dataesr/scientific-paragraphs-categorization huggingface dataset:
In the same figure (right panel) we focus on the high energy oscillations of the cross-section. Inside BlackHawk, these new metrics and their modified greybody factors and f Page factors are available through the parameters. txt file with the new parameter metric. The script fM. c has been modified to include the possibility of computing the function f (M, , a 0 ) for polymerized BHs, for 11 values of ∈ [0, 0. 79] and a 0 = {0, 0. 11}, and 11 values of ∈ [1, 100] and a 0 = 0, where the modified Page factor is given by f (M BH , ) ≡ -M 2 BH dM BH dt = M 2 +∞ 0 E 2π i dof Γ i (E, M BH , , a 0 ) e E/TLQG -(-1) si dE , (13) where Γ i (E, M BH , , a 0 ) is the modified greybody factor for the polymerized metrics with parameters and a 0. Contrary to the Kerr case, where the BH spin a * evolves during evaporation, here and a 0 are purely constant.
The Mathematica scripts used to compute them are available in the folders: /scripts/greybody factors/charged/*. m /scripts/greybody factors/LQG/*. m /scripts/greybody factors/higher/*. m accompanied by Python scripts exploitation. py to produce the fitting tables for the high and low energy limits. It is of course possible to mix the new metrics with DM contribution to the Hawking spectrum (in that case, the Page factor f must be recomputed for polymerized BHs) following the details of Section II A, at the exception of the spin 3/2 additional particle, for which the greybody factors have not been computed within the new metrics. Using the precise Hawking radiation rates for primordial black holes, Ref. [62]  derived the first ever constraints on polymerized primordial BHs as DM.
Below the pion rest masses, there is no viable QCD degree of freedom, even if light quarks and gluons are kinematically allowed. That is the scheme chosen by  [12]  when deriving the secondary photon spectrum at low energy (below the QCD scale). We thus modified BlackHawk such that it emits pions instead of single quarks if the user chooses so, with the new hadronization choice in the hadronization choice parameter. Then, we take back the development of  [12]  on the behaviour of the particles at low energy and use the public Python code Hazma  [85]  to evolve the primary particles. d 2 N γ /dE γ dt (MeV. s) -1 Primary e ± → γ π 0 → γ µ ± → γ π ± → γ total (old) total (new) FIG. 4. Comparison between the old PYTHIA extrapolated (solid red) and new Hazma computed (solid black) BlackHawk instantaneous total photon spectrum for a MBH = 5.
We follow  [12]  to compute the FSR photons thanks to the electroweak splitting functions  [86]  directly inside BlackHawk from the primary electron, muon and charged pions spectra. We also follow  [12]  and use the public code Hazma  [85]  to compute the low-energy pions and muon decay rates, which we have tabulated in: /src/tables/hazma tables/photon. txt which covers center of mass energy of 1 keV to 5 GeV. We improve on  [12]  by including the secondary low energy electron and positron spectra, from the decay rates of muons and charged pions tabulated in: /src/tables/hazma tables/electron. txt The Python script we have used to compute these tables is available at: /scripts/hazma scripts/hazma tables. py Then, we add up all the contributions to the primary photon and electron spectra to obtain the total secondary spectra.
As we can not decide (outside of a chosen model) what are the number of degrees of freedom and their nature in the QCD energy range, this hadronization method is limited to the program BlackHawk inst, because we need this information to compute the Page evolution factors inside BlackHawk tot. The PBH masses at stake are M PBH 10 14 g, thus we can consider that these PBHs are living indefinitely at our time scale -the age of the universe -and that BlackHawk inst is enough for PBH studies linked to photon or electron emission in this scheme. We show in Fig. 4  (respectively Fig. 5 ) the total photon (respectively electron) spectrum computed with the old extrapolated version of BlackHawk, compared to the new spectra computed with the method of  [12]  for a BH of mass 5. 3 × 10 14 g. We point out that this new feature is dedicated to the low energy photon and electron emission, and does not for now provide low energy spectra for neutrinos, which however are only related to sub-dominant (but complementary) constraints in the considered PBH mass range  [40, [43] [44] [45].
The seismogenic potential of the faults in the Vendée department needs therefore to be clarified. Left-hand panel: map representing the regional coverage of Bouin 1799 earthquake macroseismic data (99 point macroseismic MSK-64 intensities  (Medvedev et al. 1967 ) deduced from historical accounts and compiled in SisFrance database (https://sisf rance. irsn. f r/  Scotti et al. 2004 ). The 25, 175, 275 and 400 km radius circles delineates respectively the extent of VII-VIII (in red), VI-VII (in orange), V-VI (in yellow) and IV-V (in green) intensity area respectively (MSK-64). SASZ: South Armorican crustal Shear Zone. Right-hand panel: envelopes of macroseismic intensities for Bouin 1799 and Oléron 1972 (450 accounts) as a function of their epicentral distance. The colours correspond to the qualities of the accounts: A quality (sure intensity) in green, B quality (intensity sure enough) in orange, C quality (uncertain intensity) in red.
The objective of this study is to document the Machecoul Fault's geometry and its short and long-term activity in order to determine whether this fault could be the source of the ∼M6 1799 Bouin earthquake (France). For that purpose, we studied the area both onshore and offshore using a multidisciplinary work based on the acquisition of an extensive high-resolution seismic survey (Sparker source and single channel streamer, CHIRP echo sounder) and high resolution bathymetry data (GeoSwath), compared with onshore drilling data (BSS, BRGM), topography data (RGEALTI) and onshore gravity data (BGI). This analysis documents the geometry and potential syn-tectonic nature of the neogene sedimentary infilling of the thin Marais Breton/Baie de Bourgneuf basin and tests if the Machecoul Fault, at the northern edge of the basin, was active after the Eocene (see hereafter, geological setting).
M E T H O D O L O G Y The Machecoul Fault bounds an onshore-offshore basin, so we performed a multidisciplinary analysis (Fig. 4 ). We analysed a Lidar DEM (RGEALTI) using quantitative geomorphology and we acquired new high resolution bathymetric data  (Kaub et al. 2017)  to better describe the Machecoul Fault and to study if there is a recent relief rejuvenation associated with the fault motion. We used existing gravity data (BGI, http://bgi. obs-mip. fr/f r) combined with a drilling database (BSS, BRGM, http://infoterre. brgm. f r/page/ban que-sol-bss) and we led two new offshore seismic reflection surveys (Le  Roy et al. 2016; Kaub et al. 2017 ) in order to determine the geometry and infilling, respectively, of the onshore and offshore Marais Breton/Baie de Bourgneuf sedimentary basin. This analysis was complemented by the deployment of a temporary seismological survey dedicated to characterize the hypocentral locations and focal mechanisms of the local seismicity at depth, below the fault system in order to characterize the seismicity at depth and its eventual relation with locked or seismogenic fault segments.
Marine surveys We investigated the offshore fault segments geometry, and the sediment infilling in the Baie de Bourgneuf, using high-resolution lowpenetration offshore seismic data and high-resolution interferometric sonar bathymetry data. Those data were obtained during the RETZ 1 (Le  Roy et al. 2016 ) and RETZ 2  (Kaub et al. 2017)  campaigns operated on the French oceanographic launch Haliotis. A total coverage of 40 km 2 of high-resolution bathymetry data along the presumed offshore extension of the fault was acquired with a Geoswath interferometric sonar (Fig. 4 ). Bathymetric profiles were processed (gain filter, tidal correction, false probes automatic filtering and griding) using CARAIBES C software (developed by IFREMER). We then merged our 2 m planar resolution DEM with a bathymetric DEM of similar resolution from the previous POP-CORE 2016 cruise  (Baltzer 2016).
A total of 700 km of high-resolution seismic profiles were acquired using a single-channel (SIG C ) streamer and a SPARKER source (Fig. 4 ). Data were recorded by a DELPH acquisition system C. Sub-bottom profiler (Chirp echo sounder) data were also acquired simultaneously. Sparker seismic lines were processed using the software DELPH interpretation C and Chirp seismic data using the SUBOP C software (developed by IFREMER). All seismic lines were visualized, correlated and interpreted with the Kingdom Suite software (Seismic microtechnology INC C ). They are displayed in two-travel time in millisecond (ms). For the time-to-depth conversion, a velocity of 1600 m s -1 was used for unconsolidated sediment. The seismic data interpretations were done following the seismic stratigraphy principles  (Mitchum et al.
Drill holes and gravity onshore data To extend the sediment infilling data set and to better constrain the basin geometry, we used onshore gravity data from the Bureau Gravimétrique International (BGI) and onshore drilling data from the French national drill holes database (Banque du Sous-Sol -BSS) both available online (Fig. 4 ). We computed the complete Bouguer gravity anomaly from the free air anomaly provided by the BGI (Fig. 4 ). Topography and bathymetry were discretized in parallelepipeds of 90 and 100 m wide, respectively. We assumed for the Bouguer correction a density for the terrain and the seawater of 2670 and 1027 kg m -3 , respectively. The calculation of the gravity effect of each parallelepiped was made with the  Blakely (1995)  method. We also used a gravity modelling approach to study the thickness of the local infilling in the vicinity of the Machecoul Fault.
Automatic detections of events were processed by a standard STA/LTA (Short Term Average/Long-Term Average, e. g. Allen 1978 ) trigger algorithm procedure for the whole continuously recording raw data set. After extraction of waveforms around detection time, events were read, picked and located within the SEISAN software  (Havskov & Ottemöller 1999). We picked P and S first arrivals for 58 events around the Marais Breton and computed hypocentre location using the locator HYPOCENTER Downloaded from https://academic. oup. com/gji/article/225/3/2035/6149459 by Ifremer, Bibliothèque La Pérouse user on 30 March 2021   (Lienert et al. 1986 ). We identified and excluded blast events and regional/global earthquakes from our database. Velocity structure is poorly determined in our study area, so we used the following 4 plane-layered (1-D) crustal velocity model in the location calculations: V p = 5.
Onshore geomorphological analysis To investigate if the long-term Machecoul Fault activity could have affected landscape morphology and hydrographic network, we performed a geomorphological analysis with the RGEALTI 5 m DEM of the studied area. We extracted automatically channel networks using RiverTools software  (Peckham 2003)  from the DEM and we produced an incision map of the region. We detected drainage anomalies as stream deflections on the drainage network or knickpoints along the river longitudinal profile (e. g. Whipple & Tucker 1999). The incision map (or 'geophysical relief ',  Ahnert 1984)  Downloaded from https://academic. oup. com/gji/article/225/3/2035/6149459 by Ifremer, Bibliothèque La Pérouse user on 30 March 2021 corresponds to the difference between an envelope surface (i.
The lack of data in the Baie de Bourgneuf prevents any detailed interpretation because of artifacts created by the interpolation. Even if the signal is very weak (±5 mGal Bouguer anomaly), there is a good correlation with the overall sediment thickness deduced from the depth of top of the crystalline basement found in the BSS drillholes at 41 m depth to the north of the Marais Breton (see Appendix Fig. B1  for gravity modelling). According to the BSS drill-holes data and as expected, there is no evidence of Mesozoic, Oligocene and Miocene deposits in the Marais Breton. The Eocene deposits are overlying the crystalline basement and sediments above them are thus considered as Plio-Quaternary in age. These young sediments are poorly represented or non-existent on the Machecoul Fault footwall and their distribution is heterogeneous on the hangingwall (Fig.
2010). The Us2b facies has a more regular and subhorizontal stratification with low frequency reflectors. The amplitude varies vertically, being stronger in the upper part than in the lower part. This unit is observed mostly faulted, and by place slightly folded  (Borne 1986; Proust et al. 2001). It could correspond to the bioclastic limestones and sandy limestones of Lutetian and Bartonian ages  (Proust et al. 2010). Our marine dataset does not make easy the differentiation between Eocene formations and Palaeozoic basement on every profile. However, the boundary between these two formations and the Plio-Quaternary units is assumed to correspond to a regional reflector, defined as the top of the undifferentiated substratum and identified on most profiles. The determination of lower units geometry and axial incision depth of palaeovalleys filled by Plio-Quaternary deposits was restricted by the limited penetration of the seismic waves and the presence of a local deaf acoustic facies.
Our marine dataset thus shows that the Plio-Quaternary sediments are thicker at the bottom of the fault escarpment along the two parallel normal and south-dipping faults of the Machecoul Fault offshore system (Fig. 10 ). The offshore Plio-Quaternary infilling thickness, deduced from the mapping of the top of the undifferentiated substratum horizon, appears heterogeneous in the Baie de Bourgneuf (Fig. 10 ). This deposit increases in thickness westward (up to 25 m of Plio-Quaternary sediments in the main valleys). According to these results, the deposition of these units appears to be controlled by the southern escarpment of the Machecoul Fault (Fig. 10  and see Section 5. 1 for discussion).
However, the same data also image deeper flat-lying levels, notably around 20 km. Admittedly, our seismic database is not enough substantial nor constrained to go further in this interpretation. The stress inversion from the 8 focal solutions results into a dextral-transtensional to extensional regime. The σ 3 direction is relatively well constrained with a small plunge (N35-N50, 15 • -30 • ) and σ 1 and σ 2 are oblique and distributed along a plane normal to σ 3. This may illustrate a tendency for σ 1 and σ 2 permutation (see Appendix Fig. C1  for stress inversion).
Considering the measurement points density provided by the BGI and therefore the Bouguer anomaly resolution, the signal of these small sedimentary thicknesses (up to 40 m) is likely too weak for the current heterogeneous coverage to record. That is why we used a gravity modeling approach to study the consistency between the local infilling and the Bouguer anomaly in the vicinity of the Machecoul Fault (Fig. B1b ). In order to do that we constructed a 2-D density structure model of a fault-controlled sedimentary basin, constrained by the 05076X0005/SLM3 drill hole of the BSS database (Fig. B1c ). The Machecoul Fault is represented as a vertical interface, separating two different nature blocks, with the NE compartment (footwall) consisting of crystalline basement (density of 2. 8) and SW a sedimentary basin deposited on the base (density ranging from 1.
53 to 2. 1). The topography has also been taken into account in the upper part of the model to represent the slope fault. Then we computed its gravity response  (Blakely (1995)  method) and compared it to our Bouguer anomaly observed along a profile perpendicular to the fault (Fig. B1b ). This profile extends to 10 km on either fault side, and the sampling rate is becoming lower near the fault (ranging from 1 km to 10 m, Fig. B1a ). Thus, even if the signal is very weak (around 5 mGal), its longwavelength are compatible with the synthetic data computed with our 2-D model (Fig. B1c ). There is therefore a good correlation with the infilling thickness found in the BSS drill holes considered in the vicinity of the Machecoul Fault. However, our reductive 2-D model cannot explain the very short wavelengths gravity signal along the profile, as well as the lateral variations along the fault.
We thank  Stéphane Baize  and an anonymous reviewer for their very constructive suggestions that strongly improved the paper. This study represents part of the  PhD  project of the first author. This work, supported by the  Conseil Départemental de la Vendée (CDV) , is a joint project which benefited from an  Université de Bretagne Occidentale (UBO)  doctoral grant and  CEA  financial support. We are grateful for the technical assistance of  Jean-Pierre Laurent  (CDV, seismic installations and servicing) and  Christophe Prunier  ( UBO , seismic installations and servicing and seismic/bathymetry). We greatly thank the  RV Haliotis crew (IFREMER and GENAVIR)  for both cruises within this project. We acknowledge  Agnès Baltzer  ( IGARUN ) for sharing the POPCORE 2016 high-resolution bathymetric data.
Therefore, this study evaluated how the light availability impacts the structure of the phytoplankton community in a tropical floodplain lake system. We investigated whether multispectral K d gradients are a good framework to access phytoplankton genera in the Curuai lake. To achieve this, in situ remote sensing reflectance (R rs ) was used to semi-analytically invert K d , focusing on Sentinel-3/Ocean and Land Color Instrument (OLCI) sensor bands. These data were used to assess how the available light in the visible spectra impacts the composition of the phytoplankton community and whether different wavelengths are a determinant factor to structure in situ phytoplankton genera.
Biological Data We collected samples during two hydrological periods in 2013; rising waters (RW) and flushing waters (FW), which occurred in March and September, respectively. Whenever possible, we collected at the same points in both periods, but due to water level variation, it was not possible to repeat all points in the two sampled periods. Thus, 23 stations were collected in the RW and 36 stations in the FW period. At each station, its respective geographic coordinates were recorded using an GPS receiver (Figure  2 ). The water samples were collected at sub-surface level (approximately 20 cm); one sample at each station. The quantitative samples for phytoplankton taxonomy determination were collected and stored in amber vials and fixed with acetic Lugol solution. Phytoplankton were counted following the Utermöhl method  [60] , at 400× magnification.
For the measurements of L t , the radiometer was positioned at approximately 45 • in relation to the water surface and 135 • in relation to the sun. For measuring L sky , the radiometer was positioned at approximately 45 • in relation to the nadir, and 135 • in relation to the sun. The measurements were taken approximately 2 meters above the water surface to avoid shadow and vessel reflection. Readers should note that the HandHeld2 radiometer was manually operated by an experienced researcher, and the inclination of each measurements is approximated. For TriOS-RAMSES, a fixed support with the specific inclinations was used. Despite the difference in the sensors, both sensors were used for the same dataset in recent works in Brazilian waters and provided good results  [64, 65]. From this framework, R rs was calculated using Equation (1): R rs (λ) = (L t -p * L sky ) E s ( 1 ) where p is the air-water interface reflectance with values taken from Mobley  [50] , based on sensor geometry settings and wind speed.
The next steps of this study are to apply this approach to a new dataset and to compare the results with K d retrieved from OLCI images collected simultaneously with the in situ biological data. It would also be interesting and very enlightening to add the biological diversity indices to the analysis and use data from an entire hydrological cycle, with data collection carried out at different times in the cycle. However, organizing data collection campaigns of this size in the Amazon region is a challenge in itself, due to several factors, mainly financial, since the cost of each of these campaigns tends to be high.
Result Molecular clock signal of HCV-3a sequences The 507 HCV-3a sequences from the BOSON clinical trial were collected during 2013-2014 period  (24). Due to the short collection interval, these sequences lack temporal signal of measurable evolution (Supplementary Figure  1 ). To address this, we added 48 previously published HCV-3a whole genomes, the earliest of which was collected in 1991 in Canada. To explore the temporal signal of the updated dataset, we estimated a maximum likelihood tree from whole genomes and calculated the correlation between root-to-tip genetic distance and sampling dates of the sequences (Supplementary Figure  1 ). The results showed sufficient molecular clock signal with an estimated substitution rate of 2. 13x10 -3 (95% CI: 1. 61x10 -3 -2. 64x10 -3 ) per site per year, which is larger than previous estimate for HCV-3a (1.
Enrichment of South Asian ancestry individuals among HCV-3a infected patients The principal components (PCs) of host genome-wide genotyping data for the BOSON cohort were projected onto the genetic PCs of the 1000 Genomes project  (26). These projections were then used to validate and adjust the self-reported host ancestry of BOSON cohort patients (Figure  1 , Supplementary Figure  2 , see methods) and allowed us to distinguish between South Asian and East Asian host ancestry (both were self-reported as Asian). For BOSON hosts with HCV-3a infection where genetic data were not available, host ancestries were designated as their self-reported ancestries (19 individuals). The host ancestries corresponding to HCV-3a sequences downloaded from the public repositories (where we do not have access to host genetic data) were designated as the majority ethnic group of the country where the samples were collected.
We observed that majority of the patients had white European ancestry (N=433, 80%) and South Asians were the second largest group (N=69, 13%). The other host ancestries present in this dataset were of Admixed American (N=12), East Asian (N=6), African (N=4) and other ethnic groups (N=16). Although the patients with HCV-3a in the BOSON cohort were recruited from the United Kingdom (N=211), the USA (N=65), Canada (N=64), Australia (N=113) and New Zealand (N=35) which are mainly of white European ancestry, we observed an enrichment of patients of South Asian ancestry in this cohort, especially in the United Kingdom (19%, 41/211, p-value = 1. 4x10 -13 ), where South Asians make up 5% of the population). ancestries after adjusting the self-reported ethnicities in the BOSON cohort using ethnicity data from the 1000 Genomes project.
The growth of the pandemic stopped in the 1980s. A similar pattern of growth has been observed in HCV subtypes 1a and 1b  (18)  , where the end in population size growth was attributed to the rise of awareness of post-transfusion hepatitis, which led to better regulations around blood donation and needle sharing. During this time, voluntary blood donation, which has been shown to be safer than paid blood donation due to the difference in the demographics of the donors, was promoted in the United States as well as European countries. Also, while this is before the anti-HCV screening in the early 1990s, screening for HBsAg effectively reduced blood donation from high risk populations  (39). In this study we used the largest HCV subtype 3a whole genome dataset to date and combined it with the host genetic data and reconstructed virus epidemic history and identified its origin in South Asia.