Abstract: Palaeomagnetic investigations of the Corso-Sardinian block and Maures–Estérel show that there has been a change in their magnetic orientation during the Late Carboniferous–Early Permian period (305–280 Ma). This trend is interpreted in terms of a large-scale 90° clockwise rotation of the southern branch of the Variscan belt that matches the successive change in shortening directions revealed by structural geology. The evidence is based on existing structural studies of the fabrics of syntectonically emplaced granitoids partly based on the anisotropy of magnetic susceptibility, combined with a large database of isotopic ages. The chronological match between the palaeomagnetic and tectonic datasets is interpreted here as a result of large-scale dextral wrench movements in the lithosphere between the Gondwana and Laurussia supercontinents. This wrench deformation is regarded as a sequel to the dextral rotation of the northern branch of the Variscan belt during 330–315 Ma which terminated in frontal collision with Avalonia. The continuation of movement in the southern Variscan realm was due to shearing along the southern margin of the Avalonian block. An additional clockwise rotation is inferred to have taken place during the Triassic period. The age of this motion remains to be determined.

Early Permian 90° clockwise rotation of the Maures–Estérel–Corsica–Sardinia block confirmed by new palaeomagnetic data and followed by a Triassic 60° clockwise rotation;J.-B. Edel;2016;Geological Society of London


Abstract: Middle Devonian–Permian magmatic rocks from the northern Vosges Mountains show temporal and chemical variations which are linked to the continuous subduction of the Rhenohercynian oceanic crust and the Avalonian Devonian passive margin underneath the Saxothuringian continental crust. Major and trace elements and Sr–Nd isotopes of the northern Vosges basic to acidic magmatic rocks show that they evolved through time from: (1) Middle Devonian tholeiitic to calc-alkaline volcanic Rabodeau–Schirmeck sequence derived from partial melting of a depleted mantle, with these primary magmas having triggered anatexis of young crustal material of the Saxothuringian crust; (2) calc-alkaline Bande Médiane volcanic belt (c. 334 Ma), diorite and Hohwald granodiorite intrusion (c. 329 Ma) originated from enriched mantle contaminated and metasomatized by fluids expelled from a subduction zone; (3) high-K calc-alkaline Belmont granite (c. 318 Ma), whose chemical signature suggests magma-mixing between enriched mantle-derived melts and magmas from a young crustal source; (4) Mg–K Younger granite (c. 312 Ma) might be related to partial melting of enriched mantle which interacted with juvenile crustal material; and (5) Kagenfels S-type granite and Permian volcanic rocks generated by anatexis of meta-igneous and minor metasedimentary rocks.

Earth and related environmental sciences

Devonian–Permian magmatic pulses in the northern Vosges Mountains (NE France): result of continuous subduction of the Rhenohercynian Ocean and Avalonian passive margin;Anne-Sophie Tabaud;2016;Geological Society of London


Abstract: Geochronology, structural and anisotropy of magnetic susceptibility data from the northern Vosges batholith, which belongs to the Northern Vosges–Mid-German Crystalline Rise arc, show contrasting emplacement modes of southern granodiorites and northern granites. The ENE–WSW-trending fabrics of granodiorites (346–334 Ma) are parallel to the metamorphic cleavage affecting the host rocks developed during regional compression. The NNW–SSE-trending fabrics of younger granitoids (c. 330 Ma) reveal an extensional emplacement mode, associated with a normal shear zone separating the two magmatic suites. Palaeomagnetism shows that the switch from a compressive to an extensional regime coincides with a regional counterclockwise rotation. The 330–325 Ma extension is further supported by palaeomagnetic and seismic data indicating southeastward tilt of the whole batholith. Finally the system is rotated clockwise without any structural overprint. Data from the Early Carboniferous northern Vosges magmatic arc and remote Bohemian Massif suggest that this evolution is valid for the whole eastern branch of the European Variscan belt, for which the following model is proposed: (1) Late Devonian–Early Carboniferous east–west shortening of the Variscides above the Rhenohercynian subduction zone; (2) axial NNW–SSE shortening of the assembled Variscan orogen associated with (3) ‘internal’ sinistral rotation of inherited Rhenohercynian transform faults and shortening of intervening blocks; (4) east–west extension and dextral ‘external’ rotation of blocks between dextrally reactivated transforms.

Tectonic evolution of the European Variscan belt constrained by palaeomagnetic, structural and anisotropy of magnetic susceptibility data from the Northern Vosges magmatic arc (eastern France);J. B. Edel;2016;Geological Society of London


Abstract: Among innate cells, natural killer (NK) cells play a crucial role in the defense against cytomegalovirus (CMV). In some individuals, CMV infection induces the expansion of NKG2C+ NK cells that persist after control of the infection. We have previously shown that KIR2DL+ NK cells, in contrast to NKG2C+ NK cells, contribute to controlling CMV infection using a CMV-infected monocyte-derived dendritic cell (MDDC) model. However, the nature of CMV-infected cells contributing to the expansion of the NKG2C+ NK cell subset remains unclear. To gain more insight into this question, we investigated the contribution of NKG2C+ NK cell activation by CMV-infected primary human aortic endothelial cells (EC) isolated from kidney transplant donors, which constitutively express the human leukocyte antigen (HLA)-E molecule. Here, we show that, although classic HLA class I expression was drastically downregulated, nonclassic HLA-E expression was maintained in CMV-infected EC. By comparing HLA expression patterns in CMV-infected EC, fibroblasts and MDDC, we demonstrate a cell-dependent modulation of HLA-E expression by CMV infection. NKG2C+ NK cell degranulation was significantly triggered by CMV-infected EC regardless of the nature of the HLA-E allele product. EC, predominantly present in vessels, may constitute a privileged site for CMV infection that drives a ‘memory' NKG2C+ NK cell subset.

Supplementary Material for: Cytomegalovirus-Infected Primary Endothelial Cells Trigger NKG2C+ Natural Killer Cells;Zakia Djaoud;2016;Karger Publishers


Abstract: Gastrointestinal metastases from lung cancer are rare and usually asymptomatic. We report a case of small bowel metastases from primary lung cancer revealed by abdominal pain and severe recurrent anaemia. The diagnosis was obtained with capsule endoscopy. This non-invasive procedure thus represents a valuable method contributing to a rapid and detailed diagnosis while reducing underdiagnosis, and it should thus be considered for lung cancer patients complaining of abdominal symptoms, which may indeed be related to gastrointestinal metastases.

Supplementary Material for: Diagnosis of Jejunal Metastases from Lung Cancer Using Capsule Endoscopy;C. Leduc;2016;Karger Publishers


Abstract: Activating mutations of the NRAS (neuroblastoma rat sarcoma viral oncogene) protein kinase, present in many cancers, induce a constitutive activation of both the RAS-RAF-MEK-ERK mitogen-activated protein kinase (MAPK) signal transduction pathway and the PI(3)K-AKT-mTOR, pathway. This in turn regulates the formation of the eIF4F eukaryotic translation initiation complex, comprising the eIF4E cap-binding protein, the eIF4G scaffolding protein and the eIF4A RNA helicase, which binds to the 7-methylguanylate cap (m(7)G) at the 5′ end of messenger RNAs. Small molecules targeting MEK (MEKi: MEK inhibitors) have demonstrated activity in NRAS-mutant cell lines and tumors, but resistance sets in most cases within months of treatment. Using proximity ligation assays, that allows visualization of the binding of eIF4E to the scaffold protein eIF4G, generating the active eIF4F complex, we have found that resistance to MEKi is associated with the persistent formation of the eIF4F complex in MEKi-treated NRAS-mutant cell lines. Furthermore, inhibiting the eIF4A component of the eIF4F complex, with a small molecule of the flavagline/rocaglate family, synergizes with inhibiting MEK to kill NRAS-mutant cancer cell lines.

Synergistic effects of eIF4A and MEK inhibitors on proliferation of NRAS-mutant melanoma cell lines;Hélène Malka-Mahieu;2016;Taylor & Francis


Abstract: Supplementary material from "Scratch that itch: revisiting links between self-directed behaviour and parasitological, social and environmental factors in a free-ranging primate"

ESM Table S1 dataset to the article "Scratch that itch: revisiting links between self-directed behaviour and parasitological, social and environmental factors in a free-ranging primate";Julie Duboscq;2016;The Royal Society


Abstract: Background: Considerable variations in diagnosis and therapeutic practices are reported for hyperthyroidism (HT) between countries. Methods: A clinical study was conducted among a representative sample of 263 endocrinologists in France. All consecutive patients seen for HT during the study period were included. Diagnosis and treatment modalities were recorded from hyperthyroid patients with Graves disease (GD, n = 802), multinodular goiter (MNG, n = 121), and toxic adenoma (TA, n = 69). Results: Antithyroid antibodies were measured in half of the population (anti-TPO in 48.5% and anti-TSH receptor in 57.8%). Patients had thyroid ultrasonography and scintigraphy in 93.8 and 40.3%, respectively. Therapeutic management depended on the etiology: for the first episode of GD, antithyroid drugs (ATDs) were the first-line treatment in 91% of the patients, combined with surgery in 6.1% and with radioiodine in 2.9%. Surgery was preferred to radioiodine in MNG (52.6 vs. 22.4%) and TA (59.1 vs. 24.2%). Euthyroid status was achieved after 3 months in 64.4% of GD. A “block and replace” protocol was used in 41.2% of patients. After 3 months, 73% of patients were euthyroid in the “block and replace” group compared to 56.2% in the group with ATDs alone (p = 0.009). For MNG and TA, more than 75% of patients were euthyroid at the 3-month follow-up. Conclusions: Large discrepancies remain between clinical practice and international guidelines. These results should boost efforts to improve adherence to these guidelines.

Supplementary Material for: Survey of Clinical Practice Patterns in the Management of 992 Hyperthyroid Patients in France;B. Goichot;2017;Karger Publishers


Abstract: Objectives: Mast cells (MCs) and nerves play an important role in allergic rhinitis (AR), but little is known about their crosstalk in AR. The aim of this study was to investigate MC-nerve interaction in the human nasal mucosa during AR. Methods: The association between MCs and nerves, the expression of neuropeptide receptors (neurokinin 1 receptor [NK1R], neurokinin 2 receptor [NK2R], calcitonin gene-related peptide receptor [CGRPR], and MrgX2) on MCs, and protease-activated receptor 2 (PAR2) and tyrosine receptor kinase A (TrkA) on nerve fibres in the human nasal mucosa were investigated with immunofluorescence and real-time PCR. Results: The association between MCs and nerves was found to be significantly increased, although the numbers of MCs and nerve fibres were unchanged during AR. MCs expressing tryptase-chymase (MCtc) were frequently associated with nerve fibres and these contacts increased significantly in AR. Neuropeptide receptors NK1R, NK2R, and CGRPR were firstly found to be largely localised on MCs. The number of MCs expressing NK1R and NK2R, but not CGRPR, was significantly increased in AR. Interestingly, MCtc mostly expressed these neuropeptide receptors. The newly discovered tachykinin receptor MrgX2 was not expressed on nasal MCs, but was expressed on gland cells and increased in AR. Additionally, tachykinergic nerve fibres were found to express PAR2 or TrkA as receptors for MCs. Conclusions: This study revealed for the first time an increase of MC-nerve association and neuropeptide receptor expression on MCs during AR as well as nerve fibres containing receptors for MCs. These results suggest that targeting or controlling airway sensory nerve function as a modulator of MCs may prevent allergic airway inflammation such as AR.

Supplementary Material for: Increase of Mast Cell-Nerve Association and Neuropeptide Receptor Expression on Mast Cells in Perennial Allergic Rhinitis;D.D. Le;2016;Karger Publishers


Abstract: We report the preparation and characterisation of new emissive materials based on the insertion of platinum(II) and iridium(III) complexes inside the Al(OH)(bipyridine dicarboxylate) metal organic framework (MOF-253). Guest incorporation is performed by coordination of a metal complex precursor, and provides increased robustness to the system compared to guest inclusion by its physical diffusion. Powder X-ray diffraction analysis highlights the high degree of crystallinity of the materials, with a complete change in the lattice parameters upon metal complex insertion. The photophysical properties of the resulting materials were thoroughly investigated. This synthetic approach is particularly attractive since, as we show, it is possible to tune the emission maxima of our materials over the entire visible range.

Tuning luminescent properties of a metal organic framework by insertion of metal complexes;Youssef Atoini;2017;Taylor & Francis


Abstract: Using the phase-space formulation of quantum mechanics, we derive a four-component Wigner equation for a system composed of spin-½ fermions (typically, electrons) including the Zeeman effect and the spin–orbit coupling. This Wigner equation is coupled to the appropriate Maxwell equations to form a self-consistent mean-field model. A set of semiclassical Vlasov equations with spin effects is obtained by expanding the full quantum model to first order in the Planck constant. The corresponding hydrodynamic equations are derived by taking velocity moments of the phase-space distribution function. A simple closure relation is proposed to obtain a closed set of hydrodynamic equations.

supplementary from Phase-space methods for the spin dynamics in condensed matter systems;Jérôme Hurst;2017;The Royal Society


Abstract: Purpose: The host immune reaction during endophthalmitis, studied in particular through the intraocular cytokine network, is essential for the comprehension of the disease and the development of new therapies. Therefore, the purpose of this study was to elucidate the cytokine composition of aqueous humor during endophthalmitis. Methods: In a multicenter case-control study, forty-nine patients with postoperative endophthalmitis and 60 controls (cataract surgery) were included. Visual acuity, local inflammatory grading, medical history and intraocular levels of 27 cytokines and chemokines (measured by multiplex immunoassay) were recorded. Results: During endophtalmitis, an increase in total cytokines was observed. The raise of Th1 cytokines was particularly noticeable. Chemokines, such as IL-8, MIP-1 β, MCP-1, G-CSF and IP-10, also increased. Pearson’s correlation analyses showed a poor visual prognosis with high levels of IL-8, MCP-1 and VEGF and a low level of IL-10 at admission. Conclusion: An increase in inflammatory cytokines is noticeable during endophthalmitis, with a particular emphasis on IL-8, MCP-1 and VEGF. Targeted anti-inflammatory and anti-VEGF treatments may be of interest in the future.

Intraocular Cytokine Levels in Post-Cataract Endophthalmitis and their Association with Visual Outcome;Arnaud Sauer;2017;Taylor & Francis


Abstract: Nexus file of the genome wide phylogeny for 10 Equus taxa.

Genome phylogeny from Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies;T. Cucchi;2017;The Royal Society


Abstract: Information for the 345 specimens of the morphometric dataset regarding Museum location, identifiers in the collection, sex, age and geographic origin.

Specimens details from Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies;T. Cucchi;2017;The Royal Society


Abstract: 356 x and y coordinates extracted from the enamel outline of the 4 mandibular cheek teeth digitized for each of the 345 specimens. Anatomic and Taxonomic factors are provided.

Geometric morphometric dataset from Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies;T. Cucchi;2017;The Royal Society


(benzo[f]pyrido[2,3-h]quinoxalin-9-yl)-bis(1,10-phenanthroline)-ruthenium hexafluorophosphate unknown solvate

CCDC 1889279: Experimental Crystal Structure Determination;Solís-Ruiz, Jorge Andrés;2020;Cambridge Crystallographic Data Centre

Related Article: Jorge Andrés Solís-Ruiz, Anaïs Barthe, Gilles Riegel, Rafael Omar Saavedra-Díaz, Christian Gaiddon, Ronan Le Lagadec|2020|J.Inorg.Biochem.|208|111080|doi:10.1016/j.jinorgbio.2020.111080


Abstract: Double-stranded RNA binding (DRB) proteins are generally considered as promoting cofactors of Dicer or Dicer-like (DCL) proteins that ensure efficient and precise production of small RNAs, the sequence-specificity guide of RNA silencing processes in both plants and animals. However, the characterization of a new clade of DRB proteins in Arabidopsis has recently challenged this view by showing that DRBs can also act as potent inhibitors of DCL processing. This is achieved through sequestration of a specific class of small RNA precursors, the endogenous inverted-repeat (endoIR) dsRNAs, thereby selectively preventing production of their associated small RNAs, the endoIR-siRNAs. Here, we concisely summarize the main findings obtained from the characterization of these new DRB proteins and discuss how the existence of such complexes can support a potential, yet still elusive, biological function of plant endoIR-siRNAs.

New DRB complexes for new DRB functions in plants;Thomas Montavon;2017;Taylor & Francis


Supplementary Material to BEH 3443

Abstract: Video clips made during Canteloup et al.’s (2016) visual perspective-taking study. The study took place in three experimental areas (Canteloup et al., 2016) and subjects’ participation was voluntary. Subjects were assigned as dominant or subordinate depending on which other monkey came to participate in a given session. Each monkey started on opposite sides of the middle test area, and both were given access to the test area after an experimenter had placed two pieces of food there. One piece was placed on top of one of two breezeblocks so as to be visible to both individuals; the second piece was placed inside the other breezeblock so as to be hidden from the dominant. No training was used in this experiment.We ran two conditions, as follows: In condition 1 the subordinate was released into the test area simultaneously with the dominant; in condition 2 the subordinate had a short head start on the dominant (i.e., the dominant was released as soon as the subordinate’s entire body was in the test area). nalyses were done on a total of 360 trials involving 20 different dominant-subordinate dyads.

Supplementary Material to BEH 3443;Charlotte Canteloup;2017;Brill Online


Abstract: Background: The precise clinical description of skin lesions observed in some patients with hidradenitis suppurativa (HS) can be extremely difficult. Objective: Establishing a validated glossary of terms allowing the best possible description of lesions observed in HS patients. Material and Methods: Five international experts of HS were to assess a series of 25 photos representing typical lesions of this disorder. For each photo, the experts were asked whether naming of the lesions was possible or not and, if yes, by using which noun. Agreement of their responses was calculated using Fleiss's kappa index. Using a Delphi strategy, photos with disagreement were discussed, and photos were reevaluated on the next day. In case of agreement on the impossibility of naming some clinical situations, new terms, to be included into the glossary, were agreed upon. Results: After the first round of photos, agreement between the experts was poor with a kappa index of only 0.33 (95% CI 0.22-0.46). After extensive discussion of cases with disagreement, the kappa index increased on day 2 to 0.75 (95% CI 0.60-0.87), allowing to conclude on good interobserver agreement on terminology. Furthermore, a few clinical situations were identified in which naming with established semantics is so far not possible. For these situations, the terms ‘multicord', ‘multipore', ‘multitunnel' and ‘retraction' were defined. Discussion: This is the first validation of clinical terms used to describe lesions in patients with HS. This should be helpful in better defining the clinical phenotypes observed in this disorder.

Supplementary Material for: The ABC of Hidradenitis Suppurativa: A Validated Glossary on how to Name Lesions;D. Lipsker;2016;Karger Publishers


Abstract: Background: Bronchoscopic coil treatment has been shown to improve pulmonary function, exercise capacity, and quality of life in patients with severe emphysema. Objectives: To perform a meta-analysis of the results of four independent European clinical trials investigating this coil therapy for emphysema. Methods: Data on all patients included in the four European clinical trials were analyzed for efficacy and safety outcomes. Results: A total of 2,536 coils were placed during 259 procedures in 140 patients. A total of 37 chronic obstructive pulmonary disease exacerbations and 27 pneumonias were recorded as serious adverse events up to 1 year after treatment. The pneumothorax rate was 6.4%. Both 6 and 12 months after treatment, significant (all p < 0.001) improvements were observed for: forced expiratory volume in 1 s [+0.08 liters (±0.19) and +0.08 liters (±0.21)], residual volume [RV; -510 ml (±850) and -430 ml (±720)], 6-min walking distance [6MWD; +44.1 m (±69.8) and +38.1 m (±71.9)], and St. George's Respiratory Questionnaire score [SGRQ; -9.5 points (±14.3) and -7.7 points (±14.2)]. No differences in any outcome measures were observed between heterogeneous and homogeneous emphysema patients. Only a high baseline RV was found to be an independent predictor of successful treatment. Conclusions: Bronchoscopic coil treatment improves pulmonary function, 6MWD, and quality of life in patients with severe emphysema up to 1 year after treatment, independent of the distribution of the disease.

Erratum: Bronchoscopic Coil Treatment for Patients with Severe Emphysema: A Meta-Analysis;D.-J. Slebos;2017;Karger Publishers


Abstract:
Video showing the 3D structure of the human ribosome revealing chemical modifications of the ribosomal RNA.

File is provided in .mp4 format, compatible with most standard video playing software.
This visualization, along with the related article, presents for the first time chemical modifications of rRNA in the human ribosome introduced during biogenesis and maturation, and highlights their structural and functional role within their 3D molecular environment. Visualizations include:
Universally conserved rRNA modification sites (Class I)Predicted rRNA modification sites (Class II)Unpredicted human specific rRNA modifications (Class III)
The structure of the human 80S ribosome was determined by single particle cryo electron microscopy (cryo-EM) and refined using focused refinement of the 60S ribosomal subunit and the 40S head and body parts during image processing (resolved to 2.9, 3.0 and 3.1 Å average resolution, respectively (see methods in linked article).
See background below and related article linked from this data record for further details.
Background:Chemical modifications of the ribosomal RNA (rRNA) of the human ribosome are introduced during biogenesis and are implicated in human protein synthesis dysregulations such as cancer and other diseases but their role therein is unknown. Here we visualize over 130 individual rRNA modifications in the three dimensional structure of the human ribosome explaining their structural and functional roles. Beyond some universally conserved sites, many eukaryote/human specific modifications and new unique sites are found that form an evolutionary extended shell compared to bacterial ribosomes and which stabilize the RNA. A series of modifications are located in vicinity to 3 bound antibiotics or are associated with degenerated states in cancer such as keto alkylations at nucleotide bases reminiscent of specialized ribosomes. This high-resolution structure of the human 80S ribosome paves the way to understanding the role of rRNA modifications in human diseases and drug-design.

Visualization of chemical modifications in the human 80S ribosome structure;S. Kundhavai Natchiar;2017;figshare


Abstract: Assisted reproductive technologies, including in vitro fertilization (IVF), are now frequently used, and increasing evidence indicates that IVF causes gene expression changes in children and adolescents that increase the risk of metabolic diseases. Although such gene expression changes are thought to be due to IVF-induced epigenetic changes, the mechanism remains elusive. We tested whether the transcription factor ATF7, – which mediates stress-induced changes in histone H3K9 tri- and di-methylation, typical marks of epigenetic silencing – is involved in the IVF-induced gene expression changes. IVF up- and down-regulated the expression of 688 and 204 genes, respectively, in the liver of 3-week-old wild-type (WT) mice, whereas 87% and 68% of these were not changed, respectively, by IVF in ATF7-deficient (Atf7—/—) mice. The genes, which are involved in metabolism, such as pyrimidine and purine metabolism, were up-regulated in WT mice but not in Atf7—/— mice. Of the genes whose expression was up-regulated by IVF in WT mice, 37% were also up-regulated by a loss of ATF7. These results indicate that ATF7 is a key factor in establishing the memory of IVF effects on metabolic pathways.

Dataset for: The transcription factor ATF7 mediates in vitro fertilization-induced gene expression changes in mouse liver;Yang Liu;2017;Wiley


Abstract: Additional file 2. List of insertion sites of all the tested conditions. Raw sequencing reads are available upon request.

MOESM2 of Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails;Mohamed Benleulmi;2017;figshare


Abstract: Additional file 1: Figure S1. Structure of the native and tailless mononucleosomes used in the work. The globular structure of the nucleosomes was analyzed by loading 250 ng of native or tailless MN on 0.8% native agarose gel run 4 h at 50 V and 4 °C then stained with SYBR®Safe 20 min. Assembled MNs migrate between 600 and 700 bp and the naked 601 DNA fragment at 147 bp. Figure S2. A. Effect of LEDGF/p75 on HIV-1 integration in vitro. Integration assay was performed as done in Fig. 2 using naked 601 DNA coupled to magnetic beads and increasing concentration of LEDGF in the presence or absence of PEG and DMSO. B. Integration activity catalyzed by IN and IN/LEDGF complex on native or tail less nucleosomes in the absence of PEG and DMSO. Integration assay was performed as done in Fig. 2 using native or tail less nucleosomes coupled to magnetic beads and either IN or IN/LEDGF complex. All values are shown as the mean ± standard deviation (error bars) of three independent sets of experiments. The p values were calculated by Student’s t test and are shown as *p

MOESM1 of Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails;Mohamed Benleulmi;2017;figshare


Abstract: This fileset includes figures S1 to S4, and a KML file including the detailed map of the 1905 T-B EQs surface rupture. To open the KML file, change the (.txt) extension of the file name to (.kml).

Suplementary materials for the 2017JB013962;Jin-Hyuck Choi;2018;figshare


Abstract: Cold adaptation is an evolutionary process that has dramatic impact on enzymatic activity. Increased flexibility of the protein structure represents the main evolutionary strategy for efficient catalysis and reaction rates in the cold, but is achieved at the expense of structural stability. This results in a significant activity-stability tradeoff, as it was observed for several metabolic enzymes. In polymerases, however, not only reaction rates, but also fidelity plays an important role, as these enzymes have to synthesize copies of DNA and RNA as exact as possible. Here, we investigate the effects of cold adaptation on the highly accurate CCA-adding enzyme, an RNA polymerase that uses an internal amino acid motif within the flexible catalytic core as a template to synthesize the CCA triplet at tRNA 3′-ends. As the relative orientation of these residues determines nucleotide selection, we characterized how cold adaptation impacts template reading and fidelity. In a comparative analysis of closely related psychro-, meso-, and thermophilic enzymes, the cold-adapted polymerase shows a remarkable error rate during CCA synthesis in vitro as well as in vivo. Accordingly, CCA-adding activity at low temperatures is not only achieved at the expense of structural stability, but also results in a reduced polymerization fidelity.

Cold adaptation of tRNA nucleotidyltransferases: A tradeoff in activity, stability and fidelity;Felix G. M. Ernst;2018;Taylor & Francis


Abstract: We present an updated version of the European landslide susceptibility map ELSUS 1000 released through the European Soil Data Centre in 2013. The ELSUS V2 map shows the landslide susceptibility zonation for individual climate-physiographic zones across Europe. ELSUS V2 covers a larger area of Europe than ELSUS 1000 at a higher spatial resolution (200 × 200 m). The updated map was prepared using the same semi-quantitative method as for ELSUS 1000, combining landslide frequency ratios information with a spatial multi-criteria evaluation model of three thematic predictors: slope angle, shallow subsurface lithology and land cover. However, the new map was prepared using also: (i) an extended landslide inventory, containing 30% of additional locations for model calibration, map validation and classification and (ii) a new lithological data set derived from the International Hydrogeological Map of Europe (IHME). The new version of the map increases the overall predictive performance of ELSUS by 8 %.

Pan-European landslide susceptibility mapping: ELSUS Version 2;Martina Wilde;2019;Taylor & Francis


Abstract: Figure S3. Inhibitory effect of indomethacin on plasma electrolyte level induced by EFPA in rats. Rats were treated over a 24 h period with a single dose of either vehicle (control group), EFPA (10 mg/kg) or EFPA (10 mg/kg) + indomethacin (5 mg/kg, 1 h pretreatment) administered i.p. Data are given as means ± SEM of 6 different experiments. Statistical analyses were assessed using two-way analysis of variance (ANOVA) followed by Bonferroni’s post- test. *p

Additional file 3: of The acute diuretic effect of an ethanolic fraction of Phyllanthus amarus (Euphorbiaceae) in rats involves prostaglandins;Alain Yao;2018;figshare


Abstract: Figure S2. Inhibitory effect of indomethacin on urinary electrolyte excretion induced by EFPA in rats. Rats were treated over a 24 h period with a single dose of vehicle (control group), EFPA (10 mg/kg) or EFPA (10 mg/kg) + indomethacin (5 mg/kg, 1 h pretreatment) administered i.p. Data are given as means ± SEM of 6 different experiments. Statistical analyses were assessed using two-way analysis of variance (ANOVA) followed by Bonferroni’s post- test. *p

Additional file 2: of The acute diuretic effect of an ethanolic fraction of Phyllanthus amarus (Euphorbiaceae) in rats involves prostaglandins;Alain Yao;2018;figshare


Abstract: Figure S1. Urinary volumetric excretion induced by increasing doses of EFPA in rats. The urinary volumetric excretion values are expressed as a percentage of the initial hydric overload (50 mL/kg). Data are given as means ± SEM of 6 different experiments. Statistical analyses were assessed using two-way analysis of variance (ANOVA) followed by Bonferroni’s post- test. *p ˂ 0.001 versus control. (TIFF 216 kb)

Additional file 1: of The acute diuretic effect of an ethanolic fraction of Phyllanthus amarus (Euphorbiaceae) in rats involves prostaglandins;Alain Yao;2018;figshare


Abstract: Monthly availability of Culicoides trap data in the participating countries during the selected seven-year study period (2007–2013). X symbol indicates months when data were available. (XLSX 12 kb)

Additional file 1: Table S1. of Spatial and temporal variation in the abundance of Culicoides biting midges (Diptera: Ceratopogonidae) in nine European countries;Ana Cuéllar;2018;figshare


Abstract: Nanoparticles (NPs) typically accumulate in lysosomes. However, their impact to lysosome function, as well as autophagy, a lysosomal degradative pathway, is still not well known. We have previously reported in 1321N1 cell line that amine-modified polystyrene (NH2-PS) NPs induce apoptosis through damage initiated in the lysosomes leading ultimately to release of lysosomal content in the cytosol, followed by apoptosis. Here by using a combination of biochemical and cell biological approaches, we have characterized in a mouse embryonic fibroblast cell line that the lysosomal alterations induced by NH2-PS NPs is progressive, initiating from mild lysosomal membrane permeabilization (LMP), to expansion of lysosomal volume and intensive LMP before the summit of cell death. Though the cells seem to induce initially autophagy as a surviving mechanism, the damage of NH2-PS NPs to lysosomes likely results into lysosomal dysfunctions, leading to blockage of autophagic flux at the level of lysosomes and the eventual cell death.

Supplementary Figures from Lysosome-dependent cell death and deregulated autophagy induced by amine-modified polystyrene nanoparticles;Fengjuan Wang;2018;The Royal Society


Abstract: The Algerian hedgehog Atelerix algirus is an insectivorous species. However, the exact composition of its natural diet remains largely undetermined, especially in relation to seasonal variations in food availability. From March to November, we simultaneously analysed the composition of 180 hedgehog faecal samples and food availability in the Soumman Valley, Algeria to assess food selection in this species. The faeces contained 196 different prey species, of which 92% belonged to the class Insecta. The highest prey species diversity was found in the Coleoptera order (100 species recorded) and the highest species occurrence was found in Hymenoptera (65% of the prey items, mainly represented by the harvester ant Messor barbarus, a crop-ravaging species). This study shows that the Algerian hedgehog is mainly a generalist species with a diet that is strongly linked to food availability. However, seasonal variations were observed in prey selection, and a notable shift in food preference was observed during autumn. The exact nature of these changes in feeding behaviour remains to be investigated, notably in relation to changes in energy requirements of this species before hibernation, in terms of quantity and/or quality.

Seasonal variations in the diet and food selection of the Algerian hedgehog <i>Atelerix algirus</i>;Chafika Mouhoub-Sayah;2018;Taylor & Francis


Abstract: Table S2. Comparison of genes altered at the copy number level between ATM-associated tumours and tumours from TCGA. (XLSX 13 kb)

Additional file 3: of Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers;Anne-Laure Renault;2018;figshare


Abstract: Figure S1. Copy number variation profiles of ATM-associated tumours analysed with the OncoScan array. a Genome-wide view of cumulative CNVs present in the 19 ATM-associated tumours from participants carrying one or two copies of a TV. Gains are indicated in red, losses in blue, and LOH in orange. b Cluster dendrogram and genomic regions altered in at least 70% of the 19 analysed tumours. AT children are indicated by asterisks. Loss: the two alleles are present in the tumour; Loss/LOH: only one allele is present in the tumour; Loss/LOH or Loss: consecutive segmental regions characterized as either ‘Loss/LOH’ or ‘Loss’. (PNG 510 kb)

Additional file 2: of Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers;Anne-Laure Renault;2018;figshare


Abstract: Table S1. Genomic regions showing copy number loss or loss/LOH in at least 70% of ATM-associated tumours. (XLSX 70 kb)

Additional file 1: of Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers;Anne-Laure Renault;2018;figshare


Abstract: The influence of alternating electric field (AC) in the structure and dynamics of giant unilamellar vesicles (GUVs) comprised of 1,2-dilauroyl-sn-glycero-3-phosphatidylcholine (DLPC) is reported. The investigations were conducted by using optical fluorescence microscopy as the method of analysis. The lipid membrane of the DLPC GUVs at the fluid phase can be deformed and they migrate towards the electrodes under AC electric field. Nevertheless, membrane disruption or vesicle fusion was never noticed. The addition of concentrated glucose solution influences the osmotic pressure of the system leading to the formation of filaments at the outer region of the GUVs. These long flexible cylinders do not retract spontaneously. However, the application of AC electric field (20 V/mm, 20 Hz) enables the filaments to be retracted back to the GUVs membrane at a calculated speed of 0.18 µm.s-1

Study on the Application of Electric Field to Giant Vesicles Comprised of 1,2-Dilauroyl-Sn-Glycero-3-Phosphatidylcholine Using Optical Fluorescence Microscopy;Yasmine Miguel Serafini Micheletto;2018;SciELO journals


Eckbo_2018_data_BLGU.xlsx

Abstract: Contaminant data (pg/g, plasma, except Hg; red blood cells), lipid % in plasma, sex, telomere length (red blood cells), oxidative stress (plasma), dietary signatures (d15N, d13C), body measures, calculated body condition (BCI, SMI), field records (date of sampling, location, GPS, trapping method, brood patch, amount of sample (whole blood), sample matrices). See details of the methods in Eckbo et al. 2018.


Abstract: Aims: Limited research has been done on the functional connectivity in visuoperceptual regions in dementia with Lewy bodies (DLB) patients. This study aimed to investigate the functional connectivity differences between a task condition and an inter-task resting state condition within a visuoperceptual paradigm, in DLB patients compared with Alzheimer disease (AD) patients and healthy elderly control subjects. Methods: Twenty-six DLB, 29 AD, and 22 healthy subjects underwent a detailed clinical and neuropsychological examination along with a functional MRI during the different conditions of a visuoperceptual paradigm. Functional images were analyzed using group-level spatial independent component analysis and seed-based connectivity analyses. Results: While the DLB patients scored well and did not differ from the control and AD groups in terms of functional activity and connectivity during the task conditions, they showed decreased functional connectivity in visuoperceptual regions during the resting state condition, along with a temporal impairment of the default-mode network activity. Functional connectivity disturbances were also found within two attentional-executive networks and between these networks and visuoperceptual regions. Conclusion: We found a specific functional profile in the switching between task and resting state conditions in DLB patients. This result could help better characterize functional impairments in DLB and their contribution to several core symptoms of this pathology such as visual hallucinations and cognitive fluctuations.

Supplementary Material for: Functional Disconnectivity during Inter-Task Resting State in Dementia with Lewy Bodies;E. Chabran;2018;Karger Publishers


Abstract: Table S2. Data analysis of the microarray experiments. Lists of genes with significant differential expression levels (fold changes of ±2 fold; p

Additional file 2: of Telomerase regulation by the long non-coding RNA H19 in human acute promyelocytic leukemia cells;Joëlle El Hajj;2018;figshare


Abstract:
This dataset contains artifacts relating to the results presented in the Euro-Par 2018 conference paper entitled "Efficient Strict-Binning Particle-in-Cell Algorithm for Multi-Core SIMD Processors".
The paper describes a multi-core PIC algorithm that achieves close-to-minimal number of memory transfers with the main memory, while at the same time exploiting SIMD instructions for numerical computations and exhibiting a high degree of OpenMP-level parallelism.
A README file titled Overview_document.pdf outlines the purpose and dependencies of the software, as well as instructions for compiling and running it.
The processes used to demonstrate the performance, validation and verification of the software are also described.
This artifact is composed of several folders:
# include and src contain all the modular code for Pic-Vert (as .h and .c files). By opening them, it is possible to check that we implemented the data structures we describe in thepaper:– compiler_test.h: compiler check to know which features we can use.– diagnostics.c/h: electric field diagnostics.– fields.c/h: data structure for the electric fields.– hdf5_io.c/h: handling of HDF5 outputs.– initial_distributions.c/h: possible initial distributions of particles.– math_functions.h: useful mathematical functions not already in standard libraries.– matrix_functions.c/h: dynamic allocation of arrays.– meshes.c/h: data structure for the grid.– output.c/h: handling of outputs other than HDF5.– papi_handlers.c/h: handling of PAPI performance counters.– parameter_reader.c/h: reading parameter files for simulations.– parameters.h: useful parameters (architecture, mathematics, simulation. . . )– particle_type_concurrent_chunkbags_of_soa_XXX.c/h: data structure for particles.– poisson_solvers.c/h: data structure for the FFT Poisson solver.– random.c/h: pseudo-random number generators available.– rho.c/h: data structure for the charge density.– space_filling_curves.c/h: use of space-filling curves in the code.– variadic.h: allows to write function with default arguments in C.# simulations contains the PIC simulations that we used for this article, and that uses the files in the previous point.# scripts contains the compile and run scripts for our simulations.# memory contains spread sheets to compute the number of particles you should put in the simulation, given your architecture (prior to compilation).# Stream-test contains the Stream benchmark# post-process contains scripts to “automate data extraction and the production of plots”.# sample-outputs contains “files that represent expected outputs”.

Software artifacts for Euro-Par 2018 paper: "Efficient Strict-Binning Particle-in-Cell Algorithm for Multi-Core SIMD Processors";Yann Barsamian;2018;figshare


Abstract: is a Microsoft Excel file listing the consensus sequences of each bovine repetitive element as defined in Repbase and the average methylation percentages for CpGs 5-500 and CpGs > 500 in each RRBS sample. (XLSX 16 kb)

Additional file 4: of A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific features;Jean-Philippe Perrier;2018;figshare


Abstract: is a Microsoft Excel file listing the DMRs identified using MeDIP. This file includes three datasheets corresponding to the pairwise comparisons between sperm, fibroblasts and liver. One DMR may be present in several lanes if shared by several promoters. (XLSX 821 kb)

Additional file 3: of A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific features;Jean-Philippe Perrier;2018;figshare


Abstract: is a Microsoft Excel file listing the DMCs identified using RRBS. This file includes three datasheets corresponding to the pairwise comparisons between sperm, fibroblasts and monocytes. (XLSX 84756 kb)

Additional file 2: of A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific features;Jean-Philippe Perrier;2018;figshare


Abstract: Background: English plantain (Plantago lanceolata) is an important weed pollen allergen source triggering allergic symptoms during summer. To elucidate genuine versus cross-reactive sensitization, we investigated IgE reactivity patterns and inhibition capacities of plantain-sensitized patients. Methods: Sera of 35 rhinoconjunctivitis patients from the north-east of France with positive skin prick tests (SPT) to Plantago lanceolata pollen were tested with clinically relevant allergen sources using ELISA, ImmunoCAP, and immunoblot inhibition. Results: The patients were multisensitized with additional reactivity to grass (94.3%), ash (74.3%), birch (71.4%), and mugwort (55.2%) pollen in SPT. Sensitization prevalence to allergen molecules was 34.3% (Pla l 1), 94.3% (Phl p 1/5), 60.0% (Ole e 1), 65.7% (Bet v 1), 37.1% (profilin), and 40.0% (CCD). In immunoblot, IgE reactivity to plantain pollen was inhibited with relevant pollen extracts and purified rPla l 1. Two sera did not reveal any IgE cross-reactivity, while reactivity to plantain was efficiently inhibited by grass pollen in the sera of 10 patients. The sera from 17 different patients could be inhibited by grass, birch, or ash pollen to varying degrees. Thus, only 37.1% of our patients demonstrated true plantain pollen sensitization, while 62.9% were solely positive due to IgE cross-reactive molecules from other clinically relevant pollen. Conclusions: Plantain pollen-sensitized patients are multi-reactors demonstrating varying and complex IgE-reactivity profiles. In vivo and in vitro tests using extracts are typically blurred due to the presence of homologous allergens or CCD in grass, birch, or ash pollen. So far, Pla l 1 represents the only indicative marker allergen for the diagnosis of genuine plantain pollen sensitization.

Supplementary Material for: Do Plantago lanceolata Skin Prick Test-Positive Patients Display IgE to Genuine Plantain Pollen Allergens? Investigation of Pollen Allergic Patients from the North-East of France;T. Stemeseder;2018;Karger Publishers


Abstract: Packaging the mouse mammary tumor virus (MMTV) genomic RNA (gRNA) requires the entire 5ʹ untranslated region (UTR) in conjunction with the first 120 nucleotides of the gag gene. This region includes several palindromic (pal) sequence(s) and stable stem loops (SLs). Among these, stem loop 4 (SL4) adopts a bifurcated structure consisting of three stems, two apical loops, and an internal loop. Pal II, located in one of the apical loops, mediates gRNA dimerization, a process intricately linked to packaging. We thus hypothesized that the bifurcated SL4 structure could constitute the major gRNA packaging determinant. To test this hypothesis, the two apical loops and the flanking sequences forming the bifurcated SL4 were individually mutated. These mutations all had deleterious effects on gRNA packaging and propagation. Next, single and compensatory mutants were designed to destabilize then recreate the bifurcated SL4 structure. A structure-function analysis using bioinformatics predictions and RNA chemical probing revealed that mutations that led to the loss of the SL4 bifurcated structure abrogated RNA packaging and propagation, while compensatory mutations that recreated the native SL4 structure restored RNA packaging and propagation to wild type levels. Altogether, our results demonstrate that SL4 constitutes the principal packaging determinant of MMTV gRNA. Our findings further suggest that SL4 acts as a structural switch that can not only differentiate between RNA for translation versus packaging/dimerization, but its location also allows differentiation between spliced and unspliced RNAs during gRNA encapsidation.

The bifurcated stem loop 4 (SL4) is crucial for efficient packaging of mouse mammary tumor virus (MMTV) genomic RNA;Farah Mustafa;2018;Taylor & Francis


Abstract: Database 2. Clinical manifestations of Lyme borreliosis associated with strains grouped per ST and CC. Analyses were conducted on CCs using both DLV and SLV thresholds. (XLSX 78 kb)

Additional file 2 of Multilocus sequence typing of clinical Borreliella afzelii strains: population structure and differential ability to disseminate in humans;Floriane Gallais;2018;figshare


Abstract: Database 1. Detailed information relating to strains included in this study. All strains are listed, including those typed for this study, those extracted from the online database, and those sequenced by Coipan et al. [15]. Information is provided on the geographical origin, the clinical symptom, and sequence data relating to each strain. A list featuring the countries where each ST was identified is also available. (XLSX 103 kb)

Additional file 1: of Multilocus sequence typing of clinical Borreliella afzelii strains: population structure and differential ability to disseminate in humans;Floriane Gallais;2018;figshare


Abstract: Additional file 2: Figure S1. Impact of cherry consumption on pancreatic oxidative stress 4 months into the experimental period. Oxidative stress is assessed by dihydroethidine fluorescent probe (DHE) after 4 months of normal diet (ND), high fat high fructose (HFHF) diet, HFHF 2 months + ND 2 months (HFHF/ND), HFHF 2 months + ND with cherry supplementation 2 months (HFHF/NDCherry) and HFHF 2 months + HFHF with cherry supplementation 2 months groups (HFHFCherry). Bar scale = 100. All the results are shown as the mean ± SEM of 6 different experiments. Asterisk represents significant results vs. ND; $ vs. HFHF.

MOESM2 of Beneficial effects of cherry consumption as a dietary intervention for metabolic, hepatic and vascular complications in type 2 diabetic rats;Remmelt Werf;2018;figshare


Abstract: Additional file 1: Table S1. Food composition and food and beverage consumption.

MOESM1 of Beneficial effects of cherry consumption as a dietary intervention for metabolic, hepatic and vascular complications in type 2 diabetic rats;Remmelt Werf;2018;figshare


Abstract: Additional file 8: Table S7. The 16S rRNA gene amplicon sequencing results of 1-year monthly time series of 20 AD reactors located in Luxembourg and Belgium. Blast search results for bOTUs analysed in this study against the 8000 metagenome-reconstructed genomes from the study by Parks et al. [54].

MOESM8 of 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: Additional file 7: Table S6. The 16S rRNA gene amplicon sequencing results of 1-year monthly time series of 20 AD reactors located in Luxembourg and Belgium. Spearman correlation matrix between operational data and dominant microbial groups/ OTUs.

MOESM7 of 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: Additional file 5: Table S5. The 16S rRNA gene amplicon sequencing results of 1-year monthly time series of 20 AD reactors located in Luxembourg and Belgium. Relative abundance (%, normalised number of reads) and taxonomic affiliation of the 16S rRNA amplicon sequencing OTUs for bacteria and archaea.

MOESM5 of 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: Additional file 2: Table S1. Characterisation of the studied AD reactors. Detailed (per sample) characterisation of the studied AD reactors.

MOESM2 of 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: Stata do-file of the analysis. (TXT 10 kb)

Additional file 3: of Behavioural and demographic correlates of undiagnosed HIV infection in a MSM sample recruited in 13 European cities;Ulrich Marcus;2018;figshare


Abstract: Sialon II dataset used for the analysis presented in this manuscript. (CSV 11362 kb)

Additional file 2: of Behavioural and demographic correlates of undiagnosed HIV infection in a MSM sample recruited in 13 European cities;Ulrich Marcus;2018;figshare


Abstract: Description of data: clinical and radiological data collected for the study in the 122 newborns patients. (XLSX 48 kb)

Additional file 1: of 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: ANI and average AAI of S. lugdunensis (A-B), S. aureus (C-D), and S. epidermidis (E-F) using the EDGAR interface. ANIs were calculated as the mean identity of all BLASTN matches that showed more than 30% overall sequence identity over at least 70% of an alignable region. (PPTX 667 kb)

Additional file 2: of Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer;Xavier Argemi;2018;figshare


Abstract: Additional file 3: Figure S1. Kaplan–Meier curves of all patients with hyperlactatemia (lactate > 2 mmol/L) (n = 230) and those with lactates ≤ 2 mmol/L at baseline (n = 167).

MOESM3 of Hyperoxia toxicity in septic shock patients according to the Sepsis-3 criteria: a post hoc analysis of the HYPER2S trial;Julien Demiselle;2018;figshare


Abstract: The involvement of macroautophagy/autophagy proteins in B-cell receptor (BCR) trafficking, although suspected, is not well understood. We show that ATG5 (autophagy related 5) contributes to BCR polarization after stimulation and internalization into LAMP1 (lysosomal-associated membrane protein 1)+ and major histocompatibility complex class II (MHC-II)+ compartments. BCR polarization is crucial in the context of immobilized antigen processing. Moreover, antigen presentation to cognate T cells is decreased in the absence of ATG5 when the model antigen OVAL/ovalbumin is provided in an immobilized form in contrast to the normal presentation of soluble OVAL. We further show that ATG5 is required for centrosome polarization and actin nucleation in the immune synapse area. This event is accompanied by an increased interaction between ATG16L1 (autophagy related 16-like 1 [S. cerevisiae]) and the microtubule-organizing center-associated protein PCM1 (pericentriolar material 1). In the human B cell line BJAB, PCM1 is required for BCR polarization after stimulation. We thus propose that the ATG12 (autophagy related 12)–ATG5-ATG16L1 complex under BCR stimulation allows its interaction with PCM1 and consequently facilitates centrosome relocalization to the immune synapse, optimizing the presentation of particulate antigens. Abbreviations: ACTB: actin beta; ACTR2/3: ARP2/3 actin-related protein 2/3; APC: antigen-presenting cells; ATG: autophagy-related; BCR: B cell receptor; BECN1/Beclin 1: beclin 1, autophagy related; CDC42: cell division cycle 42; Cr2: complement receptor 2; CSFE: carboxyfluorescein succinimidyl ester; DAPI: 4ʹ,6-diamidino-2-phenylindole dihydrochloride; EEA1: early endosome antigen 1; ELISA: enzyme-linked immunosorbent assay; FITC: fluorescein isothyocyanate; GC: germinal center; GJA1/CX3: gap junction protein, alpha 1; Ig: immunoglobulin; LAMP1: lysosomal-associated membrane protein 1; LAP: LC3-associated phagocytosis; LM: littermate; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAPK/ERK: mitogen activated protein kinase; MHC-II: major histocompatibility complex class II; MIIC: MHC class II compartment; OVAL: ovalbumin; PBS: phosphate-buffered saline; PCM1: pericentriolar material 1; PtdIns3K: phosphatidylinositol 3-kinase; PTPRC/CD45RB/B220; Protein tyrosine phosphatase, receptor type, C; SYK: spleen tyrosine kinase; TBS: Tris-buffered saline; TCR: T cell receptor; ULK1: unc-51 like kinase 1

ATG5 is required for B cell polarization and presentation of particulate antigens;Florent Arbogast;2018;Taylor & Francis


Abstract: Figure S1. Time-to-event analysis for period between neurological onset and appearance of neurological manifestations of interest. VSGP and hearing loss were not taken into account in determining neurological onset. Cognitive and psychiatric symptoms were considered as a single category because they frequently overlap and their separation according to respective ages at onset may be arbitrary. Psychosis, which is part of the ‘Cognitive/Psychiatric’ category, was also analysed separately. (TIF 1229 kb)

Additional file 2: of Adult Niemann-Pick disease type C in France: clinical phenotypes and long-term miglustat treatment effect;Yann Nadjar;2018;figshare


Abstract: Representative Poales HESO1 alignment. Related to Figure 5.

Supplementary_Dataset4_Representative Poales HESO1 alignment. from RNA uridylation and decay in plants;Caroline De Almeida;2018;The Royal Society


Abstract: Alignment of HESO1 and URT1 sequences. Related to Figures 3 and 4.

Supplementary_Dataset3_HESO1 and URT1 alignment. from RNA uridylation and decay in plants;Caroline De Almeida;2018;The Royal Society


Abstract: HESO1 sequences in FASTA format. Related to Figures 3 and 4.

Supplementary_Dataset1_HESO1sequences. from RNA uridylation and decay in plants;Caroline De Almeida;2018;The Royal Society


Abstract: URT1 sequences in FASTA format. Related to Figures 3 and 4.

Supplementary_Dataset2_URT1sequences. from RNA uridylation and decay in plants;Caroline De Almeida;2018;The Royal Society


Abstract: Representative Poales URT1 alignment. Related to Figure 5.

Supplementary_Dataset5_Representative Poales URT1 alignment. from RNA uridylation and decay in plants;Caroline De Almeida;2018;The Royal Society


Abstract: Phylogeographic, chronological pattern and subsequent migrations of ancient dogs A- Pre-Neolithic dogs; B- during and after the Neolithic transition. Archaeological sites are numbered according to Table S1. Red: Haplogroup A, Blue: Haplogroup B, Yellow: Haplogroup C, Green: Haplogroup D.

Figure S1 from Dogs accompanied humans during the Neolithic expansion into Europe;Morgane Ollivier;2018;The Royal Society


Abstract: Chronological and geographical representation of ancient dog haplogroup frequencies in five geographic regions. Dotted line corresponds to the Neolithic transition in each region. Squares correspond to the different haplogroups. The 99 ancient dog sequences considered were grouped according to Table S2 Red: Haplogroup A, Blue: Haplogroup B, Yellow: Haplogroup C, Green: Haplogroup D.

Figure S3 from Dogs accompanied humans during the Neolithic expansion into Europe;Morgane Ollivier;2018;The Royal Society


Abstract: Probability of reaching haplogroup D observed frequencies under a drift model in A) Whole Europe during the Neolithic/Post-Neolithic period (Neolithic/Post-Neolithic frequency = 33%); B) in Southeastern Europe during the Neolithic/Post-Neolithic period (Neolithic/Post-Neolithic frequency = 94%); C) in Southeastern Europe during the Neolithic/Post-Neolithic period (Neolithic/Post-Neolithic frequency = 69%)). See text of supplementary data-$6 for details of the hypothesis tested.The X axis represents the number of generations; the Y axis represents the starting frequency of Hg D. Black dashed line: upper limit of the confidence interval calculated for the observed frequency; white dashed line: upper number of generation representative of duration of neolithization in each region.

Figure S4 from Dogs accompanied humans during the Neolithic expansion into Europe;Morgane Ollivier;2018;The Royal Society


Abstract: Size of the first upper molar (in centimeter, estimated by the first factor of the Fourier elliptic transform) in various Upper Paleolithic to Neolithic dogs from Eurasia (modified after Pionnier-Capitan, 2010)

Figure S5 from Dogs accompanied humans during the Neolithic expansion into Europe;Morgane Ollivier;2018;The Royal Society


Abstract: Minimum spanning network of the 2375 ancient and modern dog sequences used for this study.Nodes were coloured a posteriori considering both network and DomeTree results (Frantz et al, 2016). Red: Haplogroup A, Blue: Haplogroup B, Yellow: Haplogroup C, Green: Haplogroup D, pink: Haplogroup E, ligth blue: Haplogroup F, grey: unassigned sequences. black line: number of mutation between two haplotypes. Star: presence of ancient DNA sequences in the node.

Figure S2 from Dogs accompanied humans during the Neolithic expansion into Europe;Morgane Ollivier;2018;The Royal Society


Abstract: Summary of the mtDNA data set used in this study

Table S2 from Dogs accompanied humans during the Neolithic expansion into Europe;Morgane Ollivier;2018;The Royal Society


Abstract: Additional file 2. Raw size-exclusion chromatograms. We provide in this file the raw data of size-exclusion chromatograms used in the study (absorbance at 280 nm versus elution volume). The protein (MBP-16E6mut, MBP-8E6), resin (N1…N6, A), elution method (filter, decant) and contact time for optimization assays (2 h, 30 min, 5 min) are indicated in the worksheet names. The first worksheet entitled Readme contains explanations on the nomenclature used for worksheet titles.

MOESM2 of 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: Table S1. The top five of the most important variables by species group for each month. The variable importance is scaled from 0 to 100. Within each month (columns), the most important variable has a value of 100. (XLSX 67 kb)

Additional file 1: of 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: Ageing is characterized by the impairment of the acute innate immune response and the upregulation of low-grade inflammation, i.e. inflammaging. At the cellular level, telomeres are considered as a marker of biological ageing as their length is progressively eroded in the absence of repair mechanisms. However, the link between telomeres and inflammaging remains underexplored. We aimed to identify proteins that are differentially expressed between age classes in response to an acute inflammatory challenge. We challenged young (two months) and old (12 months) C57BL/6 mice using bacterial lipopolysaccharide (LPS) and measured telomere length and proteomic profiles in splenocytes. In total, 233 out of the 1966 proteins we quantified differed among experimental groups. A hierarchical clustering analysis revealed that nine of those 233 proteins were differently expressed among the experimental groups. Young mice responded to LPS by increasing the expression of proteins involved in the innate immune response, and interestingly, in telomere length maintenance. However, this regulation was impaired at older ages. These results are in agreement with the assumption that the strength of selection declines with age, potentially explaining the maintenance of costly, dysregulated, immune responses at old age. We suggest that the immune response is competing with the telomere maintenance process, highlighting how telomeres reflect the ageing trade-off even in a species where telomere length is not related to lifespan.

Raw proteomic data from Age-related response to an acute innate immune challenge in mice: proteomics reveals a telomere maintenance-related cost;François Criscuolo;2018;The Royal Society


Abstract: Objective:S-nitrosogluthatione (GSNO), a S-nitrosothiol, is a commonly used as nitric oxide (NO•) donor. However, its half-life is too short for a direct therapeutic use. To protect and ensure a sustained release of NO•, the encapsulation of GSNO into nanoparticles may be an interesting option. Methods: In this work, we have investigated the early (4 h) and late (24 h) transcriptomic response of THP-1 human monocytes cells to two doses (1.4 and 6 µM) of either free or Eudragit® nano-encapsulated GSNO using RNA microarray. Results: After exposure to free GSNO, genes mainly involved in apoptosis, cell differentiation, immune response and metabolic processes were differentially expressed. Although, cells exposed to free or encapsulated GSNO behave differently, activation of genes involved in blood coagulation, immune response and cell cycle was observed in both conditions. Conclusions: These results suggest that the encapsulation of low doses of GSNO into Eudragit® nanoparticles leads to a progressive release of GSNO making this compound a possible oral therapy for several biomedical applications like inflammatory bowel diseases.

Encapsulation of <i>S</i>-nitrosoglutathione: a transcriptomic validation;Ramia Safar;2020;Taylor & Francis


Abstract:
Data necessary to reproduce the figures of Elastic strain effects on wave scattering : implications for CWI (Azzola et al., 2020), accepted in Journal of Geophysical Research: Solid Earth.
- Scaterring properties and mechanical characterization of the sample from measurements obtained in the laboratory and during simulations.
- Coda Wave Interferometry data during repeated mechanical loading of an Au4G sample, in the laboratory and during simulations replicating the conditions of the laboratory experiments.

Elastic strain effects on wave scattering: implications for coda wave interferometry (CWI) (accompanies Azzola et al. (2020)).;Jérôme AZZOLA;2020;figshare


Abstract: Figure S1. Annual rate of infection by 5-years range within the hospitalized DS patients. (TIF 4139 kb)

Additional file 1: of Infection risk among adults with down syndrome: a two group series of 101 patients in a tertiary center;Aurélien Guffroy;2019;figshare


Abstract: Full genetic data. (XLSX 470 kb)

Additional file 1: of ‘Dusty core disease’ (DuCD): expanding morphological spectrum of RYR1 recessive myopathies;Matteo Garibaldi;2019;figshare


Abstract: Additional file 2. Test lists, and number of articles from the test lists retrieved by the bibliographic search.

MOESM2 of What is the evidence that ecosystem components or functions have an impact on infectious diseases? A systematic review protocol;Léa Lugassy;2019;figshare


Pyramid Quantile Regression

Abstract: We describe a Bayesian model for simultaneous linear quantile regression at several specified quantile levels. More specifically, we propose to model the conditional distributions by using random probability measures, known as quantile pyramids, introduced by Hjort and Walker. Unlike many existing approaches, this framework allows us to specify meaningful priors on the conditional distributions, while retaining the flexibility afforded by the nonparametric error distribution formulation. Simulation studies demonstrate the flexibility of the proposed approach in estimating diverse scenarios, generally outperforming other competitive methods. We also provide conditions for posterior consistency. The method is particularly promising for modeling the extremal quantiles. Applications to extreme value analysis and in higher dimensions are also explored through data examples. Supplemental material for this article is available online.

Pyramid Quantile Regression;T. Rodrigues;2019;Taylor & Francis


Abstract: Background: The geography of southern Iberia and an abundant archaeological record of human occupation are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components. Aim: To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages. Subject and methods: Four hundred and fourteen male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed. Results: Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269, whereas haplogroups E, J, I, G and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages. Conclusion: The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201 highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.

Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world;Candela L. Hernández;2019;Taylor & Francis


Abstract: Video S2. Example of “resident leaves”. Bee W25 landed on a flower occupied by bee Y35 and left second, therefore replacing bee Y35. In this example, the flower was “not-emptied” as bee Y35 fed on the flower for less than 8 s before the interaction occurred. (AVI 2069 kb)

Additional file 4: of A spatial network analysis of resource partitioning between bumblebees foraging on artificial flowers in a flight cage;Cristian Pasquaretta;2019;figshare


Abstract: Video S1. Example of “resident stays”. Bee Y67 landed on a flower occupied by bee W58 and left spontaneously. In this example, the flower was “not-emptied” as bee W58 fed on the flower for less than 8 s before the interaction occurred. (AVI 461 kb)

Additional file 3: of A spatial network analysis of resource partitioning between bumblebees foraging on artificial flowers in a flight cage;Cristian Pasquaretta;2019;figshare


Abstract: Dataset S1. Raw dataset. Flower visitation dataset containing all flower visits by each individual bee over the five days of observation. (CSV 59 kb)

Additional file 2: of A spatial network analysis of resource partitioning between bumblebees foraging on artificial flowers in a flight cage;Cristian Pasquaretta;2019;figshare


Abstract: Abstract Background Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B). However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B. Results Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B. Conclusion Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.

Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources;Camille Rustenholz;2020;figshare


Abstract: Authors’ original file for figure 2

Additional file 2 of Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources;Camille Rustenholz;2020;figshare


Additional file of Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources;Camille Rustenholz;2020;figshare


Abstract: Authors’ original file for figure 1

Additional file 1 of Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources;Camille Rustenholz;2020;figshare


Abstract: Distributions of differentially expressed genes of the FLOR-ID database in the clusters. (XLSX 28 kb)

Additional file 9: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: Best enriched biological process (BP) GO terms for the 24 clusters. The best BP GO term was extracted with its FDR from each SEA analysis. (XLSX 11 kb)

Additional file 7: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: List of genes per cluster. (XLSX 187 kb)

Additional file 6: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: List of lncTUs. (XLSX 639 kb)

Additional file 5: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: Information in PLACE and AGRIS databases on the identified motifs. (XLSX 38 kb)

Additional file 23: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: List of oligonucleotides. (XLSX 8 kb)

Additional file 22: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: Distribution of the TFBFs in the regions of the lncTUs. (XLSX 21 kb)

Additional file 21: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: Expression of lncTUs and their NATs. (XLSX 25 kb)

Additional file 19: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: Distribution of differentially expressed genes associated with chromatin biology. CR: chromatin remodeling. (XLSX 9 kb)

Additional file 18: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: Differentially expressed genes associated with chromatin biology. (XLSX 19 kb)

Additional file 17: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: TFs from the FLOR-ID. (XLSX 12 kb)

Additional file 15: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: Motifs identified with the PLM algorithm. (XLSX 87 kb)

Additional file 13: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: Distribution of the TFs among the clusters. (XLSX 38 kb)

Additional file 14: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: Hormone-related genes involved in several hormonal pathways in the clusters. (XLSX 10 kb)

Additional file 12: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: Hormone-related genes supported by genetic evidence in clusters. (XLSX 22 kb)

Additional file 10: of Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;figshare


Abstract: Table S2. List of vastus lateralis proteins identified in 2D gel spots, and exhibiting a differential abundance between hibernating (winter) and active (summer) brown bears (Ursus arctos). (XLSX 53â kb)

Additional file 2: of Metabolic reprogramming involving glycolysis in the hibernating brown bear skeletal muscle;Blandine Chazarin;2019;figshare


Abstract: Table S1. List of vastus lateralis proteins analysed in hibernating (winter) and active (summer) brown bears (Ursus arctos) using a MS-based strategy. (XLSX 4373â kb)

Additional file 1: of Metabolic reprogramming involving glycolysis in the hibernating brown bear skeletal muscle;Blandine Chazarin;2019;figshare


Abstract: Abstract: Insects are the most diverse group of animals. They can be infected by an extraordinary diversity of viruses. Among them, arthropod-borne viruses (arboviruses) can be transmitted to humans. High-throughput sequencing of small RNAs from insects provides insight into their virome, which may help understand the dynamics of vector borne infectious diseases. Furthermore, investigating the mechanisms that restrict viral infections in insects points to genetic innovations that may inspire novel antiviral strategies.

The insect reservoir of biodiversity for viruses and for antiviral mechanisms;ROENICK P. OLMO;2019;SciELO journals


Abstract: Rationale: Targeted lung denervation (TLD) is a novel bronchoscopic treatment for the disruption of parasympathetic innervation of the lungs. Objectives: To assess safety, feasibility, and dosing of TLD in patients with moderate to severe COPD using a novel device design. Methods: Thirty patients with COPD (forced expiratory volume in 1 s 30–60%) were 1:1 randomized in a double-blinded fashion to receive TLD with either 29 or 32 W. Primary endpoint was the rate of TLD-associated adverse airway effects that required treatment through 3 months. Assessments of lung function, quality of life, dyspnea, and exercise capacity were performed at baseline and 1-year follow-up. An additional 16 patients were enrolled in an open-label confirmation phase study to confirm safety improvements after procedural enhancements following gastrointestinal adverse events during the randomized part of the trial. Results: Procedural success, defined as device success without an in-hospital serious adverse event, was 96.7% (29/30). The rate of TLD-associated adverse airway effects requiring intervention was 3/15 in the 32 W versus 1/15 in the 29 W group, p = 0.6. Five patients early in the randomized phase experienced serious gastric events. The study was stopped and procedural changes made that reduced both gastrointestinal and airway events in the subsequent phase of the randomized trial and follow-up confirmation study. Improvements in lung function and quality of life were observed compared to baseline values for both doses but were not statistically different. Conclusions: The results demonstrate acceptable safety and feasibility of TLD in patients with COPD, with improvements in adverse event rates after procedural enhancements.

Supplementary Material for: Safety and Dose Study of Targeted Lung Denervation in Moderate/Severe COPD Patients;A. Valipour;2019;Karger Publishers


Abstract: Supplementary Figures and Tables (Tables S1â S4, and S6â S13). (XLSX 183 kb)

Additional file 2: of New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome;Eric Chater-Diehl;2019;figshare


Abstract: Figure S1. (A) Kaplan- Meier estimation of time to first relapse, according to clinical phenotype at the onset. The 2-year risk of the first relapse was 70.7% (95%CI 60.7–80.1) for optic neuritis (reference), 64% (95%CI 45.8–81.8; Log-rank p = 0.589) for transverse myelitis, 77.8% (95%CI 48.7–96.6; Log-rank p = 0.458) for optic neuritis and transverse myelitis, and 44.4% (95%CI 19.6–79.6; Log-rank p = 0.617) for encephalopathy/brainstem syndrome. (B) Time to NMOSD-like phenotype conversion according to clinical phenotype at the onset. The 2-year risk to NMOSD-like phenotype conversion was 17.3%; 95%CI, 8.9–36.4 for optic neuritis (as a reference), 38.2% (95%CI, 20.8–63.0; Log-rank p = 0.032) for transverse myelitis, 14.3% (95%CI, 2.14–66.6; Log-rank p = 0.199) for encephalopathy/brainstem syndrome; 100% relapsed at onset (Log-rank p

Additional file 2: of Evaluation of treatment response in adults with relapsing MOG-Ab-associated disease;Alvaro Cobo-Calvo;2019;figshare


Abstract: Timeline of the episode of care. (TIFF 1955 kb)

Additional file 1: of Retrieving a displaced third molar from the infratemporal fossa: case report of a minimally invasive procedure;Jean-Christophe Lutz;2019;figshare


Abstract: Ribosomal RNA sequences used to filter reads. (FA 20 kb)

Additional file 7 of Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods;Polina Drozdova;2019;figshare


Abstract: Sequences and characteristics of metallothionein-like transcripts. (XLSX 13 kb)

Additional file 6 of Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods;Polina Drozdova;2019;figshare


Abstract: Comparison of transcripts differentially expressed in response to temperature and/or cadmium treatments. (XLSX 51 kb)

Additional file 5 of Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods;Polina Drozdova;2019;figshare


Abstract: GO terms overrepresented in transcripts that were differentially expressed in response to elevated temperature or cadmium. For explanations of the column names please see the caption for Additional file 2. (XLSX 62 kb)

Additional file 4 of Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods;Polina Drozdova;2019;figshare


Abstract: GO terms overrepresented in transcripts that were differentially expressed between species. Terms that are robust regardless of the assembly used as a reference are shown in bold. Annotated: the number of transcripts annotated with the corresponding GO term. Significant: the observed number of DE transcripts annotated with the corresponding GO term. Expected: the expected number of DE transcripts. (XLSX 176 kb)

Additional file 2 of Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods;Polina Drozdova;2019;figshare


Abstract: List of transcripts that were differentially expressed in response to elevated temperature or cadmium. (XLSX 236 kb)

Additional file 3 of Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods;Polina Drozdova;2019;figshare


Abstract: Periodic catatonia (PC) is a psychomotor phenotype with a progressive-remitting course. While it can fit any disorder diagnosis of the schizoaffective spectrum, its core features consist of a mix of hypo- and hyperkinesias resulting in distortions of expressive movements such as grimacing and parakinesias. The replication of cerebral blood flow (CBF) increases in the left supplementary motor area (L-SMA) and lateral premotor cortex (L-LPM) in acute and remitting PC patients indicates that these increases could be used as diagnostic biomarkers. In this proof-of-concept study, 2 different MRI sequences were repeated on 3 separate days to get reliable measurement values of CBF in 9 PC and 26 non-PC patients during different cognitive tasks. Each patient was compared to 37 controls. In L-SMA [–9; +10; +60] and L-LPM [–46; –12; +43], a test was positive if the <i>t</i> value was >2.02 (α < 0.05; two tailed). The measurements had good analytical performance. Regarding the tests, their sensitivities and specificities were significantly different from the chance level on both measures, except for L-SMA sensitivities. When combining all the tests, among regions and methods, sensitivity was 98% (95% credible interval [CI] 76–100%) and specificity 88% (72–97%). Bayesian inferences of its negative predictive values for PC were >95% regardless of the context, while its positive predictive values reached 94% but only when used in combination with clinical criteria. The case-by-case analysis suggests that non-PC patients with neurological motor deficits are at risk to be false positive.

Supplementary Material for: A Brain Imaging-Based Diagnostic Biomarker for Periodic Catatonia: Preliminary Evidence Using a Bayesian Approach;J.R. Foucher;2019;Karger Publishers


Abstract: Abstract: In the present context of concerns for biodiversity, the French Academy of Sciences produced in 2017 a report entitled “Mechanisms of adaptation of biodiversity to climate change and their limits”. We briefly review here the production process and structure of the report, and summarize its conclusions and recommendations. The conclusions emphasize the role of habitat fragmentation in the expected impact of climate change on biodiversity, in particular for organisms with limited dispersal abilities, and the disparities in species responses which must be taken to understand the future of species assemblages (“communities”) under different scenarios of climate change. The recommendations cover the organization of biodiversity research and monitoring (development of observatories, key role of embedded time scales and modeling, integration of Human and Social Sciences), as well as critical domains such as Human, animal and plant health, agriculture and forestry policies, and management of the Environment.

An overview of the 2017 report of the French academy of Sciences on biodiversity;SANDRA LAVOREL;2019;SciELO journals


Abstract: Clinical, molecular, histopathological and ultrastructural findings for the patients. Table S1 Clinical and molecular findings in the DNM2 severe cases. Figure S1 Histopathological and ultrastructural findings for the patients. Patients 1, 2 and 3: Hematoxilin-eosin (HE) staining of muscles showing fibers with centralized nuclei. Patient 1: ATPase at pH 9.4 showing type I (pale) and type II (dark) fibers. Patient 3: ATPase at pH 4.6 showing type 1 fibers dark and type 2 fibers less stained. Scale bars 20 μm. (ZIP 46909 kb)

Additional file 1: of Some DNM2 mutations cause extremely severe congenital myopathy and phenocopy myotubular myopathy;Valérie Biancalana;2019;figshare


Abstract: A movie showing 3D images processed with Imaris software. The PLA (BIN1/total Tau) signal (green) was located in the vicinity of the actin staining (red) at the membrane. (ZIP 10MB)

Additional file 11: of Tau phosphorylation regulates the interaction between BIN1â s SH3 domain and Tauâ s proline-rich domain;Yoann Sottejeau;2019;figshare


Abstract: Video showing a drop detaching from a stalactite in Orgnac cave. The shape oscillations of the drop can be seen as it starts falling.

Drop detaching from a stalactite from A drop does not fall in a straight line: a rationale for the width of stalagmites;J. Parmentier;2019;The Royal Society


Abstract: Video showing a drop impacting the concave summit of stalagmite Org07 (Orgnac cave). A calcite pearl of around 1.5 cm radius, completely disjoint from the stalagmite, is visible in the center.

Drop impact on Org07 from A drop does not fall in a straight line: a rationale for the width of stalagmites;J. Parmentier;2019;The Royal Society


Abstract: Video showing a drop impacting the flat top of stalagmite Org02 (Orgnac cave).

Drop impact on Org02 from A drop does not fall in a straight line: a rationale for the width of stalagmites;J. Parmentier;2019;The Royal Society


Abstract: Additional file 1. AML building example. Source code for the ML results.

MOESM1 of Dataset’s chemical diversity limits the generalizability of machine learning predictions;Marta Glavatskikh;2019;figshare


Abstract: Additional file 2. Functional groups analysis. Complete table of all encountered functional groups in PC9 and QM9.

MOESM2 of Dataset’s chemical diversity limits the generalizability of machine learning predictions;Marta Glavatskikh;2019;figshare


Abstract: Additional file 5: Table S4. BLAST search output summaries for transcript candidates involved in the phenylpropanoid pathway for 13 berry fruit species: Enzymes of the core pathway and its decorating, modifying and regulatory proteins.

MOESM5 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics;Vera Thole;2019;figshare


Abstract: Additional file 6: Table S5. Peptide annotation for the transcriptomes of R. genevieri and R. idaeus cv. Prestige.

MOESM6 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics;Vera Thole;2019;figshare


Abstract: Additional file 4: Table S3. RNA-seq descriptors for two Rubus species at three fruit ripening stages: green, immature and ripe.

MOESM4 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics;Vera Thole;2019;figshare


Abstract: Additional file 3: Table S2. RNA-seq descriptors for 13 berry fruit species.

MOESM3 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics;Vera Thole;2019;figshare


Abstract: Additional file 1: Table S1. Classification and description of berry fruit species.

MOESM1 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics;Vera Thole;2019;figshare


Abstract: Additional file 15: Table S9. Differential expression of candidate transcripts homologous to enzymes involved in the phenylpropanoid pathway of R. genevieri and R. idaeus cv. Prestige during three fruit ripening stages: Examples of candidate enzymes of the general phenylpropanoid pathway, flavonoid regulatory enzymes, transporters, decorating and modifying enzymes.

MOESM15 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics;Vera Thole;2019;figshare


Abstract: Additional file 12: Table S8. Homologues of the regulatory genes cloned in this study in the collection of the 13 berry fruit species.

MOESM12 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics;Vera Thole;2019;figshare


Abstract: Figure S1. Pattern of voxel-wise gray matter loss in DLB patients compared with healthy elderly subjects at a more permissive significance threshold (p<0.0001 uncorrected for multiple comparisons). Abbreviations: BC: brainstem, Thal: thalamus

Additional file 2: of Changes in gray matter volume and functional connectivity in dementia with Lewy bodies compared to Alzheimer’s disease and normal aging: implications for fluctuations;Eléna Chabran;2020;figshare


Abstract: Additional file 3: Supplementary materials. Thermal properties database for samples of the Upper Rhine Graben in the dry state at ambient temperature (black), water-saturated state at ambient temperature (blue), dry state at high temperature (red). Samples are in stratigraphical order. Data include lithology, measured porosity, measuring temperature, thermal conductivity and associated standard deviation, thermal diffusivity and associated standard deviation, calculated volumetric heat capacity and associated standard deviation, effect of water saturation and slope of the trendline of thermal conductivity as a function of temperature (Fig. 8).

MOESM3 of Heat flow density estimates in the Upper Rhine Graben using laboratory measurements of thermal conductivity on sedimentary rocks;Pauline Harlé;2019;figshare


Abstract: Additional file 1: Appendix A. Equations of the trendlines of thermal conductivity as a function of temperature shown in Fig. 8. Coefficient of determination R2 are also given. The samples are ordered by lithology.

MOESM1 of Heat flow density estimates in the Upper Rhine Graben using laboratory measurements of thermal conductivity on sedimentary rocks;Pauline Harlé;2019;figshare


Abstract: Additional file 9: Table S3. Nucleotide sequences and expression profiles across the four tissues of biosynthetic genes and transcription factors involved in isoflavone and miroestrol biosyntheses.

MOESM9 of Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol;Nithiwat Suntichaikamolkul;2019;figshare


Abstract: Additional file 6: Figure S6. Ion extract chromatogram of the annotated genistein ([M-H] = 269, RT = 18.78) of methanolic extracts of GFP transiently overexpressed in N. benthamiana (a), P. mirifica Isoflavone synthase (PmIFS) transiently expressed in N. benthamiana (b), and P. mirifica Isoflavone synthase (PmIFS) and Arabidopsis MYB12 transcription factor transiently co-expressed in N. benthamiana (c), as detected by HPLC-QTOF-MS/MS in negative mode.

MOESM6 of Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol;Nithiwat Suntichaikamolkul;2019;figshare


Abstract: Additional file 5: Figure S5. Differential expressed genes (DEGs) predicted as UDP-glycosyltransferases that might be involved in isoflavone biosynthetic pathway across the four tissues of P. mirifica.

MOESM5 of Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol;Nithiwat Suntichaikamolkul;2019;figshare


Abstract: Additional file 4: Figure S4. KEGG pathway enrichment analysis of assembled unigenes in P. mirifica. a The Number of unigenes in 19 sub-categories of metabolic pathway category. b The 21 sub-categories of metabolism of terpenoids and polyketides, and other secondary metabolites.

MOESM4 of Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol;Nithiwat Suntichaikamolkul;2019;figshare


Abstract: Additional file 3: Figure S3. Gene ontology (GO) annotation for all assembled unigenes in P. mirifica. The 56 subcategories are affiliated to three main domains: biological process, cellular component, and molecular function. The GO categories were created using WEGO software.

MOESM3 of Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol;Nithiwat Suntichaikamolkul;2019;figshare


Abstract: Additional file 2: Figure S2. Clusters of orthologous groups (COG) functional classification for all assembled unigenes in P. mirifica. The vertical coordinates are function classes of COG, and the horizontal coordinates are numbers of unigenes.

MOESM2 of Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol;Nithiwat Suntichaikamolkul;2019;figshare


Abstract: Additional file 1: Figure S1. Whole plant of the approximately 3-year-old P. mirifica. (bar = 5 cm)

MOESM1 of Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol;Nithiwat Suntichaikamolkul;2019;figshare


Abstract: Abstract Background As far as we know, little data, whether obtained from self-administered questionnaires or upon dental clinical examination, has been published on the prevalence of sensitive teeth (ST) in the French adult population. The objectives of the present work were to estimate ST prevalence and characteristics in the general population of France and to explore the associated factors. Method A multicentre cross-sectional study was conducted between November 2011 and March 2013 in six French cities. Adult passers-by in public places were invited to answer an electronic questionnaire on a tablet computer. Only people who declared having at least one natural tooth were included in the study. A logistic regression model was used for the multivariate analysis. Results The prevalence of ST during the previous 12 months reported by the sample of 2413 participants was 42.2% [95% CI: 40.2–44.1%]. The final logistic regression model showed significant statistical associations between ST and female gender, use of tobacco, consumption of soft drinks, limited access to oral care and poor oral hygiene habits (p

Prevalence of sensitive teeth and associated factors: a multicentre, cross-sectional questionnaire survey in France;Alessandra Blaizot;2020;figshare


Abstract: Additional file 1. Reference catalogue of the 1348 earthquakes discussed in the paper. For each event, it contains the following parameters, in the following order: origin date and time (UTC time), northing and easting of epicenter location (Lambert II extended coordinate system, meters), depth (true vertical depth below sea level, meters), local magnitude (vertical component), azimuth and dip of the small uncertainty axis (Az1, Dip1, degrees), azimuth and dip of the middle uncertainty axis (Az2, Dip2, degrees), smallest-, middle- and largest-uncertainties (Len1, Len2 and Len3, meters) and the recorded period: 0–GRT-1 drilling, 1–GRT-1 thermal stimulation, 20–GRT-1 hydraulic stimulation, 21–GRT-1 burst of seismicity and 3–GRT-2 drilling. See text for more details on how these values were calculated.

Additional file 1 of Seismicity induced during the development of the Rittershoffen geothermal field, France;Vincent Maurer;2020;figshare


Abstract: Additional file 6: Table S5. tRNA A34I modification analysis.

Additional file 6 of A rare codon-based translational program of cell proliferation;Joao Guimaraes;2020;figshare


Abstract: Additional file 7: Table S6. Primer, adapter and coding sequences.

Additional file 7 of A rare codon-based translational program of cell proliferation;Joao Guimaraes;2020;figshare


Abstract: Additional file 5: Table S4. Differential expression analysis of mRNA and protein levels (10% vs 1% FCS).

Additional file 5 of A rare codon-based translational program of cell proliferation;Joao Guimaraes;2020;figshare


Abstract: Additional file 4: Table S3. Differential expression analysis of mRNA and ribosome occupancy (10% vs 1% FCS).

Additional file 4 of A rare codon-based translational program of cell proliferation;Joao Guimaraes;2020;figshare