Abstract: Abstract Background Post-transplant diabetes is a frequent and serious complication of kidney transplantation. There is currently no treatment to prevent or delay the disease. Nevertheless, identification of risk factors make it possible to target a population at risk of developing de novo diabetes. We hypothesized that a short-term treatment with vildagliptin may prevent new onset diabetes after transplantation (NODAT) in high-risk patients. Methods/design This is a multicenter, double-blind, placebo-controlled randomized clinical trial. Patients undergoing first kidney transplantation will be included from ten French transplant centers. Included patients will be randomized (1:1) to receive either vildagliptin 100 or 50 mg/day (depending on glomerular filtration rate) during 2 months (the first dose being administered before entering the operating theatres) or placebo. Additional antidiabetic therapy could be administered according to glycemic control. The primary outcome is the proportion of diabetic patients 1 year after transplantation, defined as patients receiving a diabetic treatment, or having a fasting glucose above 7 mmol/l, and/or with an abnormal oral glucose tolerance test. Secondary outcomes include glycated hemoglobin, the occurrence of acute rejection, infection, graft loss and patient death at 3 months, 6 months, and 12 months after transplantation. Outcomes will be correlated to clinical and general characteristics of the patient, cardiovascular history, nephropathy, dialysis history, transplantation data, biological data, health-related quality of life, and the cost-effectiveness of prevention of diabetes with vildagliptin. Discussion We have scarce data on the pharmacological prevention of post-transplant diabetes. If our hypothesis is verified, our results will have a direct application in clinical practice and could limit diabetes-associated morbidity, reduce cardiovascular complications, increase quality of life of renal transplant patients, and consequently promote graft and patient survival. Our results may possibly serve for non-transplant patients carrying a high-risk of diabetes associated with other co-morbidities. Trial registration ClinicalTrials.gov, NCT02849899 . Registered on 8 February 2016.

PRODIG (Prevention of new onset diabetes after transplantation by a short term treatment of Vildagliptin in the early renal post-transplant period) study: study protocol for a randomized controlled study;E. Gaiffe;2019;Figshare


Abstract: Abstract Background Jasmonate (JA) signaling and functions have been established in rice development and response to a range of biotic or abiotic stress conditions. However, information on the molecular actors and mechanisms underlying turnover of the bioactive jasmonoyl-isoleucine (JA-Ile) is very limited in this plant species. Results Here we explored two gene families in rice in which some members were described previously in Arabidopsis to encode enzymes metabolizing JA-Ile hormone, namely cytochrome P450 of the CYP94 subfamily (CYP94, 20 members) and amidohydrolases (AH, 9 members). The CYP94D subclade, of unknown function, was most represented in the rice genome with about 10 genes. We used phylogeny and gene expression analysis to narrow the study to candidate members that could mediate JA-Ile catabolism upon leaf wounding used as mimic of insect chewing or seedling exposure to salt, two stresses triggering jasmonate metabolism and signaling. Both treatments induced specific transcriptional changes, along with accumulation of JA-Ile and a complex array of oxidized jasmonate catabolites, with some of these responses being abolished in the JASMONATE RESISTANT 1 (jar1) mutant. However, upon response to salt, a lower dependence on JAR1 was evidenced. Dynamics of CYP94B5, CYP94C2, CYP94C4 and AH7 transcripts matched best the accumulation of JA-Ile catabolites. To gain direct insight into JA-Ile metabolizing activities, recombinant expression of some selected genes was undertaken in yeast and bacteria. CYP94B5 was demonstrated to catalyze C12-hydroxylation of JA-Ile, whereas similarly to its Arabidopsis bi-functional homolog IAR3, AH8 performed cleavage of JA-Ile and auxin-alanine conjugates. Conclusions Our data shed light on two rice gene families encoding enzymes related to hormone homeostasis. Expression data along with JA profiling and functional analysis identifies likely actors of JA-Ile catabolism in rice seedlings. This knowledge will now enable to better understand the metabolic fate of JA-Ile and engineer optimized JA signaling under stress conditions.

Characterization of Jasmonoyl-Isoleucine (JA-Ile) Hormonal Catabolic Pathways in Rice upon Wounding and Salt Stress;Mohamed Hazman;2019;Figshare


Abstract: Abstract Background Myelin oligodendrocyte glycoprotein antibodies (MOG-Ab) are related to several acquired demyelinating syndromes in adults, but the therapeutic approach is currently unclear. We aimed to describe the response to different therapeutic strategies in adult patients with relapsing MOG-Ab-associated disease. Methods This is a retrospective study conducted in France and Spain including 125 relapsing MOG-Ab patients aged ≥ 18 years. First, we performed a survival analysis to investigate the relapse risk between treated and non-treated patients, performing a propensity score method based on the inverse probability of treatment weighting. Second, we assessed the annualised relapse rates (ARR), Expanded Disability Status Scale (EDSS) and visual acuity pre-treatment and on/end-treatment. Results Median age at onset was 34.1 years (range 18.0–67.1), the female to male ratio was 1.2:1, and 96% were Caucasian. At 5 years, 84% (95% confidence interval [CI], 77.1–89.8) patients relapsed. At the last follow-up, 66 (52.8%) received maintenance therapy. Patients initiating immunosuppressants (azathioprine, mycophenolate mophetil [MMF], rituximab) were at lower risk of new relapse in comparison to non-treated patients (HR, 0.41; 95CI%, 0.20–0.82; p = 0.011). Mean ARR (standard deviation) was reduced from 1.05(1.20) to 0.43(0.79) with azathioprine (n = 11; p = 0.041), from 1.20(1.11) to 0.23(0.60) with MMF (n = 11; p = 0.033), and from 1.08(0.98) to 0.43(0.89) with rituximab (n = 26; p = 0.012). Other immunosuppressants (methotrexate/mitoxantrone/cyclophosphamide; n = 5), or multiple sclerosis disease-modifying drugs (MS-DMD; n = 9), were not associated with significantly reduced ARR. Higher rates of freedom of EDSS progression were observed with azathioprine, MMF or rituximab. Conclusion In adults with relapsing MOG-Ab-associated disease, immunosuppressant therapy (azathioprine, MMF and rituximab) is associated with reduced risk of relapse and better disability outcomes. Such an effect was not found in the few patients treated with MS-DMD.

Evaluation of treatment response in adults with relapsing MOG-Ab-associated disease;Alvaro Cobo-Calvo;2019;Figshare


Abstract: Abstract Background Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF complex. Pathogenic variants in genes that encode epigenetic regulators have been associated with genome-wide changes in DNA methylation (DNAm) in affected individuals termed DNAm signatures. Methods Genome-wide DNAm was assessed in whole-blood samples from the individuals with pathogenic SMARCA2 variants and NCBRS diagnosis (n = 8) compared to neurotypical controls (n = 23) using the Illumina MethylationEPIC array. Differential methylated CpGs between groups (DNAm signature) were identified and used to generate a model enabling classification variants of uncertain significance (VUS; n = 9) in SMARCA2 as “pathogenic” or “benign”. A validation cohort of NCBRS cases (n = 8) and controls (n = 96) demonstrated 100% model sensitivity and specificity. Results We identified a DNAm signature of 429 differentially methylated CpG sites in individuals with NCBRS. The genes to which these CpG sites map are involved in cell differentiation, calcium signaling, and neuronal function consistent with NCBRS pathophysiology. DNAm model classifications of VUS were concordant with the clinical phenotype; those within the SMARCA2 ATPase/helicase domain classified as “pathogenic”. A patient with a mild neurodevelopmental NCBRS phenotype and a VUS distal to the ATPase/helicase domain did not score as pathogenic, clustering away from cases and controls. She demonstrated an intermediate DNAm profile consisting of one subset of signature CpGs with methylation levels characteristic of controls and another characteristic of NCBRS cases; each mapped to genes with ontologies consistent with the patient’s unique clinical presentation. Conclusions Here we find that a DNAm signature of SMARCA2 pathogenic variants in NCBRS maps to CpGs relevant to disorder pathophysiology, classifies VUS, and is sensitive to the position of the variant in SMARCA2. The patient with an intermediate model score demonstrating a unique genotype-epigenotype-phenotype correlation underscores the potential utility of this signature as a functionally relevant VUS classification system scalable beyond binary “benign” versus “pathogenic” scoring. This is a novel feature of DNAm signatures that could enable phenotypic predictions from genotype data. Our findings also demonstrate that DNAm signatures can be domain-specific, highlighting the precision with which they can reflect genotypic variation.

New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome;Eric Chater-Diehl;2019;Figshare


Abstract: Abstract Background Genetic polymorphisms are known to influence milk production and composition. However, the genomic mechanisms involved in the genetic regulation of milk component synthesis are not completely understood. MicroRNAs (miRNAs) regulate gene expression. Previous research suggests that the high developmental potential of the mammary gland may depend in part on a specific miRNA expression pattern. The objective of the present study was to compare the mammary gland miRNomes of two dairy cow breeds, Holstein and Montbéliarde, which have different mammogenic potentials that are related to differences in dairy performance. Results Milk, fat, protein, and lactose yields were lower in Montbéliarde cows than in Holstein cows. We detected 754 distinct miRNAs in the mammary glands of Holstein (n = 5) and Montbéliarde (n = 6) midlactating cows using RNA-Seq technology, among which 738 were known and 16 were predicted miRNAs. The 25 most abundant miRNAs accounted for 90.6% of the total reads. The comparison of their abundances in the mammary glands of Holstein versus Montbéliarde cows identified 22 differentially expressed miRNAs (Padj ≤ 0.05). Among them, 11 presented a fold change ≥2, and 2 (miR-100 and miR-146b) were highly expressed. Among the most abundant miRNAs, miR-186 is known to inhibit cell proliferation and epithelial-to-mesenchymal transition. Data mining showed that 17 differentially expressed miRNAs with more than 20 reads were involved in the regulation of mammary gland plasticity. Several of them may potentially target mRNAs involved in signaling pathways (such as mTOR) and lipid metabolism, thereby indicating that they could influence milk composition. Conclusion We found differences in the mammary gland miRNomes of two dairy cattle breeds. These differences suggest a potential role for miRNAs in mammary gland plasticity and milk component synthesis, both of which are related to milk production and composition. Further research is warranted on the genetic regulation of miRNAs and their role in milk synthesis.

Deep RNA-Seq reveals miRNome differences in mammary tissue of lactating Holstein and Montbéliarde cows;P. Billa;2019;Figshare


Abstract: Abstract Background Integrative and complementary health approaches (ICHA) are often pursued by patients facing chronic illnesses. Most of the studies that investigated the factors associated with ICHA consumption have considered that the propensity to use ICHA is a stable or fixed characteristic of an individual. However, people may prefer using ICHA in some situations and not in others, depending on the characteristics of the illness to face. Moreover, the attitude toward ICHA may differ within a single individual and between individuals so that ICHA can be used either in addition to (i.e., complementary attitude) or in place of (i.e., alternative attitude). The present study aimed at examining distinct patterns of attitudes toward ICHA in people hypothetically facing chronic illnesses that differed according to severity and clinical expression. Methods We conducted a web-based study including 1807 participants who were asked to imagine that they had a particular chronic illness based on clinical vignettes (mental illnesses: depression, schizophrenia; somatic illnesses: rheumatoid arthritis, multiple sclerosis). Participants were invited to rate their perceived distress and social stigma associated with each illness as well as its perceived treatability. They also rated their belief in treatment effectiveness, and their treatment preference. Four patterns of treatment choice were determined: strictly conventional, weak or strong complementary, and alternative. Bayesian methods were used for statistical analyses. Results ICHA were selected as complementary treatment option by more than 95% of people who hypothetically faced chronic illness. The complementary attitude towards ICHA (in addition to conventional treatment) was more frequent than the alternative one (in place of conventional treatment). Factors driving this preference included employment status, severity of illness, age and perceived distress, social stigma and treatability of the illness. When the label of illnesses was included in the vignettes, patterns of treatment preference were altered. Conclusions This study provides evidence that “medical pluralism” (i.e., the integration of ICHA with conventional treatment) is likely the norm for people facing both mental or somatic illness. However, our result must be interpreted with caution due to the virtual nature of this study. We suggest that taking attitudes toward ICHA into account is crucial for a better understanding of patients’ motivation to use ICHA.

Alternative or complementary attitudes toward alternative and complementary medicines;Fabrice Berna;2019;Figshare


Abstract: Foraging in seasonal environments can be cognitively challenging. Comparative studies have associated brain size with a frugivorous diet. We investigated how fruit distribution (where) and preference (what) affect foraging decisions in three semi-free ranging primate species with different degrees of frugivory: Macaca tonkeana (Nindiv = 5; Ntrials = 430), M. fascicularis (Nindiv = 3; Ntrials = 168) and Sapajus apella (Nindiv = 6; Ntrials = 288). We used 36 boxes fixed on trees and filled with highly and less preferred fruits with different (weekly) spatio-temporal distributions. Individuals were tested in two conditions: (1) same fruit provided concurrently in the same quantity but in a scattered and in a clumped distribution, (2) highly preferred fruit was scattered while the less preferred was clumped. Generally, primates preferred feeding first on the boxes of the clumped distribution in both conditions, with the more frugivorous species at a higher degree than the less frugivorous species in condition (1), but not (2). Therefore, what fruit was available changed the foraging decisions of the more frugivorous species who also engaged more in goal-directed travel. When feeding on preferred fruit, primates probably maximized foraging efficiency regardless of their degree of frugivory. Our findings emphasize that the food type and distribution may be a preponderant driver in cognitive evolution.

Supplementary material from "Where and what? Frugivory is associated with more efficient foraging in three semi-free ranging primate species";Cinzia Trapanese;2019;Figshare


Abstract: Abstract Background In mammals, the hibernating state is characterized by biochemical adjustments, which include metabolic rate depression and a shift in the primary fuel oxidized from carbohydrates to lipids. A number of studies of hibernating species report an upregulation of the levels and/or activity of lipid oxidizing enzymes in muscles during torpor, with a concomitant downregulation for glycolytic enzymes. However, other studies provide contrasting data about the regulation of fuel utilization in skeletal muscles during hibernation. Bears hibernate with only moderate hypothermia but with a drop in metabolic rate down to ~â  25% of basal metabolism. To gain insights into how fuel metabolism is regulated in hibernating bear skeletal muscles, we examined the vastus lateralis proteome and other changes elicited in brown bears during hibernation. Results We show that bear muscle metabolic reorganization is in line with a suppression of ATP turnover. Regulation of muscle enzyme expression and activity, as well as of circulating metabolite profiles, highlighted a preference for lipid substrates during hibernation, although the data suggested that muscular lipid oxidation levels decreased due to metabolic rate depression. Our data also supported maintenance of muscle glycolysis that could be fuelled from liver gluconeogenesis and mobilization of muscle glycogen stores. During hibernation, our data also suggest that carbohydrate metabolism in bear muscle, as well as protein sparing, could be controlled, in part, by actions of n-3 polyunsaturated fatty acids like docosahexaenoic acid. Conclusions Our work shows that molecular mechanisms in hibernating bear skeletal muscle, which appear consistent with a hypometabolic state, likely contribute to energy and protein savings. Maintenance of glycolysis could help to sustain muscle functionality for situations such as an unexpected exit from hibernation that would require a rapid increase in ATP production for muscle contraction. The molecular data we report here for skeletal muscles of bears hibernating at near normal body temperature represent a signature of muscle preservation despite atrophying conditions.

Metabolic reprogramming involving glycolysis in the hibernating brown bear skeletal muscle;Blandine Chazarin;2019;Figshare


Abstract: Abstract Background The Integrated Disease Surveillance and Response (IDSR) strategy implemented by the World Health Organization (WHO) in Africa has produced a large amount of data on participating countries, and in particular on the Democratic Republic of Congo (DRC). These data are increasingly considered as unevaluable and, therefore, as requiring a rigorous process of validation before they can be used for research or public health purposes. The aim of this study was to propose a method to assess the level of adequacy of IDSR morbidity data in reflecting actual morbidity. Methods A systematic search of English- and French-language articles was performed in Scopus, Medline, Science Direct, Springer Link, Cochrane, Cairn, Persée, and Erudit databases. Other types of documents were identified through manual searches. Selected articles focused on the determinants of the discrepancies (differences) between reported morbidity and actual morbidity. An adequacy score was constructed using some of the identified determinants. This score was applied to the 15 weekly reported diseases monitored by IDSR surveillance in the DRC. A classification was established using the Jenks method and a sensitivity analysis was performed. Twenty-three classes of determinants were identified in 35 IDSR technical guides and reports of outbreak investigations and in 71 out of 2254 researched articles. For each of the 15 weekly reported diseases, the SIA was composed of 12 items grouped in 6 dimensions. Results The SIA classified the 15 weekly reported diseases into 3 categories or types: high score or good adequacy (value > = 14), moderate score or fair adequacy (value > = 8 and

The score of integrated disease surveillance and response adequacy (SIA): a pragmatic score for comparing weekly reported diseases based on a systematic review;Bien-Aimé Mandja;2019;Figshare


Abstract: Table S12. List of human naĂŻve CD8 T cell interactions called by ChiCMaxima from three CHi-C replicates. (XLSX 2644 kb)

Additional file 13: of ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Table S5. List of human erythroblast interactions called by ChiCMaxima from three CHi-C replicates. (XLSX 2329 kb)

Additional file 6: of ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Table S8. List of human M2 macrophage interactions called by ChiCMaxima from three CHi-C replicates. (XLSX 2433 kb)

Additional file 9: of ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Table S9. List of human megakaryocyte interactions called by ChiCMaxima from four CHi-C replicates. (XLSX 2274 kb)

Additional file 10: of ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Table S10. List of human monocyte interactions called by ChiCMaxima from three CHi-C replicates. (XLSX 2381 kb)

Additional file 11: of ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Table S11. List of human naĂŻve CD4 T cell interactions called by ChiCMaxima from four CHi-C replicates. (XLSX 2389 kb)

Additional file 12: of ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Table S7. List of human M1 macrophage interactions called by ChiCMaxima from three CHi-C replicates. (XLSX 2503 kb)

Additional file 8: of ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Table S13. List of human neutrophil interactions called by ChiCMaxima from three CHi-C replicates. (XLSX 1968 kb)

Additional file 14: of ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Abstract Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin loop detection is challenging because existing Hi-C/4C-like tools, which make different assumptions about the technical biases presented, are often unsuitable. We describe a new approach, ChiCMaxima, which uses local maxima combined with limited filtering to detect DNA looping interactions, integrating information from biological replicates. ChiCMaxima shows more stringency and robustness compared to previously developed tools. The tool includes a GUI browser for flexible visualization of CHi-C profiles alongside epigenomic tracks.

ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Table S1. List of mES interactions called by ChiCMaxima from two CHi-C replicates. (XLSX 1734 kb)

Additional file 4: of ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Table S4. List of mES interactions called by ChiCMaxima from two HiCap replicates. (XLSX 1166 kb)

Additional file 5: of ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Table S6. List of human M0 macrophage interactions called by ChiCMaxima from three CHi-C replicates. (XLSX 2738 kb)

Additional file 7: of ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C;Yousra Ben Zouari;2019;Figshare


Abstract: Abstract The inability of the yeast Saccharomyces cerevisiae to produce ethanol from xylose has hampered the biofuel production from lignocellulosic biomass. However, prior studies reveal that functional expression of xylose isomerase (XI) from Burkholderia cenocepacia (XylABc) in S. cerevisiae has remarkably improved xylose consumption and ethanol productivity. Yet, little is known about kinetic and structural properties of this enzyme. Hereby, a purified recombinant XylA was assayed in vitro, showing optimal enzyme activity at 37Â Â°C and pH 7.2. The Km of XylA for d-xylose was at least threefold lower than the Km results for any XI published to date (e.g. XylA from Piromyces sp.). In addition, oligomerization behavior as a tetramer was observed for XylA in solution. Functional and structural comparative analyses amongst three microbial XIs were further performed as theoretical models, showing that xylose orientation at the active site was highly conserved among the XIs. Mg2+ ions anchor the sugar and guide its pyranoside oxygen towards a histidine residue present at the active site, allowing an acidâ  base reaction, linearizing xylose. Electrostatic surface analyses showed that small variations in the net charge distribution and dipole moment could directly affect the way the substrate interacts with the protein, thus altering its kinetic properties. Accordingly, in silico modeling suggested the tetramer may be the major functional form. These analyses and the resulting model promote a better understanding of this protein family and pave the way to further protein engineering and application of XylA in the ethanol industry.

Understanding xylose isomerase from Burkholderia cenocepacia: insights into structure and functionality for ethanol production;Igor Vieira;2019;Figshare


Abstract: Additional file 2. Additional tables.

MOESM2 of Understanding xylose isomerase from Burkholderia cenocepacia: insights into structure and functionality for ethanol production;Igor Vieira;2019;Figshare


Abstract: Abstract Background The oleaginous yeast Yarrowia lipolytica is an organism of choice for the tailored production of various compounds such as biofuels or biopolymers. When properly engineered, it is capable of producing medium-chain-length polyhydroxyalkanoate (mcl-PHA), a biobased and biodegradable polymer that can be used as bioplastics or biopolymers for environmental and biomedical applications. Results This study describes the bioproduction and the main properties of two different mcl-PHA polymers. We generated by metabolic engineering, strains of Y. lipolytica capable of accumulating more than 25% (g/g) of mcl-PHA polymers. Depending of the strain genetic background and the culture conditions, we produced (i) a mcl-PHA homopolymer of 3-hydroxydodecanoic acids, with a mass-average molar mass (Mw) of 316,000 g/mol, showing soft thermoplastic properties with potential applications in packaging and (ii) a mcl-PHA copolymer made of 3-hydroxyoctanoic (3HO), decanoic (3HD), dodecanoic (3HDD) and tetradecanoic (3TD) acids with a Mw of 128,000 g/mol, behaving like a thermoplastic elastomer with potential applications in biomedical material. Conclusion The ability to engineer Y. lipolytica to produce tailored PHAs together with the range of possible applications regarding their biophysical and mechanical properties opens new perspectives in the field of PHA bioproduction.

Production and characterization of two medium-chain-length polydroxyalkanoates by engineered strains of Yarrowia lipolytica;Coraline Rigouin;2019;Figshare


Abstract: Abstract Background Rare diseases affecting the teeth, the oral cavity and the face are numerous, each of them present specific characteristics, and is a life-long condition. The aim of the study was to assess the association between Oral health-related quality of life (OHRQoL), and demographic characteristics, clinical and dental factors, and psycho-social characteristics to investigate that oral symptoms are not the main factors underlying a decrease in OHRQoL. Material and methods We conducted a national cohort study in French centres for rare diseases (RD) specialized in orofacial diseases. The inclusion criteria were: to have received care in RD centres over the last 5 years (2012–2017) and to have been between 6 and 17 years of age on September 1, 2017. Patients were invited to answer a questionnaire composed of socio-demographic, clinical and dental questions, psychosocial questions and then fill in the Child-OIDP Index. At the end of the questionnaire, a free space was left for the patient to add a verbatim comment to provide qualitative data. Thematic analysis was used to analyze the verbatim answers. Results Complete data were available for 110 patients. The sample included 44.5% boys and 55.5% girls. Ages ranged from 6 to 17 years old and 68.2% were between 6 to 12 years old and 31.8% were between 13 and 17 years old. Factor associated with a lower OHRQoL were: being a girl (p = 0.03), renouncement to dental care for financial reasons (p = 0.01), having syndromic disease (p = 0.01), having a problem with tooth shape and color (p = 0.03), feeling isolated, alone and different from other children (p = 0.003 and p = 0.02). Qualitative analysis highlighted very little recourse to psychological care and patients reported great anxiety and fear about the future. Conclusion OHRQoL of children suffering from these diseases is impaired, especially from the psychosocial point of view but also from that of the course of treatment and access to care. There is a need to improve the legibility of care pathways and the financial coverage of treatments.

Oral health related quality of life of children and adolescents affected by rare orofacial diseases: a questionnaire-based cohort study;Lisa Friedlander;2019;Figshare


Abstract: Abstract Several morphological phenotypes have been associated to RYR1-recessive myopathies. We recharacterized the RYR1-recessive morphological spectrum by a large monocentric study performed on 54 muscle biopsies from a large cohort of 48 genetically confirmed patients, using histoenzymology, immunohistochemistry, and ultrastructural studies. We also analysed the level of RyR1 expression in patients’ muscle biopsies. We defined “dusty cores” the irregular areas of myofibrillar disorganisation characterised by a reddish-purple granular material deposition with uneven oxidative stain and devoid of ATPase activity, which represent the characteristic lesion in muscle biopsy in 54% of patients. We named Dusty Core Disease (DuCD) the corresponding entity of congenital myopathy. Dusty cores had peculiar histological and ultrastructural characteristics compared to the other core diseases. DuCD muscle biopsies also showed nuclear centralization and type1 fibre predominance. Dusty cores were not observed in other core myopathies and centronuclear myopathies. The other morphological groups in our cohort of patients were: Central Core (CCD: 21%), Core-Rod (C&R:15%) and Type1 predominance “plus” (T1P+:10%). DuCD group was associated to an earlier disease onset, a more severe clinical phenotype and a lowest level of RyR1 expression in muscle, compared to the other groups. Variants located in the bridge solenoid and the pore domains were more frequent in DuCD patients. In conclusion, DuCD is the most frequent histopathological presentation of RYR1-recessive myopathies. Dusty cores represent the unifying morphological lesion among the DuCD pathology spectrum and are the morphological hallmark for the recessive form of disease.

Earth and related environmental sciences

‘Dusty core disease’ (DuCD): expanding morphological spectrum of RYR1 recessive myopathies;Matteo Garibaldi;2019;Figshare


Abstract: Abstract Background The optical accessibility of the eye and technological advances in ophthalmic diagnostics have put ophthalmology at the forefront of data-driven medicine. The focus of this study is rare eye disorders, a group of conditions whose clinical heterogeneity and geographic dispersion make data-driven, evidence-based practice particularly challenging. Inter-institutional collaboration and information sharing is crucial but the lack of standardised terminology poses an important barrier. Ontologies are computational tools that include sets of vocabulary terms arranged in hierarchical structures. They can be used to provide robust terminology standards and to enhance data interoperability. Here, we discuss the development of the ophthalmology-related component of two well-established biomedical ontologies, the Human Phenotype Ontology (HPO; includes signs, symptoms and investigation findings) and the Orphanet Rare Disease Ontology (ORDO; includes rare disease nomenclature/nosology). Methods A variety of approaches were used including automated matching to existing resources and extensive manual curation. To achieve the latter, a study group including clinicians, patient representatives and ontology developers from 17 countries was formed. A broad range of terms was discussed and validated during a dedicated workshop attended by 60 members of the group. Results A comprehensive, structured and well-defined set of terms has been agreed on including 1106 terms relating to ocular phenotypes (HPO) and 1202 terms relating to rare eye disease nomenclature (ORDO). These terms and their relevant annotations can be accessed in http://www.human-phenotype-ontology.org/ and http://www.orpha.net/ ; comments, corrections, suggestions and requests for new terms can be made through these websites. This is an ongoing, community-driven endeavour and both HPO and ORDO are regularly updated. Conclusions To our knowledge, this is the first effort of such scale to provide terminology standards for the rare eye disease community. We hope that this work will not only improve coding and standardise information exchange in clinical care and research, but also it will catalyse the transition to an evidence-based precision ophthalmology paradigm.

An ontological foundation for ocular phenotypes and rare eye diseases;Panagiotis Sergouniotis;2019;Figshare


Abstract: Abstract Background Management of spontaneous pneumothorax (SP) is still subject to debate. Although encouraging results of recent studies about outpatient management with chest drains fitted with a one-way valve, no data exist concerning application of this strategy in real life conditions. We assessed how SP are managed in Emergency departments (EDs), in particular the role of outpatient management, the types of interventions and the specialty of the physicians who perform these interventions. Methods From June 2009 to May 2013, all cases of spontaneous primary (PSP) and spontaneous secondary pneumothorax (SSP) from EDs of 14 hospitals in France were retrospectively included. First line treatment (observation, aspiration, thoracic drainage or surgery), type of management (admitted, discharged to home directly from the ED, outpatient management) and the specialty of the physicians were collected from the medical files of the ED. Results Among 1868 SP included, an outpatient management strategy was chosen in 179 PSP (10%) and 38 SSP (2%), mostly when no intervention was performed. Only 25 PSP (1%) were treated by aspiration and discharged to home after ED admission. Observation was the chosen strategy for 985 patients (53%). In 883 patients with an intervention (47%), it was performed by emergency physicians in 71% of cases and thoracic drainage was the most frequent choice (670 patients, 76%). Conclusions Our study showed the low level of implementation of outpatient management for PS in France. Despite encouraging results of studies concerning outpatient management, chest tube drainage and hospitalization remain preponderant in the treatment of SP.

How spontaneous pneumothorax is managed in emergency departments: a French multicentre descriptive study;S. Kepka;2019;Figshare


Abstract: Abstract Background Down syndrome (DS) is the most common form of viable chromosomal abnormality. DS is associated with recurrent infections, auto-immunity and malignancies in children. Little is known about immunity and infections in DS at adulthood. Methods We studied two separate group of adults (> 18 years old) with DS in a single referral tertiary center (Strasbourg University Hospital). The first group included 37 ambulatory DS patients between November 2014 and May 2017. We analyzed exhaustive serological and immunobiological parameters, at one point, together with the prevalence of infections, autoimmune manifestations and malignancies. The second group included 64 hospitalized patients (138 stays) in the same center, between January 2005 and December 2016. Results One hundred and one adult patients with DS were included. Unlike children and despite a global lymphopenia, adults with DS underwent few infections in our ambulatory group. They did not experience any malignancy and, apart from hypothyroidism, they presented only occasional autoimmune manifestations. Hospitalized DS patients were older than ambulatory ones (median age 47 years (18–73) vs. 27 (18–52), p

Infection risk among adults with down syndrome: a two group series of 101 patients in a tertiary center;Aurélien Guffroy;2019;Figshare


Abstract: Abstract Background Many infectious pathogens can be transmitted from animals to humans and vice versa, or by animals (especially arthropods) to humans. Such diseases are called zoonotic and/or vector-borne diseases. To control or prevent them, it is often recommended to target population reduction of host or vector species, through preventive culling or insecticide use for example. But these types of destructive interventions have shown several limits altering their efficiency, including acquired resistance of arthropods to insecticides, unpredicted change in the ecology of host populations, unexpected negative functional consequences on ecosystems, as well as economic embrittlement when livestock is concerned. An alternative pathway of action would be to rely on the functioning of ecosystems, and on their careful management, to regulate diseases and thus reduce their impact on human health. In this perspective, a thorough evaluation of the conditions that can potentially promote such a positive regulation of infectious pathogens by ecosystems, and their efficiency, is needed. Here, we present the protocol of a systematic review that will evaluate the scientific evidence existing on potential links between ecosystem components or functions and 14 vector-borne and zoonotic diseases impacting human health. Methods We will search for studies that tested the effect of changes in (i) biological communities, and (ii) habitats and landscapes, on diseases. Scientific literature from 5 publication databases will be screened in a 3-rounds process: title, abstract and full-text screening. At each stage, articles will be either rejected or kept for the next round, depending on whether they fall in the exclusion or inclusion criteria. We will present results in two parts: a systematic map and a systematic review. The systematic map will present, for the 14 diseases, the number of publications, their geographical distribution, the type of ecosystem component/function they studied, as well as the host(s) in which epidemiological measurements have been performed. From this systematic map, we will identify groups of articles that allow for critical appraisal, i.e. groups of articles that studied the effect of the same ecosystem component/function on the same disease. Only those articles will be included in the systematic review. The validity of these articles will be assessed by critical appraisal and presented as a narrative synthesis with confidence levels.

What is the evidence that ecosystem components or functions have an impact on infectious diseases? A systematic review protocol;Léa Lugassy;2019;Figshare


Abstract: Abstract Background Individual bees exhibit complex movement patterns to efficiently exploit small areas within larger plant populations. How such individual spatial behaviours scale up to the collective level, when several foragers visit a common area, has remained challenging to investigate, both because of the low resolution of field movement data and the limited power of the statistical descriptors to analyse them. To tackle these issues we video recorded all flower visits (N = 6205), and every interaction on flowers (N = 628), involving foragers from a bumblebee (Bombus terrestris) colony in a large outdoor flight cage (880 m2), containing ten artificial flowers, collected on five consecutive days, and analysed bee movements using networks statistics. Results Bee-flower visitation networks were significantly more modular than expected by chance, indicating that foragers minimized overlaps in their patterns of flower visits. Resource partitioning emerged from differences in foraging experience among bees, and from outcomes of their interactions on flowers. Less experienced foragers showed lower activity and were more faithful to some flowers, whereas more experienced foragers explored the flower array more extensively. Furthermore, bees avoided returning to flowers from which they had recently been displaced by a nestmate, suggesting that bees integrate memories of past interactions into their foraging decisions. Conclusion Our observations, under high levels of competition in a flight cage, suggest that the continuous turnover of foragers observed in colonies can led to efficient resource partitioning among bees in natural conditions.

A spatial network analysis of resource partitioning between bumblebees foraging on artificial flowers in a flight cage;Cristian Pasquaretta;2019;Figshare


Abstract: Abstract Background Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) is an autoimmune-mediated inflammatory disease of the peripheral nervous system characterized by a response directed against certain myelin proteins and for which therapies are limited. Previous studies have suggested a beneficial role of FTY720, a sphingosine 1-phosphate (S1P) receptor agonist, known to deplete lymphocytes from the peripheral blood by sequestering them into lymph nodes, in the treatment of experimental autoimmune neuritis (EAN). Therefore, we investigated whether FTY720 is also beneficial in chronic experimental autoimmune neuritis (c-EAN), a recently developed rat model mimicking human CIDP. Methods c-EAN was induced in Lewis rats by immunization with S-palm P0(180–199) peptide. Rats were treated with FTY720 (1 mg/kg) or vehicle intraperitoneally once daily from the onset of clinical signs for 18 days; clinical signs were assessed daily until 60 days post-immunization (dpi). Electrophysiological and histological features were examined at different time points. We also evaluated the serum levels of different pro- and anti-inflammatory cytokines by ELISA or flow cytometry at 18, 40, and 60 dpi. Results Our data demonstrate that FTY720 decreased the severity and abolished the chronicity of the disease in c-EAN rats. Therapeutic FTY720 treatment reversed electrophysiological and histological anomalies, suggesting that myelinated fibers were subsequently preserved, it inhibited macrophage and IL-17+ cell infiltration in PNS, and it significantly reduced circulating pro-inflammatory cytokines. Conclusions FTY720 treatment has beneficial effects on c-EAN, a new animal model mimicking human CIDP. We have shown that FTY720 is an effective immunomodulatory agent, improving the disease course of c-EAN, preserving the myelinated fibers, attenuating the axonal degeneration, and decreasing the number of infiltrated inflammatory cells in peripheral nerves. These data confirm the interest of testing FTY720 or molecules targeting S1P in human peripheral neuropathies.

FTY720 controls disease severity and attenuates sciatic nerve damage in chronic experimental autoimmune neuritis;Laurent Kremer;2019;Figshare


Abstract: Abstract Background HIV and other sexually transmitted infections remain a burden on men who have sex with men in the era of effective combination antiretroviral therapy. New prevention efforts are therefore needed. One of these approaches is the current country-wide free condom distribution at gay bars with darkrooms and gay saunas in the Netherlands. This study assessed the effects of free condom distribution on incidence and burden of disease of HIV and other sexually transmitted infections. Methods A static model was constructed to calculate the impact of free condom distribution on HIV, hepatitis C, chlamydia, gonorrhoea, and syphilis among men who have sex with men visiting these venues. Outcomes included new infections averted and disability-adjusted life years averted. Scenario studies were performed to predict the effects of a further increase of condom use, condom effectiveness and coverage. Lastly, cost-effectiveness and sensitivity analyses were performed. Results Our model showed that condom use at public sex venues increased after the intervention. Annual incidence risk decreased, ranging from 5.73% for gonorrhoea to 7.62% for HIV. The annual number of new infections averted was largest for chlamydia and gonorrhoea (261 and 394 infections, respectively), but 42 new HIV infections were averted as well. In scenarios where condom use and condom effectiveness were further increased, the number of infections reduced more extensively. Over 99% of the decrease in burden of disease was due to HIV. The intervention was cost-effective and cost-saving (for every â Ź1 spent on condom distribution, â Ź5.51 was saved) and remained this in all sensitivity analyses. Conclusions Free condoms at public sex venues could reduce the transmission of HIV and other sexually transmitted infections. Condom distribution is an affordable and easily implemented intervention that could reduce the burden of disease in men who have sex with men substantially.

The effects of free condom distribution on HIV and other sexually transmitted infections in men who have sex with men;Reinier Bom;2019;Figshare


Abstract: Polarization-resolved third-harmonic generation (P-THG) is a sensitive probe of materials anisotropy and molecular ordering. Despite its promises, this property has hardly been used in biological tissues up until now, due to the lack of imaging schemes with suitable temporal resolution. We report here on the development of a fast P-THG microscope where excitation polarization is switched within microseconds between line scans using an electro-optic modulator, associated with Fourier-based analysis. We demonstrate several novel measurements enabled by this approach: probing molecular order in deforming lipid structures undergoing phase transition; revealing crystallinity of flowing particles in the zebrafish embryo’s inner ear; detecting birefringent microstructures in live organisms. These results establish that fast P-THG is ideally suited for probing lipid organization and mineralization in dynamic biological environments.

High-speed polarization-resolved third-harmonic microscopy;Joséphine Morizet;2019;Figshare


Abstract: Abstract Docking is commonly used in drug discovery to predict how ligand binds to protein target. Best programs are generally able to generate a correct solution, yet often fail to identify it. In the case of drug-like molecules, the correct and incorrect poses can be sorted by similarity to the crystallographic structure of the protein in complex with reference ligands. Fragments are particularly sensitive to scoring problems because they are weak ligands which form few interactions with protein. In the present study, we assessed the utility of binding mode information in fragment pose prediction. We compared three approaches: interaction fingerprints, 3D-matching of interaction patterns and 3D-matching of shapes. We prepared a test set composed of high-quality structures of the Protein Data Bank. We generated and evaluated the docking poses of 586 fragment/protein complexes. We observed that the best approach is twice as accurate as the native scoring function, and that post-processing is less effective for smaller fragments. Interestingly, fragments and drug-like molecules both proved to be useful references. In the discussion, we suggest the best conditions for a successful pose prediction with the three approaches.

Binding mode information improves fragment docking;CĂŠlien Jacquemard;2019;Figshare


Abstract: Abstract Background Emergency start (ES) of dialysis has been associated with worse outcome, but remains poorly documented. This study aims to compare the profile and outcome of a large cohort of patients starting dialysis as an emergency or as a planned step in France. Methods Data on all patients aged 18 years or older who started dialysis in mainland France in 2012 or in 2006 were collected from the Renal Epidemiology and Information Network and compared, depending on the dialysis initiation condition: ES or Planned Start (PS). ES was defined as a first dialysis within 24 h after a nephrology visit due to a life-threatening event. Three-year survival were compared, and a multivariate model was performed after multiple imputation of missing data, to determine the parameters independently associated with three-year survival. Results In 2012, 30.3% of all included patients (n = 8839) had ES. Comorbidities were more frequent in the ES than PS group (≥ 2 cardiovascular diseases: 39.2% vs 28.8%, p < 0.001). ES was independently associated with worse three-year survival (57% vs. 68.2%, p = 0.029, HR 1.10, 95% CI 1.01–1.19) in multivariate analysis. Among ES group, a large part had a consistent previous follow-up: 36.4% of them had ≥3 nephrology consultations in the previous year. This subgroup of patients had a particularly high comorbidity burden. ES rate was stable between 2006 and 2012, but some proactive regions succeeded in reducing markedly the ES rate. Conclusion ES remains frequent and is independently associated with worse three-year survival, demonstrating that ES deleterious impact is never overcome. This study shows that a large part of patients with ES had a previous follow-up, but high comorbidity burden that could favor acute decompensation with life-threatening conditions before uremic symptoms appearance. This suggests the need of closer end-stage renal disease follow-up or early dialysis initiation in these high-risk patients.

Deleterious effects of dialysis emergency start, insights from the French REIN registry;Michel Alain;2018;Figshare


Abstract: Abstract Background Patients liberated from invasive mechanical ventilation are at risk of extubation failure, including inability to breathe without a tracheal tube (airway failure) or without mechanical ventilation (non-airway failure). We sought to identify respective risk factors for airway failure and non-airway failure following extubation. Methods The primary endpoint of this prospective, observational, multicenter study in 26 intensive care units was extubation failure, defined as need for reintubation within 48 h following extubation. A multinomial logistic regression model was used to identify risk factors for airway failure and non-airway failure. Results Between 1 December 2013 and 1 May 2015, 1514 patients undergoing extubation were enrolled. The extubation-failure rate was 10.4% (157/1514), including 70/157 (45%) airway failures, 78/157 (50%) non-airway failures, and 9/157 (5%) mixed airway and non-airway failures. By multivariable analysis, risk factors for extubation failure were either common to airway failure and non-airway failure: intubation for coma (OR 4.979 (2.797–8.864), P  8 days (OR 1.956 (1.087–3.518), P = 0.025), copious secretions (OR 4.066 (2.268–7.292), P

Risk factors and outcomes for airway failure versus non-airway failure in the intensive care unit: a multicenter observational study of 1514 extubation procedures;Samir Jaber;2018;Figshare


Abstract: Abstract Background Niemann-Pick disease type C (NP-C) is a neurodegenerative lysosomal lipid storage disease caused by autosomal recessive mutations in the NPC1 or NPC2 genes. The clinical presentation and evolution of NP-C and the effect of miglustat treatment are described in the largest cohort of patients with adolescent/adult-onset NP-C studied to date. Methods Observational study based on clinical chart data from adult patients with NP-C (> 18 year old) diagnosed in France between 1990 and 2015. Retrospective data from patients at diagnosis, onset of miglustat therapy (if applicable), and last follow up were analysed. Results In France, patients with an adolescent-adult neurological form constituted approximately 25% of all NP-C cases diagnosed during the study period. Forty-seven patients (46 with NP-C1 and one with NP-C2; 53% female) were included. Mean ± SD (range) ages at neurological onset and diagnosis were 23.9 ± 12.5 (8–56) years and 34 ± 13.5 (15–65) years, respectively. At presentation, patients mainly had 1) impaired gait due to cerebellar ataxia and/or dystonia, 2) and/or cognitive/behavioural manifestations, 3) and/or psychotic signs. Initially, almost half of patients had only one of the above three neuro-psychiatric manifestations. Vertical supranuclear gaze palsy, usually occurring without patient complaint, was only detected on careful clinical examination and was recorded in most patients (93%) at the time of diagnosis, several years after neurological onset. Thirty-seven patients (79%) received miglustat, among whom seventeen (46%) continued beyond 2 years (at last follow up) to a maximum of 9.8 years. Eight patients (22%) discontinued treatment early due to side effects (n = 3) or perceived lack of efficacy (n = 5).Miglustat treatment duration correlated significantly with reduced neurological worsening (p

Adult Niemann-Pick disease type C in France: clinical phenotypes and long-term miglustat treatment effect;Yann Nadjar;2018;Figshare


Abstract: Abstract Background Prenatal exposure to outdoor air pollution has been shown to have health effects in many studies; low birth weight, preterm delivery, small for gestational age, and stillbirth are the most often cited. However, exposure of pregnant women is difficult to quantify, especially with regard to their mobility, which is rarely taken into account in epidemiological studies. This study aimed to assess the impact of mobility of pregnant women living in Paris, France, on their exposure estimates to nitrogen dioxide (NO2). Methods A total of 486 pregnant women were recruited in 5 maternity hospitals in Paris between January and April 2016. A questionnaire was used to collect mothers’ characteristics (demography, education, etc.) and to assess their daily mobility during pregnancy (time spent at work, commuting time and mode used to move from residential to occupational places). Daily NO2 concentrations were estimated based on the combination of annual average concentrations modeled at the census block scale and daily concentrations measured from fixed monitoring stations. Different models were used to compare the exposure of pregnant women in residential and occupational places, also taking into account travel time and travel mode. The socioeconomic profile of the census blocks was characterized using a multi-component index. Results During the first trimester of pregnancy, women living in the least deprived census blocks were exposed to higher concentrations of NO2 than those living in the most deprived ones. Occupational mobility had a small impact on exposure levels (average increase after taking account of mobility: + 0.52 μg/m3) which was not related to the socioeconomic profile of the women. The commuting mode made a greater difference (+ 1.46 μg/m3 on average), in particular among women living in the most deprived census blocks. Conclusions Our study illustrates that air pollution exposure can be underestimated when ignoring occupational mobility and commuting mode of pregnant women. This effect might be differential according to the neighborhood deprivation profile.

Does residential mobility during pregnancy induce exposure misclassification for air pollution?;Olivier Blanchard;2018;Figshare


Abstract: While previous studies have evaluated the change in stability for the addition or removal of individual species from trophic food chains and food webs, we know of no study that presents a general theory for how stability changes with the addition or removal of trophic levels. In this study, we present a simple model of a linear food chain and systematically evaluate how stability—measured as invariability—changes with the addition or removal of trophic levels. We identify the presence of trophic cascades in the stability of species. Owing to top-down control by predation and bottom-up regulation by prey, we find that stability of a species is highest when it is at the top of the food chain and lowest when it is just under the top of the food chain. Thus, stability shows patterns identical to those of mean biomass with the addition or removal of trophic levels in food chains. Our results provide a baseline towards a general theory of the effect of adding or removing trophic levels on stability, which can be used to inform empirical studies.

Supplementary material from "Stability trophic cascades in food chains";David W. Shanafelt;2018;Figshare


Abstract: Abstract Background Despite advances in immunosuppressive therapy, kidney graft survival has failed to improve during the last decades. Ischemia/reperfusion injury (IRI) is one of the main pathophysiological mechanisms underlying delayed graft function, which is associated with poor long-term graft survival. Due to organ shortage, the proportion of grafts from expanded criteria donors (ECDs) is ever growing. These grafts may particularly benefit from IRI prevention. In preclinical models, mineralocorticoid receptor antagonists (MRAs) have been shown to efficiently prevent IRI. This study aims to assess the effect of MRA administration in the early phase of kidney transplantation (KT) among recipients of ECD grafts on mid-term graft function. Methods/design This is a multicenter, double-blind, placebo-controlled, randomized clinical trial. Patients on hemodialysis and undergoing a single or a dual KT from an ECD will be eligible for inclusion. We plan to randomize 132 patients. Included patients will be randomized (1:1) to receive either eplerenone 25 mg every 12 h during 4 days (the first dose being administered just prior to KT) or placebo. The primary outcome is graft function at 3 months, assessed by glomerular filtration rate (GFR, in mL/min/1.73m2) measured using iohexol clearance. Secondary outcomes include (1) proportion of patients with either dialysis dependency or a GFR

EPURE Transplant (Eplerenone in Patients Undergoing Renal Transplant) study: study protocol for a randomized controlled trial;Sophie Girerd;2018;Figshare


Abstract: Abstract Background Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) are small hematophagous insects responsible for the transmission of bluetongue virus, Schmallenberg virus and African horse sickness virus to wild and domestic ruminants and equids. Outbreaks of these viruses have caused economic damage within the European Union. The spatio-temporal distribution of biting midges is a key factor in identifying areas with the potential for disease spread. The aim of this study was to identify and map areas of neglectable adult activity for each month in an average year. Average monthly risk maps can be used as a tool when allocating resources for surveillance and control programs within Europe. Methods We modelled the occurrence of C. imicola and the Obsoletus and Pulicaris ensembles using existing entomological surveillance data from Spain, France, Germany, Switzerland, Austria, Denmark, Sweden, Norway and Poland. The monthly probability of each vector species and ensembles being present in Europe based on climatic and environmental input variables was estimated with the machine learning technique Random Forest. Subsequently, the monthly probability was classified into three classes: Absence, Presence and Uncertain status. These three classes are useful for mapping areas of no risk, areas of high-risk targeted for animal movement restrictions, and areas with an uncertain status that need active entomological surveillance to determine whether or not vectors are present. Results The distribution of Culicoides species ensembles were in agreement with their previously reported distribution in Europe. The Random Forest models were very accurate in predicting the probability of presence for C. imicola (mean AUC = 0.95), less accurate for the Obsoletus ensemble (mean AUC = 0.84), while the lowest accuracy was found for the Pulicaris ensemble (mean AUC = 0.71). The most important environmental variables in the models were related to temperature and precipitation for all three groups. Conclusions The duration periods with low or null adult activity can be derived from the associated monthly distribution maps, and it was also possible to identify and map areas with uncertain predictions. In the absence of ongoing vector surveillance, these maps can be used by veterinary authorities to classify areas as likely vector-free or as likely risk areas from southern Spain to northern Sweden with acceptable precision. The maps can also focus costly entomological surveillance to seasons and areas where the predictions and vector-free status remain uncertain.

Monthly variation in the probability of presence of adult Culicoides populations in nine European countries and the implications for targeted surveillance;Ana Cuéllar;2018;Figshare


Abstract: Abstract Background Bacterial expression and purification of recombinant proteins under homogeneous active form is often challenging. Fusion to highly soluble carrier proteins such as Maltose Binding Protein (MBP) often improves their folding and solubility, but self-association may still occur. For instance, HPV E6 oncoproteins, when produced as MBP-E6 fusions, are expressed as mixtures of biologically inactive oligomers and active monomers. While a protocol was previously developed to isolate MBP-E6 monomers for structural studies, it allows the purification of only one MBP-E6 construct at the time. Here, we explored a parallelizable strategy more adapted for biophysical assays aiming at comparing different E6 proteins. Results In this study, we took advantage of the distinct size and diffusion properties of MBP-E6 monomers and oligomers to separate these two species using a rapid batch preparation protocol on affinity resins. We optimized resin reticulation, contact time and elution method in order to maximize the proportion of monomeric MBP-E6 in the final sample. Analytical size-exclusion chromatography was used to quantify the different protein species after purification. Thus, we developed a rapid, single-step protocol for the parallel purification of highly monomeric MBP-E6 samples. MBP-fused HPV16 E6 samples obtained by this approach were validated by testing the binding to their prototypical peptide targets (the LXXLL motif from ubiquitine ligase E6AP) by BIAcore-SPR assay. Conclusions We have designed a rapid single-step batch affinity purification approach to isolate biologically active monomers of MBP-fused E6 proteins. This protocol should be generalizable to isolate the monomer (or the minimal biologically active oligomer) of other proteins prone to self-association.

One-step affinity purification of fusion proteins with optimal monodispersity and biological activity: application to aggregation-prone HPV E6 proteins;Anna Bonhoure;2018;Figshare


Abstract:
- Martins_Tables_Supplementary.xlsx contains Supplementary Tables S1 to S5, relative to the small RNA sequencing (Tables S1 and S2) and to the RNAseq of sorted follicular somatic cells (Tables S3-S5) of ovaries of FHV\deltaB2eGFP expressing flies.
- Martins_Figures_Supplementary contains Supplementary Figures S1 to S5.
- Martins_FileS1_Supplementary_Information.pdf includes information about the drosophila strains and plasmids used in the experiments.

Supplemental Material for Martins et al., 2018;Nelson Martins;2018;Figshare


Abstract: Abstract Background Anaerobic digestion (AD) is a microbe-driven process of biomass decomposition to CH4 and CO2. In addition to renewable and cost-effective energy production, AD has emerged in the European Union as an environmentally friendly model of bio-waste valorisation and nutrient recycling. Nevertheless, due to the high diversity of uncharacterised microbes, a typical AD microbiome is still considered as “dark matter”. Results Using the high-throughput sequencing of small rRNA gene, and a monthly monitoring of the physicochemical parameters for 20 different mesophilic full-scale bioreactors over 1 year, we generated a detailed view of AD microbial ecology towards a better understanding of factors that influence and shape these communities. By studying the broadly distributed OTUs present in over 80% of analysed samples, we identified putatively important core bacteria and archaea to the AD process that accounted for over 70% of the whole microbial community relative abundances. AD reactors localised at the wastewater treatment plants were shown to operate with distinct core microbiomes than the agricultural and bio-waste treating biogas units. We also showed that both the core microbiomes were composed of low (with average community abundance ≤ 1%) and highly abundant microbial populations; the vast majority of which remains yet uncharacterised, e.g. abundant candidate Cloacimonetes. Using non-metric multidimensional scaling, we observed microorganisms grouping into clusters that well reflected the origin of the samples, e.g. wastewater versus agricultural and bio-waste treating biogas units. The calculated diversity patterns differed markedly between the different community clusters, mainly due to the presence of highly diverse and dynamic transient species. Core microbial communities appeared relatively stable over the monitoring period. Conclusions In this study, we characterised microbial communities in different AD systems that were monitored over a 1-year period. Evidences were shown to support the concept of a core community driving the AD process, whereas the vast majority of dominant microorganisms remain yet to be characterised.

A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems;Magdalena Calusinska;2018;Figshare


Abstract: Abstract Hexanucleotide repeat expansion in C9orf72 is the most common genetic cause of frontotemporal dementia and amyotrophic lateral sclerosis, but the pathogenic mechanism of this mutation remains unresolved. Haploinsufficiency has been proposed as one potential mechanism. However, insights if and how reduced C9orf72 proteins levels might contribute to disease pathogenesis are still limited because C9orf72 expression, localization and functions in the central nervous system (CNS) are uncertain, in part due to the poor specificity of currently available C9orf72 antibodies. Here, we generated and characterized novel knock-out validated monoclonal rat and mouse antibodies against C9orf72. We found that C9orf72 is a low abundant, cytoplasmic, highly soluble protein with the long 481 amino acid isoform being the predominant, if not exclusively, expressed protein isoform in mouse tissues and human brain. As consequence of the C9orf72 repeat expansion, C9orf72 protein levels in the cerebellum were reduced to 80% in our series of C9orf72 mutation carriers (n = 17) compared to controls (n = 26). However, no associations between cerebellar protein levels and clinical phenotypes were seen. Finally, by utilizing complementary immunohistochemical and biochemical approaches including analysis of human iPSC derived motor neurons, we identified C9orf72, in addition to its association to lysosomes, to be localized to the presynapses and able to interact with all members of the RAB3 protein family, suggestive of a role for C9orf72 in regulating synaptic vesicle functions by potentially acting as guanine nucleotide exchange factor for RAB3 proteins. In conclusion, our findings provide further evidence for haploinsufficiency as potential mechanism in C9orf72 pathogenesis by demonstrating reduced protein levels in C9orf72 mutation carriers and important novel insights into the physiological role of C9orf72 in the CNS. Moreover, the described novel monoclonal C9orf72 antibodies will be useful tools to further dissect the cellular and molecular functions of C9orf72.

Novel antibodies reveal presynaptic localization of C9orf72 protein and reduced protein levels in C9orf72 mutation carriers;Petra Frick;2018;Figshare


Abstract: Abstract Background Reducing the number of people with undiagnosed HIV infection is a major goal of HIV control and prevention efforts in Europe and elsewhere. We analysed data from a large multi-city European bio-behavioural survey conducted among Men who have Sex with Men (MSM) for previously undiagnosed HIV infections, and aimed to characterise undiagnosed MSM who test less frequently than recommended. Methods Data on sexual behaviours and social characteristics of MSM with undiagnosed HIV infection from Sialon II, a bio-behavioural cross-sectional survey conducted in 13 European cities in 2013/2014, were compared with HIV-negative MSM. Based on reported HIV-testing patterns, we distinguished two subgroups: MSM with a negative HIV test result within 12 months prior to the study, i.e. undiagnosed incident infection, and HIV positive MSM with unknown onset of infection. Bivariate and multivariate associations of explanatory variables were analysed. Distinct multivariate multi-level random-intercept models were estimated for the entire group and both subgroups. Results Among 497 participants with HIV-reactive specimens, 234 (47.1%) were classified as previously diagnosed, 106 (21.3%) as incident, and 58 (11.7%) as unknown onset based on self-reported status and testing history. MSM with incident HIV infection were twice as likely (odds ratio (OR) = 2.22, 95% confidence interval (95%CI): 1.17–4.21) to have used recreational substances during their last anal sex encounter and four times more likely (OR = 3.94, 95%CI: 2.14–7.27) not to discuss their HIV status with the last anal sex partner(s). MSM with unknown onset of HIV infection were 3.6 times more likely (OR = 3.61, 95%CI: 1.74–7.50) to report testing for a sexually transmitted infection (STI) during the last 12 months. Conclusions Approximately one third of the study participants who are living with HIV were unaware of their infection. Almost two-third (65%) of those with undiagnosed HIV appeared to have acquired the infection recently, emphasizing a need for more frequent testing. Men with the identified behavioural characteristics could be considered as primary target group for HIV Pre-Exposure Prophylaxis (PrEP) to avoid HIV infection. The increased odds of those with unknown onset of HIV infection to have had an STI test in the past year strongly suggests a lost opportunity to offer HIV testing.

Behavioural and demographic correlates of undiagnosed HIV infection in a MSM sample recruited in 13 European cities;Ulrich Marcus;2018;Figshare


Abstract: Abstract Background Coagulase negative staphylococci (CoNS) are commensal bacteria on human skin. Staphylococcus lugdunensis is a unique CoNS which produces various virulence factors and may, like S. aureus, cause severe infections, particularly in hospital settings. Unlike other staphylococci, it remains highly susceptible to antimicrobials, and genome-based phylogenetic studies have evidenced a highly conserved genome that distinguishes it from all other staphylococci. Results We demonstrate that S. lugdunensis possesses a closed pan-genome with a very limited number of new genes, in contrast to other staphylococci that have an open pan-genome. Whole-genome nucleotide and amino acid identity levels are also higher than in other staphylococci. We identified numerous genetic barriers to horizontal gene transfer that might explain this result. The S. lugdunensis genome has multiple operons encoding for restriction-modification, CRISPR/Cas and toxin/antitoxin systems. We also identified a new PIN-like domain-associated protein that might belong to a larger operon, comprising a metalloprotease, that could function as a new toxin/antitoxin or detoxification system. Conclusion We show that S. lugdunensis has a unique genome profile within staphylococci, with a closed pan-genome and several systems to prevent horizontal gene transfer. Its virulence in clinical settings does not rely on its ability to acquire and exchange antibiotic resistance genes or other virulence factors as shown for other staphylococci.

Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer;Xavier Argemi;2018;Figshare


Abstract: Organogenesis involves extensive and dynamic changes of tissue shape during development. It is associated with complex morphogenetic events that require enormous tissue plasticity and generate a large variety of transient three-dimensional geometries that are achieved by global tissue responses. Nevertheless, such global responses are driven by tight spatio-temporal regulation of the behaviours of individual cells composing these tissues. Therefore, the development of image analysis tools that allow for extraction of quantitative data concerning individual cell behaviours is central to study tissue morphogenesis. There are many image analysis tools available that permit extraction of cell parameters. Unfortunately, the majority are developed for tissues with relatively simple geometries such as flat epithelia. Problems arise when the tissue of interest assumes a more complex three-dimensional geometry. Here, we use the endothelium of the developing zebrafish dorsal aorta as an example of a tissue with cylindrical geometry and describe the image analysis routines developed to extract quantitative data on individual cells in such tissues, as well as the image acquisition and sample preparation methodology.This article is part of the Theo Murphy meeting issue ‘Mechanics of development’.

Supplementary material from "Three-dimensional microscopy and image analysis methodology for mapping and quantification of nuclear positions in tissues with approximate cylindrical geometry";Pedro Campinho;2018;Figshare


Abstract: Abstract Background Intraventricular hemorrhage (IVH) is a frequent complication in extreme and very preterm births. Despite a high risk of death and impaired neurodevelopment, the precise prognosis of infants with IVH remains unclear. The objective of this study was to evaluate the rate and predictive factors of evolution to post hemorrhagic hydrocephalus (PHH) requiring a shunt, in newborns with IVH and to report their neurodevelopmental outcomes at 2 years of age. Methods Among all preterm newborns admitted to the department of neonatalogy at Rouen University Hospital, France between January 2000 and December 2013, 122 had an IVH and were included in the study. Newborns with grade 1 IVH according to the Papile classification were excluded. Results At 2-year, 18% (n = 22) of our IVH cohort required permanent cerebro spinal fluid (CSF) derivation. High IVH grade, low gestational age at birth and increased head circumference were risk factors for PHH. The rate of death of IVH was 36.9% (n = 45). The rate of cerebral palsy was 55.9% (n = 43) in the 77 surviving patients (49.4%). Risk factors for impaired neurodevelopment were high grade IVH and increased head circumference. Conclusion High IVH grade was strongly correlated with death and neurodevelopmental outcome. The impact of an increased head circumference highlights the need for early management. CSF biomarkers and new medical treatments such as antenatal magnesium sulfate have emerged and could predict and improve the prognosis of these newborns with PHH.

Post hemorrhagic hydrocephalus and neurodevelopmental outcomes in a context of neonatal intraventricular hemorrhage: an institutional experience in 122 preterm children;Vianney Gilard;2018;Figshare


Abstract: A series of hydroxamic acids linked by different lengths to a chiral imidazo-ketopiperazine scaffold were synthesized. The compounds with linker lengths of 6 and 7 carbon atoms were the most potent in histone deacetylase (HDAC) inhibition, and were specific submicromolar inhibitors of the HDAC1, HDAC6 and HDAC8 isoforms. A docking model for the binding mode predicts binding of the hydroxamic acid to the active site zinc cation and additional interactions between the imidazo-ketopiperazine and the enzyme rim. The compounds were micromolar inhibitors of the MV4-11, THP-1 and U937 cancer cell lines. Increased levels of histone H3 and tubulin acetylation support a cellular mechanism of action through HDAC inhibition.This article is part of a discussion meeting issue ‘Frontiers in epigenetic chemical biology’.

Supplementary material from "Isoform-selective HDAC1/6/8 inhibitors with an imidazo-ketopiperazine cap containing stereochemical diversity";Bertrand Lecointre;2018;Figshare


Abstract: Abstract Background Despite the growing number of discoveries during the past decades about its functions, the insula remains a mysterious ‘island’. In addition to its involvement in basic functions such as gustation and interoception, the insular cortex is now considered a key region for integrated functions such as emotion/motivation processing, decision-making and self-consciousness. We hypothesized that this structure, standing at the crossroads of such functions, could ground personal tastes in general, beyond food preferences and aesthetic judgements. Given that dementia with Lewy bodies is characterized by a focal atrophy within the insular cortex from the early stages, this condition provides an opportunity to test such a hypothesis. Methods We developed a questionnaire to assess potential changes in personal tastes, submitted it to a cohort of 23 patients with early-stage dementia with Lewy bodies and compared their questionnaire results to those of 20 age-matched healthy controls. Furthermore, we performed a global and regional neuroimaging study to test for a potential correlation between the patients’ scores for changes in personal tastes and their insular cortex volumes. Results Our results indicate that the patients presented significant changes in personal tastes compared to the controls, in both food and non-food domains. Moreover, imaging analyses confirmed the involvement of the insular cortex atrophy in the changes in personal tastes using global analysis, and in both food and non-food domains using regional analysis. Conclusions These results bring new insights into the role of the insula as a ‘grey matter of tastes’, this structure supporting personal preferences in general, beyond the food domain. The insular cortex could be involved through its role in motivational processes by the representation of subjective awareness of bodily states during the phenomenological experience of stimulus appraisal. However, we also argue that it could support the abstract representations of personal tastes as self-concepts, acutely exemplifying embodied cognition. Finally, the questionnaire on changes in tastes could constitute an interesting tool to help early diagnosis of dementia with Lewy bodies and to assess insular dysfunction more generally.

The insula, a grey matter of tastes: a volumetric MRI study in dementia with Lewy bodies;Nathalie Philippi;2020;figshare


Abstract: Abstract Farmers constitute a large professional group worldwide. In developed countries farms tend to become larger, with a concentration of farm operations. Animal farming has been associated with negative respiratory effects such as work-related asthma and rhinitis. However, being born and raised or working on a farm reduces the risk of atopic asthma and rhinitis later in life. A risk of chronic bronchitis and bronchial obstruction/COPD has been reported in confinement buildings and livestock farmers. This position paper reviews the literature linking exposure information to intensive animal farming and the risk of work-related respiratory diseases and focuses on prevention. Animal farming is associated with exposure to organic dust containing allergens and microbial matter including alive microorganisms and viruses, endotoxins and other factors like irritant gases such as ammonia and disinfectants. These exposures have been identified as specific agents/risk factors of asthma, rhinitis, chronic bronchitis, COPD and reduced FEV1. Published studies on dust and endotoxin exposure in livestock farmers do not show a downward trend in exposure over the last 30 years, suggesting that the workforce in these industries is still overexposed and at risk of developing respiratory disease. In cases of occupational asthma and rhinitis, avoidance of further exposure to causal agents is recommended, but it may not be obtainable in agriculture, mainly due to socio-economic considerations. Hence, there is an urgent need for focus on farming exposure in order to protect farmers and others at work in these and related industries from developing respiratory diseases and allergy.

Respiratory diseases and allergy in farmers working with livestock: a EAACI position paper;T. Sigsgaard;2020;figshare