dataesr/scientific-paragraphs-categorization huggingface dataset:
Briefly, viral RNA was extracted from the HIV-1-infected individual's plasma (150 ml) using the QIAamp Viral RNA Mini kit (Qiagen, Valencia, California, United States) according to the manufacturer's instructions initially. The viral RNA was then subjected to a one-step reverse transcription polymerase chain reaction (RT-PCR) to generate a fragment of pol gene (1864 base pairs) spanning protease and reverse transcriptase regions as previously described  [1, 3, 10]. The PCR products were purified (Qiagen, Valencia, Spain) and directly sequenced. The sequences generated were edited using the SeqMan II software program from the DNAStar package v. 5. 08 (Lasergene, Madison, WI). To eliminate potential contamination, all of the sequences obtained were first subjected to an HIV-1 Blast search to compare with related reference sequences in the HIV Databases, funded by the Division of AIDS of the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) (http://hivweb.
Drug resistant mutations Drug resistance mutations in protease and reverse transcriptase genes were identified by using the last updated online Stanford Resistance Database tool: HIVdb program-Genotypic Resistance Interpretation Algorithm (version 7. 0, http://sierra2. stanford. edu/sierra/servlet/JSierra?action=sequenceInput). In additional, sequence data were also submitted and evaluated by using the last updated list for surveillance of transmitted drug-resistant strains in untreated patients (ver. 6. 0 http://cpr. stanford. edu/cpr. cgi). Resistance mutations identified with HIVdb algorithm were also interpreted referring to the ''Update of the drug resistance mutations in HIV-1: March 2013'' published by IAS-USA Drug Resistance Mutations Group.
HIV-1 genotyping and phylogenetic analysis HIV-1 subtype and CRF designations were determined by uploading sequences into the REGA HIV-1 automated Subtyping Tool version 2. 0 (http://www. bioafrica. net/rega-genotype/html/ subtypinghiv. html), and confirmed by in-house phylogenetic analysis on nucleotide acid sequences of pol as previously described  [1, 3, 10]. For phylogenetic analysis, reference sequences representing overall HIV-1 group M genetic variability were obtained from the National Institutes of Health/National Institute of Allergy and Infectious Diseases (NIH/NIAID)-funded HIV database, including all subtypes, sub-subtypes, and circulating recombinant forms (CRFs) references. CRFs identified most recently, such as CRF62_BC  [11] , CRF64_BC  [12] , and CRF65_CPX  [8] , etc. , were also included.
All reference sequences and our newly obtained nucleotide sequences were aligned using Muscle  [13]  and followed by manual editing. Neighbor-joining (N-J) tree was drawn under the HKY model of evolution with 1000 bootstrap replicates in SeaView v4. 3  [14]. Sequences assigned to specific HIV-1 subtypes were finally confirmed by constructing maximum likelihood (ML) phylogenetic sub-trees as described below. To determine a recombinant virus, similarity analysis and bootscanning were performed with the Simplot version 3. 5. 1 software  [15]. Phylogenetic inter-relationships among viral sequences were estimated using maximum likelihood (ML) phylogenies with PHYML 3. 0  [16]  with the minimal number of reference sequences. The whole sequence alignment was split into 6 subdatasets based on the neighbor-joining tree, followed by gapstripping and ML phylogenetic reconstruction.
Identification of Transmission Clusters To evaluate the global profile of the local HIV-1 transmission, we split the sequence alignment into 6 sub-datasets, and implemented maximum-likelihood phylogenetic reconstruction on each sub-dataset to obtain the genetic distances. These subdatasets were designate with the data of a representative references, such as CRF08_BC (1467 base pairs remained after gap stripping), 07_BC (1666 base pairs), B/CRF51 (1711 base pairs), CRF01_AE (1194 base pairs), C/CRF57 (1752 base pairs) and B'/C URF (1708 base pairs). As screened by our criteria (bootstrap value. 98% and branch lengths,0. 015), 21. 2% (60/ 283) of all sequenced samples analyzed segregated into 21 transmission clusters (Figure  4 ). Of those 21 transmission clusters identified, 17 chains had been supported by contact tracing (including the sex, age, habitation, occupation, risk infectors in the same cluster), while four clusters (clusters 3, 6, 8 and 9) remained ambiguous.
These results indicated the local HIV-1 genotypes divergence did increase rapidly in this region. A series of novel circulating recombinant forms have recently been identified in China, especially in Yunnan province, including CRF55_01B (identified from MSM in China)  [23] , CRF57_BC  [7] , CRF59_01B (from MSM in northeast China)  [24] , CRF61_BC (CRF found among the heterosexual population in different regions in China)  [25] , CRF62_BC  [11] , CRF64_BC  [12] , CRF65_CPX (first novel HIV-1 second-generation inter-CRF in China)  [8]. In the present study, we included available sequences of CRFs in HIV-1 sequence database into our reference Table  2. Cont. pool. The breakpoints of our URFs differed apparently from those of any known CRF, implying the unidentified novel CRFs emerged in this region.
Acknowledgments We acknowledge  Liang Yu ,  Wengdi Deng ,  Veronique Jagot ,  Ju Yuan ,  Jun Zheng , and  Yingyun Zhou  for technical assistance. We thank the  Laboratory of National Key Discipline of Clinical Foundation of Chinese Medicine  and the '' Program 211'' of Guangdong province  at the  Guangzhou University of Chinese Medicine  for providing some laboratory facilities used in this study. Thank the TH-1/GZ, GuangZhou Supercomputing Center to supply support on PhyML phylogenetic reconstruction computing.
Background: Rifampicin and protease inhibitors are difficult to use concomitantly in patients with HIV-associated tuberculosis because of drug-drug interactions. Rifabutin has been proposed as an alternative rifamycin, but there is concern that the current recommended dose is suboptimal. The principal aim of this study was to compare bioavailability of two doses of rifabutin (150 mg three times per week and 150 mg daily) in patients with HIV-associated tuberculosis who initiated lopinavir/ritonavir-based antiretroviral therapy in Vietnam. Concentrations of lopinavir/ritonavir were also measured. Methods: This was a randomized, open-label, multi-dose, two-arm, cross-over trial, conducted in Vietnamese adults with HIV-associated tuberculosis in Ho Chi Minh City (Clinical trial registry number NCT00651066).
Data are presented as medians with the range in parenthesis RBT = rifabutin; OD = once daily; TPW = three times per week; Cmax = peak concentration; C0 = trough concentration. All patients: data pooled whatever the RBT dosing 150 mg OD or 150 mg TPW. doi:10. 1371/journal. pone. 0084866. t004 guinea pigs have found Cmax to be the critical pharmacokinetic parameter  [31, 32] , while other studies on mice and using hollow fibers have found that AUCt is a superior parameter  [33, 34]. For these reasons, both parameters were measured and reported on in this study, showing that rifabutin and 25-O-desacetylrifabutin levels were higher using the daily dose with LPV/r than without, and with the average concentration at a steady state being one third higher using 150 mg daily and 40% lower using 150 mg TPW compared with rifabutin alone.
Ancillary parameters Meteorological data -air temperature, relative humidity, barometric pressure, wind speed, and wind direction -were provided by the local meteorological station. Radon 222 and 220 (Rn) are monitored with a precision of 10 % on a 2 h basis. The method is described in detail by  Polian et al. (1986)  and  Kritz et al. (1990). It is assumed that 222 Rn and 220 Rn are in radioactive equilibrium with their short-lived daughters so that 222 Rn and 220 Rn concentrations can be calculated by measuring the concentration of their short-lived decay products. Upon formation these short-lived daughters are quickly and irreversibly scavenged by aerosols and sampled by filtration. The detection then relies on the measurement over time of the decrease of alpha radioactivity of these aerosols.
Quality assurance and quality control procedures Fortnightly to monthly routine maintenance operations on the denuder, RPF, soda-lime trap and filters, along with thor-ough cleaning steps and weekly site visits enabled collecting contamination-free air samples. The accuracy of flow measurements was checked twice a year with a calibrated flow meter (Definer 220). An automatic calibration step of the 2537B analyzer was carried out every 69 h with an internal mercury permeation source. The accuracy of this permeation source was annually checked against manual injections of saturated mercury vapor taken from a temperature-controlled vessel, using a Tekran 2505 mercury vapor calibration unit and a Hamilton digital syringe, and following a strict procedure adapted from  Dumarey et al. (1985). Both routine and exceptional maintenance were compiled and archived via a software program developed at the LGGE (Laboratoire de Glaciologie et Géophysique de l'Environnement).
This software program also enabled rapid data processing in order to produce clean time series of GEM, PBM and RGM. Screening criteria for data validation/invalidation were inspired by standard operative protocols used by the Canadian Atmospheric Mercury Measurement Network (CAM-Net) and the Atmospheric Mercury Network (AMNet;  Steffen et al. , 2012). To ensure uniformity across the network, GMOS is currently developing a quality control (QC) software and an intercomparison with the AMNet QC software will be undertaken. The best estimate of the detection limit (DL) for GEM measurements was 0. 10 ng m -3  (Tekran, 2011)  and 10 injections of 15 µL of saturated mercury vapor were performed to check the repeatability of the system response. The system gave a relative expanded uncertainty of 1 % (95 % confidence level).
Validated 5 min GEM data subsets were compiled into hourly average data when the hourly recovery rate exceeded 50 % (number of valid data records collected vs. that possible over the reporting period). RGM and PBM sampling resolution was shifted from 3 to 4 h after a few days due to very low concentrations, and the detection limit therefore decreased from 0. 42 to 0. 28 pg m -3 based on the sampling volumes and GEM detection limit  (Wang et al. , 2014). The mean of the distributions was estimated using the Kaplan-Meier cumulative proportion-based method. It provides more reliable results for data sets containing below-detection limit values than the substitution method, i. e. , replacement of below-detection limit values by a constant equal to 0, 0. 5 DL or DL  (Helsel, 2005). Overall, 75 and 50 % of RGM and PBM measurements, respectively, were below the limits of detection resulting in differences for mean values of up to 60 and 15 %, respectively, comparing Kaplan-Meier and normally averaged data sets.
Acknowledgements. This work contributes to the  EU-FP7  project  Global Mercury Observation System (GMOS ). Logistical and financial support was provided by the  French Polar Institute IPEV  ( Program 1028 , GMOStral). Financial support was also provided by a grant from  Labex OSUG@2020  ( ANR10 LABX56 ) and  LEFE CNRS/INSU  (program SAMOA). We deeply thank the overwintering staff:  B. Brouillard ,  J. Chastain ,  E. Coz ,  A. Croguennoc ,  M. Le Dréau  and  V. Lucaire. A. Dommergue acknowledges the  Institut Universitaire de France. We also gratefully acknowledge the MODIS mission scientists and associated  NASA  personnel for the production of the data used in this research effort, and the  NOAA Air Resources Laboratory (ARL)  for the provision of the READY website (http://www. ready. noaa.
ACKNOWLEDGEMENTS We thank  V. C. Souza  ( ESALQ/USP, Brazil ) and  Cécile Rault  ( Montpellier SüpAgro ) for the help in the identification of the plants. We also thank  L. V. Silva  for the logistical support during the survey. This study was supported by a grant of the  German Federal Ministry for Economic Cooperation and Development (BMZ)  to ICIPE.
, 2009). 454 sequences have been submitted to the European Nucleotide Archive (ENA) database (http://www. ebi. ac. uk/ena; study accession number ERP008543). For microarrays, cells were harvested at midday and midnight from cultures in early exponential growth (50 000-100 000 cells per ml) on a 14:10 light/dark cycle at 100 mmol photons m À 2 s À 1 at 171 C. A total of 28 306 clusters of Sanger expressed sequence tags (ESTs; 39 091 single EST reads from  RCC1216 and RCC1217 (von Dassow et al. , 2009)  and 72 513 from CCMP1516 downloaded from http://genomeportal. jgi. doe. gov) were represented by 84 881 60-mer probes (2-3 probes/ cluster) on 105K microarrays (Amadid: 022065) for two-color (Cy3 and Cy5) competitive array hybridizations (Agilent, Santa Clara, CA, USA). The same arrays were also used for competitive genome hybridization to compare genome content of RCC1216 and CCMP1516, using protocols previously defined for E.
huxleyi with an earlier microarray system  (Kegel et al. , 2013). Illumina whole-genome data sets from strains CCMP1516, 92A, EH2 and 92F have been previously described  (Read et al. , 2013). The genomes of two newly isolated strains (CHC428 and CHC307; ENA study accession number PRJEB7726) were sequenced by Illumina-technology (Illumina, San Diego, CA, USA) at the Leibnitz Institute for Age Research (Jena, Germany) using the same methods. The CCMP1516 JGI (Joint Genome Institute) whole-genome assembly  (Read et al. , 2013)  and the Illumina genomic resequencing contig data sets were queried with full-length axonemal and cytoplasmic dynein heavy chain (aDHC and cDHC) genes of Chlamydomonas reinhardtii by TBLASTN  (Altschul et al. , 1997). Each contig with DHC homology was analyzed by BLASTX  (Altschul et al.
, 1997)  against  Swiss-Prot (Boutet et al. , 2007). Top reciprocal alignment (to C. reinhardtii homolog) assigned DHC paralog class, determined completeness of the DHC homolog and mapped conserved DHC functional modules, including the 6 AAA ATPase modules and stalk region, onto the E. huxleyi sequences. Illumina contigs of strain 92A encoded complete homologs of DHCs in all but one case, in which the complete homology was encoded on two contigs (see Supplementary Information). BLASTN queries were conducted using the 92A contigs as queries against the CCMP1516 genome assembly and the Illumina data sets. The existence of major deletions affecting DHC homologous regions in the CCMP1516 genome was tested by mapping of the independently generated Illumina genome contigs of CCMP1516 against the JGI wholegenome assembly and, in five cases, by targeted PCR and resequencing.
reinhardtii outer arm DHCa (DYHA_CHLRE) was encoded on a single large contig in the 92A Illumina data set. Extensive regions of 497% nucleotide identity to this 92A contig were identified exclusively on scaffolds 68 and 529 in the CCMP1516 assembly. Scaffold 529 generally shows high homology and synteny to a section of the larger scaffold 68 (Figure  2a ). Scaffold 68 completely lacks sequence sections for modules A5 and A6 of the motor domain and the N-terminal and C-terminal regions, and contains only a small section for the catalytic ATPase (A1). Scaffold 529 includes a shorter predicted gene where almost the entire motor domain and most of the N-terminal tail domain have been excised. Illumina contigs from CCMP1516 (Figure  2a ) and targeted PCR (Figures  2b-d ) confirmed these structures.
0001) and more likely than not-ploidy genes to exhibit lower copy number (w 2 ¼ 628, Po0. 0001). The proportions of genome content differences attributable to 1N-specific genes (60%) and 2N-specific genes (20%) were calculated from the number of 1N-specific genes (471 genes) or 2N-specific genes (153 genes) found to be absent from CCMP1516 divided by the total genes identified as absent from CCMP1516 by the consensus of JGI, Illumina and CGH measures (778 genes). differences in geographic origin (Supplementary Data S3). In contrast, these genes failed to amplify from 37 2N E. huxleyi strains that have never been observed to produce flagellated 1N cells, even when two to four distinct primer pairs were used for each gene. Phylogenetic analysis based on the mitochondrial cox1 and cox3 genes for 83 strains indicated that loss of 1N-specific genes has occurred recently.
Biogeographic distribution of loss of flagella Loss of the flagellated phase in E. huxleyi was associated with warmer waters and lower amplitude cycles in chlorophyll and particulate inorganic carbon concentrations (Supplementary Figure  S12 ) in the relatively stable low-latitude open oceans, whereas the biphasic life cycle was preserved at high latitudes and coasts (Figure  5 ). All E. huxleyi strains isolated from regions previously observed to exhibit annual EhV-controlled blooms, and/or where EhV sequences were detected in metagenomic databases (Figure  5 ), retained the genomic capacity to form flagellated 1N cells (Table  2 ; Fisher's exact test, Po0. 0001). In low latitudes where E. huxleyi does not form blooms (see, for example,  Moore et al. , 2012) , loss of the flagellate 1N phase appeared to increase in prevalence away from the coast.
In each case, the DHC-loci pairs corresponded to only a single highly homologous contig in the 92A and 92F (diploid) Illumina genome databases. The most parsimonious interpretation is that the two sets of homologous chromosomes in the CCMP1516 diploid genome have undergone distinct rearrangements, inversions and hemizygous deletions, although duplications and translocations likely also occurred. Considering the entire JGI genome assembly, the 'diploid alleles' scaffold pairs represent 32. 9% of all unique structures, and might represent up to 19. 7% of each haploid genome present in CCMP1516. Paired scaffold regions also show large gene content differences (that is, presence/absence and gene length differences). Such high divergence between the two haploid genomes in a diploid organism arises under long-term absence of meiosis, as seen in the long-term asexual genomes of bdelloid rotifers  (Flot et al.
Acknowledgements This research was supported by a  Marie Curie International Incoming Fellowship FUNSEXDEPHYND  to PvD within the  7th European Community Framework Programme ,  FONDECYT  Projects  1110575  (to PvD) and  312004  (to DM-F), the  French Agence Nationale de la Recherche/Investissements d'Avenir Grants POSEIDON and OCEANOMICS  (Grant No. ANR-11-BTBR-0008  to CdV and IP), the  European ERA-net program BiodivERsA  under the  BioMarks  project (to EMB), funding from  NASA  and  NSF  (Grants  NNX11AF55G  and  EF-0424599  to DMG and SD), the Genoscope 2007-2008 sequencing initiative and the  PACES research program  of the  Alfred Wegener Helmholtz Institute Helmhotz Centre for Polar and Marine Research. We are very grateful to  Marco Groth  for help with Illumina sequencing.
Experimental Crystal data  Hydrogen-bond geometry (A ˚, ). The work was partially supported by the FEDER (European Fund for Regional Development) fund, the Picardie region and the French program 'investissement d'avenir' Labex Storex (ANR-10-LABX-76-01) through the acquisition of the diffractometer The ANR funding agency is gratefully acknowledged for financial support through the grant accorded for the project 'Store-ex'. [Li 2 (C 12 H 6 O 4 )(H 2 O) 2 ] M r = D-HÁ Á ÁA D -H HÁ Á ÁA D Á Á ÁA D -HÁ Á ÁA O2-H1WÁ Á ÁO1 i 0. 81 (3) 2. 10 (3) 2. 905 (2) 176 (3) O2-H2WÁ Á ÁO3 ii 0. 89 (3) 2. 01 (3) 2. 883 (2) 169 (3) Symmetry codes: (i) x; Ày þ 1; z þ 1 2 ; (ii) Àx; Ày þ 2; Àz þ 1. Supporting information for this paper is available from the IUCr electronic archives (Reference: PJ2011).
However it includes two loci located on the plasmids with two drawbacks. Firstly the plasmids are sometimes absent in environmental strains as well as some collection strains  [26, 27]  and secondly both loci have short (2 and 3 bp) repeat units, and consequently require high precision DNA fragment sizing equipment. In a search for higher discriminatory power, additional VNTR loci have subsequently been identified. Le Fleche et al. [10]  developed the Microbial Tandem Repeats database (http:// minisatellites. u-psud. fr) to facilitate the identification and selection of tandem repeats and used it to propose a MLVA20 scheme for B. anthracis including the MLVA8 loci minus the two plasmid markers and 14 newly described polymorphic markers. The MLVA15 scheme designed by Keim and col. [8, 15]  is based upon the MLVA8 selection and seven additional loci (vntr12,  16, 17, 19, 23, 32  (alias bams01 from  [10] ) and vntr35).
Lista et al. [11]  developed a 25 VNTR markers scheme (MLVA25), including MLVA8, plus 13 of the 14 additional loci proposed by Le Fleche et al. [10]  (bams01, 03, 05,  13, 15, 21, 22, 23, 24, 25, 28, 30 and 31 ; not included: bams07), and 4 new ones (bams34, 44, 51 and 53). The full set of 31 VNTR markers (MLVA31) present in the MLVA8, MLVA15 or MLVA25 panels, has been recently applied in concert with the typing of the set of SNPs called canSNPs  [8]  to evaluate the genotypic diversity found in Namibia  [16]. MLVA provides each genotype in the form of a numeric code that can be easily stored in a database for comparison, as illustrated by the publicly accessible online database (MLVAbank at http://mlva. upsud. fr/) [28, 29]  compiling the numerous genotypes identified in different studies  [6, 11, 16, 17, 19, 20, 30, 31, 32].
Taking advantage of the knowledge and data accumulated in the past thirteen years, the main aims of the present study are  (1)  to provide an update of the genetic diversity of B. anthracis strains naturally present in France, using the most recently developed MLVA31 assay,  (2)  to propose a selection of VNTR loci which could represent a reasonable first-line assay for B. anthracis MLVA genotyping (3) to present the new B. anthracis genotyping database made by taking advantage of major developments to the underlying MLVAbank software. The first-line assay should contain a minimum number of loci, compatible with typing using a large variety of DNA sizing techniques including basic agarose gel electrophoresis. In the present study, we have used the MLVA31 scheme in combination with canSNP analysis  [7, 8]  on the complete ANSES collection of strains collected from different regions of France.
The discriminatory power of the MLVA31 scheme and the contribution of individual VNTR markers were evaluated to optimize the number of markers required to accurately resolve the genetic diversity found across French strains. Congruence and linkage disequilibrium analysis were conducted for different panels of VNTR marker  [33]  and the different MLVA schemes were compared. Because databases are a key issue in terms of genotyping, we have significantly improved the software behind the http://mlva. u-psud. fr prototype by introducing three major functionalities: firstly, the new version is able to merge a number of independently curated databases so that they can be queried and browsed as a single entity, secondly, the database can host any kind of numeric genotyping data, such as canSNPs, and thirdly, a tool has been included to automatically deduce a MLVA or SNP genotype from genome sequence data.
The PCR products were diluted 1:10 and 2 ml of the dilution were added to a mix containing 30 ml of Sample Loading Solution (SLS, Beckman Coulter, Fullerton, CA. , USA) and 0. 25 ml of size marker. The samples were separated by electrophoresis in CEQ Separation Gel LPA I on a CEQ 8000 automatic DNA Analysis System (Beckman Coulter, Fullerton, CA. , USA) under the following conditions: denaturation at 90uC for 120 sec, injection at 2. 0 kV for 30 sec, separation at 4. 8 kV for 60 min (multiplexes A, C, E) or 6 kV for 70 min (multiplexes B and D). Allele sizes were estimated using the CEQ Fragment Analysis System software, by comparing the amplicon to the size marker ''DNA Size standard kit-600'' (multiplexes A, C, E; Beckman Coulter, Fullerton, CA. , USA) or a custom-made ''CST D1 100-1150 bp'' (multiplexes B, D; Bioventures, Murfreesboro, TN, USA).