In contrast, in area 18, eye removal results in many more neurons with callosal projections than in normal animals. The results suggest that the factors that determine the parcellation of cortical areas also specify their connectivity.