dataesr/scientific-paragraphs-categorization huggingface dataset:
Sub-domain IIId2 is required for replication of the picornavirus SVV, but not for SVV IRES activity In contrast to our observations that pestivirus IRES subdomain IIId2 mediates the assembly of 80S ribosomes, this study and our previous data support a model in which the picornavirus SVV sub-domain IIId2 is not required for IRES activity. Our results clearly show that eIF3 and 40S recruitment, 48S complexes and 80S ribosomes assembly are all independent from the presence of sub-domain IIId2  (28). However, deletion of sub-domain IIId2 resulted in a 2-log reduction in both viral growth and viral titre throughout a 72 h infection. These results suggest that sub-domain IIId2 is not important for SVV IRES activity, unlike in pestivirus HCV-like IRESs, but still plays a role in viral infectivity.
Monophyly has also repeatedly been found with molecular data as well  (Maekawa et al. 2003; Inward 2007; Pellens et al. 2007; Djernaes et al. 2012; Legendre et al. 2014 Legendre et al. , 2015)). Within Blaberidae, however, the phylogenetic relationships remain controversial, despite early morphological studies (e. g. ,  Grandcolas 1993 Grandcolas , 1997)). The only largely supported results are the close relationships between Zetoborinae and Blaberinae on the one hand, and Panesthiinae and Geoscapheinae on the other. The position of Panchlorinae as the first diverging lineage within the family also seems to be consistently found lately even though often based on a limited taxon sample  (Legendre et al. 2014 (Legendre et al. , 2015)). The phylogenetic positions of the seven remaining subfamilies still need to be investigated further, as do the phylogenetic positions of 24 incertae sedis genera (according to the Blattodea Species File, BSF; Beccaloni 2014).
1), one Corydiidae (Therea petiveriana Linnaeus, 1758) and one Blattidae (Blatta orientalis Linnaeus, 1758) as the rooting outgroup taxon. Among Ectobiidae, all subfamilies have been postulated as being the sister group of Blaberidae, including Pseudophyllodromiinae  (Grandcolas 1996; Inward et al. 2007; Pellens et al. 2007; Djernaes et al. 2012; Legendre et al. 2015). At first, we included several species of Pseudophyllodromiinae (Anisopygia sp. , Asemoblattana sp. , Euphyllodromia sp. , Latiblattella sp. 3) but we then discarded them because of their artifactual position within Blaberidae (among Epilamprinae, data not shown). All the species of Pseudophyllodromiinae sequenced so far show highly modified sequences, which results in high percentages of divergence with ingroup species and may cause artifacts in tree reconstruction such as long branch attraction  (Wheeler 1990; Bergsten 2005; Legendre et al.
2015). Also a couple of additional species of Blattellinae were used as outgroup taxa in preliminary analyses (Ischnoptera sp. and Xestoblatta sp. ), but were not kept because of their missing data, which might alter tree reconstruction (e. g. ,  Lemmon et al. 2013; Roure et al. 2013). Whatever the outgroup combinations used in our preliminary analyses, the supported results presented here were always retrieved. We used six molecular markers to reconstruct blaberid phylogenetic relationships: 12S rRNA (~440 bp), 16S rRNA (~440 bp), 18S rRNA (~1900 bp), 28S rRNA (~2350 bp), cytochrome oxidase subunit I (COI, 1179 bp) and cytochrome oxidase subunit II (COII, 671 bp). Primers and molecular techniques were described in  Legendre et al. (2008). We provided 175 new sequences, which were deposited in GenBank with the following accession numbers: KY497575-KY497749.
1. 7. 8  (Vaidya et al. 2011)  to produce the full dataset composed of 6991 bp. We performed separate and combined analyses in a probabilistic framework. For separate analyses, we selected the best model that does not mix I (proportion of invariant sites) and G (heterogeneity of substitution rates) using jMrModeltest v. 2. 1. 3 (Darriba et al. 2012)  with the AICc criterion. For combined analyses, we used Partitionfinder v. 1. 1. 1 (Lanfear et al. 2012 ; options: branchlengths= linked, model_selection=AICc and search=greedy) to select the best partition strategy among models supported by MrBayes. The best partitioning strategy involved nine partitions: one partition with a GTR + G model for each non-protein-coding marker; four distinct partitions for the first two positions of COI and COII with a GTR + G model; and a common partition for the third positions of COI and COII, also with a GTR + G model.
93), but with other positions in three one marker analyses (12S, 16S and 18S; Fig. 2 ). Concerning Perisphaerinae, Laxta sp. , the only Australian individual sampled, was sister group to African Perisphaerinae (BS / PP = 32 / 0. 93), a result almost only found with the combined dataset (Fig. 2 ). Two incertae sedis genera were included in the analyses: Eustegasta aff. carabidina had Asian Perisphaerinae as its sister group (BS / PP = 99 / 1); Gynopeltis spp. were monophyletic (BS / PP = 99 / 0. 9) and sister group to Gyninae (BS / PP = 89 / 0. 69).
[part 2 on next page] Optimal phylogenetic tree reconstructed in Maximum Likelihood with the combined dataset. Bootstrap values and posterior probabilities are reported for each node (bootstrap values below 25% are not displayed). The color of internal branches is proportional to bootstrap values. Geographic origin of the specimens sequenced is provided in brackets after the species names. In purple, monophyletic group congruent with morphological hypotheses; in blue, monophyletic group with geographic consistency at the continental level; in brown, incertae sedis species; in green, four species with conflicting and supported positions (Thanatophyllum akinetum Grandcolas, 1991  and Phoetalia pallida (Brunner von Wattenwyl, 1865) or congruent, but weakly supported positions (Laxta sp. and Pronauphoeta cf.
Acknowledgments This work was supported by the  network "Bibliothèque du Vivant " funded by the  CNRS , and by the  Muséum national d'Histoire naturelle, Paris (MNHN)  under the grants " ATM -taxonomie moléculaire: DNA barcode et gestion durable des collections " and "ATM -biodiversité actuelle et fossile. Crises, stress, restaurations et panchronisme: le message systématique" to F. L. We thank  Tony Robillard  for his help in several field expeditions, for collecting specimens in Mozambique and for commenting on a previous version of this manuscript. We also thank the following people for providing specimens or for their assistance in the field:  Leonid Anisyutkin  ( Zoological Institute of the Russian Academy of Sciences, Saint-Petersburg, Russia ),  Rudolf Meier  ( National University of Singapore, Singapore ),  Yayuk Suhardjono  and  Oscar Effendy  ( Museum of Bogor, Indonesia ),  Odette Morvan  and  Jean Cerda  ( French Guiana ), Eric Guilbert (MNHN), and  Henri-Pierre Aberlenc  ( Centre de Biologie pour la Gestion des Populations, Montpellier, France ).
GC-MS Analysis FAMEs were separated using a gas chromatograph (Clarus 680, Perkin Elmer, Waltham, MA, USA) fitted with a fused silica capillary column (60 m × 0. 25 mm i. d. , 0. 25 µm film thickness, Elite-WAX ETR, Perkin Elmer). Samples and standards were introduced by a 1 µL splitless injection system at 250 • C. Helium was used as the carrier gas at a constant flow of 1 mL•min -1. The oven temperature was programmed to rise continuously from 75 • C to 200 • C for a total run time of 60 min. Separated FAMEs were analyzed through electronic ionization (70 eV) with a single quadripole mass spectrometer (Clarus 600, Perkin Elmer). FAMEs were identified by comparing the obtained spectral data to a NIST database (National Institute of Standards Technology, Gaithersburg, MD, USA). Calibration standards were prepared from a commercially available mixture of standards (F.
A. M. E. Mix, C8-C22 unsaturates, Supelco, Bellefonte, PA, USA), using heptadecanoic acid (17:0) as an internal standard. Calibration standards were analyzed in triplicate and linear standard curves were established for the methyl esters of the five main fatty acids found in membrane lipids of Vigna leaves (16:0, 18:0, 18:1; 18:2, 18:3)  [21]. To maximize sensitivity and specificity, FAMEs were quantified in single-ion-recording (SIR) mode. Mass spectra of eluting FAME compounds were identified using the commercial mass spectral library supplied with the manufacturer's software (TurboMass, Perkin Elmer). For each sample of total lipids, the responses (peak areas) of FAMEs were normalized separately to the response of the internal standard 17:0 and quantified using the corresponding calibration relationship.
Statistical Analysis As described in the appropriate figure captions, parameters were measured on 3 or 4 plants per treatment, considered as independent biological replicates. At each time point and for a given cultivar, data from the different treatments (control, C; drought, D; ozone, O; ozone + drought OD) were submitted to a one-way analysis of variance (ANOVA) followed by Tukey's post-hoc tests (α = 0. 05). Homogenous subsets were indicated by appropriate letters. In addition, the effects of experimental factors (time, cultivar, drought and ozone) and their interactions were assessed through the multivariate ANOVA of the whole data set and the between-subject effects are included as supplementary information (Supporting Information Tables A2-A4. Statistical analysis were conducted using the R software  [64].
Acknowledgments: Research was supported by the  Brazilian Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)  to  Deborah Moura Reboucas  and  Yuri Maia De Sousa  in the form of a double-diploma scholarship between Brazilian and  French Laboratories. The authors would like to acknowledge  Stéphane Martin  for his technical help with the phytotronic chambers.
The cook loss (CL) was determined by the following formula: CL % = ((raw weight of steakcooked weight of steak) / raw weight of steak) * 100. All steaks were stored in a closed bag and tempered overnight at 4 °C, for subsequent Warner-Bratzler shear force (WBSF) analysis. WBSF was measured according to the procedure of  Shackelford et al. (1994). Briefly, six cores (1. 25 cm diameter) parallel to the direction of the muscle fibres were obtained and sheared using an Instron Universal testing machine, model 5543 (Instron Corporation. Bucks, UK) equipped with a Warner-Bratzler shearing device. The crosshead speed was 5 cm/ min. Instron Series IX Automated Materials Testing System software for Windows (Instron Corporation. Bucks, UK) was employed in the analysis. Three parameters were used to define the instrumental texture of meat: WBSF (N) is the peak strength or force required to shear through a meat sample, which is directly related to the myofibrillar component  (Møller, 1981) ; modulus of deformability (Mpa) was calculated as the slope in the 20% to 80% segment of the total peak, and it is mainly related to the sample elasticity  (Larmond & Petrasovits, 1972) ; total energy (J), was calculated as the total peak area and is related to the total energy used to chew the meat until it can be swallowed  (Mathoniere, Mioche, Dransfield, & Culioli, 2000).
Statistical analysis All data were analysed using the GLIMMIX procedure of SAS (SAS Inst. Inc. , Cary, NC, USA) using pen as experimental unit and gender and diet as fixed factors. The random tool of the GLIMMIX procedure was used to include "time" as a repeated measurement for the analysis of pH decline and the "position of the measurement" for the analysis of fat colour. When significant main or interaction effects were detected, the post hoc Tukey test was used to determine the differences between means. Additionally, analysis of variance (ANOVA)-partial least squares regression (APLSR) was also used to analyse the sensory data using Unscrambler® software (version 10. 3 CAMO Software AS, Oslo, Norway). The X-matrix was designed as 0/1 variables for beef samples and the Y-matrix included the sensory variables.
Conclusions Based on the results obtained in the present study it can be concluded that, despite the statistically significant differences between genders, the LT from bulls aged for 14 days was evaluated as above average by trained panellists, and the values of texture were under the consumer rejection limit (40 N). Therefore, the differences have limited commercial relevance. This finding, together with the higher performance, higher profitability and the potential added value of the greater leanness in bulls can increase the attractiveness of bulls in a grass based production system followed by a 76 days finishing period. Supplementary data to this article can be found online at http://dx. doi. org/10. 1016/j. meatsci. 2016. 11. 021. Meath with sample collection and carcass measurement is greatly appreciated.
Acknowledgments This project ( 11/SF/322 ,  "BullBeef ") was funded by the  Irish Department of Agriculture, Food  and the Marine's competitive research programmes. The authors thank  Kevin McMenamin  for managing the production part of the study and acknowledge the assistance of staff at  Teagasc Animal & Grassland Research and Innovation Centre, Grange. The assistance of staff and management at  Kepak Group, Clonee, Co.
Statistical analysis Production parameters for each hen were calculated for each 28-day period, then a mean was calculated for the whole trial duration. Daily feed consumption by hens was calculated by dividing the consumption of each group of hens by the number of hens (eight) and by the duration of the period (28 days), then a mean was used for the whole trial duration. The same calculation was made for egg quality measurements. Statistical analysis was performed using the Statview statistical program (SAS Institute, Cary, NC, USA). The results were analyzed by one factor (the diet) ANOVA, and a Fisher's test was used to compare the means. P < 0. 05 was considered to be significant. Relationships between levels of V + C and performances of the birds were tested by regression.
003, but *P < 0. 01 for day 14), and then at time 0 for the control diet and time 0 for the faba bean diet (P < 0. 001). (b) GSH levels (expressed as mmoles/ml whole blood) were measured in hen RBCs after 3 weeks of control soybean diet (black bars) and a diet supplemented with 25% high V + C faba beans (light gray bars) (check points on days 0, 7, 14 and 21). Column data represent mean values ± SD of four independent experiments, analyzed for statistical significance by two-sided Student's t-test. The differences between days 7 and 21 v. day 0 were statistically significant ( # P < 0. 05). Effects of vicine and convicine in laying hens.
001). (b) GSH levels (expressed as mmoles/ml whole blood) were measured in hen RBCs after 3 weeks of control soybean diet (black bars) and a diet supplemented with 25% high V + C faba beans (light gray bars) (check points on days 0, 7, 14 and 21). Column data represent mean values ± SD of four independent experiments, analyzed for statistical significance by two-sided Student's t-test. The differences between days 7 and 21 v. day 0 were statistically significant ( # P < 0. 05).
Acknowledgments This study was funded by the  European Union   EUFABA  project ' Faba bean breeding for sustainable agriculture ,'  QLRT-2001-02307  ( FP5-SCP ) and by  Regione Piemonte ,  Ricerca Sanitaria Finalizzata. The authors thank  Blandine Raffiot ,  UNIP Paris F. and Pierre Mangin UE INRA Domaine d'Epoisses, 21110 Bretenière F. for seed multiplication,  Philippe Dulieu ,  RD-biotech Besançon, France  for V and C measurements and  P. Carré  and  A. Quinsac  ( CETIOM-CREOL, France ) for preparation of dehulled faba beans. The authors also thank  Dorien Kleverwal  for having improved the writing of the paper.
Crystallinity An X-ray diffraction machine model X'Pert PRO ALPHA1 (PANalytical, USA) was used to analyze crystallinity. Native starch powders were exposed to X-ray beams (Cu Kα radiation λ = 1. 5405Å) of 45 kV y 40 mV, divergence and scattering openings = 0. 125, receiving opening was 0. 10 mm, the 2 angle was scanned over a range of 5 to 30, with a step of 0. 02°. The data were normalized by subtracting empty holder background with software Match! 2 ® (Crystal Impact GbR) and smoothened by the method developed by Savitsky-Golay in 1964. The relative crystallinity was estimated as the total area of the peaks in relation to the total surface of the diffractogram  (Nara & Komiya, 1983; Wang, Bogracheva, & Hedley, 1998).
Water contents were checked by thermogravimetric analysis (Q50 TGA, TA Instrument). Thermograms were obtained in a Q100 DSC (TA Instrument), previously calibrated with Indium (Tm: 429. 8 K, ΔH = 28. 55 J. g -1 ), and purged with nitrogen flow (50 cm 3. min -  ). Samples of approximately 12  0. 4 mg were weighed (XS104, Mettler Toledo) in highpressure stainless steel pans (100 bar -30 μl) and sealed hermetically, each sample was heated from 10 to 230 °C with a heating rate of 3 °C. min -. Universal Analysis 2000 ® software was used to calculate the enthalpy change (H) and melting temperatures at start (T o ), peak (T p ) and final (T m ). Since some endotherms overlapped under the measurement conditions, a mathematical deconvolution curve fitting technique was used to separate the peaks  (Liu et al.
Acknowledgements We acknowledge  M. De Carvalho  and  Jean-Eudes Maigret ,  Roselyne Desirest  ( Research Unit on Biopolymers, Interactions and Assemblies, INRA, Nantes, France ) for excellent advising and technical support. Field assistance provided by  Nelson Morante  and  Fernando Calle  and the extraction of WXCS extraction coordinated by  John Belalcazar  supervisor of the root quality laboratory at CIAT are greatly appreciated.
Funding This work was supported by the  CIAT Cassava Project , which is part of and funded by the  CGIAR Research Program on Roots, Tubers and Bananas (RTB)  with support from  CGIAR Fund Donors. http://www. cgiar. org/about-us/governing-2010june-2016/cgiar-fund/fund-donors-2/Research was conducted under the framework of a  Memorandum of Agreement between CIAT, CIRAD/INRA  and  Univalle. The  Administrative Department of Science, Technology and Innovation (COLCIENCIAS)  supported this work through the doctoral scholarships program in Colombia.
5 μg/mL. Images were captured with a Leica SP8 Confocal microscope and analyzed using the ImageJ software. Fluorescence intensity was measured with ImageJ software in wild-type, heterozygous or mutant GSCs. For each GSC, the mean fluorescence intensity was determined using three independent quantifications in three different cytoplasmic regions in the same confocal section; the number of cells analyzed (n) is indicated in the bar graphs for each genotype.
Acknowledgements We are very grateful to  D Chen ,  E Giniger ,  A Gonzalez-Reyes ,  J Knoblich ,  A Nakamura ,  LM Pai ,  M Siomi ,  P Zamore  for their gifts of fly stocks or antibodies. We thank  AL Finoux  and  W Joly  for initial work in this study. This work was supported by the  CNRS   UMR9002 ,  ANR  ( ANR-2010-BLAN-1201 01  and  ANR-15-CE12-0019-01 ), FRM ("Equipe  FRM 2013 DEQ20130326534 "). PRR held a salary from the  Labex EpiGenMed/University of Montpellier  and from the  Fondation ARC. The authors declare that they have no conflict of interest.
The same samples used for the saccharification measurements were used to prepare some KBr disks. KBr is commonly mixed with samples to be analysed by infrared spectroscopy since it is known to have a very low spectral absorption  34. Some disks containing only KBr were prepared and analysed to check KBr absorption in the range 300-800 nm was negligible (data not shown). Fluorescence spectra measurements were performed for all untreated and pretreated samples with the same acquisition parameters. Only the gain value was adapted for each biomass species to get the highest fluorescence intensity value for the untreated samples. Fluorescence spectra are presented as 3D contour maps (Fig. 1 ; Supplementary Figs  1  and 2 ). For facilitating comparison, the maximum fluorescence intensity values were determined and are reported in Table  2 , with corresponding maximum excitation and emission values.
Spectrofluorimetry. For other experiments, samples were ball-milled in a 25 mL jar with 20 × 20 mm ZrO 2 ball bearings using a Retsch MM2000 mixer mill for 2 min to achieve a size less than 80 µm. Disks were prepared by mixing 2 mg of biomass sample and 200 mg of KBr. Fluorescence spectra of the disks were measured in a Jasco FP-8300 instrument (Lisses, France). Acquisition parameters were as follows: range/precision for excitation and emission were 250-600 nm/2 nm and 260-650 nm/1 nm, respectively; excitation and emission bandwidth was 2. 5 nm; scan speed was 1000 nm/min; gain value was adapted depending on the biomass considered: 600 V, 650 V and 700 V for miscanthus, poplar and wheat straw, respectively. Spectra acquisition was performed using Jasco Spectra Manager software. Dehydrogenative polymer (DHP) synthesis was performed as previously explained  38  and their fluorescence spectra was recorded with the same parameters as above, using a gain value of 750 V.
Autofluorescence and lifetime measurements. Spectral images were acquired using laser scanning microscope LSM 710 NLO Zeiss (Zeiss SAS, Germany) coupled with Chameleon TiSa accordable 80 Mhz pulsed laser (COHERENT,USA). Sample excitation was performed at 750 nm with two-photon laser and spectral images were acquired using spectral detector of the microscope on 32 channels between 420 and 722 nm with 20× objective (NA 0. 8). Lifetime measurements were acquired using a MW-FLIM detector system along the SPC 150 photocounting card from Becker & Hickl (Becker & Hickl, Germany). This system allowed to do lifetime measurements along 12. 5 ns time-windows with a 16 spectral channels detector driven by SPCM software (Becker & Hickl). Lifetime trace of emitted photons was accumulated during 30 s simultaneously on all spectral channels of the MW-FLIM detector.
genomes. Strain CFBP7111 had no tal gene, while strain CFBP7112 contained seven tal genes located on plasmids, and strain CFBP7113 bore one tal gene located on the chromosome. This diversity may reflect different modes of adaptation of these strains to cowpea. Accession number(s). The three whole-genome sequences have been deposited at GenBank under accession numbers CP022263 to CP022266 for strain CFBP7111, CP022267 to CP022269 for strain CFBP7112, and CP022270 for strain CFBP7113.
ACKNOWLEDGMENTS This work was supported by grants from the  French National Research Agency  ( CROpTAL  project, grant number  ANR-14-CE19-0002-04 ) and Angers-Loire Metropole, France (X- HOT  project). We thank  Laurent D. Noël ,  Boris Szurek ,  Lionel Gagnevin , and  Ralf Koebnik  for recurrent scientific exchanges on the project CROpTAL led by  Laurent D. Noël. PacBio sequencing was performed at the  Icahn School of Medicine at Mount Sinai (NY, USA)  under the supervision of  Robert Sebra  and preliminary quality control of DNA was performed at the ANAN platform from the  SFR 4207 QUASAV (Angers, France). We also thank the  CIRM-CFBP (Angers, France)  for strain preservation and supply.
Genome assemblies and the MAT loci of Cryptococcus amylolentus We sequenced the genomes of the 2 C. amylolentus isolates, CBS6039 and CBS6273, which are interfertile and produce viable basidiospores, using Roche/454 (only for CBS6039), Illumina, and PacBio platforms. Hybrid assembly of this data resulted in 2 genomes, each approximately 20. 3 Mb in size and containing 14 chromosomes, with telomeric tandem arrays of C  (4, 6)  GCTAA identified at the ends of 13 chromosomes in CBS6039 and 11 chromosomes in CBS6273, respectively (Table  1 ). This is consistent with the numbers and sizes of the chromosomes in these 2 strains as visualized by contour-clamped homogeneous electric field (CHEF) electrophoresis. Chromoblot analysis using probes targeting the opposite ends of each chromosome confirmed the chromosomal organization in the assemblies (S1 Fig).