dataesr/scientific-paragraphs-categorization huggingface dataset:
Recipient age and time on dialysis Both in paediatric and adult kidney transplant recipients, recipient age has been identified as an independent risk factor of post-kidney transplant malignancies  [54, 55]. With increasing recipient age, this is an important factor in the overall increasing incidence of post-transplant cancer in kidney transplant recipients. Time on dialysis before transplantation has also been identified as a risk factor for developing post-transplant malignancy. In a study based on the ANZDATA database, Wong et al. [38]  reported a linear relationship between the duration of dialysis and the risk of solid organ cancer after transplantation, irrespective of recipient age. In a very interesting article, Yanik et al. [56]  evaluated the incidence of cancer types depending on non-renal function interval (time on dialysis either on wait list or after transplant failure) or kidney function interval (time with a functioning graft and thus on immunosuppression), applying a linkage between the SRTR and several US cancer registries.
Earlier studies have suggested an association of induction therapy with T cell-depleting antibodies with an increased risk of PTLD. In an analysis of the CTS, the SIR of lymphoma compared with a similar non-transplant population was higher with T cell-depleting antibody induction as compared with IL-2Ra or no induction therapy  [143]. Also, a study of the SRTR and the United States Renal Data System databases reported similar results (70% increased risk of PTLD in renal transplant recipients receiving monoclonal and/or polyclonal T cell-depleting antibodies as induction therapy)  [10, 14]. Also, an earlier analysis of the ANZDATA registry demonstrated that the use of T celldepleting antibodies (as induction or as treatment for rejection) was associated with a more than two-fold increased risk of early onset NHL after transplantation  [9].
Registry database studies reported results regarding rATG use and the occurrence of PTLD have been mixed. Only three studies looked at rATG specifically and two found an increased risk for PTLD while one did not  [10, 11, 151]. Other registry studies of PTLD risk have grouped multiple lymphocyte-depleting induction agents together for the purpose of analysis, in some cases including OKT3  [14, [152] [153] [154] [155]. Three prospective randomized trials followed patients up to 5 years after kidney transplantation  [156] [157] [158]. The incidence of PTLD and the follow-up time were too limited to allow for meaningful conclusions  [159] [160] [161] [162]. Finally, a systematic review by Marks et al. [13]  evaluated the rate of PTLD in recipients of kidney or heart allografts and pointed to the importance of antiviral prophylaxis, as in this study; the absence of antiviral prophylaxis was the greatest risk factor for the development of PTLD rather than the use of induction therapy.
In a study linking the US SRTR database with 15 population-based cancer registries and national pharmacy claims, cancer incidence in 32 604 sirolimus-exposed and sirolimus non-exposed kidney transplant recipients was studied. The incidence of prostate cancer was higher during sirolimus use (hazard ratio 1. 86), while the incidence of other cancers was similar or lower, with a 26% decrease in overall cancer incidence excluding prostate carcinoma (hazard ratio 0. 74). The authors postulate that the increase in prostate cancer diagnosis is due to sirolimus, effects on screen detection. In addition, two meta-analyses have been published demonstrating a lower overall cancer incidence with the use of sirolimus  [133, 194]. In the meta-analysis of Knoll et al. [133] , including 21 randomized controlled trials with patient-level data from 5876 patients, it was demonstrated that sirolimus was associated with a 40% reduction in malignancy risk and a 56% reduction in the risk of non-melanoma skin cancer (0.
Design of qPCR primers and probe The ITS sequences of pure strains (Table  1 ) were aligned using the ClustalW algorithm  [26]  and sequence motifs suitable for a species-specific analysis of A. pulchella were identified applying the software Primer express 2. 0 (Applied Biosystems, Foster City, California). Two primer binding-sites and one probe binding-site in the ITS-1 region were further tested for species-specificity: forward primer AlaPul-ITSfor (5'-TTGGAGGTCCGGCTGTGT-3'), reverse primer AlaPul-ITSrev (5'-TCCGAGGTCAACCTTAAAAAAATT-3') and TaqMan  probe AlaPul-ITSprobe (5'-CCTGCCAGCAACC-3'). The probe was labeled with 6-carboxyfluorescein at the 5'-end and MGBNFQ at the 3'-end as fluorescent reporter dye and non-fluorescent quencher, respectively. qPCR procedure qPCR reactions were performed for all DNA extracts of the inclusivity/exclusivity panel for the established assay (Table  1 ) and run on a Mastercycler 1 ep realplex S (Eppendorf, Hamburg, Germany).
These values were used to generate a calibration curve, where the mean Ct value for each standard (n = 7) was plotted as a function of the corresponding PFU. Subsequently, the LoD and LoQ were derived following the descriptions in Vrålstad et al. [28]. For a full description of the calculations for the LoD and LoQ, see S3 File. The software Real Plex 2. 2 (Eppendorf, Hamburg, Germany) and R for Mac version 3. 0. 2 [31]  were used for data analysis and preparation of figures.
g. , GenBank Accession no. KF730806, E-value: 0. 0, Identity: 100%). More importantly, sequences for species displaying the highest genetic similarity to A. pulchella showed ! 2 base mismatches at the target site for the probe (for description, see S4 File and S5 File; Figures A and B in S4 File). The only exception was found in Flagellospora curvula (GenBank Accession no. AY729939), which did not show any mismatch with the probe's sequence (Figure B in S4 File). A BLASTn-search conducted with the respective sequence, however, revealed a higher similarity to Alatospora sequences than to any other of the genus Flagellospora. Accordingly, a direct comparison of the doubtful F. curvula sequence with additional deposited sequences of the same species showed a high degree of mismatch, including the primer and probe regions (results not shown).
(maintained as pure cultures; identified morphologically and genetically) used as a source of DNA. Previously published GenBank accession numbers of reference sequences used for the genetic identification of the aquatic hyphomycete strains are displayed if accessible. Furthermore, the allocation of strains to the inclusivity panel (should be detected) and exclusivity panel (should not be detected) is shown. Newly generated GenBank accession numbers of the strains used during the present study and Ct values of the qPCR are given in the last two columns. Dashes are shown where no new GenBank accession numbers were generated, genetic identification was not possible or no positive signal was detected during qPCR. a Czech Culture Collection b Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH c EcoLab-Laboratoire ecologie fonctionnelle et environnement (Eric Chauvet) https://doi.
This work was supported by the  German Research Foundation (DFG)  (grant number  SCHU 2271/14-1 ), the  Carl Tryggers Foundation, Stockholm  (grant number  CTS 13:72 ), and the  Fix Stiftung, Landau. Financial support by the  Portuguese Foundation for Science and Technology  to  Julien Cornut  ( SFRH/BPD/108779/ 2015 ) is gratefully acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Stimuli. Eight face/anti-face pairs were used (half female; see Fig. 1  for examples; see also Fig. 1  and the Methods of ref. 13). These stimulus pairs were used in order to standardize a relatively large amount of difference within each set of facial identities (for more details, see ref. 13). They were presented exactly as in the previous study, in color with a base presentation size of approximately 5. 0 degrees of vertical visual angle. While in the upright and inverted conditions no additional stimuli were introduced, two novel stimuli were additionally presented here in the average condition: the average female and average male face. These stimuli were created from the average of the 12 female and 12 male facial identities, respectively, used in the creation of the face/anti-face pairs with JPsychoMorph software  29.
45, 9. 55, 20. 6, 34. 5, 50, 65. 5, 79. 4, 90. 5, 97. 6, and 100% (see Fig. 1A ). Stimuli were presented with carefully controlled timing through Psychtoolbox 3. 0. 9 for Windows (see ref. 52), running over MATLAB R2009a (MathWorks, USA). In addition to the low-level features of the stimulus thus varying at every screen refresh rate, to further reduce possible low-level adaptation, the size of each stimulus varied randomly at each presentation cycle among five steps in a range of 90-110% of the original presentation size  53. The structure of each trial was the same across conditions (Fig. 1B ). Each trial began with designs to reduce expectation and reaction to sudden stimulus-onset: a jittered 2-5 s of a grey background and a 2 s stimulus fade-in, during which the maximum stimulus contrast gradually increased to 100%.
webnode. com/letswave), running over MATLAB R2013b (MathWorks, USA). Since the recording was paused during breaks in between trials (with pause times indicated by an Epoch trigger), resulting changes in drifting electrode offsets were corrected by aligning the offset of each channel immediately after the pause to its prior offset. The data were then filtered with a fourth-order zero-phase Butterworth band-pass filter, with cutoff values of 0. 1-120 Hz, and a Fast Fourier Transform (FFT) multi-notch filter, with a width of 0. 5 Hz, to remove three harmonics of the 50 Hz electrical noise. Next, the data were segmented by trial, including one second before and after the time of the stimulus fade-in and fade-out, respectively. Channels which were artifact-prone across multiple trials (0 to 5 channels per participant; 1.
Acknowledgements This work was supported by grants from the  Belgian National Foundation for Scientific Research (FNRS ; grant number  FC7159  to TR) and the  European Research Council  (ERC: facessvep 284025 to BR). We would additionally like to thank  Renaud Laguesse  for preparing the original face photographs,  Milena Dzhelyova  for her help with creating the face/anti-face stimulus pairs, and  Alexy-Assaf Beck  for testing three participants.
Monte Carlo (MC) simulations are an essential tool to determine fundamental features of a neutron beam, such as the neutron flux or the γ -ray background, that sometimes can not be measured or at least not in every position or energy range. Until recently, the most widely used MC codes in this field had been MCNPX and FLUKA. However, the Geant4 toolkit has also become a competitive code for the transport of neutrons after the development of the native Geant4 format for neutron data libraries, G4NDL. In this context, we present the Geant4 simulations of the neutron spallation target of the n TOF facility at CERN, done with version 10. 1. 1 of the toolkit. The first goal was the validation of the intra-nuclear cascade models implemented in the code using, as benchmark, the characteristics of the neutron beam measured at the first experimental area (EAR1), especially the neutron flux and energy distribution, and the time distribution of neutrons of equal kinetic energy, the so-called Resolution Function.
CrsR belongs to a new family of anti-factor proteins When searching for CrsR homologs in the sequence data bank as we did for the phylogenic study, the well studied antifactors such as SpoIIAB, RsbW, and SypE were not hits. A possible explanation for this is that SpoIIAB and RsbW are organized as a single domain, and the organization of the three domains of SypE is different from that of CrsR. In fact, analysis of the sequence alignment of CrsR D3 with these three antifactors and CrsR D3 homologs obtained from the phylogenic tree highlights an additional region present in CrsR D3. Interestingly, this region is conserved in anti-factor domains of CrsR homologs presented in Fig. 4  (Fig. 5A ). The extra region stretches from Leu-469 to Ser-496 (S. oneidensis CrsR numbering) between the N and G1 boxes, which are conserved motifs of the GHKL ATPase/kinase superfamily (Fig.
5A ). On the basis of solved structures of antifactor proteins, the predictive model of the 3D structure of CrsR D3 was designed using the I-TASSER program  (14). The structural organization of the stretch of 28 amino acids described above was simulated as an unfolded loop (from Leu-469 to Asp-488) followed by a short ␣-helix (from Ser-489 to Arg-493) at the surface of the protein (Fig. 5B ). This additional region defines a new class of antifactors.
Bioinformatics analyses The proteins sharing homologies with CrsR were found in the NCBI non-redundant protein sequence database using the protein BLAST search tool. For phylogenetic tree construction, the searches were made independently on the different classes of Proteobacteria (␣-, ␤-, ␥-, ␦-, and ⑀-Proteobacteria) as well as on bacteria with the exclusion of the Proteobacteria. For the ␥-Proteobacteria, the searches were made separately on each order comprising this class. One representative sequence for each genus was subsequently selected except for Shewanella, Vibrio, and Pseudomonas. We chose the proteins sharing the highest E-value with CrsR on the whole length of the proteins. For the phylogenetic analysis, we used Phylogeny. fr software in the "one-click" mode, i. e. with the default parameters optimized by the authors (28) (http://www.
phylogeny. fr/). 4 The main steps performed by this software correspond to multiple alignments of the CrsR homologs using the MUSCLE version 3. 8. 31 method, alignment curation by GBlocks version 0. 9b, and phylogeny using the PhyML version 3. 1 method using 100 bootstrap replicates. For the tree rendering step, we used the software FigTree version 1. 4. 2 (29) (http://tree. bio. ed. ac. uk/ software/figtree/) 4 in which we entered the result in Netwick format obtained with Phylogeny. After the first phylogenetic analysis, we manually removed the unnecessary sequences, and a second phylogenetic analysis was performed. The neighborhood of the genes coding for the CrsR homologs was extracted from the databases using NCBI, Microbial Genome Annotation and Analysis Platform (MaGe) (30) (https://www.
Sequences alignment and tertiary structure prediction Representative sequences of CrsR from different classes, orders, and genera were selected. HATPase domains from these proteins and SypE (from V. fisheri) and RsbW and SpoIIAB (from B. subtilis) were aligned using the Clustal Omega program (European Molecular Biology Laboratory), and the highlighted and conserved amino acid residues were generated using the BoxShade (ExPASy) server. The secondary structure of CrsR D3 was predicted using the PSIRED server (32) (http:// bioinf. cs. ucl. ac. uk/psipred/). 4 The structure of CrsR D3 was predicted using the I-TASSER server, and the model having the highest C-score (Ϫ1. 14) was annotated and is shown in Fig. 5B   (14). Author contributions-S. B. , O. G. , V. M. , and C. I. -N. conducted experiments, analyzed the results, and wrote the paper.
It is important to note that different parameters may influence the Raman signal, such as instrumental setup, structural defects, traces elements, internal stresses or temperature  [1] [2] [3]  (Figure  1 ). Although these parameters may sometimes complicate interpretation, some of them can also be used to measure particular properties, for example, the shift related to internal stresses  [4]. Finally, the Raman effect is relatively complex to model, and the identification of a compound is generally made by comparison with reference spectra found in the literature or in databases. More information about the Raman effect can be found in this book or others  [5] [6] [7].
[14] for more information). A small grain of SiC, coming from the polishing process, is also detected (in light blue in d). (e) Optical image and (f) associated compositional Raman map of a chert sample having undergone atmospheric entry (analogue meteorite, see Ref. [15]  for more information). The quartz is in orange and the carbonaceous matter in green. The background intensity is displayed in dark blue and highlights cracks in the sample due to stresses related to atmospheric entry. To conclude, various processing methods applied to Raman mapping data set can highlight particular properties of the mineral phases in a scanned sample. Further examples of such processing include making several scans of the same area using different environmental parameters (different laser wavelengths, external stress, temperature, etc.
Acknowledgements We acknowledge  Olga A. Maslova  for the mapping and analysis of UO2 ceramics. R. Augier ,  F. Choulet ,  D. DoCouto  and  F. Rull  for the samples from  Sierra Alhamilla , Morocco and Autun, la Sioule and Tenerife, respectively. We also acknowledge  P. Bost  for his help in sampling at Chéniers.
, 2014a). The limiting amount of RNA that can be isolated from oocytes excludes the possibility of performing m 6 A-seq to determine if the consensus-containing upregulated genes in Ythdf2 mCKO MII oocytes are methylated. We therefore sought to determine if we can find evidence for their methylation in other mouse tissues using the MeT-DB database  (Liu et al. , 2015a). We found a stark enrichment for m 6 A adjacent to the stop codon in the transcripts that are upregulated in Ythdf2 mCKO MII oocytes (Figure  4G ). In summary, we find that the upregulated transcripts in the Ythdf2 mCKO MII oocytes are enriched for the m 6 A/YTHDF2 consensus motif, and for some we find evidence for their m 6 A methylation in other cell types.
Motif analysis Affymetrix identifiers were mapped to Ensembl transcripts using Biomart (32). Biomart was then used to obtain 400 nt 5 0 and 3 0 of both the start and stop codon. Sequences obtained that were shorter than 400 nt were padded to this length with the addition of 'N's. Each transcript may only be present once in the Affymetrix gene list. Where multiple transcripts are present, the one with the highest absolute fold-change is retained. Only one isoform is retained when multiple transcripts have the same sequence. Motif occurrences were directly computed using Perl regular expression matching for ''GCA[UA]'' for sequences assigned to the top 1000 most upregulated, downregulated and for 1000 transcripts from the center of the gene list. A matrix of 1000x800 elements is hence obtained for each of the three sets, indicating which sequence and at which nucleotides motifs occur.
This matrix is column summed and plotted using a cubic spline smoothing function smooth. spline from R/Bioconductor. Statistics for the motif enrichment was done with a hypergeometric test. m 6 A peaks dataset analysis Public m 6 A peak data was obtained from MeT-DB (http://compgenomics. utsa. edu/methylation/) for 12 mouse (mm9) samples. Peaks were translated into BED files with enrichment scores, lifted-over to mm10 via UCSC liftover, sorted, filtered and overlapping regions condensed into bigwig files. These bigwig files were provided to the DeepTools package v1. 5. 9. 1 (ComputeMatrix and Heatmapper)  (Ramı ´rez et al. , 2014)  to explore peak enrichments around gene-bodies from the start to the stop codon with 400 nt either side. The Ensembl GTF corresponding to GRCm38 version 79 was used for gene body coordinates.
The number of genes in the respective gates is indicated. (F) Graph representation of Loess smoothed sum of YTHDF2-binding motif GACU/A occurrences ±400 nt around the stop codon (left panel) and around the start codon (right panel). Data are shown for the top 1,000 most-upregulated transcripts (red), 1,000 downregulated transcripts (blue), and 1,000 transcripts whose expression remained unchanged (green) in Ythdf2 mCKO MII oocytes. Only enrichment of the upregulated genes compared to unchanged genes around the stop codon is statistically significant (p < 0. 05). (G) Prevalence of m 6 A peaks from public mouse datasets around the gene bodies of upregulated, downregulated, and unchanged transcripts in Ythdf2 mCKO MII oocytes. Gene bodies are scaled to the same length in each case. Only enrichment of the upregulated genes compared to unchanged genes around the stop codon is statistically significant (p < 0.
Software and Algorithms Limma  (Ritchie et al. , 2015)  https://bioconductor. org/biocLite. R Gorilla  (Eden et al. , 2009)  http://cbl-gorilla. cs. technion. ac. il Biomart (Smedley et al. , 2015) http://www. biomart. org Smooth. spline R/Bioconductor https://rdrr. io/bioc/aroma. light/src/R/likelihood. smooth. spline. R DeepTools package v1. 5. 9. 1 (Ramı ´rez et al. , 2014) http://deeptools. readthedocs. io/en/2. 0. 1/source/deeptools. html e1 Molecular Cell 67, 1059-1067. e1-e4, September 21, 2017.
0 ST Array Affymetrix N/A Deposited Data Expression data This paper E-MTAB-5056 Expression data This paper E-MTAB-5576 Mendeley Data dataset This paper http://dx. doi. org/10. 17632/zb7zyfghg3. 1 Experimental Models: Organisms/Strains Mouse: ZP3Cre:C57Bl6-Tg (de Vries et al. , 2000) N/A Mouse: Ythdf2 HA-Fl This paper N/A Mouse: Ythdf2 - This paper N/A Oligonucleotides Primers for qRT-PCR, see Table S1.
Identification of a FANCM mutation by whole-exome sequencing and molecular studies Both sisters with POI and their mother were studied by whole-exome sequencing, which generated ~45 millions of mapped read pairs per sample (91% of targeted exome at !10X). Exome capture, sequencing and data processing were performed as described in  (Fauchereau et al. , 2016). Variants were filtered according to the following criteria: minimum depth of 5 reads and variant quality of 20, with potential impact on transcript or protein, homozygosity in both affected sisters and heterozygosity in the mother and minor allele frequency (MAF) under 1%. The only variant fulfilling these criteria was the non-sense mutation chr14:45658326 C/T (rs147021911) in exon 20 of FANCM (Figure  1B , Tables  2 3 ). According to the ExAC database, its MAF is 0.
0013, slightly higher in the Finnish population (0. 0089), with only one homozygous individual described in the ExAC database. The variant and its segregation in the family were verified by Sanger sequencing of the exon 20 of the FANCM (Figure  1C ). This variant leads to the p. Gln1701* truncation at the protein level, which removes the C-terminal endonuclease and the FA associated protein 24 (FAAP24)-interaction domain (Figure  1D ). FAAP24 mediates chromatin association of FANCM. EBV-immortalized cells were obtained from patient 2 and the mother. Immunoblot with an anti-FANCM antibody confirmed the expression of a truncated FANCM protein of ~195 kDa in the cell line derived from the patient, whereas both the wild-type/WT (MW ~235 kDa) and the truncated proteins were present in the heterozygous mother (Figure  1E ).
Indeed, FANCM is targeted to damaged DNA and/or (6) Among the 110 variants detected in the genes included in the FANC pathway, only the non-sense variant found in FANCM is homozygous in both patients, is rare (below 1% in ExAC database) and predicted as pathogenic. DOI: https://doi. org/10. 7554/eLife. 30490. 007 Fouquet et al. eLife 2017;6:e30490. DOI: https://doi. org/10. 7554/eLife. 30490 stalled replication forks by its partners FAAP24, FANCM-interacting histone fold protein 1 (MHF1) and 2 (MHF2), where it recruits the FANCcore complex to monoubiquitinate FANCD2 and FANCI and coordinates DNA repair/replication rescue  (Ceccaldi et al. , 2016; Michl et al. , 2016)  allowing the faithful transmission of undamaged chromosome to the daughter cells. Consistently, the occurrence of chromosome breakages and rearrangements was higher in both POI patients than in their mother (Figure  3A  and B ).