dataesr/scientific-paragraphs-categorization huggingface dataset:
5 μ g mL -1 ) was added to the cell culture medium to select for stably transduced cells. The cells were incubated at 37 °C in a humidified atmosphere of 95% air and 5% CO 2. Construction of C6-pEIRES-HA-ferritin and C6-pEIRES-HA-ferritin-M6A cells. The murine ferritin h-chain cDNA (GenBank accession no. NM-010239) with an HA (influenza haemagglutinin) tag (HA-ferritin) and a Kozak sequence at the N-terminus was generated by RT-PCR. Additionally, a recombinant ferritin-M6A fusion protein was generated in which the M6A peptide was attached to the C-terminus of ferritin (ferritin-M6A). The two constructs were cloned into the pEIRES mammalian expression vector. Rat C6 glioma cells were transfected with pIRESHA-ferritin/HA-ferritin-M6A plasmids stably selected with puromycin. Ferritin and ferritin-M6A expression levels were monitored by Western blot analysis.
Acknowledgements We thank  ESRF (Grenoble, France ) beamline ID14-4 and SOLEIL beamline SWING for assistance during data collection. We also thank  Boaz Shaanan  and  Anat Shahar  ( MCRC unit ) for their advice during X-ray data collection and processing, and to  Ben A. Friesem ,  Yael Kalisman ,  Sharon G. Wolf  and  Eyal Shimoni  for the TEM. Hagit Dafni ,  Dorit Granot  and  Yifat Edrei  helped with some of the MRI experiments. M. N. is incumbent of the  Helen and Morris Mauerberger Chair in Biological Sciences. R. B. gratefully acknowledges the support of The Joseph and May Winston Career Development Chair in Chemical Engineering. The research leading to these results has received funding from the  EU   Seventh Framework Programme  ( FP7/2007-2013  under grant agreements ⚬  239182 ), from the  Israel Science Foundation  and the  Israeli Ministry of Science Technology and Space  (to R.
2 ). We also attempted to transfect into the mosquito-transmissible NF54 wild type background on three separate occasions without success (data not shown). Proceeding with the two lines in the D10 background, we observed both Pf apiG3PAT (À) lines were viable and grew normally as determined by frequency of subculturing, suggesting Pf apiG3PAT was indeed dispensable for blood stage growth. As we had employed a transfection strategy that relied on negative selection to eliminate wild type parasites rather than cloning by limiting dilution  (Maier et al. , 2006) , we also sought to verify the disruption of the Pf apiG3PAT locus by whole genome sequencing of one line. This analysis again confirmed the successful integration of the hDHFR cassette into the Pf apiG3PAT locus, and although three single base changes were identified between the mutant line and the wild type parent across the entire genome, targeted PCRbased sequencing of these regions in the second Pf apiG3PAT (À) line revealed that they were not conserved (sequencing data deposited in NCBI Short Read Archive under accession number SRP071808, PCR data not shown).
Pb apiG3PAT is targeted to the apicoplast and expressed in liver stage parasites Pb apiG3PAT shares strong sequence similarity with Pf apiG3PAT and is likewise predicted to possess an apicoplast targeting sequence at its N-terminus (Supplementary Fig. 1 ). To verify that Pb apiG3PAT is targeted to the apicoplast, we used a 3′ gene replacement strategy to generate the Pb apiG3PAT ha gfp transgenic line, which expressed the full-length protein fused to C-terminal hemagglutinin (HA) and GFP tags (Supplementary Fig. 4 ). We chose this approach as it resulted in the tagged protein being expressed from the endogenous promoter, and could therefore also provide information about when in the life cycle Pb apiG3PAT was expressed. No GFP fluorescence was observed in blood stage parasites, oocysts or salivary gland sporozoites by live fluorescence microscopy, indicating Pb apiG3PAT was not expressed at detectable levels in these stages (data not shown).
1% polyethyleneimine. Images were acquired using a Leica SP2 inverted confocal microscope at ambient temperature, and merged and contrast adjusted using ImageJ software (NCBI). Immunofluorescence microscopy of Pf apiG3PAT 1-70 gfp parasites was performed by fixing in paraformaldehyde/ glutaraldehyde and permeabilizing in Triton X-100 as previously described  (Tonkin et al. , 2004)  but without the sodium borohydride treatment step. Labelling was performed with mouse anti-GFP (Roche), rabbit anti-ACP (our laboratory  (Waller et al. , 2000) ), Alexa Fluor goat anti-mouse-488 and Alexa Fluor goat anti-rabbit-546 (Molecular Probes). Samples were then stained with 1 μg ml À1 DAPI and mounted in Fluorescence Mounting Medium (DAKO) before imaging as above.
, 2012). Briefly, PCR-free libraries were prepared using NEBNext DNA Library reagents (NEB) and NEXTflex DNA Barcodes (Bioo Scientific). Eight libraries were multiplexed with 8% PhiX control and run across two lanes on the Illumina HiSeq 2500 system using single-end sequencing. Sequencing data was analysed using Galaxy  (Giardine et al. , 2005; Blankenberg et al. , 2010; Goecks et al. , 2010). Reads were mapped to the P. falciparum 3D7v. 10. 0 reference genome (http://plasmodb. org/common/downloads/release-10. 0/Pfalciparum3D7/) using the Burrows-Wheeler Alignment tool  (Li and Durbin, 2009). Variants were called using Freebayes  (Garrison and Marth, 2012) , filtered for quality and read depth with GATK tools  (Auwera et al. , 2013)  (Quality > 500, Read Depth >75), and annotated using SnpEff  (Cingolani et al.
Pellets were re-extracted using methanol:water (2:1 v/v), and the second supernatants were then combined with the first extract and dried then stored at À80 C. Prior to GC-MS, extracts were partitioned into chloroform:methanol:water (1:3:3 v/v) and the apolar (lipid) phase was dried, derivatized to fatty acid methyl esters and analysed on an Agilent 7890B-5977A GC-MS system using a DB-5MS-DG column as previously described  (MacRae et al. , 2012). Data analysis was performed using MassHunter (Agilent) and fatty acid species were identified and quantified by comparison to authentic standards. Experiments were repeated with four biological replicates, and statistical significance between mean fatty acid abundances evaluated by t-test with correction for multiple testing using Prism v 6. 02 (GraphPad).
Live imaging of liver stage parasites was performed 48 h post-infection. Cells were stained briefly with 5 μg ml À1 Hoechst 33342 (Life Technologies), then imaged using a Leica SP5 inverted laser scanning confocal microscope in a 37 C temperature controlled chamber. Images were taken sequentially for the two channels and processed using ImageJ software (NCBI). Immunofluorescence microscopy of liver stage parasites was performed 48 post-infection. Cells were washed in PBS, fixed in 4% paraformaldehyde, washed again and permeabilized in 0. 15% Triton X-100 before blocking in 3% bovine serum albumin. Labelling was performed with mouse anti-GFP (Roche), rabbit anti-FabI (gift from David Fidock; used as anti-ACP antibodies were temporarily unavailable), Alexa Fluor goat anti-mouse-488 and anti-rabbit-546 secondary antibodies (Molecular Probes).
Cells were fixed as above and labelled with mouse anti-HSP70 (gift from Moriya Tsuji), goat antimouse Alexa Fluor 488 (Molecular Probes) and DAPI, before mounting in Fluorescence Mounting Medium (DAKO). Imaging was performed using an OMX V4 Blaze in wide field deconvolution mode, with z-slices acquired across the entire depth of the parasites. Image deconvolution and maximum projection were performed using softWORx software (Applied Precision), and parasite cross-sectional areas calculated using ImageJ (NCBI). Experiments were repeated three times with >50 parasites imaged per replicate, and statistical analysis was performed using Prism version 6. 0 (GraphPad). Detached cell and merosome formation by parasites was assessed by collecting culture supernatants 66 and 72 h post-infection. Cells were stained briefly with 5 μg ml À1 Hoechst 33342 (Life Technologies), the counted using the Leica SP2 inverted microscope in epifluorescence mode.
Acknowledgements MJS was supported by an  Australian Postgraduate Award. GIM gratefully acknowledges a Program Grant from the  National Health and Medical Research Council (Australia)  and a  Discovery Grant  from  Australian Research Council. CYB was supported by  ANR-RPDOC/ Atip-Avenir CNRS/ Finovi Grant/Labex Parafrap grants (Apicolipid projects ) and a  FP7 Marie Curie Actions International Outgoing Fellowship. ML was funded through generous support from the  Burroughs Welcome Fund Investigators  in the  Pathogenesis of Infectious Disease Award  ( 1007041. 01 )and start-up funding from  The Pennsylvania State University. We also thank the  Australian Red Cross  for blood.
The 4 geomorphologic landscapes were labelled l = 1 (Coastal Plain), l = 2 (Northern Chain), l = 3 (Central Massif) and l = 4 (Inini-Camopi chain)  to indicate their position on the North-South gradient that spread from the Atlantic coast to the Amazonian frontier with Brazil. Insects were captured using light traps located in the sylvatic environment during c 1 = 20, c 2 = 58, c 3 = 93, and c 4 = 85 nights spent all along the year in the 4 landscapes. Light traps consisted of a vertical white sheet lit by a 250 watts mercury vapour lamp, combined with a 400 watts lamp fixed a few meters above ground on a tower platform to increase attractiveness. According to the PLoS open access policy, these data are available on request. Specimens landing on the sheet were collected, placed in individual plastic vials and brought to the laboratory for species determination, using the systematic revision of  [43] , and molecular diagnosis of infection by T.
The sets of parameters of all models used to analyse SD and ITc data were identified by applying the equal/unequal relationships in the exact same way as for the A data. A one by one description of the 15 hypotheses and models applied to A, SD and ITc data can be found in Table  A in S2 Table. Fitting the models to data. The first step in the model selection approach consists of identifying the best fit of each of the models to the data. Each of the 15 models were then fitted to the A, SD, or ITc data observed across landscapes according to a log likelihood value that was defined as LLH m ¼ X l logpðX l ¼ O l jθ m Þ ð 1Þ where X l , O l and θ m are vectors containing statistical variables representing expected values in landscape l, observed values in landscape l, and the set of model (m) parameters to be estimated through the fitting process.
Infection by T. cruzi (ITc). We fitted the models to the ITc data for each triatomine species. The vector X l then contained a unique statistical variable I s,l corresponding to the expected number of infected individuals of species s in landscape l, O l contained the observed number i s, l of infected individuals of species s in landscape l, and θ m was the set of rates of infection r s,1 of species s in landscape l that were defined according to the hypothesis and model considered. The rates of infection in θ m were estimated by maximizing the LLH m value with the probabilities p(X l = O l |θ m ) defined according to a Binomial distribution: pðX l ¼ O l jθ m Þ ¼ n s;l i s;l ! ðr s;l Þ i s;l ð1 À r s;l Þ n s;l Ài s;l ð4Þ where n s;l i s;l ! stands for the binomial coefficient. Comparisons between models.
The second step in the model selection approach consists of comparing the 15 models according to their ability to fit to the data (as measured by the LLH obtained for the best fits) and with respect to the number of their parameters. Such comparisons can be made using the standard Akaike Information Criterion (AIC) that is calculated for each model as: AIC ¼ À2LLH þ 2P ð5Þ P was set to the number N p of parameters of the model when analysing A, and to N p (1 -(N p + 1)/N) -1 when analysing the SD and ITc. In the second case, where N = S l n l refers to the total number of adult insects in the dataset, the correction factor was introduced to minimize the risk of over-fitting associated with ratio N/N p lower than 40, which provided a 'corrected' AIC referred to as AICc  [44]. The rationale behind these comparisons is to allow evaluating when the increase in the complexity of the models (in our case from model 1 to 15) efficiently improves the description of the data.
Geographical distribution of triatomines and their infection by T. cruzi The distribution of triatomines in French Guiana was investigated by collecting insects in 22 sites covering most of this territory (Fig 1A ). A total of 731 adult specimens were captured during 256 nights of trapping. About 68. 7% were males and 31. 3% females. They belonged to 8 different species, with a dominant species (Panstrongylus geniculatus) representing 62. 8% of the community, three secondary species (Rhodnius pictipes, Panstrongylus lignarius, Eratyrus mucronatus) whose abundances add up to 32%, and a set of four other species (Panstrongylus rufotuberculatus, Rhodnius robustus, Rhodnius amazonicus, and Rhodnius paraensis) that collectively account for the remaining 5. ). None of the other models that collectively accounted for all possible kinds of geographical heterogeneity was able to provide a better fit to the data despite their additional parameters.
This work has benefited from an " Investissements d'Avenir " grant managed by  Agence Nationale de la Recherche  (CEBA, ref. ANR-10-LABX-25-01 ). This work was performed within the framework of the  LABEX ECOFECT  ( ANR-11-LABX-0048 ) of  Université de Lyon , within the program " Investissements d'Avenir"  ( ANR-11-IDEX-0007 ) operated by the  French National Research Agency (ANR). This work was supported by  PO-FEDER  contemporary loss of biodiversity.
Structural modeling and molecular dynamics simulation studies of MCs The three-dimensional (3D) structures of the four MC constructs (MC75, MC86, MC75S and MC86S) were predicted using the internal coordinate program JUMNA  (47). In particular, a closed, planar circular DNA molecule was created using the standard value of rise (3. 38 Å), and twist corresponding to linking number 7 expected for 75 bp with a helical repeat of 10. 5 bp (i. e. 33. 6 • ). A similar procedure was used to construct an 86 bp-long MC with linking number 8, using a value of twist of 33. 5 •. The presence of phased A-tracts in the sequence of the four constructs is expected to limit variations in their rotational register. In order to identify the most stable register, the sequence of each of the four constructs was threaded through the MC, by replacing each base pair with the preceding and then subjecting the resulting structures to conjugate gradient energy minimization using the AMBER parm99 force field  (48)  with the parmBSC0 modifications  (49).
Analysis of minicircle curvature In order to define whether the major groove a given location along the MC is facing toward the inside or the outside of the MC, we studied the local curvature of the predicted MC structures, using a procedure that uses the helical axis calculated by the Curves+ program  (62, 63). First, a locally optimal circle is fit through three equally spaced points along the helical axis, corresponding to base pair levels. The spacing of these points determines the sensitivity of the results to local deformations of the helical axis: best results for the present application were obtained using a spacing of 5 bp. Next, the center of the fitted circle is located, and its curvilinear helicoidal coordinates are measured using a procedure similar to that described in  (64).
Mapping of integration sites and correlative studies In order to identify the absolute position of the integration sites for each sequence of the 24 libraries, a custom python script was implemented to read these sequences and count, for each position within the region of interest, the number of integrations achieved. These positions are calculated from the distances between the acceptor and the donor primers. The output is a list of counts per position, for each library. In this study, 24 libraries of FastQ files have been analyzed, containing from 15 000 to 74 125 sequences. A first step of filtering excluded sequences without the two good primers (acceptor and donor) expected. A second filtering allowed the exclusion of sequences having the integration site outside the region of interest.
ACKNOWLEDGEMENTS We thank  M. Naughtin ,  F. Di Nunzio ,  P. Charneau  and  Céline Ralec  for scientific discussions and  L. Ma  and  C. Calmels  for technical help. High-throughput sequencing has been performed on the  Genomics Platform, member of 'France Génomique' consortium. We acknowledge  GENCI  for computer time on the CINES supercomputer OCCI-GEN.
FUNDING  ANRS  [ AO2014-02  to V. P. , M. L. ] and [ AO2012-02  to M. R. and J. B. ];  SIDACTION [AI25-1-02332  to M. P. , A. J. , M. R. , R. L. , M. L. ] and to M. R. and J. B. ;  ANR, Genomics Platform, member of 'France Génomique' consortium  [ ANR10-INBS-09-08  to C. B. ];  French Infrastructure for Integrated Structural Biology [FRISBI ,  ANR-10-INSB-05-01  to M. R. , J. B. ]; INSTRUCT, part of the  European Strategy Forum on Research Infrastructure (ESFRI)  supported by national members subscription (to M. R. , J. B. ). Funding for open access charge:  ANRS  [ A02014-02 ].
abscessus  (27). Further study found that some STB isolates lacked the insertion element IS1081, while a new ISMycA1 (GenBank accession number AJ619854) was discovered in the "M. canettii" CIPT140010059 genome  (12). ISMycA1 encodes a transposase which, surprisingly, shares 48% amino acid sequence identity with IS-encoded transposases of the Mycobacterium ulcerans plasmid  (28). ISMycA1 is a distinctive characteristic of STB in comparison with the other MTBC members  (12). Indeed, the original "M. canettii" strain (CIPT 140010059) and So93 are indistinguishable from the other MTBC members as a result of sequencing of 16S rRNA and housekeeping genes (rpoB, katG, rpsL, and gyrA)  (7). Nevertheless, further analysis of six housekeeping genes yielded 14 (A-N) STB clonal groups  (12, 17). The multiple locus variable number of tandem repeats analysis (MLVA)  (10, 11)  highlighted that ETR-A (allele 10), ETR-C (alleles 6 and 10), MIRU-02 (allele 3), MIRU-40 (allele 8), and Mtub29 (allele 5) were unique to STB strains  (10).
A, mc 2 or mc 2 ::pKirT-pstP cultures were initiated at an A 600 of 0. 1 and grown in the absence or the presence of 50 ng/ml ATc for 12 h. Whole cell lysates (WCLs) were prepared, and 35 g (for PstP) and 20 g (for GroEL1) of lysates were resolved on SDS-PAGE and probed with ␣-PstP and ␣-GroEL1 antibodies. B, mc 2 or mc 2 ::pKirT-pstP cultures were seeded at an initial A 600 of 0. 02 and grown in the absence or presence of 50 ng/ml ATc. Absorbance was measured every 3 h for 30 h. The experiment was performed in triplicate, the mean was plotted with the help of GraphPad Prism version 6 software, and the error bar represents S. D. C, cfu were enumerated at 0 and 30 h from the growth curve experiment in B. D, mc 2 or mc 2 ::pNit1-pstP cultures were seeded at an initial A 600 of 0. 1 and grown in the absence or presence of 5 M IVN.
The data were plotted using GraphPad Prism version 6 software. To enumerate cfu at 0 and 30 h, cultures were harvested, washed twice with PBST (PBS containing 0. 05% Tween 80), resuspended, and serially diluted, and different dilutions were plated on 7H10 agar plates containing OADC. In the case of M. tuberculosis (Rv) or M. tuberculosis mutant (Rv-cd-pstP), cultures were seeded at an A 600 of ϳ0. 1, either in the presence or absence of ATc, and cultures were grown for 4 days. cfu were determined on day 0, day 2, and day 4 on 7H10 agar plates in the absence of all antibiotics. Western Blotting Analysis-Cultures of M. smegmatis mc 2 , mc 2 ::KirT-pstP, mc 2 ::pNit1-pstP, mc 2 -cd-pstP, or mc 2 -cd-pstP:: pstP wt/mutant strains seeded at an A 600 of ϳ0. 1 were grown for different times in the absence or presence of ATc or IVN or ATc ϩ IVN.
Acknowledgments-We thank the Tuberculosis Aerosol Challenge Facility (TACF) of International Center for Genetic Engineering and Biotechnology,  New Delhi (ICGEB)  for support in all animal experiments. We thank  Dr. Dhiraj Kumar  for helpful discussions and for allowing use of the TACF facility. We thank the scanning electron microscopy facility and the biocontainment facility at the  National Institute of Immunology. We thank the confocal microscope facility and transmission electron microscopy facility at  CSIR-Institute of Genomic and Integrative Biology. We thank  Rekha Rani ,  Mahendra Pratap Singh , and  Manish Kumar  for support in SEM/TEM and confocal imaging. We thank  Dr. Christopher Sassetti ,  Dr. Graham Hatfull ,  Dr. Eric Rubin , and  Dr. William Jacobs  for providing the plasmids.
Study Design and Setting Data from an international, multicenter, and cross-sectional MusiQoL validation study were used. 20 Patients were recruited between January 2004 and February 2005 at neurological departments in 15 countries: Argentina, Canada, France, Germany, Greece, Israel, Italy, Lebanon, Norway, Russia, South Africa, Spain, Turkey, UK, and USA. This study was performed in accordance with the Declaration of Helsinki and all applicable regulatory authority requirements and national laws (Institutional Review Boards or Independent Ethics Committees in accordance with the local requirements of each of the 15 countries). Written informed consent from patients was obtained before any study procedures were performed.
Strengths and Limitations A limitation in our study is that we used the entire sample only for the MIRT model calibration. MCAT simulations were performed using only the complete response patterns. To overcome this issue, it should be possible to use a well-known data imputation method, such as the multiple imputations approach, and use the imputed dataset for both MIRT model calibration and MCAT simulations. Using multiple imputations on our dataset for MIRT calibration resulted in a deterioration of the model fit. This approach encouraged us to use the raw dataset in this study, given that the sample was large enough to obtain robust results. Even with the large overall sample size in this study, the representativeness of our sample should be discussed. Compared with the most important longitudinal studies that parallel the present study, our patients were younger or older (others had mean ages of 42,  53  44, 54 and 34 years),  55  had less severe baseline disability statuses (mean EDSS scores of 4.
ACKNOWLEDGMENTS We thank  A. Bendelac ,  J. Y. Bertrand , and  D. Guy-Grand  for critical reading. We are thankful to  C. Possot  to have started the breeding of the different mouse lines. We acknowledge the  Center for Human Immunology and Cytometry platform at Institut Pasteur  for support. This work was supported by the  Institut Pasteur, INSERM, UniversiteParis Diderot , and by the  Ministere de la Recherche  (to S. C. ), the  Association pour la Recherche sur le Cancer  (to S. C. and R. G. ), the  REVIVE Future Investment Program  and the  Agence Nationale de Recherche (ANR ;  grant ''Twothyme''  to A. C. ), the  Swiss National Science Foundation and Bourse Roux  (to S. S. ),  ANR  grant  ''Myeloten '' (to R. G. ), and the  Institut National du Cancer (Role  of the immune microenvironment during liver carcinogenesis, to R.
Developing eCASH The guiding principles of eCASH are clear and components of the eCASH concept are supported by current guidelines; details of this philosophy of care can be expected to evolve in response to clinical trial data. Among trials currently in progress that may be expected to influence the final form of eCASH are: SPICE III (NCT01728558); MENDS II (NCT01739933); NONSEDA (NCT0196768); AWARE (NCT01617265); DESIRE (NCT01760967); and VITAL-ITY (NCT02143661), which examines environmental influences on ICU outcomes. A longer-term goal would be to evaluate the clinical effectiveness of a prespecified eCASH bundle in a randomised clinical trial.