dataesr/scientific-paragraphs-categorization huggingface dataset:
Results Figs. 3(a) and 3(b) show superpositions of EBSD characterizations of two cross sections and the closest matching sections of the reconstructed tomography data. Here, the EBSD data are pictured as a grain boundary network, while the colored grains show the DCT reconstruction. The spacing between the two EBSD sections is approximately 3 mm. The compared grain boundary networks in Fig. 3 (a) contain 107 (DCT) and 108 grains (EBSD). The average grain size for these sections was measured by the linear intersect method and found to be 30. 1 (4) mm (DCT) and 29. 7 (4) mm (EBSD). The compared grain boundary networks in Fig. 3(b)  show cross sections containing 109 (DCT) and 110 grains (EBSD). The average grain size for these sections was found to be 31. 5 (  6 ) mm (DCT) and 28. 9 (5) mm (EBSD).
Discussion The goal of nondestructive three-dimensional imaging of microstructure evolution in ceramic materials can be realized via X-ray diffraction contrast tomography. This technique provides grain maps obtained from a complex reconstruction and post-processing procedure. We investigated the quality of these grain maps using the example of an SrTiO 3 specimen. The reconstructed microstructure was validated against EBSD data of the specimen. Therefore, grain boundary networks have been extracted from EBSD data and have been compared with corresponding two-dimensional cross sections through the reconstructed volume. The number of grains found in the EBSD and corresponding DCT maps is almost identical, with a good agreement in average grain size. The slight difference in the counting of grains (we find one grain more in the EBSD analysis of both cross sections) is the result of a number of grains being barely cut in either of the cross sections, thus appearing as really small areas.
The comparison of Euclidean distance transforms with and without pores shows clearly that, despite the higher resolution resulting from PCT data sets, the porosity data of the two characterization methods are not yet reliably comparable. This phenomenon originates from several factors: The higher number of (especially intragranular) pores in the EBSD slices can be related to ring artifacts and uncertainties in the PCT reconstructions  (Cloetens et al. , 1997). The artifacts hamper the segmentation of individual pores used for the final assembly of the reconstructed sample volume. Additionally a threshold was applied that eliminated small pores and pores with a low intensity value. Furthermore, thin material layers above pores might have collapsed during the mechanical preparation of the SrTiO 3 specimen for sectioning, thereby revealing underlying pores, so that the EBSD sections might also reveal pores that are underneath the actual section.
Refinement In the first stage of the refinement, the atomic positions of the Mo and S atoms were deduced from those in KMo 12 S 14  (Picard et al. , 2006). A subsequent difference-Fourier synthesis reveals the potassium atom and a quasi-continuous electron density along the c axis due to the sodium atoms. The latter was modelled with two partly occupied sodium sites (4 e and 2 b positions) using second-order tensors for the anisotropic displacement parameters. Anharmonic treatment of the Na1 and Na2 atoms using the program JANA2000  (Petříček & Dušek, 2000)  was unsuccessful. The final occupation factors for the Na atoms were refined freely. The highest peak and the deepest hole in the final Fourier map are located 1. 07 Å from Na2 and 0. 58 Å from Mo2, respectively. Analysis of the intensity data using the TwinRotMat routine of PLATON  (Spek, 2009)  revealed the studied crystal was twinned by merohedry with [100, 010, 001]as the twin matrix.
Computing details Data collection: COLLECT  (Nonius, 1998) ; cell refinement: COLLECT  (Nonius, 1998) ; data reduction: EVALCCD  (Duisenberg, 1998) ; program(s) used to solve structure: SHELXS97  (Sheldrick, 2008) ; program(s) used to refine structure: SHELXL97  (Sheldrick, 2008) ; molecular graphics: DIAMOND  (Bergerhoff, 1996) ; software used to prepare material for publication: SHELXL97  (Sheldrick, 2008). Extinction correction: SHELXL97  (Sheldrick, 2008) , Fc * =kFc[1+0. 001xFc 2 λ 3 /sin(2θ)] -1/4 Extinction coefficient: 0. 00032  (9).
Fitness and male mating competitiveness Females were blood fed at six days post eclosion, and aspirated into small tubes for individualized laying two days later. Eggs were matured for five days before being counted to give fecundity data and then hatched in deoxygenated water in small plastic vials. Second instar larvae were counted to give hatch rate. Uju. wMel female egg hatch was lower than for wildtype colony controls in early generations, likely as a result of variable Wolbachia density causing CI effects. Therefore, between G 6 and G 12 selection for high hatch was applied to make the Wolbachia density more uniform, by discarding approximately one quarter of broods which showed the lowest hatch rates. Longevity was assessed in 30 cm630 cm630 cm BugDorm cages (MegaView Ltd. , Taiwan) containing one hundred male and one hundred female mosquitoes (which were sexed as pupae).
Eggs were hatched five days after laying; given the complete CI (zero egg hatch) observed in both directions in crosses between wildtype and wMel-transinfected parents  [4] , the male parent was scored according to whether or not embryos hatched -hatching indicating that both contained the same Wolbachia strain. Spermathecae were dissected and examined under a dissecting microscope for the presence of stored sperm for all females that produced eggs with zero hatch, and data from any females without sperm were disregarded.
Male mating competitiveness of Uju. wMel males was compared to that of the naturally infected Uju. wt males using three independent replicates of 50 male Uju. wMel : 50 male Uju. wt : 50 females (either Uju. wMel or Uju. wt). Hatching eggs from an individual female indicated that a compatible mating had occurred with a male with the same Wolbachia strain, whilst no hatch indicated an incompatible cross (data from females with empty spermathecae were disregarded). No significant difference was found between the competitiveness of the wildtype and transinfected males under these conditions (p = 0. 652, Chi-squared analysis using a likelihood framework) (figure  3 ).
In both cases, 20 μL of L-Dopa solution (the substrate for the PO, Sigma D-9628, 4 mg/mL of dH 2 O) was added to the mixture and the colorimetric reaction was followed in a microplate reader (Versamax, Molecular Devices) at 30°C. Readings were taken for 30 min at 490 nm. Enzyme activity was analysed using the software SOFT-Max®Pro 5. 2 (Molecular Devices) and measured as the slope (V max value) of the reaction curve during the linear phase. The values reported refer to the activity present in a standard 1 μL volume of supernatant. In experiment 1, total and active PO were highly correlated and provided nearly identical results (see below). Due to a technical problem (faulty chymotrypsin), however, we were unable to reliably quantify total PO activity in experiment 2.
Statistical analyses The statistical analyses were run using the R software (v. 2. 14. 0). Variation in phenoloxidase activity was analyzed using linear mixed-effect models (lme function, nlme package). Tray (larvae) or cage (adults) effects were included as random factors, and insecticide resistance (IR), stage (larval/adult) age (adults only), sex (adults only) and size as fixed factors. Models were simplified by sequentially eliminating the least non-significant term to obtain minimal adequate models using a standard procedure of likelihood comparison (using the function anova. lme and specifying a marginal type test). When appropriate, a posteriori contrasts were carried out by aggregating factor levels that did not significantly differ from each other and by testing the fit of the simplified model  [42].
Given that PO activities were assessed from crushed extracts and that we could not have a common size estimator for larvae and adults (i. e. thorax width and wing size, respectively), the comparison of immune activity between mosquito stages needs to be taken with caution. The difference in immune investment we found between males and females agrees with previous data from other invertebrates  [60, 61]. This can be explained by two non-exclusive factors. First, by differences in lifespan and in the constraints associated with their respective reproductive schedules  [62, 63]. Indeed, males of most species, including mosquitoes, have what Zuk  [64]  described as a "live hard, die young" strategy. In contrast, the female reproductive life is made up of lengthy gonotrophic cycles, each of them consisting of a period of host seeking, followed by blood feeding, egg maturation and oviposition which, collectively, can last 2-5 days depending on the species  [65].
Acknowledgments The authors would like to thank  M. Weill  and  P. Makoundou  ( ISEM ) for providing us with the mosquito isogenic lines,  A. Nicot  for helping in the laboratory and  C. Chevillon  and  N. Pasteur  for useful discussions. AR acknowledges financial support from the  CNRS , and an  ANR   SEST "IRMAL" grant. SG acknowledges financial support from the  CNRS , an  ANR   JCJC "EPICE" grant , and an  European Research Council Starting  Grant  243054 "EVOLEPID".
Archaeocyathan database and website Establishing a database is nowadays is one of the powerful means to manage and analyze complex information. The archaeocyathan database has been produced initially to provide a flexible tool to identify archaeocyath genera  (Kerner et al. , 2011b). This has been developed with Xper², a free software to store, edit and manage descriptive data and to provide a free access key. (http://www. infosyslab. fr/lis/?q=en/resources/software/xper2 (Ung et al. , 2010). The database contains 307 valid genera, described with a set of standardized descriptive terms. Interactive identification requires the use of the same set of descriptors for each genus and an adapted terminology: terms are standardized and one term corresponds to a single morphological concept  (Kerner et al.
2011a ). An archaeocyathan description is composed of 85 morphological and ontogenetic characters. Specialists familiar with traditional terms can find a correspondence table between usual terminology and the computerized one. Each genus is illustrated by the type specimen of the type species; some additional specimens may be present. Each character and its states are associated with a definition and images. Additional data are present: Eight characters refer to stratigraphical and geographical information and 27 refer to traditional classification data. The database spans the entire Cambrian System and has world-wide coverage. As the regional Siberian stages were the traditional reference for archaeocyathan specialists before the establishment of the international stratigraphic chart, these stages are used in the database until correlations are refined.
Different tools available Xper² offers a large range of tools to explore, analyze and interpreted the knowledge base with several approaches  (Ung et al. , 2010). The identification unit is a free access key. This kind of system is very flexible and is well adapted for palaeontological specimens that are often incomplete. At each step of the identification, the user can choose the adequate descriptor and one or several states. Doubt is possible and several tools are available. As the identification key is built from the database, it is not restricted to morphological information. The presence of stratigraphical and geographical data allows the rapid creation of some lists of genera for palaeobiogeographical or stratigraphical studies. For example, all genera from Canada present during the Botomian stage are found in few seconds contrary to traditional bibliographical studies.
Conclusion The aim of this contribution is to present the current status concerning one of the most ancient fossil groups, the Archaeocyatha. Relevant studies have been published in various reviews (  (Debrenne et al. , 1990)   (Debrenne and Zhuravlev, 1992) ,  Debrenne et al. 2002, in press). A computer-aided identification tool for Archaeocyatha genera is now available online (http://www. infosyslab. fr/archaeocyatha). This database is firstly used as an identification key but can be also a driver for different areas of archaeocyathan research for instance, faunal geographical and stratigraphical distributions. The database will be an important tool for developing new palaeogeographical interpretations for the Cambrian Period.
Fig. 4B  shows typical UPLC-MS/MS chromatograms obtained with either fusion protein or maltose-binding protein as a control. Both enzymes were found to release JA from JA-Ile (Fig. 4B, e  and h ) and IAA from IAA-Ala (Fig. 4B , d and g), recombinant ILL6 appearing less active than IAR3 on all compounds tested. When incubated with 12OH-JA-Ile, TA signal was detected only with IAR3 (Fig. 4B , f), whereas after incubation with 12COOH-JA-Ile, no cleavage activity was evidenced with either enzyme (data not shown). The different activities were evaluated quantitatively after establishing standard curves with pure compounds. Under the conditions used IAR3 was about 20-fold more active on JA-Ile than ILL6, and IAR3 was itself 9-fold more active on JA-Ile than on 12OH-JA-Ile (Fig. 4C ). These results from in vitro experiments show that IAR3 and ILL6 release JA from JA-Ile and that at least IAR3 can also generate TA by cleaving 12OH-JA-Ile.
IAR3 was previously shown to cleave abscisic acid amino acid conjugates in vitro (45) and appears to be a versatile enzyme, but actual catalysis may be determined in vivo by substrate abundance. In vitro activity of recombinant ILL6 was much lower than IAR3 on either JA-Ile or IAA-Ala and no activity could be detected on 12OH-JA-Ile under our assay conditions. Previous attempts to produce active AtILL6  (36)  or the Brassica homolog BrILL6 (25) in bacteria have failed, one possible reason being the presence of potential transmembrane domain(s). These limitations leave open the possibility that the in vitro enzymatic data presented here have under evaluated the catalytic capacities of AtILL6. Genetic analysis has provided novel insights into the impact of IAR3 and ILL6 in metabolism of jasmonate conjugates in Arabidopsis.
Identifying the unique germplasm set and SSR allele data This study utilized grape accessions maintained in two of the world's largest germplasm repositories: the INRA Domaine de Vassal (Fance) collection; and combined collections housed at Davis, California (University of California, Davis and the National Clonal Germplasm Repository). Most of the University of California, Davis accessions were collected by Harold P. Olmo (Department of Viticulture and Enology, University of California, Davis) during germplasm acquisition travels in 1948 (Table  1 , Additional file 1: Table  S1 , Figure  1 ). Many of the 559 accessions tested shared identical marker profiles, thus suggesting possible cases of synonymies were observed within and among the samples from the two collections (Additional file 2: Table  S2 ).
Further analysis was based on 403 unique accessions: 296 from the Davis collections and 107 from the INRA Domaine de Vassal germplasm collection. Additional file 3: Table  S3  presents the fingerprint profiles of the 403 unique accessions based on 19 SSR markersone marker from each grape chromosome. Twenty-three accessions (interspecific hybrids, Vitis riparia, Muscadinia rotundifolia, three reference European winegrape varieties, and eight other accessions with missing data at 7 or more loci) were removed from the study set. The number of alleles per marker and percent of missing data were calculated for the remaining 380 genotypes with 34 markers (Table  2 , Additional file 4: Table  S4 ). Based on the collection records, the study set of 380 unique accessions consisted of 306 genotypes of V.
These six accessions are potential recombinants. Two Chinese species accessions, V. romanetii (C166-043) and V. yenshanensis (588421. a) had the 143 allele, but neither of them carried a resistance-associated allele at the other three markers. In the case of these two examples, we speculate that the presence of the 143 allele is either due to size homoplasy, or the alleles at other markers are lost due to recombinations. In 2009 and 2010, resistance to powdery mildew was evaluated on a 0 to 5 scale (no symptoms to severe symptoms) on all accessions from Davis that carried alleles linked to resistance at one or more markers (Table  3 , Additional file 6: Table  S6 ). Four other accessions were evaluated in 2012 (data not shown). The year effect was significant; disease pressure was more severe in 2010 (Table  3 ).
Sequencing of the resistance-linked allele of an SSR marker that co-segregates with Ren1 A 620 bp region that includes the resistance associated 143 bp allele from marker SC8-0071-014 was sequenced for the 12 powdery mildew resistant accessions and two susceptible V. vinifera subsp. sylvestris (Figure  3 ). Two accessions of Chinese species that had a 143 bp fragment at SC8-0071-014 were also sequenced. The sequences were nearly identical for all fourteen V. vinifera accessions except for occasional single nucleotide polymorphisms (SNPs) between both unrelated and genetically related accessions. The sequences of the two Chinese species, V. romanetii (C166-043) and V. yenshanensis (588421. a) were very different from one another and from the V. vinifera sequence, obvious examples of size homoplasy, where two alleles are identical in size but result from independent events (data not shown).
Distinguishing wild and cultivated types by flower phenotype Because two of the newly discovered powdery mildew resistant accessions were collected as sylvestris, it was important to confirm their true type based on morphological traits. Flower sex phenotype and seed morphology are two key criteria used to differentiate subsp. sylvestris (dioecious vines, seeds with short beaks) from cultivated sativa forms (predominantly hermaphroditic flowers, seeds with larger beaks). The flower phenotype of the subsp. sylvestris accessions collected from Armenia, Georgia and Turkmenistan could not be determined because they were young potted plants. Flower phenotype data for 15 wild V. vinifera accessions was obtained from GRIN, the National Germplasm Resource Information Network  [31]. A combination of two DNA markers was used to differentiate male, hermaphrodite and female flower phenotype for the set of 380 accessions.
Two accessions in the species group, C-166-025 and DVIT1159. 3, are recorded as male, but are hermaphrodite based on the DNA analysis. The third anomaly was the cultivar 'Neeli' (DVIT2514), which was scored as a hermaphrodite, but is listed as a female plant in the GRIN database. DNA marker analysis of flower sex in the V. vinifera subsp. sativa group of cultivars found that 223 were hermaphrodite, 57 were female, and five were identified as male (Additional file 11: Table  S10 ). One of the five males, 'Kala Kostan' (DVIT2534) is recorded as a female in GRIN; the flower phenotype could not be verified for the other four genotypically male cultivars. Eighteen of the 40 V. vinifera subsp. sylvestris accessions were male, including newly identified powdery mildew resistant accession, DVIT3351.
Discussion In this study, we exploited available genetic information on the powdery mildew resistance locus Ren1 to identify additional germplasm that shared a Ren1-like local haplotype, and then attempted to clarify the evolution of powdery mildew resistance and its domestication in cultivated V. vinifera subsp. sativa. Ten new powdery mildew resistant accessions were discovered that possess a Ren1-like local haplotype, which was earlier identified in 'Kishmish vatkana' and 'Dzhandzhal kara' (syn. 'Karadzhandal') from Central Asia  [1, 2]. We discovered that powdery mildew resistance is present in two V. vinifera subsp. sylvestris accessions, a taxon considered to be the progenitor of the cultivated form sativa. Four of the resistant accessions 'Vassarga tchernaia', 'Chirai (obak)', 'Late Vavilov' and 'Khalchili' are obscure varieties with few records in the Vitis International Variety Catalog  [32]  or the European Vitis database  [33].
We cannot determine the time period when what appears to be very active grape breeding occurred with the fingerprint database created here, but given the lack of a historical record it seems that these breeding efforts may have occurred hundreds or thousands of years ago. The discovery of powdery mildew resistance in Chinese grape species and the possible transport and role of these species in grape breeding along the Asian trade routes is also intriguing. However, with the limited amount of Chinese grape germplasm, we were unable to prove this occurred with the data presented here. Comparative sequencing of multiple lines of Ren1 from different regions and species would greatly aid our understanding of the evolution of powdery mildew resistance. Finally, it is clear that additional collections of Central Asian grape germplasm are needed to fully understand grape evolution, discover additional sources of mildew resistance, and ensure the survival of this historic and valuable resource.
In the later part of the study, fragments were separated and sized on an ABI 3130 Genetic Analyzer (Applied Biosystems, Foster City, CA). Products from up to four primers were analyzed in one injection by using different fluorescent labels (6-FAM, HEX, and NED) on different primers and taking into account the expected fragment size. PCR products were added to an 11 μl: 0. 2 μl mixture of HD-formamide and GeneScan HD 400 ROX (Applied Biosystems, Foster City, CA) as the internal size standard, respectively. The fragments were denatured for 2 min at 92°C then injected into a 36 cm capillary filled with the polymer POP-7 (Applied Biosystems, Foster City, CA). Fragment sizes were determined and rounded using Genotyper 2. 5 software (Applied Biosystems, Foster City, CA). Four to six common V. vinifera cultivars were used as an internal control and to ensure allele calls were consistent with samples run on silver stained sequencing gels.
Allele size data for 133 accessions from the INRA Domaine de Vassal germplasm collection (INRA) were generated in France for 20 SSR markers following procedures described by Laucou et al. [17]. Allele sizes were transformed to match the allele sizes from the UCD data set based on known references and samples common to both group's data sets. Multi-locus accessions from the INRA set were compared to the UCD data set to identify synonymous samples. Unique accessions from the INRA set were analyzed at UCD with an additional 14 markers to increase marker overlap with the UCD data set.
Identification of powdery mildew resistant accessions Two SSR markers reported to flank the Ren1 locus, VMCNg4E10. 1 and UDV124, were used to screen the combined datasets for additional resistant accessions  [1]. We hypothesized that resistant accessions would have both flanking resistance associated alleles with SSR markers (VMCNg4e10. 1 allele 260 and UDV124 allele 216) and powdery mildew resistance in field screens. Three additional markers (SC8_0071_014, sc47_18 and sc47_20) reported to be closely linked to the Ren1 locus  [2]  was also tested. Two of them (SC8_0071_014 and sc47_18) gave clean amplifications and were added to the entire data set of unique germplasm.