The experience of healthcare professionals treating adolescents with eating disorders in psychiatric and pediatric inpatient units for adolescents: A qualitative study

OBJECTIVES

The recommended treatment for Eating Disorders (EDs) is multidisciplinary and multimodal. Nonetheless, the complex linkage of the different disciplines involved is not necessarily simple. We analyzed the experience of healthcare professionals faced with psychiatric and psychological symptoms in adolescents with EDs in two "multidisciplinary" inpatient units embedded predominantly in different paradigms - one pediatric and one psychiatric.

METHODS

Qualitative analysis of 20 healthcare staff members' interviews from different professional backgrounds working in inpatient units for EDs in Montreal (Canada) and Paris (France).

RESULTS

The "Complex patients" theme discusses the need for a global approach to the multiplicity of symptoms presented by these patients. "Management and its limits" describes the daily management of psychiatric symptoms in both units. "Psychiatry and Adolescent medicine: from opposition to collaboration" describes the different levels at which these disciplines work together and how this cooperation may be evolving.

CONCLUSIONS

The complex entanglement intrinsic in EDs of the patients' somatic, psychosocial, psychiatric, and adolescent problems requires collaboration between disciplines, but the modalities of this collaboration are multiple and evolve non-linearly in specialized treatment units. A multilevel approach must be offered, with the degree of collaboration (multidisciplinary, interdisciplinary and transdisciplinary) appropriate to the complexity of each adolescent's issues.

Pediatric deep neck infections: Clinical description and analysis of therapeutic management

OBJECTIVES

The aim of our study was to describe clinical presentations, bacteriological results, and therapeutic management in a pediatric population presenting with acute pharyngeal suppuration. A further aim was to identify clinical, bacteriological, and radiological predictors of success associated with exclusive medical treatment.

METHOD

A retrospective study was carried out including patients under 18 years of age hospitalized between January 1, 2015 and December 31, 2017 in our center for acute pharyngeal suppuration. We identified three groups of patients: group A, treated with exclusive intravenous antibiotics; group B, surgically treated after 48 h of appropriate antibiotic therapy, due to persistent fever and/or clinical worsening and/or persistence of a collection on follow-up imaging; group C, surgically treated as first-line therapy in association with intravenous antibiotics. A total of 83 patients were included: 36 in group A, 12 in group B, and 35 in group C. These three groups were compared for several variables: age of the patients, polynuclear neutrophil counts, diameter of the collections (the largest diameter found on imaging), duration of antibiotic therapy, delay before return to apyrexia, and hospitalization duration.

RESULTS

A neck mass and torticollis were present, respectively, in 48.8 and 47.6% of cases. No breathing difficulties were reported. Streptococcus pyogenes was the most frequently identified microorganism. The average diameter of the collections from patients treated surgically as first-line therapy (group C) was significantly larger than that of the patients treated with antibiotics (group A) (27.89 mm vs. 18.73 mm, respectively, p = 0.0006). All the patients who required surgery despite 48 h of appropriate antibiotic therapy (group B) had collections with diameters greater than or equal to 15 mm. There was no significant difference between the groups concerning hospitalization duration.

CONCLUSION

Exclusive medical treatment is associated with a high cure rate, mainly for collections with small diameter. We recommend special attention to patients treated with first-line exclusive intravenous antibiotic therapy and with a collection diameter greater than or equal to 15 mm.

Oropharyngeal squamous cell carcinoma: p16/p53 immunohistochemistry as a strong predictor of HPV tumour status

AIMS

Oropharyngeal squamous cell carcinomas (OPSCC) related to human papillomavirus (HPV) infection have a better prognosis than those without HPV infection. Although p16^INK4a overexpression is used as a surrogate marker for HPV infection, 5-20% of p16-positive OPSCC are described as being unrelated to HPV infection, with worse overall survival compared to OPSCC-related HPV. There is therefore a risk of undertreating a proportion of OPSCC patients falsely considered to be HPV-driven because of p16 positivity. TP53 mutations are highly prevalent in OPSCC driven by mutagens in tobacco and alcohol. We describe herein a combined p16/p53 algorithm to predict HPV tumour status in OPSCC.

METHODS AND RESULTS

A total of 110 OPSCC were identified in the database of the pathology department and were studied using p16 and p53 immunohistochemistry. For p16-positive or p16-negative/wild-type patterns-p53 (WT-p53) cases (n = 63), DNA in-situ hybridisation for high-risk HPV was performed, and if negative the HPV status was controlled by HPV DNA polymerase chain reaction (PCR) (n = 19). A significant association between TP53 mutation and pattern of p53 expression was found (WT-p53, seven of 16, P < 0.001). The p16-positive/WT-p53 was significantly associated with HPV⁺ tumour status (p16-positive/WT-p53, 50 of 110, P < 0.001). Interestingly, a subset of p16-positive OPSCC was unrelated to HPV (13.5%, eight of 59), and showed mutant-type staining of p53 expression.

CONCLUSIONS

The p16 protein immunopositivity in conjunction with the mutant-type pattern of p53 staining helped to reclassify a subset of p16-positive OPSCC as OPSCC-unrelated HPV. This approach could be routinely applied by pathologists involved in the management of OPSCC, because of their potential therapeutic implications.

Severe neutropenia in an anorexic adolescent girl: a stigma of underfeeding syndrome?

PURPOSE

We describe a case of severe, prolonged neutropenia in an adolescent girl hospitalized for anorexia nervosa (AN) which occurred during a refeeding procedure in the absence of refeeding syndrome.

METHODS

This case report includes retrospective anamnestic, clinical and biological data from the patient's medical record. A literature review was conducted on the haematological changes described in the undernutrition and refeeding periods, and also on recent data for underfeeding syndrome in patients with anorexia nervosa.

CONCLUSION

Leuconeutropenia is an adaptive condition observed in undernutrition in AN, usually rapidly and completely reversible in the course of refeeding and weight gain. We describe a rare case of severe, prolonged neutropenia despite appropriate care in the absence of refeeding syndrome and without gelatinous bone marrow transformation. We suggest that neutropenia in adolescent anorexia nervosa could be a stigma of underfeeding syndrome resulting from an overly cautious refeeding strategy.

LEVEL OF EVIDENCE

Level V, descriptive study.

[Adjustment of healthcare and telemedicine in times of lockdown and COVID-19 pandemic: Feedback from a "Maison des Adolescents" (Teenager's House)]

La crise sanitaire de la COVID-19 a imposé une réorganisation majeure de l’offre de soins en France. Considérant la nécessité de maintenir des soins pour les adolescents souffrant de troubles physiques ou psychiques, les Maisons des Adolescents ont dû adapter en urgence leurs pratiques afin de maintenir au maximum la continuité des soins pour les adolescents et leurs familles. À travers le cas d’une adolescente qui a présenté une dégradation clinique de son anorexie mentale durant le confinement, nous présentons les réorganisations des soins au sein des différentes unités (consultations–hôpital de jour–unité d’hospitalisation temps plein) d’une Maison des Adolescents parisienne au cours de la pandémie de COVID-19. À partir de la littérature existante, nous discutons les avantages et limites de la télémédecine et les enjeux pratiques pour l’organisation future des soins pour les adolescents. Contrairement à la médecine pédiatrique ou pédopsychiatrique, il n’existe pas de protocole décrivant la mise en place de la télémédecine en médecine et psychiatrie de l’adolescent. Il est urgent d’approfondir les évaluations de l’utilisation de la télémédecine pour les adolescents. Ce type de recherche permettra d’améliorer les connaissances sur l’efficacité, l’acceptabilité et les limites de l’utilisation d’un dispositif de téléconsultation en psychiatrie de l’adolescent, en contexte de crise. Certaines modalités de soins à distance mises en place pendant la crise pourraient ainsi être maintenues dans le temps et s’inscrire en routine dans le domaine de la médecine et psychiatrie de l’adolescent.

A subset of activated fibroblasts is associated with distant relapse in early luminal breast cancer

Background

Early luminal breast cancer (BC) represents 70% of newly diagnosed BC cases. Among them, small (under 2 cm) BC without lymph node metastasis (classified as T1N0) have been rarely studied, as their prognosis is generally favorable. Nevertheless, up to 5% of luminal T1N0 BC patients relapse with distant metastases that ultimately prove fatal. The aim of our work was to identify the mechanisms involved in metastatic recurrence in these patients.

Methods

Our study addresses the role that autonomous and non-autonomous tumor cell features play with regard to distant recurrence in early luminal BC patients. We created a cohort of T1N0 luminal BC patients (tumors between 0.5–2 cm without lymph node metastasis) with metastatic recurrence (“cases”) and corresponding “controls” (without relapse) matched 1:1 on main prognostic factors: age, grade, and proliferation. We deciphered different characteristics of cancer cells and their tumor micro-environment (TME) by deep analyses using immunohistochemistry. We performed in vitro functional assays and highlighted a new mechanism of cooperation between cancer cells and one particular subset of cancer-associated fibroblasts (CAF).

Results

We found that specific TME features are indicative of relapse in early luminal BC. Indeed, quantitative histological analyses reveal that “cases” are characterized by significant accumulation of a particular CAF subset (CAF-S1) and decrease in CD4⁺ T lymphocytes, without any other association with immune cells. In multivariate analysis, TME features, in particular CAF-S1 enrichment, remain significantly associated with recurrence, thereby demonstrating their clinical relevance. Finally, by performing functional analyses, we demonstrated that CAF-S1 pro-metastatic activity is mediated by the CDH11/osteoblast cadherin, consistent with bones being a major site of metastases in luminal BC patients.

Conclusions

This study shows that distant recurrence in T1N0 BC is strongly associated with the presence of CAF-S1 fibroblasts. Moreover, we identify CDH11 as a key player in CAF-S1-mediated pro-metastatic activity. This is independent of tumor cells and represents a new prognostic factor. These results could assist clinicians in identifying luminal BC patients with high risk of relapse. Targeted therapies against CAF-S1 using anti-FAP antibody or CDH11-targeting compounds might help in preventing relapse for such patients with activated stroma.

Aire-dependent genes undergo Clp1-mediated 3'UTR shortening associated with higher transcript stability in the thymus

The ability of the immune system to avoid autoimmune disease relies on tolerization of thymocytes to self-antigens whose expression and presentation by thymic medullary epithelial cells (mTECs) is controlled predominantly by Aire at the transcriptional level and possibly regulated at other unrecognized levels. Aire-sensitive gene expression is influenced by several molecular factors, some of which belong to the 3'end processing complex, suggesting they might impact transcript stability and levels through an effect on 3'UTR shortening. We discovered that Aire-sensitive genes display a pronounced preference for short-3'UTR transcript isoforms in mTECs, a feature preceding Aire's expression and correlated with the preferential selection of proximal polyA sites by the 3'end processing complex. Through an RNAi screen and generation of a lentigenic mouse, we found that one factor, Clp1, promotes 3'UTR shortening associated with higher transcript stability and expression of Aire-sensitive genes, revealing a post-transcriptional level of control of Aire-activated expression in mTECs.

Tracheal injury complicating Sistrunk's thyroglossal cyst surgery

INTRODUCTION

Airway injury is a very rare complication of thyroglossal duct cyst surgery in children. The wound is most frequently located at the larynx, due to a confusion between the hyoid bone and the thyroid cartilage.

OBSERVATION

This is the first report of a tracheal injury complicating Sistrunk's procedure in a 3 year old child, revealed by respiratory distress. Conservative treatment was suggested, requiring a tracheostomy lasting 49 days, leading to decanulation and complete anatomical and functional recovery.

CONCLUSION

This report highlights the specificity of pediatric laryngotracheal anatomy.

Contribution of drug-induced sleep endoscopy to the management of pediatric obstructive sleep apnea/hypopnea syndrome

OBJECTIVES

The role of drug-induced sleep endoscopy (DISE) in the management of obstructive sleep apnea/hypopnea syndrome (OSAHS) is not precisely defined in children. The primary objective of this study was to describe DISE-induced revision of airway obstruction site location and the ensuing treatment changes in children with OSAHS. Secondary objectives were to analyze the correlation of number of obstruction sites found on DISE with apnea-hypopnea index (AHI) and with type of OSAHS.

MATERIAL AND METHODS

A retrospective single-center study included 31 children (mean age: 5.5±2.6years) undergoing DISE for management of OSAHS between 2015 and 2018. Revisions of airway obstruction site location and in treatment were noted. The correlation of number of obstruction sites with AHI and with type of OSAHS was analyzed.

RESULTS

Airway obstruction site location was reconsidered in 77% of children (n=24), modifying treatment in 45.2% (n=14). There was no significant correlation between number of obstruction sites and AHI: Spearman coefficient 0.20 (P=0.26). Patients with type-III OSAHS did not show more obstruction sites than others: respectively, 2.0 versus 1.8 (P=0.40).

CONCLUSION

DISE induced significant revision of the location and change in treatment of obstruction sites in children with OSAHS. Systematic implementation, especially in type-I OSAHS, would allow more precise pre-therapeutic classification and treatment adapted to actual airway obstruction.

Guidelines of the French Society of Otorhinolaryngology (SFORL): Nonsteroidal anti-inflammatory drugs (NSAIDs) and pediatric ENT infections. Short version

OBJECTIVES

To present the guidelines of the French Society of Otolaryngology-Head and Neck Surgery concerning the use of non-steroidal anti-inflammatory drugs (NSAIDs) in pediatric ENT infections.

METHODS

Based on a critical analysis of the medical literature up to November 2016, a multidisciplinary workgroup of 11 practitioners wrote clinical practice guidelines. Levels of evidence were classified according to the GRADE (Grades of Recommendation, Assessment, Development and Evaluation) system: GRADE A, B, C or "expert opinion". The first version of the text was reworked by the workgroup following comments by the 22 members of the reading group.

RESULTS

The main recommendations are: NSAIDs are indicated at analgesic doses (e.g. 20-30 mg/kg/day for ibuprofen) in combination with paracetamol (acetaminophen) in uncomplicated pediatric ENT infections (acute otitis media, tonsillitis, upper respiratory infections, and maxillary sinusitis) if: o pain is of medium intensity (visual analogue scale (VAS) score 3-5 or "Evaluation Enfant Douleur" (EVENDOL) child pain score 4-7) and insufficiently relieved by first-line paracetamol (residual VAS≥3 or EVENDOL≥4); o pain is moderate to intense (VAS 5-7 or EVENDOL 7-10). When combined, paracetamol and ibuprofen are ideally taken simultaneously every 6h. It is recommended: (1) o not to prescribe NSAIDs in severe or complicated pediatric ENT infections; (2) o to suspend NSAIDs treatment in case of unusual clinical presentation of the infection (duration or symptoms); (3) o not to prescribe NSAIDs for more than 72h.

The bio.tools registry of software tools and data resources for the life sciences

Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.

Combined genetic approaches yield a 48% diagnostic rate in a large cohort of French hearing-impaired patients

Hearing loss is the most common sensory disorder and because of its high genetic heterogeneity, implementation of Massively Parallel Sequencing (MPS) in diagnostic laboratories is greatly improving the possibilities of offering optimal care to patients. We present the results of a two-year period of molecular diagnosis that included 207 French families referred for non-syndromic hearing loss. Our multi-step strategy involved (i) DFNB1 locus analysis, (ii) MPS of 74 genes, and (iii) additional approaches including Copy Number Variations, in silico analyses, minigene studies coupled when appropriate with complete gene sequencing, and a specific assay for STRC. This comprehensive screening yielded an overall diagnostic rate of 48%, equally distributed between DFNB1 (24%) and the other genes (24%). Pathogenic genotypes were identified in 19 different genes, with a high prevalence of GJB2, STRC, MYO15A, OTOF, TMC1, MYO7A and USH2A. Involvement of an Usher gene was reported in 16% of the genotyped cohort. Four de novo variants were identified. This study highlights the need to develop several molecular approaches for efficient molecular diagnosis of hearing loss, as this is crucial for genetic counselling, audiological rehabilitation and the detection of syndromic forms.

Very high concentrations of n-3 fatty acids in peri-and postmenopausal Inuit women from Greenland

OBJECTIVES

The objectives of this study were to examine the profile of relative concentrations in plasma phospholipids of n-3 fatty acids among peri- and postmenopausal Inuit women living in Greenland and to verify their relationships with ischemic heart disease risk factors and more particularly, with concentrations of plasma triacylglycerols.

STUDY DESIGN

This study was part of a survey conducted in 2000, which aimed to assess the prevalence of osteoporosis and the associated risk factors among peri- and postmenopausal Greenland Inuit women.

METHODS

The study population consisted of 153 women aged 49-69 years (mean +/- SD: 55.3 +/- 4.4 y) randomly selected. Data were obtained through an interview (questionnaire on lifestyle habits, medical history etc) and a clinical session (physiologic and anthropologic measurements). Plasma samples were used to measure the fatty acid composition of plasma phospholipids.

RESULTS

The mean body mass index of women was 27.9 +/- 6.1. Seventy-five percent were smokers and 9% were currently on hormone replacement therapy. Relative concentrations of total n-3 fatty acids were very high (13.8%, 95% CI: 13.1-14.6), with docosahexanoic and eicosapentanoic acids accounting for 4.7% and 7.2%, respectively. The ratio of n-3:n-6 fatty acids was 0.67. n-3 fatty acids were inversely correlated to triacylglycerols.

CONCLUSION

These data show that peri- and post-menopausal Greenland Inuit women have very high plasma concentrations of n-3 fatty acids that protect them from ischemic heart disease.

Early synaptic deficits in the APP/PS1 mouse model of Alzheimer's disease involve neuronal adenosine A2A receptors

Synaptic plasticity in the autoassociative network of recurrent connections among hippocampal CA3 pyramidal cells is thought to enable the storage of episodic memory. Impaired episodic memory is an early manifestation of cognitive deficits in Alzheimer's disease (AD). In the APP/PS1 mouse model of AD amyloidosis, we show that associative long-term synaptic potentiation (LTP) is abolished in CA3 pyramidal cells at an early stage. This is caused by activation of upregulated neuronal adenosine A2A receptors (A2AR) rather than by dysregulation of NMDAR signalling or altered dendritic spine morphology. Neutralization of A2AR by acute pharmacological inhibition, or downregulation driven by shRNA interference in a single postsynaptic neuron restore associative CA3 LTP. Accordingly, treatment with A2AR antagonists reverts one-trial memory deficits. These results provide mechanistic support to encourage testing the therapeutic efficacy of A2AR antagonists in early AD patients.

Abstract P1-01-14: Do estrogen receptor negative and progesterone receptor positive breast tumors really exist? Attitude for not making them real

Background: Breast tumors with negative estrogen receptor (ER-) and positive progesterone receptor (PR+) are rare (from 0 to 3.4 % according to the studies), and their existence is contested. These markers determine cancer molecular subtypes which play a determinant role for both the management and the prognosis of breast cancers. It is then essential to document the real existence of ER-/PR+ tumors. The present study aimed at determining if ER-/PR+ tumors share more basal or luminal characteristics.

Methods: Between 2000 and 2015, 50 patients with ER-/PR+ breast tumors, representing 0.6 % of all breast cancers diagnosed in our institution, were included in this study. Their clinical (age, node status), morphological (size, histological type, Elston and Ellis (EE) grade, necrosis, inflammation, pushing margins, central scar, mitotic index) and immunohistochemical characteristics (ER, PR, HER2, CK5/6 and EGFR status) were compared with those of 50 luminal and 50 triple negative (TN) tumors randomly selected in our lab database. At the time this abstract is written, the Ki67 index determination is still in progress. Five of these ER-/PR+ tumors were also given a molecular test (Nanostring). Qualitative variables were compared using Chi2 or Fisher test, quantitative variables were compared using Student or Mann & Whitney tests. To take into account for multiple comparisons, p-values less than 0.025 were considered as significant.

Results: The results are summarized in table 1. For almost all the analyzed criteria, ER-/PR+ tumors present statistical difference with luminal ones. On the contrary, they share most of TN tumors characteristics. The 5 molecular analyzes performed on ER-/PR+ samples showed the following phenotypes: 3 basal, 1 HER2 enriched and 1 luminal. For this last one, new immunohistological analyzes reveal in fact an ER+ staining.

Table 1: Study results ER-/PR+ tumorsER+ tumorsTN tumorsp ER-/PR+ vs ER+p ER-/PR+ vs TNSize (mm)23.12525.20.00440.4822Histological type0.00120.2424 ductal9480.4100  lobular219.60  neuro-endocrine40 Differentiation&lt;10-40.4497 well09.80  moderately12.548.818  poorly87.541.582 EE grade&lt;10-40.1016 14.135.34  236.74918  359.215.778 EE differentiation&lt;10-40.3197 105.90  214.341.222  385.752.978 EE nuclear atypia&lt;10-40.2227 102  234.774.522  365.325.576 EE mitosis&lt;10-40.0123 124.580.418  230.613.710  344.95.972 Mitotic index (mitoses/mm2)9.52.210.2&lt;10-40.1252Necrosis465.952&lt;10-40.5484Inflammation0.00030.0011 yes30224  no4474.516  weak2623.560 CK5/6 +78.74.280.4&lt;10-40.8378EGFR +44.74.252.2&lt;10-40.4697HER2 +29.87.800.0051&lt;10-4Results are given in %, excepting mitotic index and size

Conclusion: This study tends to support that ER-/PR+ tumors may not exist and are likely to be TN cancers or less frequently false negative ER+ tumors. In a practical point of view, we think that 1) when a tumor shows ER-/PR+ and TN characteristics, it is probably a false positive PR staining, and the tumor has to be considered as a TN one, 2) when an ER-/PR+ tumor don't fit the triple negative tumors characteristics, ER must be retested in order to exclude a true luminal tumor.

Citation Format: Molly D, Bertaut A, Blanchet C, Beltjens F, Charon-Barra C, Loustalot C, Desmoulins I, Arnould L. Do estrogen receptor negative and progesterone receptor positive breast tumors really exist? Attitude for not making them real. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-01-14.

BioShaDock: a community driven bioinformatics shared Docker-based tools registry

Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis

With the increasingly rapid growth of data in life sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. Such approaches necessitate the use of large-scale computational resources and e-infrastructures, such as the European Grid Infrastructure (EGI). EGI, one of key the enablers of the digital European Research Area, is a federation of resource providers set up to deliver sustainable, integrated and secure computing services to European researchers and their international partners. Here we aim to provide the state of the art of Grid/Cloud computing in EU research as viewed from within the field of life sciences, focusing on key infrastructures and projects within the life sciences community. Rather than focusing purely on the technical aspects underlying the currently provided solutions, we outline the design aspects and key characteristics that can be identified across major research approaches. Overall, we aim to provide significant insights into the road ahead by establishing ever-strengthening connections between EGI as a whole and the life sciences community.

RSAT 2015: Regulatory Sequence Analysis Tools

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/.

Mucosal relapse of visceral leishmaniasis in a child treated with anti-TNFα

Visceral leishmaniasis is an enzootic parasitosis present across the Mediterranean Basin. Some consider it an opportunistic parasite. We report the case of a girl treated with anti-tumour necrosis factor alpha (anti-TNFα) for juvenile idiopathic arthritis who had previously presented with visceral leishmaniasis. Two and a half years later, she presented a tumour-like mass in the nasal mucous membrane caused by Leishmania parasites. Leishmania infantum is classically responsible for visceral leishmaniasis, but pure mucocutaneous leishmaniasis has also been described. To our knowledge, this is the first observation of a recurrence of visceral leishmaniasis in the mucocutaneous form. The occurrence of atypical forms and presentations in those on anti-TNF therapy should be considered.

A new case of pediatric laryngeal foraminal cyst: diagnostic challenges and association with hemi-facial microsomia

Laryngeal cysts are heterogeneous in their clinical presentation and several classifications have been proposed. Here, we report the case of a foraminal laryngeal cyst in a 6 year-old child who also has hemi facial microsomia (HFM). The cyst was treated surgically with laryngotracheal endoscopy followed by cervicotomy. Histological analysis revealed different types of cystic wall epithelium. This case is the first report of a laryngeal cyst associated with HFM in the literature. We discuss the diagnostic challenges of these specific cystic pathologies, and their pathogenesis as part of an oculo-auriculo-vertebral spectrum. Several hypotheses are proposed, based mainly on characterization of their embryological origin.

Nodular recurrence and hypothyroidism following partial thyroidectomy for benign nodular thyroid disease in children and adolescents

OBJECTIVES

Diagnostic and therapeutic processing of a thyroid nodule in children and adolescents may require lobectomy-isthmusectomy (LI) or nodule-resection (NR). Very few data in the literature report the long-term evolution of the remaining thyroid lobe in a defined pediatric population. In this study, we aimed to answer the following questions: Does a nodule recurrence occur in the remainder lobe? Is a post-operative thyroxine treatment necessary?

MATERIAL AND METHODS

This retrospective study describes 28 patients under 18 who underwent LI (22 cases) or NR (6 cases) from January 2004 to March 2012. Ten of them were lost to follow up, 18 could be assessed (4 NR (22%) and 14 LI (78%) - mean follow-up 45±31 months). All patients benefited of post-operative thyroid ultrasonography, and regular endocrinologic follow-up. The following data were analysed: emergence of new thyroid nodules, evolution of pre-existing nodules, occurrence of post-operative hypothyroidism and requirement for completion thyroidectomy.

RESULTS

The mean age at the time of surgery was 14.3±1.9 years. Two patients (11%) had pre-existing nodules in the remaining thyroid gland, none of which showed an increase in size after surgery. De novo nodules developed in five patients (27.8%). Three patients who underwent LI (21.4%) needed thyroxine treatment for post-operative hypothyroidism. One patient (5.5%) needed completion thyroidectomy.

CONCLUSIONS

In this children and adolescents population, after performing LI or NR, remaining thyroid tissue stays free of nodules in 72.2% of the cases. A post-operative thyroxin treatment is necessary in 21.4% of cases after LI.

Membrane lipids tune synaptic transmission by direct modulation of presynaptic potassium channels

Voltage-gated potassium (Kv) channels are involved in action potential (AP) repolarization in excitable cells. Exogenous application of membrane-derived lipids, such as arachidonic acid (AA), regulates the gating of Kv channels. Whether membrane-derived lipids released under physiological conditions have an impact on neuronal coding through this mechanism is unknown. We show that AA released in an activity-dependent manner from postsynaptic hippocampal CA3 pyramidal cells acts as retrograde messenger, inducing a robust facilitation of mossy fiber (Mf) synaptic transmission over several minutes. AA acts by broadening presynaptic APs through the direct modulation of Kv channels. This form of short-term plasticity can be triggered when postsynaptic cell fires with physiologically relevant patterns and sets the threshold for the induction of the presynaptic form of long-term potentiation (LTP) at hippocampal Mf synapses. Hence, direct modulation of presynaptic Kv channels by activity-dependent release of lipids serves as a physiological mechanism for tuning synaptic transmission.

Deficits in morphofunctional maturation of hippocampal mossy fiber synapses in a mouse model of intellectual disability

The grik2 gene, coding for the kainate receptor subunit GluK2 (formerly GluR6), is associated with autism spectrum disorders and intellectual disability. Here, we tested the hypothesis that GluK2 could play a role in the appropriate maturation of synaptic circuits involved in learning and memory. We show that both the functional and morphological maturation of hippocampal mossy fiber to CA3 pyramidal cell (mf-CA3) synapses is delayed in mice deficient for the GluK2 subunit (GluK2⁻/⁻). In GluK2⁻/⁻ mice this deficit is manifested by a transient reduction in the amplitude of AMPA-EPSCs at a critical time point of postnatal development, whereas the NMDA component is spared. By combining multiple probability peak fluctuation analysis and immunohistochemistry, we have provided evidence that the decreased amplitude reflects a decrease in the quantal size per mf-CA3 synapse and in the number of active synaptic sites. Furthermore, we analyzed the time course of structural maturation of CA3 synapses by confocal imaging of YFP-expressing cells followed by tridimensional (3D) anatomical reconstruction of thorny excrescences and presynaptic boutons. We show that major changes in synaptic structures occur subsequently to the sharp increase in synaptic transmission, and more importantly that the course of structural maturation of synaptic elements is impaired in GluK2⁻/⁻ mice. This study highlights how a mutation in a gene linked to intellectual disability in the human may lead to a transient reduction of synaptic strength during postnatal development, impacting on the proper formation of neural circuits linked to memory.

Audiological findings in 100 USH2 patients

Bilateral sensorineural hearing loss (HL), classically described as mild to severe with a typically down-sloping audiometric configuration, is the earliest symptom occurring in Usher syndrome type II (USH2). Audiological findings were analyzed in a total of 100 USH2 patients (92 families) divided into three groups according to the gene involved: 88 USH2A, 10 GPR98 and 2 DFNB31 patients. A fine analysis of audiograms was performed (pure tone average, degree of severity, configuration). The median age of HL diagnosis was 5 years (range 8 months-31 years) although the median age at USH2 diagnosis was 34.5 (range 8-76). Moderate HL was predominant (76%) and a gently down-sloping configuration characterized most audiograms (66%). No statistically significant difference was found between USH2A and GPR98 patients but a tendency was clearly noted for more GPR98 patients to present with severe hearing loss. It is not possible to predict the mutated gene from audiograms.

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

Curves+, a revised version of the Curves software for analyzing the conformation of nucleic acid structures, is now available as a web server. This version, which can be freely accessed at http://gbio-pbil.ibcp.fr/cgi/Curves_plus/, allows the user to upload a nucleic acid structure file, choose the nucleotides to be analyzed and after optionally setting a number of input variables, view the numerical and graphic results online or download files containing a set of helical, backbone and groove parameters that fully describe the structure. PDB format files are also provided for offline visualization of the helical axis and groove geometry.

Grid computing for improving conformational sampling in NMR structure calculation

MOTIVATION

Methods for automatic nuclear magnetic resonance (NMR) structure determination need to face a high level of ambiguity encountered in NMR spectra recorded by solid-state NMR and by solution NMR of partially unfolded proteins, leading to time-consuming calculations. The software package Ambiguous Restraints for Iterative Assignment (ARIA) allows for straightforward parallelization of the calculation, as the conformers can be generated in parallel on many nodes.

RESULTS

Due to its architecture, the adaptation of ARIA to grid computing can be easily achieved by using the middleware glite and JDL (Job Description Language) scripts. This adaptation makes it possible to address highly ambiguous datasets, because of the much larger conformational sampling that can be generated by use of the grid computational power.

AVAILABILITY

The version 2.3.1 of ARIA implemented on the grid is freely available from the ARIA web site: aria.pasteur.fr/downloads.

BioXSD: the common data-exchange format for everyday bioinformatics web services

Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types.

Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web.

Availability: The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community.

Contact:matus.kalas@bccs.uib.no; developers@bioxsd.org; support@bioxsd.org

Is marine mammal fat or fish intake most strongly associated with omega-3 blood levels among the Nunavik Inuit?

Here we determined the relationship between red blood cell (RBC) omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFAs) and usual dietary marine food product intake among 630 Nunavik Inuit adults. Marine food product intake was determined by a food frequency questionnaire (FFQ) and fatty acids were quantified in RBC membranes. Multiple linear regression was undertaken to determine the relationship between marine food product intake and RBC n-3 LC-PUFAs (dependent variable). Mean RBC n-3 LC-PUFA level was 9.16 ± 0.11% [SEM]. The highest correlations noted with RBC n-3 LC-PUFAs were for marine mammal fat (r(s)=0.41, P<0.0001) and fish (r(s)=0.35, P<0.0001). Age, total marine mammal fat and fish intakes were the variables that contributed the most to predicted RBC n-3 LC-PUFAs and explained 34%, 15% and 5%, respectively, of its variances. Our study indicates that marine mammal fat intake is more important than fish in accounting for RBC n-3 LC-PUFA levels among the Nunavik Inuit.

The EMBRACE web service collection

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions.

Impaired development of hippocampal mossy fibre synapses in mouse mutants for the presynaptic scaffold protein Bassoon

Bassoon, a protein highly concentrated at the synaptic active zone, is thought to participate in the organization of the cytomatrix at the site of neurotransmitter release. Bassoon is amongst the first proteins to accumulate at newly formed synaptic junctions, raising the question of the functional role of this protein in the early stages of synaptic development. Here we show that the course of synaptic maturation of hippocampal mossy fibre (MF) synapses (glutamatergic synapses with multiple release sites) is markedly altered during the first 2 weeks of postnatal development in mutant mice lacking the central region of Bassoon (Bsn(-/-) mice). At postnatal day 7 (P7), Bsn(-/-) mice display large amplitude MF-EPSCs with decreased paired pulse ratios, an abnormality which may be linked to deficits in the organization of the presynaptic active zone. Surprisingly, 1 week later, decreased MF-EPSCs amplitude is observed in Bsn(-/-) mice, consistent with the inactivation of a subset of synaptic release sites. Finally, at more mature states a decreased posttetanic potentiation is observed at MF-synapses. These results support the notion that Bassoon is important for organizing the presynaptic active zone during the postnatal maturation of glutamatergic synapses.

Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies

We use a physics-based approach termed ADAPT to analyse the sequence-specific interactions of three proteins which bind to DNA on the side of the minor groove. The analysis is able to estimate the binding energy for all potential sequences, overcoming the combinatorial problem via a divide-and-conquer approach which breaks the protein-DNA interface down into a series of overlapping oligomeric fragments. All possible base sequences are studied for each fragment. Energy minimisation with an all-atom representation and a conventional force field allows for conformational adaptation of the DNA and of the protein side chains for each new sequence. As a result, the analysis depends linearly on the length of the binding site and complexes as large as the nucleosome can be treated, although this requires access to grid computing facilities. The results on the three complexes studied are in good agreement with experiment. Although they all involve significant DNA deformation, it is found that this does not necessarily imply that the recognition will be dominated by the sequence-dependent mechanical properties of DNA.

PDB_REDO: automated re-refinement of X-ray structure models in the PDB

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

Risk and benefits from consuming salmon and trout: A Canadian perspective

Recent reports on the presence of persistent organic chemicals in wild and farmed salmon have left consumers and health professionals confused regarding the safety of regular fish consumption. The objectives of this study were (1) to compare concentrations of key contaminants and the essential nutrients omega-3 fatty acids between farmed and wild salmon and trout, and (2) to balance risks and benefits from regularly consuming these species. Concentrations of mercury, polychlorinated biphenyls, dioxins and furans as well as omega-3 fatty acids were determined in fillets from farmed salmon and trout bought in various markets located in Quebec, Canada, as well as in fillets from wild salmonids obtained from fishermen and various Canadian agencies. While differences were observed between market (farmed) and wild fish with regard to the concentrations of mercury and polychlorinated biphenyls, overall the concentrations of contaminants were low, such that the regular consumption of these fish would not cause tolerable daily intakes to be exceeded. Our results indicate that salmon and trout sold in Quebec markets, which as in markets located elsewhere in North America originate for the most part from Chilean farms, can be consumed regularly to achieve optimal nutritional benefits from omega-3 fatty acids, without incurring significant contaminant related health risks.