dataesr/scientific-paragraphs-categorization huggingface dataset:
Despite this, we obtained sufficient image resolution for detailed visualization of subcellular components of the oocytes, similar to the ones observed under conventional TEM (Fig. 1e ), ensuring the details needed for thorough examination of the mitochondria and bacteria (Fig. 2g ). Six acquisitions from different biological samples were processed, and we calculated the physical sizes of the imaged oocyte pieces between 346 and 6,302 μm 3 that were products of minimum 479 to maximum 1930 slices milled on the Z axis (Table  1 ). Subsequently, the datasets were imported to Amira (version 2019. 4) and manually segmented into separate label fields for mitochondria, bacteria, and the cytoplasm for 3D reconstruction. We examined four datasets of wild-type oocytes and two datasets of aposymbiotic oocytes from two and one semi-engorged I.
ricinus ticks, respectively (Table  1 ). Similar to our 2D images, we did not observe autophagic structures or cellular damages like in the reabsorbed oocytes of arthropods. In all six datasets, we could monitor subcellular components including mitochondria and yolk particles (Fig. 3a-f ). The presence of yolk particles indicated that the oocytes were under vitellogenesis. Based on the amount of yolk granules, we concluded that the oocytes were in different vitellogenic stages. Specifically, the wild-type oocytes were previtellogenic, early vitellogenic, vitellogenic and late vitellogenic (Fig. 3a-d ), while the aposymbiotic oocytes were vitellogenic and late vitellogenic (Fig. 3e, f ). The rodshaped bacteria were readily distinguished and exclusively present in wild-type oocytes (Fig. 3a-d ).
3g ). In the second dataset, we interpreted the aggregation of the dark particles without clear membrane as soluble vitellogenin proteins, suggesting the start of the vitellogenin transport and initiation of vitellogenesis  32  (Fig. 3b ). The cytoplasm was cleared of its contents except for vitellogenin, M. mitochondrii and mitochondria. We observed explicitly individual globular mitochondria without any reticulation, and some The sample names are based on vitellogenic stages of the oocytes. The physical size of the image, number of images stacked for the 3D images, the volume of the imaged sample, volume of the cell in the image, total number of mitochondria and bacteria counted in the image are listed. M. mitochondrii cells were present inside these globular mitochondria (Fig. 3h ). In the third and fourth datasets, large vitellin granules were fully formed and accumulated in the cytoplasm, implying on-going vitellogenisation (Fig.
3m-p ). We quantitatively characterized those subpopulations by computing the volumes of individual bacteria and mitochondria (Fig. 4a, b ) and then calculating the Volume of Overlap Fraction (V OF = V submerged part /V bacterium ). Using V OF , we classified the bacteria into four subpopulations: "free" (V OF = 0), "next" (0 < V OF < = 0. 05), "partially inside" (0. 05 < V OF < = 0. 3) or "fully inside" (V OF > 0. 3), and we then grouped the partner mitochondria as "free", "next", "partially hosting" and "fully hosting" subpopulations based on V OF of the corresponding bacteria (Fig. 4c ). When there are multiple overlaps, we classified according to the largest V OF (Fig. S2c ). After categorizing each bacterium (Fig. 4d ) and mitochondrion (Fig. 4e ) in all datasets, we found that the bacterial subpopulations "partially inside" and "fully inside" correspond to 48.
4 ± 9% of the total bacteria, while 50 ± 15% of the mitochondria were found to be partially or fully hosting when the four datasets from wild-type oocytes were combined. Intriguingly, we observed that the intramitochondrial bacteria subpopulations substantially increased upon vitellogenisation (Fig. 4d ). The percentage of the intramitochondrial M. mitochondrii increased from 42. 15% in the previtellogenic oocyte to 61. 57% in late vitellogenic oocyte (Fig. 4d ). Moreover, the proportion of mitochondria hosting bacteria increased from 38% to 70% (Fig. 4e ). In addition to this, we detected more mitochondria carrying multiple bacteria in vitellogenic and late vitellogenic oocytes (Fig. 4f-i ). The portion of the mitochondrial population that harbor more than one bacterium is around 20% in the previtellogenic and early vitellogenic oocytes (Fig.
We used solidity to quantify the disturbance in the spherical volumes  38  , defined as the ratio between the actual volume of a mitochondrion and In each box plot, the center line indicates the median, the edges of the box represent the first and third quartiles, and the whiskers extend to span a 1. 5 interquartile range from the edges. c Categorization of the bacteria and mitochondria populations into subpopulations based on the volume overlap between a bacterium and corresponding mitochondrion: 0% overlap is considered a "free" bacterium, 1-5% is designated "next", between 6 and 30% is "partially inside" and above 31 % is "fully inside". The portions of bacterial (d) and mitochondrial (e) subpopulations in each dataset are shown. As the oocytes mature, we detected more bacteria and mitochondria in intimate association (d, e).
We concluded that 2D imaging of tick oocytes is not sufficient to accurately count the subcellular populations in oocytes or to display the bacterial-mitochondrial intersection in its entirety and resorted to 3D imaging. In this study, we used FIB-SEM to obtain large 3D images displaying the complete symbiotic interface, demonstrated the interacting partners in full, and quantitatively characterized the subpopulations at oocyte level. Our FIB-SEM micrographs of six datasets had sufficient image resolution to confirm the details provided in TEM images in which we could observe the interaction between mitochondria and M. mitochondrii at different vitellogenic stages. Vitellogenisation in both wild-type and aposymbiotic oocytes was associated with organellar degradation and clearance of cytoplasm, while mitochondria remained unaffected by the decay.
The fine polishing of the surface block was performed with 5 nA at 30 kV. For the slice series, 1 nA milling current was applied, removing a 10 nm layer from the specimen block surface. Scanning EM images were recorded with an aperture of 60 μm in the high-current mode at 1. 5 kV of the in-lens EsB detector with the EsB grid set to -300 to -500 V. The voxel size is 10 nm in x, y, and z. The contrast of backscattered electron images was inverted and acquired using ATLAS 5 software (Carl Zeiss, Germany). Acquisition time of each volume lasted on average 3 days, and was sometimes accompanied by drift, loss of focus, and interruption in milling, resulting in volumes of different sizes. We acquired 2048 nm × 2048 nm images and continued until milling was interrupted. These were aligned and processed using Fiji  46  plugin Stacks-shuffling/Align Slices 47.
Three-dimensional-structure reconstruction and volume analysis Image series obtained using ATLAS 5 software were transferred to ImageJ v. 1. 52t for alignment and reconstruction of 3D images. The 3D images were analyzed using 3D visualization software Amira version. 2019. 4 (Thermo Scientific, USA). The mitochondria, bacteria and cell membrane were manually segmented, and the volume of representative data was measured using Amira. For the analysis in Fig. 5 , the volumes of total mitochondria in a unit cubic volume (1 µm 3 ) were measured using the same software. The methodology of simulations, 3D image categorization and the analyses are explained in details in supplementary material. The graphical representations of the 3D images were generated using ImageJ v. 1. 52t, Amira version 2019.
Acknowledgements We are grateful to  Dr. Valérie Choumet  and  Dr. Elisabeth Ferquel  ( Institut Pasteur, France ) for their contributions to tick handling, and  Maarteen Voourdouw  ( University of Saskatchewan, Canada ) for providing the Neuchâtel line of I. ricinus. Professor Simonetta Gribaldo ,  Professor Pascale Cossart , and  Professor John McCutcheon  are thanked for their valuable support, and  Professor John Murray  for proofreading. This research was financially supported by the  Human Frontier Science Program (HFSP) ,  Young Investigator Program  grant  RGY-0075.
1 PFig. 4 | 14 Fig. 4 | Statistical analyses of the 3D reconstructed images. Distribution of volumes of the bacteria (a) and the mitochondria (b) visualized in n = 4 wild-type and n = 2 aposymbiotic 3D datasets. In each box plot, the center line indicates the median, the edges of the box represent the first and third quartiles, and the whiskers extend to span a 1. 5 interquartile range from the edges. c Categorization of the bacteria and mitochondria populations into subpopulations based on the volume overlap between a bacterium and corresponding mitochondrion: 0% overlap is considered a "free" bacterium, 1-5% is designated "next", between 6 and 30% is.
, 2010) , if large-scale condition changes have not occurred previously. Recent field campaigns have been executed, such as ParisFOG  (Haeffelin et al. , 2010) , LANFEX  (Price, 2011) , and Fog Remote sensing and Modelling (FRAM:  (Gultepe et al. , 2009) , for which the life cycle of fog has been studied. During the former two, the effect of heterogeneity on fog was investigated. As part of ParisFOG, measurements were made over three different zones at the SIRTA observatory; the zones included (1) an area of small-scale surface heterogeneties, (2) an area of buildings, and (3) a more open area. During LANFEX, multiple measurement stations were set up in valleys and at hill tops and supplemented by data from a relatively flat area; the effect of orographic heterogeneity on the fog life cycle was studied.
The objective of this study is to provide a better understanding of the impact of forest proximity on the fog life cycle by comparing measurements of radiative fog cases at different sites which vary in their degree of sheltering by surrounding forests. We use data from the recent SOFOG3D field campaign, which are described in Section 2. Two radiation fog cases are presented in Section 3, for which data are compared from ground level up to 50 m at two different sites. Additional radiation fog cases at the two sites are then evaluated at the near-surface only in Section 3. 6. Finally, in Section 4 we introduce additional sites to explore further the effect of different degrees of sheltering on radiation fog formation.
F I G U R E 1 The top panel shows the locations of each of the SOFOG3D measurement sites for which data were used in the analysis presented here. The two 50-m mast sites, Le Couye and Jachere, are represented by the orange and purple markers, respectively. The additional sites are Charbonniere (red), Basta fog monitor station (blue), Champs-Tanon fog monitor station (black), Les Houzins (brown), and Foret-Tanon (green). The middle and bottom panels are photos looking southwest at Jachere and Le Couye, respectively. These two sites are the main focus of the work presented here; however, additional sites were also used to supplement these. The five additional sites were chosen to represent a range of smaller and larger areas within or adjacent to the forested area. All of the sites used in this analysis were contained within an area of around 7 × 15 km (Figure  1 ).
At both Le Couye and Jachere, instrumentation WAS deployed from subsoil to approximately 50 m high. The core measurements used in this study were collected at the following heights. (i) 3D wind speed and direction: at 48, 23, 10, and 2 m at Le Couye and 50, 25, 10, and 3 m at Jachere. (ii) Air temperature: 48, 23, 10, and 1. 2 m at Le Couye and 45, 25, 10, and 2 m at Jachere. Skin-temperature measurements were not available at Jachere. (iii) Visibility: 48, 23, and 2 m at Le Couye and 48, 25, and 3 m at Jachere. Relative humidity (RH) values were also available at the heights described in (ii); however, due to calibration uncertainties at Le Couye we have chosen not to use these in this work. We have, however, used these values to convert the RH into specific humidity (Q), where the data were deemed to be of sufficient quality.
From these data, heat fluxes and turbulence intensity were also calculated. Additionally, we used radiative fluxes at 2 and 1 m at Le Couye and Jachere, respectively, and soil heat-flux measurements made at 2 cm below the surface at both sites. The measurements that were collected above 10 m at Jachere were only available up until early November 2019, after which data were only available at 10 m or below. The additional sites were used for comparison of the near-surface conditions only; these consisted of the following. (i) Visibility: at 3 m at Charbonniere, Les Houzins, and Foret-Tanon; there were no visiometers at Basta or Champs-Tanon fog monitor stations (FMS). (ii) Air temperature: at 2 m at Charbonniere, Les Houzins, and Foret-Tanon, and 1. 2 m at Basta FMS and Champs-Tanon FMS. (iii) Longwave radiation: at 1 m at Les Houzins and Foret-Tanon.
The additional sites did not host as extensive a suite of instrumentation as Le Couye and Jachere, that is, heat fluxes and turbulence intensity were not available. These sites have therefore been used to supplement the findings from Le Couye and Jachere, rather than being used to introduce the concepts discussed in the following sections. The data from Jachere, Charbonniere, Les Houzins, and Foret-Tanon sites were collected, processed, and provided by Meteo-France; those from Le Couye, Basta FMS, and Champs-Tanon FMS were collected and processed by the UK Met Office. A list of instrumentation located at the UK Met Office and Meteo-France sites, along with their associated uncertainties and sampling and logging frequencies, is provided in the Appendix.
COMPARISON WITH ADDITIONAL SITES Data from additional sites have been introduced to identify any other cases where early fog formation was observed or not. The additional sites were chosen specifically to represent the range between an open site and a very sheltered site. These sites were used to supplement the main sites 1477870x, 0, Downloaded from https://rmets. onlinelibrary. wiley. com/doi/10. 1002/qj. 4558 by Cochrane France, Wiley Online Library on [22/09/2023]. See the Terms and Conditions (https://onlinelibrary. wiley. com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License.
We suggest therefore that the earlier fog formation at Les Houzins could be a consequence of sheltering by the surrounding forest, as was observed at Le Couye. At Foret-Tanon (narrow forest clearing), early fog formation near to the surface was not observed; instead, the formation of fog tended to occur after it had done so at Jachere. This is despite the near-surface temperatures at Foret-Tanon being similar to those observed at the other three sheltered sites (Le Couye, Les Houzins, Champs-Tanon). It is suggested by the longwave radiation data (not shown here), however, that the near-surface at Foret-Tanon was not cooling radiatively as rapidly in the afternoon as the other two sites (Le Couye and Les Houzins). This is due to higher levels of downwelling longwave radiation, measured near the surface, which could likely be a consequence of the trees emitting additional longwave radiation downwards.
SUMMARY AND CONCLUSIONS As part of the SOFOG3D project, we have analysed data from two 50-m mast sites over two cases of radiation fog formation and development. The two sites differed in their surroundings: Jachere was very open on agricultural land, and Le Couye was located within an agricultural field, which was surrounded by forested area. We supplemented these cases with six other radiation fog cases, and data from five additional sites, for which we had near-surface measurements available. We found that, in all eight cases of radiation fog, formation occurred earlier at Le Couye than at Jachere. These were cases of in situ formation, where the fog remained shallow and dissipated after around 2 hr. For the two radiation fog cases that occurred whilst the 50-m masts were erected, we attribute this dissipation to cloud passing over the site.
Atmospheric river catalogs The atmospheric river presence is obtained from the two catalogs built by  Wille et al. (2021). The detection is based on the integrated water vapour (IWV) and the meridional component of the integrated vapour transport (vIVT), both from 3 hourly data of the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2) reanalysis  (Gelaro et al. , 2017). The datasets provide a boolean indicator of the atmospheric river presence for each grid cell worldwide with a latitude-longitude resolution of 0. 50 • ×0. 625 •. Previous work revealed weak sensitivity to the input meteorological dataset used, between MERRA-2 (used for the tier-2 exercise of the ARTMIP project:  Collow et al. (2022) ) and ERA5, especially over East Antarctica  (Pohl et al.
Snowpack temperature The vertical profile of temperature in the upper snowpack is estimated with the surface energy budget and thermal diffusion model called Minimal Firn Model (https://github. com/ghislainp/mfm, last visited: February 2023  Picard et al. , 2009 Picard et al. , , 2012;; Domine et al. , 2019)  inspired by the Minimal Snow Model  (Essery, 2004). The model takes as input the 2 m air temperature, surface pressure, 10 m wind speed, 2 m specific humidity, surface downwelling long-wave radiation flux, surface downwelling short-wave radiation flux, extracted from the ERA5 reanalysis. Besides, the required snowpack properties are taken from the literature: the density at the surface and at 10 m depth (e. g. Leduc-Leballeur et al. (2015) ;  Tian et al. (2018) ), the thermal conductivity  (Boone, 2002) , the specific heat capacity of ice  (Picard et al.
Another potential connection may exist with the Amundsen Sea Low, but our study did not allow to accurately characterize if a co-occurrence of different critical conditions could provoke a large GSI event. Further analysis could be done using the ERA5 reanalysis in order to extend the time interval and evaluate the significance of these anomalous situations and possibly to discover some other similar configurations which had led to intense growth of the snow grain. The microwave data available in the past (e. g. Special Sensor Microwave Imager, SSM/I) miss the 150 GHz channel, but the 85-91 GHz channel could be used to find abrupt decreases in 1987-1999. However, the extension is not trivial as the grain size index is indirect and results from remote sensed observations. In situ observations should be included in the analysis, when available, in order to correct possible biases.
Data availability. ERA5 reanalysis data are available from https://cds. climate. copernicus. eu/#!/search?text=ERA5&type=dataset (Accessed on 05-Aug-2022). The AMSU-B TB values were retrieved at https://www. ncei. noaa. gov/access/metadata/landing-page/bin/iso?id=gov. noaa. 335 18 https://doi. org/10. 5194/tc-2023-61 Preprint. Discussion started: 30 May 2023 c Author(s) 2023. CC BY 4. 0 License. ncdc:C00981 (NCEI DSI 3702_01 dataset). AAO index were retrieved from https://www. cpc. ncep. noaa. gov/products/precip/CWlink/daily_ ao_index/aao/aao. shtml.
The number of samples per year for the 16 lysimeters was 145 the 1st year (one sample every 100 mm of rain), 29 the second year, 16 the third year (an annual composite sample), 48 the third year (an annual composite sample except for lysimeters 13 and 14 including a sample with each rain to follow up on the drop in pH of the drains from lysimeter 14), and 10 the fifth full year. Moderate watering was applied during the summer to maintain the plants in a vegetative state. Metal content, pH, conductivity, redox potential were measured in all the samples. Each sample represents a volume (known by weighing) and therefore a calculated liquid/solid ratio L/S in l/kg, i. e. the volume of the sample divided by the mass of mining residue for topic 3. All concentration data were expressed in mg/l and quantity data in mg/kg (concentration multiplied by the L/S ratio of the sample).
The cumulative quantities were calculated by adding the quantities of each sample. Details are given in part 1 of the paper. The results by lysimeter, by year and by parameter are presented in the supplementary data (appendix 1 and appendix 2: average concentration in mg/l of drain and annual cumulative quantity in mg/kg of MBR or mining residue, according to the themes and given in the tables). TOPIC 3 results: Remediation of sulfidic mine tailings with MBR, and revegetation. Experimental setup with Saint-Félix mine residues On-site remediation of sulfide mining residue has been evaluated, by numerous laboratory tests with different residues, and by a test plot of 30 m treated and 30 m control plot on the Saint-Félix concession. In order to estimate emissions to groundwater from this site with and without treatment, lysimeters of this mine tailing residue called "TF" were installed with: -mining residue (lysimeter # According to this latter work, an equivalent of MBR has effects for several years (14-year data available), while limestone has an effect for 2 to 4 years.
Note that for OsloCTM-emi, the hydrogen at the surface, and hence also burden, is slightly larger in CTRL compared to the prescribed fields used in the concentration-driven run. The increase in methane induced effects by hydrogen was estimated using sensitivities from PERT_CH4 from the concentration-driven OsloCTM runs. Model setup. The CTRL simulation uses present-day hydrogen surface abundances. The hydrogen surface concentration field used by all models is on monthly resolution and on a zonally averaged one-degree resolution. The field was generated using data from https://www. esrl. noaa. gov/ using data from 67 stations. The open data includes monthly averages between 1989 and 2005. The data availability varies from station to station, so to create the averaged field we used average monthly values for each month for each station.
Acknowledgements We would like to thank  Jean-François Lamarque  for providing the WACCM results and for his valuable input to the study. This study was supported by the  HYDROGEN  project grants no. 320240  funded by  Energix  and the  Norwegian Research Council. Parts of the simulations were performed on resources provided by Sigma2 -the National Infrastructure for High-Performance Computing and Data Storage in Norway, and the data was also uploaded and shared through their services through the project accounts  NN9188K  and  NS9188K.
-As sea ice is scale-invariant up to the kilometre-scale, fragmentation of sea-ice propagates from small, unresolved, scales to the larger, resolved, scales. Because the small scales are unresolved, the appearance of linear kinematic features seems to be stochastic from the resolved macro-scale point of view. Additionally, such features are inherently multifractal and propagate in an anisotropic medium  (Wilchinsky and Feltham, 2006, 2011). Finally, the found subgrid-scale parametrisation approach should be scalable to a range of resolutions, from regional models used in this study to Arctic-wide models, like neXtSIM  (Rampal et al. , 2016; Ólason et al. , 2022). As a first step towards solving these challenges for NNs, we present the aforementioned twin experiments with a regional model. We create a training dataset with an ensemble of forcing parameters and initial cohesion, which describes the strength of the sea ice against stress.