dataesr/scientific-paragraphs-categorization huggingface dataset:
Phylogenetic analyses Both strands of each PCR product were sequenced, and the ClustalW algorithm (MacVector 6. 5 software, Oxford Molecular) was implemented to align forward and reverse sequences of each segment to derive a consensus sequence of the full LTR (758-bp) region, a fragment of the gp21 env gene (522-bp), colinearized gagtax (2,346-bp) and gag-pol-env-tax (7567-bp) genes (figure  2 ). Phylogenetic trees were generated from multiple alignments of the LTR region and gp21 env together with the colinearized gag-tax and gag-pol-env-tax genes. Included in the phylogenetic analyses were the 23 new proviral sequences from Australia and the four novel sequences from Vanuatu (ESH18, ESW44, EM5, PE376) that were characterized in the present study together with appropriate sequences of previously characterized strains from PNG (MEL1, MEL2 and MEL7), the Solomon Islands (MEL3 to MEL6 and MEL 8 to MEL10), Vanuatu (PE376, VAN54, VAN136, VAN251, VAN335) and Australia (MSHR-1).
Additional representative sequences of the HTLV-1 a, b, d-g subtypes available in Genbank were also included. The sequences were aligned using the DAMBE program (version 4. 2. 13) [28]. Absence of saturation of the alignment was confirmed by 2 methods: likelihood mapping (model TN93; non uniform substitution) with Tree-Puzzle software (version 5. 2) and the test of Xia and Xie  [28]  with the DAMBE program. The final alignment was submitted to the Modeltest program (version 3. 6) and the best model was selected according to the Akaike information criterion. This was then applied to phylogenetic analyses using the PAUP program (version 4. 0b10) to infer trees according to both Neighbor-Joining (NJ) and Maximum Likelihood (ML) methods. To test the robustness of the tree topologies, 1,000 bootstrap replicates were performed.
Gp21 env gene fragment analyses The primary purpose of our work was to study the molecular relationship between the new Australian HTLV-1 proviral strains and those from HTLV-1 infected individuals in Australia and the neighboring islands whose sequences have been previously published. For most strains, the only available sequences in the Genbank database are the 522-bp fragment of the gp21 env gene. We therefore compared the gp21 env gene fragments of seven proviral sequences from Australia, including five new proviral strains (Aus-Cs, Aus-DF, Aus-NR, Aus-GN and Aus-GM) and two previously characterized sequences (MSHR-1 and Aus-RDJ) (Genbank: M92818 and JX891480, respectively)  [15, 25] , with HTLV-1 proviral strains from PNG (MEL1, MEL2 and MEL7), Vanuatu (EM5, VAN54, VAN136, VAN251 and PE376) and the Solomon Islands (MEL3 to MEL6 and MEL8 to MEL10)  [9, 13, 18, 31].
The first group includes strains from the Solomon Islands and Vanuatu (Sol/Van) while the second comprises all the HTLV-1 Australian proviral sequences (Aus) (figures 4A and 4B). Unfortunately, no complete LTR proviral sequence from PNG is available in the sequences databases. However, phylogenetic analysis based on a partial 627bp fragment of the LTR region, including the PNG-1 strain from Papua New Guinea (Genbank: M85207), clearly confirmed the existence of three distinct clades within the HTLV-1c subtype (data not shown)  [32]. Phylogenetic analyses using both gp21 env and LTR fragments were consistent with the existence of two Australian HTLV-1c clades. The nature of this relationship was further clarified by comparing larger genomic fragments using both ML and NJ methods.
Colinearized gag-pol-env-tax genomic fragment analyses These analyses were performed using the complete proviral sequences obtained from four Australian samples: Aus-CS, Aus-   3A ) and Maximum Likelihood (ML) (figure  3B ) methods performed in the PAUP program, on a 522-bp fragment of the gp21 env gene, for 53 HTLV-1 available sequences including the 5 proviral sequences generated in this work and two previously characterized Australian proviral strains (MSHR-1 and Aus-RDJ). The selected model was the Tamura Nei. a-f correspond to the major HTLV-1 subtypes. HTLV-1c subtype corresponds to the Australo-Melanesian one including the new Australian proviral sequences: Aus-CS, Aus-DF, Aus-NR, Aus-GN and Aus-GM (Genbank: KF242506, KF242505, JX891479, KF242507 and JX891478 respectively) and 2 previously described Australian sequences: MSHR-1 (M92818) and Aus-RDJ (JX891480); 9 sequences from Vanuatu: VAN54, VAN136, VAN251, VAN335, PE376, EM5, PE376, ESH18 and ESW44 (Genbank: AY549880, AY549882, AY549879, AY549881, EF061856, EF061884, EF061856, EF061885 and EF061886 respectively); 7 sequences from the Solomon Islands: MEL3, MEL4, MEL5, MEL6, MEL8, MEL9, MEL10 (Genbank: M94198, M94199, M94200, M93099, U11578, U11580, U11566 respectively) and 3 sequences from Papua New Guinea: MEL1, MEL2 and MEL7 (Genbank: L02533, M94197 and U11576, respectively).
doi:10. 1371/journal. pntd. 0002418. g003 NR, Aus-DF and Aus-GM (Genbank: KF242506, JX891479, KF242505 and JX891478 respectively). In addition, two of these complete proviral sequences were selected as the representative prototypes of each Australian clade (''Northern'' clade, Aus-NR; ''Southern'' clade, Aus-GM. The general genomic organization of these two prototypic sequences is similar to that of HTLV-1 prototypes ATK-1 and MEL5 strains (Genbank: J02029 and L02534, respectively). The overall range of nucleotide divergence of the first complete Australian strains from the prototypes ATK-1 and MEL5 was 7. 8-8% and 3. 3-3. 4% respectively. The nucleotide homology between these two Australian prototypic sequences was 98. 9% (102 differences over 9,046-bp). Phylogenetic analyses using both NJ and ML methods of the colinearized gag-pol-env-tax (6,000-bp) genomic fragments, including HTLV-1, HTLV-2 and HTLV-3 representative sequences available in Genbank, confirmed the existence of an Australian subgroup that was highly supported phylogenetically (figures 6A and 6B).
Figure2. PCR strategy for amplifying both the complete HTLV-1c proviral genome (figure2A) and the entire Long Terminal Repeat (LTR) region (figure2B). Both LTR-gag, pro-pol, pol-env and tax-LTR fragments, which were amplified by PCR and sequenced are shown (orange arrows) as well as internal primers pairs (purple arrows) designed for sequencing reactions (see table 2 for oligonucleotide primers sequences). Nucleotide numbering is according to the HTLV-1 ATK-1 prototypic sequence (Genbank: J02029). doi:10. 1371/journal. pntd. 0002418. g002.
This work was supported by the  Northern Territory Rural Clinical School , which is an initiative of the  Australian Department of Health and Ageing (LE) , from the  CNRS  ( UMR 3569 ) (OC, PVA, AG), the  Institut Pasteur, France (OC, PVA, AG) , and through the  Investissement d'Avenir as part of a Laboratoire d'Excellence (LabEx) French research program :  Integrative Biology of Emerging Infectious Diseases (IBEID)  (OC, PVA, AG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Cells were imaged on an Olympus FV1000 MPE laser scanning confocal microscope with environmental chamber to maintain 37 C, 40% humidity and 5% CO 2 ; 488 nm (GFP) and 559 nm (TAMRA) were used as laser lines, and images were collected with an 60Â oil immersion lens. Alternatively, a Zeiss 510 Meta laser scanning confocal microscope was used. For kinetic studies, images were captured every minute for 5 min before the addition of Retro-1 (100 mM) and for 20 min after. Quantification was performed in FV10-ASW software. Co-localization is represented as the Pearson Coefficient (50) of GFP and TAMRA overlap within the cytoplasm of the cell. Nuclear intensity is the ratio of nuclear and whole cell means of TAMRA fluorescence.
In vivo experiments Non-obese diabetic (NOD) scid mice (Jackson Laboratories) received bilateral sub-cutaneous xenografts of 2 Â 10 6 A375Luc705 human melanoma cells, and tumours were allowed to grow to $0. 5 cm. Thereafter, on successive days, mice received intra-peritoneal injections of 200 ml of buffered saline or of SSO 623 in buffered saline (20 mg/kg 2Â, 40 mg/kg 1Â). At 18 h after the last injection, the mice were imaged for luciferase activity. Immediately thereafter, a cohort of the mice received a single 40 ml intra-venous injection of 2 mg of Retro-1 using DMSO/PEG400 (50/50) as a diluent. At 6 h after receiving the Retro-1, all animals were imaged again. For quantitation of luciferase induction (51), the mice were injected subcutaneously with luciferin and imaged in a Xenogen IVIS TM system with continuous isoflurane anesthesia; luminescence was measured and analysed using Living Image Õ software.
Titration of PleD with c-di-GMP To study the binding of c-di-GMP to PleD, increasing concentrations of c-di-GMP were added to a sample containing 10 mM of PleD in 20 mM Tris, pH 8, 100 mM NaCl, 10 mM MgCl 2 , 1 mM BeCl 2 and 10 mM NaF. CD spectra were taken at 25 C after equilibration of the system. The spectra of the samples containing 25, 30, 35 and 40 mM c-di-GMP were measured again after the addition of MnCl 2 to a final concentration of 2. 5 mM. The order of addition of the three components in the mixture (i. e. PleD+c-di-GMP+Mn 2+ or c-di-GMP+PleD+Mn 2+ or c-di-GMP+Mn 2+ +PleD) did not change the final spectrum (data not shown). The experiment was performed in triplicate.
Crystallization, data collection and structure solution Single crystals of [Mn(H 2 O) 4 (c-di-GMP) 2 ] 2+ complex suitable for X-ray diffraction were obtained by hanging drop vapor diffusion method. The best diffracting crystals grew from drops of 6 ml, obtained by mixing 5 ml of c-di-GMP solution (c-di-GMP 4. 3 mM; MnCl 2 30 mM; cacodilate, pH 6. 5, 50 mM) and 1 ml of reservoir solution (2-methyl-2,4-pentanediol 50% v/v; cacodilate, pH 6. 5, 50 mM). A crystal (0. 5 Â 0. 5 Â 0. 2 mm 3 ) was mounted at room temperature on a Bruker-Nonius Kappa CCD diffractometer equipped with a graphite monochromatedMoKa radiation ( = 0. 71073 A ˚, CCD rotation images). The crystal was tetragonal with space group I4 1 and unit cell parameters: a = b = 20. 05, c = 39. 55 A ˚. Semi-empirical absorption correction (SADABS) was applied.
Fourier reflection pairs were not merged to consider anomalous scattering from manganese and phosphorous atoms. The structure was solved by direct methods [SIR97 package  (37) ] and refined by the full matrix least-squares method on F 2 against all independent measured reflections [SHELXL program of SHELX97 package  (38) ]. All non-hydrogen atoms were refined anisotropically. The final refinement converged to an R-value of 0. 0969, for reflection with I > 2s(I). Twinning by merohedry [180 rotation about (1 1 0)] was detected and contemplated in the refinement (the calculated twinning fraction was 0. 186). Crystal data and refinement details are summarized in Supplementary Table  S1. CCDC 913765 contains the supplementary crystallographic data for this article. These data can be obtained free of charge at www.
The results obtained by CD analysis (point measurements) are fully consistent with data obtained by reverse-phase HPLC. The comparison of the kinetics as followed by real-time measurements with that obtained by point measurements (see Figure  6 ) clearly shows (more evidently in the case of RocR) that the real-time approach is an absolute requirement for an accurate determination of the time course of the reaction. The time course of the reaction of RocR was also measured in the absence of Mn 2+ (with Mg 2+ ions alone), and no difference was observed in the kinetic parameters (data not shown), suggesting that the real-time measurement can be carried out, if needed, also in the presence of Mg 2+ ions alone (using a consistent calibration curve). Interestingly, we have also observed that, in the presence of the diguanylate cyclase PleD, the CD signal of c-di-GMP increases even in absence of manganese in the buffer (Figure  7 , black circles).
ACKNOWLEDGEMENTS The authors wish to thank  Manuela Caruso  ( Rome, I ) for skilful technical assistance. The plasmid expressing the RocR gene is a kind gift of H. Sondermann (USA). A. B. acknowledges support from  Deutscher Akademischer Auslandsdienst  (DAAD) and  Konrad-Adenauer-Stiftung. FUNDING Ministero della Universita`e Ricerca of Italy  [ RBRN07BMCT  and  20094BJ9R7  to F. C,  RBFR10LHD1  to S. R. ];  Sapienza University of Rome ;  Fondazione Italiana Fibrosi Cistica  [13/2009-with the contribution of  Delegazione Novara  and  Delegazione Cosenza2  to F. C. ]. Funding for open access charge:  Ministero della Universita`e Ricerca of Italy.
The OMC-2 cloud core contains a number of protostars, including OMC-2 FIR 4 as the dominant Class 0 object. It is among the closest intermediatemass protostellar cores and possibly an example of triggered star formation  (Shimajiri et al. 2008). While earlier studies attributed a luminosity of 400 or 1000 L to OMC-2 FIR 4  (Mezger et al. 1990; Crimier et al. 2009) , recent Herschel and SOFIA observations found 30 to 50 L  (Adams et al. 2012). Adams et al. (2012)  further found an envelope mass of 10 M for FIR 4, while previous authors found it to be ∼ 30 M  (Mezger et al. 1990; Crimier et al. 2009)  and continuum interferometry has yielded even larger estimates, 60 M  (Shimajiri et al. 2008). The factor of 20 difference in luminosity is apparently related to the improved spatial resolution of the Herschel and SOFIA data used by  Adams et al.
Observations and data reduction The data, presented in Fig. 1 , were obtained with the HIFI spectrometer on the Herschel Space Observatory in 2010 and 2011, as part of the Herschel/HIFI guaranteed-time key program CHESS  (Ceccarelli et al. 2010). The spectral scan observations were carried out in dual beam switch (DBS) mode, using the Wide Band Spectrometer (WBS) with a native resolution of 1. 1 MHz (0. 7 to 0. 2 km/s). The data were downloaded from the Herschel Science Archive, re-pipelined, reduced, and then deconvolved with the HIPE software  (Ott 2010, version 6. 2. 0 for the SIS bands and 8. 0. 1 for the HEB bands). Kelvinto-Jansky conversions were carried out with the factors given by  Roelfsema et al. (2012) , which is also the standard reference for other instrumental parameters. The spectrum on which line identification was carried out was obtained by stitching together the deconvolved spectral scans and single-setting observations.
Data quality after reduction After default pipelining, the data quality is already very high. However, in several bands unflagged spurious features (spurs) prevent the deconvolution algorithm from converging. This problem is resolved by manually flagging the spurs missed by the pipeline. The baseline level in all bands is mostly gently sloping, but has occasional noticeable ripples. The data quality after spur flagging and baseline subtraction is excellent, as seen in Fig. 1. Updated reductions will be provided on the CHESS KP and Herschel Science Center websites. In bands 1 through 5, an important concern is ghosts from bright (T a ≥ 3 K) lines  (Comito & Schilke 2002). The effect of ghosts on the overall noise properties is negligible, but they may locally imitate or damage true lines. To check this, we performed a separate reduction where bright lines are masked out and not used in the deconvolution.
Lines in the survey were mostly identified using the JPL 5   (Pickett et al. 1998 ) and CDMS 6  (Müller et al. 2005)  catalogs. The literature was consulted for H 2 O +. The line identification was carried out in two phases and relied on the fact that the OMC-2 FIR 4 spectrum, while relatively rich in lines, is sufficiently sparse at our sensitivity that most lines can be individually and unambiguously identified. In phase 1, we employed the CASSIS 7  software to look for transitions of more than 80 molecules or isotopologs that had been previously reported in spectral surveys or were expected to be seen in the HIFI data. Reasonable cutoffs were applied to limit the number of transitions investigated. For example, for CH 3 OH, we set E u < 10 3 K, A ul > 10 -4 s -1 and |K u | ≤ 5, yielding > 2000 transitions in the HIFI range.
The location of each of these transitions was then visually inspected in the survey data. Once marked as a potential detection, a feature was not excluded from re-examination as a candidate for another species, with the intention of producing a conservative list of blend candidates. For suspected detections, the line flux was measured in a range covering the line and accommodating potential weak wings (typically ∼ 20 km/s in total). The local RMS noise was determined from two line-free nearby regions for each line, and the line flux signal-to-noise ratio was calculated from Eq. 1. The majority of the investigated transitions were not deemed even candidate detections, and ∼ 10% of all chosen candidates turned out to be below the S = 5 limit. The identification process was greatly sped up by the use of the CASSIS software as well as custom HIPE scripts.
Of all the lines in our survey, 10% are in overlapping sections of HIFI bands, which we use to obtain a repeat measurement of their fluxes after deconvolution, and thus an estimation of the calibration and processing uncertainties. Focussing on the overlap of bands 1b and 2a, where the SBR variations are known to be large  (Higgins 2011) , we find that the line flux uncertainty is at the ∼ 10% level, although this may depend to a substantial degree on how the data reduction is carried out. To estimate the SBR impact in the centers of the HIFI bands, we analyze the fluxes of 12 CO lines in the double sideband data. In Fig. 2 , we show the fractional difference from the mean for the integrated intensity of each CO line observed in Spectral Scan mode, i. e. with multiple LO settings. H and V polarization are shown in blue (x) and red (+), respectively.
The broad blue is traced by SO and  --Two lines (7 -6 is excluded). Notes. Uncertainties for the parameters were calculated including the effects of RMS noise and the relative flux calibration errors (10%), and were found to always be < 10%. u > 200 K. Species Size E u < 200 K E u > 200 K Notes T rot [K] N [cm -2 ] T rot [K] N [cm -2 ] CO beam- is unique for its combination of blueshifted velocity and large linewidth, both ∼ 9 km/s. Other species may have contributions from this component. The foreground slab refers to narrow lines at ∼ 9 km/s, most of them in absorption. We use the term other for line profile features which do not fall in the above categories. The velocities of all components shift around by ∼ 1 km/s with species and excitation energy, pointing to further substructure in the emitting regions, although part of this variation is certainly due to measurement uncertainties and could also be due to uncertainties of order 1 MHz in the database frequencies of some species.
The continuum While continuum emission studies are not the main goal of our HIFI survey, the high quality of the spectra allows a continuum level to be determined for use in line modeling. For example, local wiggles in the baseline can mimick a continuum and distort the absorption line to continuum ratio. We provide here a global second-order polynomial fit to the continuum in bands 1a through 5a, where the data quality is highest and the frequency coverage is complete. We stitched the spectra with baselines intact and sampled every 10th channel to reduce the data volume. All spectral regions containing line detections were excluded from the fit. For a polynomial of the form T mb [K] = a + b • ν[GHz] + c • (ν[GHz]) 2 , (2) we find the parameters to be a = -0. 51979, b = 0. 0015261 and c = -4.
3. The CI line fluxes from the bulk of OMC-2 FIR 4 are underestimated due to the self-absorption. The CII line peaks at 9. 5 km/s and likely represents emission from the foreground slab. The CII absorption in the 11. 15 km/s velocity range is an artefact caused by emission in the reference position spectra. To estimate the amount of flux lost due to this at the line peak, we reprocessed the data with one DBS reference spectrum at a time. We established that, while the 11. 15 km/s absorption features vary strongly with the choice of reference spectrum, the 9. 5 km/s peak varies only by ∼ 10%, suggesting that the amount of line flux lost in this component through reference subtraction is small or that the large-scale emission at this velocity around OMC-2 is remarkably uniform. The latter is unlikely as the difference spectrum of the two reference positions shows a strong positive-negative residual, indicating a velocity offset between the components.
For example, the number of species found in the HIFI spectral survey of OMC-2 FIR 4, 26 excluding isotopologs, is smaller than that found in similar data for the high-mass star forming regions NGC 6334I (46 species,  Zernickel et al. 2012)  and Sagittarius B2(N) (≥ 40 species,  Neill et al. 2012 ). This may be related to the substantially lower luminosity of OMC-2 FIR 4 compared to the more massive sources.
Acknowledgements. The authors would like to thank  Charlotte Vastel  for help with the spectroscopic data; our CHESS, HEXOS and WISH colleagues for useful discussions; and the  HIFI Instrument Control Center and Herschel Science Center  teams for their efforts. M. K. gratefully acknowledges funding from the  Netherlands Organisation for Scientific Research (NWO) Toptalent  grant number  021. 002. 081 , the  Leids Kerkhoven-Bosscha Fonds  and the  COST Action on Astrochemistry. A. L. S. and C. C. acknowledge funding by the  French Space Agency CNES  and from  ANR  contract  ANR-08-BLAN-022. A. F. acknowledges support from the  CONSOLIDER INGENIO 2010 program , grant  CSD2009-00038. Herschel is an  ESA  space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from  NASA.
-In terms of composition and dominant chemical species, OMC-2 FIR 4 is well in line with results for other protostars from ground-based instruments. It is thus a nearby intermediate-mass star formation laboratory for which an exceptional spectral dataset is now available. velope of OMC-2 FIR 4, at least one outflow, a newly discovered foreground PDR and other components. The broad outflow emission has a redshifted offset of 1. 5 km/s from the source velocity. Narrow, blue-shifted self-absorption on broad emission lines of H 2 O, NH 3 , and possibly HCO + , may originate in an expanding layer in the inner envelope. Broad, blue-shifted SO lines trace a new component of unclear nature. -The cooling budget of OMC-2 FIR 4 between 480 and 1250 GHz is dominated by continuum radiation, with lines contributing 2%.
DNA extraction, amplification and phylogenetic analyses DNA extraction was carried out on each isolated cyst as previously described  [15]. Single-cell Polymerase Chain Reaction (PCR) was used to amplify 18S and 28S (D1 and D2 regions) ribosomal DNA markers with Radiolaria-specific primers (see 15 for primer details). Following amplification, the PCR products were purified by EXOSAP-IT (GE Healthcare Bio-Sciences Corp. ), and bidirectionally sequenced using the ABI-PRISM Big Dye Terminator Cycle Sequencing Kit (Applied Biosystems). Accession numbers of the 18S and 28S rRNA sequences of cysts are given in Table  S1. The matrices of 18S rRNA and partial 28S rRNA sequences were individually aligned with Muscle, implemented in Seaview  [32]. As the topology of 18S and 28S rRNA genes are congruent  [15] , the two aligned matrices were concatenated with Sequence Matrix  [33] , forming a 2386 bp-long dataset containing 104 taxa.