dataesr/scientific-paragraphs-categorization huggingface dataset:
More detailed validation for each stereo video dataset can be found at the acquisition documentation (see  10, 12, 27, 31  ). However, this kind of comparison was not always available for all the data provided in this study. As a consequence, the quantization error is the most direct value to estimate the expected accuracy of the observations. Table  3  reports the root-mean-square (RMS) values of the three components of err qu , namely vertical (RMS z ) and 2-D horizontal (RMS x , RMS y ), and the estimated low-high frequency limits ( f lim ) for each experiment. The assessment presented in Table  3  was optimized according to different research objectives. So these results could be adjusted for other study purposes, for example, in most of the cases, the quantization error could be reduced by looking at a smaller region closer to the cameras, and the high and low-frequency limits may be improved by applying different filtering techniques.
Usage Notes The stereo-image data set is archived at 30 https://sextant. ifremer. fr/eng, https://doi. org/10. 12770/af599f42-2770-4d6d-8209-13f40e2c292f. Data provided in this repository are organized according to the station and year of the experiment (e. g. BS_2011, BS_2013, AA_2014 …). Each record is characterized by the time that the acquisition starts and the frame rate in Hz, e. g. BS_2011/2011-10-01_16-18-00_15 Hz. The following data are publicly available there: Here we provide a full dataset for twelve stereo video records, including examples of post-processed Netcdf outputs, the raw images and the link to the codes repository. So the users can either work with the surface elevation map samples or download the images and reprocess it according to their needs.
code availability All the data processed in this dataset used the WASS ("An open-source pipeline for 3-D stereo reconstruction of ocean waves") code version 1. 4 provided by  9  and available at http://www. dais. unive. it/wass (the WASS is a fullframe and dense-matching evolution of the previous stereo code developed by  8, 26  and further refined by  10  ). This tool is able to (i) reconstruct the sea surface by means of a dense cloud of 3-D points from stereo images, (ii) compute the extrinsic parameters of the stereo rig without the need of tedious calibration on-the field, and (iii) provide the parameters necessary to transform the wave data to a local geographical reference system. The fast 3-D dense stereo reconstruction is based on the OpenCV library  29  and analyzes the photometrically distinctive features of the water surface to eventually provide the 3-D surface elevation map.
When the stereo images are processed by WASS, the generated 3-D point cloud is re-sampled in a uniform grid and the final space-time surface elevation is stored in a standard NetCDF4 file. We developed an additional tool (https://github. com/fbergama/wassncplot) that provides the mapping between each image pixel (either from left or right camera) to the 3-D geographical reference frame of the grid stored in the NetCDF4 file. This way, any further processing can take into account both the luminance of each pixel and its 3-D location onto the sea-surface. Possible applications include the analysis of white-capped areas, the 3-D tracking of floating objects and measuring the shape and extent of individual waves. Note that this mapping is in general oneway (ie. from image to 3-D space) since cameras are angled with respect to the sea-surface and some 3-D points in the back-side of the waves are occluded by the crests.
acknowledgements This work has been done in the framework of the DiMe, CARAVELE projects, which benefit from French government support managed by the  Agence Nationale de la Recherche  under the  program Investissement d' Avenir   ANR-10-IEED-0006-14 ,  ANR-10-IEED-0006-26. YS data collection was supported by the project " Construction of Ocean Research Stations and their Application Studies ", funded by the  Ministry of Oceans and Fisheries, Republic of Korea. AA data collection was funded by the Flagship Project RITMARE-The Italian Research for the Sea-coordinated by the  Italian National Research Council  and funded by the  Italian Ministry of Education, University and Research  within the  National Research Program   2011-15. This work has been partially supported by the  Copernicus Marine Environment Monitoring Service (CMEMS)   LATEMAR  project.
All IHC staining results (Table  1 ) show that in cases with both DCIS and IDC the TMEM165 levels increased in IDC in the same tissue section. We have further investigated the expression of TMEM165 in early invasive disease using the MCF10DCIS xenograft model. The MCF10DCIS cell line slowly progresses from DCIS to invasive lesions in 10 weeks. Data shown in Figure  2B  demonstrate that TMEM165 is not expressed in the non-invasive stage, increases in the focal invasive stage while still contained within the basement membrane and continues to expand expression in the invasive stage. Next we looked at expression levels for TMEM165 in the TCGA breast carcinoma database  [23]. The expression profile of TMEM165 among the histological subtypes of invasive breast cancer indicate that TMEM165 expression occurs in all subtypes with the highest percentages in the ER negative subtypes (Table  2 , IDC subtypes).
We evaluated NCSTN glycoforms in control and TMEM165KO for each of these cell lines and compared this to MDAMB231 cells. Our data show that TMEM165KO in HEK293T and HeLa cells display NCSTN glycoforms with migration to a lower molecular weight than the MDAMB231 breast cancer TMEM165KO cells (Figure  5B ) These results indicate that the NCSTN glycoprotein from MDAMB231 breast cancer cells have different glycosylation compared with HEK293T and HeLa cells. To rescue the altered NCSTN glycoforms in TMEM165KO cells both TMEM165WT plasmid and empty vector were transiently transfected in MDAMB231 cells. These results further confirmed that altered glycosylation pattern observed in NCSTN was rescued only in TMEM165KO cells after transfected with TMEM165WT plasmid and not vector (Figure  5C ). Interestingly, when CDG mutant forms of TMEM165 (R126H and G304R) were transiently expressed in MDAMB231 cells, N-linked glycosylation was also present with NCSTN glycoforms as observed in control cells (Figure  5D ).
For example, fucose changes detected by AAL are distributed in low and high molecular weight glycoproteins. However, changes in sialylation detected by SNA were limited to high molecular weight glycoproteins. We performed a lectin blot with ConA to demonstrate an equivalent loading of glycoproteins in each lane. Glycan levels are often changing as a result of changes in the levels of glycosyltransferase (GT) enzymes. We measured the levels of certain GT enzymes that produce the N-glycan structures that were increased in TMEM165KO xenograft tumors using real-time PCR analysis. Data shown in Figure  5G  show the fold change in relative normalized expression levels for each enzyme.
Gene expression analysis via UALCAN UALCAN (http://ualcan. path. uab. edu/) is an online, open-access platform for visualization of gene expression alterations occurring between cancerous and paired normal tissues relative to clinical pathological features, which are sourced from the TCGA database  [18]. In the current study, UALCAN was applied to analyze the transcriptional levels of TMEM165 in primary breast cancer tissues and its association with molecular subtypes. All the breast cases available on UALCAN were included in our research.
Scratch wound assay MDAMB231 cells were seeded into a 6-well plate at high density in DMEM (Invitrogen) with 10% FBS (Gemini Bioproducts, West Sacramento, CA) and 100 mg/ mL streptomycin (Invitrogen). A clear area was scraped into the cell monolayer using a pipet tip. Cells were washed gently with PBS to remove the detached cells, placed in complete growth media for 2 days. Migration of cells into the wounded area was monitored by microscopy using a Cytation 3 (BioTek) and images were captured at different time points after the scratch (0 hr, 24 hr and 48 hr). Wound closure was quantified using ImageJ software (http://imagej. nih. gov/ij/docs/index. html).
The present work proposes a continuous solar adsorption refrigerator for a positive cold storage room of 231 m 3 used for fruits and vegetables preservation and installed in the south of Tunisia. After the estimation of the storage room cooling load, which is equal to 13 kW, a parametric study, aims to improve, the performance of the chiller is done in order to achieve the storage room need and to estimate the required heat in the refrigerator generator. A theoretical model, based on the thermodynamics of the adsorption process, heat and mass transfer within the porous medium and energy balance in the system components, is developed and a simulation with Matlab/Simulink, is carried out. The model was established and validated with the literature experimental data. A maximum coefficient of performance of 0.
Computing results According to the Tunisian National Institute of Meteorology, the average ambient temperature in Sfax for the summer months is 35 °C. Therefore, an average ambient temperature of 35°C is considered, as well as a storage temperature of 9°C. A MATLAB code was established to predict the needed refrigeration capacity of the studied system, and permits to find that, an average power of 13 kW is enough for the cold room's running. The parts that Products, walls, and other heat sources respectively represent on this refrigeration needed power are depicted in Fig. 4. As shown the major input data, are the heat gained by products (68 %) then the heat gained through walls (24%) and the rest are the heat released by lights, fans and people. The driven heat source is solar radiation that is absorbed by a solar thermal collector and then transferred to the adsorption refrigeration chiller.
Simulink modelling for adsorption chiller As shown by equations 1-15, the dynamic response of the adsorption cooling systems are governed by a set of ordinary differential equations. Various simulation tools have been reported in literature to simulate the dynamic response of these systems like Modelica, Java language, Fortran, Matlab programing, Transys. Generally, these simulation tools develop defined functions and additional subroutines for the analysis of thermal systems. Simulink is a dynamic solver that uses mathematical and signal blocks with minimum need for additional user coding  [19]   [20]. Therefore, it is more robust for the analysis and comparative studies. Fig. 7  shows a schematic diagram of a Simulink model for a two-bed adsorption cooling system consisting of four main subsystems describing the governing equations for the two adsorber/desorber beds, condenser and evaporator.
2009; Rabeling and Kronauer 2013). So far, few studies have investigated how Ne varies among Hymenoptera, and all were restricted to the effect of eusociality alone  (Owen 1985; Berkelhamer 1983; Reeve et al. 1985; Bromham and Leys 2005; Romiguier et al. 2014; Imrit et al. 2020). Only recent studies with genome-wide datasets have detected associations between eusociality and decreases in Ne  (Romiguier et al. 2014; Imrit et al. 2020) , but these studies are typically restricted to few taxa compared to studies that rejected any significant effect  (Bromham and Leys 2005). Disregarding the joint effect of other potential Ne determinants (e. g. , body-size, parasitism, pollen-feeding, haplo-diploidy) may bias results and explain the discrepancy among studies with low vs high number of species comparisons.
Here, we tried to better assess the respective effects of potential Ne determinants in Hymenoptera. We used a phylogenomic dataset of 3256 genes in 169 species of Hymenoptera  (Peters et al. 2017) , including 10 eusocial species distributed among 4 independent origins of eusociality (Formicidae: 3 species; Polistinae/Vespinae wasps: 3 species; Stenogastrinae wasps: 1 species; Corbiculate bees: 3 species), 112 parasitic species and 32 solitary pollinating bees. We estimated mean genomic dN/dS for each species and compared these estimations between solitary and eusocial taxa, as well as between free and parasitic taxa (see figure  S3 ),. We also correlated these to body size, life-history descriptor variables of parasitoids (see table  S1  for details) and geographical range descriptors (see table  S5  for details).
Results dN/dS distribution across the Hymenoptera phylogeny We estimated dN/dS in 3241 gene alignments of 169 species of Hymenoptera using the mapNH program  (Romiguier et al. 2012 ; https://github. com/BioPP/testnh) from the testnh program suite  (Dutheil and Boussau 2008; Guéguen and Duret 2017). We used the tree obtained by  Peters et al. (2017)  and its topology through all analyses to correct for phylogenetic inertia. As eusocial Hymenoptera are known to have high recombination rates  (Wilfert et al. 2007; Sirviö et al. 2011; Wallberg et al. 2015; Jones et al. 2019) , which in turn are known to inflate dN/dS when associated to biased gene conversion in vertebrates  (Duret and Galtier 2009; Lartillot 2012; Galtier et al. 2018)  , we estimated dN/dS considering GC-conservative substitutions only.
1086 ± 0. 0352sd). This last clade of bees does not clearly stand out however, as most bees in the dataset (Anthophila, species characterized by pollen feeding of larvae: Apidae, Megachilidae, Halictidae, Colettidae, Andrenidae, and Melittidae) show high dN/dS ratios (0. 1190 ± 0. 0302sd, 41 species) with no dependence on their social organization. Finally, only two purely solitary taxa displayed comparable dN/dS ratios: Siricoidea (0. 1025 ± 0. 0251sd, 3 species) and Cynipoidea (0. 1005 ± 0. 0175sd, 5 species). We further used simple linear modeling to try and relate variation in dN/dS ratios to life history traits and geographical range descriptors. Phylogenetic independent contrasts were used to transform the data and account for phylogenetic relationships  (Felsenstein 1985). We also used terminal branch length as a covariable in all models.
2010). This translated into a relatively better power for gene prediction by  Peters et al. (2017)  in eusocial species, and thus into a significant (T=3. 0567, df=9. 3549, p-value=0. 01305) overrepresentation of these eusocial species in alignments (mean number of alignments available per species: 2732. 40 ± 88. 09sd) compared to solitary species  (2276. 7 ± 90. 74sd ). To control for potential biases originating from varying precision in estimations, we replicated all the analyses of this study using a balanced subsampled dataset containing 134 alignments, each of them containing data for the same 88 species (most represented half of the species, referred later as the 88-species dataset). Unless specified otherwise, presented results were obtained with the full dataset. Average corrected genomic dN/dS estimated using the 88-species subsampled dataset are displayed along the Hymenoptera tree in figure  S2.
We further tried to test for an association between dN/dS ratios of reproductive strategy and diet specialization within parasitoids using life-history and host range descriptors found in the literature  (Traynor and Mayhew 2005a; Traynor and Mayhew 2005b; Jervis et al. 2003; Mayhew 2016) , and summarized in table  S1. However these descriptors were very seldom available for the species contained in the present phylogenomic dataset, forcing us to use genus-level averaging for both traits and dN/dS ratios. We detected no significant associations between average dN/dS ratios and life-history in parasitoids at the genus-level. We also tested for an association between dN/dS ratios and four proxies of species geographical range obtained using occurrence data available on the GBIF database. dN/dS ratios showed no significant correlation with mean latitude of occurrences, maximal distance between occurrences, or two additional estimators of species range (table  S5 ).
Anthophila bees and eusocial taxa reveal relaxed selection at the genomic scale High dN/dS ratios in Anthophila bees is by far the strongest pattern observed in our results. Treating Anthophila as a covariable allows to significantly explain (df=167; F=175. 84; p-val < 2. 2. 10-16) more than half the observed variation (R2=0. 512). Despite Anthophila being only one monophyletic group, this effect is still present when accounting for phylogeny (table  1 ), and when accounting for sampling effort variation by using the 88-species subsampled dataset (table  S3 ). This effect is strong enough to completely mask the effect of eusociality when using the full dataset. Indeed, the social status of a terminal branch significantly explains dN/dS variations in the dataset only if removing all Anthophila samples from the analysis.
This is because eusocial corbiculate bees do not show any increase in dN/dS values when compared to other Anthophila. The increase of dN/dS in ants and eusocial wasps, remains significant when accounting for sampling effort variation by using the 88-species subsampled dataset (table  S3 ). To ensure that previous results stem from a relaxation of selection and not from strong positive selection, we applied the Hyphy RELAX procedure  (Pond et al. 2005; Wertheim et al. 2014 ) on each available alignment separately. This procedure allows to formally test for selection relaxation by modelling the distribution of dN/dS ratios along the branches a phylogeny and by comparing the distribution fitted on a focal group of branches (eusocial taxa and Anthophila, alternatively) to the distribution fitted for the rest of the tree.
Out of 3236 realized tests, 1743 (53. 9%) detected relaxed selection on eusocial branches (including eusocial bees) and 184 (5. 7%) detected intensified selection. Genes under relaxation of selection thus represent 90% of the genes for which a difference of selection efficiency between eusocial branches and focal branches could be detected. Results of a gene ontology enrichment analysis conducted with genes under intensified selection in eusocial species as focal genes are presented in table S4, but revealed no clear pattern. Using a conservative bonferroni correction for multiple testing in this procedure still leads to the detection of selection relaxation in 751 genes and of selection intensification in 28 genes. These results also hold if the more balanced 88species subsampled dataset is used, as out of 134 alignments, 68 genes supported a relaxation of selection and 16 genes supported an intensification of selection.
Long-lived reproductive female with delayed sexual maturity, as well as a biased sex-ratio and monopolization of the reproductive labor by few individuals, are typical features of eusocial species, which are bound to reduce effective population size. The hypothesis of a life-history effect matches well with the observation of a higher dN/dS in the highly eusocial formicoids ants Acromyrmex echinatior and Camponotus floridanus than in Harpegnatos saltator, which possesses a less complex social organization  (Hölldobler and Wilson 1990 ). These results are however to be taken with care, as the number of eusocial species in the dataset is low, and as no significant increase in dN/dS due to eusociality has been detected within bees. In this study, a choice was made not to increment the original dataset with additionnal eusocial species, because this addition would have introduced heterogeneity in sample treatment, and translated into new bias in the estimation of dN/dS ratios.
It might be necessary to replicate our analyses using a separate, tailor-made and more exhaustive dataset in terms of eusocial species number in order to confirm the effect of eusociality on demography. Another exciting prospect will be to study Ne variation within eusocial groups. Ants, which display a variety of complexity levels in their social organisation, could represent an ideal model for a more quantitative approach (Bourke 1999), allowing to test for an effect of variation in eusocial characteristics of species on selection efficiency.
One previous study in Teleost fishes has shown that species of temperate regions display lower Ne than species of tropical regions  (Rolland et al. 2020) , while another found no such link across Metazoans  (Romiguier et al. 2014b). Similarly to the latter, we found no associations between mean latitude (or other range descriptors) and dN/dS ratios in Anthophila (see table  S5 ). However this result might be simply due to the massive overrepresentation of species from temperate regions in our dataset, and more thorough studies focusing on more tropical species will be necessary to draw any conclusions. In any case, specialized feeding on flowers appears here as a specialization to ecosystems with relatively low carrying capacity  (Orr et al. 2020)  requiring high parental investment for a scarce resource.
Data cleaning Each amino-acid alignment was first checked for potential false homology using HmmCleaner  (Di Franco et al. 2019; Philippe et al. 2017 ) with default settings. The resulting maskings were then reported on corresponding nucleotide sequences using the reportMaskAA2NT program from the MASCE program suite  (Ranwez et al. 2011). At this point, we discarded individual sequences containing less than 50% of informative site within one alignment.
dN/dS ratios estimation Cleaned alignments were then used, along with the tree topology inferred by  Peters et al. (2017)  and the mapNH binary  (Romiguier et al 2012;  https://github. com/BioPP/testnh), to estimate synonymous and nonsynonymous substitution rates along the branches of the Hymenoptera tree. MapNH allows a fast estimation of those rates by using tree-wide parameters obtained a priori by fitting a homogeneous model (YN98) to the data with the help of bppml  (Dutheil and Boussau 2008) , to parsimoniously map observed substitutions to the supplied topology. Estimated substitution counts for specific branches, obtained separately for each alignments, can then be summed to obtain genome-wide substitution rates. We used this method to obtain dN/dS ratios of terminal branches, susceptible to carry information about the long-term drift regime of extant lineages.
Controlling for sampling bias Four Hymenoptera (Apis mellifera and the three ants), which represent nearly half the eusocial species considered, are species with published genomes. This translates into a better power for gene prediction and thus, into an over-representation of these species in the dataset. Imprecisions in dN/dS ratios estimations are in turn known to yield higher values, because the real value of this ratio in functional sequences is often close to its zero boundary. We thus applied an additional sub-sampling procedure, designed to correct for any potential bias in our estimations that could stem from variation in the quantity of information available for each species. We applied every analysis mentioned before to a reduced but complete dataset containing data only for the most represented half of the species (88 species), and only alignments containing information for each of these species (135 alignments).
Linear modelling of dN/dS ratios Estimated rates, corrected rates and rates obtained from the 88-species subsampled dataset were then modelled through simple linear models using the R software environment, using adult size, social status (eusocial or solitary) and membership to Anthophila as covariables. We also used this statistical setting to evaluate the effect of branch length. Short branches are known to bias dN/dS estimations upward because they yield more inaccurate and thus generally higher estimations of this parameter. The phylogenetic setting was taken into account by using phylogenetic independent contrast  (Felsenstein 1981)  for each variable. This was done using the pic() function in the R package ape. To try and further uncover the potential links between dN/dS ratios and life-history within Hymenoptera, we also attempted to correlate dN/dS ratios with major descriptors of parasitic type within parasitoid Hymenoptera.