dataesr/scientific-paragraphs-categorization huggingface dataset:
All panels contain information about the coefficient of determination r 2 obtained for each fit. Adapted from  Vasseur et al. (2017). (A, B, E, F ) are the data for two porosities, for which the ML-TROL power-law model is fit using increasing fractions of the data. f = 1 represents the full dataset, while f = 0. 7, for example, would indicate that 70% of the total data set, measured from the beginning, has been used in the fitting. Panels (C,G) are the effect of taking increasing fractions of the data on the failure time accuracy. Contrastingly, in panels (D,H), the curves at f < 1 refers to a case when data at the beginning of the sequence is missing. A normalized failure forecast of unity (zero on this log axis), represents a perfect forecast. (A,B,E,F) contain information about the coefficient of determination r 2 obtained for each fit.
Probability and Accuracy For 0. 7 ≤ f ≤ 1. 0, we show in Figure  5  the effect of taking different proportions of the sequence on the forecast error. A complete sequence f = 1. 0 relates to the forecast error for a complete sequence, and therefore represents a limiting case where the entire dataset is known ahead of time. Any reports of the predicted failure time for f = 1. 0 are therefore not forecasts and are instead useful for assessing the quality of the functional forms for ˙ (t) that could be used in forecasts. Here we see the strong dependence of the error on the sample porosity, with high-porosity materials being fully predictable with nearzero error. However, at f = 0. 7, for which the uncertainty on the signal is higher, we note that the variability in the forecast error for high-porosity materials is larger than for materials with φ < 0.
CONCLUSIONS We show that it is the heterogeneity of the system that most effects the efficacy of forecasts of material failure. Given this insight, we have presented the simplest scaling from the laboratory to the natural case on the basis of the relationship between rupture lengthscale and radiated frequency. On the laboratory scale, it is the inter-pore lengthscales that fail in each individual acoustic event, which leads to larger scale failure at the critical time. By scaling, we see that these events and the associated frequencies would be equivalent to seismic events at volcanoes with much larger rupture lengthscales. However, independent tests of the rupture lengthscales at active volcanoes are poorly known and would represent fruitful future work. We explore the effect of having an incomplete dataset during a deformation episode.
This project was funded by the European Union's collaborative Seventh Framework Program for research, technological development, and demonstration under the NMI3-II Grant number 283883 (FP7-NMI3), being part of the contributions submitted to ESS  [10]. The large high-efficiency multi-layered Micromegas thermal neutron detector, built under this framework FP7-NMI3, was presented in detail in Reference  [11]  and its main aspects are shown in the next section. Based on the same concept, CEA designed and simulated another neutron-sensitive Micromegas detector using the Microbulk Micromegas detector technology for the SINE2020 project that received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No. 654000, materialized in ESS. The European Spallation Source (ESS) now under construction in Sweden, will produce intense beams of neutrons for determining the structure and dynamics of materials.
Three-dimensional (3D) electrostatic field numerical simulations were carried out using the Garfield  [13]  simulation framework with the addition of the neBEM  [14, 15]  toolkit in order to investigate how the thickness of the mesh affects the electron transparency. The outcome indicates the need of very thin meshes to achieve high electron transmission. Therefore, nickel meshes of 5 μm thickness were ordered, coated, and tested. A comprehensive and accurate set of Monte Carlo simulations was performed to optimize the thickness of the 10 B4C layer for maximizing the conversion efficiency, defined as the probability for a neutron to produce an α particle and/or a Li ion that enter into the gas gap. For the current work, the FLUKA Monte-Carlo simulation package  [16, 17]  was used (simulation results using the GEANT4 platform were compared to cross-validate the code), where the low energy neutron transport package was activated and employed for thermal neutron detection.
A comprehensive and accurate set of Monte Carlo simulations was performed to optimize the thickness of the 10 B 4 C layer for maximizing the conversion efficiency, defined as the probability for a neutron to produce an α particle and/or a Li ion that enter into the gas gap. For the current work, the FLUKA Monte-Carlo simulation package  [16, 17]  was used (simulation results using the GEANT4 platform were compared to cross-validate the code), where the low energy neutron transport package was activated and employed for thermal neutron detection. The demanded detection efficiency is given by the number of entries in the energy deposition histograms inside the gas volume divided by the total number of thermal neutrons hitting the detector. A 10 B layer thicker than 2-3 µm is not effective due to the absorption of the reaction products.
The data indicate that the detector response is ~0. 65 Hz (noise) when no neutron source is used. Having placed the detector on top of the neutron source and varying the applied voltages, the contribution of each 10  V, a rate of ~9. 24 Hz was recorded, which comes from the 10 B 4 C layer 1. Higher recorded counting rates of ~36 Hz can be obtained with a higher multiplication factor of F = 10. We establish here that the proposed detector works; however, for obtaining more reliable results, we should optimize the applied voltages and the drift distances in order to increase the ionization, and maximize the electron transmission through the meshes by having the peaks of the rate distributions from different drift regions overlapping with each other. The performance of this configuration and set-up was compared to a calibrated reference 3 He tube detector (see Figure  4 ).
Acknowledgments: We thank our technician colleagues from  CEA/Saclay  for many months of collaborative work,  R. de Oliveira  and his team at  CERN  for the manufacturing of the microbulk and GEM detectors. We also acknowledge the support of  LLB  staff during our tests of our detector prototype at Orphée reactor as well as all our colleagues from  Linköping University  and the ESS detector coatings workshop who participated in the depositions of our meshes.
thaliana root cells, in which we used DAPI to stain DNA (Fig. 2C ). Transcriptomic data from the AtGenExpress database show that the four A. thaliana NOC genes are coexpressed at similar developmental stages, while data from ATTED-II additionally show these genes to be coregulated under similar stress conditions (Fig. S1B )  [17, 18]. Further to the correlation between SWA2 and AtNOC2 expression shown by Li et al. [16] , we show a correlation between AtNOC3 and RBL expression (Fig. S1C ). Moreover, data from ATTED-II indicate that AtNOCs are coexpressed with many genes encoding nucleolar proteins, such as OLIGOCELLULA2, TORMOZ, and APUM23 (Fig. S1D )  [19] [20] [21].
5A ). The OBE1 contains a PHD zinc finger domain (IPR001965) known to act in the regulation of chromatin states  [22, 23]. OBE1 was characterized as a regulator of apical and root meristem development in the embryo  [24, 25]. VFP3/ENAP1 belongs to the trihelix family proteins, which includes ASIL1 and ASIL2 that are involved in seed maturation  [26, 27]. It has been recently shown that VFP3/ENAP1 is involved in ethylene response. VFP3/ENAP1 interacts with EIN2, EIN3, SRT1 and SRT2 and regulates change in histone H3 acetylation levels and ethylene-dependant transcription  [28] [29] [30]. Using a GFP transcriptional fusion protein, we investigated the subcellular localization of OBE1 and VFP3/ENAP1. DAPI staining of DNA in transgenic A. thaliana root cells showed that OBE1 is a nucleoplasmic protein which is mainly colocalized with heterochromatin, in agreement with the role of OBE1 in chromatin remodeling (Fig.
Yeast two-hybrid experiments A cDNA library of etiolated A. thaliana seedlings (Stock CD4-22: https://www. arabidopsis. org/servlets/TairObject? type=stock&id=88570) was initially screened using fulllength RBL cloned in pAS2. 1 (Clontech). The cDNA library was cloned in the pADGAL4-2. 1 vector  [45]. Y2H experiments were performed by mating, using S. cerevisiae AH109 and Y187 strains and selection on triple (-Leu, -Trp, -His) or quadruple (-Ade) selective media  [41]. Computer-based sequence analysis to identify putative interactors was performed using VectorNTI (Informax) and SEQUENCHER (Gene Codes Corporation, Ann Arbor, MI, USA) software. The interaction of RBL with OBE1 and VFP3 were confirmed by mating between AH109 (carrying pADGAL4-2. 1 and full-length cDNAs of interactors, or cDNAs containing frameshift mutations caused by deletions) and Y187 (carrying the empty pAS2.
Accession numbers RBL (At3g55510), SWA2 (At1g72440), AtNOC2 (At2g18220), AtNOC3 (At1g79150), OBE1 (At3g07780), VFP3/ENAP1 (At3g11100) and IN analyzed and interpreted the data. SdB, PM, CT, and IN wrote the manuscript.
Acknowledgements We thank  Olivier Hamant ,  Matthieu Bourdon , and  Charlie Scutt  for their constructive remarks on our work and the manuscript. We are grateful to all the researchers who provided biological material used in this work. We also thank  Claire Lionnet  and  Christophe Chamot (PlaTIM, SFR BioSciences Lyon-Gerland)  for their help with confocal microscopy. SdB has been funded by a grant of  R egion Rhône-Alpes.
Analysis of tRNA genes The genome of 'Candidatus Spiroplasma holothuricola' was obtained from the hindgut of a sea cucumber recently  (21). Coding sequences (CDSs) were predicted with Prodigal (v2. 6)  (22)  and manually refined in some cases. The deduced proteins of all the CDSs were probed against the NCBI-nr database with BLASTp program with e-value cutoff of 1e-4 and seed size of 3. tRNA genes in the genome were searched using tRNAscan  (23). The genes for potential tRNA posttranscriptional modifications and their targets were predicted with tRNAmodpred  (24). Phylogeny-based filtration and NCBI SmartBLAST were performed to examine the output of tRNAmodpred.
10. 1 (http://www. bioinformatics. babraham. ac. uk). Low-quality bases (quality threshold was set to 5) at both ends were trimmed using Trimmomatic-0. 36  (27). The reads with an average quality lower than 15 were also removed by Trimmomatic-0. 36. All the trimmed reads were retained for subsequent analysis without a further length filtration. Paired-end reads were merged using PEAR v0. 9. 5  (28)  with a minimum assembly length of 10 bp. The resulted sequences along with unpaired reads were searched against tRNA sequences of 'Ca. Spiroplasma holothuricola' using BLASTn alignment (Blast+ 2. 2. 29) with megablast task for sequences longer than 50 bp or with blastn-short task for those shorter than 50 bp, and with an e-value threshold of 1e-5. The fragments with a similarity of >95% to the tR-NAs were collected and re-examined by searching against the NCBI nt database.
Despite this highly important consideration, a lot of authors consider that the study of the flow can be done with a sequence of discrete stationary orientations of the oar. For instance, Coppel et al. [3]  use the RANS solver ANSYS Fluent to run simulations essentially of stationary nature, without free surface, using the threedimensional geometries of a flat blade and a Big Blade. The rotation of the blade is done with a cylindrical sliding mesh. As the configuration radically simplifies the physical problem, the numerical results for the drag and lift coefficients get far from the experimental ones of Caplan and Gardner  [2]. Sliasas and Tullis  [18]  also replicate the same case using the same solver but taking account of the free surface and therefore obtain better results. Kinoshita et al.
[6]  were the first ones to carry out threedimensional unsteady computations for this flow. However, the configuration was simple and unrepresentative of a real rowing stroke since the blade rotates around a vertical axis passing at mid-chord, with a uniform flow velocity and without free surface. Sliasas and Tullis  [19]  also performed unsteady computations using ANSYS CFX and demonstrated that the maxima of unsteady forces are significantly higher than the steady ones. Yet the results are unphysical at some point, especially for the propulsive force which is momentarily and unexpectedly negative. This default was corrected in another paper published later  [20]. Leroyer et al. [8]  performed simulations reproducing a simplified rowing stroke but with a dynamic similar to a real one, especially for the free surface deformation.
Results Figure  6  shows snapshots of the flow for rowing stroke 154, obtained by a numerical simulation performed with a coarse grid of 1. 2. ⋅ 10 6 cells. The characteristics of a real rowing strokes are well reproduced. In particular, one can observe the breaking of the free surface and the creation of an air cavity behind the blade. Two grid convergence studies were carried out with the three levels of mesh fineness of Table  2. They are based on two different experimental trials whose parameters are voluntarily chosen as different as possible in the available database: the smallest velocity against the largest simultaneously Fig. 6  Visualisation, from a stationary location, looking in the hull-to-bank direction, of a simulation of a simplified rowing stroke. The free surface is coloured according to its vertical coordinate z (in m) with the largest immersion angle against the smallest (trials 67 and 154).
The total CPU time needed for those computations is between about 1000 h (on 56 cores) for the coarse grids and 10000 h (on 224 cores) for the fine grids. Using the quite rich database of results from the experimental campaign, two sets of rowing strokes were selected where only one parameter varies in each of them: the immersion and roll angles. The objective is to analyse the influence of those parameters and to check if the trends obtained experimentally are similar to those of the numerical simulations. Figure  8  shows the influence of the immersion angle on the force F z and moment M z. F z has been chosen rather than the propulsive force F x or the transversal force F y because these curves show similar trends compared to the one of M z , so the comments would be identical. Curves of the same marker shape represent the same immersion angle.
Conclusions The frame of modelling and numerical simulation of a rowing stroke was tested and validated using an experimental database coming from trials performed in a towing-tank, whose measurements are less prone to uncertainties than those of experiments carried out in situ  [15]. The counterpart of this configuration lies in the simplification of the rowing stroke, where two DOFs are lost for the propulsive phase: the rotation allowing the immersion of the oar on the water and the vertical translation. In addition the carriage of the towing tank moves at a constant velocity while a rowing boat has an unsteady kinematics. In this more controlled configuration better results were obtained. The simulations are able to capture the profiles of the forces and to reproduce the trend induced by the variations of two parameters: the immersion and roll angles of the oar.
Background Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common Mendelian genetic disorders with an incidence of 1/400 to 1/2000 affected individuals worldwide  [1]. The disorder is heterogeneous with two main genes, polycystic kidney disease 1 (PKD1) and 2 (PKD2), which are responsible for most disease cases  [2, 3]. While PKD1 accounts for 75-80% of patients, 10-15% of patients have defects in PKD2. A third gene, GANAB has recently been identified as accounting for less than 1% of affected patients  [4]. Although more than 1200 PKD1 and almost 200 PKD2 pathogenic mutations have been reported (ADPKD Mutation Database, http://pkdb. mayo. edu/), a significant proportion of patients with ADPKD symptoms (5-10%) do not appear to carry these pathogenic gene mutations  [5] [6] [7].
PKD2 contact regions display characteristics of regulatory elements Some of the 5′ and 3′ regions engaged in long-range contacts with the PKD2 promoter might correspond to DNA elements important for its regulation. We therefore tested if some of these regions displayed features of enhancers by using available databases for different markers of regulatory elements. We aligned our 5C interaction profiles from the four CRC samples with datasets from the human Renal Proximal Tubule Epithelial Cells (RPTECs). We assumed that the regulatory elements controlling PKD2 in this cell line should be, at least in part, similar to the regulatory network in cyst epithelial cells. We specifically looked for the presence of DHS or H3K27Ac marks because these often reflect the presence of regulatory elements.
Databases and URLs The Hi-C data from human A549 were downloaded from computational and functional Genomics/Epigenomics Yue Lab website at http://promoter. bx. psu. edu/ hi-c/view. php. The Hi-C data shown in a heatmap format were binned at 40 kb. TAD and sub-TADs were outlined manually based on clustering of interaction frequencies. DHS peaks, CTCF binding sites datasets of H3K27Ac marks for RPTEC and A549 and transcription factor ChIP-seq data of 161 factors from 91 cell types were obtained and visualized using the UCSC genome browser (http://genome. ucsc. edu) [79]. The "my5C-primer" and "my5C-heatmap" bioinformatics tools are found at http://3dg. umassmed. edu/ my5Cheatmap/heatmap. php.
Luciferase assay Cells (2. 5 × 10 5 ) were seeded in 6-well plates. Transfections were done 24 h later with the transit 2020 reagent (Mirus). 800 ng of the P PKD2 construct and 200 ng of the pCMV-LacZ construct (as internal control) were used for each condition. Every condition was carried out in triplicates. The cells were washed once with 1X PBS and lysed with Passive lysis buffer (Promega) 48 h post-transfection. Cell lysates were clarified by centrifugation at 15,000 g for 5 min at 4 °C. 20 μL of each protein extract was used to assay the luciferase activity and 25 μL for beta-galactosidase activity. We used Promega reagents and a multiwell plate reader Varioskan (Thermo Fisher). The results were presented as relative luciferase activity with the P PKD2 construct activity equal to 1. Significance determination of the increased luciferase activity was performed using unpaired t-tests using the GraphPad Prism® software.
Availability of data and materials The Hi-C data from human A549 were downloaded from computational and functional Genomics/Epigenomics Yue Lab website. The Hi-C data shown in a heatmap format were binned at 40 kb (http://promoter. bx. psu. edu/hi-c/ view. php?species=human&assembly=hg19&source=inside&tissue=A549&ty pe=raw-rep1&resolution=40&c_url=&transfer=&chr=chr4&start=87720000 &end=90000000&sessionID=&browser=none). DHS peaks, CTCF binding sites datasets of H3K27Ac marks for RPTEC and A549 and transcription factor ChIP-seq data of 161 factors from 91 cell types were obtained and visualized using the UCSC genome browser (http://geno me. ucsc. edu/cgi-bin/hgTracks?db=hg19&lastVirtModeType=default&lastVirt ModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&posi tion=chr4%3A88576500-89070500&hgsid=676703611_3vY26dSGrdehcr939 HtB3zszv3tE)  [79].
The volume of the loudspeaker was standardized and the intensity of each acoustic stimuli was adjusted using the Audacity ® software to reach 80 db at 20 m (measured using a Phonic ® PAA3 decibelmeter) to match the intensity measured during handling routines. The playback trials started after a six week period of habituation to the experimenter and his recording and playback (with no sound played) equipment. The position of the loudspeaker was standardized, i. e. at the door of the enclosure, making credible the presence of a person. The observer was placed close to the loudspeaker. The playback was performed early in the morning (i. e. between 7:30 and 8:30), before the park was opened to public or staff in order to avoid incongruence or distraction and to standardize the context preceding the playback.
e. change in posture and/or locomotor movement) were compared between the familiar and unfamiliar voice playbacks. Individuals who did not exhibit any behavioural change were assigned the maximum latency score of 150 s. Nonparametric Wilcoxon signed-rank tests were then used on Statistica software version 13 to compare the behaviours of subjects in the 150 s following the playback of a familiar versus unfamiliar voice. In addition, the number of individuals showing a reaction was compared between familiar and unfamiliar voices using Binomial tests on Statistica software version 13. To control for the reliability of our video rating, a second blind viewing (with the sound switched off) of 25% of the dataset (half familiar and half unfamiliar voice trials randomly chosen) was conducted by a naive observer.
2 07 2 Sep 2018, (F1000 Faculty Rev):1429 (doi: First published: 7 ) 10. 12688/f1000research. 15081. 1 07 Sep 2018, (F1000 Faculty Rev):1429 (doi: Latest published: 7 ) 10. 12688/f1000research. 15081. 1 v1.
MAtERiAl And MEthodS Microorganisms. The B. amyloliquefaciens Y1 strain was isolated in our previous study from the field soil of Chonnam National University, South Korea (35. 1764°N, 126. 9081°E) and deposited with accession number KJ616752 in GenBank  (Jamal et al. 2015). It was kept in a 25% glycerol solution at -70°C for further use. Plant growth promoting traits of B. amyloliquefaciens Y1. For the qualitative estimation of hydrogen cyanide production, a picrate assay was used  (Castric 1975). For phosphate solubilisation, Y1 isolate was streaked on Pikovskaya's agar medium  (Pikovskaya 1948 ) and incubated at 28°C for 6 days. Plates were observed for clearing zones around the bacterial colony which indicate phosphate solubilising activity  (Gaur 1990 ). For the qualitative estimation of chitinase, chitin agar plate amended with 2% phenol red was prepared and isolates were spot inoculated and incubated at 27 ± 2°C for 120 hours.
Enzyme activity assay in soil. To check the effect of Y1 on soil enzymes, chitinase and dehydrogenase activities in the rhizosphere soil samples were determined using a modified method of  Trevors (1984)  and  Yedidia et al. (2000) , respectively. Each experiment was conducted with three replications, and is expressed per gram dry weight of soil. Dry weight determinations were calculated after drying soil samples for 24 h at 105°C. Statistical analysis. The data was subjected to analysis of variance using SAS v9. 1 software  (SAS Institute 2003). Mean values among treatments were compared by the least significant difference (lSD) test at 5% level (P = 0. 05) of significance and presented as the mean values ± standard deviation (SD). https://doi. org/10. 17221/154/2016-PPS.
RNA Isolation and Reverse Transcription Total RNA was isolated from the frozen tissue according to the TRIZOL method (Invitrogen/Life technologies, Carlsbad, Cal, USA). Total RNA concentration was measured by spectrophotometry using a NanoVuePlus (GE Healthcare, Chicago, Illinois, USA), and all samples were normalized at 500 ng /µl before storage at -80°C until cDNA generation. The integrity of total RNA was analyzed by electrophoresis. cDNA was obtained by reverse transcription using the enzyme Superscript III (Invitrogen/Life technologies, Carlsbad, Cal, USA) and a mix of oligo dT and random primers (Promega, Fitchburg, Wisconsin, USA). 3 µg of total RNA was used, and the absence of contamination by DNA was verified by two negative controls (without RNA and without Superscript). The reaction was carried out in a StepOne (Applied Biosystem, Waltham, Massachusetts, USA) for 25° C / 5 min, 55° C / 60 min, 70° C / 15 min and retention at 4°C until storage at -20°C.