dataesr/scientific-paragraphs-categorization huggingface dataset:
We sought to answer the following general questions: (a) Does this phytophagous insect lineage exhibit long-term climatic specialization? (b) Do aphids occur in the full range of climate conditions occupied by their host plants, or do they only occupy a subset of the host's climatic niche? Concordance between the insects' and hosts' climatic niches would suggest that observed insect climatic niches are limited by the hosts' presence rather than their own set of physiological constraints. Aphids are particularly well-suited to address these questions as they are generally host-specific, they spend their whole life cycle on their hosts, and their range of host preference and their geographic distribution are generally well-known due to the pest status of numerous species. Using a georeferenced occurrence dataset and a comprehensive phylogeny, we studied the evolution of climate tolerance of the conifer-feeding aphid genus Cinara Curtis, 1835 (Aphididae: Hemiptera) in relation to their Pinus spp.
We compiled a total of 6,135 Cinara occurrence records for 106 species. These include data from online databases (GBIF with 2,359 records and IBOL with 1,334 records) and aphid taxonomic databases from the entomological collection of the University of Montreal (1,705 records), the Institute of Zoology of the Chinese Academy of Sciences (221 records), and the INRA collection (516 records). All occurrences were reviewed and ambiguous accessions (e. g. , occurrences for which the location names did not correspond with the given GPS coordinates or were assigned to county centroids) and duplicate records were removed. Occurrence data for Pinus species hosting Cinara were retrieved from the Conifers of the World database  (Farjon & Filer, 2013). In order to estimate the aphid climatic niches and those of their associated Pinus hosts, we selected a subset of the bioclimatic variables developed by  Hijmans, Cameron, Parra, Jones, and Jarvis (2005) , at the finest grid resolution (30s), that likely influence aphid biology: the maximum (BIO 5) and minimum (BIO 6) temperatures of the warmest and coldest months of the year; the mean temperature of the warmest and coldest quarters of the year (BIO 10 and BIO 11 respectively).
| Taxonomic validation and association of occurrences with phylogenetic species The identification of aphids based on morphological criteria can be ambiguous because aphids show considerable overlap in their morphological characteristics  (Coeur d'acier et al. , 2014). Specimen misidentification or other taxonomic ambiguity can lead to an erroneous geographic occurrence record of a species. We therefore sought to cure the occurrence dataset of misidentifications: We downloaded 743 Cinara barcode sequences (i. e. , cytochrome oxidase I DNA sequences available in IBOL [http://www. bolds ystems. org/] and GenBank [https ://www. ncbi. nlm. nih. gov/genba nk/]) representing 105 species and corresponding to 638 records in our occurrence dataset. Cross-referencing the datasets allowed us to assess whether some of the species included in this study were not monophyletic and could thus be subject to taxonomic ambiguities.
To this end, we reconstructed a maximum-likelihood tree using a Kimura-2-parameter model of base substitution  (Kimura, 1980)  and 1,000 bootstrap replications as implemented in RaxML 8. 2. 10 (Stamatakis, 2014). The COI tree revealed some polyphyletic and paraphyletic species. In most cases, we defined monophyletic species groups of closely related species that seem to be regularly mixed. We then grouped occurrence data accordingly and assigned them to their respective species group. In cases where sequences assigned to a species were found in distant phylogenetic lineages, the species was either entirely removed from our occurrence dataset and the final phylogenetic tree, or just the evidently problematic occurrences were deleted. Details on the curation of the occurrence dataset and clustering of specimens into species groups are given in Appendices S1 and S2.
| Phylogenetic methods and molecular dating In order to obtain the most comprehensive Cinara phylogeny, we complemented the nucleotide dataset published by  Meseguer et al. (2015)  with sequences available on GenBank. We used one marker from the aphid nuclear genome (elongation factor 1-α, EF) and two from its mitochondrion (COI; cytochrome b, CytB). Then, we considered two markers from the aphid's primary symbiont, Buchnera aphidicola: a chaperonin molecule involved in protein folding, GroEL, and "His" including the ATP phosphoribosultransferase, HisG, and the histidinol dehydrogenase, HisD. The final dataset included 82 Cinara species, 15 more than the  Meseguer et al. (2015)  study. Following  Meseguer et al. (2015) , 12 species belonging to seven genera of the Lachninae subfamily (Lachnus, Longistigma, Maculolachnus, Pterochloroides, Stomaphis, Trama, and Tuberolachnus) and two species belonging to two other aphid subfamilies (Mindarus sp.
| Climatic niche evolution in Cinara For the following analyses, we pruned from the tree the species for which we had gathered fewer than five georeferenced occurrence records. The phylogenetic signal of each selected climate variable was estimated with the λ of  Pagel (1999)  on the time-calibrated tree. λ varies between 0 (no phylogenetic signal, i. e. , the character evolved independently of the phylogeny) and 1 (there is phylogenetic signal, i. e. , the phylogeny fully represents the trait covariance among species). From the occurrence data, we calculated the median, minimum, and maximum values of each bioclimatic variable for each species or species group included in the tree and optimized the value of λ using the phylosig function of the phytools package in R (R  Core Team, 2013; Revell, 2012).
| Cinara and Pinus niche equivalency tests The clades B 2 , B 3 , and B 5 of the Cinara tree (see below) encompass species feeding exclusively on pines (44 species in our dataset). We restricted our analyses of niche equivalency to these species because Pinus-Cinara associations are particularly well documented  (Blackman & Eastop, 1994). In addition, occurrences available in public databases often specify the Pinus species whereas the identification of other Cinara hosts frequently does not reach the species level. We retrieved the association of each Cinara species with species of Pinus from  Blackman and Eastop (2019)  and from our own dataset. When Cinara species were clustered into species groups, the host niche represented the combination of the occurrences of all the hosts of all aphid species included in the group.
| Occurrences and taxonomic validation After filtering for duplicates and dubious locations, 1,756 of the 6,135 occurrences were retained. The COI tree revealed a few polyphyletic and paraphyletic species, suggesting these nominal species are regularly misidentified or harbor cryptic taxonomic entities (Appendix S1). Indeed, they represent well-known cases of ambiguously defined species and represent taxonomic challenges in need of work (Appendix S2). This kind of phenomenon represents a possible source of error when using georeferenced data from unverified databases (e. g. , GBIF) to plot on the tips of a phylogenetic tree. We defined 13 species groups that each encompassed closely related species that were regularly mixed in the COI tree and grouped occurrence data accordingly (Table  2 ).
| Cinara niche characterization and evolution After pruning the tree of species represented by fewer than five occurrences, the dataset included 67 species, with 5-93 occurrences each (mean = 26. 9, SD = 20. 2). Mapping the bioclimatic scores on the tips of the phylogenetic tree showed that none of the clades is restricted to specific climatic conditions (Figure  1 ). There is no phylogenetic clustering of climatic tolerance observed among the tips, with each species occupying a different subset of the climatic range of Cinara genus as a whole. The phylogenetic signal was low for four out of the five selected bioclimatic variables (Table  3 ).
In order to understand the relative role of climatic niche and the evolution of host preference evolution on phytophagous insect history, a species-level association matrix is needed. These matrices are particularly hard to compile for insects that do not feed on their hosts as adults. Aphids feed on their hosts during their entire life and are thus good models for studying plant-insect associations. Using an occurrence dataset and a robust phylogeny, we show that climatic niche tolerance is evolutionarily labile in the aphid genus Cinara, with the most of the analyzed temperature and precipitation climate variables displaying a weak phylogenetic signal (Table  3 ). These results suggest that none of the Cinara clades appeared specialized for any specific climate conditions. On the contrary, all clades encompassed most of the climatic niche variation described within the genus and the observed disparity values for closely related species are greater than simulated under neutral evolution (Figures  1  and 2 ).
Alternatively, the narrow range of climatic tolerance in some Cinara species may be due to historical barriers limiting their expansion throughout the full geographic range of their hosts  (Meseguer et al. , 2015). This explanation does not seem to fit our dataset; however, as These species, however, are only known from very restricted areas, suggesting that the small number of occurrences is not a sampling artifact but probably indicative of their true distribution. In any case, species that were represented by few occurrences (fewer than 10) always failed to reject the equivalency test. Hence, undersampling did not to generate type I errors (i. e. , claiming that aphids live in a subset of their hosts niche because of an inaccurate sampling). We nevertheless noted several cases where sampling did seem incomplete: That is, cases where there was no overlapping distribution between Cinara species and at least one of their host plant species,for example, P.
banksiana-C. watsoni (Figure  3 , C. watsoni) failed to reject the null hypothesis, so again we do not think that undersampling led to a false positive in this case. Finally, the sampling of Cinara species is relatively uniform within their known geographic range with no obvious biases toward particular areas and a map superimposing all sampling points shows that a large geographic range has been covered for the entire group. We emphasize also that when Cinara species were sampled (at least by the authors of this study) the aphids were sampled broadly on many conifer hosts, with no focus on any particular species in any particular locations. Therefore, the absence of a particular species in a well-covered area in our dataset, such as Southern California, is probably not a sampling artifact.
Niches were then compared with Schoener's (1968) D statistic. The ecospat. niche. equivalency. test function pools all of the Cinara and host species occurrence data and randomly splits them into two datasets of the same size as the original datasets with which the niche overlap D is then calculated. This process is repeated 100 times and a histogram of the simulated values is constructed which allows a p-value calculation: If the observed D falls into the density of 95% of the simulated values, the null hypothesis (i. e. , the two niches are equivalent) cannot be rejected.
We cannot ignore the possibility that the climatic differences detected in the niche equivalency tests are the result of an incomplete characterization of the aphids' geographic ranges. Although we gathered a relatively large occurrence dataset (see Boucher et al. , 2012; Burbrink & Pyron, 2010; Nürk, Uribe-Convers, Gehrke, Tank, & Blattner, 2015  for studies on vertebrates an plants with a similar number of occurrences per species), some Cinara species were represented by relatively few occurrences; for example, there were only five occurrences for C. solitaria and C. harmonia.
Research funding was provided by the French government through a ANR grant (Phylospace) to EJ. ASM was supported by a Marie-Curie FP7-COFUND (AgreenSkills fellowship-26719) and by an "Investissements d'Avenir" grant managed by Agence Nationale de la Recherche (CEBA, ref. ANR-10-LABX-25-01). Many thanks to.
Protein concentrations were determined with the BioRad Bradford Protein Assay Kit (BioRad, Marnes-la-Coquette, France) and TAM protein levels were assessed by immunoblotting. RNA extraction and real-time reverse transcription-quantitative PCR RNA was isolated from cell lines and xenografts with RNeasy Mini kit (Qiagen, Courtaboeuf, France). Reverse transcription was performed with 1 µg of total RNA, and a high-capacity cDNA reverse transcription kit (ThermoFisher Scientific). A predesigned assay was used to quantify expression of the TATA-box binding protein (TBP) reference gene (ThermoFisher Scientific, Ref: 4326322E). Custom-designed assays were used to measure expression of the TYRO3, AXL, MERTK and GAS6 genes. Primers and probes were designed with Probe Finder software at the Universal Probe Library Assay Design Center (Roche).
DNA array For the identification of genes displaying changes in expression after TYRO3 knockdown in MGH-U3, RT112 and UM-UC-5 cells, we transfected the cells for 40 h with TYRO3 siRNA#1, TYRO3 siRNA#2 or TYRO3 siRNA#3. mRNA was extracted and purified with RNeasy Mini kit (Qiagen). Total RNA (200 ng) from control and siRNA-treated MGH-U3, RT112 and UM-UC-5 cells was analysed with the Affymetrix U133 Plus 2. 0 DNA array. Raw gene expression data were normalised and summarised by the RMA (robust multi-array averaging) method (R package affy) with a customised chip definition developed by Microarray Lab, BrainArray (HGU133Plus2_Hs_ENTREZG_v18). 14, 15 ne log2-transformed signal value per gene was obtained. The microarray data described here are available from GEO (https:// www. ncbi. nlm. nih.
gov/geo/) under accession number GSE100025. The LIMMA algorithm was used to identify genes differentially expressed between TYRO3 siRNA-treated (n = 9) and lipofectaminetreated control (n = 9) cells. 16 The p values were adjusted for multiple testing by the Benjamini-Hochberg FDR procedure. Genes with |log 2 FC| ≧ 0. 58, and with a FDR below 5% were considered to be differentially expressed. Xenograft models Six-week-old female Swiss nu/nu mice (Charles River Laboratories, Saint-Germain-Nuelles, France) were raised in the animal facilities of Institut Curie, in specific pathogen-free conditions. They were housed and cared for in accordance with the institutional guidelines of the French National Ethics Committee (Ministère de l'Agriculture et de la Forêt, Direction de la Santé et de la Protection Animale, Paris, France), under the supervision of authorised investigators.
TYRO3 is highly expressed in bladder carcinomas We first investigated the role of TAM receptors in human bladder carcinoma, by analysing, using RT-qPCR, the levels of expression of AXL, MERTK, TYRO3 and GAS6 in our previously described CIT cohort of 169 bladder tumours encompassing 87 NMIBCs and 82 MIBCs. 5, 11 Seven normal urothelium samples were used as controls (Fig. 1a ). Expression levels for the three receptors and their ligand were heterogeneous in tumours, with only TYRO3 significantly elevated in NMIBCs and MIBCs relative to normal samples. GAS6 was more strongly expressed in MIBCs than in NMIBCs, suggesting that GAS6 might increase the autocrine or paracrine activation of TYRO3 in muscle-invasive tumours (Fig. 1a ). Higher TYRO3 expression in MIBCs relative to normal samples was confirmed by an analysis of publicly available RNA-seq data from the TCGA cohort for 405 MIBCs (primary tumours only) and 14 normal samples  17  (Supplementary Figure  S1 ).
However, strong MERTK expression was surprisingly detected in 8 of 21 tumours. Different migration profiles in immunoblotting assays were observed for TYRO3, possibly due to post-translational modifications of the receptor (Fig. 1b ). An analysis of the TYRO3 sequence with NetNGlyc1. 0 software identified seven potent N-glycosylation sites (not shown). The treatment of two tumour protein samples with peptide Nglycanase F (PNGaseF), an enzyme that removes N-linked glycans, shifted the TYRO3 band to the expected theoretical molecular weight of 96 kDa, confirming the N-glycosylation of this receptor (Fig. 1c ). We examined the protein expression pattern of TYRO3 in clinical samples from the CIT cohort by immunohistochemistry using an anti-TYRO3 antibody. We had validated the specificity of the antibody using paraffin-embedded 5637 cells expressing the three TAM receptors and that were transfected or not with TYRO3 siRNA (Supplementary Figure  S3 ).
The data shown are means ± SD (n = 4). Statistical analysis was performed with t-tests No alteration of the TYRO3 copy number was detected (data not shown), the mechanisms increasing the expression of TYRO3 in bladder tumour cells remain to be determined. TYRO3 was detected at the plasma membrane in several bladder cancer cell lines by flow cytometry, but IHC staining on human bladder tumour sections showed it to be present mostly in the cytoplasm and only weakly expressed at the plasma membrane of tumour cells. A similar RTK distribution has already been reported for TYRO3 and AXL in human colorectal cancer and pancreatic cancer, respectively. 18, 29 onsistent with this general higher level of expression of TYRO3 in bladder tumours compared to normal samples, TYRO3 expression was detected in most of the UBC cell lines, whereas AXL and MERTK had more heterogeneous expression patterns in UBC cell lines.
Given the current interest in agonistic anti-CD137 antibodies for cancer treatment,  35  TYRO3 inhibition might be useful for both inhibiting tumour growth and boosting the antitumour immune response. In line with this hypothesis, a phase 1b clinical trial (NCT03170960) has recently begun to test the combination of a pan-TAM inhibitor (cabozantinib) with an anti-PD-L1 antibody (atezolizumab) in patients with advanced urothelial carcinoma (including bladder, renal pelvis, ureter, or urethra carcinoma) or renal cell carcinoma. Overall, our data suggests that TYRO3 is a promising potential therapeutic target for both muscle-invasive and non-muscle invasive bladder cancers. Although our pharmaceutical inhibition experiments with TAM inhibitors reproduced the results obtained with TAM knockdown, we cannot rule out the possibility that other activities of UNC-2025 or BMS-777607 could impact tumour cell viability.
ACKNOWLEDGEMENTS We thank  Jacqueline Fontugne (MD, PhD  student) for the pathological examination of TYRO3 staining in normal urothelium samples and peritumoural tissue. We would like to thank  David Gentien  and  Audrey Rapinat  from the  Translational Research Department of Institut Curie  for performing transcriptome experiments. We thank the Cell and  Tissue Imaging  ( PICT-IBiSA ) and  Nikon Imaging Centre, Institut Curie , a member of the  French National Research Infrastructure France-BioImaging  ( ANR10-INBS-04 ). We also thank the  Flow Cytometry Core Facility of Institut Curie. Ethics approval and consent to participate: All patients provided informed consent, and the study was approved by the institutional review boards of the  Henri Mondor, Foch and Institut Gustave Roussy Hospitals (Comité de Protection des Personnes de l'hôpital Henri Mondor, Comité de Protection des Personnes de Boulogne-Ambroise Paré , and  Comité de Protection des Personnes de Bicêtre)  in accordance with the French laws and the  World Medical Association's Declaration of Helsinki.
5,11Mice were housed and cared for in accordance with the institutional guidelines of the  French National Ethics Committee  ( Ministère de l'Agriculture et de la Forêt, Direction de la Santé et de la Protection Animale, Paris, France ). Funding: This work was supported by  La Ligue Nationale Contre le Cancer , through the funding of an accredited team ( FR, IBP, FD, LS, HNK, AMV, CK, NK, MDG, EC, YA, NS, Equipe labellisée ), by  ANR Emergence Bio  and by  ElsaLys Biotech. This project also received funding from the  European Union 's  Horizon 2020 research and innovation program , under  Marie Skłodowska-Curie  grant agreement No. 666003. Data availability: The microarray data are available from  GEO  (https://www. ncbi. nlm. nih. gov/geo/) under accession number  GSE100025. Note: This work is published under the standard license to publish agreement.
Later,  Ginoux and Deroubaix (2017)  used FoO derived from the MODIS Deep Blue dust optical depth (DOD) record to retrieve the wind erosion threshold over East Asia. For individual dust events, the threshold of friction velocity can also be determined by fitting a second-order Taylor series to dust saltation flux measurements  (Barchyn and Hugenholtz, 2011; Kok et al. , 2014b). Nonetheless, a global distribution of threshold of wind erosion based on observation that may be implemented in climate models is still lacking. In this study, we propose a method to retrieve monthly global threshold of wind erosion (hereafter, V threshold ) for dry and sparsely-vegetated surface using high-resolution satellite products and reanalysis datasets. This two-dimensional threshold is then implemented into the Geophysical Fluid Dynamics Laboratory (GFDL) coupled land-atmosphere model, AM4.
1) AERONET The AErosol RObotic NETwork (AERONET;  Holben et al. , 1998)  provides quality assured cloud-screened (level 2) aerosol measurements from sunphotometer records. In this paper we used the data products of the version 3. 0 AERONET processing routine. To examine model simulated DOD, we used coarse mode AOD (COD) at 500 nm processed by the Spectral Deconvolution Algorithm  (O'Neill et al. , 2003; hereafter SDA). SDA COD monthly data is first screened to remove those months with less than AERONET monthly aerosol optical thickness (AOT) data around 550 nm (e. g. , 500 nm, 551 nm, 531 nm, 440 nm, 675 nm, 490 nm, 870 nm, etc. ) and the Ångström exponents across the dual wavelength of 440-675 nm, 440-870 nm, and 500-870 nm are used to calculate AOD at 550 nm ( !!" ). If AOT for 551 nm, 555 nm, 531 nm or 532 nm exist, then these values are directly used as AOD 550 nm.
2) RSMAS surface dust concentration The Rosenstiel School of Marine and Atmospheric Science (hereafter RSMAS dataset) at University of Miami collected mass concentration of dust, sea salt, and sulfate over stations globally, with most of stations on islands  (Savoie and Prospero, 1989). The dataset has been widely used for model evaluation (e. g. ,  Ginoux et al. , 2001; Huneeus et al. , 2011). Only stations with records longer than four years were used and of those stations 1998. So here we also assume that the climatology of the surface dust concentrations do not change greatly from the 1980s to the 2000s.
3) IMPROVE surface fine dust concentration The Interagency Monitoring of Protected Visual Environments (IMPROVE) network has collected near-surface particulate matter 2. 5 (PM 2. 5 ) samples in the U. S. since 1988  (Malm et al. , 1994; Hand et al. , 2011). IMPROVE stations are located in national parks and wilderness areas, and PM 2. 5 sampling is performed twice weekly (Wednesday and Saturday;  Malm et al. , 1994)  prior to 2000 and every third day afterwards. Fine dust (with aerodynamic diameter less than 2. 5 µm) concentration is calculated using the concentrations of aluminum (Al), silicon (Si), calcium (Ca), iron (Fe), and titanium (Ti) by assuming oxide norms associated with predominant soil species  (Malm et al. , 1994; their Eq. 5). This dataset has been widely used to study variations in surface fine dust in the U.