Abstract: Abstract Background Hibernation has been a key area of research for several decades, essentially in small mammals in the laboratory, yet we know very little about what triggers or ends it in the wild. Do climatic factors, an internal biological clock, or physiological processes dominate? Using state-of-the-art tracking and monitoring technology on fourteen free-ranging brown bears over three winters, we recorded movement, heart rate (HR), heart rate variability (HRV), body temperature (Tb), physical activity, ambient temperature (TA), and snow depth to identify the drivers of the start and end of hibernation. We used behavioral change point analyses to estimate the start and end of hibernation and convergent cross mapping to identify the causal interactions between the ecological and physiological variables over time. Results To our knowledge, we have built the first chronology of both ecological and physiological events from before the start to the end of hibernation in the field. Activity, HR, and Tb started to drop slowly several weeks before den entry. Bears entered the den when snow arrived and when ambient temperature reached 0Â Â°C. HRV, taken as a proxy of sympathetic nervous system activity, dropped dramatically once the bear entered the den. This indirectly suggests that denning is tightly coupled to metabolic suppression. During arousal, the unexpected early rise in Tb (two months before den exit) was driven by TA, but was independent of HRV. The difference between Tb and TA decreased gradually suggesting that bears were not thermoconforming. HRV increased only three weeks before exit, indicating that late activation of the sympathetic nervous system likely finalized restoration of euthermic metabolism. Interestingly, it was not until TA reached the presumed lower critical temperature, likely indicating that the bears were seeking thermoneutrality, that they exited the den. Conclusions We conclude that brown bear hibernation was initiated primarily by environmental cues, but terminated by physiological cues.

Drivers of hibernation in the brown bear;A. Evans;2016;Figshare


Abstract: Abstract Background We aimed to describe specific changes in brain perfusion in patients with dementia with Lewy bodies (DLB) at both the prodromal (also called mild cognitive impairment) and mild dementia stages, relative to patients with Alzheimer’s disease (AD) and controls. Methods Altogether, 96 participants in five groups (prodromal DLB, prodromal AD, DLB with mild dementia, AD with mild dementia, and healthy elderly controls) took part in an arterial spin labeling MRI study. Three analyses were performed: a global perfusion value comparison, a voxel-wise analysis of both absolute and relative perfusion, and a linear discriminant analysis. These were used to assess the global decrease in perfusion, regional changes, and the sensitivity and specificity of these changes. Results Patterns of perfusion in DLB differed from AD and controls in both the prodromal stage and dementia, DLB having more deficits in frontal, insular, and temporal cortices whereas AD showed reduced perfusion in parietal and parietotemporal cortices. Decreases but also increases of perfusion in DLB relative to controls were observed in both absolute and relative measurements. All these regional changes of perfusion classified DLB patients with respect to either healthy controls or AD with sensitivity from 87 to 100 % and specificity from 90 to 96 % depending on the stage of the disease. Conclusions Our results are consistent with previous studies. We extend the scope of those studies by integrating prodromal DLB patients and by describing both hypo- and hyperperfusion in DLB. While decreases in perfusion may relate to functional impairments, increases might suggest a functional compensation of some brain areas.

Brain perfusion in dementia with Lewy bodies and Alzheimer’s disease: an arterial spin labeling MRI study on prodromal and mild dementia stages;Daniel Roquet;2016;Figshare


Abstract: Abstract Background Genetically induced hepatocellular carcinoma (HCC) models are generally used to investigate carcinogenesis pathways, but very few attempts were made to valorize them for pharmacological testing. This study describes a micro-computed tomography (micro-CT) - based methodology for the diagnostic and lifelong follow-up of HCC in the hepatocyte-specific Trim24-null mouse line. Myo-inositol trispyrophosphate (ITPP) was tested as anti-cancer drug. Methods Partial hepatectomy was performed in 2 months-old Trim24-null mice, in order to accelerate the carcinogenesis process. HCC diagnosis was obtained by micro-CT scan with double contrast agent: 10 μl/g Fenestra™ LC was injected intraperitoneally 6 h prior to imaging and 10 μl/g Fenestra™ VC was injected intravenously 15 min prior to imaging. Twenty three hepatocyte-specific Trim24-null mice were considered for ITPP testing (3 mg/g/week intraperitoneally during 10 months in 12 mice, versus 11 controls). Lifelong follow-up was performed using micro-CT. Comparative analysis was performed using unpaired t test with Welch correction and survival curves were compared by log-rank test. Gene expression analysis was performed using the RT q-PCR technique. Results Double contrast micro-CT scan allowed HCC diagnosis as hypodense, isodense or hyperdense nodules. Positive predictive value was 81.3 %. Negative predictive value was 83.3 %. Tumor growth could be objectified by micro-CT scan before the ITPP treatment was started, and at 3 and 9 months follow-up. Significant progression of tumor volume was demonstrated in the both groups, with no difference between groups (p > 0.05). In the ITPP group, a mild decrease in tumor doubling time was first observed (31.9 +/− 12 days, p > 0.05) followed by a significant increase (59.8 +/− 18.3 days, p = 0.008). However, tumor doubling time was not different between groups (p > 0.05). Median survival after treatment initiation was 223 days (controls) versus 296 days (ITPP group, p = 0.0027). HIF1α, VEGF, glutamine synthase, osteopontin expression levels were not significantly modified at the end of follow-up. In the ITPP group, the p53 expression profile was inversed as compared to the control group, higher in non-tumor livers than in tumors. Conclusion ITPP treatment allowed for a two-month survival improvement, with better tolerance of tumor burden and apoptosis increase in non-tumor, pathological livers.

Development of a methodology for in vivo follow-up of hepatocellular carcinoma in hepatocyte specific Trim24-null mice treated with myo-inositol trispyrophosphate;Mihaela Ignat;2016;Figshare


Abstract: Abstract Background Alterations in genetic and epigenetic landscapes are known to contribute to the development of different types of cancer. However, the mechanistic links between transcription factors and the epigenome which coordinate the deregulation of gene networks during cell transformation are largely unknown. Methods We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. We applied a systems biology approach by combining transcriptome and epigenome data for each step during transformation and integrated transcription factorâ  target gene associations in order to reconstruct the gene regulatory networks that are at the basis of the transformation process. Results We identified 142 transcription factors and 24 chromatin remodelers/modifiers (CRMs) which are preferentially associated with specific co-expression pathways that originate from deregulated gene programming during tumorigenesis. These transcription factors are involved in the regulation of divers processes, including cell differentiation, the immune response, and the establishment/modification of the epigenome. Unexpectedly, the analysis of chromatin state dynamics revealed patterns that distinguish groups of genes which are not only co-regulated but also functionally related. Decortication of transcription factor targets enabled us to define potential key regulators of cell transformation which are engaged in RNA metabolism and chromatin remodeling. Conclusions We reconstructed gene regulatory networks that reveal the alterations occurring during human cellular tumorigenesis. Using these networks we predicted and validated several transcription factors as key players for the establishment of tumorigenic traits of transformed cells. Our study suggests a direct implication of CRMs in oncogene-induced tumorigenesis and identifies new CRMs involved in this process. This is the first comprehensive view of the gene regulatory network that is altered during the process of stepwise human cellular tumorigenesis in a virtually isogenic system.

Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis;Valeriya Malysheva;2016;Figshare


Abstract: Abstract Background The aim of this volumetric study was to explore the neuroanatomical correlates of the Free and Cued Selective Reminding Test (FCSRT) and the Delayed Matching-to-Sample—48 items (DMS-48), two tests widely used in France to assess verbal and visual anterograde memory. We wanted to determine to what extent the two tests rely on the medial temporal lobe, and could therefore be predictive of Alzheimer’s disease, in which pathological changes typically start in this region. Methods We analysed data from a cohort of 138 patients with mild cognitive impairment participating in a longitudinal multicentre clinical research study. Verbal memory was assessed using the FCSRT and visual recognition memory was evaluated using the DMS-48. Performances on these two tests were correlated to local grey matter atrophy via structural MRI using voxel-based morphometry. Results Our results confirm the existence of a positive correlation between the volume of the medial temporal lobe and the performance on the FCSRT, prominently on the left, and the performance on the DMS-48, on the right, for the whole group of patients (family-wise error, P

Exploring anterograde memory: a volumetric MRI study in patients with mild cognitive impairment;N. Philippi;2016;Figshare


Abstract: Abstract Background In HIV-1 infected cells, the integrated viral DNA is transcribed by the host cell machinery to generate the full length HIV-1 RNA (FL RNA) that serves as mRNA encoding for the Gag and GagPol precursors. Virion formation is orchestrated by Gag, and the current view is that a specific interaction between newly made Gag molecules and FL RNA initiates the process. This in turn would cause FL RNA dimerization by the NC domain of Gag (GagNC). However the RNA chaperoning activity of unprocessed Gag is low as compared to the mature NC protein. This prompted us to search for GagNC co-factors. Results Here we report that RPL7, a major ribosomal protein involved in translation regulation, is a partner of Gag via its interaction with the NC domain. This interaction is mediated by the NC zinc fingers and the N- and C-termini of RPL7, respectively, but seems independent of RNA binding, Gag oligomerization and its interaction with the plasma membrane. Interestingly, RPL7 is shown for the first time to exhibit a potent DNA/RNA chaperone activity higher than that of Gag. In addition, Gag and RPL7 can function in concert to drive rapid nucleic acid hybridization. Conclusions Our results show that GagNC interacts with the ribosomal protein RPL7 endowed with nucleic acid chaperone activity, favoring the notion that RPL7 could be a Gag helper chaperoning factor possibly contributing to the start of Gag assembly.

Earth and related environmental sciences

Characterization of the interaction between the HIV-1 Gag structural polyprotein and the cellular ribosomal protein L7 and its implication in viral nucleic acid remodeling;Hala Mekdad;2016;Figshare


Abstract: Abstract Background Comprehensive assessment of sedentary behavior (SB) and physical activity (PA), including transport-related activities (TRA), is required to design innovative PA promotion strategies. There are few validated instruments that simultaneously assess the different components of human movement according to their context of practice (e.g. work, transport, leisure). We examined test-retest reliability and validity of the Sedentary, Transportation and Activity Questionnaire (STAQ), a newly developed questionnaire dedicated to assessing context-specific SB, TRA and PA. Methods Ninety six subjects (51 women) kept a contextualized activity-logbook and wore a hip accelerometer (Actigraph GT3X + TM) for a 7-day or 14-day period, at the end of which they completed the STAQ. Activity-energy expenditure was measured in a subgroup of 45 subjects using the double labeled water (DLW) method. Test-retest reliability was assessed using intra-class-coefficients (ICC) in a subgroup of 32 subjects who filled the questionnaire twice one month apart. Accelerometry was annotated using the logbook to obtain total and context-specific objective estimates of SB. Spearman correlations, Bland-Altman plots and ICC were used to analyze validity with logbook, accelerometry and DLW data validity criteria. Results Test-retest reliability was fair for total sitting time (ICC = 0.52), good to excellent for work sitting time (ICC = 0.71), transport-related walking (ICC = 0.61) and car use (ICC = 0.67), and leisure screen-related SB (ICC = 0.64-0.79), but poor for total sitting time during leisure and transport-related contexts. For validity, compared to accelerometry, significant correlations were found for STAQ estimates of total (r = 0.54) and context-specific sitting times with stronger correlations for work sitting time (r = 0.88), and screen times (TV/DVD viewing: r = 0.46; other screens: r = 0.42) than for transport (r = 0.35) or leisure-related sitting-times (r = 0.19). Compared to contextualized logbook, STAQ estimates of TRA was higher for car (r = 0.65) than for active transport (r = 0.41). The questionnaire generally overestimated work- and leisure-related SB and sitting times, while it underestimated total and transport-related sitting times. Conclusions The STAQ showed acceptable reliability and a good ranking validity for assessment of context-specific SB and TRA. This instrument appears as a useful tool to study SB, TRA and PA in context in adults.

Assessment of sedentary behaviors and transport-related activities by questionnaire: a validation study;Keitly Mensah;2016;Figshare


Abstract: Abstract Background Volatile thiols largely contribute to the organoleptic characteristics and typicity of Sauvignon blanc wines. Among this family of odorous compounds, 3-sulfanylhexan-1-ol (3SH) and 4-methyl-4-sulfanylpentan-2-one (4MSP) have a major impact on wine flavor. These thiols are formed during alcoholic fermentation by the yeast from odorless, non-volatile precursors found in the berries and the must. The present study investigates the effects of vine nitrogen (N) status on 3SH and 4MSP content in Sauvignon blanc wine and on the glutathionylated and cysteinylated precursors of 3SH (Glut-3SH and Cys-3SH) in the berries and the must. This is paralleled by a RNA-seq analysis of gene expression in the berries. The impact of N supply on the expression of the glutathione-S-transferase 3 and 4 (VviGST3 and VviGST4) and the γ-glutamyltranspeptidase (VviGGT), considered as key genes in their biosynthesis, was also evaluated. Results N supply (N100 treatment) increased the 3SH content in wine while no effect was noticed on 4MSP level. Furthermore, N supply increased Glut-3SH levels in grape berries at late berry ripening stages, and this effect was highly significant in must at harvest. No significant effect of N addition was noticed on Cys-3SH concentration. The transcript abundance of the glutathione-S-transferases VviGST3 and VviGST4 and the γ-glutamyltranspeptidase (VviGGT), were similar between the control and the N100 treatment. New candidate genes which might be implicated in the biosynthetic pathway of 3SH precursors were identified by whole transcriptome shotgun sequencing (RNA-seq). Conclusions High vine N status has a positive effect on 3SH content in wine through an increase of Glut-3SH levels in grape berries and must. Candidate GSTs and glutathione-S-conjugates type transporters involved in this stimulation were identified by RNA-seq analysis.

Vine nitrogen status and volatile thiols and their precursors from plot to transcriptome level;Pierre Helwi;2016;Figshare


Abstract: Abstract Background Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europeâ  s megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamics during the Pleistocene. Results Through ancient DNA analysis we show that the emblematic European bison has experienced several waves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic diversity during the Holocene. Fifty-seven complete and partial ancient mitogenomes from throughout Europe, the Caucasus, and Siberia reveal that three populations of wisent (Bison bonasus) and steppe bison (B. priscus) alternately occupied Western Europe, correlating with climate-induced environmental changes. The Late Pleistocene European steppe bison originated from northern Eurasia, whereas the modern wisent population emerged from a refuge in the southern Caucasus after the last glacial maximum. A population overlap during a transition period is reflected in ca. 36,000-year-old paintings in the French Chauvet cave. Bayesian analyses of these complete ancient mitogenomes yielded new dates of the various branching events during the evolution of Bison and its radiation with Bos, which lead us to propose that the genetic affiliation between the wisent and cattle mitogenomes result from incomplete lineage sorting rather than post-speciation gene flow. Conclusion The paleogenetic analysis of bison remains from the last 50,000 years reveals the influence of climate changes on the dynamics of the various bison populations in Europe, only one of which survived into the Holocene, where it experienced severe reductions in its genetic diversity. The time depth and geographical scope of this study enables us to propose temperate Western Europe as a suitable biotope for the wisent compatible with its reintroduction.

Past climate changes, population dynamics and the origin of Bison in Europe;Diyendo Massilani;2016;Figshare


Abstract: Abstract Background Proximity ligation-mediated methods are essential to study the impact of three-dimensional chromatin organization on gene programming. Albeit significant progress has been made in the development of computational tools that assess long-range chromatin interactions, next to nothing is known about the quality of the generated datasets. Method We have developed LOGIQA ( www.ngs-qc.org/logiqa ), a database hosting quality scores for long-range genome interaction assays, accessible through a user-friendly web-based environment. Results Currently, LOGIQA harbors QC scores for >900 datasets, which provides a global view of their relative quality and reveals the impact of genome size, coverage and other technical aspects. LOGIQA provides a user-friendly dataset query panel and a genome viewer to assess local genome-interaction maps at different resolution and quality-assessment conditions. Conclusions LOGIQA is the first database hosting quality scores dedicated to long-range chromatin interaction assays, which in addition provides a platform for visualizing genome interactions made available by the scientific community.

LOGIQA: a database dedicated to long-range genome interactions quality assessment;Marco-Antonio Mendoza-Parra;2016;Figshare


Abstract: Abstract The observation showing that Lewy type synucleinopathy (LTS), the pathological hallmark of Parkinson’s disease (PD), is found in the gut of almost all PD subjects led to a substantial amount of research to develop a diagnostic procedure in living patients based on endoscopically obtained gastrointestinal biopsies. However, the existing studies have provided conflicting results regarding the sensitivity and specificity of gastrointestinal biopsies for the detection of LTS. We therefore undertook a multi-center staining and blinded judging of a common set of slides from colonic biopsies to determine the optimal protocol for the detection of LTS. Four different immunohistochemical methods, developed in four separate expert laboratories, were evaluated for their sensitivity and specificity to detect enteric LTS. Test sets of formalin-fixed, paraffin-embedded sections from biopsies of 9 PD subjects and 3 controls were stained with the 4 methods and graded by 4 different observers. Four types of staining morphology (granular staining in the lamina propria, perivascular/vascular wall staining in the submucosa, lacy-granular pattern in the submucosa and epithelial cell nuclear staining) were variably observed in the slides stained by the 4 methods. Positive alpha-synuclein staining was observed by all 5 judges in most of the slides from control cases, regardless of the staining methods that were used. Moreover, none of the tested method or staining pattern had a specificity and sensitivity more than 80 % regarding to PD. Overall, our study suggest that the tested methods are not adequate for the prediction of PD using gastrointestinal biopsies. Future studies are warranted to test new immunostaining methods.

Evaluation of alpha-synuclein immunohistochemical methods for the detection of Lewy-type synucleinopathy in gastrointestinal biopsies;Anne-Gaëlle Corbillé;2016;Figshare


Abstract: Abstract Background Deficient nucleotide excision repair (NER) activity causes a variety of autosomal recessive diseases including xeroderma pigmentosum (XP) a disorder which pre-disposes to skin cancer, and the severe multisystem condition known as Cockayne syndrome (CS). In view of the clinical overlap between NER-related disorders, as well as the existence of multiple phenotypes and the numerous genes involved, we developed a new diagnostic approach based on the enrichment of 16 NER-related genes by multiplex amplification coupled with next-generation sequencing (NGS). Methods Our test cohort consisted of 11 DNA samples, all with known mutations and/or non pathogenic SNPs in two of the tested genes. We then used the same technique to analyse samples from a prospective cohort of 40 patients. Multiplex amplification and sequencing were performed using AmpliSeq protocol on the Ion Torrent PGM (Life Technologies). Results We identified causative mutations in 17 out of the 40 patients (43 %). Four patients showed biallelic mutations in the ERCC6(CSB) gene, five in the ERCC8(CSA) gene: most of them had classical CS features but some had very mild and incomplete phenotypes. A small cohort of 4 unrelated classic XP patients from the Basque country (Northern Spain) revealed a common splicing mutation in POLH (XP-variant), demonstrating a new founder effect in this population. Interestingly, our results also found ERCC2(XPD), ERCC3(XPB) or ERCC5(XPG) mutations in two cases of UV-sensitive syndrome and in two cases with mixed XP/CS phenotypes. Conclusions Our study confirms that NGS is an efficient technique for the analysis of NER-related disorders on a molecular level. It is particularly useful for phenotypes with combined features or unusually mild symptoms. Targeted NGS used in conjunction with DNA repair functional tests and precise clinical evaluation permits rapid and cost-effective diagnosis in patients with NER-defects.

Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing;Nadège Calmels;2016;Figshare


Abstract: Abstract Background Acacia ataxacantha (Fabaceae), used in traditional medicine grows in the South-West of Bénin. Ethyl acetate extract of the barks of this species was previously reported to display various bioactivities, including antibacterial, antifungal and antioxidant activities. In the present study, we investigate the antimicrobial and antioxidant activities of compound isolated from ethyl acetate extract of Acacia ataxacantha. Methods Purification, isolation and structural identification of isolated compound were done using various chromatographic and spectroscopic methods. Antimicrobial activity was investigated using a two-fold serial microdilution method. The inhibitory potency of isolated compound was evaluated by kinetic experiments. The antioxidant activity was also determined using 2, 2-diphenyl-1-picrylhydrazyl. Results The isolated compound was identified as 7-hydroxy-2-methyl-6-[β-galactopyranosyl-propyl]-4H-chromen-4-one. As far as we know, this compound, named “acthaside”, reported for the first time, was active against all tested microorganisms with minimal inhibitory concentration ranging from 25 to 50 μg/ml. At 50 μl/ml, no growth was observed in almost all tested microbial after 24 h of exposure. The isolated compound had significant antioxidant activity with an IC50 value of 3.61 ± 0.12 μg/ml compared to quercetin (IC50 1.04 ± 0.01 μg/ml). Conclusion The present work demonstrates that the new chromen derivative isolated from A. ataxacantha may help treat bacterial and yeast infections. However, further studies are required to clarify the mechanism of action of this compound.

Acthaside: a new chromone derivative from Acacia ataxacantha and its biological activities;Abdou Amoussa;2016;Figshare


Abstract: Abstract Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses;Shaman Narayanasamy;2016;Figshare


Abstract: Abstract Background Genome-wide association (GWA) mapping has recently emerged as a valuable approach for refining the genetic basis of polygenic resistance to plant diseases, which are increasingly used in integrated strategies for durable crop protection. Aphanomyces euteiches is a soil-borne pathogen of pea and other legumes worldwide, which causes yield-damaging root rot. Linkage mapping studies reported quantitative trait loci (QTL) controlling resistance to A. euteiches in pea. However the confidence intervals (CIs) of these QTL remained large and were often linked to undesirable alleles, which limited their application in breeding. The aim of this study was to use a GWA approach to validate and refine CIs of the previously reported Aphanomyces resistance QTL, as well as identify new resistance loci. Methods A pea-Aphanomyces collection of 175 pea lines, enriched in germplasm derived from previously studied resistant sources, was evaluated for resistance to A. euteiches in field infested nurseries in nine environments and with two strains in climatic chambers. The collection was genotyped using 13,204 SNPs from the recently developed GenoPea Infinium® BeadChip. Results GWA analysis detected a total of 52 QTL of small size-intervals associated with resistance to A. euteiches, using the recently developed Multi-Locus Mixed Model. The analysis validated six of the seven previously reported main Aphanomyces resistance QTL and detected novel resistance loci. It also provided marker haplotypes at 14 consistent QTL regions associated with increased resistance and highlighted accumulation of favourable haplotypes in the most resistant lines. Previous linkages between resistance alleles and undesired late-flowering alleles for dry pea breeding were mostly confirmed, but the linkage between loci controlling resistance and coloured flowers was broken due to the high resolution of the analysis. A high proportion of the putative candidate genes underlying resistance loci encoded stress-related proteins and others suggested that the QTL are involved in diverse functions. Conclusion This study provides valuable markers, marker haplotypes and germplasm lines to increase levels of partial resistance to A. euteiches in pea breeding.

Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: Follow-up of hepatocellular carcinoma (HCC) growth by 3D reconstruction. Follow-up of hepatocellular carcinoma (HCC) growth by 3D reconstruction of micro-CT rendering. Micro-CT imaging was performed at 12, 15, and 21 months of age respectively in hepatocyte specific Trim24-null mice. A, B, C Exponential growth of unifocal HCC. A. Micro-CT-scan rendering in coronal slides (strips indicate vertical diameter of HCC). B. 3D reconstruction of the micro-CT-scan (HCC is depicted in green). C. Macroscopic appearance of the liver and HCC at dissection at 22 months old (black arrow indicates tumor). D, E, F. Multifocal growth of HCC. D. Micro-CT scan rendering in coronal slides (strips indicate vertical diameters of the HCCs). E. 3D reconstruction of the micro-CT-scan (HCCs are depicted in green). F. Macroscopic appearance of the liver and HCCs at dissection at 23 months old (black arrows indicate tumors). (JPG 4259 kb)

Additional file 4: of Development of a methodology for in vivo follow-up of hepatocellular carcinoma in hepatocyte specific Trim24-null mice treated with myo-inositol trispyrophosphate;Mihaela Ignat;2016;Figshare


Abstract: In Staphylococcus aureus, peptidoglycan metabolism plays a role in the host inflammatory response and pathogenesis. Transcription of the peptidoglycan hydrolases is activated by the essential 2-component system WalKR at low cell density. During stationary growth phase, WalKR is not active and transcription of the peptidoglycan hydrolase genes is repressed. In this work, we studied regulation of expression of the glycylglycine endopeptidase LytM. We show that, in addition to the transcriptional regulation mediated by WalKR, the synthesis of LytM is negatively controlled by a unique mechanism at the stationary growth phase. We have identified 2 different mRNAs encoding lytM, which vary in the length of their 5′ untranslated (5′UTR) regions. LytM is predominantly produced from the WalKR-regulated mRNA transcript carrying a short 5′UTR. The lytM mRNA is also transcribed as part of a polycistronic operon with the upstream SA0264 gene and is constitutively expressed. Although SA0264 protein can be synthesized from the longer operon transcript, lytM cannot be translated because its ribosome-binding site is sequestered into a translationally inactive secondary structure. In addition, the effector of the agr system, RNAIII, can inhibit translation of lytM present on the operon without altering the transcript level but does not have an effect on the translation of the upstream gene. We propose that this dual regulation of lytM expression, at the transcriptional and post-transcriptional levels, contributes to prevent cell wall damage during the stationary phase of growth.

Various checkpoints prevent the synthesis of <i>Staphylococcus aureus</i> peptidoglycan hydrolase LytM in the stationary growth phase;Efthimia Lioliou;2016;Figshare


Synthesis of 1,3-thiazines by a three-component reaction and their transformations into β-lactam-condensed 1,3-thiazine and 1,4-thiazepine derivatives;Flavie Peudru;2016;Figshare


Abstract: Detailed information on CRISPR/Cas9 cleavage efficiency studies. Number of guides, cell types, delivery, and expression method of the guide RNA and comments. (XLS 36 kb)

Additional file 10: Table S5. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR;Maximilian Haeussler;2016;Figshare


Abstract: Genetic loci associated with Aphanomyces resistance, earliness and plant height detected by genome-wide association mapping using the MLMM method. (a) Genetic positions are estimated on the genetic map resulting from the projection of the marker map from Hamon et al. [43] onto the consensus map from Tayeh et al. [49]; (b) A linkage disequilibrium (LD) block is designed with all markers in LD (r 2 > 0.2) with the associated marker. LD blocks are named in consecutive numerical order following their linkage group (LG) name and their genetic position; (c) Aphanomyces resistance and earliness Meta-QTL (quantitative trait loci) described in [43]; (d) Initial QTL for Aphanomyces resistance and earliness before meta-analysis described in [41, 43]; (e) Trait-associated marker(s) and their genetic position(s) in the LD blocks. PsCam- markers are SNPs developed by Tayeh et al. [49], Af is a morphological gene involved in leaves shape, other markers are SSRs (detected allele in brackets); (f) Minor allele frequency (MAF) of each detected marker in the collection; (g) Variables are coded as described in Additional file 4; (h) significant p-value of the marker-trait association < 2.5E-5; (i) mean value of the trait corrected with the effect of all markers included in the MLMM analysis; (j) allelic effect of the marker on the variable, the sign depends on the allele code; (k) standard error at the marker around the mean value of the trait in the collection. (XLSX 32 kb)

Additional file 11: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: Simple sequence repeat (SSR) markers used to genotype the pea-Aphanomyces collection. (a) main Aphanomyces resistance quantitative trait loci (QTL) defined in [43]. (XLSX 14 kb)

Additional file 2: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: Least square means (LSMeans) of phenotypic data in the pea-Aphanomyces collection after ANOVA. Variables are coded as in Additional file 4. NA: missing data. (XLSX 71 kb)

Additional file 16: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: Marker haplotype composition of the pea-Aphanomyces collection. (a) Name of marker haplotype carried by each line as described in Additional file 13, at each of the 14 consistent linkage disequilibrium (LD) blocks detected; dark green and red: favourable and unfavourable marker haplotypes, respectively, as defined in the Material and Methods section of the manuscript; (b) coordinates of each line of the collection on the first Multiple Factor Analysis principal component; the pea lines of the collection are ranked according to these coordinates; (c) Composition of each line in favourable and unfavourable haplotypes, is described in Additional file 13; (d) marker haplotypes with either a missing value or heterozygous score for at least one marker of a LD block. (XLSX 66 kb)

Additional file 14: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: Annotation of markers in detected linkage disequilibrium (LD) blocks for putative candidate genes. (a) LD block were constructed with markers detected by genome-wide association mapping and markers in LD with them, LD block are named according to Additional file 11; (b) genetic positions are estimated as described in Additional file 11; For each LD block:(c) traits associated with markers in the LD block; (d) Pairwise LD between each marker and the marker(s) detected by GWA in the LD block (detected marker in bold); (e) putative protein annotation underlying each marker based on comparative Blast X data from Tayeh et al. [49], see Methods section; (f) putative function of the protein in plant disease resistance based on the literature; (g) putative function of the protein in plant development based on the literature; (h) reference for protein function involved in plant disease resistance or plant development; (i) Pea cloned genes referred in literature; (j) extract of annotation data from Tayeh et al. [49], Blast X of marker sequence onto P. sativum, M. truncatula, G. max and A. thaliana proteins. (XLSX 131 kb)

Additional file 15: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: Variable contribution in the two first Multiple Factor Analysis (MFA) principal components. (a) Variables are coded as described in Additional file 4, (b) percentage of variable contribution in the construction of the MFA axis, ‘*’: the six highest contributions; (c) cos2 indicates the representation quality of the variable on the MFA axis, ‘*’: 0.2 < cos2 < 0.5, ‘**’: cos2 > 0.5; (d) correlation between variable and MFA axis, ‘*’: 0.5 < r 2 < 0.8, ‘**’: r 2 > 0.8. (XLSX 17 kb)

Additional file 7: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: Description of linkage disequilibrium (LD) block haplotypes in the pea-Aphanomyces collection. (a) LD blocks are named as described in Additional file 11; (b) Each LD block is subdivided into marker haplotypes according to its allelic composition. Marker haplotypes are named with the LD block name followed by an Arabic numeral. Only haplotypes without missing values or heterozygous markers are shown; For each LD block: (c) list of markers significantly detected by genome-wide association in the LD block; (d) the first line is a list of the markers included in the LD block (detected markers in bold font and their markers in (LD) in plain font); (e) the second line is the genetic positions of the listed markers on the genetic map described in Additional file 11; (f) following lines are the pairwise LD r 2 values between each marker defined in the LD block and the marker detected by GWA; (g) For SNP markers, ‘AA’ and ‘BB’ are allele codes of Genome Studio analysis while for SSR markers, amplicon lengths are indicated. For each Aphanomyces resistance associated marker, enhancing allele(s) is in bold dark green font and unfavourable allele(s) in bold dark red font; (h) the first line is the list of the variables significantly associated with a marker in the LD block, variables are described as in Additional file 4; (i) next lines are p-values of the marker-trait associations; (j) grey or coloured lines are mean phenotypic values ± standard error for marker haplotypes carried by more than 5 % of the lines from the pea-Aphanomyces collection, letters indicate significantly different means (Tukey-HSD, α < 0.05); dark green and red haplotypes: favourable and unfavourable haplotypes of the LD block, respectively, as defined in the Materiel and Methods section of the manuscript. (XLSX 73 kb)

Additional file 13: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: Genotyping data of the pea-Aphanomyces collection used for the GWA analysis before filters and imputation. NA: missing data. (a) Morphological gene genotyping data are coded “AA” when phenotypes are white flowers, normal leaves or smooth seeds for A, Af and R genes, respectively, and “BB” when they are colored flowers, afila leaves or wrinkled seeds; (b) PCR specific genotyping data are coded “AA” or “BB” when specific to the first or second allele; (c) SSR genotyping data are presented with the allele size (in bp); (d) SNP genotyping data are coded “AA” or “BB” when homozygous for the first or second allele, “AB” when heterozygous. (XLSX 7252 kb)

Additional file 17: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: Information on the connectivity between projected maps. (a) HMap: consensus map from Hamon et al. [43]; (b) TMap: consensus map from Tayeh et al. [49]; (c) number of common markers between HMap and TMap for each linkage group (LG); (d): Number of inversions of marker positions on each LG; (e) number of inversions of marker positions in confidence intervals of the quantitative trait loci (QTL) described by Hamon et al. [43]. (XLSX 11 kb)

Additional file 12: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: Description of the pea-Aphanomyces collection. (a) Line categories, as referred in Fig. 1b and Additional file 9 in legends; (b) Line codes in the Biological resource center (CRB) database of INRA Dijon, France; (c) Country codes ISO3166-1; (d) Cv: Cultivar, Bl: breeding line, Gmp: germplasm, Lv: local variety, Wa: wild accession; (e) Fd: fodder, Gd: garden; (f) Ws: winter sown, Ss: spring sown; (g) Nl: normal leaves, af: afila leaves, (h) W: white, Pu: purple, Pi: pink; (i) Wr: wrinkled, Sm: smooth; #: parents of GSP breeding programs; $: parents of RIL populations. (XLSX 29 kb)

Additional file 1: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: Statistical analysis results of Aphanomyces resistance, earliness and height scoring data in the pea-Aphanomyces collection. (a) CC: controlled condition experiment, Field: Infested field experiment, RRI: Root rot index, ADI1: First aerial decline index, ADI2: Second aerial decline index, FLO1: date to 50 % bloom, FLO2: date to 100 % bloom, RIPE: date to 100 % dried plants, HT: height of plants, 09 to 13: year of experiment, All: global variables over all field environments, DI: Dijon-Epoisses, Burgundy, France, RI: Riec-sur-Belon, Brittany, France, REN: Rennes-Le Rheu, Brittany, France, KEN: Kendrick, ID, USA, ‘$’ Residual normality statistics are not exact but graphs of residuals are correct, (b) Mean, minimum, maximum and standard error in the pea-Aphanomyces collection; (c) ANOVA significance p-value codes: 0 < ‘***’ < 0.001≤ ‘**’ < 0.01≤‘*’ < 0.05≤ ‘ns’ < 1; (d): Genotype effect; (e): Replicate effect; (f): Environment effect; (g): Genotype x Environment interaction effect; (h) mean-based heritability. (XLSX 16 kb)

Additional file 4: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea;Aurore Desgroux;2016;Figshare


Abstract: MYC target genes as determined by the analysis of publically available ChIP-seq profiles and defined by the association of the MACS peaks (p value threshold = −30) with the TSS of genes using a 10-kb distance as an association criterion. (XLS 199 kb)

Additional file 12. of Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis;Valeriya Malysheva;2016;Figshare


Abstract: Transcriptome data summary provided in Excel format. (XLS 1293 kb)

Additional file 10. of Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis;Valeriya Malysheva;2016;Figshare


Abstract: Reproducibility of the guide VEGFA GGGTGGGGGGAGTTTGCTCCTGG across three different assays. Shown are the numbers and locations of the mismatches, the off-target score, the modification frequencies found by the different studies, and whether the off-target was predicted by the CRISPR Design website ( http://crispr.mit.edu/ ). (XLS 45 kb)

Additional file 5: Table S3. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR;Maximilian Haeussler;2016;Figshare


Abstract: Collection of all off-targets and their frequencies from all off-target studies. The fields of the table are: name of the guide (guide), its sequence (guideSeq), the sequence of the off-target (otSeq), the specificity score of the guide determined with up to four mismatches (guideSpecScore4MM), the GC content of the guide (guideGcCont), the fraction of reads or lentiviral integration sites for this off-target (readFraction), the number of mismatches of the off-target to the guide (mismatches), the Hsu et al. off-target score (outscore), a string indicating with stars where the mismatches are located over the length of the guide sequence (otLogo), the minimal number of mismatches if a deletion is allowed in the guide sequence (bulgeRnaMmCount), the guide sequence with this deletion marked in parentheses (bulgeRnaGuideSeq), the minimal number of mismatches if a deletion is allowed in the off-target sequence (bulgeDnaMmCount), and the off-target sequence with the deletion marked (bulgeDnaOtSeq). Bulge information is shown only if the number of mismatches obtained by the deletion is at least three less than the number of mismatches without the deletion; otherwise the fields are set to “−1”. (TSV 98 kb)

Additional file 2: of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR;Maximilian Haeussler;2016;Figshare


Abstract: Scatterplots of predicted versus obtained cleavage efficiency for all studies shown in Figs. 4 and 5 and Additional file 13: Figure S5 for all scoring models, including 3′ GC content-related heuristics. One row per dataset, one column per prediction score. The previously published datasets shown are, in order: the training data from the Wang, Doench 2014 (human and mouse) and Chari (293 T and K562) studies, Wang 2015, Doench 2016 (AZD and PLX treatment), Hart 2016 averaged over all time points (Rpe1 and the two Hct116 replicates), the data from studies by Moreno-Mateos, Varshney, Gagnon, Liu, Ren, Housden, Farboud, and Gandhi. For details and references on these datasets, see “Methods” or Additional file 10: Table S5. The last six rows represent datasets from this study: “Concordet” is a cell culture dataset quantified with T7 endonuclease and on gels, the datasets “Schönig” and “Eschstruth” ranked guides 1–3 by efficiency, “Shkumatava” by number of mutated sequencing clones obtained from zebrafish embryos, “Teboul” the percentage of mutant mouse embryos. For details on these datasets, see the “Methods” section and also Additional file 15: Table S7 for the Teboul dataset. (TSV 8773 kb)

Additional file 14: of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR;Maximilian Haeussler;2016;Figshare


Abstract: Collection of guide sequences and their frequencies from all published cleavage efficiency studies, including this one. The fields of the table are: the name of the study, the guide name (guide) and its sequence (seq), its extended sequence context (longSeq), the genome database used (db), the chromosomal position (0-based, half-open), the cleavage frequency (modFreq) reported by the study, and all scores calculated from the extended sequence, e.g., the Wang et al. score, the Chari et al. score, etc. (PNG 4950 kb)

Additional file 12: of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR;Maximilian Haeussler;2016;Figshare


Abstract: Comparison of the off-target prediction sensitivity of the CRISPR Design website ( http://crispr.mit.edu/ ), CRISPOR, and CasOffFinder by the number of mismatches. Only off-targets with the PAM NGG were taken into account as the non-standard PAMs differ among the tools. Shown are the number of mismatches in the first columns, then over three columns the number of off-targets predicted for each tool, then two columns with the number of sites found by CRISPOR and CasOffFinder but not by the MIT site, then two columns with the number of sites found by the MIT site but not the other two tools (always 0). The next column shows an example sequence that was missed by the MIT site. The final column contains the distribution of mismatches for each nucleotide over the length of the guide sequence, for all sequences missed by the MIT site. (XLS 30 kb)

Additional file 8: Table S4. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR;Maximilian Haeussler;2016;Figshare


Abstract: Detailed information about CRISPR/Cas9 off-target studies, including first author, PMID, name of the primary assay, type of genome change detected, cell type, sensitivity, number of guides studied, off-targets found, and whether the off-targets found with the primary assay where subsequently validated by PCR and sequencing. (XLS 36 kb)

Additional file 1: Table S1. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR;Maximilian Haeussler;2016;Figshare


Abstract: Reproducibility of the guide EMX1 GAGTCCGAGCAGAAGAAGAAGGG across three different assays. Shown are the numbers and locations of the mismatches, the off-target score, modification frequencies found by the different studies, and whether the off-target was predicted by the CRISPR Design website ( http://crispr.mit.edu/ ). (XLS 31 kb)

Additional file 4: Table S2. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR;Maximilian Haeussler;2016;Figshare


Abstract: Details of the Teboul mouse dataset of this study. (XLS 70 kb)

Additional file 15: Table S7. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR;Maximilian Haeussler;2016;Figshare


Abstract: Correlations between knock-out efficiency results in different studies and cell types. (XLS 40 kb)

Additional file 11: Table S6. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR;Maximilian Haeussler;2016;Figshare


Abstract: Supplementary tables. Tables S1â  S12. Detailed table legends available within file. (XLSX 4350 kb)

Additional file 2: of IMP: a pipeline forÂ reproducible reference-independent integrated metagenomic and metatranscriptomic analyses;Shaman Narayanasamy;2016;Figshare


Abstract: Map showing the location of the various sites in Western Europe that yielded the samples described in this study. (PPTX 1296 kb)

Additional file 6: Figure S4. of Past climate changes, population dynamics and the origin of Bison in Europe;Diyendo Massilani;2016;Figshare


Abstract: Uncorrected percentage sequence distances, mean with range shown in parentheses. Intraspecific distances are shown in bold along the diagonal, interspecific distances are shown in the lower triangle (NA indicates comparison not possible due to singleton specimen present; number of specimens per species (n) shown in brackets with the number of specimens originating from this study; followed by the number originating from GenBank in parentheses). (XLSX 17 kb)

Additional file 2: Table S3. of DNA barcoding and surveillance sampling strategies for Culicoides biting midges (Diptera: Ceratopogonidae) in southern India;Lara Harrup;2016;Figshare


Abstract: Description of all samples analyzed. Table S2. Population diversity parameters based on the HVR sequences. Table S3. GenBank accession numbers of the sequences used in the Bayesian analysis of the HVR phylogeny of Fig.Â 2. Table S4. Depth of coverage and number of covered positions of the captured mitogenomes. Table S5. GenBank accession numbers of the sequences used in the Bayesian analysis of the mitogenome phylogeny of Fig.Â 3. Table S6. PCR primers used for amplification of the mitochondrial HVR DNA of Bison sp. Table S7. Primer sequences for amplification of the mitochondrial genome of Bos taurus to synthesize capture baits. (XLSX 177 kb)

Additional file 1: Table S1. of Past climate changes, population dynamics and the origin of Bison in Europe;Diyendo Massilani;2016;Figshare


Abstract: Distribution of the SNP density along the mitogenome for sequences analyzed in this study. Each bison mitogenome was aligned pairwise to the same outgroup, the bovine mitogenome reference sequence. The quantity of SNPs in 50 bp-long sliding windows (step of 5 bp) is plotted in ordinate alongside the length of the mitogenome in abscissa. Protein and RNA coding genes, and the HVR are schematized below in green, purple and pink, respectively. (PPTX 271 kb)

Additional file 4: Figure S3. of Past climate changes, population dynamics and the origin of Bison in Europe;Diyendo Massilani;2016;Figshare


Abstract: Genes differentially expressed in response to N at (v + 28) and (v + 35) in 2013. p value ≤ 0.05 and │LFC│ ≥ 0.6. C, control; ns, not significant. (XLSX 49 kb)

Additional file 1: of Vine nitrogen status and volatile thiols and their precursors from plot to transcriptome level;Pierre Helwi;2016;Figshare


Abstract: Genes differentially expressed in response to N at (v + 28) and (v + 35) in 2013 and 2014. p value ≤ 0.05 and │LFC│ ≥ 0.6. C, control; ns, not significant. (XLSX 10 kb)

Additional file 3: of Vine nitrogen status and volatile thiols and their precursors from plot to transcriptome level;Pierre Helwi;2016;Figshare


Abstract: Alignment of Cdk1-type kinases. A. Multiple alignment (MUSCLE) of Cdk1 (H. sapiens), Cdk2 (H. sapiens), Cdk3 (H. sapiens), CDC28p (S. cerevisiae), Cdc2+ (S. pombe) and CDKA;1 (A. thaliana). The amino acid modified in the gatekeeper mutant (F80 in CDKA;1) is marked by a star. B. Overlay of the computed 3D model of Arabidopsis CDKA;1 (turquoise ribbon) and the experimentally achieved X-ray structure of human Cdk2 (gray cartoon; PDB ID: 1B38) underscores the high conservation at the structural level of both kinases. The lack of gray ribbon on the lower left hand is due to a not resolved part of the structure in the template file. Given that HsCdk2 is a very good model for Arabidopsis CDKA;1, it can be used to further monitor the changes after mutation in its plant homologue as shown in Fig.Â 1b. Homology model built using SWISS-MODEL and graphics output generated using PyMOL ( www.pymol.org ). (JPG 2215 kb)

Additional file 1: Figure S1. of Modulation of plant growth in vivo and identification of kinase substrates using an analog-sensitive variant of CYCLIN-DEPENDENT KINASE A;1;Hirofumi Harashima;2016;Figshare


Abstract: Primer sequences used in this study. (XLSX 28 kb)

Additional file 2: Table S1. of Modulation of plant growth in vivo and identification of kinase substrates using an analog-sensitive variant of CYCLIN-DEPENDENT KINASE A;1;Hirofumi Harashima;2016;Figshare


Abstract: Showing partial correlations between the normalized behavioural scores and the normalized volumes of the clusters: normalized scores were obtained taking into account nuisance covariates (i.e. age of the subjects, EL, total GM volume, site of acquisition) for the mean FCSRT (Fig. S1.a-c for TR and S1.d. for DTR) or DMS-48 scores (Fig. S1.e.) and the mean GM volume of the clusters found using FWE correction in the whole group of patients (group ABC). (TIF 278 kb)

Additional file 1: Figure S1. of Exploring anterograde memory: a volumetric MRI study in patients with mild cognitive impairment;N. Philippi;2016;Figshare


Abstract: Showing group analyses: local GM loss in group A1 S2.a and group B1 S2.b as compared with group C1 and in group A2 S2.c and group B2 S2.d as compared with group C2 including age, gender, EL, total GM volume and centre as nuisance covariates, with a threshold of P = 0.001 S2.a, S2.b, S2.d or P = 0.005 S2.c, uncorrected. (TIF 709 kb)

Additional file 2: Figure S2. of Exploring anterograde memory: a volumetric MRI study in patients with mild cognitive impairment;N. Philippi;2016;Figshare


Abstract: Poorly covered amplicons (mean coverage

Additional file 2: of Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing;Nadège Calmels;2016;Figshare


Abstract: Clinical picture and molecular results of patients #17 (mutated in ERCC3(XPB)). A: clinical picture of patient #17. B: Patient #17 reads alignment (thanks to Alamut Visual) showing that both mutations c.296 T > C and c.325C > T were never observed on the same read. Forward reads are in green and reverse reads are in blue. (PPTX 477 kb)

Additional file 7: of Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing;Nadège Calmels;2016;Figshare


Abstract: Clinical pictures of patients #8 (A) and #9 (B) (mutated in ERCC8(CSA)). (PPTX 403 kb)

Additional file 5: of Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing;Nadège Calmels;2016;Figshare


Apollo-University Of Cambridge Repository

Research data supporting Tissue folding at the organ-meristem boundary results in nuclear compression and chromatin compaction;Kateryna Fal;2021;Apollo - University of Cambridge Repository

Original confocal microscopy stacks and segmented stacks used in the paper. See the Readme.md file for a detailed description of the dataset contents.


Abstract: Alignment of the HVR sequences obtained in the present study. Alignment of the sequences originating from the samples listed in Table S1 using the primers listed in Additional file 1: Table S6. (PPTX 131 kb)

Additional file 2: Figure S1. of Past climate changes, population dynamics and the origin of Bison in Europe;Diyendo Massilani;2016;Figshare


Abstract: Schematic representation of the two hypotheses describing the mtDNA segregation pattern between B. p taurus, B. bonasus, and B. priscus/bison. Species tree and embedded mtDNA tree are shown with the age estimate of the two nodes and the 95 % HPD bar are represented to scale using the values estimated with the Bayesian analyses of the complete mitogenomes presented in Fig.Â 3. Hypothesis 2 of the post-speciation gene flow requires a rapid speciation event taking place just during the short time-interval between the two nodes. This hypothesis appears less parsimonious because speciation is clearly gradual since it has not yet completely prevented interfertility between Bos and Bison even 800 kyr after the hypothesized rapid speciation event. (PPTX 45 kb)

Additional file 3: Figure S2. of Past climate changes, population dynamics and the origin of Bison in Europe;Diyendo Massilani;2016;Figshare


Abstract: Genes differentially expressed in response to N at (v + 28) and (v + 35) in 2014. p value ≤ 0.05 and │LFC│ ≥ 0.6. C, control; ns, not significant. (XLSX 12 kb)

Additional file 2: of Vine nitrogen status and volatile thiols and their precursors from plot to transcriptome level;Pierre Helwi;2016;Figshare


Research data supporting "Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping";MN Bongiovanni;2016;Apollo - University of Cambridge Repository

Supplementary video for data analysis.


Abstract: False negative results in microCT scan imaging in two mice. A, B, C. Aspects corresponding to the first animal. A, B. Axial and frontal view of microCT scan imaging of an isodense, poorly delineated right liver lobe tumor. Prospective and retrospective interpretation of images could only identify an enlargement of the right liver lobe. The border between normal and pathological tissue could not be identified on the microCT scan rendering. C. Gross appearance of the poorly delineated right liver lobe tumor, depicted in A and B. D, E, F. Aspects corresponding to the second animal. D. Retrospective interpretation of microCT scan rendering with identification of a centroabdominal in-homogeneous, isodense tumor (arrowheads). E. Gross appearance of the centroabdominal tumor which was not identified at the prospective interpretation of the microCT scan images. F. Histological assessment of the presence of a hepatocellular carcinoma (HE, x240). (JPG 3580 kb)

Additional file 3: of Development of a methodology for in vivo follow-up of hepatocellular carcinoma in hepatocyte specific Trim24-null mice treated with myo-inositol trispyrophosphate;Mihaela Ignat;2016;Figshare


Abstract: Plant architecture of atring1a;atring1b;stm-7 mutant. (A) Adult plant of stm-7 mutant. (B) Adult plant of atring1a;atring1b;stm-7 mutant. Bars = 2 cm. (C) Schematic structure of the stm-7 mutant allele GK-100 F11 containing a transfer DNA (T-DNA) insertion in the second intron of STM. Gray box represents UTR, black box represents exon, and line represents intron. (JPG 623 kb)

Additional file 2: Figure S2. of Arabidopsis PRC1 core component AtRING1 regulates stem cell-determining carpel development mainly through repression of class I KNOX genes;Donghong Chen;2016;Figshare


Abstract: Original data and statistical analysis for qRT-PCR analyses. (XLSX 12 kb)

Additional file 8: Table S2. of Arabidopsis PRC1 core component AtRING1 regulates stem cell-determining carpel development mainly through repression of class I KNOX genes;Donghong Chen;2016;Figshare


Abstract: Expression pattern of AtRING1a in the reproductive stage examined by in situ hybridization using a specific AtRING1a probe. (A) Leaf primordia. (B) and (C) SAM. (D) FM. (E) Young flower. (F) Developing ovule. (G) Developing ES. (H) Developing seed in globular stage. (I) Heart stage. (J) Mature green stage. Bars = 50 μm in (A)–(J). (JPG 951 kb)

Additional file 1: Figure S1. of Arabidopsis PRC1 core component AtRING1 regulates stem cell-determining carpel development mainly through repression of class I KNOX genes;Donghong Chen;2016;Figshare


Abstract: Phenotype analysis of atring1a;atring1b;as1-1 mutant. (A) Adult plant architecture of as1-1 mutant. (B) Adult plant architecture of atring1a;atring1b;as1-1 mutant. Barsâ  =â  2Â cm. (JPG 665 kb)

Additional file 4: Figure S4. of Arabidopsis PRC1 core component AtRING1 regulates stem cell-determining carpel development mainly through repression of class I KNOX genes;Donghong Chen;2016;Figshare


Abstract: Phenotype analysis of atring1a;atring1b;wus-8 triple mutant. (A) Adult plant of wus-8 mutant. (B) Adult plant of atring1a;atring1b;wus-8 triple mutant. (C) Close-up view of (B), showing the main florescence of atring1a;atring1b;wus-8 triple mutant. Bars = 2 cm in (A) and (B) and 500 μm in (C). (D) The wus-8 allele (SAIL_150_G06) harboring a T-DNA insertion in the second intron of WUS. Gray box represents UTR, black box represents exon, and line represents intron. (JPG 599 kb)

Additional file 5: Figure S5. of Arabidopsis PRC1 core component AtRING1 regulates stem cell-determining carpel development mainly through repression of class I KNOX genes;Donghong Chen;2016;Figshare


Abstract: Phenotype analysis of atring1a;atring1b;bp-1 plant. (A) Adult bp-1 plant (Ler). (B) Adult bp-1 control. (C) Adult atring1a;atring1b;bp-1 plant. The control bp-1 -/- mutant (B) and atring1a;atring1b;bp-1 triple mutant (C) are derived from the same F2 generation of atring1a -/+ ;atring1b -/+ ;bp-1 -/- . Insets indicate the close-up view of downward branch related to corresponding mutant. Bars = 2 cm in (A)–(C) and 1 mm in the corresponding insets. (JPG 711 kb)

Additional file 3: Figure S3. of Arabidopsis PRC1 core component AtRING1 regulates stem cell-determining carpel development mainly through repression of class I KNOX genes;Donghong Chen;2016;Figshare


Abstract: Phenotype analysis of atring1a;atring1b;clv3-2 triple mutant. (A) Whole plant architecture of clv3-2 mutant. (B) Whole plant architecture of atring1a;atring1b;clv3-2 triple mutant. The control clv3-2 -/- mutant and atring1a;atring1b;clv3-2 triple mutant are derived from the same F2 generation of atring1a -/+ ;atring1b -/+ ;clv3-2 -/- . Barsâ  =â  2Â cm. (JPG 521 kb)

Additional file 6: Figure S6. of Arabidopsis PRC1 core component AtRING1 regulates stem cell-determining carpel development mainly through repression of class I KNOX genes;Donghong Chen;2016;Figshare


Abstract: AF TableÂ 3: detailed medical history. Detailed medical history of each patient focussed on medical conditions at risk of cramps. (CSV 9Â kb)

Additional file 4: of Prevalence of cramps in patients over the age of 60 in primary care : a cross sectional study;Hubert Maisonneuve;2016;Figshare


Abstract: Novel POLH splice mutation in non-related XP-variant patients. A: Pedigrees of the 4 XP-variant families coming from Northern Spain and mutated in the POLH gene. The arrows indicate the four patients studied by NGS. Patients #11, 12 and 13 were homozygous for the splice mutation c.764 + 1G > A whereas patient #10 was compound heterozygous for mutations c.764 + 1G > A and c.1445C > A (p.Ser482*). B: RT-PCR using RNA from patients #10 and 11, with forward primer in exon 5 and reverse primer in exon 8, showed a single 365 bp band in normal cells and two bands at323 bp and 261 bp in the homozygous patient #11. The diagram indicates partial deletion (42 bp) of exon 6 in the type I splice variant and deletion of the entire 104 bp of exon 6 in the type-II splice variant. The normal transcript was the major transcript in the heterozygous patient #10, with a fain band corresponding to the type I splice variant. (PPTX 92 kb)

Additional file 3: of Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing;Nadège Calmels;2016;Figshare


Abstract: Spectrum of previously identified variations within the validation cohort of 11 patients. 11 patients already tested by Sanger sequencing of ERCC6(CSB) and/or ERCC8(CSA) genes were explored by targeted NGS strategy. All 63 previously identified single base variations were identified in their correct heterozygous/homozygous state. A heterozygous 4.6 Mb deletion of chromosome 10q11, encompassing the whole ERCC6(CSB) gene, was clearly detected but the method was not sensitive enough to detect an ERCC6(CSB) deletion limited to the first two exons of the gene. (XLSX 14 kb)

Additional file 1: of Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing;Nadège Calmels;2016;Figshare


Abstract: Clinical pictures and brain MRI of patients #16 (mutated in ERCC5(XPG)). Sagittal T1 and axial T2-Flair (PPTX 970 kb)

Additional file 6: of Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing;Nadège Calmels;2016;Figshare


Abstract: POLH founder mutation in Northern Spain. Haplotype analysis was performed on the 6 XP-variant patients coming from Northern Spain with mutations in the POLH gene (chr6:43,543,878-43,588,260[hg19]). Despite a genome wide study using the Illumina HumanOmniExpress-24 SNP chip, the table focuses on the SNP localized in the vicinity of the POLH gene on chromosome 6 (between 42,000,000 and 44,000,000). Patient #11, patient #12 and her sister and patient #13 and his sister were homozygous for the c.764 + 1G > A mutation. Patient #10 was compound heterozygous c.[764 + 1G > A(;)1445C > A]. Parents of patient #13 were heterozygous carriers of the splice mutation. The five homozygous patients share a region of homozygosity (975 kb) including the POLH gene (from rs3800291 at position 42,751,457 to rs866236 at position 43,726,956). The compound heterozygous patient #10 and the carrier parents have at least one allele in common with the founder haplotype all along the 975 kb region. (XLSX 46 kb)

Additional file 4: of Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing;Nadège Calmels;2016;Figshare


Abstract: AF TableÂ 1: detailed prevalence of cramps in the study population. Detailed presence of cramps, cramps related with sleep disturbance, cramps more frequent than 3 times a month, gender and age-group among the study population. (CSV 8Â kb)

Additional file 2: of Prevalence of cramps in patients over the age of 60 in primary care : a cross sectional study;Hubert Maisonneuve;2016;Figshare


Abstract: AF TableÂ 4: detailed treatment. Detailed treatment of each patient, reporting also phytotherapy and homeopathy, without targeting medication at risk of cramps. (CSV 27Â kb)

Additional file 5: of Prevalence of cramps in patients over the age of 60 in primary care : a cross sectional study;Hubert Maisonneuve;2016;Figshare


Abstract: AF TableÂ 2: detailed occurrence of cramps. Detailed occurrence for each cramps sufferer of the study population. (CSV 5Â kb)

Additional file 3: of Prevalence of cramps in patients over the age of 60 in primary care : a cross sectional study;Hubert Maisonneuve;2016;Figshare


Abstract: AF Table 5: duration of cramps detailed for each cramps sufferer of the study population. Date of onset of cramps specified for each patient reporting cramps. (CSV 5Â kb)

Additional file 6: of Prevalence of cramps in patients over the age of 60 in primary care : a cross sectional study;Hubert Maisonneuve;2016;Figshare


Abstract: Studying wildlife space use in human-modified environments contributes to characterize wildlife-human interactions to assess potential risks of zoonotic-pathogens transmission, and to pinpoint conservation issues. In central African rainforests with human dwelling and activities, we conducted a telemetry study on a group of males of Hypsignathus monstrosus, a lek-mating fruit bat identified as a potential maintenance host for Ebola virus. During a lekking season in 2020, we investigated the foraging-habitat selection and the individual nighttime space use during both mating and foraging activities close to villages and their surrounding agricultural landscape. At night, marked individuals strongly selected agricultural lands and more generally areas near watercourses to forage, where they spent more time compared to forest ones. Furthermore, the probability and duration of the presence of bats in the lek during nighttime decreased with the distance to their roost site but remained relatively high within a 10 km radius. Individuals adjusted foraging behaviors according to mating activity by reducing both the overall time spent in foraging areas and the number of forest areas used to forage when they spent more time in the lek. Finally, the probability of a bat revisiting a foraging area in the following 48 hours increased with the previous time spent in that foraging area. These behaviors occurring close to or in human-modified habitats can trigger direct and indirect bat-human contacts, which could thus facilitate pathogen transmission such as Ebola virus.

Data from: Foraging and mating behaviors of Hypsignathus monstrosus at the bat-human interface in central African rainforest;Elodie Schloesing;2024;Movebank Data Repository


Abstract: The Middle Allochthon of the Galicia-Trás-os-Montes Zone (GTMZ) in NW Iberia is an assemblage of oceanic units representing the Variscan suture of one or more peri-Gondwanan oceans. This contribution brings new geochronological and geochemical data from the Middle Allochthon of the Morais Complex, in northern Portugal. There, the oceanic ensemble consists of a stack of five tectonic units which from bottom to top are the Junqueira, Pombais and Izeda oceanic supracrustals and the Remondes and Morais-Talhinhas ophiolitic units. The Junqueira and Pombais units consist of greenschists and metapelites. No age data are available for these two units, but a correlation is established with a Cambro-Ordovician unit in the Órdenes Complex of Galicia (NW Spain) dated at 500 Ma. The Izeda Unit consists of fine-grained, low-grade amphibolites transitional to epidote-amphibolites and greenschists, for which an age of 484 ± 3 Ma has been obtained for a metabasic tuff. In the ophiolitic ensemble, the Remondes and Morais-Talhinhas units consist of fine-grained amphibolites associated with deformed metagabbros, mafic cumulates and serpentinized ultramafics. In this study, two plagiogranite samples from the Remondes Unit yielded a complex spread of age data with Silurian ages representing the dominant population. This suggests that the newly defined Remondes Unit is younger than the Izeda Unit but older than the previously published age for these rocks, which are considered part of the overlying Morais-Talhinhas Unit, dated as Devonian (406–395 Ma) in a previous study. The geochemistry of the basic rocks in the five units is that of NMORB with a subduction-derived component that varies from weak to null. The ages, together with new and previously published whole rock geochemical data obtained from basic igneous samples, are interpreted to date and reflect the formation of igneous protoliths in oceanic ridge settings associated with the Mid-Variscan Ocean, a part of the Rheic oceanic realm that registered magmatic activity between the late Cambrian and the Lower Devonian.

Environmental Sciences not elsewhere classified

Chemical Sciences not elsewhere classified

Mathematical Sciences not elsewhere classified

The mid-Variscan suture in the Morais complex of Trás-os-Montes (Portugal): insights from geochemistry and geochronology of oceanic rocks;Jérémie Malecki;2024;Taylor & Francis


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.

Related Article: Luca Münzfeld, Milena Dahlen, Adrian Hauser, Nolwenn Mahieu, Senthil Kumar Kuppusamy, Jules Moutet, Maxime Tricoire, Ralf Köppe, Léo La Droitte, Olivier Cador, Boris Le Guennic, Grégory Nocton, Eufemio Moreno‐Pineda, Mario Ruben, Peter W. Roesky|2023|Angew.Chem.,Int.Ed.|62|e202218107|doi:10.1002/anie.202218107

CCDC 2125022: Experimental Crystal Structure Determination;Münzfeld, Luca;2023;Cambridge Crystallographic Data Centre


CCDC 2125023: Experimental Crystal Structure Determination;Münzfeld, Luca;2023;Cambridge Crystallographic Data Centre


Abstract: We describe the new version (v2.73y) of the code hfodd which solves the nuclear Skyrme Hartree-Fock or Skyrme Hartree-Fock-Bogolyubov problem by using the Cartesian deformed harmonic-oscillator basis. In the new version, we have implemented the following new features: (i) full proton-neutron mixing in the particle-hole channel for Skyrme functionals, (ii) the Gogny force in both particle-hole and particle-particle channels, (iii) linear multi-constraint method at finite temperature, (iv) fission toolkit including the constraint on the number of particles in the neck between two fragments, calculation of the interaction energy between fragments, and calculation of the nuclear and Coulomb energy of each fragment, (v) the new version 200d of the code HFBTHO, together with an enhanced interface between HFBTHO and HFODD, (vi) parallel capabilities, significantly extended by adding several restart options for large-scale jobs, (vii) the Lipkin translational energy correction method with pairing, (viii) higher-order Lipkin particle-number corrections, (ix) interface to a program plotting single-particle energies or Routhians, (x) strong-force isospin-symmetry-breaking terms, and (xi) the Augmented Lagrangian Method for calculations with 3D constraints on angular momentum and isospin. Finally, an important bug related to the calculation of the entropy at finite temperature and several other little significant errors of the previous published version were corrected.

Solution of the Skyrme-Hartree-Fock-Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis. (VIII) HFODD (v2.73y): A new version of the program.;N. Schunck;2017;Mendeley


Spectra of stellar stream with MEGARA

Spectra of stellar stream with MEGARA;D. Martinez-Delgado;2024;Centre de Donnees Strasbourg (CDS)

VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' Once in a blue stream. Detection of recent star formation in the NGC 7241 stellar stream with MEGARA.' (bibcode: 2024A&A...684A.157M)


Tomography of Betelgeuse

Tomography of Betelgeuse;D. Jadlovsky;2024;Centre de Donnees Strasbourg (CDS)

VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' The Great Dimming of Betelgeuse: The photosphere as revealed by tomography during the past 15 years.' (bibcode: 2024A&A...685A.124J)


3 main-sequence galaxy systems datacubes;T. Devereaux;2024;Centre de Donnees Strasbourg (CDS)

VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' The ALMA-ALPINE CII survey: The sub-kpc morphology of three main sequence galaxy systems at z~4.5 revealed by ALMA.' (bibcode: 2024A&A...686A.156D)


STONKS Multi-Mission X-ray Catalog

STONKS Multi-Mission X-ray Catalog;E. Quintin;2024;Centre de Donnees Strasbourg (CDS)

VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' STONKS: Quasi-real time XMM-Newton transient detection system.' (bibcode: 2024A&A...687A.250Q)


CARLA cluster sample study

CARLA cluster sample study;S. Mei;2023;Centre de Donnees Strasbourg (CDS)

VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' Morphology-density relation, quenching, and mergers in CARLA clusters and proto-Clusters at 1.4 < z < 2.8.' (bibcode: 2023A&A...670A..58M)


CCDC 2281377: Experimental Crystal Structure Determination;Guo, Jia-Dong;2024;Cambridge Crystallographic Data Centre

Related Article: Jia-Dong Guo, Feven-Alemu Korsaye, Dorian Schutz, Ilaria Ciofini, Laurence Miesch|2024|Chemical Science|15|17962|doi:10.1039/D4SC05190D


CCDC 2281378: Experimental Crystal Structure Determination;Guo, Jia-Dong;2024;Cambridge Crystallographic Data Centre


CCDC 2310786: Experimental Crystal Structure Determination;Guo, Jia-Dong;2024;Cambridge Crystallographic Data Centre


CCDC 2296149: Experimental Crystal Structure Determination;Steinmetz, Maxime;2024;Cambridge Crystallographic Data Centre

Related Article: Maxime Steinmetz, Christophe Gourlaouen, David Sémeril|2024|Organics|5|1|doi:10.3390/org5010001


CCDC 2296150: Experimental Crystal Structure Determination;Steinmetz, Maxime;2024;Cambridge Crystallographic Data Centre


COSMOS2020-MIPS-PACS-SPIRE-SCUBA catalog;L. Wang;2024;Centre de Donnees Strasbourg (CDS)

VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' Probabilistic and progressive deblended far-infrared and sub-millimetre point source catalogues. I. Methodology and first application in the COSMOS field.' (bibcode: 2024A&A...688A..20W)


CCDC 2343757: Experimental Crystal Structure Determination;Krešáková, Lenka;2024;Cambridge Crystallographic Data Centre

Related Article: Lenka Krešáková, Miroslava Litecká, Itziar Oyarzabal, Ján Titiš, Michaela Červeňáková, Elizabeth A. Hillard, Jerome Robert, Juraj Černák|2024|New J.Chem.|48|17750|doi:10.1039/D4NJ03545C


CCDC 2343756: Experimental Crystal Structure Determination;Krešáková, Lenka;2024;Cambridge Crystallographic Data Centre


Abstract: Stargardts Disease (SD) is the most common human inherited macular degeneration, leading to irreversible loss of central vision in children and young adults. Despite identification of the causal gene, Abca4, over 25 years ago, animal models of SD have been only partially successful. Although knockout mouse models show some features, such as lipofuscin accumulation, most lines show little to no cell loss or functional decline characteristic of the human disease. We reasoned that use of a diurnal cone-rich rodent whose retina resembles those of humans more closely would be a better model. Using virally mediated transfer of CRISPR-CAS9 sequences to inhibit Abca4 expression, which show that indeed such animals exhibit the complete disease phenotype, with rapid widespread photoreceptor, especially cone, loss accompanied by significant declines in visual sensitivity and lipid accumulation. Such models represent a significant step forward in this field of research and will facilitate better understanding of disease mechanisms and development of therapeutic strategies.

raw data for Psammomys model of Stargardts Disease;David Hicks;2024;figshare


CCDC 2296142: Experimental Crystal Structure Determination;Steinmetz, Maxime;2024;Cambridge Crystallographic Data Centre


CCDC 2296144: Experimental Crystal Structure Determination;Steinmetz, Maxime;2024;Cambridge Crystallographic Data Centre


CCDC 2368117: Experimental Crystal Structure Determination;Marie, Nicolas;2024;Cambridge Crystallographic Data Centre

Related Article: Nicolas Marie, Kim Uyen Ly, Norio Shibata, Vincent Bizet, Dominique Cahard|2024|Org.Lett.|26|9168|doi:10.1021/acs.orglett.4c03760


Abstract: Survival data set of European rabbit during an outbreak of RHDV2 and related modeling files in E-SURGE program

Data set - Impact of RHDV2 outbreak on wild rabbit;Jérôme LETTY;2024;figshare


Supplementary Material

Abstract: Supplementary Material

Supplementary Material;Liam Bond;2024;AIP Publishing


CCDC 2296536: Experimental Crystal Structure Determination;Appleton, Jordan L.;2024;Cambridge Crystallographic Data Centre

bis[2,9-bis(4-t-butylphenyl)-4,7-diphenyl-1,10-phenanthroline]-copper hexafluorophosphate diethyl ether solvate

Related Article: Jordan L. Appleton, Lavinia Ballerini, Sylvie Choua, Christophe Gourlaouen, Romain Ruppert, Matteo Mauro|2024|Eur.J.Inorg.Chem.|27|e202400278|doi:10.1002/ejic.202400278


CCDC 2296537: Experimental Crystal Structure Determination;Appleton, Jordan L.;2024;Cambridge Crystallographic Data Centre

bis[2,9-bis(4-t-butylphenyl)-1,10-phenanthroline]-copper hexafluorophosphate dichloromethane solvate


CCDC 2296538: Experimental Crystal Structure Determination;Appleton, Jordan L.;2024;Cambridge Crystallographic Data Centre


CCDC 2296539: Experimental Crystal Structure Determination;Appleton, Jordan L.;2024;Cambridge Crystallographic Data Centre


CCDC 2328279: Experimental Crystal Structure Determination;Papangelis, Evangelos;2024;Cambridge Crystallographic Data Centre

(1,1'-(pyridine-2,6-diyl)bis[3-mesityl-1,3-diazinan-2-ylidene])-bromo-nickel(ii) bromide toluene unknown solvate

Related Article: Evangelos Papangelis, Katrin Pelzer, Christophe Gourlaouen, Dominique Armspach, Pierre Braunstein, Andreas A. Danopoulos, Corinne Bailly, Nikolaos Tsoureas, Dimitrios Triantafyllos Gerokonstantis|2024|Chem.Asian J.|19|e202400169|doi:10.1002/asia.202400169


CCDC 2328280: Experimental Crystal Structure Determination;Papangelis, Evangelos;2024;Cambridge Crystallographic Data Centre


Abstract: AbstractUrban stormwater contains various micropollutants, such as biocides, which are washed off from facades during wind-driven rain events. Biocides can reach the groundwater via stormwater infiltration systems (SIS), although the soil layer acts as a reactive barrier preventing the leaching of biocides but producing transformation products (TPs). Little is known about the occurrence and concentration of biocides in SIS soils, their distribution and temporal behavior. Here, we present a first systematic screening of three commonly used biocides (diuron, octylisothiazolinone (OIT), terbutryn) and four TPs of terbutryn in 46 French and German SIS. Overall, biocide occurrence in SIS topsoils was ubiquitous but low, while point source inputs to specific SIS were high but rare. Low concentrations (< 2ng g-1) of terbutryn were detected in 78% of the SIS. Maximum concentrations occurred in recently constructed SIS, suggesting that this is due to higher biocide loads entering the SIS. The frequent detection of terbutryn supports the idea that it is a non-point source marker, as it is relatively stable in soil (t1/2 > 90 days) and widely used in renders and paints. In contrast, high concentrations of diuron (168 ng g-1) and OIT (58 ng g-1) were observed in only one sample, suggesting an urban point source contamination, possibly from a freshly repainted facade. The distinction between source types provides a basis for targeted measures to prevent biocide entry to groundwater. Altogether, this study opens the door to a more systematic consideration of micropollutant dissipation and ecotoxicological effects in SIS design and monitoring.

Biocides in soils of urban stormwater infiltration systems : indications of inputs from point and non-point sources;Felicia Linke;2023;Universität Stuttgart

Open Access funding enabled and organized by Projekt DEAL. Albert-Ludwigs-Universität Freiburg im Breisgau


VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' A3COSMOS & A3GOODSS: Continuum source catalogues and multi-band number counts.' (bibcode: 2024A&A...685A...1A)

A3COSMOS and A3GOODSS Data Version 20220606;S. Adscheid;2024;Centre de Donnees Strasbourg (CDS)


Euclid preparation. XXXVIII

VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' Euclid preparation. XXXVIII. Spectroscopy of active galactic nuclei with NISP.' (bibcode: 2024A&A...685A.108E)

Euclid preparation. XXXVIII;Euclid Collaboration;2024;Centre de Donnees Strasbourg (CDS)


Sgr dSph members RV and [Fe/H]

VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' The metallicity distribution in the core of the Sagittarus dwarf spheroidal: Minimising the metallicity biases.' (bibcode: 2023A&A...669A..54M)

Sgr dSph members RV and [Fe/H];A. Minelli;2023;Centre de Donnees Strasbourg (CDS)


Galaxies outside clusters

VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' Origin of the differences in rotational support among early-type galaxies: The case of galaxies outside clusters.' (bibcode: 2023A&A...672A..27B)

Galaxies outside clusters;M. Bilek;2023;Centre de Donnees Strasbourg (CDS)


VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' Gaia Data Release 3: Specific processing and validation of all sky RR Lyrae and Cepheid stars: The Cepheid sample.' (bibcode: 2023A&A...674A..17R)

Gaia Data Release 3. The Cepheids sample;V. Ripepi;2023;Centre de Donnees Strasbourg (CDS)


Gaia DR3. The RR Lyrae sample

VizieR online Data Catalogue associated with article published in journal Astronomy and Astrophysics with title ' Gaia Data Release 3: Specific processing and validation of all-sky RR Lyrae and Cepheid stars: The RR Lyrae sample.' (bibcode: 2023A&A...674A..18C)

Gaia DR3. The RR Lyrae sample;G. Clementini;2023;Centre de Donnees Strasbourg (CDS)


VizieR online Data Catalogue associated with article published in journal Astrophysical Journal with title ' A panoramic landscape of the Sagittarius Stream in Gaia DR2 revealed with the STREAMFINDER spyglass.' (bibcode: 2020ApJ...891L..19I)

Gaia DR2 stars in the Sgr stream with STREAMFINDER;R. Ibata;2024;Centre de Donnees Strasbourg (CDS)


Stars of the LMS-1 stream with sp. obs.

VizieR online Data Catalogue associated with article published in journal Astrophysical Journal with title ' Evidence of a dwarf galaxy stream populating the inner Milky Way halo.' (bibcode: 2021ApJ...920...51M)

Stars of the LMS-1 stream with sp. obs.;K. Malhan;2024;Centre de Donnees Strasbourg (CDS)


VizieR online Data Catalogue associated with article published in journal Astrophysical Journal with title ' The CO emission in the Taffy galaxies (UGC 12914/15) at 60pc resolution. I. The battle for star formation in the turbulent Taffy bridge.' (bibcode: 2022ApJ...931..121A)

CO emission in the Taffy galaxies. I. ALMA obs.;P.N. Appleton;2024;Centre de Donnees Strasbourg (CDS)


Pristine Inner Galaxy Survey PIGS VIII

VizieR online Data Catalogue associated with article published in journal Monthly Notices of the Royal Astronomical Society with title ' The Pristine Inner Galaxy Survey (PIGS). VIII: Characterising the orbital properties of the ancient, very metal-poor inner Milky Way.' (bibcode: 2024MNRAS.530.3391A)

Pristine Inner Galaxy Survey PIGS VIII;A. Ardern-Arentsen;2024;Centre de Donnees Strasbourg (CDS)


CCDC 2367268: Experimental Crystal Structure Determination;Printz, Gaël;2024;Cambridge Crystallographic Data Centre

Related Article: Gaël Printz, Redoy Gazi Shuvo, Antoine Schweizer, Dmytro Ryzhakov, Christophe Gourlaouen, Lielou Lantigner, Béatrice Jacques, Samir Messaoudi, Franck Le Bideau, Samuel Dagorne|2024|Polym.Chem.|15|3901|doi:10.1039/D4PY00778F


DWR-hyperelastic-soft-tissue

Abstract: Enhancing Biomechanical Simulations Based on A Posteriori Error Estimates: The Potential of Dual Weighted Residual-Driven Adaptive Mesh Refinement


CCDC 1823831: Experimental Crystal Structure Determination;Jewula, Pawel;2023;Cambridge Crystallographic Data Centre

Related Article: Pawel Jewula, Mickaël Grandmougin, Mélanie Choppin, Anna Maria Chiara Tivelli, Agnese Amati, Yoann Rousselin, Lydia Karmazin, Jean-Claude Chambron, Michel Meyer|2023|Eur.J.Inorg.Chem.|26|e202300038|doi:10.1002/ejic.202300038


CCDC 1823832: Experimental Crystal Structure Determination;Jewula, Pawel;2023;Cambridge Crystallographic Data Centre


CCDC 2056438: Experimental Crystal Structure Determination;Jewula, Pawel;2023;Cambridge Crystallographic Data Centre


Supplementary Material

Abstract: Supplementary Material

Supplementary Material;Wilfred Franse;2024;AIP Publishing


CCDC 2372720: Experimental Crystal Structure Determination;Xu, Xuejuan;2024;Cambridge Crystallographic Data Centre

Related Article: Xuejuan Xu, Jordan Parmentier, Christophe Gourlaouen, Béatrice Jacques, Samuel Dagorne|2024|Dalton Trans.|53|15849|doi:10.1039/D4DT02152E


Abstract:
Experimental STM, STS and STML data studying the fluorescent behaviour of a PTCDA molecule attached to the metallic apex of a scanning tunneling microscope.

Treated source data of all Figures included in the publication.

Experimental data supporting the paper "Fluorescence from a single-molecule probe directly attached to a plasmonic STM tip";Niklas Friedrich;2024;Zenodo


CCDC 2372716: Experimental Crystal Structure Determination;Xu, Xuejuan;2024;Cambridge Crystallographic Data Centre


CCDC 2372717: Experimental Crystal Structure Determination;Xu, Xuejuan;2024;Cambridge Crystallographic Data Centre


CCDC 2372718: Experimental Crystal Structure Determination;Xu, Xuejuan;2024;Cambridge Crystallographic Data Centre


CCDC 2372719: Experimental Crystal Structure Determination;Xu, Xuejuan;2024;Cambridge Crystallographic Data Centre


CCDC 2373743: Experimental Crystal Structure Determination;Xu, Xuejuan;2024;Cambridge Crystallographic Data Centre

(1,3-di(adamantan-1-yl)imidazol-2-ylidene)-ethyl-zinc tetrakis(pentafluorophenyl)borate pentane solvate


Abstract: Weaned Southern elephant seal (SES) quickly transition from terrestrial to aquatic life after a 4-week postweaning period. Previous studies have highlighted the importance of the post-weaning period for the physiological challenges of their future sea-life. However, very little is known about how their body condition during this period may influence the development of their behaviour and brain activities. Therefore, we characterised the behaviour changes before ocean departure, for individuals in different body conditions, with a multi-disciplinary approach combining behaviour scoring (overall activity) and brain electrical activity during this period. Newly weaned SES-pups (n=20, Kerguelen Islands) were equipped with Axytreks (TechnoSmArt) combining accelerometer and GPS loggers, during 5 to 26 days. A subgroup of animal (n=4) was equipped with electroencephalogram-logger (Evolocus LLC) to explore the brain activity in relation with accelerometer. As pups age, the amount of time allocated to resting decreases in favour of physical activity. Most resting (9.6± 1.2 h/day) takes place during daytime, with periods of slow-wave sleep representing 4.9± 0.9 h/day during the first 2 weeks. Furthermore, an increasing proportion of physical activity transitions from land to shore. Additionally, pups in poorer condition are more active earlier than those in better condition. Surprisingly, clear circadian activity with two peaks at dawn and dusk is observed just after weaning, remaining unchanged during the 4 weeks on land. This circadian pattern matches the one observed in adults at sea, raising the question of whether it is endogenous or triggered by the mother during lactation.

One month for southern elephant seal pups to acquire aquatic skills before their first ocean trip: Stay longer or leave earlier?;Society for Experimental Biology 2024;2024;Underline Science Inc.


Abstract: Repeated hypoxic events are reported in various brain pathologies. Mammal brain is highly vulnerable to hypoxia, because brain functions require high oxygen and energy demands. Marine mammals, such as pinnipeds, were naturally selected to cope with daily repeated hypoxic events during foraging dives, when human brain can only cope with minor repeated hypoxia. How do pinnipeds cope with repeated severe hypoxic events at the blood-brain interface? We performed a comparative physiological approach using for model the Southern Elephant Seal (SES), which is the most extreme diver of all seals and being exposed to severe peripheral hypoxia. Immunolabelling of various blood-brain interface markers (endothelium, astrocytes, neurons) were performed on brain cortical slices from freshly dead post-weaning pups (n=4) and reproductive adults (n=5) collected at Kerguelen Island. Immunolabelling were visualised using confocal microscope and images were analysed using ImageJ. Cerebral vascularisation exhibits significant differences between pups and adults: 1) in the grey matter, the vascular volume fraction was around 62% higher in adults than in pups; 2) the vessels were significantly more ramified and tortuous in adults (e.g. 6% more tortuous in the white matter); 3) some large blood vessels exhibited abnormalities in adults suggesting blood-brain interface dysfunctions. Interestingly, adult SES vessels share similar phenotypes to pathological cerebral-blood vessels described in human neurodegenerative diseases. Then, abnormal vessel-morphologies raise the question of the potential pathological situation for adult SES. To study blood-flow velocity in brain-vessels and premature aging in SES, biomechanical fluid modelling, additional staining for neurodegenerative landmarks and blood-biomarkers are currently performed.

Does cerebral blood vessel phenotype represent and adaptative response to repeated hypoxia in the southern elephant seal?;Society for Experimental Biology 2024;2024;Underline Science Inc.


Supplementary Material

Abstract: Supplementary Material for 'Topological comparison of flexible and semiflexible chains in polymer melts with θ-chains'

Supplementary Material;Maurice Schmitt;2024;AIP Publishing


Related Article: Andreas A. Danopoulos, Pierre Braunstein, Jörg Saßmannshausen, David Pugh, Joseph A. Wright|2020|Eur.J.Inorg.Chem.|2020|3359|doi:10.1002/ejic.202000429

CCDC 1999526: Experimental Crystal Structure Determination;Danopoulos, Andreas A.;2020;Cambridge Crystallographic Data Centre


CCDC 1999547: Experimental Crystal Structure Determination;Danopoulos, Andreas A.;2020;Cambridge Crystallographic Data Centre


Abstract: This dataset is attached to the research paper "<b>Mind the polar sun: Solar radiations trigger frequent heat stress in breeding king penguins, despite relatively cool air temperatures.</b>", which investigates the heat stress response of cold-adapted king penguins when breeding on land. For this, observations of behavioural thermoregulation of parents while taking care of the egg or chick (panting, wing spreading, exposure of the brood pouch) are confronted to air temperature, solar radiation, wind speed and relative humidity recorded at the colony location. Sub-cutaneous temperatures (from the back of the individuals) are also measured.

HotKing dataset: heat stress in breeding king penguins.;Aude Noiret;2024;figshare


Related Article: Dang Ho Binh, Mustapha Hamdaoui, Diane Fischer-Krauser, Lydia Karmazin, Corinne Bailly, Jean-Pierre Djukic|2018|Chem.-Eur.J.|24|17577|doi:10.1002/chem.201804048

CCDC 1826970: Experimental Crystal Structure Determination;Binh, Dang Ho;2018;Cambridge Crystallographic Data Centre


CCDC 1843843: Experimental Crystal Structure Determination;Binh, Dang Ho;2018;Cambridge Crystallographic Data Centre


Related Article: Maxime Florent, Nathalie Kyritsakas, Jean-Marc Planeix, Aurélie Guenet, Mir Wais Hosseini|2021|Dalton Trans.|50|15924|doi:10.1039/D0DT00822B

CCDC 1980612: Experimental Crystal Structure Determination;Florent, Maxime;2021;Cambridge Crystallographic Data Centre


Related Article: Anna Bonfiglio,  Conor McCartin,  Ulises Carrillo,  Cristina Cebrián,  Philippe C. Gros,  Sylvie Fournel,  Antoine Kichler,  Chantal Daniel,  Matteo Mauro|2021|Eur.J.Inorg.Chem.|2021|1551|doi:10.1002/ejic.202100132

CCDC 1983105: Experimental Crystal Structure Determination;Bonfiglio, Anna;2021;Cambridge Crystallographic Data Centre


Semi-Overcomplete Convolutional Auto-Encoder Embedding As Shape Priors For Deep Vessel Segmentation;Amine Sadikine;2022;IEEE


CCDC 1867496: Experimental Crystal Structure Determination;Ulm, Franck;2018;Cambridge Crystallographic Data Centre

Related Article: Franck Ulm, Amalia I. Poblador-Bahamonde, Sabine Choppin, Stéphane Bellemin-Laponnaz, Michael J. Chetcuti, Thierry Achard, Vincent Ritleng|2018|Dalton Trans.|47|17134|doi:10.1039/C8DT03882A


CCDC 1867502: Experimental Crystal Structure Determination;Ulm, Franck;2018;Cambridge Crystallographic Data Centre


CCDC 1867501: Experimental Crystal Structure Determination;Ulm, Franck;2018;Cambridge Crystallographic Data Centre


CCDC 1867503: Experimental Crystal Structure Determination;Ulm, Franck;2018;Cambridge Crystallographic Data Centre


CCDC 1887748: Experimental Crystal Structure Determination;Zeng, Minghua;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 1893245: Experimental Crystal Structure Determination;Carvalho, Mary-Ambre;2019;Cambridge Crystallographic Data Centre

Related Article: Mary-Ambre Carvalho,  Hervé Dekkiche,  Mayumi Nagasaki,  Yoshihiro Kikkawa,  Romain Ruppert|2019|J.Am.Chem.Soc.|141|10137|doi:10.1021/jacs.9b02145


CCDC 1590361: Experimental Crystal Structure Determination;Ren, Xiaoyu;2019;Cambridge Crystallographic Data Centre

Related Article: Xiaoyu Ren, Marcel Wesolek, Pierre Braunstein|2019|Dalton Trans.|48|12895|doi:10.1039/C9DT02400J


CCDC 1590362: Experimental Crystal Structure Determination;Ren, Xiaoyu;2019;Cambridge Crystallographic Data Centre


CCDC 1590359: Experimental Crystal Structure Determination;Ren, Xiaoyu;2019;Cambridge Crystallographic Data Centre