dataesr/scientific-paragraphs-categorization huggingface dataset:
We thank the French National Research Agency (grant no. ANR-13-BSV6-0004) and the German Research Society (DFG grant no. He 1848/14-1, He1848/15-1, and SFB 1036/TP13) for support of W. V. B. and E. L. , R. H. and M. W. , respectively. T. V. D. was funded by the Ministry of Education and Training of Vietnam and the Schmeil Foundation, Heidelberg. This study has benefited from the facilities and expertise of the SICaPS platform of I2BC (Institute for Integrative Biology of the Cell).
MBP-AtNAA70 or other plant NAAs should reveal Ntermini of proteins acetylated by the recombinant plant proteins. As controls, the already characterized enzymatically active subunit, AtNAA10, and its auxiliary subunit, AtNAA15, of the plant NatA complex were also expressed in E. coli as His 6 -MBP-tagged fusion proteins [Linster et al. , in revision]. After SCX-LC enrichment, N-termini enriched fractions were analyzed by LC-MS/MS to determine the NTA frequency of the bacterial proteome induced by the expression of the plant Nat subunit. Using this large-scale proteomics approach more than 2000 peptides were identified, which correspond to more than 400 non-redundant protein N-termini in each sample (PRoteomics IDEntifications database, http://www. proteomexchange. org/databases/pride: PXD001947).
His 6 - 6 MBP-AtNAA70 or other plant NAAs should reveal Ntermini of proteins acetylated by the recombinant plant proteins. As controls, the already characterized enzymatically active subunit, AtNAA10, and its auxiliary subunit, AtNAA15, of the plant NatA complex were also expressed in E. coli as His 6 -MBP-tagged fusion proteins [Linster et al. , in revision]. After SCX-LC enrichment, N-termini enriched fractions were analyzed by LC-MS/MS to determine the NTA frequency of the bacterial proteome induced by the expression of the plant Nat subunit. Using this large-scale proteomics approach more than 2000 peptides were identified, which correspond to more than 400 non-redundant protein N-termini in each sample (PRoteomics IDEntifications database, http://www. proteomexchange. org/databases/pride: PXD001947).
A digital analytical balance model HM-120 (A&D Weighing, San Jose, USA) was used to measure egg weight, with physical dimensions of 249 Â 330 Â 327 mm 3 , capacity of 120 g and precision of 70. 001 g. The balance was placed at the same height as the eggshell basket to ensure similar airflow direction and pattern. The weighing chamber of the balance was kept open to reflect similar air speed conditions around the eggshells (0. 5-0. 6 m/s). The software WinCT™ was used to transmit the weighing data from the balance to the computer via a RS-232C communication port. The frequency of eggshell weight was 1 measurement per second. Signal acquisition for both T egg and egg weight for each eggshell were synchronized and stored on the same computer for succeeding data analysis.
Measured effects of simultaneous heat and mass transfer in eggshells Measurements of both T egg and T air aligned with M egg and M water throughout the evaporation study, including the spraying event, comprised a valuable dataset for further analyses on the mechanisms of simultaneous heat and mass transfer in eggshells. An example of the obtained M egg values and the corresponding T egg of an eggshell are shown in Fig. 2. Fig. 2  demonstrates the characteristic profile curves of simultaneous heat and mass transfer in one of the eggshell samples over a time of approximately 12,000 s. The average M egg just before water spraying for this specific eggshell sample was 5. 3370. 02 g. An amount of about 1. 870. 04 g of water was sprayed into the eggshell at 2960 s increasing the egg weight (M egg þM water ) to 7.
The purities of SDS and DTAB were confirmed using surface tension measurements, which showed no evidence of a dip at the critical micelle concentration (CMC), which would be indicative of surface-active impurities. XPS. XPS measurements were taken at the NEXUS laboratory (Newcastle University, U. K. ) using the AXIS Nova XPS spectrometer. XPS spectra were recorded for the films as-sputtered and also for those cleaned using UV/ozone (30 min). Spectra were fitted using the CasaXPS software and calibrated by setting the C 1s peak to 285. 0 eV. XRR. XRR measurements were carried out at the Cavendish Laboratories in Cambridge using a Bruker D8 X-ray diffractometer with a copper target and a Goebel mirror. An accelerating voltage of 40 kV  and a primary beam size of 0. 1 mm were used. The detector was operated in single pixel (0D) mode.
Samples were cleaned with UV/ozone (30 min) before being soaked in ultrapure water (UPW) adjusted to the required pH by the requisite volume of nitric acid for 2 h and dried using a flow of N 2 gas before measurement. Data were fitted to a structural model using GenX 2. 0 software to minimize the figure of merit (FOM). 30 The Parratt algorithm was used to generate the model fits. 31  Potential. To measure the ς potential of the NiO powder over a range of pH values, solutions of sodium nitrate (concentrations 1-100 mM) were adjusted to each pH as required using nitric acid or sodium hydroxide. NiO powder (1 mg mL -1 ) was then dispersed in the solution, and the average particle size and ς potential were measured using a Brookhaven ZetaPALS dynamic light scatterer. Further profiles were measured at 10 mM sodium nitrate concentration, with the addition of either 7 mM SDS or DTAB to the dispersion.
Both substrates were characterized under pure H 2 O and pure D 2 O in order to extract the nickel film and oxide layer thicknesses and roughnesses. To substrate 1, a 5 mM solution of SDS at pH 6 was then added, and the surfactant layer was characterized under both water contrasts. Solutions (5 mM) at pH 4 and 2 were consecutively flushed through the sample cell, and neutron reflectivity profiles were obtained at each pH for both water contrasts. The same approach was adopted for substrate 2, using 5 mM DTAB as the additive rather than SDS. The concentration value of 5 mM, lying below the CMC of both SDS and DTAB over the whole pH range of interest here, was chosen from the depletion isotherm data as a concentration at which significant SDS adsorption was known to occur. The PNR data were fitted to a structural model using the Rascal fitting program to minimize χ 2.
Potential explanations are discussed in the PNR section below. PNR. Neutron reflectivity profiles (plots of the measured reflectivity as a function of momentum transfer perpendicular to the surface) were initially collected for both nickel substrates 1 and 2 under D 2 O and H 2 O in order to characterize the nickel and oxide layers before adding surfactant. For substrate 1, a nickel film of thickness 116 (±3) Å (agreeing well with the estimated deposition thickness) and roughness 5 Å and a NiO film of thickness 23 (±2) Å and roughness 7 Å were modeled. Similar parameters were observed for substrate 2, with a nickel film of 123 (±3) Å thickness and 5 Å roughness and a NiO thickness of 19 (±2) Å with roughness 7 Å. While the XPS data clearly show a mixture of nickel hydroxide, Ni(OH) 2 , and oxide, NiO, at the surface, the hydroxide is harder to see in the PNR data; the best fit is obtained with an oxide of high density (i.
For example, for between two and six clusters, the PAM algorithm can be challenged on 100 subsamples made of 80% of the original data set, reshuffled for each iteration. Robustness will then be computed as the propensity for two observations to be assigned to the same cluster throughout the 100 iterations. If all the couples of observations are assigned to the same clusters at each iteration, then the result is likely to be robust and reliable. Such resampling-based methods are also used to address the sensitivity to initial conditions.
A simple, theoretical example We created a data set of 200 patients, originating from four different groups in terms of height and weight. For the purpose of this example, let us postulate that we have a group of young frail children, one of obese adolescents, one of relatively small female adults and a group of relatively large male adults. We assume that heights and weights within a group follow a Gaussian distribution, centered on their respective mean. Data have been generated with the R software version 2. 14. 2 (64 bits), running on Windows 7, and the clusterCons package. The R code we used for data generation as well as for the following analysis is provided in the supplementary data. Our training objective is to distinguish between four qualitative groups to be discovered in these data using clustering algorithms.
A real data application: searching for specific profiles in healthcare resource utilization data The data presented here were extracted from the French SIRS cohort study, with the latest data collected in 2010 in a representative sample of 3000 French-speaking adults in the Paris metropolitan area (Paris and its suburbs, a region with a population of 6. 5 million). The SIRS methodology and further detailed characteristics have been previously described elsewhere, for example in  [43]. For a more comprehensible view of how the French healthcare system is solicited -or not -by its users, one may want to identify specific and homogeneous profiles of healthcare resource utilization. The SIRS cohort study provides us with numerous variables that account for various aspects of the healthcare system utilization.
Available software and packages Either free or commercial suites, the main statistical packages available provide at least partial solutions for pattern recognitionclustering: SAS (proc fastclust), SPSS (SPSS TwoStep Cluster Component), STATA (linkage, k-means), R, and Matlab. In some cases, proprietary solutions can even be found (e. g. , SPSS). For R, several packages can be used, such as cluster  [45] , clusterCons  [40] , and clv  [46] , clValid  [47]. The R software runs on Linux or Windows machines, is freely downloadable, and all packages are fully documented and often comewith code examples. Dissimilarity matrices can be computed using a dedicated algorithm, called DAISY  [22] , also available in the R Cluster package.
In most cases, these two angles were measured at different moments of time. Generally, using the observations published during the 19th and at the beginning of the 20th centuries posed many problems. For instance, it was not possible sometimes to identify from publication the time-scale; sometimes it was not clear whether reductions were made when data were prepared for publication. At the beginning of the 20th century photographic observations began to be used, and at the end of this century observations made with CCD cameras appeared. Such observations can be relative or absolute. Relative observations provide us with Triton's coordinates relative to Neptune while absolute observations give us satellite positions relative to stars. Absolute observations always have a systematic error resulting from inaccuracy in star coordinates taken from star catalogues.
We have also used the observations made by the Voyager 2 spacecraft in 1988-1989 (the results have been published in Jacobson 1991). It is reported in  Jacobson (2009)  that the spacecraft trajectory was reconstructed, i. e. refined and transformed into the International Celestial Reference Frame. The corresponding computer file vgr2-nep081. bsp available at the Jet Propulsion Laboratory (JPL;  Acton et al. 2015)  site http://naif. jpl. nasa. gov/ pub/naif/VOYAGER/kernels/spk/ allows to obtain refined coordinates of the Voyager 2 spacecraft. Earlier, we used these coordinates in  Emelyanov & Arlot (2011)  to fit the orbit of the Neptunian moon Nereid to observations. The old Voyager 2 position published in  Jacobson (1991)  were replaced by the positions calculated with the SPICE software of JPL using the new kernel file.
Other drugs, e. g. aminoglycosides, should be considered as alternative or combined therapeutic options against infections caused by AMC-resistant isolates. In these circumstances, an analysis of resistance to aminoglycosides in AMC-resistant E. coli is relevant for clinical and epidemiological reasons. According to the European Antimicrobial Resistance Surveillance Network (EARS-Net) (http://www. ecdc. europa. eu/en/ healthtopics/antimicrobial resistance/database/Pages/database. aspx), in the last decade aminoglycoside-resistant E. coli isolates from blood have increased from 6. 8% (2001) to 15. 6% (2012) in Spain. Different mechanisms are known to play a role in the development of aminoglycoside resistance in E. coli and other Gram-negative bacteria, but the production of aminoglycosidemodifying enzymes (AMEs) is the most important.
DNA sequencing The amplified products were purified with a QIAquick PCR Purification Kit (QIAGEN Inc. , Barcelona, Spain). DNA sequences on both strands were determined using an external resource (Macrogen Inc. , Amsterdam, The Netherlands). The BLAST program was used to compare the nucleotide and protein sequences with those available on the National Center for Biotechnology Information (NCBI) website (http://www. ncbi. nlm. nih. gov). Amplicons representative of all AME genes obtained were sequenced and 100% homology with the GenBank sequences was found. The presence of the aac(6 )-Ib-cr variant conferring additional resistance to ciprofloxacin  [19]  was inferred from the sequence of the corresponding amplicons.
The X-ray beam was focused down to 400 Â 500 nm in the vertical and horizontal directions, respectively, using KB mirrors  (Ulrich et al. , 2011). The diffracted X-rays were recorded by a Mar CCD (MAR165) consisting of 2048 Â 2048 pixels with a size of 80 mm. It was mounted in top reflection geometry at 90 with respect to the incident beam at a distance of 70 mm, thus covering a solid angle of X-ray collection of around 100. X-ray fluorescence excited by the focused beam was monitored using an energy-dispersive point detector (Rontec XFlash 1001, 3. 4 mm opening, 10 mm 2 area). In addition to the three-point bending experiment, the nanowire deformation was simulated by FEA using the COMSOL Multiphysics software (http://www. uk. comsol. com/), taking into account the complete elastic stiffness tensor C for bulk Au.
This reversible displacement of the gold Laue spot shows a purely elastic deformation of the wire which was verified both by mLaue diffraction mapping of the whole wire after the in situ experiment and by scanning electron microscopy studies (not shown here). None of these later studies indicated the presence of plastic deformation or any deviation of the selfsuspended wire from its original horizontal position. From the Laue diffraction patterns the orientation, i. e. both bending and rotation of the wire part illuminated by the X-ray beam, was determined from the orientation matrices (UB). Taking into account at least eight Au Laue spots, the standard Laue pattern analyses were performed using the LaueTools software  (Micha, 2014). The bending angle Â is inferred from the dot product between crystallographic directions under load and their initial state as follows: Â ¼ arccos q load Á q init jq load jjq init j ; ð1Þ with the scattering vector q ¼ UB Á G Ã , where G Ã ¼ ha Ã þ kb Ã þ lc Ã is the reciprocal-lattice vector defined with Miller indices hkl.
Moreover, recording the onset of plasticity will allow for studying the nucleation of the first defects and dislocations as well as their evolution and propagation. The authors gratefully acknowledge financial support from the French National Research Agency through the project ANR-11-BS10-01401 MecaNIX. They further thank the French Review Commitee for the allocated experiments at CRISTAL (SOLEIL) and the BM32 beamline at ESRF.
TFIIS1 is present in two or three copies; TFIIS2 and TFIIS3 are present in one or two copies, while in all species TFIIS4 is encoded by a single gene (Michael Lynch's lab data from ParameciumDB). The fact that all four TFIIS families have been conserved during Paramecium evolution may indicate that each family has a specific function that cannot be replaced by another family.
Expression patterns of TFIIS genes reveal a strong induction of TFIIS4 during autogamy We investigated the expression of all six TFIIS genes during the sexual cycle of P. tetraurelia. Expression profiles were extracted from published microarray data  [28]  and showed that TFIIS1a, 1c and 3 are expressed at significant levels during vegetative growth and also during autogamy (Fig  1B ). In contrast, little or no expression is detected in vegetative cells for TFIIS2a, 2b and 4, while these genes are specifically induced during autogamy. All expression patterns were confirmed using northern blots for an independent autogamy time-course experimentsee S3 Fig. The different expression patterns of TFIIS genes make P. tetraurelia a promising model for the study of potentially divergent roles of TFIIS proteins.
Interestingly, among autogamy up-regulated genes, TFIIS4 is the most highly induced. Its transcription increases sharply early during autogamy, at the time when only vegetative and meiotic cells can be detected in the samples and remains high throughout autogamy. In all subsequent functional analyses, therefore, we paid closer attention to this gene. The multigenic TFIIS family in Paramecium tetraurelia and its expression profiles. (A) Domain organization and neighbor-joining tree of P. tetraurelia TFIIS proteins. The evolutionary history was inferred in MEGA4  [76]  based on the alignment of entire protein sequences (342 positions in the final dataset) and the following parameters: deletion of gaps in pairwise sequence comparisons, uniform rates among sites, bootstrap 1000 (bootstrap values displayed next to the branches), Poisson correction.
The scale is in the units of the number of amino acid substitutions per site. Accession numbers in ParameciumDB: TFIIS1a-GSPATP00003556001, TFIIS1c-GSPATP00008714001, TFIIS2a-PTETP1100023001, TFIIS2b-GSPATP00003298001, TFIIS3-GSPATP00019582001, TFIIS4-GSPATP00025792001. The Dst1 protein from S. cerevisiae was used as an outgroup. (B) Mean expression signals obtained in microarray experiment "Paramecium tetraurelia autogamy series 1" from  [28]. Values obtained for TFIIS2a were recalculated using the signals obtained only for microarray probes covering the corrected gene annotation. V: vegetative; -3. 5: meiosis; 0: 50% of cells with fragmented MAC; 5 to 20: 5 to 20 hours after "0" time point. Y-axis shows mean signals. doi:10. 1371/journal. pgen. 1005383. g001.
As a control we used sequencing data for the DNA sample obtained from autogamous cells of the same strain, but with no silencing (  [19] , see Materials & Methods for details). In both datasets, IES retention scores were determined for each IES by calculating the ratio of IES-containing reads (IES+) over the sum of: (i) the number of reads that map to the IES excision junction (IES-reads), and (ii) the number of IES-containing reads (IES+). Hence a retention score of 0 means complete excision whereas a score of 1 means complete retention of the IES as described in  [19]. The results are in good agreement with the above molecular data: IESs shown to be retained by PCR or Southern blot hybridization exhibit higher retention scores in the sequencing experiment  (Fig 4C). To ensure that the IES retention observed in the TFIIS4 RNAi sample is indeed due to the silencing of this gene, we performed statistical comparison of IES retention scores between control condition and TFIIS4-RNAi (for details see Materials and methods).
Construction of GFP fusions Plasmid pGFP-TFIIS4-e encoding an N-terminal GFP fusion to TFIIS4 was constructed by inserting a 1294-bp fragment containing the TFIIS4 open reading frame and its potential 179-bp terminator region (bp 151716. 150423 from accession number NW_001799642. 1) between the BamHI and PstI sites of plasmid pZCΔRIX (kindly provided by E. Meyer & S. Malinsky), directly downstream of the EGFP coding sequence optimized for Paramecium codon usage  [44]. Then, the putative promoter of TFIIS4 (bp 151832. 151714) was inserted between the SalI and XbaI sites of the plasmid. The other N-terminal GFP fusions (pGFP-TFIIS1a, pGFP-TFIIS1c, pGFP-TFIIS2a, pGFP-TFIIS2b, pGFP-TFIIS3) were obtained by an overlapping PCR method  [67]. In general, each construct contained the putative promoter, coding sequence and putative terminator region of the appropriate TFIIS gene (exact coordinates of cloned genomic fragments are given in S1 Table ).
Microarray analysis of gene expression Five samples (V, St, T0, T5, T10 and T20) from a TFIIS4 silencing and a control (ICL7 silencing) autogamy time-course experiment were selected and sent to PartnerChip (Evry, France) for cDNA labeling and hybridization on NimbleGen (Roche Nimblegen, Madison, WI) microarrays "101018_Paramecium_L_EXP" (GEO no. GPL18944, SET01). The data were processed and normalized as previously described  [28]  (GEO no. GSE64682).
Only reads with unambiguous alignments were counted. Each read was counted only once to avoid over-counting owing to paralogous matches. Reads were only counted at IES ends, to avoid length biases resulting from IES length variation. The fraction of IES+ reads/(IES+ and IES-) reads gives the RS. Then, we compared the RS of a given IES to the control RS observed for the control DNA sequencing (as described in  [19] ) to make sure that the observed retention can be attributed to TFIIS4 silencing. First we calculated the confidence interval (alpha = 0. 95) of the control RS value, using the Pearson-Klopper exact method as implemented by the R binom package version 1. 0-5  [74]. Then we tested for higher retention in the experiment, thanks to a frequency comparison test (based on a binomial law of probability) between the experimental RS and the upper bound of the confidence interval in the control.
Normalization was performed relative to the cDNA of the constitutively expressed T1b gene, which encodes a trichocyst matrix protein (TMP1b). Oligonucleotide sequences are listed in S2 Table. transcripts corresponding to the gene are no efficiently down-regulated-probably due to lower amount of siRNA present in the cells after long starvation period. This may explain some residual survival in post-autogamous cells and delayed partial excision of some IESs. 17S rRNA probe was used as a loading control. (B) Microarray hybridization data obtained using the same RNA samples as in panel A. Gene expression heatmap was plotted using the previously obtained hierarchical clusterization of the set of 2467 genes that are most differentially expressed during autogamy  [28]. The plot displays the samples both for TFIIS4-silencing and the control (ICL7-silencing) as columns, and the genes as rows.
Acknowledgments We kindly thank  Casey McGrath ,  Tom Doak , and  Michael Lynch  ( Department of Biology, University of Indiana, Bloomington ) for the access to the preliminary assembly of the genomes of the other Paramecium species obtained in course of the project " The Evolutionary Consequences of Whole-genome Duplication : the  Paramecium aurelia complex" (NSF  grant  MCB 1050161 ) that we used to find TFIIS proteins. We thank  Dorota Adamska  and  Anna Labno  from  Andrzej Dziembowski lab  for their help in Illumina sequencing. We thank  Eric Meyer  and  Sophie Malinsky  for the kind gift of plasmid pZCΔRX1, and  Antoine Marmignon  for providing RNA samples from a  PiggyMac-RNAi  experiment. We are grateful to  Emeline Dubois  and  Aurélie Kapusta  for their technical assistance during KM-O PhD training.