Automation of Wilms' tumor segmentation by artificial intelligence.

BACKGROUND: 3D reconstruction of Wilms' tumor provides several advantages but are not systematically performed because manual segmentation is extremely time-consuming. The objective of our study was to develop an artificial intelligence tool to automate the segmentation of tumors and kidneys in children. METHODS: A manual segmentation was carried out by two experts on 14 CT scans. Then, the segmentation of Wilms' tumor and neoplastic kidney was automatically performed using the CNN U-Net and the same CNN U-Net trained according to the OV2ASSION method. The time saving for the expert was estimated depending on the number of sections automatically segmented. RESULTS: When segmentations were performed manually by two experts, the inter-individual variability resulted in a Dice index of 0.95 for tumor and 0.87 for kidney. Fully automatic segmentation with the CNN U-Net yielded a poor Dice index of 0.69 for Wilms' tumor and 0.27 for kidney. With the OV2ASSION method, the Dice index varied depending on the number of manually segmented sections. For the segmentation of the Wilms' tumor and neoplastic kidney, it varied respectively from 0.97 to 0.94 for a gap of 1 (2 out of 3 sections performed manually) to 0.94 and 0.86 for a gap of 10 (1 section out of 6 performed manually). CONCLUSION: Fully automated segmentation remains a challenge in the field of medical image processing. Although it is possible to use already developed neural networks, such as U-Net, we found that the results obtained were not satisfactory for segmentation of neoplastic kidneys or Wilms' tumors in children. We developed an innovative CNN U-Net training method that makes it possible to segment the kidney and its tumor with the same precision as an expert while reducing their intervention time by 80%.

An 8-Week Course of Bifidobacterium longum 35624® Is Associated with a Reduction in the Symptoms of Irritable Bowel Syndrome.

Irritable bowel syndrome (IBS) is one of the disorders most frequently diagnosed by gastroenterologists. Probiotics are promising tools for the management of IBS. The objective of the present study was to evaluate the effectiveness and tolerability of a probiotic (Bifidobacterium longum 35624®) in adults (aged 18 or over) with IBS (as defined by the Rome IV criteria). In an open-label, observational, post-market study conducted in Germany, adults with IBS and a prior recommendation for the intake of B. longum 35624® were recruited by family physicians. During the 8-week course of treatment, the study participants filled out a weekly questionnaire that enabled calculation of a total IBS symptom score (TISS, the sum of abdominal pain, bloating, passage of gas, constipation, and diarrhea individual symptom scores) and the well-known IBS severity scoring system (IBS-SSS) score. Thirty-seven patients were included. The course of B. longum 35624® was associated with a significant reduction (43.4%) in the TISS vs. baseline. The mean individual symptom grades for passage of gas and bloating fell significantly from "moderate" at baseline to "very mild to mild" after 8 weeks of treatment, whereas those for abdominal pain and diarrhea fell significantly from "mild to moderate" to "very mild to mild." Over 60% of the participants achieved clinically meaningful reductions in the TISS (> 30%) and the IBS-SSS score (> 50 points). The effectiveness of B. longum 35624® was rated as "good to satisfactory" by study participants and the investigating physicians. One mild adverse event (nausea) was potentially linked to the study treatment. We conclude that an 8-week course of B. longum 35624® was associated with significant, clinically meaningful symptom relief in a typical population of adult patients with IBS.

French survey of sedation practices for pediatric magnetic resonance and computed tomography imaging.

BACKGROUND: Pediatric magnetic resonance imaging (MRI) and computed tompgraphy (CT) require patient immobility and therefore often require sedation or general anesthesia of patients. Consensus on these procedures is lacking in France. OBJECTIVE: Thus, the aim of this study was to describe the current sedation practices for pediatric MRI and CT in France. MATERIAL AND METHODS: From January 2019 to December 2019, an online questionnaire was delivered by electronic mail to a representative radiologist in 60 pediatric radiology centers registered by the French-speaking pediatric and prenatal imaging society. Questions included protocols, drugs used, monitoring and side effects. RESULTS: Representatives of 40 of the 60 (67%) radiology centers responded to the survey. Among them, 31 performed sedation including 17 (55%) centers where radiologists performed sedation without anesthesiologists present during the procedure. The premedication drugs were hydroxyzine (n = 8, 80%) and melatonin (n = 2, 20%), Sedation drugs used for children ages 0 to 6 years old were pentobarbital (n = 9, 60%), midazolam (n = 2, 13%), chloral hydrate (n = 2, 13%), diazepam (n = 1, 6.5%) and chlorpromazine (n = 1, 6.5%). A written sedation protocol was available in 10/17 (59%) centers. In 6/17 (35%) centers, no monitoring was used during the procedures. Blood pressure monitoring and capnography were rarely used (< 10%) and post-sedation monitoring was heterogeneous. No life-threatening adverse effect was reported, but 6 centers reported at least one incident per year. CONCLUSION: For half of the responding radiology centers, radiologists performed sedation alone in agreement with the local anesthesiology team. Sedation procedures and monitoring were heterogenous among centers. Adjustment and harmonization of the practices according to the capacity of each center may be useful.

Expending the Phenotypic Spectrum of Encephalocraniocutaneous Lipomatosis: About a Prenatal Case With Complete Autopsy.

Encephalocraniocutaneous lipomatosis (ECCL) or Haberland syndrome (MIM #613001) is a rare congenital neurocutaneous disorder. It is characterized by unilateral ocular, cutaneous and central nervous system anomalies. Key clinical features include hairless fatty tissue nevus of the scalp, choristoma of the eye and intraspinal and intracerebral lipomas. We report one of the first cases diagnosed after termination of pregnancy at 35 WG, including antenatal and post-mortem imaging, complete autopsy and genetic analysis. Prenatal ultrasound and MRI of the third trimester showed multifocal spinal lesions and left lateral cerebral ventriculomegaly with cerebral atrophy. Diagnosis of ECCL was suggested at complete autopsy which revealed nevus psiloliparus of the scalp, facial hamartomas and intracranial and spinal lipomas. In addition, our case also exhibited a cardiac rhabdomyoma and a multicystic dysplastic kidney, both never reported to date in this syndrome. ECCL was confirmed by the identification of a postzygotic FGFR1 mutation. We reviewed the literature and discuss the pathogenesis of this syndrome.

Genotype-first in a cohort of 95 fetuses with multiple congenital abnormalities: when exome sequencing reveals unexpected fetal phenotype-genotype correlations.

PURPOSE: Molecular diagnosis based on singleton exome sequencing (sES) is particularly challenging in fetuses with multiple congenital abnormalities (MCA). Indeed, some studies reveal a diagnostic yield of about 20%, far lower than in live birth individuals showing developmental abnormalities (30%), suggesting that standard analyses, based on the correlation between clinical hallmarks described in postnatal syndromic presentations and genotype, may underestimate the impact of the genetic variants identified in fetal analyses. METHODS: We performed sES in 95 fetuses with MCA. Blind to phenotype, we applied a genotype-first approach consisting of combined analyses based on variants annotation and bioinformatics predictions followed by reverse phenotyping. Initially applied to OMIM-morbid genes, analyses were then extended to all genes. We complemented our approach by using reverse phenotyping, variant segregation analysis, bibliographic search and data sharing in order to establish the clinical significance of the prioritised variants. RESULTS: sES rapidly identified causal variant in 24/95 fetuses (25%), variants of unknown significance in OMIM genes in 8/95 fetuses (8%) and six novel candidate genes in 6/95 fetuses (6%). CONCLUSIONS: This method, based on a genotype-first approach followed by reverse phenotyping, shed light on unexpected fetal phenotype-genotype correlations, emphasising the relevance of prenatal studies to reveal extreme clinical presentations associated with well-known Mendelian disorders.

Butyrate mediates anti-inflammatory effects of Faecalibacterium prausnitzii in intestinal epithelial cells through Dact3.

The commensal bacterium Faecalibacterium prausnitzii plays a key role in inflammatory bowel disease (IBD) pathogenesis and serves as a general health biomarker in humans. However, the host molecular mechanisms that underlie its anti-inflammatory effects remain unknown. In this study we performed a transcriptomic approach on human intestinal epithelial cells (HT-29) stimulated with TNF-α and exposed to F. prausnitzii culture supernatant (SN) in order to determine the impact of this commensal bacterium on intestinal epithelial cells. Moreover, modulation of the most upregulated gene after F. prausnitzii SN contact was validated both in vitro and in vivo. Our results showed that F. prausnitzii SN upregulates the expression of Dact3, a gene linked to the Wnt/JNK pathway. Interestingly, when we silenced Dact3 expression, the effect of F. prausnitzii SN was lost. Butyrate was identified as the F. prausnitzii effector responsible for Dact3 modulation. Dact3 upregulation was also validated in vivo in both healthy and inflamed mice treated with either F. prausnitzii SN or the live bacteria, respectively. Finally, we demonstrated by colon transcriptomics that gut microbiota directly influences Dact3 expression. This study provides new clues about the host molecular mechanisms involved in the anti-inflammatory effects of the beneficial commensal bacterium F. prausnitzii.

Retraction Note to: Lactobacillus casei BL23 regulates Treg and Th17 T-cell populations and reduces DMH-associated colorectal cancer.

This article has been retracted. Please see the retraction notice for more detail: https://doi.org/10.1007/s00535-015-1158-9 .

3D reconstruction of Wilms' tumor and kidneys in children: Variability, usefulness and constraints.

INTRODUCTION: Wilms' tumor (WT) is the most common type of malignant kidney tumor in children. Three-dimensional reconstructions can be performed pre-operatively to help surgeons in the planning phase. OBJECTIVES: The main objective of this study was to determine the variability of WT segmentation and 3D reconstruction. The secondary objectives were to assess the usefulness of these 3D reconstructions in the surgical planning phase and in the selection of patients for nephron-sparing surgery (NSS). METHODS: 14 scans from 12 patients were manually or semi-automatically segmented by 2 teams using 3D Slicer software. Inter-individual variability of 3D reconstructions was measured based on the Dice index. The utility of 3D reconstructions for the surgical planning was evaluated by 4 pediatric surgeons using a 5-point Likert scale. The possibility of undertaking NSS was evaluated according to the criteria defined in the Umbrella SIOP-RTSG 2016 protocol. RESULTS: Segmentation of the WT, healthy kidney, pathological kidney, arterial and venous vascularization could be performed for all of the patients in this study. Urinary cavities segmentation could only be performed for 5 out of 14 scans that had a delayed acquisition phase. The mean time required to carry out these segmentations was 8.6 h [3-15 h]. The mean Dice index for all of the scans was good (mean: 0.87; range [0.83-0.91]). Considering each anatomical structure, the Dice index was very good for the WT (mean: 0.95; range [0.91-0.97]) and the healthy kidney (mean: 0.95; range [0.93-0.96]), good for the pathological kidney (mean: 0.87; range [0.69-0.96]) and arterial vascularization (mean: 0.84; range [0.74-0.91]). The Dice index was lower than 0.8 for venous vascularization only (mean: 0.77; range [0.58-0.86]). All the surgeons who were interviewed agreed that the 3D reconstructions were realistic representations and useful for the surgical planning phase. The images reconstructed in 3D allowed most of the criteria defined by the Umbrella SIOP-RTSG 2016 protocol to be evaluated regarding the selection of patients who could benefit from NSS. CONCLUSION: The inter-individual variability of 3D reconstructions of WT is acceptable. Three-dimensional representation appears to assist surgeons with the surgical planning phase by allowing them to better anticipate the operative risks. 3D reconstructions can also be an additional tool to better select patients for NSS. However, the manual or semi-automatic method used is very time-consuming, making it difficult for a routinely use. Developing techniques to automate this segmentation process, therefore, appears to be essential if surgeons and radiologists are to use it in daily practice.

A new case of KIAA0753-related variant of Jeune asphyxiating thoracic dystrophy.

A narrow thorax with shortening of long bones is usually pointing to dysfunction of the primary cilia corresponding clinically to ciliopathies with major skeletal involvement. Mutations in at least 23 genes are likely to correspond to this clinical presentation: IFT43/52/80/81/122/140/172, WDR19/34/35/60, DYNC2H1, DYNC2LI1, CEP120, NEK1, TTC21B, TCTEX1D2, INTU, TCTN3, EVC 1/2 and KIAA0586. In addition to these, KIAA0753 variants were recently described in seven patients with Jeune asphyxiating thoracic dystrophy (ATD) (two first cousins, one unrelated patient and one fetus), Joubert syndrome (two siblings) and orofaciodigital syndrome type 6 (one patient). We present the clinical characteristics of a eighth such patient. This 4 year-old boy with narrow thorax, short limbs, severe respiratory and feeding difficulties from birth on had a history of hypotonia and developmental delay. On skeletal survey, short tubular bones (height - 5,5 SD) and a trident appearance of the pelvis were seen. Brain MRI showed cervical canal stenosis. Renal function was normal and moderate hepatomegaly was noted. A homozygous c.943C > T mutation in KIAA0753 was identified on whole exome sequencing, resulting in Gln315Ter premature termination of the corresponding protein. This case provides confirmation of an additional molecular basis for skeletal dysplasia and illustrates how ciliopathies due to mutations in a single gene may present as apparently distinct syndromes.

Cutis laxa and excessive bone growth due to de novo mutations in PTDSS1.

The cutis laxa syndromes are multisystem disorders that share loose redundant inelastic and wrinkled skin as a common hallmark clinical feature. The underlying molecular defects are heterogeneous and 13 different genes have been involved until now, all of them being implicated in elastic fiber assembly. We provide here molecular and clinical characterization of three unrelated patients with a very rare phenotype associating cutis laxa, facial dysmorphism, severe growth retardation, hyperostotic skeletal dysplasia, and intellectual disability. This disorder called Lenz-Majewski syndrome (LMS) is associated with gain of function mutations in PTDSS1, encoding an enzyme involved in phospholipid biosynthesis. This report illustrates that LMS is an unequivocal cutis laxa syndrome and expands the clinical and molecular spectrum of this group of disorders. In the neonatal period, brachydactyly and facial dysmorphism are two early distinctive signs, later followed by intellectual disability and hyperostotic skeletal dysplasia with severe dwarfism allowing differentiation of this condition from other cutis laxa phenotypes. Further studies are needed to understand the link between PTDSS1 and extra cellular matrix assembly.

Lactobacillus casei BL23 regulates Treg and Th17 T-cell populations and reduces DMH-associated colorectal cancer.

BACKGROUND: Chronic intestinal inflammation alters host physiology and could lead to colorectal cancer (CRC). We have previously reported beneficial effects of the probiotic strain of Lactobacillus casei BL23 in different murine models of intestinal inflammation. In addition, there is an emerging interest on the potential beneficial effects of probiotics to treat CRC. We thus explored whether L. casei BL23 displays protective effects on CRC. METHODS: Mice were subcutaneously injected with 1,2-dimethylhydrazine (DMH) weekly during 10 weeks and orally administered with L. casei BL23 in the drinking water until the 10th week. Multiple plaque lesions in the large intestine were observed macroscopically and counted and intestinal tissues were also histologically analyzed. Finally, T-cell populations and cytokine production were evaluated after co-incubation of L. casei BL23 with spleen cells from non-treated mice to determine the immuno-modulatory effects of this bacterium. RESULTS: Our results show that oral treatment with this probiotic bacterium modulates host immune responses and significantly protect mice against DMH-induced CRC. This protection may be associated with the modulation of regulatory T-cells towards a Th17-biased immune response accompanied by the expression of regulatory cytokines (IL-6, IL-17, IL-10 and TGF-ß), as demonstrated in L. casei BL23-treated splenocytes, but also with the colonic expression of IL-22 observed in vivo on L. casei BL23-treated mice; suggesting the induction of a fine-tune Th17-biased response. CONCLUSIONS: Altogether our results reveal the high potential of L. casei BL23 to treat CRC and opens new frontiers for the study of immunomodulatory functions of probiotics.

Identification of novel anti-inflammatory probiotic strains isolated from pulque.

Probiotics are live microorganisms which when administered in adequate amounts, confer health benefits on the host. Their use is more and more widespread for both prevention and treatment of diseases, including traveler's diarrhea and inflammatory bowel diseases (IBDs). In this work, we isolated and characterized novel candidate probiotic strains from pulque (xaxtle), a traditional Mexican alcoholic fermented beverage. A total of 14 strains were obtained from xaxtle samples isolated from three different Mexican regions. Species identification was performed by biochemical methods and 16S rRNA gene targeted PCR. The isolates belonged to the Lactobacillus plantarum, Lactobacillus paracasei, Lactobacillus brevis, and Lactobacillus composti phylogenetic groups, with L. brevis being the most dominant group. Bacteria were tested for lysozyme, low pH, and bile acid resistance. Moreover, the strains were tested for adherence to human intestinal epithelial cells and screened for their immunomodulatory properties using a cellular model. Selected bacterial strains with anti-inflammatory properties were then tested in vivo in a dinitro-benzene sulfonic acid (DNBS)-induced chronic colitis mouse model, and weight loss, gut permeability, and cytokine profiles were measured as readouts of inflammation. One of the selected strains, Lactobacillus sanfranciscensis LBH1068, improved mice health as observed by a reduction of weight loss, significant decreases in gut permeability, and cytokine modulation. Altogether, our results highlighted the potential of lactobacilli isolated from pulque and in particular the strain L. sanfranciscensis LBH1068 as a novel probiotic to treat IBD.

Factors influencing the diagnostic yield and accuracy of image-guided percutaneous needle biopsy of pediatric tumors: single-center audit of a 26-year experience.

BACKGROUND: Image-guided percutaneous core needle biopsy is a common procedure for diagnosis of both solid tumors and hematological malignancies in children. Despite recent improvements, a certain rate of non-diagnostic biopsies persists. OBJECTIVE: To assess the factors influencing the diagnostic yield and accuracy of percutaneous core needle biopsies of pediatric tumors. MATERIALS AND METHODS: We conducted a single-center retrospective study of a 26-year experience with image-guided biopsies in children and young adults. Using uni- and multivariate analysis, we evaluated the association of diagnostic yield and accuracy with technical factors (image-guided procedure, pathological technique) and clinical factors (complication rate, histological type and anatomical location). RESULTS: We retrieved data relating to 396 biopsies were performed in 363 children and young adults (mean age: 7.4 years). Overall, percutaneous core needle biopsy showed a diagnostic yield of 89.4% (95% confidence interval [CI] 85.9-92.2) and an accuracy of 90.9% (CI 87.6-93.6) with a complication rate of 2.5% (CI 1.2-4.6).The diagnostic yield increased with the use of advanced tissue assessment techniques (95.7% with immunohistochemistry versus 82.3% without immunohistochemistry; P < 0.0001) and an increased number of passes (mean: 3.96 for diagnostic biopsies versus 3.62 for non-diagnostic biopsies; P = 0.044). CONCLUSION: The use of advanced pathological techniques and an increased number of passes are the two main factors influencing the diagnostic success of biopsies in pediatric tumors.

Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii.

UNLABELLED: Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified on the basis of human clinical data. The mechanisms underlying its beneficial effects are still unknown. Gnotobiotic mice harboring F. prausnitzii (A2-165) and Escherichia coli (K-12 JM105) were subjected to 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced acute colitis. The inflammatory colitis scores and a gas chromatography-time of flight (GC/TOF) mass spectrometry-based metabolomic profile were monitored in blood, ileum, cecum, colon, and feces in gnotobiotic mice. The potential anti-inflammatory metabolites were tested in vitro. We obtained stable E. coli and F. prausnitzii-diassociated mice in which E. coli primed the gastrointestinal tract (GIT), allowing a durable and stable establishment of F. prausnitzii. The disease activity index, histological scores, myeloperoxidase (MPO) activity, and serum cytokine levels were significantly lower in the presence of F. prausnitzii after TNBS challenge. The protective effect of F. prausnitzii against colitis was correlated to its implantation level and was linked to overrepresented metabolites along the GIT and in serum. Among 983 metabolites in GIT samples and serum, 279 were assigned to known chemical reactions. Some of them, belonging to the ammonia (α-ketoglutarate), osmoprotective (raffinose), and phenolic (including anti-inflammatory shikimic and salicylic acids) pathways, were associated with a protective effect of F. prausnitzii, and the functional link was established in vitro for salicylic acid. We show for the first time that F. prausnitzii is a highly active commensal bacterium involved in reduction of colitis through in vivo modulation of metabolites along the GIT and in the peripheral blood. IMPORTANCE: Inflammatory bowel diseases (IBD) are characterized by low proportions of F. prausnitzii in the gut microbiome. This commensal bacterium exhibits anti-inflammatory effects through still unknown mechanisms. Stable monoassociated rodents are actually not a reproducible model to decipher F. prausnitzii protective effects. We propose a new gnotobiotic rodent model providing mechanistic clues. In this model, F. prausnitzii exhibits protective effects against an acute colitis and a protective metabolic profile is linked to its presence along the digestive tract. We identified a molecule, salicylic acid, directly involved in the protective effect of F. prausnitzii. Targeting its metabolic pathways could be an attractive therapeutic strategy in IBD.

TCF12 microdeletion in a 72-year-old woman with intellectual disability.

Heterozygous mutations in TCF12 were recently identified as an important cause of craniosynostosis. In the original series, 14% of patients with a mutation in TCF12 had significant developmental delay or learning disability. We report on the first case of TCF12 microdeletion, detected by array-comparative genomic hybridization, in a 72-year-old patient presenting with intellectual deficiency and dysmorphism. Multiplex ligation-dependent probe amplification analysis indicated that exon 19, encoding the functionally important basic helix-loop-helix domain, was included in the deleted segment in addition to exon 20. We postulate that the TCF12 microdeletion is responsible for this patient's intellectual deficiency and facial phenotype.

Splenic infarction in a child revealing chronic myeloid leukemia.

A 7-year-old girl was admitted with a severe abdominal pain. Abdominal ultrasound and CT revealed a large splenic infarction, leading to the diagnosis of chronic myeloid leukemia.

Childhood onset diabetes posttransplant in a girl with TCF2 mutation.

Heterozygous mutations of TCF2 (transcription factor 2) have been associated with maturity onset diabetes of the young, renal malformations, hyperuricemia, and occasionally internal genital malformations in female. We report a female patient with bilateral renal hypodysplasia and de novo heterozygous TCF2 gene mutation. At the age of 9 yr, she developed transient ketoacidosis immediately posttransplant, temporarily requiring insulin. During glucocorticoid tapering, impaired glucose tolerance persisted and overt insulin-dependent diabetes mellitus developed 1 yr later. Pathogenic factors which might have played a role in the acceleration of diabetes were (i) switch from cyclosporine to tacrolimus, (ii) weight excess, and (iii) cytomegalovirus infection. TCF2 analysis might, therefore, be of interest in patients with congenital abnormalities of the kidney and the urinary tract in order to improve posttransplant management in terms of steroid and tacrolimus exposure.

Prenatal US evaluation of the spinal cord using high-frequency linear transducers.

We illustrate the contribution of high-frequency linear abdominal transducers in the prenatal US examination of the spinal cord. After birth, such transducers are commonly used in US examination of the spinal cord. During the third trimester of gestation, the fetal spine is commonly facing anteriorly and US images of the spinal cord can be acquired using a high-frequency linear abdominal transducer. Images of the normal spinal cord, normal variants (ventriculus terminalis, cyst of filum terminale) and spinal cord abnormalities (myelomeningocele, meningocele, diastematomyelia, tethered spinal cord and caudal regression syndrome) are presented. In this pictorial essay, comparison between images acquired with low- and high-frequency transducers are provided as well as correlation with postnatal data. In the normal spine, anatomical details such as the conus medullaris, the filum terminale and the nerve root bundles are exquisitely depicted, making it possible to differentiate normal variants from abnormalities. In abnormal cases, the position of the conus medullaris, its shape and the nerve roots can be analyzed in detail. We describe the benefits of using high-frequency linear transducers in US examination of the spinal cord, which is common after birth but has not been hitherto reported in fetuses.