dataesr/scientific-paragraphs-categorization huggingface dataset:
Comparative genomics We used OrthoMCL v2. 0. 9 (59,60) to examine speciesspecific genes and gene families with species disparities in copy number. Protein sets from B. bovis T2Bo, B. bigemina BOND and B. divergens 1802A were clustered using Or-thoMCL, set to maximize cluster size (i. e. minimized sequence identity requirements for clustering). From these data we calculated the number of genes shared by all three species in single copy ('conserved') or as part of gene families with variable copy number ('semi-conserved'). We also extracted the number of ves1 homologs and ves1-like shortened forms (i. e. ves2) in each genome. Finally, we calculated the number of species-specific genes in single or multiple copies. In comparisons of chromosomal rearrangements across species, and in comparisons of conserved ves1/ves2 loci across strains, we used the Artemis Comparison Tool [ACT  (61) ] to visualize conservation in gene order.
We checked the B. bovis genomes for genuine orthologs to ves2 and discovered a tandem gene pair (BBOV III002570/2580), which encode homologs to BbigVes2 in both B. bovis strains. Hence, these genes may be the sole remaining representatives of a BbovVes2 family now largely lost, perhaps replaced by smORF. Ves1 genes share a 3 region that encodes the conserved VESA C-terminus. This is the only region for which a multiple sequence alignment can be made across all species. A maximum likelihood phylogeny was estimated from the 840-character sequence alignment using PHYML (see Figure  4a ). The phylogeny indicates that, while the ancestor of these Babesia species possessed a ves1 gene family, the dimorphism evident in B. bovis (BbovVes1α/1β) and B. bigemina (BbigVes1a/1b) is not ancestral and has independent origins in these lineages.
Multiple VESA2 proteins may be expressed with greater abundance than VESA1 Genome comparison indicates that ves-like genes lacking the conserved 3 region have been independently derived from the canonical ves1 genes during Babesia evolution. Sequence comparison indicates that these ves2 genes are not non-functional ves1 pseudogenes but, in fact, encode highly abundant and polymorphic proteins. To explore the biological differences between ves1 and ves2, we carried out proteomic analyses of global gene expression in B. bigemina PR. We identified 1777 peptides corresponding to 366 predicted proteins in the B. bigemina BOND reference genome (i. e. 8. 2% of the predicted proteome; see Supplementary Table  S1 ). Figure  5  shows the abundance of VESA1 and VESA2 protein relative to each other, and to all other proteins identified in our data set.
Sequence read data have been submitted to the European Nucleotide Archive (http://www. ebi. ac. uk/ena) with the accession numbers ERP000167 and ERP000252. BioProject identifiers (http://www. ncbi. nlm. nih. gov/bioproject/) for the B. bigemina BOND and B. divergens 1802A reference genomes are PRJEB5046 and PRJNA230984, respectively. Genome sequences for B. bigemina strains JG29, BbiS3P and PR, B. bovis C9. 1 and B. divergens Rouen1987 are available from the Wellcome Trust Sanger Institute FTP site (ftp://ftp. sanger. ac. uk/pub/pathogens/ Babesia/). Mass spectrometry and proteomic data have been deposited in the ProteomeXchange Consortium (http: //proteomecentral. proteomexchange. org) via the PRIDE partner repository (http://www. ebi. ac. uk/pride/) with the dataset identifier PXD000629.
ject identifiers (http://www. ncbi. nlm. nih. gov/bioproject/) for the B. bigemina BOND and B. divergens 1802A reference genomes are PRJEB5046 and PRJNA230984 respectively. Genome sequences for B. bigemina strains JG29, BbiS3P and PR, B. bovis C9. 1 and B. divergens Rouen1987 are available from the Wellcome Trust Sanger Institute FTP site (ftp://ftp. sanger. ac. uk/pub/pathogens/ Babesia/). Mass spectrometry and proteomic data have been deposited in the ProteomeXchange Consortium (http: //proteomecentral. proteomexchange. org) via the PRIDE partner repository (http://www. ebi. ac. uk/pride/) with the dataset identifier PXD000629.
CRC samples and patients CRC resection specimens with documented MMR status and available frozen tissue samples containing at least 50% tumor cells were at the pathology departments of the Val d'Aurelle Cancer Centre and Rouen University Hospital. In total, 110 CRC samples, of which 48 had MSI, were selected for this study. Among the 48 MSI CRCs, 11 were from patients with Lynch Syndrome, as defined by the presence of a deleterious The amount of each factor was quantified using two multiplex assays and expressed as pg/µg of total protein extracted from Mss or Msi tumor samples containing at least 50% tumor cells. Data were compared using a non-parametric Mann-Whitney test. abbreviations: crc, colorectal cancers; Mss, microsatellite stable; Msi, microsatellite instable. www. landesbioscience.
72 The first multiplex assay detected 27 proteins (27-plex assay: IL-1β, IL-1ra,    Coupled beads were incubated with 25 µg of total protein in a final volume of 50 µL. Data on the antibody reactions were acquired using the Bio-Plex system, which is a dual-laser, flowbased microplate reader system (BioRad). The concentrations of each target protein (expressed as pg/µg of total protein) were matched to the clinicopathologic data.
Evaluation of tumor-infiltrating inflammatory cells Tissue microarray sections were incubated with monoclonal antibodies against CD3 (clone LN10, Menarini), CD8 (clone C8/144B, Dako), CD45RO (clone UCHL1, Dako), FoxP3 (clone 236A/E7, AbCam), T-Bet (clone 4B10, SCB), CD20 (clone L26, Dako), and CD68 (clone KP1, Dako) on a Autostainer Link48 platform (Dako) using the Flex ® system for signal amplification and diaminobenzidine tetrahydrochloride-chromogen (DAB) as a chromogen. Immunoreactive cells were automatically quantified with the Spot Browser software (Excilone), as previously described. 5 asurements were recorded as the number of positive cells per mm 2 of tissue surface. Results were exported into an Excel file and data from triplicate cores were consolidated into a single score that was matched to the clinicopathologic data.
Acknowledgments This work was supported by grants from  Inserm  ( Institut national de la santé et de la recherche médicale), University of Rennes 1, ANRS 2010, Ligue Nationale Contre le Cancer (Comité d'Ille et Vilaine ) 2009, IFR 140 2010, and BioSit 2012. The authors thank  Dr. Butterfield  for generously providing the HMC1. 1 human mast cell line, the  Biological Resource Center (BRC) of Rennes University Hospital , and the  H2P2 platform of BioSit.
Protein concentrations were determined, using the Bio-Rad protein assay kit (BIO-RAD, Hercules, CA, USA). Protein lysates (40 mg of protein) were subjected to SDS-PAGE and Western blotting using anti-IR, antiphospho-AKT, anti-phospho-S6K1 and anti-phospho-S6. After washing, membranes were incubated with an IRDye infrared secondary antibody (Li-COR Inc. Biotechnology, Lincoln, NE, USA). Bands were visualized by Infrared Fluorescence, using the Odyssey Imaging System (Li-COR Inc. Biotechnology, Lincoln, NE, USA) and quantified by Odyssey infrared imaging system software (Application Software, version 1. 2). Gels were then stripped and total protein forms and B tubulin were quantified to normalize protein expression.
Statistical analysis Statistical analyses followed the methods outlined by Zar  [42]. All data were tested for homogeneity of variances by Leven's tests, and then submitted to one-way ANOVA at each sampling point or to two-way ANOVA with time and diet as independent variables. When diet x time interactions were significant (P#0?05), individual means were compared using Tukey's test. For growth performance data (Table  2 ) the experimental unit was the tank, after pooling 3 fish (3/20), and for the remaining analysis, the experimental unit was individual fish. All data were analysed using IBM SPSS statistics version 19 (IBM Corp. , New York, USA). Differences were considered significant when P,0. 05.
Results Data on weight gain, feed efficiency, nutrient intake and gain and whole body composition of Senegalese sole fed the two diets for 88 days are presented in Table  2. Weight gain and daily growth index were similar with both dietary treatments, although sole fed on LL/HC diet reached a slightly higher final weight than those fed on HL/LC diet. Protein and energy intake were similar between treatments however lipid and starch intake were significantly different due to difference in feed formulae (p, 0. 05). As expected, fish fed on HL/LC diet had a higher lipid intake than those fed on LL/HC diet (1. 78 vs 0. 48), whereas the opposite was recorded for starch intake (HL/LC = 1. 45 and LL/ HC = 2. 38). Protein gain was significantly higher in fish fed the LL/HC diet and no significant differences were recorded for lipid gain, although the value was slightly higher in fish fed the HL/LC diet.
Study population, serum samples, data collection, and ethics statement We obtained sera from 51 adult patients consented and evaluated for participation in the Eramune 02 clinical trial (http://clinicaltrials. gov/ct2/show/NCT00976404) at the Northwestern University clinical site in Chicago, USA. Patients were assessed if they had current CD4+ cell counts $350 cells/ml, continuous suppression of HIV RNA ,50 copies/mL for at least one year and ,500 copies/mL for at least three years. We excluded patients from evaluation who had any of the following conditions: diagnosis of cancer within the last five years, history of autoimmune disease, immunologic therapeutic intervention within the past year, and any co-morbid condition with an expected survival of less than twelve months. As per Eramune 02 evaluation procedures, serum and cell pellets were obtained for evaluation of adenovirus antibodies and total proviral HIV DNA assessment.
Virus production and neutralization assay Pseudotyped viruses (HIV-1 JR-FL , VSV-g pseudotyped HIV-1) were produced as described recently  [44]. Replication competent viruses (HIV-2/HIV-1 chimeras) were generated identically but in the absence of the HIV-1 backbone plasmid pSG3DEnv. To evaluate patient samples for their neutralization potency, serum was heat inactivated and 0. 2 mm filtered before virus incubation. In a preliminary neutralization experiment, crude serum samples were tested against pseudotyped HIV-1 JR-FL. Over 65% of the sera were able to neutralize HIV-1 JR-FL with a reciprocal serum dilution factor ranging from 100 up to. 2700 (data not shown). To minimize false positive results due to the presence of antiretroviral drugs (e. g. efavirenz) in serum, IgG was purified prior to testing.
This also explains the difficulty of accurate characterization of diseases caused by this organism and highlights 16S rRNA PCR and sequencing as the only reliable means to identify it. Genome sequencing was performed using the MiSeq sequencer (Illumina, San Diego, CA) with a 2ϫ 250-bp paired-end run after library preparation with the Nextera Xt sample preparation kit (Illumina). De novo assembly was done using CLC Genomics Workbench v7. 0. 4, and the resulting 48 contigs (Ͼ200 bp and Ͼ20ϫ coverage with an N 50 of 216,921) were used for open reading frame (ORF) prediction and gene annotation, carried out using the Prodigal software in the Prokka annotation suite (http://www. vicbioinformatics. com/software. prokka. shtml). RNAmmer (5) and tRNAscan-SE (6) were used to identify rRNA and tRNAs.
Signal peptides were identified using SignalP v4. 1  (7). The clustered regularly interspaced short palindromic repeats (CRISPR) were identified using CRISPRFinder  (8). The draft genome sequence of Necropsobacter rosorum is made of 48 chromosomal contigs exhibiting an average length and coverage of 52,618. 5 bp and 223ϫ, respectively. The draft genome length is 2,525,687 bp with a GϩC content of 48. 9%. The chromosome contains 2,301 protein-encoding genes and 7 rRNAs (1 rRNA contig and 4 additional 5S rRNAs), 51 tRNAs, 1 transfermessenger (tmRNA), 27 other RNAs, and 188 signal peptides. Of the 2,301 genes, 2,146 (93. 2%) and 1,850 (80. 3%) were assigned a putative function by comparison to the Clusters of Orthologous Groups (COG) and KEGG databases, respectively. In addition, 155 genes (6.
7%) encoded proteins classified as hypothetical. One CRISPR array was detected. Two intact (79. 9-kb and 26. 1-kb) and one questionable (6-kb) phage regions were identified in the genome using PHAST (9) with a total of 133 phage related genes. Using PathogenFinder, a Web server for the prediction of bacterial pathogenicity  (10) , three positive hits for pathogenic genes predicted a potential for human pathogenicity. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers CCMQ01000001 to CCMQ01000048.
Risk factor analysis The risk for a herd to be detected as a carrier of antibodies against C. burnetii in BTM in relation to the two independent variables was assessed using logistic regression: (equation 1) where p(x) is the risk for a herd to be detected as positive, α the intercept, DENS the local cattle density variable (5 classes), ID the in-degree parameter variable (3 classes) and CO the country variable (2 classes). β 1 , β 2 and β 3 are the adjusted regression coefficients associated with the variables estimated by the model. Logistic regressions were performed using R software (R Development Core Team, 2012). ID parameters were calculated using the "EpiContactTrace" package 1 of R software.
Descriptive statistics The local cattle density varied markedly between the two studied areas. The local cattle density was higher in Finistère District than on the Gotland logit p(x) = log = α + β 1 DENS + β 2 ID + β 3 CO p(x) 1 -p(x) ( ) AF ID = P ID x (OR ID -1) 1 + P ID x (OR ID -1) 1 Stefan Widgren and Maria Noremark, 2012. EpiContactTrace: Epidemiological tool for contact tracing. R package version 0. 6. 9. http://CRAN. Rproject. org/package=EpiContactTrace. Island (Fig. 3a ); the average local cattle densities were 75. 4 and 24. 9 animals per km², respectively. During the 2-year period before the ELISA tests, a herd received animals directly from a maximum of 25 other herds (Fig. 3b ), with a similar distribution of the ID parameter in the Finistère and on Gotland (Finistère: median = 0, mean = 1.
The standard curve for calibration was made by 5-fold serial dilutions from 250,000, to 16 parasites per milliliter (7 points) with double-distilled water. A QuantiTect multiplex PCR NoROX (Qiagen, Germany) was used, and the PCR mixture was prepared using 1ϫ QuantiTect buffer, 0. 4 M each primer, and 0. 2 M hydrolysis probe. The temperature profiles were 95°C initial denaturation for 15 min, and then 50 cycles of denaturation (94°C) for 15 s followed by annealing (60°C) for 60 s. An internal control was multiplexed in the reaction based on the human beta-actin gene (GenBank accession number, NM_001101. 3). The primer and probe sequences were obtained from ShineGene Bio-Technologies, Inc. (primers, 5=-ACCGAGCGCGGCTACAG [forward] and 5=-CTTAA TGTCACGCACGATTTCC [reverse]; 6-carboxytetramethylrhodamine [TAMRA] probe, 5=-VIC-TTCACC ACCACGGCCGAG C-3=).
An estimate of the parasite numbers in each sample was derived from extrapolation of the threshold cycle (C T) value obtained for the unknown sample to the standard curve using the Rotor-Gene Q series software v. 2. 0. 2. Based on the calibration experiments, the cutoff C T value was set prospectively to 40. For samples where the qPCR was positive, an attempt was made to determine the Plasmodium species present using nested PCR protocols specific to P. falciparum (microsatellite marker name Pk2), P. vivax (microsatellite marker name 3. 502) and Plasmodium malariae (18S rRNA) as described previously  (18) (19) (20). Positive samples for which there was insufficient DNA to do this or no amplification was obtained were reported as being malaria of indeterminate species. qPCR protocol validation.
In order to rule out cross-contamination of samples during DNA extraction or PCR processing, negative controls consisting of only water were added in a proportion of 8 for every 48 samples. Scale-up. To scale up for high-throughput testing, automated procedures were developed. The samples were labeled using barcodes created from the sample management software Freezerworks (Dataworks Development, Inc. , Lynnwood, Seattle, WA). Automated DNA extraction was performed using a QIA Symphony automated nucleic acid extraction integrated system (Qiagen, Germany), and then the QIAgility liquid handling system was used to prepare master mixes for the PCRs and for adding the DNA template.
The results were determined by a probit analysis using SPSS 11 (SPSS, Inc. , Chicago, IL). A graphical illustration of the probit analysis is shown in Fig. 2. The analytical detection limit (LOD) derived from the plots is 22 (standard deviation [SD], 5) parasites/ml (Fig. 2 ). This implies that when the assay is applied to the 3D7 parasite strain, there is a 95% probability of detecting a parasitemia as low as 22/ml. Given that the sequence of the target fragment amplified from the P. falciparum 18S RNA genes is exactly the same as that in the 18S RNA genes present in P. vivax, P. ovale, P. malariae, and Plasmodium knowlesi, it is unlikely that the analytical sensitivities for these species would be substantially different than that for P. falciparum. Nonetheless, this would need to be confirmed prospectively.
(v) Analytical specificity. The specificity of the qPCR protocol was tested by three approaches: (i) BLAST analysis of the primers and probe sequences against the NCBI databases, (ii) testing of different field samples harboring the four Plasmodium species that infect humans, and (iii) screening for sequence polymorphisms in the 18S RNA Plasmodium gene fragments amplified. (a) BLAST analysis. The specificity of the qPCR was maximized by the selection of primers and probes highly specific to the Plasmodium genes, which were then used under stringent reaction conditions. The primers and hydrolysis probes selected had already been validated by  Kamau et al. (2011)   (11) , and were shown to have very high specificity for Plasmodium sp. 18S RNA. We conducted updated (9 January 2014) searches using Nucleotide BLAST to confirm that these primers would be unlikely to hybridize and amplify any unrelated genes that have been sequenced recently.
The precision data were calculated on the basis of the C T values of the amplification curves and the parasitemia/ml values. The data obtained were used to determine the standard deviation and the variance. Assessment of precision was undertaken by testing five of the serially diluted calibration samples (corresponding to 10000, 2000, 400, 80, and 16 parasites/ml, see above) on six separate occasions. The mean coefficient of variation for the cycle threshold across the five samples was 0. 78% (Table  4 ), which translated to a coefficient of variation for parasites/ml of 13. 9% (Table  5 ). (vii) Robustness. Thirty confirmed Plasmodium-negative blood samples were spiked with 100 parasites/ml of P. falciparum 3D7 control samples. After extraction using the automated DNA extraction machine QIAsymphony and the DSP DNA midi kit (Qiagen, Germany), these samples were analyzed with the qPCR.
ACKNOWLEDGMENTS We thank  Mehul Dhorda  and  Anna Maria Annerberg  for their help. This study was supported by  Mahidol University , the  Wellcome Trust  as part of the WT101148MA strategic award "Eliminating malaria to counter artemisinin resistance. "Funding was also obtained from the  Bill and Melinda Gates Foundation , SIgN, and from the  Horizontal Pro-gramme on Infectious Diseases  under the  Agency for Science, Technology and Research (A*STAR) (Singapore) , the  Wellcome Trust Mahidol University Oxford Tropical Medicine Research Programme. We declare that we have no conflicts of interest.
For the supplementary tests in the age subgroup 0-2 years, a Bonferroni correction was applied, and resulting p values were interpreted at a significance level of 1. 25%. Missing data were handled by using the last available assessment. For confirmatory purposes, analyses were performed on the microbiologically positive per protocol set (MPPS) and for the contralateral infected eye. Tolerance and safety were evaluated for the safety population (all patients who used study medication).
Clinical efficacy On D3, the clinical cure rate for the worse eye was significantly higher in the azithromycin group compared with the tobramycin group for patients in the MFAS (47. 1% vs 28. 7%, respectively; p=0. 013) (table  2 ). On D7, there was no statistically significant difference in clinical cure rates between treatment groups (89. 2% vs 78. 2%, respectively; p=0. 077), and non-inferiority of azithromycin to tobramycin was demonstrated. Similar rates were found for the contralateral eye and in the MPPS (data not shown). Improvements of other ocular signs (folliculo-papillary reaction, eyelid erythema, eyelid swelling) were also noted on D3 and D7, but were not significantly different between groups (D3: p=0. 067, 0. 662 and 0. 498, respectively; D7: p=0. 172, 0. 421 and 0. 165, respectively).
DISCUSSION Randomised controlled studies with, when possible, stratification by age group (ie, neonates, infants, children and adolescent) and designed to establish the efficacy and safety of medicinal products in the paediatric population are strongly encouraged by regulatory health authorities  19. Most currently licensed topical antibiotics for bacterial conjunctivitis have been approved based on clinical studies conducted mainly in adults  11  , with insufficient clinical data in newborns and infants (ie, <24 months). This study has now established the efficacy and safety of azithromycin 1. 5% eye drops in children with an average age of 3 years old. Patients were mainly recruited in hospital centres where usually only very young children are seen for treatment of bacterial conjunctivitis.
RESULTS AND DISCUSSION This study was initiated after we encountered a patient with peripheral T cell lymphoma who developed chronic GVHD and simultaneous HE. Because HE was present at the time of diagnosis of lymphoma, a relapse of the lymphoma was suspected, but this was ruled out by a different TCR rearrangement on Southern blot analysis. Five additional patients with HE were then analyzed for TCR d locus recombination by Southern blot analysis, which revealed clonal T cell expansion (data not shown). We studied these T cell expansions through quantitative determination of Vb usage using real time PCR and CDR3 size polymorphism (spectratyping or immunoscope analysis). Ten patients were studied, 6 of whom exhibited a clonal expansion profile. Comparisons of these 6 patients with HE and 4 controls showed massive expansions in the HE group (with >40% of families in 2 patients), especially within the Vb3 and Vb6 families (Figure  1A  and Supplemental Figure  S1 ).
This work was supported by grants to G. H. from the  University of Franche-Comte(UFC)  and the  Region Franche-Comte ( RECH-FON12-000013 ). W. A. is a recipient of a doctoral scholarship from the  Higher Education Commission, Pakistan. A. K. is a recipient of a postdoctoral fellowship of the  Region Franche-Comte  ( 2012C-06102 ). The authors thank  Diasorin SA  for its financial support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.