dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments We thank  Stefano Frixione  for his suggestions and interest at the early stage of this project. D. P. , I. T. and M. Z. acknowledge also  Fabio Maltoni  for his strong encouragement and support in pursuing this study. The work of M. C. is supported in part by grants of the DFG and  BMBF. The work of D. H. and A. M. is supported by the  UK STFC  grants  ST/L002760/1  and  ST/K004883/1. A. M. is also supported by the  European Research Council   Consolidator Grant  " NNLO-forLHC2 ". The work of D. P is partially supported by the  ERC  grant  291377  "LHCtheory: Theoretical predictions and analyses of LHC physics: advancing the precision frontier" and by the  Alexander von Humboldt Foundation , in the framework of the  Sofja Kovalevskaja Award Project  " Event Simulation for the Large Hadron Collider at High Precision ".
The work of I. T. is supported by the  F. R. S. -FNRS "Fonds de la Recherche Scientifique" (Belgium)  and in part by the  Belgian Federal Science Policy Office  through the  Interuniversity Attraction Pole   P7/37. The work of M. Z. is supported by the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Sklodovska-Curie  grant agreement No  660171  and in part by the  ILP LABEX  ( ANR-10-LABX-63 ), in turn supported by  French  state funds managed by the  ANR  within the  "Investissements d'Avenir" programme  under reference  ANR-11-IDEX-0004-02.
HHsearch  (Söding, 2005)  against the PANTHER protein family database  (Mi et al. , 2016)  reported the RING finger protein family PTHR22663 (which includes human ZHP3/RNF212 and RNF212B, budding yeast Cst9/Zip3, and Caenorhabditis elegans Zhp-3 and F55A12. 10) as the only significant hit (E = 0. 0014) and the only hit with E < 0. 01. Using the HHpred server  (Söding et al. , 2005)  to search against a database of nine eukaryotic proteomes resulted in three significant hits: Drosophila melanogaster CG31053, C. elegans F555A12. 10, and human ZHP3, all of which belong to the PTHR22663 family. HMMsearch against the National Center for Biotechnology Information nonredundant protein database obtained a single significant hit in addition to TTHRM_00049220, namely protein XP_002996515 of the microsporidian Nosema ceranae, which is also a member of the PTHR22663 family.
5) containing 1% Triton X-100, once with wash buffer without Triton X-100, and then four times with 50 mM ammonium bicarbonate. All buffers except for ammonium bicarbonate contained cOmplete proteinase inhibitor (Roche, Indianapolis, IN). Beads were sent for mass spectrometry analysis, and Zhp3 was eluted from a small aliquot for Western blotting with an anti-HA antibody to confirm precipitation. Note added in proof. Gene TTHERM_00460720 (SA15 ) is now named BIME1 in the Tetrahymena Genome Database (http://ciliate. org/).
Database and fitting parameters The measured FTIR spectra result from infrared absorption by a molecular population which is not in thermal equilibrium. To be able to accurately analyze these spectra, an algorithm has been developed to calculate and fit these non-equilibrium infrared transmittance spectra. The basic flowchart for the algorithm can be seen in figure  2. The algorithm makes use of the HITEMP-2010 database  [26] , which contains transition energies, Einstein A coefficients, broadening constants, etc, of a wide variety of molecules. Transition data for CO 2 is available up to 6 7 3 n =  , while vibrational transitions of CO are documented as far as  14 15  CO n = . Transitions of both these vibrational quanta (i. e. , , , , 1 l l 1 2 3 1 2 3 2 2 n n n n n n  + ( ) ( ) and 1 CO CO n n  + ( ) ( )) are present in the region of interest of 1975-2400cm -1.
It prevents the normalization being significantly influenced by the previously mentioned overpopulation of higher vibrational states resulting from the Treanor distribution. T T T i rot th = = , equation ( 3. 2. 2. Calculate line strengths. The next step is the calculation of the line strength, starting from the Einstein A coefficient A ul for spontaneous emission from upper state u to lower state l. This coefficient is listed in the HITEMP database. The line strength S j of transition j can be calculated as follows  [31] : S I g A c N g N N g N 8 , 1 2 j a j rot,u ul 2 l l u u p n = - ⎛ ⎝ ⎜ ⎞ ⎠ ⎟ ˜( ) where I a is the fractional abundance of the isotopologue as listed in  [31] , j n ˜is the transition energy as listed in the HITEMP database, and g l and g u are the total rovibrational degeneracy of the lower and upper state, respectively 6.
Equation (  8 ) is now used to compute the lower and upper state densities, N l and N u , respectively. Although equation (  12 ) is derived using the relations between spontaneous emission and stimulated emission and absorption coefficients under the assumption of thermalequilibrium black-body radiation, it is also valid in situations where there is no thermal equilibrium  [37]. 3. 2. 3. Apply temperature and pressure broadening. The HITEMP database lists for each line a self-and airbroadened half-width, as well as a CO 2 -broadened halfwidth for CO. Broadening due to pressure from other molecular species is approximated as if it were from air. The Lorentzian pressure broadening profile is convolved with the Gaussian shaped Doppler broadening and multiplied by the line strength S j. This results in a Voigt-shaped cross section j s n ( ˜), unique for every line j  [38, 39].
However, g rot,u is used because of how A ul is determined in the HITEMP database  [31]. where L is the length of the reactor. The transmittance is constructed from a product of four exponents, i. e. the contributions of thermal and non-thermal CO 2 and CO. 3. 2. 5. Apply instrumental broadening. In the last step, the broadening of the instrument is applied. The final transmittance is obtained by convolving T n ˜with the instrumental line shape of the FTIR. A three-term Blackman-Harris is used as the apodization function for the Fourier transform, resulting in a spectral line shape which can be very well approximated by a Gaussian  [41]. For the spectrometer settings used in this study, the full-width at halfmaximum of this Gaussian is determined to be 0. 27cm -1.
Adding thermal-volume fraction Figure  4  shows a measurement taken at 2ms in the discharge of a 5-10ms on-off duty cycle of 50mA at 6. 7mbar. The spectrum is fitted once with f th set to 0 and once with the default value of 0. 26, in order to illustrate the effect of adding a thermal-volume fraction to the calculation of the transmittance spectra. Both fits are respectively shown in panels (a) and (b), including residuals. The effect of adding thermal gas is most visible around 2349cm -1 , which is the central wavenumber of the line structure of the 0, 0 , 0 0, 0 , 1 0 0  ( ) ( ) transition of C O 12 16 2. In panel (a), symmetrically around this point an oval shape indicates a discrepancy between data and fit. This discrepancy is further exposed in the residual. The general shape of the residual is typical for a transmittance spectrum of CO 2 in the vibrational ground state, which is fitted with a too high rotational temperature.
In panel (b), this discrepancy has disappeared by adding to the fitting conditions that 26% of the gas in the reactor volume is thermal. The temperature of the thermal gas fraction is fitted at 363K, while the rotational temperature of the non-thermal fraction increased from 661K in (a) to 729K in Figure  3. A fit, using the algorithm, on CO 2 data from Dang et al  [9]. Transmission data is digitally extracted from the article and divided by an artificial background. (b). Also T 1,2 and T 3 from the fitted spectra significantly increase from (a) to (b). These temperatures largely represent the ratio of the ground state density over the density of vibrationally excited states. At temperatures below 400K, thermally distributed CO 2 and CO mainly populate the ground state (82% and 99. 96%, respectively).
Background and introduction -Schefflera is the largest genus in Araliaceae, with approximately 900 species. However, recent studies have shown that Schefflera is polyphyletic, representing no fewer than five distinct clades, each corresponding to a specific geographic region: Asia, continental Africa plus Madagascar, Melanesia, the Neotropics, and a small clade in several archipelagos of the Pacific Ocean. The Afro-Malagasy clade comprises 49 species distributed throughout tropical Africa, Madagascar, the Comoro Islands, and the Seychelles. Previous studies have suggested that this group is monophyletic, identifying two subclades (which largely correspond to informal morphogroups identified as 'Meiopanax' and 'Sciodaphyllum'). Methods -Using sequence data from nuclear rDNA and chloroplast spacers derived from 33 of the 49 currently circumscribed species of Afro-Malagasy Schefflera, this study tested the group's monophyly and that of its two informal subgroups.
We utilized alternative partitioning schemes to explore the combinability of datasets from the distinct genomic regions sampled. Key results -Our results support the monophyly of Afro-Malagasy Schefflera and its two informal subgroups, 'Meiopanax' and 'Sciodaphyllum'. Each of these subgroups include species from both continental Africa and Madagascar, although species diversity in 'Meiopanax' is heavily based in Madagascar. In 'Sciodaphyllum', species diversity is much greater in continental Africa, despite evidence for more widespread dispersal events that have led to subsequent speciation in both Madagascar and the Seychelles Islands. Among several species that appear to be non-monophyletic, S. myriantha stands out as particularly problematic. This species, which shows very little morphological variation across its wide distribution in Africa and Madagascar, forms two subclades, one restricted to Africa, and another from Madagascar that also includes two additional, morphologically distinctive species.
) and then purified using the Mul-tiScreen 384 SEQ filtration system (Millipore Corp. ) or the BigDye XTerminator purification kit (Applied Biosystems Corp. ). Capillary gel electrophoresis of cleaned products was performed on a MegaBACE 1000 DNA Sequencing System (GE Healthcare, Inc. ) or an ABI 3730 DNA Analyzer (Applied Biosystems Corp. ) and then assembled and edited using the Sequencher 4. 7 software package (Gene Codes Corp. ). Sequence alignment was adjusted manually following an initial alignment using ClustalX  (Thompson et al. 1997). All sequences have been deposited in the GenBank database.
Phylogenetic analyses Three complementary approaches to phylogenetic analysis were used in this study, maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI). Five separate datasets were used, (1) ITS, (2) ETS, (3) combined ITS + ETS, (4) the plastid markers (trnK-rps16, ndhF-rpl32, and rpl32-trnL, treated together), and (5) a set combining sequences from all five markers. To test for congruence among the separate datasets, the incongruence length difference (ILD) test of  Farris et al. (1994)  was performed using the partition homogeneity test in PAUP* 4. 0b10  (Swofford 2002). Three partitions were established, representing the ITS, ETS, and combined plastid markers. An ILD test was   Fiaschi & Plunkett (2011). b  Linder et al. (2000). c  White et al. (1990). d  Wen & Zimmer (1996).
The model-based analyses were performed using GARLI (version 2. 01; Zwickl 2006) for ML and MrBayes (version 3. 2. 6; Ronquist & Huelsenbeck 2003)  for BI. ML analyses were performed by applying most of the default parameters in GARLI and MrBayes and the appropriate model of sequence evolution selected according to the corrected Akaike Information Criterion (AICc) using the program PartitionFinder (version 1. 1. 1; Lanfear et al. 2012). For the ML analyses, the maximum number of generations was set to 5 million, saving the ML tree with the best score. ML bootstrap values were also calculated using GARLI (with the same parameters) with 100 bootstrap replicates. Maximum Likelihood bootstrapping analyses and Bayesian inference (for four million generations, sampling every 1,000 generations) were both run using the CIPRES Science Gateway  (Miller et al.
Sequence characteristics A total of 162 accessions were sequenced for each of the five DNA spacer regions employed in this study, although four specimens did not amplify for the ndhF-rpl32 marker and one specimen did not amplify for the trnK-rps16 marker (table 2). After examining the sequences for redundancy, 37 samples were removed because they shared identical sequences with others in the dataset. The remaining 125 accessions representing 33 species were used for phylogenetic analyses. Uncorrected pairwise distances were calculated between all sequences for each molecular marker (treating the three plastid markers separately). Pairwise distances were also calculated for plastid markers. Sequence characteristics for each marker, including the primer name and sequence, are provided in table 2.
Significant incongruence among the three partitions established in this study could not be rejected based on results of the ILD test (p = 0. 01), suggesting that the partitions may not be combinable. There is a wide body of literature weighing the merits of the ILD test  (Yoder et al. 2001 , Barker & Lutzoni 2002 , Hipp et al. 2004 ) and suggesting that it be used in combination with the consideration of other factors. Although significant incongruence could not be rejected in this study, taken together, our analyses support the topologies produced by each partition and individual cases of incongruence do not reflect 'hard' incongruence between datasets (see  Farris et al. 1994 ). Thus we conclude that the incongruence detected by the ILD test is likely an artifact of insufficient data and we chose to compare topologies resulting from the analysis of each nuclear marker independently and from three concatenated matrices comprising both nuclear markers, all three plastid markers, and the combined nuclear and plastid markers, respectively.
What little incongruence exists does not appear to significantly alter conclusions regarding species relationships among Afro-Malagasy Schefflera. Rather, the concatenated dataset disrupts what appears to be a soft polytomy produced by limited variation in chloroplast markers, and our measure of incongruence may also be affected by missing data (table 2). To explore the effects of combining the datasets, all three partitions were concatenated and analysed simultaneously. We have provided results from the strict consensus of MP analyses from each of the three concatenated datasets (figs 1-3) as well as the results from the ML analysis for the combined nuclear (ETS+ITS) dataset because it shows branch lengths for groups resolved in this analysis (fig. 4 ). Results from all other analyses are provided as electronic appendices, including the strict consensus trees from the separate MP analyses of ETS and ITS (electronic appendix 1A & B), ML analyses for all remaining datasets (electronic appendix 2A-D), and majority-rule consensus topologies resulting from Bayesian Inference with all datasets (electronic appendix 3A-E).
Results from analysis of the combined plastid dataset produced topologies with the least resolution (fig. 3 , electronic appendices 2C & 3D), but a clade comprising all species of African and Malagasy Schefflera is well supported. Two additional clades that are well supported in other analyses are likewise moderately supported in the strict consensus MP analysis of the combined plastid dataset  ('Meiopanax' and 'Sciodaphyllum', fig. 2, BS = 75 and 76, respectively ; see also electronic appendices 2C & 3D). The combined plastid analyses did not yield strong internal resolution of branching patterns within either the 'Meiopanax' or 'Sciodaphyllum' clades; only two moderately to well supported subclades were recognized, referred to as the 'Goetzenii' subclade (BS = 90, PP = 1. 0, fig. 2 ) and the 'African myriantha' subclade (BS = 93, fig.
2 ). In the combined nuclear (ETS + ITS) analyses, all species of African and Malagasy Schefflera are strongly supported as a clade, within which the 'Meiopanax' and 'Sciodaphyllum' clades are likewise well supported (figs 1 & 4, electronic appendix 3C). Relationships suggested by the combined nuclear analyses provide support for five subclades. These included the two subclades in 'Sciodaphyllum' that are resolved in the combined plastid analyses along with a third subclade (viz. the 'Myriantha-monophylla' subclade, figs 1 & 4, electronic appendix 3C), and two additional subclades in the 'Meiopanax' clade, which we refer to as the 'Diversifolia  3 & 4, electronic appendix 3C). These seven clades/subclades are also well supported in our combined analysis of nuclear and chloroplast data (fig.
Results from both the ML and BI analyses of the combined plastid datasets place S. umbellifera among a large polytomy in the 'Meiopanax' clade, but branch support for this is low (electronic appendices 2C & 3D). The 'Palmate-vantsilana' subclade is so named because of the shared tendency toward palmately compound leaves among its members together with the inclusion of Schefflera vantsilana, whose epithet is also the Malagasy vernacular name for most species of Schefflera. Within this subclade, several additional subclades are resolved containing accessions assigned to two species, identified as S. longipedicel lata and S. vantsilana, as well as a smaller subclade that in-Gostel, Plunkett & Lowry II, Afro-Malagasy Schefflera phylogeny cludes the samples of four undescribed species (referred to herein as Schefflera sp.
Both the separate and combined analyses of the nuclear and plastid datasets indicate paraphyly in S. myri antha with strong branch support (fig. 1 , BS = 97, PP = 1. 0; fig. 3 , BS = 69, PP = 1. 0; fig. 4 , BS = 91, electronic appendices 1-3). Lower branch support in the plastid and combined nuclear + plastid topologies appears to result from inconsistent placement of a single accession of S. monophylla (Randrianasolo 131). The morphological distinctions among S. humblotiana, S. monophylla, S. myriantha, as well as Schefflera sp. ined. 9, are quite strong. Despite its epithet, S. monophylla is typically not truly unifoliolate, but instead generally has a comparatively large central leaflet with two smaller lateral leaflets that are sometimes scarcely evident but only rarely absent. Morphologically, S.
humblotiana is the most distinctive of these three species, possessing extremely long, narrow leaflets, whereas those of S. myrian tha are elliptical (sometimes broadly so). On the other hand, the lack of any apparent morphological differences between S. myriantha from Africa and Madagascar suggests the need for further analysis in light of the relationships revealed in this study. Given the molecular divergence (in both the plastid and nuclear datasets) among the lineages belonging to the 'myriantha-monophylla' and 'African myriantha' subclades, it seems that S. myriantha, as currently circumscribed, represents two distinct but cryptic species. The only alternative treatments would include the recognition of S. myriantha as a paraphyletic species or including the material of all three taxa in a single, highly variable and broadly defined species.
Harms (fig. 1, BS = 73, PP = 1. 0; fig. 2, BS = 90, PP = 1. 0; fig. 3, BS = 96, PP = 1. 0; fig. 4, BS = 79, electronic appendices 1-3). Resolution is poor within this clade, and while some phylogenetic structuring can be detected, the topology varies among the datasets. Only one member of this clade, S. procumbens, forms a species-specific subclade (figs 2-3, BS = 89, PP = 0. 99-1. 0; electronic appendices 2C & D, 3D & E).
ACKNOWLEDGEMENTS Support for field and laboratory work was provided by grants from the  U. S. National Science Foundation  ( DEB 9981641 ,  0613728 ,  0614152  and  0743355 ). The authors wish to thank the  Botanic Garden Meise in Belgium (BR)  for access to their collections. We are grateful for field assistance provided by several colleagues in Madagascar, including  P. Antilahimena ,  R. Bernard ,  J. Rabenantoandro ,  C. Rakotovao ,  O. Randriambololomamonjy ,  R. Randrianaivo ,  D. Ravelonarivo , and  R. Razakamalala. MG also thanks  A. Nicolas  and  P. Fiaschi  for assistance in the laboratory, and  B. De Villiers  and  C. Rodrigues  for help with herbarium specimens. Fieldwork in Madagascar was carried out under collaborative agreements between the  Missouri Botanical Garden  and the  Parc Botanique et Zoologique de Tsimbazaza  and the  Direction de la Recherche Forestière et Piscicole, FOFIFA.
Taxon Genbank accession no. (ETS/ITS/ndhF-rpl32/rpl32-trnL/ trnk-rps16) * indicates missing sequence Source and accession no. Outgroups Astrotricha pterocarpa Benth. KY203609/AF229761/KY203616/ KY203623/KY203630 Queensland, Australia, Plunkett 1527 (NY) Cussonia holstii Harms ex Engl. KY203614/AY389031/ KY203621/ KY203628/ KY203635 Arusha, NP, Tanzania, Lowry 4986 (MO) Cussonia paniculata Eckl. & Zeyh. KY203615/AT389032/ KY203622/ KY203629/ KY203636 Amatole Mountains, South Africa, Phillipson 5263 (MO) Cussonia thyrsiflora Thunb. KY203613/KY203638/ KY203620/ KY203627/ KY203634 Kenton-on-sea, South Africa, Phillipson 5110 (MO) Osmoxylon pectinatum (Merr. ) Philipson KY203610/AY389045/KY203617/ KY203624/KY203631 Green Is. , Taiwan, Huang 756 (HAST) Schefflera digitata J. R. Forst. & G. Forst.
The colors of the individual cells were then analyzed quantitatively. Owing to the perinuclear localization of the NPs, each labeled cell appeared as a separate region of high density of dots, which facilitated greatly an automated image analysis using an ImageJ macro (Supplementary file 1). The measured relative intensities of the three channels provided RGB barcodes for each cell, which were then represented in a ternary diagram of an RGB color triangle (Figure  4D ). Analysis of over 2000 cells, showed 13 well-separated populations, which implies robust color coding of live cells by at least 13 different barcodes. It should be noted that incubation of cells with a simple mixture of dyes (DiI and DiD) without nanoparticles resulted rather heterogeneous color code (Figure  S13 ). The latter could be explained by very poor solubility of these dyes in water, so that the aggregates of these dyes in water do not provide as homogeneous cell staining as PLGA NPs loaded with these dyes.
The different channels were recorded as follows: excitation 405 nm, emission recorded from 430 nm to 480 nm; excitation 488 nm, emission recorded from 495 nm to 560 nm; excitation 561 nm, emission recorded from 570 nm to 610 nm; excitation 635 nm, emission recorded from 650 nm to 750 nm. The power of the 405 nm laser was adjusted as needed. The power of the 488, 561, and 635 nm lasers was set either to 10 or to 20 % of the nominal power (same for all three) and the gain and offset were set to the same value for all three. Three successive sequences were recorded for each image. Image analysis: Image analysis was performed using the Fiji software and, for data analysis, the R software. The three consecutive images were averaged for each channel. The intensity levels were set to the same levels for the three NP channels for all images presented here.