dataesr/scientific-paragraphs-categorization huggingface dataset:
Proline was then used to perform a compilation, grouping and MS1-based label-free quantification of the protein groups from the different samples. Statistical analysis was performed using ProStaR  94. Proteins identified in the reverse and contaminant databases, proteins identified with only 1 peptide, proteins identified by MS/MS in less than 3 replicates of one condition and proteins exhibiting less than 4 quantification values in one condition were discarded. After log2 transformation, abundance values were normalized using the variance stabilizing normalization procedure before missing value imputation (slsa method for POV and DetQuantile with quantile and factor set to 1 for MEC). Statistical testing was conducted using limma. Differentially expressed proteins were sorted out using a log2 (fold change) cut-off of ± 0.
Therefore, the GMO Panel considers that its previous conclusions on the safety of the single maize events remain valid. For the six-event stack maize, the risk assessment included the molecular characterisation of the inserted DNA and analysis of protein expression. An evaluation of the comparative analysis of agronomic, phenotypic and compositional characteristics was carried out, and the safety of the newly expressed proteins, of the dsRNAs and the whole food and feed were evaluated with respect to potential toxicity, allergenicity and nutritional characteristics. Environmental impacts and post-market environmental monitoring (PMEM) plan were also evaluated. The molecular characterisation data establish that the events stacked in maize MON 87427 9 MON 87460 9 MON 89034 9 1507 9 MON 87411 9 59122 have retained their integrity.
Agronomic and phenotypic analysis Field study, US, 2014, eight sites (a)  MPA640B (b)  18 (c)   Compositional analysis GM: genetically modified. (not treated), the comparator MPA640B and four non-GM maize reference varieties (hereafter referred to as 'non-GM reference varieties'). The agronomic, phenotypic and compositional data were analysed as specified by the EFSA GMO Panel (2010b, 2011a). This includes, for each of the two treatments of the six-event stack maize, the application of a difference test (between the GM maize and the non-GM comparator) and an equivalence test (between the GM maize and the set of non-GM commercial reference varieties). The results of the equivalence test are categorised into four possible outcomes (I-IV, ranging from equivalence to non-equivalence). 11 3. 4.
Dietary exposure assessment to new constituents In line with Regulation (EU) No 503/2013 the applicant provided dietary exposure estimates to CP4 EPSPS, CspB, NPTII, Cry1A. 105, Cry2Ab2, Cry1F, PAT, Cry3Bb1, Cry34Ab1 and Cry35Ab1 proteins newly expressed in MON 87427 9 MON 87460 9 MON 89034 9 1507 9 MON 87411 9 59122 maize. Dietary exposure was estimated based on protein expression levels reported in this application for the six-event stack maize treated with the intended herbicides, the current available consumption data and feed practices, the foods and feeds currently available in the market and the described processing conditions. Table  8  describes the protein expression levels derived from replicated field trials in United States during 2014 (five locations, four replicates) and used to estimate both human and animal dietary exposure to CP4 EPSPS, CspB, NPTII, Cry1A.
Human dietary exposure 28 Human dietary exposure was estimated across different European countries on different population groups 29 : young population (infants, toddlers, 'other children'), adolescents, adult population (adults, elderly and very elderly) and special populations (pregnant and lactating women). Mean protein expression values on fresh weight basis (Table  8 ) are considered as the most adequate to estimate human dietary exposure (both acute and chronic) when working with raw primary commodities that are commonly consumed as processed blended commodities  (EFSA, 2019). Since no specific consumption data were available on commodities containing, consisting of or obtained from the six-event stack maize grains, a conservative scenario with 100% replacement of conventional maize by the GM maize was considered.
Consumption figures for all relevant commodities (e. g. corn flakes, sweet corn, popcorn, etc. ) were retrieved from the EFSA Comprehensive European Food Consumption Database (EFSA consumption database). 30 Corn oil was excluded from the assessment since no proteins are expected to be present in the oil. For the acute dietary exposure estimations, the applicant directly assigned to processed commodities the mean value reported for the concentration of the newly expressed proteins in maize grains (Table  8 ). Overall, this is a conservative approach as neither recipes nor the effect of processing on the final concentration of newly expressed proteins are considered, except for corn oil which is eventually excluded from the exposure estimations. Summary statistics from the EFSA consumption database were used.
105, Cry2Ab2, Cry1F, PAT, Cry3Bb1, Cry34Ab1 and Cry35Ab1 proteins. Individual consumption data of the (e): Expression levels for Cry1A. 105 are not corrected for the cross-reactivity between Cry1F and Cry1A. 105 observed in the ELISA for Cry1A. 105. As a consequence, the Cry1A. 105 expression levels are overestimated by ~7%. (f): PAT protein levels were below the limit of detection in all grain samples (LOD = 0. 025 lg/kg). The reported LOD was used for both human and animal dietary exposure estimations. 28 Dossier: Part II -Section 2. 4 and Additional information 26/8/2019. 29 For infants, very elderly population and vulnerable groups only chronic dietary exposure estimations are provided. 30 http://www. efsa. europa. eu/en/data/food-consumption-data 31 Summary statistics from the EFSA Comprehensive European Food Consumption Database accessed in September 2016.
32 Dominant food commodity refers to the food that will lead to the highest exposure among all consumed foods. relevant food commodities were retrieved from the EFSA Consumption Database, using dietary surveys with at least two days consumption and covering a total of 23 European countries. 33 Different recipes and factors were considered to estimate the amount of maize in the consumed commodities before assigning newly expressed protein levels to the relevant commodities. 34 No losses in the newly expressed proteins during processing were considered, except for certain commodities excluded from the exposure estimations (maize oil, corn starch, corn syrup). The 95th percentile chronic exposure (highly exposed population) was derived from the distribution of the individual dietary exposure estimates within each dietary survey and age class.
The highest chronic dietary exposure was estimated in the age class 'Infants' with exposure estimates that ranged between 0. 024 lg/kg bw per day and 144 lg/kg bw per day for NPTII and Cry34Ab1 proteins, respectively. The main contributor to the exposure in the dietary survey with the highest estimates was sweet corn. Consumption data on pollen supplements are available for few consumers across nine different European countries. 35 However, since no data on the presence of newly expressed proteins in pollen were available, the potential dietary exposure to CP4 EPSPS, CspB, NPTII, Cry1A. 105, Cry2Ab2, Cry1F, PAT, Cry3Bb1, Cry34Ab1 and Cry35Ab1 proteins from the consumption of pollen supplements could not be estimated.
34 100 grams of maize bread are made with approximately 74 g of maize flour, and a reverse yield factor of 1. 22 from the conversion of maize grains into flour is used. This results in 26. 2 µg of Cry34Ab1 per gram of maize bread as compared to 34 µg/g in the maize grains. 35 https://www. efsa. europa. eu/en/food-consumption/comprehensive-database. Data accessed April 2020. 36 Dossier: Part II -Section 2. 4 and Additional Information 27/8/2019. their total intake and the magnitude and direction of the observed changes were considered during the nutritional assessment.
Leucine and lysine are essential amino acids; the observed increase in leucine content (%AA) in maize grains is not a concern for animal nutrition. Also, the magnitude of the decrease of lysine (%AA) in maize grains does not pose a problem for animal nutrition. Both amino acids are usually balanced and supplemented in complete diets (e. g. for monogastric animals). In animal nutrition, amino acids are also expressed as the percentage of dry weight (dw) to calculate directly the amount of each amino acid consumed daily by animals. According to Regulation (EC) No 767/2009 37 , if, 'in complete or complementary feed, amino acids, vitamins and/or trace elements are indicated under the heading of analytical constituents, they shall be declared, along with the total amount thereof'. Therefore, variations in the amino acids described above were also assessed taking in consideration data expressed as % dw, which did not change the overall assessment.
Comparison of the levels of the newly expressed proteins between the six-event stack maize and those of the single maize events did not reveal an interaction at protein expression level. In addition, the potential impact of the DvSnf7 dsRNA on the levels of the newly expressed proteins was assessed by comparing the protein expression levels in the six-event stack and the respective single events. The data indicate that there is no impact of the DvSnf7 dsRNA on the expression levels of the newly expressed proteins. Considering the combined traits and their interactions, the outcome of the agronomic and phenotypic analysis, and routes and levels of exposure, the GMO Panel concludes that six-event stack maize would not raise safety concerns in the event of accidental release of viable GM maize grains into the environment.
4. 1. 3 and Appendix B). In addition, the potential impact of the DvSnf7 dsRNA on the levels of the newly expressed proteins was assessed by comparing the protein expression levels in the six-event stack and the respective singles. The data indicate that there is no impact of the DvSnf7 dsRNA on the expression levels of the newly expressed proteins. This supports the conclusion that interactions affecting the expression levels of the newly expressed proteins are not expected in the 39 subcombinations not previously assessed and included in the scope of application EFSA-GMO-NL-2017-139.
In this study, we make and compare estimates of slip rate measured using both geodesy and geomorphology, and spanning time periods ranging from decadal to 100 ka. To image the present-day accumulation of strain, we process 7 years  (2003) (2004) (2005) (2006) (2007) (2008) (2009) (2010)  of data from six ENVISAT tracks covering the fault, with interferograms produced for 400-km-long strips of data to image the longwavelength signals associated with interseismic strain accumulation across the locked fault. Our analysis shows that less than 4 mm/yr-and likely only 1-3 mm/yr-of slip accumulates across the fault. Using high-resolution optical satellite imagery, we make reconstructions of displacement across six alluvial fans whose surfaces cross the fault, in four separate river catchments. We determine the ages of these fans using infra-red-stimulated luminescence dating combined with U-series dating of pedogenic carbonates.
10. 1029/2020TC006256 the two-channel margins on the downstream side. When more than one displaced stream is present within a landform, we make a single best-fit restoration. Further details of our geomorphic interpretations and restorations are provided on a site-by-site basis in Section 5. For age constraint, we predominantly use infra-red stimulated luminescence (IRSL), with results shown in Table  1 , and full data presented in Tables  A1  and A2. A full description of the methods is given in the Appendix, which vary slightly from those described in  Fattahi et al. (2014). We also performed U-series dating of pedogenic carbonates found at one site. We milled individual growth layers of carbonate from two samples and dated them using the U-Series method. All preparatory and analysis steps are as reported in  Gregory et al.
Decadal Strain Accumulation From InSAR We used SAR images from the ASAR instrument (5. 6-cm wavelength) on board the ENVISAT satellite to investigate the interseismic deformation across the Doruneh fault. In the "image mode" of the ASAR instrument (swath of 100 km), the studied area is covered by several tracks of the satellite (Figure  1b ). We chose to use 400-km-long interferograms to be able to integrate regions far from the fault trace, in contrast to an earlier study of  Pezzo et al. (2012)  that considers only 100-km interferograms centered on the fault trace and does not correct for DEM errors and atmospheric effects. The 100-km-long strips of data used by  Pezzo et al. (2012)  may be too short to discriminate between the long-wavelength orbital error signal and the elastic interseismic deformation around the fault.
Processing Raw radar images from 2003 to 2010 (Processing Level 0) were processed with ROI_PAC software  (Rosen et al. , 2004)  using the NSBAS package  (Doin et al. , 2011). The topographic phase contribution was estimated from the SRTM Digital Elevation Model (DEM) at 90-m spatial resolution  (Farr et al. , 2007). Precise DORIS orbital data for the ENVISAT satellite provided by ESA were used for interferometric processing. We produced single look complex (SLC) images with a common Doppler frequency band. A single master image was chosen following the approach of  Zebker and Villasenor (1992)  and  Hooper et al. (2007) , and all other SLCs were co-registered in the master image geometry using the DEM. We processed all possible interferograms having baseline differences less than 500 m to minimize de-correlation of the signal.
e. , to a depth of 35 cm from the surface). Two IRSL samples were taken from the silt unit at depths of 30-35 cm. These two samples yield ages of 98. 6 ± 7. 3 ka (KASHMAR-1, 35-cm depth) and 89. 2 ± 6. 8 ka (KASHMAR-2, 30-cm depth). We also dated the rinds of carbonate found on the underside of gravel clasts at a depth of 55 cm. Detritally corrected ages are plotted in Figure  13. The data shows a clear correlation of growth at the 92. 4-98. 0 ka isochron age. A further correlation between samples exists at ∼20-30 ka implying a younger generation of carbonate. There is also a single data point at ∼80 ka, which could either represent an episode of growth, or cross-contamination of the two sample groups. The data strongly suggests the onset of carbonate growth around 100 ka, in agreement with the IRSL ages.
The best fit line is shown in red, with two-sigma uncertainty in the regression represented by the pink area. In the plot shown, the best fit line is constrained to pass through the origin. If the best fit line is not constrained to pass through the origin the mean slip-rate does not change, but the uncertainty increases from ± 0. 2 to ± 0. 3 mm/yr. post-depositional processes are the dominant control on scatter within the boulder populations, at least in those few sites with independent age control. A similar post-depositional signal can be seen in the full dataset of 10 Be boulder ages in  Farbod et al. (2016) , which show a general increase in scatter in progressively older surfaces, as seen in their Figure  10 , but again show broad agreement with our own chronology of alluvial fan deposition.
To correct for the effect of detrital contamination on the calculated ages, we first determined detrital composition by assuming a crustal elemental abundance of Uranium and Thorium archived in the EarthChem database (http://www. earthchem. org), and then derived a 230 Th/ 238 U ratio of 0. 7607 ± 0. 0139 and a 234 U/ 238 U ratio of 1. 2679 ± 0. 172 from the isochron relationship (e. g. ,  Bischoff & Fitzpatrick, 1991; Luo & Ku, 1991)  using the four "C-Inner" samples and "B-Outer-2" (Table  A3 ). To constrain the uncertainty of detrital isotopic concentration, the isochron slopes and intercepts were calculated using a York fit, with error weighted in both x and y.
Acknowledgments The authors thank the  European Space Agency (ESA)  for providing Envisat SAR images and IKONOS imagery through CAT-1 projects 6462 and 7023. The authors are grateful to  JPL/Caltech  for use of the ROI_PAC software. The authors thank the  Geological Survey of Iran  for their continued support of our work. Mr. Hosseini  of the Kerman office of the Geological Survey and  Mr. Soltani  of the International.
Data Availability Statement Maps were prepared using Generic Mapping Tools software  (Wessel & Smith, 1995). FAIR data access statement: For the interferometry, we used Envisat data, which was originally obtained through a European Space Agency Category 1 project (7023), and which is now archived and freely available through the ESA online catalog (http://esar-ds. eo. esa. int/socat/SAR-ASA_IMS_1P/pair_search). Commercial Quickbird satellite imagery used within this analysis was obtained at no cost through ESA Category 1 project (6462). The data were obtained under license and are available for purchase from Maxar (https://www. maxar. com/). All data derived from IRSL and U-series dating are provided in full within the main body of the study.
Currently, this approach is still widely used in the engineering process design (see for example the MFIX open source software  [4] ). Some DEM weaknesses, reported in  [2] , include the small time steps inherent in the explicit time scheme or the damping introduced for stability matters. Moreau established the theoretical concepts to properly handle the non-smooth mechanics featured by nondifferentiable laws in its common definition. Thus, he introduced the second-order sweeping process as the framework of mathematical analysis and numerical schemes designed for granular materials. The cornerstone is the formulation for the Signorini problem in terms of velocities and impulses, leading to the Moreau-Jean time-stepping approach  [5]. This numerical scheme is implicit and the energy conservation property holds unlike the DEM framework.
The RNA was quantified using the Qubit kit (Fisher Life Science). 10 g of RNA was treated with Turbo DNase (Fisher Scientific) to remove contaminating DNA. Ribosomal RNA was removed using Ribozero (Illumina) according to the manufacturer's instructions. To form the chimeric RNAs between RNAs crosslinked with AMT, the protocol described by Sharma et al. was followed as described in the supplemen-tary data  (30). The only modification was the use of CircD-NAligase (Epicentre) instead of CircRNAligase as this has been discontinued. RNAseq. Following reversal of crosslinking at UV 254 nm, RNA was purified and resuspended in 10 l H 2 O and processed through the TruSeq stranded total RNA library kit (150 bp) (Illumina) according to the manufacturer's instructions. The resulting libraries were sequenced on a MiSeq (Illumina).
Analysis. STAR aligner was used to map reads (Version STAR 2. 6. 0c 08-11)  (39). This mapping tool is designed to analyse splicing of introns and exons, which is similar to what is created through the formation of chimeric reads where two different RNA fragments have been joined together. By identification of reads that map to different features (protein coding sequences, sRNAs, UTRs, transcripts for ncRNAs such as rRNA and tRNA, or transcribed intergenic regions) it is possible to identify RNA interactions. STAR aligner was set to single end read mode to map read 1 and read 2 separately, the chimeric detection mode activated, as this has been reported to be more sensitive to chimeric junctions. The allowed mismatches in mapping was set to default for STARaligner. The output from STAR was merged in to one Sam file, before being annotated using featureCounts within the package subread-1.
05  (40). To gain further confidence in pairs that form the most likely interactions, interacting pairs were further assessed by in silico prediction with IntaRNA2. 0, which predicts the stability and binding position between two interacting RNAs  (41, 42). The gene and any untranslated region that has been identified associated with the gene of interest  (12)  were included in the prediction to take into account the transcriptional start and stop sites. If no UTR had been identified for an mRNA, the 50 bp up and downstream of the start and stop site were employed. The analysis pipeline can be found in the following GitHub repository, https://github. com/StephenLi55/ Bacillus RNA crosslinking analysis.
Tandem MS was performed by isolation at 1. 2 Th using the quadrupole, HCD fragmentation with normalized collision energy of 33, and rapid scan MS analysis in the ion trap. The MS2 ion count target was set to 3 × 103 and maximum injection time was 200 ms. Precursors with charge state 2-6 were selected and sampled for MS2. The dynamic exclusion duration was set to 60 s with a 10 ppm tolerance around the selected precursor and its isotopes. Monoisotopic precursor selection was turned on and instrument was run in top speed mode. Thermo-Scientific raw files were analysed using MaxQuant software v1. 6. 0. 16 (http://www. maxquant. org) (44)  against the UniProtKB B. subtilis database (UP000001570, 4260 entries). Peptide sequences were assigned to MS/MS spectra using the following parameters: cysteine carbamidomethylation as a fixed modification and protein N-terminal acetylation and methionine oxidations as variable modifications.
The FDR was set to 0. 01 for both proteins and peptides with a minimum length of seven amino acids and was determined by searching a reversed database. Enzyme specificity was trypsin with a maximum of two missed cleavages. Peptide identification was performed with an initial precursor mass deviation of 7 ppm and a fragment mass deviation of 20 ppm. The MaxQuant feature 'match between runs' was enabled. Label-free protein quantification (LFQ) was done with a minimum ratio count of 2. Data processing was performed using the Perseus module of MaxQuant v1. 6. 0. 16  (45). Proteins identified by the reverse, contaminant and only by site hits were discarded. Only protein groups identified with at least two assigned peptides were accepted and LFQ intensities were log 2 transformed. Significantly regulated proteins were identified in two rounds of analysis.
Plate reader experiments Experiments to monitor promoter activity were carried out in a 96-well format in a BioTek Synergy Plate reader, with measurements every 10 min and analysed as described previously  (36, 37). Briefly, cultures were monitored for both optical density (O. D. 600 nm ) and GFP fluorescence (excitation 485/20 nm, emission 528/20 nm). Background fluorescence from the isogenic WT control strain not expressing GFP was subtracted. Arbitrary units represent changes in promoter activity and were calculated using the equation (GFP t -GFP t-1 )/O. D. 600t (where t represents a given time point at which fluorescence was measured, and t -1 the preceding time point at which fluorescence was measured). Curves were smoothed using a moving average of three data points.
A similar arrest of the reverse transcriptase in the presence of RoxS was observed previously for sucCD and ppnkB mRNA  (14). To confirm the key regions of interaction between FsrA and RosA, we also performed EMSA assays with RosA and FsrA mutants. The 4 C's of the CRR1 sequence of FsrA were first mutated to four A's (FsrA CRR1/4A ) and 2 C's of CRR2 to 2 A's (FsrA CRR2/2A ) (Figure  2B ). Mutation of FsrA CRR1 did not affect FsrA binding to RosA, while the FsrA CRR2/2A mutation abolished the interaction (Figure  5D ), confirming that FsrA CRR2 is more important for pairing. This was confirmed by mutation of the complementary GRR1 and GRR2 regions of RosA (RosA GRR1/2U and RosA GRR2/4U ). WT FsrA still bound to RosA GRR2/4U but failed to form a complex with RosA GRR1/2U. Together, these results show that the CRR2 sequence of FsrA and the GRR1 region of RosA, the site of the most stable interaction predicted by the IntaRNA program  (42) , are most likely to be involved in the pairing between the two RNAs.