dataesr/scientific-paragraphs-categorization huggingface dataset:
All dilutions were performed in running buffer. The sensor chip surface was regenerated after each experiment by injecting 20 l of 3 M MgCl 2. The kinetic parameters were calculated using BIAeval 4. 1 software. Analysis was performed using the simple Langmuir binding model. The specific binding profiles were obtained after subtracting the response signal from the control anti-myc antibody alone channel and from blank-buffer injection. The fitting to each model was judged by the chi square (2) value and randomness of residue distribution compared with the theoretical model. Active concentration was determined under mass transfer condition where the slope of the curves is directly correlated with the active concentration of the protein  (18). Luciferase Reporter Assay-HEK293 cells stably expressing either wt CD40 or CD40-K29A were cultured in 24 well plates at 3 ϫ 10 5 cell/ml.
Detection of firefly luciferase and Renilla luciferase expression was done using the dual luciferase assay detection kit (Promega). Monocyte-derived Dendritic Cell Differentiation and Maturation-Elutriated monocytes were obtained from the Etablissement Français du Sang (EFS; Strasbourg, France). Monocytes were cultured in RPMI 1640 medium with Ultraglutamine (Lonza) supplemented with 10 g/ml gentamycin, 2 mM HEPES, and 10% heat-inactivated fetal calf serum. At day 0, cells were seeded at a density of 4 ϫ 10 6 cells/well in a 6-wells plate, and differentiation into CD209-positive dendritic cells was induced by addition of 5 ng/ml GM-CSF HuXp and 5 ng/ml IL-4 HuXp (Humanzyme, Chicago, IL). At day 5, when Ͼ80% of the cells expressed CD209 (data not shown), cells were incubated with the indicated stimuli in the presence or absence of 100 g/ml polymyxin B (Fluka).
After 24 h of culture, cells were harvested and washed with 2 ml of cold PBS, and maturation maker expression was analyzed by flow cytometry. Flow Cytometry Analysis-Cells were stained in PBS containing 2% fetal calf serum at 4 °C for 20 min with the various antibodies used at concentration recommended by the manufacturer. After two washes in PBS, cells were analyzed by flow cytometry with a Gallios flow cytometer (Beckman Coulter). At least 10,000 events were acquired for each experiment, and the data were processed with the Kaluza Flow Analysis Software (Beckman Coulter). Statistical Analysis-FRET experiments were analyzed using one-way ANOVA with Tukey post test, and luciferase NF-B and monocyte-derived dendritic cell maturation assays were analyzed using two-way ANOVA with Bonferroni post test, using GraphPad Prism version 5.
1B ). Although glycosylation interfered with ionization of soluble CD40 in native mass spectrometry (supplemental Fig. 1 ), the deglycosylated protein behaved well in this assay which allowed detection of two peaks at masses of 23. 94 and 47. 86 kDa, corresponding relatively closely to expected theoretical values for the nonglycosylated monomeric (23. 4 kDa) and dimeric (46. 7 kDa) CD40 (Fig. 1C ). Taken together, these results indicate that at least a fraction of CD40 can self-assemble in the absence of ligand, most probably as a noncovalent homodimer. CD40-CRD1 Mediates Self-interaction of CD40-To define the site required for CD40 self-assembly, we first constructed a model of a CD40 dimer based on the structures of the parallel TNFR1 dimer (PDB ID code1NCF) and ligand-bound CD40 (PDB ID code 3QD6).
16 ϫ 10 Ϫ3 s Ϫ1 ), as determined by surface plasmon resonance analysis, whereas no binding was detected for both cysteine mutants (Fig. 4B  and supplemental Fig. 6 ). These data show the importance of an adequate CRD1 folding for binding to CD40. Of note, using surface plasmon resonance, the active concentration of CD40-CRD1 was estimated to be 4. 7% of the total protein. In all experiments, the mentioned concentration of CD40-CRD1 is that of the active protein. The concentration of CRD1 mutants was estimated also as 4. 7% of the total protein although it was not possible to estimate its active fraction because there is no detectable binding to CD40. Recombinant CD40-CRD1 Induces a Mild Ligand-like Activity and Potentiates CD40L Signals-As expected, an overnight stimulation of CD40-expressing cells with CD40L activated the NF-B transcription factor and induced expression of a NF-B luciferase reporter gene (Fig.
Acknowledgments-We thank  Dr. Sylviane Muller  ( UPR 9021 Strasbourg, France ) for constant support and encouragement;  Laure Willen  ( University of Lausanne ) for expert technical assistance in plasmid cloning;  Marie-Christine Rio  and  Fabien Alpy  for kindly providing the ERBB2-EYFP construct; and  Pedro Romero  and  Petra Baumgaertner  ( University of Lausanne ) for helpful discussions, advice, and assistance in monocyte-derived dendritic cell assay.
* This work was supported by the  Centre National de la Recherche Scientifique  (to S. F. and G. G. ), the  Swiss National Science Foundation  (to P. S. ), and the  Agence Nationale Recherche  Grant  ANR-08-PCVI-0034-01 ) (to G. G. ). □ S This article contains supplemental Figs. 1234567. 1 Recipient of grants from the  Agence Nationale de la Recherche  and the  University of Strasbourg.
Genome assemblies Sequencing of the type strains of the five Nakaseomyces species; Candida nivariensis CBS9983, Candida bracarensis CBS10154, Nakaseomyces (Kluyveromyces) delphensis CBS2170, Candida castellii CBS4332, and Nakaseomyces (Kluyveromyces) bacillisporus CBS7720, was performed at Genoscope (Evry, France), using a combination of Illumina and 454 technologies (see Methods). Genome data has been deposited at the EMBL. Final assemblies showed a close correspondence between scaffolds and chromosomes (Additional file 1), and were annotated for coding and non-coding genes (see Methods). Flow cytometry results show that species are haploid, except N. bacillisporus which is diploid (Additional file 2). All species have an haploid genome size of 10 to 12 Mb. Chromosome numbers, as estimated by Pulsed-Field Gel Electrophoresis (not shown), range from eight in C.
Species names in red and with an asterisk indicate human fungal pathogens. Underlined species names correspond to the newly sequenced Nakaseomyces species. Important evolutionary events such as the Whole Genome Duplication (WGD) or the genetic code transition in the Candida clade (CTG) are marked on the tree. All aLRT-based supports were maximal and a single node with a bootstrap support below 100% is indicated. This topology is also the most parsimonious in terms of inferred duplications in 4,965 individual gene phylogenies, as assessed by a Gene Tree Parsimony approach implemented in duptree  [20]. congruent, for the shared species, with our current understanding of Saccharomycotina phylogeny  [21]. This topology supports the the existence of the Nakaseomyces genus, and defines two clear sub-groups separated by an ancient split.
Variations in gene repertoires The total numbers of protein-coding genes range from 5400 to 5900, which is similar to what is found in C. glabrata  [2] , and lower than in S. cerevisiae. Indeed, the number of true protein-coding genes in S. cerevisiae is estimated at around 5800, but this rises to around 6600 when dubious and other non-experimentally characterized ORFs are included, a figure more comparable to our predicted gene sets (SGD, 12 January 2012, http://www. yeastgenome. org, and Additional file 7). To assess the coverage of the predicted gene repertoires we tested for the presence of a set of 2,007 protein families previously found to be widespread in Saccharomycotina  [21]. Our proteomes contained 99. 4-100% of this core dataset, attesting for a high coverage in our procedures.
Sequence and annotation of protein-coding genes Sequencing was done by the Genoscope (Evry, France). Briefly, a whole genome shotgun (WGS) strategy associating different types of sequencing technologies was performed for each strain. An mean 24. 8 genome equivalent (from 15. 4 up to 41) was achieved using 454 GSFlx approach using a mixture of 8 kb mate pairs sequencing and single reads. Genome assembly was performed using 454 Newbler software. Subsequently, a mean 70 genome equivalent coverage for each strain was obtained using Illumina GAIIx technology 36 or 76 bp single reads, and these data were used to correct assembly errors  [67]  Probably because of the complete sequence identity between segments of the three MAT-like cassettes, most of these loci were absent from the automated assembly generated from the Illumina and 454 reads.
Identification of centromeres was done by searching with fuzznuc from the Emboss suite  [70]  [GT]N  (7, 15) TTCCGAA"  [75] , and by manually checking for conservation of synteny in case of multiple hits within a single scaffold. Telomeric repeats were searched for by using the repeat motif from C. glabrata, CAGCACCCAGACCCCA, as blastn queries against the genomic sequences. This also revealed the putative template inside the TLC1 gene. ncRNA discovery and annotation tRNA genes were identified by both cloverleaf structure detection  [76]  and tRNAscan-SE  [77]. BLAST  [78]  and Infernal  [79]  searches were performed on each of the five Nakaseomyces genomes for other ncRNA genes; using annotated ncRNAs from the Genolevures database  [80]  as queries for BLAST, and the covariance models from RFam database  [81]  for the Infernal search.
0  [91]. The two evolutionary models best fitting the data were determined by comparing the likelihood of the used models according to the AIC criterion  [92] ; Then, ML trees were derived using these two models. All trees and alignments have been deposited in PhylomeDB  [82]  and can be browsed on-line (www. phylomedb. org, phylome codes 78 to 83). Trees were scanned to i) define orthology and paralogy relationships using a phylogeny-based, species overlap approach  [28] ; ii) detect and date duplication events  [29] , including large expansions of gene families; and iii) transfer functional annotations from one-to-one orthologs in S. cerevisiae. Unless indicated otherwise, all operations with phylogenetic trees were performed using scripts implemented within the ETE package  [50]. To reconstruct a species phylogeny, alignments of 603 proteins that had a single ortholog in all species considered in the phylome were concatenated into a single trimmed alignment of 288,995 positions.
e. , affecting different species in the group), which would be consistent with either the relaxation of selective constraints or with the action of positive selection. We used the program codeml in the paml 4 package  [93]  to estimate the d N /d S rate ratio variation in each individual one-to-one ortholog, along particular branches in the tree. Subsequently, we compared pairs of nested models by means of a likelihood ratio test (LRT) where the degrees of freedom correspond to the difference in the number of parameters estimated in each model, and the distribution of the d N /d S rate is assumed to follow a chi square distribution. Values of d N /d S larger than 5 were filtered out. We hypothesized an acceleration in gene evolution rate, and possible cases of positive selection, preceding the diversification of the 'glabrata group' , that were perhaps involved in the capability of these species to become pathogenic.
Acknowledgements We thank  Brendan Cormack  for sharing unpublished results about EPA genes and access to sequences. We thank our colleagues from the  Genolevures network  for their continued enthusiasm and support. TG's research leading to these results has received funding from the  European Research Council  under the European Union's  Seventh Framework Programme  (FP/2007-2013)/ ERC  Grant Agreement n. 310325 , a Grant from the  Qatar National Research Fund  grant ( NPRP 5-298-3-086 ), and by a grant from the  Spanish Ministry of Economy and Competitiveness  ( BIO2012-37161 ). CF's research is funded in part by an  "Attractivité" grant  from the  University Paris Sud. GA is a recipient of a  Marie Curie grant  ( FP7-PEOPLE-2010-IEF-No. 274223 ). SB, HD and RA are recipients of, respectively, a shared post-doctoral grant and a Ph.
2 mg of total RNA obtained was used as a template to synthesize cDNAs with the SuperScriptH III First-Strand Synthesis System for RT-PCR (Invitrogen, Life technologies). Real-time quantitative PCR assays were then performed in triplicate on these cDNAs in the presence of the PCR Master Mix (Power SYBRHGreen, Applied Biosystems, Warrington, UK) to detect the amplification products. Samples were analyzed simultaneously for ribosomal protein 36B4 mRNA as an internal control using an ABI Prism 7300 sequence detector (Applied Biosystems, Foster City, CA, USA), and the data were analyzed using Sequence Detection software v. 3. 0. (Applied Biosystems). The primer sequences for quantitative PCR are indicated in Table  1.
Data analysis and statistical procedures The results are reported as the means 6 SEM and they were analyzed with the SPSS package for Windows, version 15. 0 (SPSS, Chicago, IL,USA). All measurements were taken in triplicate from three independent experiments. The Shapiro Wilks test was used to evaluate the fit of the data to a normal distribution and the Levene test to evaluate the homogeneity of variance. Significance was tested using one-way ANOVA followed by a Tukey's multiple range test.
Significant differences existed from 6 weeks of age onwards in females (P < 0. 05) and from 7 weeks onwards in males (P < 0. 01; Student's t-test, N = 18-24, error bars represent SEM). A star indicates difference between genotypes within the same sex (P values between 0. 036 and < 0. 001). (B and C) Male and female growth velocity was calculated as weight gain per day using data from (A). Peaks of growth velocity at 4 weeks of age are blunted in IGF-1R   S1  and S2. For comparison, mean lifespan in B6 control groups from the recent literature is on average 811 days in females and 822 days in males (Table  S3 ). IGF-1R, lifespan, and genetic background, J. Xu et al. we detected elevated plasma levels of acid-labile subunit (ALS) in 129S2 mice (Fig. 2D ), consistent with their high IGF-I. Plasma GH in contrast was lower in 129S2 mice compared with B6 (Fig.
Statistical analysis Two-tailed Student's t-test, Mann-Whitney U-test, and one-way ANOVA with Bonferroni's post hoc test were performed to determine statistical significance of differences between groups. GH pattern was analyzed by log-rank test. Survival curves were evaluated by Cox's regression and log-rank test. Tests were performed using SPSS (SPSS Institute Inc. , Chicago, USA). Results are presented as means AE SEM.
felis and deposited in GenBank  [14, 16]. Domestic cat hepatozoonosis has been reported from several countries worldwide including: India, South Africa, Nigeria, the USA, Brazil, Israel, Spain and France  [7, 9, 11, 12, [17] [18] [19] [20]. Most studies have focused on reporting the detection of feline hepatozoonosis and almost no information has been published on its pathogenesis, transmission, life cycle and epidemiology. In that context, the aims of this study were to carry out a survey on domestic feline hepatozoonosis, characterize its causative agents genetically and morphologically in blood and tissues, and evaluate its possible transplacental transmission.
Cat survey Blood samples were collected in EDTA tubes during 2010 and 2011 from multiple locations and sources in Israel. These included convenience sampling of cats whose Hepatozoon infection status was unknown from animal shelters in 5 cities in central Israel (Tel-Aviv; Jerusalem; Rehovot; Beit Dagan; Rishon Le-Zion), cats brought for routine spay to HUVTH, cats admitted to private veterinary clinics in 5 cities and villages in Israel (Haifa; Nahariya; Carmiel; Kfar Vradim; Yodfat) and to the to the HUVTH in central Israel whose samples were taken for routine diagnostic purposes. Serum samples were also collected from the same cats. Data collected on the cats included: sex, age, source of cats (e. g. shelter or private ownership), geographic location, indoors or outdoors access, and feline immunodeficiency (FIV) status as tested during this study.
Sequencing and phylogenetic analysis All PCR amplicons amplified from positive cats included in each part of the study were sequenced. The DNA products were sequenced using the BigDye Terminator v3. 1 Cycle Sequencing Kit (PerkinElmer/Applied Biosystems) and an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems). Sequences were evaluated with the ChromasPro software version 1. 33 and compared to sequence data available from GenBank using the BLAST 2. 2. 9 program (http://www. ncbi. nlm. nih. gov/BLAST/). The Hepatozoon species identity found was determined according to the closest BLAST match with an identity of 97% -100% to an existing GenBank accession. Only samples that produced amplicons with a sequence compatible with a Hepatozoon sp. were considered positive for Hepatozoon and included accordingly in the study analysis.
A phylogenetic analysis, which included DNA sequences from the blood of 18 cats from the study, was carried out to compare these sequences to Hepatozoon spp. described in other animal hosts and in domestic cats and had previously been deposited in GenBank. Sequences were analyzed using the MEGA version 3. 0 (www. megasoftware. net) and a phylogenetic tree was constructed by the Maximum-Likelihood, Minimum-Evolution and the Neighbor-Joining algorithms using the Kimura2-parameter model. Bootstrap replicates were performed to estimate the node reliability, and values were obtained from 1000 randomly selected samples of the aligned sequence data.
Genetic identity and phylogenetic analysis GenBank accessions A 358 bp fragment of the Hepatozoon 18S rRNA gene was amplified by PCR using the Piroplasmid primers from the blood and tissues of all cats considered infected in this study. DNA sequencing revealed that all positive cats, except for two, had a sequence whose closest match by BLAST, with an identity of 97%-100%, was an H. felis GenBank accession. Most sequences were 98%-100% identical to H. felis [GenBank:AY628681] (H. felis isolate Spain 2  [16] ). The DNA sequences similar to H. felis included those obtained from the 55 positive survey cats, sequences from all cats from which paraffin embedded or fresh frozen tissues were tested, and sequences from 17 of the 19 cats included in the collection of samples identified by blood smear microscopy during 2002-2011.
The Hepatozoon sequence obtained from the blood of the cat in which infection was detected antemortally and also in necropsy tissue was 99% identical to H. felis [GenBank: AY628681]. The sequence amplified from the paraffinembedded myocardial tissue of the French cat with hepatozoonosis was also 99% identical to H. felis [GenBank:AY628681] as was the sequence amplified from the paraffin-embedded myocardial tissue of the local cat with panleukopenia, and a sequence amplified from the amniotic fluid of a fetus from a blood-positive queen. Only 2 cats had DNA sequences that matched H. canis and not H. felis. Samples 9617 and 9618 from the collection of positive blood smear spp. were 99% identical to H. canis [GenBank:EU289222] and other H. canis accessions. Although the piroplasmid primers can also amplify DNA from piroplasms such as Babesia spp.
, none of the amplified sequences were positive for Babesia, Theileria or Cytauxzoon spp. Further investigation of the genetic identity of Hepatozoon parasites found in cats from this study was carried out using the HAM-1 F and HPF-2R primers which amplified a 1400 bp fragment of the H. felis 18S rRNA gene. Amplification of this large fragment of the 18S rRNA gene was carried out for selected samples included in the phylogenetic analyses. In addition to the DNA sequences from cats, fragments of H. canis from local Israeli dogs were also amplified using the two sets of primers and sequenced in order to compare H. felis and H. canis from cats with a local H. canis from dogs. Details on Hepatozoon sequences from this study submitted to GenBank are included in Table  1. A Neighbor Joining phylogenetic tree based on 345 bp from the shorter 18S rRNA fragment amplified by the Piroplasmid primers (Figure  1 ) indicated that sequences from 14 Israeli cats detected as infected with H.
felis clustered with H. felis [GenBank:AY628681] (H. felis isolate Spain 2), whereas the H. canis sequences found in 2 cats from the study clustered together with H. canis from dogs. Similar clustering was obtained also with the Maximum-Likelihood and the Minimum-Evolution algorithms. A Maximum Likelihood tree based on 970 bp from the longer 18S rRNA fragment amplified by primers HAM-1 F and HPF-2R (Figure  2 ) also indicated that H. felis sequences from Israeli cats clustered together with the H. felis Spain1 and Spain 2 sequences. Likewise, H. canis from 2 Israeli cats clustered together with H. canis [GenBank:AY461378] from a dog in Spain. These were separated from H. americanum and Hepatozoon spp. reported from other animal hosts.
Surveys of Hepatozoon sp. infection in domestic cats describe variable rates of infection in different areas. A study of myocardium specimens from 100 cats brought to necropsy in Israel found that 36% of cats harbored cardiac Hepatozoon-like meronts  [9]. Interestingly, this was the same rate of infection found in Israel almost 40 years later in the current study, indicating that feline hepatozoonosis The GenBank accession numbers, species of infected animals and country of origin from which the sequences were derived are included for each sequence. New GenBank accessions derived from the present study are indicated in bold letters. is not a new emerging infection in this country. Studies using PCR detection from Spain have shown diverse prevalence rates with 0. 6% in one study  [16] , 16% in a cat colony from Barcelona  [14] , and 4% in cats from the Barcelona area  [20].
A comparative study carried out in several districts of Bangkok, Thailand, where both canine and feline hepatozoonosis are prevalent, has reported a high infection rate of 32% in 300 cats by PCR. A positive association was found between the rates of infected dogs and cats in the same districts and 18S rDNA sequences from cats and dogs were closest to H. canis  [28]. These findings encouraged the authors to hypothesize that H. canis was the cause of both canine and feline infections. However, the genetic analyses in this study were probably made before the sequences designated as H. felis were deposited in GenBank  [16]. Therefore, the identity of some feline sequences may have been misinterpreted. A study from Brazil evaluated 200 blood samples from Sao Luis in Brazil and found only one cat infected with a Hepatozoon sp.
Acknowledgements We thank all the veterinarians from the HUVTH who helped to collect samples from cats,  Drs. Sigal Riten ,  Orly Harari , and  Lilach Zadik ,  Prof. Shmuel Perl  from the  KVI Pathology department ,  Dr. Harold Salant  for performing the T. gondii PCR and helping to collect samples,  Maria Griber  and  Tamar Shapiro  from the  HUVTH lab.
The CMS detector The analysis presented in this Letter uses experimental data collected by the Compact Muon Solenoid (CMS) experiment at the LHC in 2011. The central feature of the CMS apparatus is a superconducting solenoid of 6 m internal diameter, providing a magnetic field of 3. 8 T. Within the superconducting solenoid volume are a silicon pixel and strip tracker, a lead tungstate crystal electromagnetic calorimeter, and a brass/scintillator hadron calorimeter. The inner tracker measures charged particles within the pseudorapidity range |η| < 2. 5, where η = ln[tan(θ/2)] and θ is the polar angle with respect to the direction of the counterclockwise proton beam that is the z-axis of the CMS reference frame. The tracker provides an impact parameter resolution of ∼15 µm and a transverse momentum (p T ) resolution of about 1.