dataesr/scientific-paragraphs-categorization huggingface dataset:
Patient Population Patients included retrospectively were of over 18 years of age, with histologically proven ovarian cancer that was suspected of recurrence, and had been treated in our institution between 2006 and 2010. All patients of the institution received written information on the possibility of use of their medical data in retrospective studies. After initial diagnosis, the patients were monitored by physical examination, CA 125 assay, and CT every 6 months over a 5year period. Recurrent disease was suspected following abnormal examination results and/or symptoms suggestive of recurrence, equivocal results on CI, and/or the isolated elevated serum tumor marker (CA 125). PET scans were acquired only if recurrence was suspected from the different criteria described above. The International Federation of Gynecology and Obstetrics (FIGO) classification was used for clinical staging  (8).
Qualitative Imaging Analysis CT and PET/CT clinical reports were collected and retrospectively analyzed. All PET/CT images were interpreted independently by two nuclear medicine physicians. The observers were aware of the clinical data and findings obtained with other anatomic imaging modalities. When abnormal FDG uptake was observed, its exact anatomical location was indicated on the CT scans. On PET images, the presence of a relapse tumor was suspected when accumulation of FDG was moderately to markedly increased, in comparison with that of comparable normal contralateral structures or surrounding tissues, excluding physiological bowel and urinary activity. For both ethical and practical reasons, not every suspected involved lesion was evaluated by histology. A gold standard reference was therefore established based on histology and 6 months follow-up data (significant tumor progression on clinical examination or on CT according to RECIST Criteria).
Statistical Analysis Results are expressed as mean values ±SD or median (range) in the case of small group sizes. Qualitative variables were compared using the Pearson test or the Fisher exact test where necessary (small sample size). Paired qualitative variables were compared using the Mac Nemar test. Quantitative variables were compared using the Student's t-test or the Mann-Whitney U test where necessary. Survival curves were calculated by means of the Kaplan-Meier method and compared by a log rank test. Multivariate analysis was performed by means of a Cox regression model. Analyses were performed using SAS 9. 1 (SAS Institute Inc. , Cary, NC, USA) and Stata/SE 10 (StataCorp LP, College Station, TX, USA). All tests were performed at a two-sided significance level of α = 0. 05.
3 Å at room temperature. 9  Figure  2   , $ ! "# ! ! To visualize HS domain nucleation and coarsening during the phase change, temperature dependent TEM measurements were performed on the CTIST heating branch using a liquid He cooled specimen holder. The sample was gradually cooled to about 100 K to achieve the IM state (Figure  1 ) and then slowly heated to observe changes as the IM state transitions back to the room temperature HS phase. The sample is easily damaged by the TEM experiment below the freezing point of the ionic liquid (~210 K) so the study is restricted to temperatures above this point (Figure3). Figure  4  shows 3D charts of Co-Fe distances on a ~900 nm crystal plane along with histograms of the distribution of Co-Fe distances obtained at several temperatures. Note that the data have not been adjusted for TEM calibration, so measured values have a constant offset of 0.
Acknowledgements M. G. acknowledges support from the  European Research Council Advanced  Grant  STRATUS (ERC-2011-AdG No. 291198 ). S. M. gratefully acknowledges the support from the  National Science Foundation  through Grant No. CHE-1361516  and the  Chemical Sciences, Geosciences , and  Biosciences division, Office of Basic Energy Sciences, Office of Science, U. S. Department of Energy. A. G. acknowledges financial support from  Italian Ministry of Education and Research (MIUR) -Grant No. RBFR1248UI. B. P. F. gratefully acknowledges support from the  German Research Foundation (DFG)  within the  Emmy Noether Programme  ( FI 2034/1-1 ). A. N. wishes to acknowledge the help of the  Hamiltonian of Design studio  (http://hamiltonianofdesign. worldpress. com) for creating the graphical abstract.
Background: As more and more genotypes become available, accuracy of genomic evaluations can potentially increase. However, the impact of genotype data on accuracy depends on the structure of the genotyped cohort. For populations such as dairy cattle, the greatest benefit has come from genotyping sires with high accuracy, whereas the benefit due to adding genotypes from cows was smaller. In broiler chicken breeding programs, males have less progeny than dairy bulls, females have more progeny than dairy cows, and most production traits are recorded for both sexes. Consequently, genotyping both sexes in broiler chickens may be more advantageous than in dairy cattle. Methods: We studied the contribution of genotypes from males and females using a real dataset with genotypes on 15 723 broiler chickens.
Data The dataset and variance components used in this study were provided by Cobb-Vantress Inc. (Siloam Springs, AR). The dataset consisted of phenotypes recorded on purebred broiler chickens across four generations for four production traits referred to as T1, T2, T3, and T4; heritabilities for all traits ranged from 0. 22 to 0. 49, genetic correlations ranged from -0. 02 to 0. 21 and phenotypic correlations from -0. 02 to 0. 46 (Table  1 ). The first trait (T1) was recorded on 196 613 birds, whereas the three other traits (T2, T3 and T4) were recorded on 26, 5, and 26 % of the birds with records for T1, respectively. Traits T1 and T3 were measured on birds at 35 days of age, whereas traits T2 and T4 were measured within a 2-week period after 35 days of age. Multiple measurements for T2 and T4 were combined into a unique record for T2 and for T4.
Thus, each trait was analyzed as a single record. The number of birds in the pedigree relationship matrix (A) was 198 915. Genotypes from the 60 k SNP (single nucleotide polymorphism) panel developed by Groenen et al. [15]  were available for 15 723 birds. Quality control of genomic data retained SNPs with call rates greater than 0. 9, minor allele frequencies greater than 0. 05, and departures from Hardy-Weinberg equilibrium (difference between expected and observed frequency of heterozygous) less than 0. 15. Parent-progeny pairs were tested for discrepant homozygous SNPs, and progenies were eliminated when the conflict rate was greater than 1 %. Also, SNPs with an unknown position or located on sex chromosomes were excluded from the analyses. After quality editing, 39 102 autosomal SNPs for 15 723 birds remained for analysis.
The genotype file was split by sex and the three genotype datasets (males, females, and both sexes) were used in different analyses. The total numbers of genotyped males and females were 6149 and 9574, respectively and the numbers of genotyped birds with phenotypes for each trait are in Table  2. The birds that were genotyped were chosen randomly or based on phenotypes, depending on the trait. The dataset available for this study was split into training and validation populations according to date of birth. Thus, 2975 birds born in generation 4 were chosen as validation animals and their phenotypes were removed from the analyses.
Weights were assigned for G (α = 0. 95) and A 22 (β = 0. 05) to avoid singularity problems  [13]. Coefficients a and b were used to match pedigree and genomic relationships  [14, 19, 20]. Different H matrices were used based on different G that contained 2975 birds from the validation population plus one of the three training populations: males (n = 4648), females (n = 8100), and both sexes (n = 12 748). Traditional and genomic evaluations were computed using the software BLUP90IOD  [21, 22]. The convergence criterion was set to 10 -14 for all evaluations. Variance components used in all analyses were pre-computed by Cobb-Vantress Inc. using the same data and model as presented here.
For quality control, Fig. 2  contains the distribution of genomic relationships for full-sibs. The quality of genomic relationships can also be evaluated for other groups of siblings or by checking all genomic relationships against all pedigree relationships. Broiler chickens have large full-sib families and a greater gain in accuracy is expected from genomic evaluations over traditional evaluations in this case, provided genomic relationships are based on high-quality SNP genotypes. Although the expected relationship among full-sibs in the absence of inbreeding is equal to 0. 50, the average (SD) genomic relationship for this dataset was 0. 47 (0. 05). The standard deviation of 0. 05 and the skewed shape agree with theory  [12, 23]. However, if the distribution of genomic relationships is not centered on the expected relationship and is long-tailed, genotyping and pedigree errors are present.
g. , insufficient modeling of factors associated with T3, structure of the validation population, unaccounted selection, or sexual dimorphism  [35]. Our study ignored sexual dimorphism  [16, 35, 36 ] because genetic correlations between sexes were assumed to be equal to 1. If this assumption does not hold, realized accuracies could be higher with proper modeling. Followup research is required to evaluate the change in ranking for animals evaluated for different traits when sexual dimorphism is accounted for and genomic information is available. Realized accuracy and accuracy from the inverse of the coefficient matrix of the mixed model equations In spite of a large number of genotyped birds, the overall accuracies obtained for the dataset used in this study were below expectations. The maximum theoretical accuracy with PA is 0.
Acknowledgements This study was partially supported by  USDA Agriculture and Food Research Initiative  (Grant no. 2009-65205-05665  from the  USDA National Institute of Food and Agriculture Animal Genome Program). We would like to thank  Cobb-Vantress Inc. (Siloam Springs, AR)  for providing access to the dataset, and  Robyn Sapp  for helping with data details. Helpful comments from the anonymous reviewers are also gratefully acknowledged.
We are convinced that this study will open the way for multiple applications of this particularly interesting substrate as well as the dual copper-iminium activation. The Agence Nationale pour la Recherche (ANR-13-PDOC-0007-01), the Centre National de la Recherche Scientifique (CNRS) and the Aix-Marseille Universiteare gratefully acknowledged for financial support. The authors warmly thank Marion Jean and Nicolas Vanthuyne (Aix-Marseille Universite) for chiralphase HPLC analysis.
Samples were fi xed, stained for OCT4 expression (an indicator of pluripotency) and images acquired using an automated fl uorescence microscope. Images were automatically processed to quantify cell response to each polymer spot (using CellProfi ler software). This initial screen was used to identify 24 "hit" materials on the basis of their ability to support high HUES7 hESC attachment across six replicates whilst maintaining OCT4 expression (>90%) (Figure  1  b,c -"hit" monomer structures presented in Figure  S3  in the Supporting Information). To explore the effect of copolymerization the 24 hit monomers were mixed pairwise (70/30% v/v mixtures to explore each monomer as a major and minor component of each copolymer) to form a second-generation array design comprising 576 unique materials in triplicate (Figure  1 d ).
Poly(HPhMAco -HEMA) gave transparent coatings that did not crack, even after 1 month of incubation in medium. XPS analysis of poly(HPhMAco -HEMA) coatings confi rmed the composition of the material (Figure  1 k ). To evaluate hPSC expansion on these substrates we fi rst assessed whether preconditioning with culture medium or ECM proteins was required for hPSCs to retain pluripotency in six-well plates coated with poly(HPhMAco -HEMA). Attachment and distribution of hPSCs 24 h after seeding in StemPro was similar irrespective of preconditioning, as was the time required to reach confl uency (72 h). Therefore, preconditioning was omitted in subsequent experiments. This approach enabled cells to be cultured through fi ve serial passages with accutase on the poly(HPhMAco -HEMA) substrate maintaining expression of OCT4, TRA181, and SSEA4 in >93% cells, as measured by quantitative immunofl uorescence using an automated plate reader (Operetta) and high-content image analysis software (CellProfi ler), with retention of a 46,XY karyotype by G-banding 30 cells ( Figures 2 a,b and S5, Supporting Information).
Assistance with ToF-SIMS measurements from D. Scurr and XPS analysis from E. Smith and A. Barlow is kindly acknowledged. X-ray photoelectron spectra were obtained at the National EPSRC XPS User's Service (NEXUS) at Newcastle University, UK, an EPSRC Mid-Range Facility. Data collected as part of this project is available from https://rdmc. nottingham. ac. uk/ handle/internal/15 (DOI: 10. 17639/nott. 12). Note: The structure of the HEMA monomer was missing from Figure  1h  in the manuscript when originally published. This was added here as Figure  1l  on July 15 2015. The acknowledgements were also updated.
Acknowledgements A. D. C. and J. G. W. S. contributed equally to this work. D. C. H. was supported by the  UK Regenerative Medicine Platform  ( MR/K026666/1  and  MR/L022974/1 ). L. E. H. was supported by  BBSRC. C. D. was supported by  EPSRC ,  MRC ,  British Heart Foundation  ( Centre for Regenerative Medicine and Programme Grant ),  Heart Research UK and National Centre for the Replacement, Refi nement and Reduction of Animals in Research  ( NC3Rs ). M. R. A. gratefully acknowledges  EPSRC  (Grant No. EP/H045384/1 ) for funding, and the  Royal Society  for the provision of.
Genomics Data j o u r n a l h o m e p a g e : h t t p : / / w w w. j o u r n a l s. e l s e v i e r. c o m / g e n o m i c s -d a t a / the remaining hematopoietic cell fraction in these cultures. A cytometric control was carried out on the cells prior to performing molecular biology experiments. CD105, CD73 and CD90 marker positivity was verified to validate the mesenchymal cell phenotype. The negativity of the CD45 marker was also carried out to prove the absence of residual hematopoietic cells in culture. Each culture of mesenchymal stromal cell is isolated from the bone marrow of an individual. In total, the bone marrow samples were studied individually from 6 healthy donors (6 controls: GSM1084994, GSM1084995, GSM1084996, GSM1084997, GSM1084998, GSM1084999) and from 6 patients with primary myelofibrosis (6 PMF: GSM1085000, GSM1085001, GSM1085002, GSM1085003, GSM1085004, GSM1085005).
The hybridization procedure was performed using Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1. 65 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 h, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4 * 44k using Agilent's in hybridization chamber. The fluorescence signals were detected using Agilent's Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) v9. 1 was used to read out and process the microarray image files. The software determines feature intensities including background subtraction. The signal intensities from single experiment raw data lists are normalized by dividing the intensities values by their median. Normalized data were accessible on public database: (GEO submission number GSE44426, http://www.
ACS consensus determination From ARS coordinates (at G0), sequences were extracted from the reference genome to constitute an ARS database. In order to detect conserved motifs, GIMSAN  [68]  was run on the ARS library. The null model used by GIMSAN was built from sequences that were not in the ARS database. Motif sizes of 8, 14, or 20 bp were used as input parameters. When the 20-bp size was used, the consensus sequence was not significant beyond 14 bp, therefore a 14-bp consensus was kept. The GIMSAN output file was reformatted in the MEME file format. The 14-bp consensus was subsequently researched in all ARS sequences extended 200 bp upstream and downstream, using MAST  [69]. Recalculation of the S. cerevisiae ACS was made using the same approach as for C. glabrata, using as a library the 337 ARSs identified in the budding yeast genome  [70].
Phylogenetic analyses All chromosome C proteins were extracted from the Génolevures database  [71] , and compared to Naumovozyma castellii, Kluyveromyces polysporus, and Zygosaccharomyces rouxii complete proteomes. Gene families containing paralogous genes were removed, so that only orthologous families containing one and only one gene in each of the four yeast species were retained for subsequent comparisons. On chromosome C left arm, 105 genes were found to be in orthologous gene families, whereas 39 orthologous gene families were found on the right arm. In each family, the distance between the C. glabrata gene and each of its three orthologues was calculated and a Z-score was determined for this distance. Average Z-scores were slightly higher for genes located on the right arm than for the left arm for all three species (Fig.
05°, using a neutron wavelength λ = 1. 594 Å and a standard He cryostat. The NTO polymorph was also cooled down to 4 K, where a long scan was measured under the same conditions. The evolution of the magnetic structures was studied using the sequential patterns collected at each degree from 3 K up to 55 K on the high intensity D1B instrument. Each pattern was measured in the angular range 0°≤ 2θ ≤ 130°with a step-width of 0. 1°using λ = 2. 520 Å. Long scans were also taken at 3 K. The nuclear structures were refined from room temperature D2B data, using Rietveld analysis through the FullProf software package  19  and considering a Thomson-Cox-Hastings function to optimize the shape of the peaks. The magnetic symmetry analysis of the low temperature D1B data was performed by means of the program BasIreps.
1 top) and the IL-type model obtained from XRD refinement showed a poor fit to the neutron data. The data can be fitted assuming a LN-type ordering (R3c) with R wp = 4. 40% and R p = 3. 41% agreement factors. In order to clarify this situation, electron microscopy experiments were performed. The SAED patterns exhibit the reflection conditions: hkil: -h + k + l = 3n, hki0: -h + k = 3n, 000l: l = 3n, h -h00: h = 3n, h -h0l: h + l = 3n and the only feasible space groups are R3 ˉand R3 (Fig. 2a-c ). Fig. 2d  and e  show the microdiffraction of the [2 -1 -1 0] zone axis. The no periodicity difference between the zero and first order Laue zones (ZOLZ and FOLZ) indicates the absence of a c-glide plane, in agreement with XRD. Moreover, the analysis of the whole pattern (WP) of the [2 -1 -1 0] and [0 1 -1 0] zone axes (Fig.
The nature and strength of these interactions is defined by the Mn-O-Mn angles, which take the values of 104 (1)°, 113 (1)°and 123 (1)°. According to the Goodenough-Kanamori rules  27  these angles rule the antiferromagnetic interactions among d 5 cations, as observed in the magnetization curves (see SF3 † bottom). From the Rietveld refinement, it has been found that 9. 1% of A-sites are occupied by diamagnetic Sc 3+ cations, resulting in a magnetic dilution effect on the overall Mn 2+ sublattice. The magnetic structure of DPv_Mn 2 ScSbO 6 was determined by NPD using data from the D1B instrument. Additional magnetic neutron diffraction peaks are observed below 22 K. Fig. 5a  (bottom) shows the fit to the 3 K data. The magnetic reflections can be indexed with the k = [0 0 0] propagation vector in the P2 1 /n space group.
Irreducible representations and their basis vectors were obtained by using the program BASIREPS. Fig. 5b  shows the resulting magnetic structure. It can be described as an antiparallel orientation of Mn 2+ spins located in the ac-plane, with a total moment of 4. 54 (1) μ B at 3 K. The deviation of the spins with respect to the c axis has been calculated to be γ = 20. 34 (1)°, resulting in 1. 58 (1) μ B and 4. 26 (1) μ B components along the a-and c-axes respectively. The inset in Fig. 5a  shows the thermal evolution of the ordered magnetic moment, fitted to the critical law. The fitting results in T N = 22. 3 K and β = 0. 37, where β agrees again with 3D Heisenberg antiferromagnetic behaviour.
Results Using a combination of X-ray reectivity and high resolution diffraction, it is then possible to build up a full structural picture of the thin lm and the substrate/lm and lm/air interface. This article is licensed under a Creative Commons Attribution 3. 0 Unported Licence. calculations of the reectivity and the high angle diffraction are represented by solid red lines. These data were taken at the I07 beamline of the Diamond Light Source. The photon ux at a synchrotron source is between 4 and 5 orders of magnitude greater than a laboratory source and so allows one to probe the reectivity far further in q z and better resolve the fringes at higher angles. It is also ideal to study buried interfaces, which in our case will be the UO 2 /water interaction, since we are interested in the potential dissolution of UO 2 in groundwater.
The following data were taken on the I07 beamline at the Diamond Light Source, UK. The beam energy was monochromated to 17. 116 keV (50 eV below the U L 3 absorption edge), which was then focused in the vertical and horizontal directions to give an approximate beam size at the sample position of 200 mm Â 200 mm. The incident beam slits were set to 100 mm Â 100 mm for all measurements and the scattered photons were detected, using a Pilatus 100K detector. In Fig. 3 (a) and (b) we present data at three points in time, 30 s, 90 s and 120 s. The thin layer surface tension cell was lled with Milli-Q ultra pure type 1 water and the incident slits were set to a 200 micron square. The surface was exposed at This article is licensed under a Creative Commons Attribution 3. 0 Unported Licence. an incident angle of $0.
Acknowledgements The authors wish to thank  Paul Thompson  and  Laura Glaubes  for their assistance in the rst experiments on this project at the XMaS beamline  BM28 ,  ESRF. Ross Springell  would like to thank the  Royal Commission for the Exhibition of 1851  for the receipt of a research fellowship. The authors would also like to thank the  EPSRC  for funding the DISTINCTIVE consortium grant on nuclear waste.
MATERIALS AND METHODS Study design. The Elderly Woman GINECO Trial 3 was an open-label phase II multicentric trial approved by the Independent Ethics Committee of Lyon University Hospital (EUDRACT No. 2006-005504-13). The study design, population and assessments have been described elsewhere  [1]. Written informed consent was obtained from each patient and included authorization for collection of a blood sample for TL measurement. Patients were treated with up to six cycles of carboplatin AUC5 (5 mg/mL/min for 30 min every 3 weeks). In this ancillary study, TL at inclusion was evaluated, along with the impact of TL on patient outcome and the correlation between TL and geriatric covariates. Patient population. Eligible patients were ≥70 years old, with a life expectancy ≥3 months, and histologically or cytologically proven epithelial FIGO stage III-IV ovarian cancer.