dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGMENTS We thank  Eric Deziel  for helpful discussions and the generous gift of the transcriptional reporters pTNS2, pML03, and  pGX1 ,  Everett C. Pesci  for the generous gift of the transcriptional reporters pLPRI, pPCS223, pPCS1001, and  pPCS1002 ,  Joe Harrison  for the generous gift of the vector mini-CTX2T2. 1-GWand the construct pJJH187, and  Sudha Chugani  and  E. Pete Greenberg  for the generous gift of the pSC301 vector. We thank  Sylvain Millot  for his technical assistance with the LC-MS. We recognize the  Canadian Institutes for Health Research  for research and salary support to D. N. and the  Burroughs Wellcome Fund  for research support to D. N.
Inclusion Criteria for Papers The database search on PubMed was performed using the following string: "fmri AND (navigation OR egocentric OR allocentric OR map) NOT gene NOT genetic NOT DNA NOT heart NOT patients NOT cellular NOT social NOT psychopathy". A total of 42 studies were found. Our a-priori inclusion criteria for papers were: 1) Inclusion of whole-brain analysis performed using functional magnetic resonance imaging (fMRI); thus, we excluded positron emission tomography (PET) studies, electrophysiology studies and papers that reported only results from ROI analysis. 2) Provision of coordinates of activation foci, either in Montreal Neurological Institute (MNI) or Talairach reference space. 3) All participants in the studies had to be young and healthy. Studies that included healthy elderly adults were excluded to avoid the effects of aging on navigation.
Our results suggest that glycosylases involved in the first steps of the BER pathway may be cancer risk modifiers in BRCA1/2 mutation carriers and should be more comprehensively studied. If confirmed, these findings could have implications not only for risk assessment, but also for treatment of BRCA1/2 mutation carriers with PARP inhibitors. non-independence among related individuals, we accounted for the correlation between the genotypes by estimating the kinship coefficient for each pair of individuals using the available genomic data  [34, 38, 39]. These analyses were performed in R using the GenABELlibraries and custom-written functions in FORTRAN and Python. To estimate the magnitude of the associations (HRs), the effect of each SNP was modeled either as a per-allele HR (multiplicative model) or as genotype-specific HRs, and was estimated on the logscale by maximizing the retrospective likelihood.
The retrospective likelihood was fitted using the pedigree-analysis software MEN-DEL. The variances of the parameter estimates were obtained by robust variance estimation based on reported family membership. All analyses were stratified by country of residence and based on calendar-year and cohort-specific breast cancer incidence rates for mutation carriers. Countries with small number of mutation carriers were combined with neighbouring countries to ensure sufficiently large numbers within each stratum. USA and Canada were further stratified by reported Ashkenazi Jewish (AJ) ancestry. Imputation. Genotypes were imputed separately for BRCA1 and BRCA2 mutation carriers using the v3 April 2012 release (Genomes Project et al. , 2012) as reference panel. To improve computation efficiency we used a two-step procedure which involved pre-phasing in the first step and imputation of the phased data in the second.
Pre-phasing was carried out using the SHAPEIT software  [40]. The IMPUTE version 2 software was used for the subsequent imputation  [41]. SNPs were excluded from the association analysis if their imputation accuracy was r2,0. 3 or MAF,0. 005 in any of the data sets. For the final analysis we only took in account those SNPs with an imputation accuracy r2. 0. 7, MAF. 0. 01 and being located in the region comprised within 15 kilo bases (kb) downstream and upstream the gene where the genotyped SNP showing an association was located (Table  1 ). Associations between imputed genotypes and breast cancer risk were evaluated using a version of the score test as described above but with the posterior genotype probabilities replacing the genotypes.
Latvia (BFBOCC-LV) is partly supported by  LSC  grant  10. 0010. 08  and in part by a grant from the  ESF Nr. 2009/0220/1DP/1. 1. 1. 2. 0/09/APIA/VIAA/016  and Liepaja's municipal council. BRICOH study:  NIH R01CA74415  and  P30 CA033752. SLN was partially supported by the  Morris and Horowitz Families Professorship. CBCS work was supported by the  NEYE Foundation. The  City of Hope Clinical Cancer Genetics Community Research Network  is supported by Award Number  RC4A153828  (PI: JNW) from the  National Cancer Institute  and the Office of the Director,  National Institutes of Health. The members of CONSIT TEAM were funded by grants from the  Italian Association for Cancer Research (AIRC)  to PP, LO and PR;  FiorGen Foundation  for Pharmacogenomics to LP;  Associazione CAOS Varese  to MGT and by funds from  Italian  citizens who allocated the 561000 share of their tax payment in support of the  Fondazione IRCCS Istituto Nazionale Tumori , according to Italian laws ( INT-Institutional strategic projects '561000 ') to SMan and PR.
RE and Elizabeth Bancroft are supported by  Cancer Research UK  Grant  C5047/A8385. FCCC study: The authors acknowledge support from  The University of Kansas Cancer Center  ( P30 CA168524 ) and the  Kansas Bioscience Authority   Eminent Scholar Program. AKG was funded by  5U01CA113916 ,  R01CA140323 , and by the  Chancellors Distinguished Chair in Biomedical Sciences Professorship. The  German Consortium of Hereditary Breast and Ovarian Cancer (GC-HBOC)  is supported by the  German Cancer Aid  (grant no  109076 , RKS) and by the  Center for Molecular Medicine Cologne (CMMC). This study was kindly supported by the  German Cancer Aid  to RKS (grant no  109076 ) and by the  Center for Molecular Medicine Cologne (CMMC). GEMO study: The study was supported by the  Ligue National Contre le Cancer ; the Association ''Le cancer du sein, parlons-en!''Award; and the  Canadian Institutes of Health Research  for the '' CIHR Team in Familial Risks of Breast Cancer '' program.
The HEBON study is supported by the  Dutch Cancer Society  grants  NKI1998-1854 ,  NKI2004-3088 ,  NKI2007-3756 , the  Netherlands Organization of Scientific Research  grant  NWO 91109024 , the  Pink Ribbon  grant  110005  and the  BBMRI grant   NWO 184. 021. 007/CP46. Hungarian Breast  and  Ovarian Cancer Study  was supported by  Hungarian Research Grant   KTIA-OTKA CK-80745. IHCC study: KJB is a fellow of  International PhD program ,  Postgraduate School of Molecular Medicine, Warsaw Medical University , supported by the  Polish Foundation of Science. The ILUH group was supported by the  Nordic Cancer Union ,  Icelandic Association ''Walking for Breast Cancer Research' ' and by the  Landspitali University Hospital Research Fund. INHERIT: This work was supported by the  Canadian Institutes of Health Research  for the '' CIHR Team in Familial Risks of Breast Cancer'' program , the  Canadian Breast Cancer Research Alliance -grant # 019511  and the  Ministry of Economic Development, Innovation and Export Trade  -grant #  PSR-SIIRI-701.
Methods stage I Selection and genotyping of SNPs. Eighteen genes (UNG, SMUG1, MBD4, TDG, OGG1, MUTYH, NTHL1, MPG, NEIL1, NEIL2, APEX1, APEX2, LIG3, XRCC1, PNKP, POLB, PARP1 and PARP2) involved in the BER pathway were selected, based on the information available at http://www. cgal. icnet. uk/ DNA_Repair_Genes. html as at the 31 st December, 2009. Tag SNPs for the selected genes were defined using Haploview v. 4. 0 (http://www. broad. mit. edu/mpg/haploview) with an r 2 threshold of 0. 8 and a minimum minor allele frequency of 0. 05. In addition, SNPs with potentially functional effects already described in the literature were selected. A final number of 144 SNPs was included in an oligonucleotide pool assay for genotyping using the Illumina Veracode technology (Illumina Inc. , San Diego, CA).
Three hundred nanograms of DNA from each sample were genotyped using the GoldenGate Genotyping Assay with Veracode technology according to the published Illumina protocol. Genotype clustering and calling were carried out using the GenomeStudio software. SNPs with a call rate ,0. 95 were excluded from further analysis. Duplicate samples and CEPH trios (Coriell Cell Repository, Camden, NJ) were genotyped across the plates. SNPs showing Mendelian allele-transmission errors or showing discordant genotypes across duplicates were excluded. Statistical analysis. To test for departure from Hardy-Weinberg equilibrium (HWE), a single individual was randomly selected from each family and Pearson's X 2 Test (1df) was applied to genotypes from this set of individuals. The association of the SNPs with breast cancer risk was assessed by estimating hazard ratios (HR) and their corresponding 95% confidence intervals (CI) using weighted multivariable Cox proportional hazards regression with robust estimates of variance  [34].
Three seeding experiments during oligotrophic period in the oligotrophic waters of the Mediterranean Sea The methodology concerning the "large clean mesocosms" (diameter: 2. 3 m, surface area: 4. 15 m 2 , and volume: 52 m 3 ) setup is fully described in  Guieu et al. (2010)  and the 2 field campaigns main features are described in a companion paper  (Guieu et al. , 2014b). In this paper we will report on primary production (PP), bacterial respiration (BR) and particulate organic carbon export (POC export ) data acquired during the campaigns DUNE-1 in June 2008 and DUNE-2 in June-July 2010. DUNE-1 consisted in two distinct 8 day experiments: a first simulation of a Saharan wet deposition event (hereafter named "DUNE-P") and a second simulation of a Saharan dry deposition event (hereafter named "DUNE-Q").
Oxygen concentration was measured through a spectrophotometric approach based on measuring the absorbance at 466 nm of the colored I 2 and I that the used technique, involving pre-filtration and long incubation time, can lead to an overestimation of the BR rates (see for example,  Aranguren-Gassis et al. , 2012). This potential overestimation should not be a big problem as far as results are compared with literature data (mostly obtained with the same method) and/or relative changes after dust addition are concerned. We are aware, however, that absolute values of BR or net CO 2 fluxes must be taken with caution. NPP -One sample per depth was collected at both 0. 1 and 5 m depth during DUNE-P and -Q and at 5 m depth only during DUNE R, for the determination of NPP using the 13 C uptake determination method.
Statistical tests The mean relative changes (RC, in %) after the P, Q, R1 and R2 seedings were calculated as (X Dust -X Control )×100/(X Dust ) for each parameter (X = NPP, BR and POC export ), where X Control is the mean for the 3 mesocosms CONTROL. In order to compare the results between experiments), means were compared using a one-way ANOVA and a Fisher Least Significant Difference (LSD) means comparison test (α = 0. 05). When assumptions for ANOVA were not respected, means were compared using a Kruskal-Wallis test and a post hoc Dunn's test. The statistical tests and the box plots were performed using the Addinsoft TM XLstat software (http://www. xlstat. com).
A strong heterotrophic character remains after seeding Although there are some variations in between the triplicate mesocosms as one may expect in natural systems responding to external forcing such as atmospheric deposition, the DUNE data show an increase in both BR and NPP fluxes after seeding (except for NPP for DUNE-Q). The first important point is to note that NPP/BR are below 1 with the average value for the whole data set being 0. 32±0. 25. As seen on Fig. 3 , NPP/BR tends to be significantly lower in DUST-Meso compared to CONTROL-Meso for P and Q indicating that the dust deposition induced an increase in the net heterotrophic character of the tested waters in these experiments. Indeed, when normalizing to CONTROL values (Fig. 4 ), there is evidence that the net heterotrophic character of the waters is increasing after seeding for P and Q experiments.
Such mechanism could counterbalance in part the drawdown of DOC necessary to explain the net consumption observed in the absence of allochtonous input of DOC in our setup. Nevertheless, this budget illustrates that in the absence of lateral advection from coastal sources or upwelling from deep waters, such heterotrophic system boosted by atmospheric deposition could decrease significantly the stock of dissolved organic carbon in the surface ocean, a question largely debated at the moment (see for ex. Duarte et al. , 2013; Ducklow and Doney, 2013). Although the net heterotrophy character of the tested waters remained (or even was increased) after the dust addition, POC export was still observed: so the DUNE data also illustrate that a system can be dominated by heterotrophy and still maintain an export of particulate organic carbon even in the absence of allochthonous carbon inputs on the short time scale concerned by the dust deposition event.
Acknowledgements. The  DUNE  project, a DUst experiment in a low Nutrient, low chlorophyll Ecosystem, is a fundamental research project funded by the  ANR  under the contract " ANR-07-BLAN-0126-01 ". It was conducted in partnership with the laboratory of LISA (Créteil),  LEMAR (Brest) ,  LOCEAN (Paris) , and in collaboration with the laboratories LSCE ( Gif-sur-Yvette ),  LOMIC (Banyuls) ,  IRD/LOBP/COM (Marseille) ,  CEFREM (Perpignan) ,  CERES/ERTI ,  ENS (Paris)  and the  Regional Parc of Corsica, Preservation Area of Scandola. DUNE was also conducted in strong collaboration with foreign research institute including the  Institut des Régions Arides (IRA) ,  Médenine (Tunisie) ,  IFM-GEOMAR, Kiel (Germany) ,  Stazione Zoologica Anton Dohrn ,  Napoli (Italy)  and  Alfred Wegener Institute, Bremerhaven (Germany).
The Y-chromosome haplotype, determined with the AmpFlSTR Identifiler PCR amplification Kit is unique in a current European database with over 21,000 individuals, suggesting that any matching with other individuals would likely support a paternal relationship between them. The subsequent analysis of the mummified head 8 of the king Henri IV (1553-1610) 9 , separated by seven generations from Louis XVI, provided a partial Y-chromosome profile that with the exception of one genetic marker, was concordant with that found in the gourd's blood. Since one allelic difference is not unexpected in pedigrees of several generations, the results still supported that both remains were paternally related 9. However, a later analysis of three male living Bourbons from two different family branches revealed identical Y-chromosome haplotypes that were different to those found in the remains of Henri IV and the gourd's individual 10.
While contamination can still remain problematic a lower coverages, we have estimated that in the case of 123 coverage the remaining contamination, according to a Bernoulli statistical model and conditional probabilities, range between 0. 25% and 0. 39% (Supplementary Methods). The second set has a higher confidence due to the increased coverage; nevertheless we have calculated a genotype concordance between both datasets of 98%. Obviously, the conservative procedure selected had the side effect of removing real heterozygotes from the gourd's genome. Subsequent Sanger sequencing of 9 sites confirmed the undercalling of heterozygous SNPs (false negative rate of 33. 3%) (Supplementary Table  S8 ). Combining the two datasets in a nonredundant set of SNPs, we characterized a total of 1,208,005 SNPs contained in dbSNP, from which 314,549 (26.
We first determined the gourd's blood paternal ancestry, using diagnostic SNPs in the Y-chromosome, as defined by ISOGG (2014). Several derived SNPs define a G2a2a haplogroup (Supplementary Table  S5 ); again, this result is concordant with that previously found with the AmpFlSTR Identifiler kit  7. An identity-by-descent (IBD) tract sharing analysis showed very few IBD tracts with extant Europeans, likely due to gaps in the genomic coverage and undercalling of heterozygous sites. The sequenced individual shared the highest number of fragments with a French individual, but shared the longest tract with a Belgium individual (Supplementary Table  S10 ). We also performed a principal component analysis (PCA) on the. 93 SNP exome dataset, using 236 individuals from the 1000 Genomes Project 1 for comparison (16,635 SNPs).
To minimize differences between our low coverage genome and the reference genotypes, we randomly sampled a single haploid allele from each individual prior to PCA analysis  13. The gourd's individual can be found close to the CEU distribution, slightly displaced towards the Iberian samples and Tuscan samples from Northern Italy (Fig. 3 ). Subsequently, to place the gourd's genome in a more precise European context, we performed a genome wide PCA using the European populations of POPRES  14. Because only 3% of our exome data intersect with POPRES markers, we utilized all SNPs passing our filters genome-wide in this analysis -SNP dataset increased to about 100,000. We found the sequenced individual clusters with Northern Italian individuals (Fig. 4a ) which is not what we could expect owing the known ancestry of Louis XVI.
This data set is obviously more influenced by the contamination of the sample, due to the less efficient allele imbalance removal associated to the low coverage. To explore if Louis XVI ancestry at the level of his great-great grandparents was compatible with the PCA results, we have randomly generated 30 composite genomes with the proportions of his known ancestry and generated a PCA with POPRES European populations. This simulation showed that the expected position of the king in the PCA is among present day Central European populations (Germany and Poland) (Fig. 4b ). In summary, the results of these analyses do not support the royal identity of the sequenced genome. However, given Louis XVI's complex great-great-grandparental ancestry, the low coverage and the aggressive filtering to remove minor alleles from the current dataset, we consider it could still be possible, although implausible, that the gourd's blood could be that of the French king.
Discussion We have retrieved a draft genome from the gourd's blood, supposed to be that of king Louis XVI, and we have conducted several genomic analyses to characterize this individual. First, we have generated a population analysis with different current European datasets as reference populations. These analyses show that the position of the gourd's individual in the context of modern Europeans is somewhat complex -we see IBD sharing with contemporary French individuals, but also ancestry that is somewhere between contemporary CEU samples and Northern Italian samples. Although it can be argued that Northern Italian populations have clear ancestral ties with Central Europe, this discernible component cannot be easily reconciled with the known Louis XVI family history, given that just one in sixteen great-great-grandparents -Victor Amadeus II, Duque of Savoy (1666-1732)-has some possible Northern Italian ancestry.
Acknowledgments We are indebted to the owners of the gourd for allowing access to the blood sample inside it and to  John Novembre  for advice and assistance with the ancestry analysis. This work is supported by  FEDER  and  Spanish Government  grants  BFU2012-38236  and the  Spanish Multiple Sclerosis Netowrk (REEM)  of the  Instituto de Salud Carlos III  ( RD12/0032/0011 ) to A. N. ,  BFU2011-28549  and  ERC Starting Grant  ( 260372 ) to T. M. -B. and  BFU2012-34157  to C. L. -F. and S. C. , and a predoctoral fellowship from the  Basque Government (DEUI)  to I. O.
A total of 277,762,784 sequences were mapped, from which 9,565,693 remained after removing duplicates, thus achieving a final global coverage of ,7. 323. SNP assessment from Linkage disequilibrium patterns. To recapture non-available SNPs and to confirm genotyped SNPs, we first searched for those SNPs present in the NHGRI GWAS Catalog 22 through a custom-designed pipeline. As a primary input, we intersected the HapMap SNPs (CEU population) with the SNP positions analysed in the gourd's genome. The rationale behind is that any SNP in HapMap would have a frequency high enough to be detected in a GWAS study. This resulted in an input dataset of 2,031,376 SNPs that were further analysed to ascertain LD patterns among them. 100 kbp regions around each of these ,2 million SNPs were defined and all the SNPs with a LD threshold of R 2 5 1 were considered.
We then searched those recaptured SNPs associated to our selected traits at the GWAS Catalog. Afterwards, based on sequence data for the CEU population from the 1,000 Genomes Project 1 , pairwise haplotypes with recaptured and genotyped SNPs were built using PLINK-1. 07  23. With the pairwise haplotypes we could infer if a particular non-genotyped risk allele is segregating in LD with any of the known positions. We subsequently filtered the obtained SNP dataset and considered only those SNPs recaptured by at least three neighboring SNPs, with no incongruities (Supplementary Methods). Furthermore, the pipeline was used not only to recapture unknown SNPs, but also to verify that the SNPs for which we already had a genotype were correct. We considered as valid those SNPs that were in a congruent haplotype with at least six other SNPs (Supplementary Table  S17 ).
This marker placement was based on a previously published article focusing on the lower limb during such lateral reactive jumps  (Fleischmann et al. , 2010). Markers were captured with a 12-camera motion analysis system (Vicon V-MX, VICON Motion Systems Ltd. , Oxford, UK) with a sampling frequency of 200 Hz. A static trial with the subject standing in a pre-defined neutral position was used to define the kinematic model and to calculate segment lengths and joint centres  (Grood & Suntay, 1983; Wu et al. , 2002). The kinematic modelling was performed with the motion analysis software (Vicon Nexus 1. 6. 1, VICON Motion Systems Ltd. , Oxford, UK). Joint kinematics in three rotational degrees of freedom were determined using an yxz Euler rotation sequence of the respective segment coordinate system according to the global reference system defined in Vicon.
Data analysis Kinematic data for the ankle, knee and hip joints in the sagittal (positive values dorsiflexion, knee flexion, hip flexion) and frontal (positive values for ankle inversion, knee adduction, hip abduction) planes were analysed. Comparison of mechanically identical landing modalities (e. g. stable landing in the predictable setting vs. stable landing in the unpredictable setting) served to identify differences in the feedforward motor control strategy. Kinematic parameters were investigated at the time of the initial contact (IC) with the ground and at 140 ms after initial touchdown as it was previously proposed that this time reflects the end of the reflex induced activity  (Fleischmann et al. , 2010). Data obtained at this later instant gave further information about the consequences of changes in the feedforward motor control adaptation.
30 (glycerol) objective and TD 488/561/633 beam splitter). Images were acquired via three channels (430e525 nm, 500e550 nm and 600e700 nm) excited with laser diode 405 nm/50 mW, laser OPSL 488 nm/ 270 mW, and DPSS 561 nm/20 mW. The confocal images were analyzed with Imaris program (Bitplane) and either slice or surpass images were constructed. The possible deconvolution was done with AutoQuant X program (MediumCybernetics).
The fluorophores were excited with lasers Argon 488 nm/35 mW and HeNe 633 nm/12 mW. Emission was acquired at 500e550 nm (fluorescein) and 650e750 nm (Draq5 TM ). The transmitted light was also collected. The confocal images were analyzed with Imaris 7. 4 program (Bitplane) and either slice or surpass images were constructed.