dataesr/scientific-paragraphs-categorization huggingface dataset:
To further confirm this interaction, a complementary mutation was introduced into the ilvA transcript changing the predicted SD region from GAGG to CACC, and the construct was designated ilvA-SD CACC (Figure  4(a) ). Differences in the labelling efficiencies between sRli47 and sRli47 GGUG were consistently observed (Figure  4  and S5 ). In silico analysis predicted several RNA structures with similar folding patterns for both sRli47 and sRli47 GGUG (ΔG ranging from -66. 10 to -63. 30 kcal/mol). The single-stranded loop, where the mutated region resides, was preserved in all of the proposed mfold structures, implying that the differences in labelling efficiencies are most likely due to changes in the tertiary structure of the sRNA species. Further secondary structure predictions on ilvA and ilvA-SD CACC mRNAs revealed that the mutation caused differences in folding.
Transcriptomic analysis shows that amino acid transport and metabolism is affected by rli47 deletion To complement the in silico and in vitro data described above, and investigate the overall impact of Rli47 on gene transcription, a transcriptomic analysis of L. monocytogenes Δrli47 mutant and the parental strain EGD-e was performed using RNA-seq during growth at 37°C in DM, a condition where Rli47 is strongly expressed in the WT (Figure  2 ). Significant changes in the transcript levels of 155 genes were detected between the two strains (Figure  7 (a)). The relative abundance of each COG category in the set of differentially transcribed genes was determined. Overall, genes involved in amino acids transport and metabolism were highly represented in both upregulated and downregulated sets of genes, suggesting a direct and/or indirect role of rli47 in modulating amino acid metabolism (Figure  7(b) ).
While the appearance copB in the RNA-seq data set does not provide evidence of a direct interaction between it and Rli47 this certainly remains a distinct possibility. It could be that the in vitro binding conditions  Figure 8. Proposed model of the regulatory effect of Rli47 on isoleucine biosynthesis in L. monocytogenes. Transcription of rli47 is under σ B control and when it is expressed it interacts directly with mRNA from the ilv-leu operon at the predicted Shine-Dalgarno sequence upstream from the ilvA start codon. The Rli47-ilv interaction blocks the first step of isoleucine biosynthesis by preventing the translation of ilvA to produce threonine deaminase (TD), and also by affecting the stability of the ilv-leu transcript. σ B negatively influences the activity of TD through an Rli47-independent route which remains to be identified.
Modelling of rli47 secondary structure in vivo The data on dimethyl sulphate (DMS) reactivity of Rli47 RNA were imported from NCBI's Gene Expression Omnibus (GEO Series accession number GSE118387). In that study, DMS reactivity of L. monocytogenes non-coding RNAs was probed using the DMS-MaPseq protocol during mid-exponential growth at 37°C in BHI medium  [62]. DMS methylates unpaired adenines (A) or cytosines (C) but not A or C engaged in pairing. In brief, DMS (3%) was added to growing cells for 3 min before quenching and RNA-preparation. cDNA of the RNA were synthesized using TGIRTIII reverse transcriptase which incorporates a random base if encountering a methylated A or C. After sequencing and aligning of the cDNA, any mismatch from the reference sequence was indicative of an unpaired A or C in the RNA at the time of DMS addition.
Northern blot Total RNA (10 μg) was resolved on a 6% or 8% polyacrylamide 8 M urea gel as previously described  [65] ; alternatively, 20 μg of total RNA were separated on a formaldehyde agarose gel for 3 h and 15 min prior to capillarity blotting on a Zeta-Probe membrane (Bio-Rad)  [66]. Membranes were hybridized with 32 P-labeled DNA single-stranded probes listed in Table  S1. RNA bands were visualized using a Typhoon FLA9000 (GE Healthcare) and analyzed with IQTL 8. 0 quantification software (GE Healthcare). For mapping the 3ʹ-end of Rli47, three probes were used. The first probe used annealed in the middle of Rli47 (Rli47_NB), the second one Rli47(2)_NB annealed before the predicted stop site, and the third probe Rli47(3)_NB annealed after this predicted stop site.
05 were considered as DE. The transcriptomic data have been deposited on the Sequence Read Archive (SRA) database and is accessible through the SRA accession SUB5067488. Volcano plots were drawn by R software, with the integration of the ggplot2 and ggrepel graphical packages for data analysis  [70]. The top 20 most significantly upregulated and downregulated expressed genes in the deletion mutant were labelled. The negative log 10 of p-value was plotted on the Y-axis, and the log 2 FC was plotted on the X-axis. The blue points on this graph represent sRNAs and mRNAs that are significantly differently expressed in the rli47 deletion mutant (p-value <0. 05), the red points represent sRNAs and mRNAs with p-value >0. 05. The horizontal line represents a p-value >0. 05 cutoff. The horizontal lines represent a -0.
Three sets of cDNA were analyzed, originating from three sets of RNA extracted as described above. Primers efficiency was calculated prior to sample runs, in the same system. The relative expression ratio was used to analyze RT-qPCR results. The samples were run on a LightCycler® 480 System (Roche) with an initial step at 95°C for 15 min, 45 cycles of 15 s at 95°C, 15 s at 53°C and 30 s at 72°C, a melting curve was drawn for 5 s at 95°C, 1 min at 55°C followed by increases of 0. 11°C s -1 until 95°C, and a cooling for 30 s at 40°C. Cycle quantification values were calculated by the software LightCycler® 480 Software version 1. 5. 1 (Roche) and the Pfaffl relative expression formula  [71, 72]. The 16s rDNA gene served as a reference gene. The experiment was carried out in three biological replicates, each in technical triplicates.
monocytogenes rli47 deletion mutant comparatively to the wildtype EGD-e. Left pie chart, percentage of genes belonging to each COGs in the whole genome of L. monocytogenes EGD-e (NC_003210. 1). Right upper pie chart, genes upregulated compared with wild-type; right down pie chart, genes downregulated compared with wild-type. Colours correspond to categories in the COGs database.
(b) Relative abundance of categories of genes differentially expressed by L. monocytogenes rli47 deletion mutant comparatively to the wildtype EGD-e. Left pie chart, percentage of genes belonging to each COGs in the whole genome of L. monocytogenes EGD-e (NC_003210. 1). Right upper pie chart, genes upregulated compared with wild-type; right down pie chart, genes downregulated compared with wild-type. Colours correspond to categories in the COGs database.
Participants We included studies which: (1) genotyped both the HP CNV and rs2000999 and (2) genotyped the CNV using gold-standard PCR approaches (Table  1 ), rather than imputation from genome-wide array screening (GWAS). Three studies were identified at the time of study planning, and data was made available by the authors. The Avon Longitudinal Study of Parents and Children (ALSPAC) is a general population cohort study  [14, 15] ; lithium heparin plasma Hp level and HP genetic data was available from 325 participants (159 females and 166 males, Caucasian, age 18 ± 0. 33 years). The ALSPAC study website (http://www. bristol. ac. uk/alspac/researchers/our-data/) contains details of all the data that is available through a fully searchable data dictionary and variable search tool. Ethical approval for the study was obtained from the ALSPAC Ethics and Law Committee and the Local Research Ethics Committees.
Contribution of HP polymorphism to expression Data from the two mixed gender British and Japanese cohorts and the female-only French cohort was used to assess the contribution of the two HP genetic polymorphisms to circulating Hp level. All cohorts were in Hardy-Weinberg equilibrium (HWE) for both genetic variants (Supplementary File 1, Table  S1 ). We found evidence of LD between the two polymorphisms in each cohort (Supplementary File 1, Table  S1 ). To determine the contribution of HP genetic variation to circulating Hp level we performed multivariate linear regression where HP CNV was the exposure and rs2000999 was the covariate and combined the effects of each cohort in a fixed-effects meta-analysis. The analysis identified that the rs2000999 minor allele (A) was associated with a Hp change of -0.
SuperWASP, the Northern hemisphere WASP observatory, has been observing the skies from La Palma since 2004. In that time, more than 50 planets have been discovered with data contributions from SuperWASP. In the process of validating planets, many false-positive candidates have also been identified. The TESS telescope is set to begin observations of the northern sky in 2019. Similar to the WASP survey, the TESS pixel size is relatively large (13 arcsec for WASP and 21 arcsec for TESS), making it susceptible to many blended signals and false detections caused principally by grazing and blended stellar eclipsing binary systems. In order to reduce duplication of effort on targets, we present a catalogue of 1 041 Northern hemisphere SuperWASP targets that have been rejected as planetary transits through follow-up observation.
The raw-image data are corrected using bias frames, thermal dark-current exposures, and flat-field exposures. Typically the light curves for stars in the USNO-B1. 0 catalogue that are brighter than an R magnitude of 15 are extracted. The light curves for each star are taken from three different circular apertures with radii of 2. 5, 3. 5, and 4. 5 pixels, corresponding to 34, 48, and 62 arcsec on the sky. Checking whether the transit signal appears stronger in the larger apertures gives an indication of whether the object is blended with a nearby star, and thereby helps to eliminate photometric blends from further analysis  (Pollacco et al. 2006). The WASP pipeline also performs several other corrections for trends in the photometry, including the effects of extinction, instrumental colour response, and the system's zero point.
This includes transit depth, period, inclination, and secondary radius. As of 2019 April 18, the SuperWASP and WASP-South project have produced 163 published planets: 1 30 with SuperWASP, 109 with WASP-South, and 24 joint north and south. In addition, SuperWASP has contributed to rejecting an additional 1041 objects after follow-up data was taken. These objects, shown in Fig. 1 , are presented in this work. The WASP data base contains information of all stars with an R 15. 0 in the USNO-B1. 0 catalogue, and the BLS transit detection 1 https://wasp-planets. net/wasp-planets/ runs are only made for stars with more than 1000 data points. The archive contains all data available from the beginning of the SuperWASP project through March of 2014. The members of the WASP team have access to all of the light curves on an online data base.
The SuperWASP project relies on follow-up observations from a wide range of instruments to observe targets of interest. The contribution from each instrument is shown in Fig. 2. For further information about each instrument, refer to Appendix A. The observatory locations can be seen in Fig. 3. Once the nature of the light curve is known, it can be dispositioned in the catalogue as a planet (P), an eclipsing binary (EB), a blend with nearby objects (Blend), a low-mass companion (EBLM), a variable star (V), a false detection (X), or simply rejected after follow-up (RAF). If follow-up data was taken by another instrument to make the disposition determination, an additional, optional follow-up flag can be used to add further information. This can include information from spectroscopic follow-up, such as single or double lined eclipsing binary (SB1 or SB2) or line bissector (LB) variations.
An 'SB1' can also be indicative of a low-mass eclipsing binary (EBLM). This category reflects an object more massive than a planet or a brown dwarf, but with a radius comparable to a gasgiant planet or a very low mass star close to the mass limit for hydrogen burning. These are of particular interest for TESS as their flat-bottomed transits can pass almost every vetting test. In general, radial velocity data is needed to constrain the mass and confirm the EBLM status. However, in a few cases, the EBLM label was assigned based on the radius alone with the justification being the most likely explanation for an object larger than 2. 2R Jup is a small star and not a hyper inflated planet. Several EBLMs reported in this catalogue have significantly larger radii than this limit. This reflects the fact that the catalogue contains properties of the secondary mass estimates from the WASP archive, not values determined after follow-up.
As with the EBs, EBLMs will not have a follow-up flag if determined photometrically. Note that 18 of the EBLMs included in this catalogue have already been reported by  Triaud et al. (2017). These have been denoted with a ' * ' after the SWASP ID. The 'X' flag in this catalogue is a broad category and can either indicate that the light curve was a non-astrophysical false positive due to systematics, in which case the follow-up flag is 'FP' for false positive, or that the light curve was otherwise rejected. Again, the comments column will provide further detail. Some follow-up flags can be used for several different primary flags. The 'RR' follow-up flag indicated the star is rapidly rotating, defined in the WASP data base as having an FWHM > 8 km s -1. The 'G' flag indicates that the primary target star is a giant.
In the case that the giant status was deduced prior to follow-up by looking at the reduced proper motion of the star, the star is not included in the catalogue. However, in some cases, the giant status of the star was not known until spectral data were obtained. The recent Gaia data release has now greatly reduced the risk for spending follow-up effort of evolved stars. Finally 'O' stands for 'other', meaning that none of the follow-up flags provided captures why the object was categorized as it was. When possible, further information about the classification is included in the 'Comments' column of the table. In some cases, a star in the catalogue is labelled as rejected without further classification (denoted as 'RAF'). The flags in the false positive catalogue have therefore been updated to reflect the true disposition.
Furthermore, presence in the false positive catalogue does not necessarily mean that there is not a planet in the system, only that there is not a planet of the predicted size and period found in the WASP data. The catalogue highlights several interesting features in the population of stars that have been observed. One trend that is apparent in the data is the magnitude sensitivity of SuperWASP. Fig. 6  shows that the vast majority of stars observed with WASP have V-band magnitudes less than 14, even though the input catalogue contains all stars brighter than a magnitude of 15. The reason for this is twofold. First, brighter objects have better signal to noise, with objects brighter than a V magnitude of 9. 4 having precision around 0. 004 mag. By a V magnitude of 11. 5, the precision drops to.
In order to try to quantify the effect of blended light on follow-up stars, we use Gaia photometry to make a rough prediction on the dilution of light from the primary target. We search the Gaia DR2 data base  (Gaia Collaboration et al. 2016 , 2018 ) for all objects Figure  5. A manual 'decision tree' describing the general criteria for dispositioning objects in the WASP database. In many cases, there is not enough data to completely go through the decision tree. When this happens, only branches containing known information are used. For example, if only spectroscopic follow-up is available, we bypass the branch pertaining to aperture and photometric blends. within the middle WASP aperture of 3. 5 pixels (48 arcsec) in radius surrounding the target star. We then combine the relative magnitude of the surrounding stars to the target star to measure the total dilution.
Higher dilution values mean increased light from other sources within the aperture. As can be seen in Fig. 9 , there is a clear tendency for planets to be found where few other stars are present to dilute the target light. This is most apparent when comparing to the population of blends, although a similar trend is seen when comparing planets to eclipsing binaries and other low-mass eclipsing companions. This demonstrates another way which Gaia data can be used to help with candidate prioritization.
S U M M A RY A N D C O N C L U S I O N S Here, we have presented a catalogue of all stars displaying transitlike signals in SuperWASP data that were shown to not be planets after further follow-up. Objects that are currently undergoing additional observations or that do not have a definitive disposition are not included. In total, 1041 false positives have been included in the catalogue, while 54 planets have been discovered with SuperWASP or jointly with WASP-South. This false positive rate is similar to that reported by the KELT team which found 1128 false positives and 30 reported planets  (Collins et al. 2018). In addition to the WASP planets, the data base includes many planets that have been discovered by other survey missions, and therefore have not been assigned a WASP name. While not all of these planets are visible in the WASP data due to poor signal to noise, lack of sufficient data on the star, or periods outside of the WASP search space, nearly 50 additional planets can be identified in the SuperWASP data.
Solution structure and dynamics of RodA The structure of RodA was studied by NMR spectroscopy. Comparison of the 1 H-15 N HSQC spectra of recombinant RodA (rRodA) and the HPLC purified hydrofluoric acid-extracted RodA from conidia indicated that both proteins have the same structure, the same cysteine redox state and potential disulfide pairing (Supplementary Material Fig. S1 ). Additionally, the native protein did not contain any post-translational modification such as an O-or N-glycosylation. This was confirmed by mass spectrometry (MS) of proteolysis fragments of the fulllength conidia-extracted protein before or after chemical treatment with the N-and O-deglycosylating agent trifluoromethanesulfonic acid (data not shown). We thus performed further work using the recombinant protein expressed in E.
S8);  (2) while parental rodlets coated the entire conidium, the coverage of the conidium surface by the mutated rodlets was incomplete, with a coverage ranging from 20 to 50% of the conidial surface for the I115S/I146G mutant (Fig. 7 ). In addition, the surfaces of the conidia of the I146G and I115S/ I146G mutants were covered at least partially by an amorphous material. MS analysis of the extract obtained after incubation of the conidia in formic acid for 2 h indicated that over 1200 proteins were quantified in the I115S/I146G mutant conidia and this number greatly exceed the number of proteins detected with its parental strain, demonstrating the presence of a much higher concentration of proteins in the mutant cell wall (Data are available via ProteomeXchange with the identifier PXD008503).
8 ). The most important recruitment was observed with the ΔrodA mutant and was similar in mice infected with the ΔrodA and the quadruple cysteine mutants (Fig. S11 ). Interestingly, the cellular recruitment with the RodA I115S/I146G mutant was similar to the parental strain, suggesting that the presence of disorganized rodlets on the conidial surface is sufficient to immunosilence the conidia. After 24 h, no difference in the GM concentration was found between all RodA mutants and the parental strain in mice lungs (data not shown). This result was in agreement with previous results  (Thau et al. , 1994. Valsecchi et al. , 2017)  indicating that rodlets are not a virulence factor for A. fumigatus. Long-term exposure was investigated with fixed conidia and human dendritic cells (DC) for 2 reasons: (i) DCs are major players in deciding the fate of the immune response and (ii) the use of fixed conidia was necessary since unfixed conidia would germinate and thus interfere with the specific immune response towards intact conidia of the parental and mutant strains.
The quality of the structures was assessed with PROCHECK 3. 5. 4 (Laskowski et al. , 1993) , WHATCHECK  (Hooft et al. , 1996) , MOLPR-OBITY  (Chen et al. , 2010)  and PROSA  (Sippl, 1993). The coordinates have been deposited to the pdb under the accession code 6GCJ.
Lag phase and t 1/2 were determined by the last time point before the normalized ThT fluorescence reached a value of 0. 1 and the time at which normalized 0. 5 ThT fluorescence reached 0. 5, respectively. Statistical analysis was performed on GraphPad Prism (version 6. 04 for Windows, GraphPad Software, CA, USA, www. graphpad. com). Data was evaluated using one-way ANOVA followed by Tukey's multiple comparisons test.
The HOPG surfaces were scanned with tapping mode using a silicon scanning probe with tip radius < 10 nm, force constant of 40 N/m and resonance frequency of 300 kHz (Tap300AI-G, BudgetSensors™, Bulgaria). The images were further processed with Gwyddion software (version 2. 38, http://gwyddion. net). For TEM, a 20-µL droplet of peptide (200 µg/mL) was placed on a formvar/carbon coated copper TEM grid (200-mesh, ProSciTech), and incubated for 2 min at room temperature. Excess solution was removed with filter paper and grids were washed twice by floating the grids on water droplets and wicking away the excess solution. Samples were stained with 2% uranyl acetate and imaged on a JEOL 1400 JEOL TEM equipped with a Morada G3 16 megapixel side camera. All images were analyzed with ImageJ.
Atomic force microscopy of conidia Conidial surfaces were analyzed by AFM, using a Multimode VIII AFM (Bruker, Santa Barbara, CA). A. fumigatus conidia were immobilized by mechanically trapping them into porous polycarbonate membranes with a pore size similar to the conidium diameter (it4ip SA, Belgium). After filtering a concentrated suspension of conidia, the filter was rinsed with deionized water, carefully cut and attached to a metallic puck using double-sided sticky tape. The mounted sample was then transferred to the AFM liquid cell. Images were performed in contact mode under minimal applied force, using oxide-sharpened microfabricated Si 3 N 4 tips (MSCT, Bruker) with a nominal spring constant of 0. 01 N/m. The surface coverage of the amorphous layer and the rodlets were determined visually using ImageJ software.
Treatment of DCs with RodA proteins and conidia Immature DCs (0. 5x10 6 /ml) were cultured in the presence of GM-CSF and IL-4 alone or with parental or mutant conidia (1:1) for 48 h. In other experiments, DCs were incubated with p-formaldehyde fixed conidia or various forms of RodA (1 μg/0. 5 × 10 6 DCs/ml) or LPS (100 ng/0. 5 × 10 6 DCs/ml) as described in  Aimanianda et al, 2009. After 48 h of incubation, cell-free culture supernatants were collected for analysis of IL-6 and TNFα DC-cytokines (ELISA Ready-SET-Go, eBioscience). DCs were processed for flow cytometry by surface staining with fluorochrome-conjugated antibodies. Data were acquired on a LSR II (BD Biosciences) flow cytometer and analyzed using the BD FACS DIVA software (BD Biosciences).
DCs-naïve CD4 + T cell co-culture To explore the effect of A. fumigatus conidia-stimulated DCs on CD4 + T cell polarization, after stimulation, DCs were extensively washed and co-cultured with 0. 1 × 10 6 CD4 + CD45RA + CD25 -autologous naïve T cells at a 1:20 ratio for five days in serum-free X-VIVO medium. Cell-free supernatants were collected after 5 days. Surface staining of T cells was performed with fluorescence-conjugated mAbs against CD4, CD25 or CD127. Then, cells were fixed, permeabilized using an intracellular staining kit (eBioscience) and incubated at 4 °C with fluorochrome-conjugated mAbs against FoxP3. Data were recorded on a LSR II (BD Biosciences) flow cytometer and analyzed with the BD FACS DIVA software (BD Biosciences). The cell-free culture supernatants were collected and analyzed for various T cell cytokines by ELISA (IFNγ, IL-4, and IL-17A; ELISA Ready-SET-Go, eBioscience).