dataesr/scientific-paragraphs-categorization huggingface dataset:
Molecular evolution analysis The sequences employed for the evolutionary survey were retrieved from the NCBI, Ensembl and JGI databases. Human RAN was the initial query sequence employed for tBlastn searches  [42]  from unicellular eukaryotes to vertebrates, and reciprocal Blasts were carried out. The identity of Ran proteins was further assessed by using the domain bank of PROSITE database  [43]  and manually aligned as in Coppola et al. [44]. Synteny between Ran and Stx was mapped manually through the examination of public databases (Ensembl, NCBI). The Stx and Ran proteins were aligned employing Clustal Omega  [45]  and the phylogenetic reconstructions were computed with the Maximum Likelihood (ML) estimation using MEGA6 with 1,000 replicates and the WAG matrix (γ = 4 and proportion of invariable sites = 0.
We have measured direct photons for pT < 5 GeV/c in minimum bias and 0%-40% most central events at midrapidity for Cu+Cu collisions at √ s N N = 200 GeV. The e + e -contribution from quasi-real direct virtual photons has been determined as an excess over the known hadronic contributions in the e + e -mass distribution. A clear enhancement of photons over the binary scaled p+p fit is observed for pT < 4 GeV/c in Cu+Cu data. The pT spectra are consistent with the Au+Au data covering a similar number of participants. The inverse slopes of the exponential fits to the excess after subtraction of the p+p baseline are 285±53(stat)±57(syst) MeV/c and 333±72(stat)±45(syst) MeV/c for minimum bias and 0%-40% most central events, respectively. The rapidity density, dN/dy, of photons demonstrates the same power law as a function of dN ch /dη observed in Au+Au at the same collision energy.
A detail description on constraint parameterization can be found in Ref. [25]. The p+p data points measured by the EMCal in 4 < p T < 10 GeV/c are included in the fit in addition to the virtual photon measurement covering p T < 6 GeV/c. Here the lowest p T data point is just an upper limit. The best fit gives χ 2 /NDF=18. 9/17, which is the minimum obtained by variation of the p Tcorrelated errors. The uncertainty of the p+p fit is calculated using the error matrix of the fit parameters and is indicated as bands on the scaled p+p fits. A different empirical parameterization, employed in Ref. [9] , was tested as well. We treat the small deviation we find above 1 GeV/c as a maximum-extend error. We divide the deviation by √ 12 and add it in quadrature to the uncertainty of the fit. An exponential fit to the excess yield above the scaled p+p fits gives inverse slopes of 285±53(stat)±57(syst) MeV/c for MB and 333±72(stat)±45(syst) MeV/c for 0%-40% centrality.
V. SUMMARY AND CONCLUSIONS Low-p T direct photons have been measured using the virtual photon method for MB and 0%-40% most central collisions in √ s N N = 200 GeV Cu+Cu collisions. A clear excess yield of direct photons over the binary-scaled p+p baseline is seen for Cu+Cu as in the previously reported Au+Au results. The Cu+Cu direct photon p T spectra are consistent with the Au+Au data for similar N part. The exponential fits to the excess over the binary-scaled p+p baseline give inverse slopes of 285±53(stat)±57(syst) MeV/c for MB and 333±72(stat)±45(syst) MeV/c for 0%-40% centrality. The Cu+Cu data points improve our knowledge of the system size dependence of the excess yield of the direct photons, especially in the small-N part region. The Cu+Cu results on dN/dy for p T > 1 GeV/c follow the same dN ch /dη dependence as the Au+Au data as de-scribed by a simple power law.
ACKNOWLEDGMENTS We thank the staff of the  Collider-Accelerator and Physics Departments at Brookhaven National Laboratory  and the staff of the other PHENIX participating institutions for their vital contributions. We acknowledge support from the  Office of Nuclear Physics in the Office of Science of the Department of Energy , the  National Science Foundation ,  Abilene Christian University Research Council, Research Foundation of SUNY, and Dean of the College of Arts and Sciences, Vanderbilt University (U. S. A) ,  Ministry of Education, Culture, Sports, Science, and Technology  and the  Japan Society for the Promotion of Science (Japan) ,  Conselho Nacional de Desenvolvimento Científico e Tecnológico and Fundação de Amparo à Pesquisa do Estado de São Paulo (Brazil) ,  Natural Science Foundation of China (People's Republic of China) ,  Croatian Science Foundation and Ministry of Science and Education (Croatia) ,  Ministry of Education, Youth and Sports (Czech Republic) ,  Centre National de la Recherche Scientifique ,  Commissariat à l' Énergie Atomique , and  Institut National de Physique Nucléaire et de Physique des Particules (France) ,  Bundesministerium für Bildung und Forschung ,  Deutscher Akademischer Austausch Dienst , and  Alexander von Humboldt Stiftung (Germany) ,  J.
Four partial models were estimated. The first three models examined releasing additional thresholds based on changes in the χ 2 value, starting with those for item 10, followed by those for item 12, and item 5 (see Table  1 ) 5. These three items were 5 Modification indices were used to identify thresholds that would lead to the biggest improvement in model fit if they were allowed to differ between the groups. Modification indices reflect the change in χ 2 that would occur if a certain threshold would be allowed to vary between the two groups. Higher Modification indices indicate a larger decrease in χ 2 and thus a larger improvement of model fit. all part of the Psychosocial Issues subscale of the CushingQoL. For each of these models, the χ 2 difference test indicated that the model still fit the data worse than the metric model from phase 2.
Gel imaging After SDS-PAGE, the gels were scanned with a Typhoon 9400 Imager (GE Healthcare) at 200 μm resolution (pixel size) using appropriated excitation and emission wavelengths, filter and photomultiplier (PMT) sensitivity for each dye (PMT values: 415, 400 and 430 for Cy2, Cy3 and Cy5, respectively). Gel images were processed with the DeCyder software (v5. 00. 08; GE Healthcare), which allows quantification, gel matching and statistical analyses. First, the Differential In-gel Analysis (DIA) module co-detected the 3 images from a single gel (i. e. , the internal standard as the primary image and two samples as secondary and tertiary images, respectively), measured spot volume in each image, and expressed these values as a spot ratio of the internal standard. Second, the Biological Variation Analysis (BVA) module used those images to match protein spots across comparable gels, using the internal standard for gel-to-gel matching.
Protein identification Preparative gels were matched with the DIGE images to edit the picking list. Spots with a very weak intensity or bad-defined in preparative gels were excluded from the list. Tentative identification was thus performed on 182 spots. These spots were excised, digested, and peptides were processed as previously described  [18]. Mass fingerprints were acquired using a matrix-assisted laser desorption ionization-time (MALDI) combined with a time-of-flight (TOF)/TOF mass spectrometer (Ultraflex, Bruker Daltonics). When applicable, precursor ions in the MALDI-MS mass spectrum were subjected to fragment ion analysis in the tandem (MS/MS) mode. Lists of monoisotopic peaks were submitted to SwissProt sequence database restricted to Mammalia taxonomy (65,132 sequences) and NCBI non-redundant sequences databases of mammalian proteins (845,127 sequences) using the MASCOT search engine (version 2.
2. 07; http://www. matrixscience. com) and stored in ProteinScape bioinformatics platform (v1. 3 SR2; Burker Daltonics). Search conditions were as follows: initial rather open mass window of 70 ppm for an internal calibration, one missed cleavage allowed, fixed modifications of cysteines by iodoacetamide, and methionine oxidation as variable modifications. Results were scored using the probability-based Mowse score. A score greater than 61 for the SwissProt database and 72 for the NCBInr database, respectively, was retained for identification. For the MS/MS experiment, the mass tolerance was set at 100 ppm for the parent ion and at 0. 5 Da for the fragment ions. A score greater than 27 indicated peptides with significant homology, and scores greater than 32 (for the SwissProt database) or 43 (for the NCBInr database) indicated a significant identification.
Gene-ontology based pathway analysis Lists of identified proteins were clustered using annotation categories included in Gene Ontology (GO) Biological Process, KEGG Pathways, and PIR SuperFamily Names, which were collected in the DAVID knowledgebase (Database for Annotation, Visualization and Integrated Discovery bioinformatics tool; v6. 7, https://david. ncifcrf. gov/). Orthologous gene identifiers for Homo sapiens were associated to the lists of identified proteins and further explored with the functional annotation clustering tool. Significance levels of functional annotations over-represented were appreciated by the modification of Fisher's exact test (P < 0. 05) and the enrichment calculated for individual specific terms in each functional group. To order the relative importance of the gene groups, the E score was calculated by minus log transformation of the geometric mean of the modified Fisher Exact EASE Scores of all the annotation terms that belong to the cluster.
Expression levels of selected genes by qPCR in adipose tissue Expression levels of encoded proteins that were identified with differential abundance due to age and(or)genotype by proteomics were investigated by qPCR. Other selected genes encode proteins that cannot be visualized on 2D gels: the fatty acid synthase (FASN), a whole enzymatic system composed of two identical 272 kDa multifunctional polypeptides acting in lipogenesis, and well-known transcriptional regulators of adipogenesis and lipid metabolism. Gene primers (Additional file 3) were designed using PrimerExpress software (version 3. 0, Applied Biosystems, Foster City, CA, USA) from pig sequences, taking into account intron-exon organization. Samples of subcutaneous adipose tissue were homogenized in Trizol reagent (Invitrogen, Cergy-Pontoise, France) using a TissueLyser (Qiagen, Courtaboeuf, Paris) and treated as described previously  [23].
Statistical analysis Protein spots abundance, triglycerides content, expression levels of target genes in adipose tissue, and plasma concentrations of nutrients and IGF-I were compared by ANOVA for the effects of developmental age, fetal genotype and the interaction between age and genotype (A × G), by using the GLM procedure of the SAS software (SAS Institute, Cary NC, New-York). Protein spot abundance values were analyzed after logarithmic transformation to fit normal distribution. A P-value of less than 0. 05 was used as the cut-off. Lists of spots identified with a differential abundance due to age, fetal genotype and(or) an interaction effect between age and genotype were edited in picking lists. Benjamini-Hochberg (BH) multiplicity correction of the P-values for a control of the FDR was also calculated.
Taken together, these data suggest that ROS generation was lower and/or that ROS scavenging was more effective in MeiS adipose tissue. The increased abundance of CLIC1, a chloride intracellular channel whose knockdown in cells led to increased sensitivity to hydrogen peroxide  [42] , was another element supporting this assumption. Differences in the abundance of adipose proteins with regulatory roles in cellular growth were revealed between fetal genotypes At the two examined time points of gestation, proteins participating in the regulation of cytoskeleton organization and a b Fig. 6  Plasma concentrations of IGF-I and nutrients in purebred and crossbred Large White or Meishan fetuses gestated by sows of either breed. Blood samples taken from 4 fetal genotypes at d 90 or d 110 of development were analyzed (n = 6 per age and per genotype).
Acknowledgements The authors are very grateful to all the staff of experimental pig facilities ( INRA, GenESI, Saint-Pierre d'Amilly, France ) for expert assistance in surgeries and  Sandrine Tacher ,  Christine Tréfeu ,  Sophie Daré-Michelot  and  Nathalie Bonhomme  ( INRA, PEGASE, Saint-Gilles, France ) for laboratory technical analyses.
03 (1H d, J = 1. 5 Hz) in compound 1; δ H 7. 67 (1H d, J = 1. 6 Hz) in compound 4) and the replacement of the indole ∆ 2 double bond by a hydroxyl group at C-3 and a carbonyl group at C-2. The latter was confirmed by the HMBC correlation observed between H-8 and C-2 (Figure  2 ). The structure proposed for compound Further examination of the NMR data revealed that spectroscopic data of compound 1 were very similar to those of compound 4  [10] , with the main differences being the upfield shift of the H-7 resonance (δH 7. The configurations of two chiral centers at C-3 and C-12 in compound 1 were determined using a combination of techniques. The absolute configuration of C-3 was determined by comparison of the ECD spectra (Figure  3 ) of the hydrogenolysis product of compound 1 with the compound (R)-3-propyldioxindole  (8) , which share the dioxindole core structure.
Anti-Inflammatory Activity To evaluate the potential anti-inflammatory activity of compounds 1-7, their effects on DC secretion of the pro-inflammatory cytokine IL-12p40 and the anti-inflammatory cytokine IL-10 was determined. The tested compounds did not show cytotoxic effects on the DCs, with the cell viability being more than 90% in the presence of the compounds at 10 µg/mL (data not shown). Compound 4 inhibited by more than 50% secretion of both IL-12p40 and IL-10. Compounds 2 and 6 decreased DC secretion of IL-12p40 by 29 and 32%, respectively, without affecting secretion of IL-10, which suggests an overall anti-inflammatory activity of these compounds. Compound 3 slightly decreased DC secretion of IL-12p40 (13%) but increased secretion of the anti-inflammatory cytokine IL-10 by 40%, which also suggests an anti-inflammatory activity.
Anti-Inflammatory Activity To evaluate the potential anti-inflammatory activity of compounds 1-7, their effects on DC secretion of the pro-inflammatory cytokine IL-12p40 and the anti-inflammatory cytokine IL-10 was determined. The tested compounds did not show cytotoxic effects on the DCs, with the cell viability being more than 90% in the presence of the compounds at 10 μg/mL (data not shown). Compound 4 inhibited by more than 50% secretion of both IL-12p40 and IL-10. Compounds 2 and 6 decreased DC secretion of IL-12p40 by 29 and 32%, respectively, without affecting secretion of IL-10, which suggests an overall anti-inflammatory activity of these compounds. Compound 3 slightly decreased DC secretion of IL-12p40 (13%) but increased secretion of the anti-inflammatory cytokine IL-10 by 40%, which also suggests an anti-inflammatory activity.
Extraction and Isolation The frozen sponge material was cut into small pieces and lyophilized prior to extraction with CH 2 Cl 2 :CH 3 OH (v/v, 1:1) mixture (3 × 20 L, each for 24 h) at room temperature. The combined extracts were concentrated under vacuum to yield a dark gum and stored at -20 • C. The crude extract (1. 8 g) was submitted to a modified Kupchan partition to yield five subextracts, namely hexane (fraction A), chloroform (fraction B), dichloromethane (fraction C), n-butanol (fraction D), and water (fraction E). Each fraction was analyzed by UPLC-qTOF-MS before preparative-scale isolation work commenced and the data were processed and analyzed by MassLynx programme and compared to available references in ChemSpider database  [51]  and SciFinder Scholar (Chemical Abstracts Service, Columbus, OH, USA).
Statistical Analysis Data are presented as the mean values ± standard error of the mean (SEM). As the data were not normally distributed, Mann-Whitney U test or Kruskal Wallis one-way ANOVA with Tukey's post-hoc test were used to determine statistical differences between treatments (SigmaStat 3. 1, Systat Software, San Jose, CA, USA) and p < 0. 05 was considered as statistically significant.
Acknowledgments: The authors would like to thank  Hans Tore Rapp  at the  University of Bergen  for the identification of animal material,  Nathalie Kringlstein  for technical assistance,  Annaliese Franz  at  University of California, Davis , for the generous gift of 8a,  Sigridur Jonsdottir  at  University of Iceland  for running NMR spectra on a Bruker AM-400 spectrometer,  Finnur Freyr Eiriksson  and  Margret Thorsteinsdottir  for running UPLC-qTOF-MS and  Kare Telnes  for giving the permission to use the sponge picture in the Graphical abstract.
Fixation of RTX to CD20, density of CD20 molecules, GM1 and SM levels, complement inhibitor proteins CD55, CD59 and Factor H were evaluated in CLL cells in the two groups of patients. Although these preliminary data are promising, this study has potential limitations. The developed in vitro assay necessitates long term incubations with RTX and we could not exclude that chemotherapy protocols have an effect on sialylation and CDC regulator expression. The sample size is quite small and is heterogeneous with respect to treatments. The analysis of the relationship between CDC status and clinical response were not adjusted for treatment, cytogenetic status, and immunoglobulin mutational status. In future studies it will be important to investigate dependence to these factors because existing data suggest that they are contributing factors in CLL relapse.
RTX was introduced as first line treatment in combination with fludarabine and cyclophosphamide (RFC, n=28) or with bendamustine (RB, n=6). Response to therapy was assessed according to the 2008 IW-CLL guidelines  [71]  by determining the CR at the end of RTX infusions, TTR was defined as the time from RTX initiation to the time of disease progression (≥5 ×10 9 peripheral B cells/L), and the OS rate from the inclusion to death from any cause. Blood was also withdrawn from 21 healthy volunteers. Consent was obtained from all individuals and the protocol approved by the Ethical Board at the Brest University Medical School Hospital (https://clinicaltrials. gov/ct2/show/NCT03294980; CRB Brest, collection 2008-214), in accordance with the Declaration of Helsinki.
Mutational status of IGHV As previously described  [68, 69] , the IGHV gene mutation status was determined by sequencing after conducting a PCR multiplex amplification. Briefly, for multiplex PCR, 100ng of genomic DNA, 0. 25μl of Ampli Taq Gold DNA Polymerase (Applied Biosystems, Foster City, CA, USA), 10pmol of each primer, 0. 2mM dNTP Mix, 1. 5mM MgCl2, 1x PCR Buffer II, were adjusted to 50μl with DNase/RNase free ultrapure distilled water. Next, PCR products were visualized on 2% agarose gel, and purified with ExoSAP-IT PCR product cleanup kit (Affymetrix, High Wycombe, UK). Finally, amplicons were sequenced with a Big Dye Terminator v3. 1 cycle sequencing kit (Applied Biosystems). Results were analyzed with the database IMGT/HighV-Quest (The international ImMunoGeneTics information system, Montpellier) and a homology sequence >98% defined an UM status.
ACKNOWLEDGMENTS The authors would like to thank  Mariam Hammadi  and  Charlotte Laot  for their technical help,  Geneviève Michel  and  Simone Forest  for secretarial assistance, and  Dr Wesley H Brooks  for editorial assistance (Tampa, USA). The authors thank the  Brest Biological Resources Center   BB-0033-00037  (" CRB Santé de Brest" ) for providing high quality and annotated samples and  Cragg MS  ( Southampton, UK ) for the generous gift of  B1.
10 µm for both cases. The derived complex refractive indices are 1. 52(±0. 05) + i0. 021(±0. 010) and 1. 55(±0. 05) + i0. 028(±0. 014) for Palaiseau and Lille data. The retrieved aerosol properties were used to calculate the direct radiative forcing (DRF) effect specific to the UTLS aerosol layers. The simulations derive daily net DRF efficiency of -79. 6 Wm -2 τ -1 at the bottom of the atmosphere for Lille observations. At the top of the atmosphere, the net DRF efficiency is -7. 9 Wm -2 τ -1. The results indicate that the UTLS aerosols strongly reduce the radiation reaching the terrestrial surface by absorption. The heating rate of the UTLS layers is estimated to be 3. 7 Kday -1. The inversion of Palaiseau data leads to similar results. The heating rate predicts a temperature increase within the UTLS aerosol layer, which has been observed by the radiosonde temperature measurements.
, 2014). As a branch of GRASP algorithm, GARRLiC (Generalized Aerosol Retrieval from Radiometer and Lidar Combined data) algorithm was developed for the inversion of coincident single or multi-spectral Lidar and sun photometer measurements  (Lopatin et al. , 2013; Bovchaliuk et al. , 2016). The two main modules of GARRLiC/GRASP are the forward model and the numerical inversion module. The forward module simulates the atmospheric radiation by using radiative transfer and by accounting for the interaction between light and trace gases, aerosols and underlying surfaces. The numerical inversion module follows the multi-term least squares method strategy and derives several groups of unknown parameters that fit the observations. Therefore, we can use the forward model of GARRLiC/GRASP to estimate the radiative effect of the UTLS aerosols.
For the layer observed in Lille on 24 August, the top and base of the UTLS are selected as: 18. 4 km and 16. 7 km and for Palaiseau observations, they are 20 km and 17. 0 km. At the top of the atmosphere, the net DRF flux is estimated to be -1. 2 Wm -2 and -3. 5 Wm -2 for Lille and Palaiseau data, respectively. The corresponding forcing efficiencies are -7. 9 Wm -2 τ -1 and -21. 5 Wm -2 τ -1. At the bottom of the atmosphere, the net DRF flux is estimated to -12. 3 Wm -2 for Lille data and -14. 5 Wm -2 for Palaiseau data. The corresponding forcing efficiencies are -79. 6 Wm -2 τ -1 and -89. 6 Wm -2 τ -1. We noticed that the difference in net DRF flux between the layer top and layer base is significant. For Lille data, we obtained 9. 9 W/m 2 of difference between the top and the base of the UTLS layer and for Palaiseau, we obtained 11.
1 W/m -2. Because of the high imaginary part of refractive indices, the UTLS aerosols have the capacity of absorbing the incoming radiation, thus reducing the upward radiation at the top of the UTLS layer and the downward radiation at the base of the UTLS aerosol layer. The heating rate of the UTLS layer is estimated to be 3. 3 K/day for Palaiseau data and 3. 7 K/day for Lille data. This qualitatively explains the increase of temperature within the UTLS layer, as observed by the radiosonde measurements shown in Figure  2.
(2007b). In particular, the retrieved particle size agrees well with the observed smoke aerosol transported from Canada to Europe  (Wandinger et al. , 2002; Müller et al. , 2005). Müller et al. (2007b)  found that the effective radius increased from 0. 15 -0. 25 µm (2 -4 days after the emission) to 0. 3 -0. 4 µm after 10 -20 days of transport time, which is consistent with our results. Colarco et al. (2004)  assessed that the coagulation process during the transport could explain the growth of particle size and the decrease of extinction-related Ångström exponent. The real part of the refractive indices obtained in this study is 1. 52±0. 05 for Palaiseau data and 1. 55±0. 05 for Lille data, without considering the spectral dependence. The values are consistent with the results for smoke aerosol in the troposphere  (Dubovik et al.
Mallet et al. (2008)  studied the radiative forcing of smoke and dust mixture over Djougou and derived -68 Wm -2 τ -1 to -50 Wm -2 τ -1 for the DRF efficiency at the bottom of the atmosphere. The uncertainties of the DRF estimation could be large, because the uncertainty of the retrieved microphysical properties is high. Our results show stronger forcing efficiencies, but are comparable with the values in the publications. Additionally, the mean heating rate of the UTLS aerosol layer is estimated to be 3. 7 K/day for Lille data and 3. 3 K/day for Palaiseau data, which qualitatively supports the temperature increase within the UTLS smoke layer. The warming effect in the layer is potentially responsible for the upward movements of soot-containing aerosol plumes observed by  Laat et al. (2012).