dataesr/scientific-paragraphs-categorization huggingface dataset:
Supplemental tables: Table  S1 : Description of 937 Tara Oceans metagenomes. Table  S2 : DNA-dependent RNA polymerase subunit B genes characterized from the sunlit ocean. Table  S3 : Metabins containing DNA-dependent RNA polymerase subunit B genes of interest and used for genome-resolved metagenomics. Table  S4 : Genomic and environmental statistics for the GOEV database. Table  S5 : Occurrence of gene clusters with remote homologies for the GOEV database. A summary of core gene clusters and statistics are included.
Acknowledgments: Our survey was made possible by two scientific endeavors: the sampling and sequencing efforts by the  Tara Oceans Project , and the bioinformatics and visualization capabilities afforded by anvi'o. We are indebted to all who contributed to these efforts, as well as other open-source bioinformatics tools for their commitment to transparency and openness. Tara Oceans (which includes the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the  Tara Oceans Foundation  and the continuous support of 23 institutes (https://oceans. taraexpeditions. org/). Some of the computations were performed using the platine, titane and curie HPC machine provided through  GENCI  grants ( t2011076389 ,  t2012076389 ,  t2013036389 ,  t2014036389 ,  t2015036389  and  t2016036389 ).
This study was in part supported by  Japan Society for the Promotion of Science (JSPS) KAKENHI  ( 18H02279 ,  22H00384 ),  Research Unit for Development of Global Sustainability, Kyoto University Research Coordination Alliance , and the  International Collaborative Research Program of the Institute for Chemical Research, Kyoto University  ( 2022-26 ,  2021-29 ,  2020-28 ). M. K. was supported by grants from the  l'Agence Nationale de la Recherche  ( ANR-20-CE20-0009-02  and  ANR-21-CE11-0001-01 ). Part of computational work was performed at the  SuperComputer System, Institute for Chemical Research, Kyoto University. This article is contribution number XXX of Tara Oceans.
Three-point bend fracture tests have been conducted at different loading rates with a quadratic martensitic steel. The failure energy has been found to increase with loading rate. To get insights in this increase a numerical investigation has been undertaken with different strategies using ABAQUS and IMPETUS softwares in order to address quasi-static and dynamic loading conditions. Simulations were conducted with the ABAQUS software in order to carry out a comparative analysis of both implicit and explicit approaches. In addition to standard Finite Element Method (FEM) applied to quasi-static and dynamic conditions, the eXtended-Finite Element Method (X-FEM) was applied to quasistatic conditions. In both approaches, implicit and explicit, crack initiation and propagation were governed by a critical plastic strain threshold combined with a displacement-based damage evolution criterion.
Introduction The influence of loading rate on the fracture strength of a quadratic martensitic steel has been investigated with threepoints bend fracture tests. To interpret the experimental data, a numerical investigation has been undertaken with different computational approaches in order to deal with quasi-static and dynamic loading conditions. A special attention was given to the influence of numerical methods on the results, considering that standard constitutive laws and "off-the-shelf" fracture criteria have been retained for the studied ductile martensitic steel. In that perspective, two softwares have been considered: ABAQUS  [1]  and IMPETUS  [2] , the former allowing both implicit and explicit approaches not only with standard finite elements but also with X-FEM elements (yet, limited to the implicit approach)  [3] , the latter, despite a limitation to pure explicit approaches, provides high order fully integrated finite elements.
Material models and crack propagation In both approaches, implicit and explicit, and with both softwares, ABAQUS and IMPETUS, the material constitutive model is based on a tabulated plasticity flow stress versus plastic strain coupled with a tabulated damage parameter D. Both data sets are extracted from quasi-static uniaxial tests performed on 8 mm diameter and 40 mm length round samples. The damage parameter D induces a progressive loss of material properties, as illustrated in Fig. 4. In ABAQUS, as shown in Fig. 4 , the damage parameter D is triggered by a critical plastic strain value, the crack opening occurring when D equals 1. In IMPETUS, this damage parameter is initiated once the plastic energy reaches a given ratio of the plastic energy at failure implemented in the Cockcroft-Latham criterion, as expressed in Eqn.
(  5 )  [7]. The crack opening then occurrs when this plastic energy at failure is attained. ( ) 5 where Dd is the ductile Cockcroft-Latham damage parameter, Wc is the plastic energy at failure, σ1 is the maximum principal stress and is the effective plastic strain. Then, the modelling of the crack propagation is "approach and software" dependent: -In the case of the implicit X-FEM calculations performed with ABAQUS, the crack opening is modelled through a further (and imposed) enrichment of nodal displacements of the cracked element, -In the case of the explicit (coupled with mass-scaling) calculations performed with ABAQUS, the crack opening is represented by the numerical erosion of the cracked element, -In the case of the explicit (coupled with mass-scaling) calculations performed with IMPETUS, a mass conservative node-splitting technique is used.
Material models and crack propagation With both softwares, ABAQUS and IMPETUS, the material behavior is represented by means of a Johnson-Cook constitutive model  [8]  which defines flow stress as: (6) where σy is the Von Mises flow stress, εp is the equivalent plastic strain, is the equivalent plastic strain rate, * is the normalized strain rate, T is the normalized temperature, A is the initial yield strength, B is the hardening parameter, n is the hardening exponent, C is the strain rate parameter, and m is the thermal softening exponent. This flow-stress model allows considering, to a certain extent, dynamic hardening and thermal softening phenomena. Associated parameters have been fitted from dynamic compression tests conducted on diameter 9 mm height 5 mm compression samples. These parameters are as follows: A=810 MPa ; B = 600 MPa ; C = 0.
Simulation results and comparison with experience 6. 1 Quasi-static simulations Experimental and numerical results obtained with both softwares are confronted to the experimental response in Fig. 8. Explicit calculations show an acceptable accordance with experience. The fitted parameters for the damage models are as follows: -For the ABAQUS calculation, the critical plastic equivalent strain is 21%, -For the IMPETUS calculation, the Cockcroft Latham criterion is fitted to 750. 10 6 J/m 3 A direct comparison of these criteria and, hence, of the two softwares is not trivial but it appears that the critical plastic strain at which damage is initiated is quite equivalent in both softwares: this critical strain εc is found to be around 18% in IMPETUS, so quite close from the 21% used in ABAQUS.
Conclusion The failure energy of three-point bend fracture specimens made of a quadratic martensitic steel was found to increase with the increase of the applied displacement rate, from quasi-static loading conditions, 0. 002 m/s, to dynamic conditions 82 m/s. This increase was interpreted through an increase of the macroscopic deformation of the notch with displacement rate. To get insights in this failure energy increase, a numerical investigation was undertaken with different strategies using the ABAQUS and IMPETUS softwares in order to address quasi-static and dynamic loading conditions. The former software includes both implicit and explicit approaches whereas the latter is limited to a pure explicit resolution scheme. Numerical analyzes have been split in two steps, with a first step addressing quasi-static conditions, and a second step dealing with the dynamic loading conditions.
For both analyzes, the ductile fracture propagation has been modelled through a damage-driven law, this damage being initiated by a threshold plastic strain value for the ABAQUS approach and by a given plastic energy for the IMPETUS approach. In the scope of the quasi-static loading condition, an implicit X-FEM approach uses with the ABAQUS software leads to reproduce the damage initiation process. However, the simulation diverges and fails to represent the final breakup due to a smoothing effect. A potential way of improvement could be the use of smaller step times in order to restitute more accurately stress-strain field singularities and, as a consequence, valorize this approach recognized to be not meshdependent. However, the quasi-static loading condition has been correctly reproduced with an explicit approach for both ABAQUS and IMPETUS softwares, with the successful use of a mass-scaling technique to reduce calculation time.
Additional numerical simulations are currently in progress to allow for a complete comparison of the two codes in terms of local plastic strains and energy responses. In the scope of dynamic conditions, both softwares led to satisfying results. More precisely, the increase of fracture energy with loading rate was reproduced with the increase of the plastic-strain for the ABAQUS damage initiation criterion and of the energy-based IMPETUS criterion. These simulations have demonstrated the ability of these two softwares to model three-point bend fracture tests as a function of the displacement rate. Furthermore, these simulations provide perspectives to refine fracture modelling, with the mesh-independent X-FEM method, embedded in the ABAQUS software, and the node-splitting technique associated with high order elements in the IMPETUS software.
Additionally, a fine-polishing step with Struers OP-U 0. 04 μm colloidal silica suspension was done to obtain a proper smooth surface for post-deformation analysis. Interrupted LCF tests and tests up to failure were undertaken at room temperature at several constant strain ranges (Δε t = 0. 8%, 0. 9%, 1%, 1. 2%, and 1. 6%) using a reversal triangular waveform with a constant strain rate of 4x10 - 3 s -1 and a strain ratio Rε = -1. The bulk specimen and its surface prior and after cyclic straining were investigated by Electron Backscatter Diffraction (EBSD-SEM) in a Hitachi SU-5000 FEG-SEM system operated at 20 kV with an Oxford Instruments® EBSD system having a minimum angular resolution of 0. 5 •. The post-processing of the data was perfomed using the EDAX/TSL OIM 7. 3 software. For each considered condition, two EBSD acquisitions of at least an approximate area of 60 μm × 40 μm in order to cover about 100 blocks and 47 packets The scan step size of 100 nm was adopted focusing on optimization of the acquisition data according to the methods proposed by Chen et al.
and Kamaya et al. [17] [18] [19] , where a small step size can collect background data inducing errors, and higher values lead to loss of information. Grain dilation with a tolerance angle of 15 • was applied to clean up the artifacts present on the material surface  [5]. To achieve a better understanding of the relationship between crystallography character and the susceptibility to fracture, Martensite Parent Grain Reconstruction based on the 24 Kurdjumov-Sachs variant orientation relationship was accomplished by an algorithm developed for MTEX analysis toolbox in MATLAB  [21]. To observe the dislocation structures in a wider area, EBSD-based controlled Electron Channeling Contrast Image (c-ECCI) was carried out in the same microscope. The two-beam diffraction condition for a well-oriented crystal was obtained with the aid of the TOCA software using the c-ECCI methodology developed by Zaefferer and Elhami  [20].
7. The plastic strain range was measured on the loop recorded at mid-life by the wideness of the loop at zero stress. The elastic strain range was measured by the difference between the total strain range and the plastic strain range. Under all of the experimental strain ranges, the elastic strain range was nearly constant and the associated line (the Basquin curve) stays above the plastic strain range data. This is encountered for some martensitic steels  [24]. However, fitting the plastic strain range data according to the number of cycles to failure with a single line (the Manson-Coffin curve) was not possible. Indeed, a bilinear behavior of the quenched microstructure with a transition state at Δε p = 0. 2% (Δε t = 1%) is observed. To provide an explanation of this change in slope of the fatigue resistance curve, it was decided to investigate the microstructure after fatigue at low and high strain tests (Δε t = 0.
Acknowledgements The  SEM  and  TEM national facility in Lille (France)  is supported by the  Conseil Regional des Hauts-de-France  and the  European Regional Development Fund (ERDF). The authors thank technical engineer  J. Golek  for his help in the fatigue experiments. One of the authors (M. A. C. A) would like to acknowledge the partial financial support of the  Roberto Rocca Education Program.
Images were recorded using a FEI Eagle 4kx4k CCD camera and AnalySIS v3. 2 camera control software (Olympus). Ten representative images were taken at a magnification of x1650. Following adjustment of images to 32-bit grayscale of 4090 Â 4090 pixels, the black-top hat filter was used to enhance casein gel network and Otsu thresholding algorithm to convert into binary image. Two different microstructural parameters were determined from binary images: the average area density, i. e. the ratio between the protein matrix area with respect to the total area of the image (dimensionless), and the size distribution of particle aggregates (mm) using the procedure previously developed by J. Silva, Legland, Cauty, Kolotuev, and Floury  [92] , described in Thevenot, et al. [96]  and implemented in FIJI software with MorphoLibJ, Granulometry, Geodesics plugins  [52, 53, 54].
Acknowledgements We acknowledge the support of the  Australian Nuclear Science and Technology Organization (ANSTO)  in providing USANS and SANS beam facilities (proposal no. 7399) used in this work. The authors would like to thank  AINSE Limited  for providing financial assistance (Award -PGRA) to enable work on QUOKKA and KOO-KABURRA. The authors thank  Jonathan Thévenot  ( INRAE-STLO ) for providing FIJI macro for automatised image analysis. The authors also acknowledge the advice provided by  Allison Williams and Roderick Williams (CSIRO Agriculture and Food ) during the digestion experiments. Charlotte E. Conn was the recipient of an  RMIT Vice Chancellor's Senior Research Fellowship.
We present the new version v2. 0 of the public code BlackHawk designed to compute the Hawking radiation of black holes, with both primary and hadronized spectra. This new version aims at opening an avenue toward physics beyond the Standard Model (BSM) in Hawking radiation. Several major additions have been made since version v1. 0: dark matter/dark radiation emission, spin 3/2 greybody factors, scripts for cosmological studies, BSM black hole metrics with their associated greybody factors and a careful treatment of the low energy showering of secondary particles; as well as bug corrections. We present, in each case, examples of the new capabilities of BlackHawk. CONTENTS I. Introduction 1 II. New features 3 A. Adding a DM particle 3 B. Spin 3/2 particle 4 C. Time dependent features, cosmological studies 5 D.
However, people use most of the time the high-energy limit for the greybody factors given in these papers, resulting in order-of-magnitude constraints. There was thus a need for an automatic program to compute the precise spectra for any BH mass and spin, with a wide choice of parameters that allow for any kind of HR study. This was the context of creation of the public code BlackHawk v1. 0  [34]. Since its first release, the code has received some modifications and has reached version 1. 2. The previous version of the manual can be found on the arXiv  [34]  (v2), while the code is publicly available on HEPForge: https://blackhawk. hepforge. org/ The code has been recently presented to the TOOLS 2020 conference  [35]. BlackHawk is used by many groups from very different domains of astrophysics and cosmology to perform striking studies including, to the knowledge of the authors, evolution of BHs spin  [36] , EGRB constraints with extended mass distributions and spinning BHs  [37]  or with higher dimensional Schwarzschild BHs  [38] , electron and positrons signals from the galaxy with the 511 keV line  [39, 40] , current  [41]  or prospective  [42]  X-ray limits, neutrino constraints from Super-Kamiokande  [40] , JUNO  [43]  or prospective neutrino detectors  [44, 45] , gamma ray constraints from INTEGRAL  [46] , COMPTEL with improved lowenergy secondary particles treatment  [12] , prospective AMEGO instrument  [12, 47] , LHASSO  [48]  or fine modelisation of the Galaxy  [49] , prediction of signals from Planet 9 within the PBH hypothesis  [50] , archival galactic center radio observations  [51] , interstellar medium temperature in dwarf galaxies  [52] [53] [54]  or 21 cm measurements by EDGES with Schwarzschild  [55]  or Kerr PBHs  [56] , Big Bang nucleosynthesis (BBN)  [57] , heat flow from a small BH captured in the Earth core  [58] , warm DM from light Schwarzschild  [22]  and Kerr  [23]  PBHs, dark radiation from light spinning PBHs  [23, 24] , (extended) dark sector emission  [13, 59] , axion-like particle emission  [60] , HR from extended BH metrics  [61, 62].
While this release note was being written, the authors became aware of Refs. [63, 64]  which analyze the production of DM by PBH evaporation in the early universe; while these do not explicitly use the code BlackHawk, apart from the spin 2 greybody factors, they provide results compatible with those of BlackHawk with mostly the same spirit in the numerical part. This paper is a release note of a new version of BlackHawk v2. 0 that includes some primordial new features linked to the physics described above: dark sector emission, spin 3/2 greybody factors, BH remnants, BSM BH metrics, low energy hadronization; as well as bug corrections. It then completes the manual published in European Physics Journal C  [34]  and goes together with the updated version of the code available on the BlackHawk website mentioned above, and an updated version of the manual available on the arXiv  [34]  (v3).
All the installation and run procedures, as well as the complete set of parameters and routines are described in the latter, while we focus here on the new features only. It is organized as follows: in Section II we describe the physics of the new features added to the code and illustrate them with examples of BlackHawk results, in Section III we list the new input parameters, in Section IV we mention some improvements on the optimisation of the code and we conclude in Section V. In the following, we use the natural system of units G = = c = k B = 1.
Indeed, in the integration over the total spectrum to obtain the mass and spin change of the BH, additional dofs provide additional contributions: the mass and spin loss rates are enhanced, thus the BH evaporates faster. When considering only one additional dof, as in  [22] [23] [24] , the change in the lifetime is negligible, but it could be much higher with numerous additional dof as considered in  [13]. In BlackHawk, this change has been taken into account in alternative f (M, a * ) and g(M, a * ) tables computed by an updated (and simplified) version of the script fM. c. Tables fM add*. txt, fM add* nograv. txt, gM add*. txt and gM add* nograv. txt are read instead of the usual fM. txt, fM nograv. txt, gM. txt and gM nograv. txt, for the addition of a single massless dof of spin *. The tables f (M, a * ) and g(M, a * ) have further been recomputed with increased precision.
The greybody factor tables and fits necessary to recompute the f, g tables are also given in the code source. All these files are available in the folder: /scripts/greybody scripts/fM If the additional particle considered has a rest mass µ that has to be taken into account, new tables must be computed using the fM. c script to limit the emission of this particle to the usual condition E > µ. Finally, the primary spectrum output is modified by the addition of one column to the file instantaneous primary spectra. txt (program BlackHawk inst) or by a new file DM primary spectrum. txt (program BlackHawk tot). The additional dof is assumed to have no interaction with the SM. Hence, there is no modification of the SM secondary spectra. If it were the case, the user would have to modify the routines computing the secondary spectra to implement any new branching ratio (e.
2 , (2) where the superscript "out" refers the the outgoing part of the wave. For the moment, in BlackHawk, we have only implemented the Schwarzschild special case of the spin 3/2 Hawking radiation. The massive spin 3/2 particle can be treated as the other spins, by putting an artificial energy cutoff in the Hawking spectrum at the particle rest mass E > µ. We have computed the greybody factors thanks to a script similar to the ones used for spins 0, 1, 2 and 1/2 particles, in the Schwarzschild case. The Mathematica script for spin 3/2 is spin 1. 5. m; it has been added to the BlackHawk folder: /scripts/greybody scripts/greybody factors This script performs the integration of Eq. (  1 ) and tabulates the greybody factors summed over the spherical harmonics decomposition of the wave function.
For details about this computation see the complete manual  [34]. We advise to use as a "spatial infinity" boundary condition at least r * ∞ /r H > 300/x, where x ≡ Er S is the adimensioned energy, for good numerical convergence. This is particularly important for the low energy greybody factors. The script fM. c has also been updated as already developed in Section II A to include spin 3/2 emission in the BH lifetime computation. In Fig. 1  (left panel) we show the Hawking radiation rate for all massless spins fields with a single dof Q s (E, M BH ) ≡ d 2 N s dtdE = Γ s e E/TBH -(-1) 2s , (3) where s is the particle spin, T = 1/4πr S is the Schwarzschild BH temperature and Γ s (E, M BH ) ≡ +∞ l=0 (2l + 1)Γ l s (E, M BH ) , (4) where Γ l s is the greybody factor for angular momentum l, energy E and BH mass M BH.
C. Time dependent features, cosmological studies Several studies performed with BlackHawk consider Hawking radiation through cosmological eras, e. g. the early universe before BBN  [22] [23] [24]. It can be relevant to consider not the full time-dependent spectrum of emitted particles, but only the stacked spectrum of those particles at some time after the BH evaporation. This quantity must be computed by taking the redshift into account. Indeed, particles emitted at the beginning of the BH evaporation see their energy diluted compared to those emitted at the end of the BH lifetime. We thus provide into BlackHawk a C script stack. c that performs this integration, with adjustable cosmology parameters such as the matter/radiation domination at the time of evaporation, the time of matter-radiation equality, etc.
This script is available in the folder: /scripts/cosmology scripts and is accompanied by a README. txt file containing instructions. This kind of integration requires that we can extract the time steps of the BH evaporation precisely. It was not possible with the previous version of BlackHawk as only the absolute time was available in the output files, with a exponential precision of 5 digits. At the end of the BH evaporation, the time steps become so tiny that this precision is not sufficient to distinguish the time steps, making the integration procedure incomplete. Thus, we have added the output file dts. txt to the result set of a BlackHawk run which contains the explicit time steps on top of the absolute time. This file is read by the script stack. c. The script computes the integrated spectrum Qi of particle i from BH formation t form to total evaporation t eva Qi (E) = teva t form (1 + z(t)) d 2 N i dtdE (t, (1 + z(t))E) dt.