Abstract: Additional file 3: Table S2. Codon scores across different experiments.

Additional file 3 of A rare codon-based translational program of cell proliferation;Joao Guimaraes;2020;figshare


Abstract: Additional file 2: Table S1. Codon usage of different gene sets (G1-specific, G2M-specific and All genes).

Additional file 2 of A rare codon-based translational program of cell proliferation;Joao Guimaraes;2020;figshare


CCDC 2008001: Experimental Crystal Structure Determination;Bao, Shu-Jin;2020;Cambridge Crystallographic Data Centre

Related Article: Shu-Jin Bao, Ze-Ming Xu, Yun Ju, Ying-Lin Song, Heng Wang, Zheng Niu, Xiaopeng Li, Pierre Braunstein, Jian-Ping Lang|2020|J.Am.Chem.Soc.|142|13356|doi:10.1021/jacs.0c07014


CCDC 2008003: Experimental Crystal Structure Determination;Bao, Shu-Jin;2020;Cambridge Crystallographic Data Centre


CCDC 2008013: Experimental Crystal Structure Determination;Bao, Shu-Jin;2020;Cambridge Crystallographic Data Centre


Abstract: Fecal cortisol metabolites and life history information on female Columbian ground squirrels. Data from publication Sosa, Dobson, Bordier, Neuhaus, Saraux, Bosson, Palme, Boonstra & Viblanc. 2020. Behavioral Ecology and Sociobiology.

Social stress in female Columbian ground squirrels: density-independent effects of kin contribute to variation in fecal glucocorticoid metabolites;Sebastian Sosa;2020;figshare


Abstract: Additional file 2: Figure 1. Control experiments for IHC.

Additional file 2 of Distribution of Parkinson’s disease associated RAB39B in mouse brain tissue;Yujing Gao;2020;figshare


Abstract: Data set corresponding to the publication by Viblanc, Schull, Stier, Durand, Lefol, Robin, Zahn, Bize, Criscuolo (2020). Foster rather than biological parental telomere length predicts offspring survival and telomere length in king penguins

Foster rather than biological parental telomere length predicts offspring survival and telomere length in king penguins;Vincent A Viblanc;2020;figshare


Abstract: Additional file 8 Answers according to large et small volume centers. The groups were defined on the median of lung transplants performed in 2017 (n = 28). LTx: lung transplantation.

Additional file 8 of Worldwide clinical practices in perioperative antibiotic therapy for lung transplantation;Benjamin Coiffard;2020;figshare


Abstract: Additional file 7. Answers to Case 5.

Additional file 7 of Worldwide clinical practices in perioperative antibiotic therapy for lung transplantation;Benjamin Coiffard;2020;figshare


Abstract: Additional file 4. Answers to Case 2.

Additional file 4 of Worldwide clinical practices in perioperative antibiotic therapy for lung transplantation;Benjamin Coiffard;2020;figshare


Abstract: Additional file 5. Answers to Case 3.

Additional file 5 of Worldwide clinical practices in perioperative antibiotic therapy for lung transplantation;Benjamin Coiffard;2020;figshare


Abstract: Additional file 6. Answers to Case 4.

Additional file 6 of Worldwide clinical practices in perioperative antibiotic therapy for lung transplantation;Benjamin Coiffard;2020;figshare


Abstract: Additional file 3. Answers to Case 1.

Additional file 3 of Worldwide clinical practices in perioperative antibiotic therapy for lung transplantation;Benjamin Coiffard;2020;figshare


Abstract: Additional file 2. Raw anonymized answers of the 99 participants

Additional file 2 of Worldwide clinical practices in perioperative antibiotic therapy for lung transplantation;Benjamin Coiffard;2020;figshare


Abstract: Additional file 7: Figure S3. Maximum likelihood phylogenetic tree using 28S rDNA. Values at the nodes represent bootstrap values greater than 800 for the most important nodes (1000 replicates).

Additional file 7 of The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level;Antoine Mignotte;2020;figshare


Abstract: Additional file 6: Figure S2. Maximum likelihood phylogenetic tree using cox1. Values at the nodes represent bootstrap values greater than 800 for the most important nodes (1000 replicates).

Additional file 6 of The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level;Antoine Mignotte;2020;figshare


Abstract: Additional file 5: Figure S1. Maximum likelihood phylogenetic tree using 16S rDNA. Values at the nodes represent bootstrap values greater than 800 for the most important nodes (1000 replicates).

Additional file 5 of The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level;Antoine Mignotte;2020;figshare


Abstract: Additional file 3: Table S3. Reference sequences used for specific assignation.

Additional file 3 of The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level;Antoine Mignotte;2020;figshare


Abstract: Additional file 4: Table S4. Information on all Culicoides sequenced and GenBank accession numbers.

Additional file 4 of The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level;Antoine Mignotte;2020;figshare


Abstract: Additional file 2: Table S2 Primers used for PCRs and sequencing in this study.

Additional file 2 of The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level;Antoine Mignotte;2020;figshare


Abstract: Additional file 1: Table S1. Information on adult female Culicoides sampling sites and results of specific assignation using cox1.

Additional file 1 of The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level;Antoine Mignotte;2020;figshare


Abstract: Additional file 2 : Table S1 Overview of the S. cerevisiae collection. Profile id column indicates the unique combination of CDS alleles. Columns reporting the CDS alleles indicate the id of the sequence as reported in the multi fasta database of the unique sequences (http://1002genomes.u-strasbg.fr/files/MitochondrialGenomes/allNonRedundantAlleles.tar.gz). Introns and endonucleases presence/absence is coded 1, for presence, or 0, for absence. NA indicate unavailable sequence. Endonucleases and omega intron were identified by blast search using a cut-off of 90% of identity on 90% of sequence overlap with a reference sequence (see materials and methods). nt in the reference are indicated with the upstream nucleotide position. Positions of the GC cluster refers to the starting position in the reference sequence. Cluster which are absent in the reference sequence are indicated with the first upstream position.

Additional file 2 of Discordant evolution of mitochondrial and nuclear yeast genomes at population level;Matteo De Chiara;2020;figshare


Abstract: R Script containing the functions associated to the R Script Behavioural inference of sea turtle

R Functions Behavioural inference of sea turtle from Behavioural inference from signal processing using animal-borne multi-sensor loggers: a novel solution to extend the knowledge of sea turtle ecology;Lorène Jeantet;2020;The Royal Society


Abstract: R-script containing the overall procedure to automatically predict the behaviours from raw acceleration, angular speed and depth data

R Script Behavioural inference of sea turtle from Behavioural inference from signal processing using animal-borne multi-sensor loggers: a novel solution to extend the knowledge of sea turtle ecology;Lorène Jeantet;2020;The Royal Society


Abstract: R script containing the required package and script to visualise the raw acceleration signals associated with the behavioural labels of the immature green turtles

R Script Visualisation of the raw data associated with the behaviours of sea turtle from Behavioural inference from signal processing using animal-borne multi-sensor loggers: a novel solution to extend the knowledge of sea turtle ecology;Lorène Jeantet;2020;The Royal Society


Abstract: Background: Mobilization after surgery is recommended to reduce the risk of adverse effects and to improve recovery. The aim of this study was to examine the associations between perioperative physical activity and postoperative outcomes in colorectal surgery. Methods: The daily number of footsteps was recorded from preoperative day 5 to postoperative day 3 in a prospective cohort of patients using wrist accelerometers. Timed Up and Go Test (TUGT), 6 Min Walking Test (6MWT), and peak expiratory flow (PEF) were assessed preoperatively. ROC curves were used to assess the performance of physical activity as a diagnostic test of complications and prolonged length of stay (LOS) of more than 5 days. Results: A total of 50 patients were included. Patients with complications were significantly older (67 years) than those without complications (53 years, p = 0.020). PEF was significantly lower in the group with complications (mean flow 294.3 vs. 363.6 L/min, p = 0.038) while there was no difference between groups for the other two tests (TUGT and 6MWT). The tests had no capacity to discriminate the occurrence of complications and prolonged LOS, except the 6MWT for LOS (AUC = 0.746, p = 0.004, 95% CI: 0.604–0.889). There was no difference in the mean number of preoperative footsteps, but patients with complications walked significantly less postoperatively (mean daily footsteps 1,101 vs. 1,243, p = 0.018). Conclusions:Colorectal surgery patients with complications were elderly, had decreased PEF, and walked less postoperatively. The 6MWT could be used preoperatively to discriminate patients with potentially increased LOS and foster mobilisation strategies.

Supplementary Material for: Physical Activity and Outcomes in Colorectal Surgery: A Pilot Prospective Cohort Study;D. Martin;2020;Karger Publishers


Abstract: Dispersion of data for the first three dimensions of the PCAs in each species of macaques and social context

3D cluster graphs from Tolerant and intolerant macaques show different levels of structural complexity in their vocal communication;Nancy Rebout;2020;The Royal Society


Abstract: It includes all raw data and scripts for running experiments, cleaning data and plotting. A detailed introduction could be found in the zip file package.

Artifact for Euro-Par2020 Paper -- Improving mapping for sparse direct solvers: A trade-off between data locality and load balancing;Changjiang Gou;2020;figshare


Abstract: Additional file 3.

Additional file 3 of The insula, a grey matter of tastes: a volumetric MRI study in dementia with Lewy bodies;Nathalie Philippi;2020;figshare


Abstract: Additional file 2.

Additional file 2 of The insula, a grey matter of tastes: a volumetric MRI study in dementia with Lewy bodies;Nathalie Philippi;2020;figshare


Abstract: Additional file 1 : Supplemental figure. VBM analyses for changes in tastes (food scores) in the DLB group. GM volumes within bilateral insular cortices negatively correlated with the total score on the questionnaire on changes in tastes, using a threshold of P = 0.001 uncorrected, including age and TGM as nuisance covariates, k = 50.

Additional file 1 of The insula, a grey matter of tastes: a volumetric MRI study in dementia with Lewy bodies;Nathalie Philippi;2020;figshare


Abstract: Additional file 9: Figure S4. Correlation of viral isoform abundances quantified by ONT sequencing between T cell replicates. The relative abundances of HIV-1 spliced RNAs were calculated as a % of the total number of spliced viral RNAs. Results were compared between infected T cell samples obtained from 3 different donors using a linear regression model supplied by Prism 7: (a) donor 1 vs donor 2; (b) donor 1 vs donor 3; (c) donor 2 vs donor 3. Pearson correlation coefficients r are indicated. p<0.0001.

Additional file 9 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Additional file 7: Table S5. Details on read counts in infected CD4+ T cells.

Additional file 7 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Additional file 5: Figure S1. Viral isoform levels in different models of HIV-1 expressing cells. (a) Exon combinations identified by ONT sequencing in infected T cells (INF T cells), transfected (TF HeLa) or infected (INF HeLa) HeLa cells. (b) Exon combinations ≥5 copies amongst replicates and considered as existing viral isoforms in the rest of the analysis.

Additional file 5 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Additional file 2: Table S2. Read mapping statistics of HIV-1 expressing HeLa cell samples, sequenced with ONT device. ONT sequencing reads were mapped to both the human and HIV NL4-3 genomes, using Minimap2. NI: non-infected HeLa cells; INF: infected HeLa cells; TF: transfected HeLa cells; WT U1 HeLa: wild type U1 snRNA co-transfected HeLa cells; U1 D2upEx HeLa: modified U1 D2upEx snRNA co-transfected HeLa cells.

Additional file 2 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Additional file 4: Table S4. HIV-1 transcripts identified in the different cellular models. Reads mapping to each isoform were counted and pooled for each HIV-1 expression model. Isoforms represented by ≥5 reads in T cells were highlighted in grey. The class of transcripts, the splice junctions involved and the study where they were first identified are indicated. New exon combinations represented by less than 5 reads were not named (ND: not defined). N: New isoform identified in this study.

Additional file 4 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Additional file 3: Table S3. NL4-3 splice site counts in HIV-1 expressing samples. Reads overlapping potential SD/SA sites were counted and pooled for each HIV-1 expressing sample (infected T cells; Transfected HeLa cells; Infected HeLa cells; WT U1 HeLa: HeLa cells co-transfected with wild-type U1 snRNA and NL4-3 provirus; U1 D2upEx HeLa: HeLa cells co-transfected with modified U1D2upEx snRNA and NL4-3 provirus). Splice sites observed at least 5 times in a same splice junction of a transcript are highlighted in grey. Known SA/SD were named according to the established classification. Putative splice sites were considered as new only if they were represented in a splice junction of a transcript represented at least 5 times and if they were involved in a consensus splice junction (GT-AG).

Additional file 3 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Additional file 1: Table S1. Read mapping statistics of HIV-1 infected T cell samples, sequenced with ONT device. Activated CD4+ T cells from 3 different donors were infected with NL4-3 VSV-G pseudotyped virus, harvested 24 h later and RNA was extracted. cDNA libraries were prepared and sequenced using MinION device from ONT. Raw reads from 3 different CD4+ T cell samples were mapped onto the human and the HIV-1 NL4-3 genome using Minimap2.

Additional file 1 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Additional file 16: Table S8. List of primers used in this study.

Additional file 16 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Additional file 14: Table S7. Viral transcripts identified in HIV-1 infected T cells between 12 h and 24 h of infection and in viral particles. ONT sequencing reads mapping to each isoform expressed in infected CD4+ T cells from donor 4 at each time point, as well as reads produced from ONT sequencing of viral particles produced at 24 hpi were counted. The number of reads, the class of transcripts and the splice junctions involved are indicated. New exon combinations represented by less than 5 reads were not annotated (ND: not defined). N: New isoform identified in this study.

Additional file 14 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Additional file 13: Table S6. ONT read mapping statistics of T cell sample infected with HIV-1 between 12 h and 24 h. Primary CD4+ T cells from donor 4 were infected with VSV-G pseudotyped NL4-3 virus, RNA was extracted at 12, 14, 16, 20, 24 hpi, cDNA libraries were prepared and sequenced using ONT device. ONT sequencing reads were mapped to both the human and HIV NL4-3 genomes, using Minimap2.

Additional file 13 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Additional file 10: Figure S5. Relative abundances of viral isoforms in infected and transfected HeLa cells. (a) Relative levels of viral RNA classes in HeLa cell were estimated as described for infected T cells (Fig. 3 and Additional file 8: Fig. S3). (b) Correlation of viral isoform abundances expressed in infected T cells versus transfected HeLa cells according to ONT sequencing. (c) Correlation of viral isoform abundances expressed in infected T cells versus infected HeLa cells according to ONT sequencing. Pearson correlation coefficients r are indicated. p<0.0001.

Additional file 10 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Additional file 5: Figure S5. Correlation between Dp71 expression and histological lesions In 28 biopsies from 6 muscles sampled from 8 different LRMD dogs the proportion of Dys2+ fibres was quantified and compared to the pathological index on H&E stained serial sections. The correlation was not significant (Pearson’s R= -0.32; p =0.069).

Additional file 5 of X-linked muscular dystrophy in a Labrador Retriever strain: phenotypic and molecular characterisation;Inès Barthélémy;2020;figshare


Abstract: Additional file 4: Figure S4. Immunohistochemical characterization of the expressed dystrophins in LRMD muscles. Serial sections from a biceps femoris (LRMD3), immunohistochemistry using the following antibodies: A: Dys2 (dystrophin, C-terminal part), B: βDG (beta-dystroglycan), C : MANEX1A (dystrophin, N-terminal part), D : MANEX1011C (dystrophin, exons 10-11), E: Dys1 (dystrophin, central rod domain repeats 8-10), F: MANDYS107 (dystrophin, central rod domain repeat 15). Most of the myofibres show a marked immunoreactivity with the Dys2 (C-term) antibody, associated with a beta-dystroglycan relocalization. Some of the Dys2 negative myofibres (asterisks) were positive for the antibodies specific for the N-terminal part of the protein (MANEX1A, MANEX1011C). No immunoreactivity was seen in any case when using antibodies specific for the central rod domain.

Additional file 4 of X-linked muscular dystrophy in a Labrador Retriever strain: phenotypic and molecular characterisation;Inès Barthélémy;2020;figshare


Abstract: Additional file 3: Figure S3. Histological findings in LRMD skeletal muscles. A: evolution of the muscle pathology with age. H&E stained biopsies x20. Illustration of the aspect of the biceps femoris at 5 different ages: 2 months, 4 months, 1 year, 2 years and 6 years. A significant number of necrosis-regeneration lesions are noted at early stages; these lesions are associated with inflammatory foci and sporadic calcifications. With time endomysial fibrosis and adiposis dominate the pathological context. B: illustration of all the elementary lesions found in LRMD muscles. Entire section and details of an extensor carpi radialis biopsy taken at the age of 4 months (LRMD7). This biopsy had an elevated pathological index (62.5 %). Abbreviations: BF: biceps femoris.

Additional file 3 of X-linked muscular dystrophy in a Labrador Retriever strain: phenotypic and molecular characterisation;Inès Barthélémy;2020;figshare


Abstract: Additional file 2: Figure S2. Phenotype in the neonatal period: fulminating form and growth retardation. A: Serial sections of muscle tissue sampled on a deceased LRMD neonate stained with H&E (left) and Alizarin red S (right)., Necrosis and calcium overload were seen in the diaphragm, and to a lesser extent, in the tongue and the sartorius cranialis muscle. Other muscles, such as the triceps brachii, the tibialis cranialis or the biceps femoris, were relatively spared by this rhabdomyolysis process. The results observed are consistent with the muscle lesions observed in the GRMD neonatal fulminating form. B: Whole section view of a diaphragm biopsy taken from a deceased LRMD neonate. The strong staining with Alizarin red S indicates that there is a significant calcium overload in this muscle. C: Kaplan-Meier survival curve during the neonatal period (from birth to 2 months of age) showing that half of the LRMD dogs died within their first days of life due to neonatal fulminating forms. Only 47 % of the LRMD dogs survived to weaning (2 months of age). D: Weight curves during the neonatal period (from birth to weaning, 2 months of age) from 5 different litters, showing growth retardation in most LRMD dogs (in black) relative to healthy littermates (in grey). E: Picture of a 15-week-old LRMD dog (LRMD7, on the right) compared to a healthy littermate (carrier female) illustrating the difference in size F: Picture of a one month-old LRMD dog (LRMD13, on the right) compared to a healthy male littermate.

Additional file 2 of X-linked muscular dystrophy in a Labrador Retriever strain: phenotypic and molecular characterisation;Inès Barthélémy;2020;figshare


Abstract: Additional file 1: Figure S1. Pedigree of the LRMD colony. The colony was founded by crossing an affected male with his carrier sister. Ten subsequent litters were obtained, and a total of 14 LRMD dogs survived the neonatal period. The colony presented high levels of inbreeding (consanguinity coefficients min 25 % max 41 %).

Additional file 1 of X-linked muscular dystrophy in a Labrador Retriever strain: phenotypic and molecular characterisation;Inès Barthélémy;2020;figshare


Abstract: Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in <i>Arabidopsis thaliana</i>, which exhibited many anciently conserved similarities with humans but also positions that appear to be ‘hot spots’ for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification;Jessica M. Warren;2020;Taylor & Francis


CCDC 976399: Experimental Crystal Structure Determination;Gebers, Jan;2020;Cambridge Crystallographic Data Centre

Related Article: Jan Gebers, Bilal Özen, Lucia Hartmann, Michel Schaer, Stéphane Suàrez, Philippe Bugnon, Rosario Scopelliti, Hans-Georg Steinrück, Oleg Konovalov, Andreas Magerl, Martin Brinkmann, Riccardo Petraglia, Piotr Silva, Clémence Corminboeuf, Holger Frauenrath|2020|Chem.-Eur.J.|26|10265|doi:10.1002/chem.201904562


CCDC 1043812: Experimental Crystal Structure Determination;Gebers, Jan;2020;Cambridge Crystallographic Data Centre


Abstract: Abstract Background Alternative splicing is a key step in Human Immunodeficiency Virus type 1 (HIV-1) replication that is tightly regulated both temporally and spatially. More than 50 different transcripts can be generated from a single HIV-1 unspliced pre-messenger RNA (pre-mRNA) and a balanced proportion of unspliced and spliced transcripts is critical for the production of infectious virions. Understanding the mechanisms involved in the regulation of viral RNA is therefore of potential therapeutic interest. However, monitoring the regulation of alternative splicing events at a transcriptome-wide level during cell infection is challenging. Here we used the long-read cDNA sequencing developed by Oxford Nanopore Technologies (ONT) to explore in a quantitative manner the complexity of the HIV-1 transcriptome regulation in infected primary CD4+ T cells. Results ONT reads mapping to the viral genome proved sufficiently long to span all possible splice junctions, even distant ones, and to be assigned to a total of 150 exon combinations. Fifty-three viral RNA isoforms, including 14 new ones were further considered for quantification. Relative levels of viral RNAs determined by ONT sequencing showed a high degree of reproducibility, compared favourably to those produced in previous reports and highly correlated with quantitative PCR (qPCR) data. To get further insights into alternative splicing regulation, we then compiled quantifications of splice site (SS) usage and transcript levels to build “splice trees”, a quantitative representation of the cascade of events leading to the different viral isoforms. This approach allowed visualizing the complete rewiring of SS usages upon perturbation of SS D2 and its impact on viral isoform levels. Furthermore, we produced the first dynamic picture of the cascade of events occurring between 12 and 24 h of viral infection. In particular, our data highlighted the importance of non-coding exons in viral RNA transcriptome regulation. Conclusion ONT sequencing is a convenient and reliable strategy that enabled us to grasp the dynamic of the early splicing events modulating the viral RNA landscape in HIV-1 infected cells.

Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection;Nam Nguyen Quang;2020;figshare


Abstract: Abstract Background In the general population, metabolic syndrome (MetS) is predictive of major adverse cardiovascular events (MACE). Waist circumference (WC), a component of the MetS criteria, is linked to visceral obesity, which in turn is associated with MACE. However, in haemodialysis (HD) patients, the association between MetS, WC and MACE is unclear. Methods In a cross-sectional study of 1000 HD patients, we evaluated the prevalence and characterised the clinical predictors of MetS. The relationship between MetS and its components, alone or in combination, and MACE (coronary diseases, peripheral arteriopathy, stroke or cardiac failure), was studied using receiver operating characteristics (ROC) curves and logistic regression. Results A total of 753 patients were included between October 2011 and April 2013. The prevalence of MetS was 68.5%. Waist circumference (> 88 cm in women, 102 cm in men) was the best predictor of MetS (sensitivity 80.2; specificity 82.3; AUC 0.80; p

Metabolic syndrome in haemodialysis patients: prevalence, determinants and association to cardiovascular outcomes;Arnaud Delautre;2020;figshare


Abstract: Abstract Background Canine models of Duchenne muscular dystrophy (DMD) are a valuable tool to evaluate potential therapies because they faithfully reproduce the human disease. Several cases of dystrophinopathies have been described in canines, but the Golden Retriever muscular dystrophy (GRMD) model remains the most used in preclinical studies. Here, we report a new spontaneous dystrophinopathy in a Labrador Retriever strain, named Labrador Retriever muscular dystrophy (LRMD). Methods A colony of LRMD dogs was established from spontaneous cases. Fourteen LRMD dogs were followed-up and compared to the GRMD standard using several functional tests. The disease causing mutation was studied by several molecular techniques and identified using RNA-sequencing. Results The main clinical features of the GRMD disease were found in LRMD dogs; the functional tests provided data roughly overlapping with those measured in GRMD dogs, with similar inter-individual heterogeneity. The LRMD causal mutation was shown to be a 2.2-Mb inversion disrupting the DMD gene within intron 20 and involving the TMEM47 gene. In skeletal muscle, the Dp71 isoform was ectopically expressed, probably as a consequence of the mutation. We found no evidence of polymorphism in either of the two described modifier genes LTBP4 and Jagged1. No differences were found in Pitpna mRNA expression levels that would explain the inter-individual variability. Conclusions This study provides a full comparative description of a new spontaneous canine model of dystrophinopathy, found to be phenotypically equivalent to the GRMD model. We report a novel large DNA mutation within the DMD gene and provide evidence that LRMD is a relevant model to pinpoint additional DMD modifier genes.

X-linked muscular dystrophy in a Labrador Retriever strain: phenotypic and molecular characterisation;Inès Barthélémy;2020;figshare


CCDC 1996297: Experimental Crystal Structure Determination;Wu, Fule;2020;Cambridge Crystallographic Data Centre

Related Article: Fule Wu, Christophe Deraedt, Yann Cornaton, Julia Contreras-Garcia, Mélanie Boucher, Lydia Karmazin, Corinne Bailly, Jean-Pierre Djukic|2020|Organometallics|39|2609|doi:10.1021/acs.organomet.0c00253


CCDC 1996299: Experimental Crystal Structure Determination;Wu, Fule;2020;Cambridge Crystallographic Data Centre


CCDC 1996300: Experimental Crystal Structure Determination;Wu, Fule;2020;Cambridge Crystallographic Data Centre


CCDC 1996301: Experimental Crystal Structure Determination;Wu, Fule;2020;Cambridge Crystallographic Data Centre


CCDC 1996302: Experimental Crystal Structure Determination;Wu, Fule;2020;Cambridge Crystallographic Data Centre


CCDC 1996306: Experimental Crystal Structure Determination;Wu, Fule;2020;Cambridge Crystallographic Data Centre


Related Article: Richard C. Knighton, Lohona K. Soro, Thibault Troadec, Valerie Mazan, Aline M. Nonat, Mourad Elhabiri, Nathalie Saffon-Merceron, Saifou Djenad, Raphaël Tripier, Loïc J. Charbonnière|2020|Inorg.Chem.|59|10311|doi:10.1021/acs.inorgchem.0c01456

CCDC 1990767: Experimental Crystal Structure Determination;Knighton, Richard C.;2020;Cambridge Crystallographic Data Centre


CCDC 1990768: Experimental Crystal Structure Determination;Knighton, Richard C.;2020;Cambridge Crystallographic Data Centre


CCDC 1990765: Experimental Crystal Structure Determination;Knighton, Richard C.;2020;Cambridge Crystallographic Data Centre


Abstract: Abstract Background General practitioners (GPs) regularly feel challenged by the care of depressed patients and may encounter several barriers in providing best management. GPs’ perspectives on barriers to depression care are a subject of growing interest but there is a lack of validated assessment tools. The aim of this study was to develop and validate a questionnaire assessing barriers to depression care (BDC-Q) encountered by GPs in France and the French-speaking part of Switzerland. Methods The BDC-Q was constructed in five steps: Item development, content validation, pretesting, testing phase and test-retest reliability. The questionnaire items were generated through a literature search. An expert panel of GPs (n = 16) and psychiatrists (n = 3) validated the content and 20 GPs pretested the questionnaire to provide response process validity evidence. We then tested the questionnaire among 116 GPs and used principal component analysis and internal consistency testing (Cronbach’s alpha) to structure it into consistent dimensions. Test-retest reliability using Pearson correlation coefficient was assessed with 30 GPs who completed the questionnaire twice after an interval of at least 2 weeks. Results The 25 items BDC-Q was structured in five dimensions: (i) provision of care by the general practitioner, (ii) considering patients’ attitudes towards depression, (iii) guidance for care, (iv) collaboration with mental health specialists and (v) access to mental health care. Conclusions The BDC-Q displays evidence of validity and reliability to meaningfully assess GPs’ perspectives on barriers to depression care. It can be used both at a practice level within a quality improvement strategy, and at a broader level, to inform health planners and tailor appropriate strategies to improve depression care in the community.

General practitioners’ perspectives on barriers to depression care: development and validation of a questionnaire;Arun Senchyna;2020;figshare


Abstract: We tested the social complexity hypothesis which posits that animals living in complex social environments should use complex communication systems. We focused on two components of vocal complexity: diversity (number of categories of calls) and flexibility (degree of gradation between categories of calls). We compared the acoustic structure of vocal signals in groups of macaques belonging to four species with varying levels of uncertainty (i.e. complexity) in social tolerance (the higher the degree of tolerance and the higher the degree of uncertainty): two intolerant species, Japanese and rhesus macaques, and two tolerant species, Tonkean and crested macaques. We recorded the vocalizations emitted by adult females in affiliative, agonistic and neutral contexts. We analysed several acoustic variables: call duration, entropy, time and frequency energy quantiles. The results showed that tolerant macaques displayed higher levels of vocal diversity and flexibility than intolerant macaques in situations with a greater number of options and consequences, i.e. in agonistic and affiliative contexts. We found no significant differences between tolerant and intolerant macaques in the neutral context where individuals are not directly involved in social interaction. This shows that species experiencing more uncertain social interactions displayed greater vocal diversity and flexibility, which supports the social complexity hypothesis.

Supplementary material from "Tolerant and intolerant macaques show different levels of structural complexity in their vocal communication";Nancy Rebout;2020;The Royal Society


Abstract: Continental carbonate bodies are widespread in the Tabernas basin, eastern Betic Cordillera. Their relationships with the topographic evolution, climate changes and extensional regional tectonic processes recognized in the region are, however, still unclear. Travertine deposits exhibit facies of cascade and pool environments often reported as related to water-air surface processes. Calcretes show a large panel of facies, indicating a control by groundwater and pedogenic processes. New U/Th dates on both travertine and calcrete reveal that they precipitated from 354 ka ± 76 to 8 ka ± 0.2. The U/Th dates obtained on calcretes are in good agreement with global climate changes and support that precipitation of recent CaCO3 is episodic and occur mainly during warm and wet conditions. C and O stable isotopes geochemistry reveal travertines are thermogenic and characterized by hydrothermal fluids enriched in CO2 that interacted with aquifers. This thermogenic origin suggests a deep source of CO2 (higher positive δ13C values) likely triggered by the presence of an anomalously hot mantle that reflects thinning of the regional lithosphere and volcanism. Further analyses of the distribution of calcrete show they are carbonate-rich fluvial terraces, whose formation is controlled by the response of the river network to regional uplift and climate.

Quaternary tectonic and climate changes at the origin of travertine and calcrete in the eastern Betics (Almería region, SE Spain);Marine Larrey;2020;Geological Society of London

Earth and related environmental sciences


Abstract: Abstract Background Culicoides obsoletus is an abundant and widely distributed Holarctic biting midge species, involved in the transmission of bluetongue virus (BTV) and Schmallenberg virus (SBV) to wild and domestic ruminants. Females of this vector species are often reported jointly with two morphologically very close species, C. scoticus and C. montanus, forming the Obsoletus/Scoticus Complex. Recently, cryptic diversity within C. obsoletus was reported in geographically distant sites. Clear delineation of species and characterization of genetic variability is mandatory to revise their taxonomic status and assess the vector role of each taxonomic entity. Our objectives were to characterize and map the cryptic diversity within the Obsoletus/Scoticus Complex. Methods Portion of the cox1 mitochondrial gene of 3763 individuals belonging to the Obsoletus/Scoticus Complex was sequenced. Populations from 20 countries along a Palaearctic Mediterranean transect covering Scandinavia to Canary islands (North to South) and Canary islands to Turkey (West to East) were included. Genetic diversity based on cox1 barcoding was supported by 16S rDNA mitochondrial gene sequences and a gene coding for ribosomal 28S rDNA. Species delimitation using a multi-marker methodology was used to revise the current taxonomic scheme of the Obsoletus/Scoticus Complex. Results Our analysis showed the existence of three phylogenetic clades (C. obsoletus clade O2, C. obsoletus clade dark and one not yet named and identified) within C. obsoletus. These analyses also revealed two intra-specific clades within C. scoticus and raised questions about the taxonomic status of C. montanus. Conclusions To our knowledge, our study provides the first genetic characterization of the Obsoletus/Scoticus Complex on a large geographical scale and allows a revision of the current taxonomic classification for an important group of vector species of livestock viruses in the Palaearctic region.

The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level;Antoine Mignotte;2020;figshare


Abstract: The identification of sea turtle behaviours is a prerequisite to predicting the activities and time-budget of these animals in their natural habitat over the long term. However, this is hampered by a lack of reliable methods that enable the detection and monitoring of certain key behaviours such as feeding. This study proposes a combined approach that automatically identifies the different behaviours of free-ranging sea turtles through the use of animal-borne multi-sensor recorders (accelerometer, gyroscope and time-depth recorder), validated by animal-borne video-recorder data. We show here that the combination of supervised learning algorithms and multi-signal analysis tools can provide accurate inferences of the behaviours expressed, including feeding and scratching behaviours that are of crucial ecological interest for sea turtles. Our procedure uses multi-sensor miniaturized loggers that can be deployed on free-ranging animals with minimal disturbance. It provides an easily adaptable and replicable approach for the long-term automatic identification of the different activities and determination of time-budgets in sea turtles. This approach should also be applicable to a broad range of other species and could significantly contribute to the conservation of endangered species by providing detailed knowledge of key animal activities such as feeding, travelling and resting.

Supplementary material from "Behavioural inference from signal processing using animal-borne multi-sensor loggers: a novel solution to extend the knowledge of sea turtle ecology";Lorène Jeantet;2020;The Royal Society


Abstract: Abstract Background Mitochondria are essential organelles partially regulated by their own genomes. The mitochondrial genome maintenance and inheritance differ from the nuclear genome, potentially uncoupling their evolutionary trajectories. Here, we analysed mitochondrial sequences obtained from the 1011 Saccharomyces cerevisiae strain collection and identified pronounced differences with their nuclear genome counterparts. Results In contrast with pre-whole genome duplication fungal species, S. cerevisiae mitochondrial genomes show higher genetic diversity compared to the nuclear genomes. Strikingly, mitochondrial genomes appear to be highly admixed, resulting in a complex interconnected phylogeny with a weak grouping of isolates, whereas interspecies introgressions are very rare. Complete genome assemblies revealed that structural rearrangements are nearly absent with rare inversions detected. We tracked intron variation in COX1 and COB to infer gain and loss events throughout the species evolutionary history. Mitochondrial genome copy number is connected with the nuclear genome and linearly scale up with ploidy. We observed rare cases of naturally occurring mitochondrial DNA loss, petite, with a subset of them that do not suffer the expected growth defect in fermentable rich media. Conclusions Overall, our results illustrate how differences in the biology of two genomes coexisting in the same cells can lead to discordant evolutionary histories.

Discordant evolution of mitochondrial and nuclear yeast genomes at population level;Matteo De Chiara;2020;figshare


Abstract: Abstract Background Within the genus Culicoides (Diptera: Ceratopogonidae), the subgenus Avaritia is of particular interest as it contains a significant number of economically important vector species. Disagreements about the systematic classification of species within this subgenus have resulted in a taxonomic imbroglio. Methods A molecular phylogeny of the subgenus Avaritia was conducted to test the existing systematic classification, which is based on phenetic assessment of morphological characters. Three nuclear ribosomal markers, internal transcribed spacer 1 and 2 (ITS1, ITS2), 5.8S, and three mitochondrial markers, cytochrome c oxidase subunit 1 and 2, and cytochrome b (cox1, cox2 and cytb), were obtained for 37 species of the subgenus Avaritia from all six biogeographical regions. Phylogenetic reconstructions using these genes independently and in combination were implemented using Bayesian inference analysis and maximum likelihood methods. Results Phylogenetic reconstructions gave strong support to several monophyletic groups within the subgenus Avaritia. Both C. actoni and C. pusillus formed a single clade with C. grahamii so their respective groups, the Actoni and Pusillus groups, have been merged with the Grahamii group. Some support was provided for the Boophagus and Jacobsoni groups. A group of species currently placed into the Orientalis group clustered in a clade with poor support. The Obsoletus group was defined as a sister clade to all other Avaritia groups. The clade including the Imicola group was well supported based on phylogenetic criteria. Conclusions This phylogenetic study combining five distinct molecular markers has provided meaningful insights into the systematic relationships of Culicoides (Avaritia) and highlighted future directions to continue the study of this subgenus. While the cox2 marker appeared to be useful to investigate closely related species, the 5.8S marker was highly conserved and uninformative. Further investigations including species absent from this work are needed to confirm the proposed systematic scheme. However, this systematic scheme can now serve as a foundation to investigate cryptic species affiliation within the subgenus. We advocate that future studies employ a combination of morphological and molecular analyses.

A phylogenetic analysis of the biting midges belonging to Culicoides Latreille (Diptera: Ceratopogonidae) subgenus Avaritia using molecular data;Bruno Mathieu;2020;figshare


Abstract: Abstract Background Infection is the most common cause of mortality within the first year after lung transplantation (LTx). The management of perioperative antibiotic therapy is a major issue, but little is known about worldwide practices. Methods We sent by email a survey dealing with 5 daily clinical vignettes concerning perioperative antibiotic therapy to 180 LTx centers around the world. The invitation and a weekly reminder were sent to lung transplant specialists for a single consensus answer per center during a 3-month period. Results We received a total of 99 responses from 24 countries, mostly from Western Europe (n = 46) and the USA (n = 34). Systematic screening for bronchial recipient colonization before LTx was mostly performed with sputum samples (72%), regardless of the underlying lung disease. In recipients without colonization, antibiotics with activity against gram-negative bacteria resistant strains (piperacillin / tazobactam, cefepime, ceftazidime, carbapenems) were reported in 72% of the centers, and antibiotics with activity against methicillin-resistant Staphylococcus aureus (mainly vancomycin) were reported in 38% of the centers. For these recipients, the duration of antibiotics reported was 7 days (33%) or less (26%) or stopped when cultures of donor and recipients were reported negatives (12%). In recipients with previous colonization, antibiotics were adapted to the susceptibility of the most resistant strain and given for at least 14 days (67%). Conclusion Practices vary widely around the world, but resistant bacterial strains are mostly targeted even if no colonization occurs. The antibiotic duration reported was longer for colonized recipients.

Worldwide clinical practices in perioperative antibiotic therapy for lung transplantation;Benjamin Coiffard;2020;figshare


Abstract: Previous studies to understand the evolution of interspecific variation in mammalian social organization (SO; composition of social units) produced inconsistent results, possibly by ignoring intraspecific variation. Here we present systematic data on SO in artiodactyl populations, coding SO as solitary, pair-living, group-living, sex-specific or variable (different kinds of SOs in the same population). We found that 62% of 245 populations and 83% of species (83/100) exhibited variable SO. Using Bayesian phylogenetic mixed-effects models, we simultaneously tested whether research effort, habitat, sexual dimorphism, breeding seasonality or body size predicted the likelihood of different SOs and inferred the ancestral SO. Body size and sexual dimorphism were strongly associated with different SOs. Contingent on the small body size (737 g) and putative sexual monomorphism of the earliest fossil artiodactyl, the ancestral SO was most likely pair-living (probability = 0.76, 95%CI = 0–1), followed by variable (p = 0.19, 95%CI = 0–0.99). However, at body size values typical of extant species, variable SO becomes the dominant form (p = 0.74, 95% CI = 0.18–1.00). Distinguishing different kinds of ‘variable’ highlights transitions from SOs involving pair-living to SOs involving solitary and/or group-living with increasing body size and dimorphism. Our results support the assumption that ancestral artiodactyl was pair-living and highlight the ubiquity of intraspecific variation in SO.

Supplementary material from "Variable social organization is ubiquitous in Artiodactyla and likely evolved from pair-living ancestors";A. V. Jaeggi;2020;The Royal Society


Abstract: Abstract Background Castleman disease (CD) is a rare non-malignant lymphoproliferation of undetermined origin. Two major disease phenotypes can be distinguished: unicentric CD (UCD) and multicentric CD (MCD). Diagnosis confirmation is based on histopathological findings in a lymph node. We attempted to survey all cases of paediatric CD identified to date in France to set up a national registry aiming to improve CD early recognition, treatment and follow-up, within the context of a new national reference center (http://www.castleman.fr). Methods In 2016, we e-mailed a questionnaire to members of the French paediatric immunohaematology society, the paediatric rheumatology society and the Reference Centre for Castleman Disease to retrospectively collect cases of paediatric CD (first symptoms before age 18 years). Anatomopathological confirmation was mandatory. Results We identified 23 patients (12 girls) with a diagnosis of UCD (n = 17) and MCD (n = 6) between 1994 and 2018. The mean age at first symptoms was 11.47 ± 4.23 years for UCD and 8.3 ± 3.4 years for MCD. The mean diagnosis delay was 8.16 ± 10.32 months for UCD and 5.16 ± 5.81 years for MCD. In UCD, the initial symptoms were isolated lymph nodes (n = 10) or lymph node associated with other symptoms (n = 7); fever was present in 3 patients. Five patients with MCD presented fever. No patients had HIV or human herpesvirus 8 infection. Autoinflammatory gene mutations were investigated in five patients. One patient with MCD carried a K695R heterozygous mutation in MEFV, another patient with MCD and Duchenne myopathy carried two variants in TNFRSF1A and one patient with UCD and fever episodes carried two heterozygous mutations, in IL10RA and IL36RN, respectively. Treatment of UCD was mainly surgical resection, steroids, and radiotherapy. Treatment of MCD included tocilizumab, rituximab, anakinra, steroids, chemotherapy, and splenectomy. Overall survival after a mean of 6.1 ± 6.4 years of follow-up, was 100% for both forms. Conclusion Paediatric CD still seems underdiagnosed, with a significant diagnosis delay, especially for MCD, but new international criteria will help in the future. Unlike adult CD, which is strongly associated with HIV and human herpesvirus 8 infection, paediatric CD could be favored by primary activation of innate immunity and may affect life expectancy less.

The French paediatric cohort of Castleman disease: a retrospective report of 23 patients;Charlotte Borocco;2020;figshare


Abstract: Abstract Background Borrelia miyamotoi is a relapsing fever Borrelia species transmitted by ticks of the Ixodes ricinus complex. Human disease caused by B. miyamotoi was first described in Russia and later in the USA and Japan. Additionally, five cases of meningoencephalitis in immunocompromised patients and one case in an apparently immunocompetent patient were described. Methods We investigated the presence of B. miyamotoi in I. ricinus nymphs and in patients suspected of human granulocytic anaplasmosis, in Alsace (France), an endemic area for I. ricinus ticks and Lyme borreliosis, using direct (PCR) and indirect diagnosis (glycerophosphoryldiester-phosphodiesterase (GlpQ) serology). Results Borrelia miyamotoi was found in 2.2% of 4354 ticks collected between 2013 and 2016. None of the 575 blood samples, collected from the patients suspected of HGA, was found positive for B. miyamotoi by PCR. Acute and late sera from 138 of these 575 patients were available. These paired sera were tested for IgM and IgG antibodies against the B. miyamotoi GlpQ antigen. A total of 14 out of 138 patients had at least one positive parameter (i.e. anti-GlpQ IgG and/or IgM). One patient seroconverted for IgG, and three had isolated IgM in the acute serum. These three patients were treated with doxycycline which could have prevented seroconversion. After reviewing clinical data and other biological tests performed, co-exposure among different microorganisms vectored by ticks or serological cross-reactivity could not be ruled out in these different cases. One patient had persistent IgG, which strongly suggests previous exposure to B. miyamotoi. Conclusions Humans can be exposed to B. miyamotoi through tick bites in Alsace. We present serological data for possible B. miyamotoi exposure or infection of patients with fever after tick bite. Future studies should determine the incidence, clinical course and burden of this emerging tick-borne disease in other parts of Western Europe.

Assessment of Borrelia miyamotoi in febrile patients and ticks in Alsace, an endemic area for Lyme borreliosis in France;Pierre H. Boyer;2020;figshare


Abstract: Abstract Background The draft genome assemblies produced by new sequencing technologies present important challenges for automatic gene prediction pipelines, leading to less accurate gene models. New benchmark methods are needed to evaluate the accuracy of gene prediction methods in the face of incomplete genome assemblies, low genome coverage and quality, complex gene structures, or a lack of suitable sequences for evidence-based annotations. Results We describe the construction of a new benchmark, called G3PO (benchmark for Gene and Protein Prediction PrOgrams), designed to represent many of the typical challenges faced by current genome annotation projects. The benchmark is based on a carefully validated and curated set of real eukaryotic genes from 147 phylogenetically disperse organisms, and a number of test sets are defined to evaluate the effects of different features, including genome sequence quality, gene structure complexity, protein length, etc. We used the benchmark to perform an independent comparative analysis of the most widely used ab initio gene prediction programs and identified the main strengths and weaknesses of the programs. More importantly, we highlight a number of features that could be exploited in order to improve the accuracy of current prediction tools. Conclusions The experiments showed that ab initio gene structure prediction is a very challenging task, which should be further investigated. We believe that the baseline results associated with the complex gene test sets in G3PO provide useful guidelines for future studies.

A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms;Nicolas Scalzitti;2020;figshare


Abstract: Abstract Background Culicoides biting midges transmit viruses resulting in disease in ruminants and equids such as bluetongue, Schmallenberg disease and African horse sickness. In the past decades, these diseases have led to important economic losses for farmers in Europe. Vector abundance is a key factor in determining the risk of vector-borne disease spread and it is, therefore, important to predict the abundance of Culicoides species involved in the transmission of these pathogens. The objectives of this study were to model and map the monthly abundances of Culicoides in Europe. Methods We obtained entomological data from 904 farms in nine European countries (Spain, France, Germany, Switzerland, Austria, Poland, Denmark, Sweden and Norway) from 2007 to 2013. Using environmental and climatic predictors from satellite imagery and the machine learning technique Random Forests, we predicted the monthly average abundance at a 1 km2 resolution. We used independent test sets for validation and to assess model performance. Results The predictive power of the resulting models varied according to month and the Culicoides species/ensembles predicted. Model performance was lower for winter months. Performance was higher for the Obsoletus ensemble, followed by the Pulicaris ensemble, while the model for Culicoides imicola showed a poor performance. Distribution and abundance patterns corresponded well with the known distributions in Europe. The Random Forests model approach was able to distinguish differences in abundance between countries but was not able to predict vector abundance at individual farm level. Conclusions The models and maps presented here represent an initial attempt to capture large scale geographical and temporal variations in Culicoides abundance. The models are a first step towards producing abundance inputs for R0 modelling of Culicoides-borne infections at a continental scale.

Modelling the monthly abundance of Culicoides biting midges in nine European countries using Random Forests machine learning;Ana Carolina Cuéllar;2020;figshare


Abstract: Abstract Pathogenic variants in the gene encoding the small GTPase Ras analogue in Brain 39b (RAB39B) are associated with early-onset parkinsonism. In this study we investigated the expression and localization of RAB39B (RNA and protein) in mouse brain tissue to gain a better understanding of its normal physiological function(s) and role in disease. We developed novel resources, including monoclonal antibodies directed against RAB39B and mice with Rab39b knockout, and performed real-time PCR and western blot analysis on whole brain lysates. To determine the spatial localization of Rab39b RNA and protein, we performed in-situ hybridization and immunohistochemistry on fresh frozen and fixed brain tissue. Our results show that RAB39B is localized throughout the cortex, hippocampus and substantia nigra of mice throughout postnatal life. We found high levels of RAB39B within MAP2 positive cortical and hippocampal neurons, and TH positive dopaminergic neurons in the substantia nigra pars compacta. Our studies support and extend current knowledge of the localization of RAB39B. We validate RAB39B as a neuron-enriched protein and demonstrate that it is present throughout the mouse cortex and hippocampus. Further, we observe high levels in the substantia nigra pars compacta, the brain region most affected in Parkinson’s disease pathology. The distribution of Rab39b is consistent with human disease associations with parkinsonism and cognitive impairment. We also describe and validate novel resources, including monoclonal antibodies directed against RAB39B and mice with Rab39b knockout, both of which are valuable tools for future studies of the molecular function of RAB39B.

Distribution of Parkinson’s disease associated RAB39B in mouse brain tissue;Yujing Gao;2020;figshare


Abstract: Abstract Background Evaluation of the action of various traditional plants to treat metabolic syndrome are strongly studied. In our study, we investigated the effect of the Tunisian jojoba seed on a metabolic syndrome induced in rat by the High Fat diet and High Fructose (HFHF) and its renal and hepatic complications. Methods The rats were fed with HFHF or Normal Diet (ND) for a period of 8 weeks. After that, a switch from HFHF to ND or Normal Diet Jojoba (NDJ),(jojoba diet approach) or High Fat and High Fructose and Jojoba diet (HFHFJ) (nutraceutical approach) has been done. Metabolic disorder was evaluated by measuring the fasting body weight, glycemia and C-peptide and leptin. Oxidative stress parameters like ThioBarbituric Acid Reactive Substances (TBARS) and Total Antioxidant Capacity (TAOC) were analyzed in the plasma and renal and hepatic function were determined by the measure of creatinine and alanine transferase (ALT) respectively. Histological analysis was performed on the liver, kidney and pancreas. Results HFHF diet exhibited characteristics of metabolic syndrome presented by insulin resistance, hyperinsulinemia, hyperleptinemia, fat mass with hepatic steatosis and renal disorder. HFHF diet was associated with oxidative stress (OS) presented by an increase in TBARS and a decrease in TAOC. Adding jojoba seeds to HFHF rat group diet induced a decrease in body weight, fat mass (58 and 41%), insulin resistance (59 and 56%), oxidative stress (60 and 41%), liver steatosis (from a score = 3 to a score = 0) and renal complications (25 and 42%). This effect was emphasized with diet approach. Conclusion The results demonstrated the beneficial effect of jojoba against metabolic syndrome and oxidative stress, suggesting that jojoba could be used in the prevention and treatment of metabolic syndrome. Graphical abstract

Anorexic and metabolic effect of jojoba: potential treatment against metabolic syndrome and hepatic complications;Sahla Belhadj;2020;figshare


Abstract: Abstract Background To assess the presence of a seasonal effect on fatigue, pain and dryness in primary Sjögren’s syndrome (pSS). Methods Data (date; visual analogue scales (VAS) for pain, fatigue and dryness) were extracted from three randomised placebo-controlled trials (RCTs) evaluating infliximab (TRIPSS; n = 103 patients), hydroxychloroquine (JOQUER; n = 120 patients) and rituximab (TEARS; n = 120 patients) and from the 5-year follow-up of the ASSESS prospective cohort (n = 395 patients). Data were analysed at each visit for each patient, according to the day, the month of the year and the season. Linear mixed models were used to take into account the repeated structure of the data and to analyse a potential cyclic effect. Results A total of 744, 584, 848 and 682 pain, fatigue and dryness VASs were collected on 632 subjects in spring, summer, fall and winter, respectively. No significant difference was observed in pain, fatigue and dryness, according to the month of the year or the season (all p values > 0.05). Conclusion In pSS, seasonality does not affect patient-reported outcomes (PROs) on fatigue, pain and dryness.

Seasonal effect on fatigue, pain and dryness in primary Sjögren’s syndrome;Pierre-Marie Duret;2020;figshare


Abstract: Abstract Background The speed of translation elongation is primarily determined by the abundance of tRNAs. Thus, the codon usage influences the rate with which individual mRNAs are translated. As the nature of tRNA pools and modifications can vary across biological conditions, codon elongation rates may also vary, leading to fluctuations in the protein production from individual mRNAs. Although it has been observed that functionally related mRNAs exhibit similar codon usage, presumably to provide an effective way to coordinate expression of multiple proteins, experimental evidence for codon-mediated translation efficiency modulation of functionally related mRNAs in specific conditions is scarce and the associated mechanisms are still debated. Results Here, we reveal that mRNAs whose expression increases during cell proliferation are enriched in rare codons, poorly adapted to tRNA pools. Ribosome occupancy profiling and proteomics measurements show that upon increased cell proliferation, transcripts enriched in rare codons undergo a higher translation boost than transcripts with common codons. Re-coding of a fluorescent reporter with rare codons increased protein output by ~â€‰30% relative to a reporter re-coded with common codons. Although the translation capacity of proliferating cells was higher compared to resting cells, we did not find evidence for the regulation of individual tRNAs. Among the models that were proposed so far to account for codon-mediated translational regulation upon changing conditions, the one that seems most consistent with our data involves a global upregulation of ready-to-translate tRNAs, which we show can lead to a higher increase in the elongation velocity at rare codons compared to common codons. Conclusions We propose that the alleviation of translation bottlenecks in rapidly dividing cells enables preferential upregulation of pro-proliferation proteins, encoded by mRNAs that are enriched in rare codons.

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


Abstract: Abstract Understanding paintings as physical systems is fundamental for advancing environmental specifications that would allow for effective management of museum environments in terms of reducing energy use and carbon emissions while maintaining high standards of collection care. The current environmental specifications were derived using the criterion of the crack initiation in undamaged, usually new, material. In reality, historical paintings exhibit complex crack patterns called craquelures. The present paper analyses painted wood which is among the category of cultural objects most vulnerable to relative humidity and temperature fluctuations and frequently found in museum collections of various kinds. Fracture toughness determined experimentally for the most brittle component of pictorial layer—the ground layer (gesso) is used as a ‘failure criterion’. Comparison of energy release rate—calculated for the model of the gesso laid on a wooden substrate using finite element analysis—with the structure toughness, allowed the fracture saturation expressed as the ratio of spacing between cracks S to gesso layer thickness t to be determined for various combinations of the gesso stiffness and geometries of structural flaws at which cracks initiate. For flat geometry of a panel painting and panel thickness of 40 mm, representing the worst-case, largest stresses in the gesso layer, the fracture saturation occurs when S/t is larger than 5, even if flaws in the gesso layer are present. The paper shows that the fracture saturation significantly changes vulnerability of paintings to climate variations—a panel painting with developed craquelure network is significantly less vulnerable to climate variations than an undamaged one.

Fracture saturation in paintings makes them less vulnerable to environmental variations in museums;Łukasz Bratasz;2020;figshare


Abstract: Abstract The development of the Rittershoffen deep geothermal field (Alsace, Upper Rhine Graben) between 2012 and 2014 induced unfelt seismicity with a local magnitude of less than 1.6. This seismicity occurred during two types of operations: (1) mud losses in the Muschelkalk formation during the drilling of both wells of the doublet and (2) thermal and hydraulic stimulations of the GRT-1 well. Seismicity was also observed 4Â days after the main hydraulic stimulation, although no specific operation was performed. During chemical stimulation, however, no induced seismicity was detected. In the context of all field development operations and their injection parameters (flow rates, overpressures, volumes), we detail the occurrence or lack of seismicity, its magnitude distribution and its spatial distribution. The observations suggest the presence of the rock stress memory effect (Kaiser effect) of the geothermal reservoir as well as uncritically stressed zones connected to the GRT-1 well and/or rock cohesion. A reduction of the seismic rate concurrent with an increase of injectivity was noticed as well as the reactivation of a couple of faults, including the Rittershoffen fault, which was targeted by the wells. These results are derived from the homogeneous and consistent catalogue of more than 1300 local earthquakes that is provided. This reference catalogue is based on a standard detection method, whose output was manually verified and improved. The given absolute locations have been computed in a calibrated, geologically realistic 3D velocity model. Our work builds on previous analyses addressing the seismicity induced by the GRT-1 hydraulic stimulation and places the results into a historical context, thus considering the full dynamics of the observed phenomena. This paper also complements existing descriptions of the hydrothermal characteristics of the deep reservoir by providing insights separate from the wells.

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


Abstract: Abstract Background To evaluate the prevalence and management of heart failure (HF) in very old patients in geriatric settings. Methods Members of the French Society of Geriatrics and Gerontology throughout France were invited to participate in a point prevalence survey and to include all patients ≥80 years old, hospitalized in geriatric settings, with HF (stable or decompensated) on June 18, 2012. General characteristics, presence of comorbidities, blood tests and medications were recorded. Results Among 7,197 patients in geriatric institution, prevalence of HF was 20.5% (n = 1,478): (27% in acute care, 24.2% in rehabilitation care and 18% in nursing home). Mean age was 88.2 (SD = 5.2) and Charlson co morbidity score was high (8.49 (SD = 2.21)). Left ventricular ejection fraction (LVEF) was available in 770 (52%) patients: 536 (69.6%) had a preserved LVEF (≥ 50%), 120 (15.6%) a reduced LVEF (

National survey on the management of heart failure in individuals over 80 years of age in French geriatric care units;Clémence Boully;2019;Figshare


Abstract: The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~ years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the 'two-layer' hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing ancient human genomes ( from SEA, Japanese Jomon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hoabinhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.

The prehistoric peopling of Southeast Asia;Hugh McColl;2017;Online Ancient Genome Repository


Abstract: Abstract Background The appropriate management of postoperative complication of wisdom teeth removal is of utmost importance as it can result in legal procedures. The accidental displacement of a maxillary third molar in the infratemporal fossa (ITF), is a rare complication that can occur even with experienced surgeons. The numerous retrieval techniques reported are invasive and provide an unpredictable access. Our aim was to achieve the safe and swift retrieval of the tooth displaced to an area of such complex anatomy. Case presentation We describe the case of a 17-year-old female patient whose right upper third molar was accidentally pushed upward to the ITF and became unreachable. Retrieval based on interventional radiology using the CT-guided placement of a bone trocar above the displaced tooth was successfully performed. The postoperative course was uneventful. Conclusions CT scan assisted interventional radiology provides both, real-time assessment of the tooth position through image refreshment, and steady stabilization of the displaced tooth. Therefore, it allows a safe and non-traumatic retrieval with a time-efficient procedure achieved through a minimally-invasive approach with inconspicuous scaring. We believe that such a procedure is an interesting treatment option for optimal outpatient care. To our knowledge, no such case has been previously described.

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


Mouse_rest_multicentre


Abstract: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

CCDC 1912482: Experimental Crystal Structure Determination;C. Werlé;2019;Cambridge Crystallographic Data Centre

Related Article: C. Werlé, C. Bailly, L. Karmazin, J.-P. Djukic|2019|IUCrData|4|x190573|doi:10.1107/S241431461900573X


CCDC 1897489: Experimental Crystal Structure Determination;Jan Holub;2019;Cambridge Crystallographic Data Centre

Related Article: Jan Holub, Antonio Santoro, Jean-Marie Lehn|2019|Inorg.Chim.Acta|494|223|doi:10.1016/j.ica.2019.05.017


CCDC 1897491: Experimental Crystal Structure Determination;Jan Holub;2019;Cambridge Crystallographic Data Centre


CCDC 1898383: Experimental Crystal Structure Determination;Eufemio Moreno-Pineda;2019;Cambridge Crystallographic Data Centre

Related Article: Eufemio Moreno-Pineda, Gheorghe Taran, Wolfgang Wernsdorfer, Mario Ruben|2019|Chemical Science|10|5138|doi:10.1039/C9SC01062A


CCDC 1898384: Experimental Crystal Structure Determination;Eufemio Moreno-Pineda;2019;Cambridge Crystallographic Data Centre


CCDC 1904162: Experimental Crystal Structure Determination;Pierre Thuéry;2019;Cambridge Crystallographic Data Centre

Related Article: Pierre Thuéry, Youssef Atoini, Jack Harrowfield|2019|Inorg.Chem.|58|6550|doi:10.1021/acs.inorgchem.9b00804


CCDC 1904163: Experimental Crystal Structure Determination;Pierre Thuéry;2019;Cambridge Crystallographic Data Centre


CCDC 1904164: Experimental Crystal Structure Determination;Pierre Thuéry;2019;Cambridge Crystallographic Data Centre


CCDC 1904166: Experimental Crystal Structure Determination;Pierre Thuéry;2019;Cambridge Crystallographic Data Centre


CCDC 1904167: Experimental Crystal Structure Determination;Pierre Thuéry;2019;Cambridge Crystallographic Data Centre


CCDC 1904168: Experimental Crystal Structure Determination;Pierre Thuéry;2019;Cambridge Crystallographic Data Centre


CCDC 1904169: Experimental Crystal Structure Determination;Pierre Thuéry;2019;Cambridge Crystallographic Data Centre


CCDC 1904170: Experimental Crystal Structure Determination;Pierre Thuéry;2019;Cambridge Crystallographic Data Centre


CCDC 1904171: Experimental Crystal Structure Determination;Pierre Thuéry;2019;Cambridge Crystallographic Data Centre


CCDC 1887931: Experimental Crystal Structure Determination;Zhenxing Liu;2019;Cambridge Crystallographic Data Centre

Related Article: Zhenxing Liu, Chaofan Xu, Juan del Pozo, Sebastian Torker, Amir H. Hoveyda|2019|J.Am.Chem.Soc.|141|7137|doi:10.1021/jacs.9b02318


CCDC 1887932: Experimental Crystal Structure Determination;Zhenxing Liu;2019;Cambridge Crystallographic Data Centre


CCDC 1891841: Experimental Crystal Structure Determination;Lara Faour;2019;Cambridge Crystallographic Data Centre

Related Article: Lara Faour, Catherine Adam, Christelle Gautier, Sébastien Goeb, Magali Allain, Eric Levillain, David Canevet, Marc Sallé|2019|Chem.Commun.|55|5743|doi:10.1039/C9CC02498K


CCDC 1871933: Experimental Crystal Structure Determination;Chloé Batisse;2019;Cambridge Crystallographic Data Centre

Related Article: Chloé Batisse, Maria F. Céspedes Dávila, Marco Castello, Amélia Messara, Bertrand Vivet, Gilbert Marciniak, Armen Panossian, Gilles Hanquet, Frédéric R. Leroux|2019|Tetrahedron|75|3063|doi:10.1016/j.tet.2019.04.037


Abstract: Abstract Background The floral transition is a complex developmental event, fine-tuned by various environmental and endogenous cues to ensure the success of offspring production. Leaves are key organs in sensing floral inductive signals, such as a change in light regime, and in the production of the mobile florigen. CONSTANS and FLOWERING LOCUS T are major players in leaves in response to photoperiod. Morphological and molecular events during the floral transition have been intensively studied in the shoot apical meristem. To better understand the concomitant processes in leaves, which are less described, we investigated the nuclear changes in fully developed leaves during the time course of the floral transition. Results We highlighted new putative regulatory candidates of flowering in leaves. We observed differential expression profiles of genes related to cellular, hormonal and metabolic actions, but also of genes encoding long non-coding RNAs and new natural antisense transcripts. In addition, we detected a significant increase in ploidy level during the floral transition, indicating endoreduplication. Conclusions Our data indicate that differentiated mature leaves, possess physiological plasticity and undergo extensive nuclear reprogramming during the floral transition. The dynamic events point at functionally related networks of transcription factors and novel regulatory motifs, but also complex hormonal and metabolic changes.

Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction;Stefania Prete;2019;Figshare


CCDC 1024872: Experimental Crystal Structure Determination;Sébastien Dhers;2019;Cambridge Crystallographic Data Centre

Related Article: Sébastien Dhers, Humphrey L. C. Feltham, Mathieu Rouzières, Rodolphe Clérac, Sally Brooker|2019|Inorg.Chem.|58|5543|doi:10.1021/acs.inorgchem.8b03455


CCDC 1024873: Experimental Crystal Structure Determination;Sébastien Dhers;2019;Cambridge Crystallographic Data Centre


CCDC 1024874: Experimental Crystal Structure Determination;Sébastien Dhers;2019;Cambridge Crystallographic Data Centre


CCDC 1024877: Experimental Crystal Structure Determination;Sébastien Dhers;2019;Cambridge Crystallographic Data Centre


CCDC 1851468: Experimental Crystal Structure Determination;Hao Wang;2019;Cambridge Crystallographic Data Centre

Related Article: Hao Wang, Zheng-Xin Zhou, Mohamedally Kurmoo, Yue-Jin Liu, Ming-Hua Zeng|2019|Org.Lett.|21|2847|doi:10.1021/acs.orglett.9b00851


CCDC 1891452: Experimental Crystal Structure Determination;Jia-Wei Li;2019;Cambridge Crystallographic Data Centre

Related Article: Jia-Wei Li, Liang-Neng Wang, Ming Li, Pan-Ting Tang, Xiao-Peng Luo, Mohamedally Kurmoo, Yue-Jin Liu, Ming-Hua Zeng|2019|Org.Lett.|21|2885|doi:10.1021/acs.orglett.9b00888


CCDC 1891453: Experimental Crystal Structure Determination;Jia-Wei Li;2019;Cambridge Crystallographic Data Centre


CCDC 1881595: Experimental Crystal Structure Determination;Hao Wang;2019;Cambridge Crystallographic Data Centre


CCDC 1881597: Experimental Crystal Structure Determination;Hao Wang;2019;Cambridge Crystallographic Data Centre


CCDC 1881598: Experimental Crystal Structure Determination;Hao Wang;2019;Cambridge Crystallographic Data Centre


CCDC 1865691: Experimental Crystal Structure Determination;Hao Wang;2019;Cambridge Crystallographic Data Centre


CCDC 1865692: Experimental Crystal Structure Determination;Hao Wang;2019;Cambridge Crystallographic Data Centre


CCDC 1881602: Experimental Crystal Structure Determination;Hao Wang;2019;Cambridge Crystallographic Data Centre


CCDC 1881603: Experimental Crystal Structure Determination;Hao Wang;2019;Cambridge Crystallographic Data Centre


CCDC 1883107: Experimental Crystal Structure Determination;Jia-Wei Li;2019;Cambridge Crystallographic Data Centre


CCDC 1883108: Experimental Crystal Structure Determination;Jia-Wei Li;2019;Cambridge Crystallographic Data Centre


CCDC 1883110: Experimental Crystal Structure Determination;Jia-Wei Li;2019;Cambridge Crystallographic Data Centre


CCDC 1883111: Experimental Crystal Structure Determination;Jia-Wei Li;2019;Cambridge Crystallographic Data Centre


CCDC 1883112: Experimental Crystal Structure Determination;Jia-Wei Li;2019;Cambridge Crystallographic Data Centre


CCDC 1883113: Experimental Crystal Structure Determination;Jia-Wei Li;2019;Cambridge Crystallographic Data Centre


CCDC 1883116: Experimental Crystal Structure Determination;Jia-Wei Li;2019;Cambridge Crystallographic Data Centre


CCDC 1878911: Experimental Crystal Structure Determination;Zhi Wang;2019;Cambridge Crystallographic Data Centre

Related Article: Zhi Wang, Hao-Tian Sun, Mohamedally Kurmoo, Qing-Yun Liu, Gui-Lin Zhuang, Quan-Qin Zhao, Xing-Po Wang, Chen-Ho Tung, Di Sun|2019|Chemical Science|10|4862|doi:10.1039/C8SC05666H


CCDC 1878912: Experimental Crystal Structure Determination;Zhi Wang;2019;Cambridge Crystallographic Data Centre


CCDC 1865458: Experimental Crystal Structure Determination;Bougar Sarr;2019;Cambridge Crystallographic Data Centre

Related Article: Bougar Sarr, Abdou Mbaye, Cheikh A.K. Diop, Mamadou Sidibe, Frederic Melin, Petra Hellwig, Francis Maury, Francois Senocq, Philippe Guionneau, Michel Giorgi, Romain Gautier|2019|Inorg.Chim.Acta|491|84|doi:10.1016/j.ica.2019.03.037


CCDC 1865459: Experimental Crystal Structure Determination;Bougar Sarr;2019;Cambridge Crystallographic Data Centre


CCDC 1865460: Experimental Crystal Structure Determination;Bougar Sarr;2019;Cambridge Crystallographic Data Centre


CCDC 1897130: Experimental Crystal Structure Determination;Qin Yu;2019;Cambridge Crystallographic Data Centre

Related Article: Qin Yu, Jian Su, Jian-Ping Ma, Chanel F. Leong, Deanna M. D’Alessandro, Hai-Ying Wang, Mohamedally Kurmoo, Jing-Lin Zuo|2019|Cryst.Growth Des.|19|3012|doi:10.1021/acs.cgd.9b00239


CCDC 1897131: Experimental Crystal Structure Determination;Qin Yu;2019;Cambridge Crystallographic Data Centre


CCDC 1897132: Experimental Crystal Structure Determination;Qin Yu;2019;Cambridge Crystallographic Data Centre


CCDC 1897133: Experimental Crystal Structure Determination;Qin Yu;2019;Cambridge Crystallographic Data Centre


CCDC 1414184: Experimental Crystal Structure Determination;Patrick Larpent;2019;Cambridge Crystallographic Data Centre

Related Article: Patrick Larpent, Abdelaziz Jouaiti, Nathalie Kyritsakas, Mir Wais Hosseini|2019|CrystEngComm|21|2534|doi:10.1039/C9CE00113A


CCDC 1414185: Experimental Crystal Structure Determination;Patrick Larpent;2019;Cambridge Crystallographic Data Centre


CCDC 1414186: Experimental Crystal Structure Determination;Patrick Larpent;2019;Cambridge Crystallographic Data Centre


CCDC 1414187: Experimental Crystal Structure Determination;Patrick Larpent;2019;Cambridge Crystallographic Data Centre


CCDC 1414188: Experimental Crystal Structure Determination;Patrick Larpent;2019;Cambridge Crystallographic Data Centre


CCDC 1414189: Experimental Crystal Structure Determination;Patrick Larpent;2019;Cambridge Crystallographic Data Centre


CCDC 1862242: Experimental Crystal Structure Determination;Ivan Šalitroš;2019;Cambridge Crystallographic Data Centre

Related Article: Ivan Šalitroš, Radovan Herchel, Olaf Fuhr, Rodrigo González-Prieto, Mario Ruben|2019|Inorg.Chem.|58|4310|doi:10.1021/acs.inorgchem.8b03432


CCDC 1862243: Experimental Crystal Structure Determination;Ivan Šalitroš;2019;Cambridge Crystallographic Data Centre


CCDC 1893848: Experimental Crystal Structure Determination;Stéphane A. Baudron;2019;Cambridge Crystallographic Data Centre

Related Article: Stéphane A. Baudron, Hubert Chevreau|2019|CrystEngComm|21|1853|doi:10.1039/C9CE00168A


CCDC 1893849: Experimental Crystal Structure Determination;Stéphane A. Baudron;2019;Cambridge Crystallographic Data Centre


CCDC 1893850: Experimental Crystal Structure Determination;Stéphane A. Baudron;2019;Cambridge Crystallographic Data Centre


CCDC 1893851: Experimental Crystal Structure Determination;Stéphane A. Baudron;2019;Cambridge Crystallographic Data Centre


CCDC 1893852: Experimental Crystal Structure Determination;Stéphane A. Baudron;2019;Cambridge Crystallographic Data Centre


CCDC 1893853: Experimental Crystal Structure Determination;Stéphane A. Baudron;2019;Cambridge Crystallographic Data Centre


CCDC 1866279: Experimental Crystal Structure Determination;Frédéric Beltran;2019;Cambridge Crystallographic Data Centre

Related Article: Frédéric Beltran, Laurence Miesch|2019|Org.Lett.|21|1569|doi:10.1021/acs.orglett.8b03987


CCDC 1866280: Experimental Crystal Structure Determination;Frédéric Beltran;2019;Cambridge Crystallographic Data Centre


CCDC 1895442: Experimental Crystal Structure Determination;Frédéric Beltran;2019;Cambridge Crystallographic Data Centre


CCDC 1855648: Experimental Crystal Structure Determination;Chun-Yu Liu;2019;Cambridge Crystallographic Data Centre

Related Article: Chun-Yu Liu, Xue-Rui Wei, Yuan Chen, Hui-Fang Wang, Jian-Feng Ge, Yu-Jie Xu, Zhi-Gang Ren, Pierre Braunstein, Jian-Ping Lang|2019|Inorg.Chem.|58|3690|doi:10.1021/acs.inorgchem.8b03298


CCDC 1855649: Experimental Crystal Structure Determination;Chun-Yu Liu;2019;Cambridge Crystallographic Data Centre


CCDC 1855650: Experimental Crystal Structure Determination;Chun-Yu Liu;2019;Cambridge Crystallographic Data Centre


CCDC 1879640: Experimental Crystal Structure Determination;Bao-Qian Ji;2019;Cambridge Crystallographic Data Centre

Related Article: Bao-Qian Ji, Hai-Feng Su, Marko Jagodic, Zvonko Jaglicic, Mohamedally Kurmoo, Xing-Po Wang, Chen-Ho Tung, Zao-Zhen Cao, Di Sun|2019|Inorg.Chem.|58|3800|doi:10.1021/acs.inorgchem.8b03406


CCDC 1882970: Experimental Crystal Structure Determination;Hamzé Almallah;2019;Cambridge Crystallographic Data Centre

Related Article: Hamzé Almallah, Mélodie Nos, Virgile Ayzac, Eric Brenner, Dominique Matt, Christophe Gourlaouen, Mohamad Jahjah, Akram Hijazi|2019|Comptes Rendus Chimie|22|299|doi:10.1016/j.crci.2019.01.008


CCDC 1893175: Experimental Crystal Structure Determination;Fan Zhang;2019;Cambridge Crystallographic Data Centre

Related Article: Fan Zhang, Audrey Fluck, Stéphane A. Baudron, Mir Wais Hosseini|2019|Dalton Trans.|48|4105|doi:10.1039/C9DT00377K


CCDC 1893176: Experimental Crystal Structure Determination;Fan Zhang;2019;Cambridge Crystallographic Data Centre


CCDC 1893177: Experimental Crystal Structure Determination;Fan Zhang;2019;Cambridge Crystallographic Data Centre


CCDC 1893178: Experimental Crystal Structure Determination;Fan Zhang;2019;Cambridge Crystallographic Data Centre


CCDC 1874333: Experimental Crystal Structure Determination;Jian Su;2019;Cambridge Crystallographic Data Centre

Related Article: Jian Su, Tian-Hao Hu, Ryuichi Murase, Hai-Ying Wang, Deanna M. D’Alessandro, Mohamedally Kurmoo, Jing-Lin Zuo|2019|Inorg.Chem.|58|3698|doi:10.1021/acs.inorgchem.8b03299


CCDC 1874334: Experimental Crystal Structure Determination;Jian Su;2019;Cambridge Crystallographic Data Centre


CCDC 1874335: Experimental Crystal Structure Determination;Jian Su;2019;Cambridge Crystallographic Data Centre


CCDC 1874336: Experimental Crystal Structure Determination;Jian Su;2019;Cambridge Crystallographic Data Centre


CCDC 1874337: Experimental Crystal Structure Determination;Jian Su;2019;Cambridge Crystallographic Data Centre


CCDC 1882361: Experimental Crystal Structure Determination;Elodie Chevallot-Beroux;2019;Cambridge Crystallographic Data Centre

Related Article: Elodie Chevallot-Beroux, Ayuk M. Ako, Wolfgang Schmitt, Brendan Twamley, Joseph Moran, Boudon Corinne, Laurent Ruhlmann, Samir Mameri|2019|Dalton Trans.|48|4830|doi:10.1039/C8DT04807J


CCDC 1531086: Experimental Crystal Structure Determination;Noviyan Darmawan;2019;Cambridge Crystallographic Data Centre

Related Article: Noviyan Darmawan, Letizia Sambri, Constantin G. Daniliuc, Luisa De Cola|2019|Dalton Trans.|48|3664|doi:10.1039/C8DT04833A


CCDC 1887730: Experimental Crystal Structure Determination;Minghua Zeng;2019;Cambridge Crystallographic Data Centre

Related Article: Minghua Zeng, Jun-Quan Zhang, De-Shan Zhang, Qiu-Jie Chen, Hai-Bing Xu, Mohamedally Kurmoo, Ming-Hua Zeng|2019|Chem.-Eur.J.|25|5177|doi:10.1002/chem.201900204


CCDC 1887731: Experimental Crystal Structure Determination;Minghua Zeng;2019;Cambridge Crystallographic Data Centre


CCDC 1887733: Experimental Crystal Structure Determination;Minghua Zeng;2019;Cambridge Crystallographic Data Centre


CCDC 1887734: Experimental Crystal Structure Determination;Minghua Zeng;2019;Cambridge Crystallographic Data Centre


CCDC 1887735: Experimental Crystal Structure Determination;Minghua Zeng;2019;Cambridge Crystallographic Data Centre


CCDC 1887747: Experimental Crystal Structure Determination;Minghua Zeng;2019;Cambridge Crystallographic Data Centre


CCDC 1887732: Experimental Crystal Structure Determination;Minghua Zeng;2019;Cambridge Crystallographic Data Centre


CCDC 1974740: Experimental Crystal Structure Determination;Liu, Chun-Yu;2020;Cambridge Crystallographic Data Centre

Related Article: Chun-Yu Liu, Xu-Ran Chen, Hui-Xian Chen, Zheng Niu, Hajime Hirao, Pierre Braunstein, Jian-Ping Lang|2020|J.Am.Chem.Soc.|142|6690|doi:10.1021/jacs.0c00368


Apollo-University Of Cambridge Repository

Research data supporting "Complex coding and regulatory polymorphisms in a restriction factor determine the susceptibility of Drosophila to viral infection";Chuan Cao;2016;Apollo - University of Cambridge Repository

All data and scripts for Cao et al "Complex coding and regulatory polymorphisms in a restriction factor determine the susceptibility of Drosophila to viral infection." This folder contains R scripts and raw data used in this manuscript. ERC [281668], Cambridge Commonwealth, European & International Trust and China scholarship Council


Abstract: Abstract Background MSCs isolated from bone marrow (BM-MSCs) have well-established chondrogenic potential, but MSCs derived from the synovial membrane (SM-MSCs) and synovial fluid (SF-MSCs) are thought to possess superior chondrogenicity. This study aimed to compare the in vitro immunophenotype and trilineage and chondrogenic potential of BM-MSCs to SM-MSCs and SF-MSCs. Methods MSCs were isolated from bone marrow (BM-MSCs), synovial membrane (SM-MSCs), and synovial fluid (SF-MSCs) extracted from the hips (BM) and knees (SM and SF) of advanced OA patients undergoing arthroplasty. Flow cytometric analysis was used at P2 to evaluate cell stemness. The trilinear differentiation test was performed at P2. At P3, MSC-seeded collagen sponges were cultured in chondrogenic medium for 28 days. Chondrogenic gene expression was quantified by qRT-PCR. Finally, the implants were stained to assess the deposition of proteoglycans and type II collagen. Results Despite variability, the immunophenotyping of BM-MSCs, SM-MSCs, and SF-MSCs was quite similar. All cell types were positive for the expression of stem cell markers and negative for exclusion markers. Additionally, chondrogenic differentiation and hypertrophy were more pronounced in BM-MSCs (ACAN, SOX9, COL2B, and COL10A) than in SF-MSCs, with SM-MSCs having intermediate characteristics. Concerning matrix synthesis, the three cell types were equipotent in terms of GAG content, while BM-MSC ECM synthesis of type II collagen was superior. Conclusions Chondrogenic MSCs are easily collected from SM and SF in advanced human OA, but in vitro chondrogenesis that is superior to age-matched BM-MSCs should not be expected. However, due to intra-articular priming, SF-MSCs did not overexpress hypertrophic gene.

Respective stemness and chondrogenic potential of mesenchymal stem cells isolated from human bone marrow, synovial membrane, and synovial fluid;Paul Neybecker;2020;figshare


CCDC 1970242: Experimental Crystal Structure Determination;Brzechwa-Chodzyńska, Anna;2020;Cambridge Crystallographic Data Centre

tris[5-([2,2'-bipyridin]-5-yl)pyrimidin-2-amine]-iron(ii) bis(tetrafluoridoborate) dihydrate unknown solvate

Related Article: Anna Brzechwa-Chodzyńska, Michał Zieliński, Mirosław Gilski, Jack M. Harrowfield, Artur R. Stefankiewicz|2020|Inorg.Chem.|59|8552|doi:10.1021/acs.inorgchem.0c01019


CCDC 1999612: Experimental Crystal Structure Determination;Romo-Islas, Guillermo;2020;Cambridge Crystallographic Data Centre

Related Article: Guillermo Romo-Islas, Guillermo Moreno-Alcántar, Marcos Flores-Álamo, Hugo Torrens|2020|J.Fluorine Chem.|236|109578|doi:10.1016/j.jfluchem.2020.109578


CCDC 1942248: Experimental Crystal Structure Determination;Qiu, Ya-Ru;2020;Cambridge Crystallographic Data Centre

Related Article: Ya-Ru Qiu, Long Cui, Pei-Yu Cai, Fei Yu, Mohamedally Kurmoo, Chanel F. Leong, Deanna M. D'Alessandro, Jing-Lin Zuo|2020|Chemical Science|11|6229|doi:10.1039/D0SC02388D


CCDC 1974741: Experimental Crystal Structure Determination;Liu, Chun-Yu;2020;Cambridge Crystallographic Data Centre


CCDC 1974738: Experimental Crystal Structure Determination;Liu, Chun-Yu;2020;Cambridge Crystallographic Data Centre


CCDC 1981722: Experimental Crystal Structure Determination;Wei, Yi;2020;Cambridge Crystallographic Data Centre

Related Article: Yi Wei, Abing Duan, Pan-Ting Tang, Jia-Wei Li, Rou-Ming Peng, Zheng-Xin Zhou, Xiao-Peng Luo, Mohamedally Kurmoo, Yue-Jin Liu, Ming-Hua Zeng|2020|Org.Lett.|22|4129|doi:10.1021/acs.orglett.0c01208


CCDC 1835730: Experimental Crystal Structure Determination;Qiu, Ya-Ru;2020;Cambridge Crystallographic Data Centre


CCDC 1969978: Experimental Crystal Structure Determination;Brzechwa-Chodzyńska, Anna;2020;Cambridge Crystallographic Data Centre


CCDC 1835731: Experimental Crystal Structure Determination;Qiu, Ya-Ru;2020;Cambridge Crystallographic Data Centre


CCDC 1974742: Experimental Crystal Structure Determination;Liu, Chun-Yu;2020;Cambridge Crystallographic Data Centre


CCDC 1879198: Experimental Crystal Structure Determination;Fan, Kun;2020;Cambridge Crystallographic Data Centre

Related Article: Kun Fan, Feng Xu, Mohamedally Kurmoo, Xin-Da Huang, Chwen-Haw Liao, Song-Song Bao, Fei Xue, Li-Min Zheng|2020|Inorg.Chem.|59|8935|doi:10.1021/acs.inorgchem.0c00762


CCDC 1974739: Experimental Crystal Structure Determination;Liu, Chun-Yu;2020;Cambridge Crystallographic Data Centre


CCDC 1991682: Experimental Crystal Structure Determination;Fan, Kun;2020;Cambridge Crystallographic Data Centre


CCDC 1987944: Experimental Crystal Structure Determination;Ristić, Predrag;2020;Cambridge Crystallographic Data Centre

Related Article: Predrag Ristić, Tamara R. Todorović, Vladimir Blagojević, Olivera R. Klisurić, Ivana Marjanović, Berta Barta Holló, Predrag Vulić, Mihaela Gulea, Morgan Donnard, Miguel Monge, María Rodríguez-Castillo, José M. López-de-Luzuriaga, Nenad R. Filipović|2020|Cryst.Growth Des.|20|4461|doi:10.1021/acs.cgd.0c00287


CCDC 1992970: Experimental Crystal Structure Determination;Debrauwer, Vincent;2020;Cambridge Crystallographic Data Centre

Related Article: Vincent Debrauwer,  Aneta Turlik,  Lénaic Rummler,  Alessandro Prescimone,  Nicolas Blanchard,  K. N. Houk,  Vincent Bizet|2020|J.Am.Chem.Soc.|142|11153|doi:10.1021/jacs.0c03556


CCDC 1879196: Experimental Crystal Structure Determination;Fan, Kun;2020;Cambridge Crystallographic Data Centre


CCDC 1991681: Experimental Crystal Structure Determination;Fan, Kun;2020;Cambridge Crystallographic Data Centre


CCDC 1987949: Experimental Crystal Structure Determination;Ristić, Predrag;2020;Cambridge Crystallographic Data Centre


CCDC 1987947: Experimental Crystal Structure Determination;Ristić, Predrag;2020;Cambridge Crystallographic Data Centre

catena-[(mu-thiomorpholine-4-carbonitrile)-(3,5-dicarboxybenzoato)-silver benzene-1,3,5-tricarboxylic acid solvate]


CCDC 1879197: Experimental Crystal Structure Determination;Fan, Kun;2020;Cambridge Crystallographic Data Centre


CCDC 1991680: Experimental Crystal Structure Determination;Fan, Kun;2020;Cambridge Crystallographic Data Centre


CCDC 1992927: Experimental Crystal Structure Determination;Debrauwer, Vincent;2020;Cambridge Crystallographic Data Centre

6,8-dimethoxy-2-methyl-3-(triphenylgermyl)isoquinolin-1(2H)-one ethanol solvate monohydrate


CCDC 1992925: Experimental Crystal Structure Determination;Debrauwer, Vincent;2020;Cambridge Crystallographic Data Centre


CCDC 1992926: Experimental Crystal Structure Determination;Debrauwer, Vincent;2020;Cambridge Crystallographic Data Centre


CCDC 2000304: Experimental Crystal Structure Determination;Debrauwer, Vincent;2020;Cambridge Crystallographic Data Centre


CCDC 1955690: Experimental Crystal Structure Determination;Moreno-Alcántar, Guillermo;2020;Cambridge Crystallographic Data Centre

Related Article: Guillermo Moreno-Alcántar, Luis Turcio-García, José M. Guevara-Vela, Eduardo Romero-Montalvo, Tomás Rocha-Rinza, Ángel Martín Pendás, Marcos Flores-Álamo, Hugo Torrens|2020|Inorg.Chem.|59|8667|doi:10.1021/acs.inorgchem.9b03131


CCDC 1955693: Experimental Crystal Structure Determination;Moreno-Alcántar, Guillermo;2020;Cambridge Crystallographic Data Centre


CCDC 1955698: Experimental Crystal Structure Determination;Moreno-Alcántar, Guillermo;2020;Cambridge Crystallographic Data Centre


CCDC 1920843: Experimental Crystal Structure Determination;Estrada-Montaño, Aldo S.;2020;Cambridge Crystallographic Data Centre

tris(4,4'-dimethyl-2,2'-bipyridine)-iron bis(chloride) deuterochloroform solvate

Related Article: Aldo S. Estrada-Montaño, Alexandre Gries, José A. Oviedo-Fortino, Carolina Torres-Gutierrez, Amira Grain-Hayton, Raymundo Marcial-Hernández, Longzhu Shen, Alexander D. Ryabov, Christian Gaiddon, Ronan Le Lagadec|2020|Organometallics|39|1842|doi:10.1021/acs.organomet.0c00107


CCDC 1983165: Experimental Crystal Structure Determination;Thuéry, Pierre;2020;Cambridge Crystallographic Data Centre

Related Article: Pierre Thuéry, Youssef Atoini, Jack Harrowfield|2020|Inorg.Chem.|59|6953|doi:10.1021/acs.inorgchem.0c00450


CCDC 1983166: Experimental Crystal Structure Determination;Thuéry, Pierre;2020;Cambridge Crystallographic Data Centre


CCDC 1983168: Experimental Crystal Structure Determination;Thuéry, Pierre;2020;Cambridge Crystallographic Data Centre


CCDC 1983167: Experimental Crystal Structure Determination;Thuéry, Pierre;2020;Cambridge Crystallographic Data Centre


CCDC 1920845: Experimental Crystal Structure Determination;Estrada-Montaño, Aldo S.;2020;Cambridge Crystallographic Data Centre


CCDC 1920844: Experimental Crystal Structure Determination;Estrada-Montaño, Aldo S.;2020;Cambridge Crystallographic Data Centre


CCDC 1908272: Experimental Crystal Structure Determination;Ren, Yufeng;2020;Cambridge Crystallographic Data Centre

Related Article: Yufeng Ren, Jeremy Forté, Khaled Cheaib, Nicolas Vanthuyne, Louis Fensterbank, Hervé Vezin, Maylis Orio, Sébastien Blanchard, Marine Desage-El Murr|2020|iScience|23|100955|doi:10.1016/j.isci.2020.100955


CCDC 1978288: Experimental Crystal Structure Determination;Normand, Adrien T.;2020;Cambridge Crystallographic Data Centre

Related Article: Adrien T. Normand, Raluca Malacea-Kabbara, Rosita Lapenta, Aymeric Dajnak, Philippe Richard, Hélène Cattey, Anaëlle Bolley, Alfonso Grassi, Stefano Milione, Audrey Auffrant, Samuel Dagorne, Pierre Le Gendre|2020|Dalton Trans.|49|6989|doi:10.1039/D0DT00972E


CCDC 1978287: Experimental Crystal Structure Determination;Normand, Adrien T.;2020;Cambridge Crystallographic Data Centre


CCDC 1978290: Experimental Crystal Structure Determination;Normand, Adrien T.;2020;Cambridge Crystallographic Data Centre


CCDC 1978292: Experimental Crystal Structure Determination;Normand, Adrien T.;2020;Cambridge Crystallographic Data Centre


CCDC 1978293: Experimental Crystal Structure Determination;Normand, Adrien T.;2020;Cambridge Crystallographic Data Centre


CCDC 1978289: Experimental Crystal Structure Determination;Normand, Adrien T.;2020;Cambridge Crystallographic Data Centre