dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements. We thank the anonymous Referee for their insightful remarks that helped us improving both this paper and the online catalogue. The authors were supported by the  LabEx UnivEarthS :  Interface  project  I10  "Binary rEvolution: from binary evolution towards merging of compact objects". SC is grateful to the  CNES  ( Centre National d'Études Spatiales)  for the funding of  MINE (Multi-wavelength INTEGRAL Network ). FG is CONICET researcher. FG acknowledges support by  PIP 0113 (CONICET) ,  PICT-2017-2865  ( ANPCyT ) and PIBAA 1275 (CONICET). This work made use of  NASA 's Astrophysics Data System (ADS) web services, and of the services associated to the  Centre de Données Astronomiques de Strasbourg (CDS) Simbad and Vizier. This work has made use of data from the  European Space Agency (ESA) mission Gaia  (https://www.
Study Design We hypothesized that surgical treatment would have superior visual outcomes (a 2-line improvement in vision) than PD with an acceptable safety profile. This was a prospective, randomized, multicenter, open-label superiority trial in patients with nAMD comparing the visual outcomes and safety of SMH management via surgery (PPV plus subretinal tPA, SF 6 tamponade) or PD (intravitreal SF 6 plus tPA). In addition, an intravitreal injection with 0. 5 mg ranibizumab (0. 5 mg Lucentis; Genentech, Inc. / Novartis) was performed at the end of the procedure in both groups. The STAR study was funded by the French national research program "Programme Hospitalier Recherche Clinique," with Dijon University Hospital as the sponsor. The STAR study was approved by the institutional review boards (French ethics committee [Comité de Protection des Personnes] and the French data protection agency [Commission Nationale de l'Informatique et des Libertés]), complied with the ethical standards defined by the Declaration of Helsinki and Good Clinical Practice, and was registered at ClinicalTrials.
gov (identifier, NCT02557451). An independent data and safety monitoring board reviewed safety data. All patients provided informed consent before participating in the study. Potential patients were provided with information at selection visit. Patients who agreed to participate then attended the enrollment visit for baseline assessments and randomization and subsequently were treated according to the randomized treatment strategy (surgery or PD). All visual outcomes and safety were assessed monthly up to month 6. No major changes to the study design took place after the study started. Overall, 90 patients were enrolled from 13 hospitals in France between April 28, 2016, and October 28, 2019, with the last patient's final visit on May 5, 2020.
A second analysis was carried out using multiple imputations by fully conditional specification to impute missing VA at month 3. Imputation for VA change to month 3 was based on treatment allocation, baseline VA, age, sex, pretreated AMD status, and clinical center. No interim analyses were planned or performed. Finally, for exploration purposes, we performed a post hoc subgroup analysis of visual outcomes according to SMH diameter and thickness. Analyses were performed with SAS software version 9. 4 (SAS Institute). All tests were 2-sided with a P value of less than 0. 05 as the significance level. The main conclusion of the trial was based on the intention-to-treat analysis.
Théa This study was funded by the  French research program Programme Hospitalier Recherche Clinique  with  Dijon University Hospital  as the sponsor. The funding organization had no role in the design or conduct of the research. Presented at: American Academy of Ophthalmology Annual Meeting, Chicago, Illinoisby the institutional review boards (French ethics committee [CPP] and the French data protection agency [CNIL]), complied with the ethical standards defined by the  Declaration of Helsinki and Good Clinical practice , and was registered on Clinicaltrials. gov( NCT02557451 ). N/A; Study was performed as part of the authors' regular employment duties. No additional funding was provided.
To this end, we fitted the detection-adjusted model to Bd infection data obtained from free-living populations of the southern Darwin's frog (Rhinoderma darwinii) in Chile. As our data come from hosts individually identified using photographs taken at the time of sampling, we were also able to evaluate the effects of individual pseudoreplication in our prevalence estimates. We expected the naïve (i. e. observed) Bd infection prevalence to be negatively biased in our system, given the results obtained by previous studies assessing either Bd swab detection probability or qPCR detection probability  (DiRenzo, Campbell Grant, et al. , 2018; Hollanders & Royle, 2022; Miller et al. , 2012). We also predicted that pseudoreplication would exacerbate the underestimation of Bd prevalence, since R. darwinii individuals are highly susceptible to lethal chytridiomycosis and infected individuals are less likely to be recaptured than uninfected individuals  (Valenzuela-Sánchez et al.
| Removing individual pseudoreplication Our sampling of individuals was not instantaneous; therefore, we expected the presence of individual pseudoreplication because a single frog could have been sampled during multiple months. As R. darwinii individuals were identified using photographs, we could remove pseudoreplicates from our dataset. To achieve this, we followed this procedure:  (1)  for individuals never captured as Bd-positive, a single capture occasion was randomly retained in the dataset; (2) for individuals captured multiple times but only once as Bd infected, the Bd-positive occasion was retained and (3) for individuals captured multiple times as Bd-positive (this occurred only with three individuals: No. 270, 313, 487), we randomly retained one of the Bd-positive occasions. Depending on which positive occasions is selected for these individuals, different final datasets without pseudoreplicates were possible, but we showed that this had little impact on the estimation of prevalence (see Figure  S1  for details).
| Accounting for imperfect pathogen detection resulting from sampling and diagnostic errors We used the sampling and diagnostic detection-adjusted model described by  DiRenzo, Campbell Grant, et al. (2018)  to account for imperfect pathogen detection resulting from sampling and diagnostic errors. We fitted this model to the dataset with and without pseudoreplicates. An alternative approach for dealing with individual pseudoreplication would be to use a multi-season occupancy model to estimate point prevalence, but developing such a model was beyond the scope of our study. Briefly, the detection-adjusted model is a static multiscale occupancy model considering two latent ecological processes, the probability of a host being infected (ψ, which can be seen as the infection prevalence; here a host corresponds to a 'site' in classical site occupancy models) and, if yes, its infection intensity; and two observational processes, the sampling process and diagnostic testing.
For each, pathogen detection probability is modelled by a classical logistic regression based on the history of pathogen detections in the series of samples (i. e. swabs), taken from the same capture, and in the series of diagnostic tests (qPCR), performed on the same sample, respectively. The model also accounts for heterogeneity in detection probabilities that arises due to variation in infection intensity. The full description and parametrisation of the model are available in the Appendix S1: Description of the detection-adjusted model. All parameters were estimated in a Bayesian framework by Markov Chain Monte Carlo methods using JAGS  (Plummer, 2003)  through the R package jagsUI  (Kellner, 2015).
| Removing individual pseudoreplication Of 1085 captures, we captured only 641 individuals, of which 282 were captured more than once (in total, there were 444 recaptures). Three individuals were captured multiple times as infected. Eleven individuals gained infection while three apparently cleared it over the study period (Table  S2 ). Removing pseudoreplicates from our dataset led to a 5-month period prevalence of 6. 2% (40/641) and 5. 3% (34/641) in the 'double swab without pseudoreplicates' and 'classic Bd investigation without pseudoreplicates' scenarios, respectively. In other words, not properly accounting for individual pseudoreplication resulted in a considerable underestimation (of roughly 36%-38%) of the infection prevalence estimates, regardless of the scenario considered (Figure  1 ; Table  S1 ).
Acknowledgements This paper was developed by the  European Society of Cardiology  with special contribution from the  European Association of Cardiovascular Imaging (EACVI)  and was then endorsed by the  European Society of Cardiology Associations : the  Association of Cardiovascular Nursing & Allied Professions (ACNAP) , the  Association for Acute CardioVascular Care (ACVC) , the  European Association of Preventive Cardiology (EAPC) , the  European Association of Percutaneous Cardiovascular Interventions (EAPCI) , the  European Heart Rhythm Association (EHRA) , and the  Heart Failure Association (HFA). The document was reviewed by the  European Association of Cardiovascular Imaging (EACVI) Board  and approved by the  ESC Scientific Documents Committee. We are grateful to  Celeste McCracken  for her help in creating the figures containing certification data;  Liliana Szabo  for her help in creating the graphical abstract; and  Matthieu Depuydt  ( European Society of Cardiology ) for coordination support to the manuscript development.
Polyglutamylation is a reversible modification; deglutamylation is catalyzed by enzymes from the cytosolic carboxypeptidase (CCP) family  [8] [9] [10]. In our proteomic datasets, we discovered Dishevelled (DVL), a highly conserved regulatory protein in the Wnt signaling pathway, as a candidate binding partner of several TTLLs. Wnt pathways represent evolutionary conserved signaling modules that are required for multiple processes during development and maintenance of homeostasis. The best studied is the Wnt/β-catenin pathway (also referred to as "canonical") where DVL is necessary for membrane signalosome complex formation  11, 12  which triggers the disruption of cytoplasmic β-catenin destruction complex and subsequent stabilization of β-catenin. β-catenin is translocated into the nucleus where it activates T-cell factor/lymphoid enhancer factor (TCF/LEF) dependent transcription  13.
DVL proteins are polyglutamylated by TTLL11 We have recently identified several members of the TTLL protein family in the pulldowns of DVL3 (datasets partially published in  34  , see Suppl. Table  1 ), suggesting that TTLLs and DVL can interact. To assess whether any of TTLLs can polyglutamylate DVL we overexpressed all 13 mouse TTLL paralogs together with Flag-tagged human DVL3 and performed western blotting (WB) analysis (Fig. 1A, B ). We detected a change in the electrophoretic mobility of DVL3 when overexpressed with TTLL11, which indicated that TTLL11 might have modified DVL3. Moreover, analysis of polyglutamylation by an anti-polyE antibody, which specifically recognizes C-terminal polyglutamate peptides comprising at least 3 glutamates 9 revealed a prominent specific band in presence of TTLL11 (in addition to signal corresponding to tubulin that served as a positive control) at the size of DVL3 (Fig.
S3 ). Altogether, our data strongly support the notion that TTLL11 catalyzes a so-far unknown type of polyglutamylation that extends the primary peptide sequence of DVL3 by the addition of multiple glutamates beyond the C-terminal methionine residue. In order to directly prove C-terminal polyglutamylation at M716, we immunoprecipitated DVL3 that was co-expressed with TTLL11 and performed cyanogen bromide (CNBr) cleavage of the mixture of DVL3 tryptic peptides. CNBr cleaves peptide bonds at the C-terminus of non-oxidized methionine residues, releasing peptides with Cterminal homoserine (Hse) or homoserine lactone (Hsl) (Fig  2E ). After CNBr cleavage, the peak series corresponding to polyglutamylated MAMGNPSEFFVDVM disappeared (Fig. 2Ea ), and instead non-glutamylated peptides terminated either by Hse or Hsl appeared (Fig.
FRAP RPE cells were seeded to µ-Slide 8 Well (Ibidi) chambers at density 10000 cells per cm  2  24 hours prior to transfection. Cells were transfected with corresponding plasmids of ECFP tagged DVL3 construct (Supplementary table  S2  and S3 ) and incubated another 24 h. Live cell imaging and photobleaching was performed on Zeiss LSM 880 microscope equipped with thermostat and CO2 chamber using Plan-Apochromat 63x objective. After transferring of cells into the microscope, they were left for 30 minutes to rest. Then, protein condensates of similar size were bleached using 458nm laser and images were taken every 5 seconds. Only condensates that stayed in the plane of focus were considered for analysis. Raw images were processed using ImageJ software using jay plugins (https://github. com/jayunruh/Jay_Plugins) from Jay Unruh at Stowers Institute for Medical Research in Kansas City, MO.
LC-MS analysis of polyglutamylated DVL Selected 1D gel bands were excised manually and after destaining and washing Under equivalent ionization and fragmentation conditions, peptide standards at a concentration 0. 01 mg/ml (in 50% ACN, 0. 1% FA) were directly injected at 3 µl/min flow rate to the ion source by using a syringe pump. The processing of the mass spectrometric data including recalibration, compounds detection, charge deconvolution and further MS/MS data analysis was carried out in DataAnalysis software (4. 2 SR1; Bruker). Mascot MS/MS ion searches (Matrixscience, London, UK; version 2. 5. 1) were done against in-house database containing expected protein sequences extended with polyE motifs added to the protein C-term or introduced into the sequence after sites tentatively forming side chains.
cRAP contaminant database (downloaded from http://www. thegpm. org/crap/) was searched in advance to exclude contaminant spectra prior the main database search. Mass tolerance for peptides and MS/MS fragments were 10 ppm and 0. 1 Da, respectively, with the option of one 13C atom to be present in the parent ion. Oxidation of methionine, carbamidomethylation (C), deamidation (N, Q) were set as optional modifications. In case of CNBr digests, methionine modification to homoserine or homoserine lactone was also allowed. All searches were done without enzyme specificity. Presence of modified C-terminal peptides was verified by checking the corresponding extracted ion chromatograms (± 0. 015 m/z) and by manual verification of the MS/MS data obtained. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE  73  partner repository with the dataset identifier PXD034237.
LC-MS analysis of protein complexes LC-MS/MS analyses of all peptide mixtures were done using RSLCnano system connected to Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific). Prior to LC separation, tryptic digests were online concentrated and desalted using trapping column (100 μm × 30 mm) filled with 3. 5-μm X-Bridge BEH 130 C18 sorbent (Waters). After washing of trapping column with 0. 1% FA, the peptides were eluted (flow rate -300 nl/min) from the trapping column onto an analytical column (Acclaim Pepmap100 C18, 3 µm particles, 75 μm × 500 mm; Thermo Fisher Scientific) by 100 min nonlinear gradient program (1-56% of mobile phase B; mobile phase A: 0. 1% FA in water; mobile phase B: 0. 1% FA in 80% ACN). Equilibration of the trapping column and the column was done The analysis of the mass spectrometric RAW data files was carried out using the MaxQuant software (version 1.
Acknowledgments Funding:  Czech Science Foundation  grant  GX19-28347X  (VB)  French National Research Agency  grant  ANR-10-IDEX-0001-02  (CJ)  LabEx Cell 'n' Scale  grant  ANR-11-LBX-0038  (CJ)  Institut de convergence Q- life grant  ANR-17-CONV-0005  (CJ)  French National Research Agency  grant  ANR-12-BSV2-0007  (CJ)  French National Research Agency  grant  ANR-17-CE13-0021  (CJ)  Czech Academy of Sciences  grant RVO:  86652036  (CB)  Czech Science Foundation  (Project  GA22-25365S ) (CB)  Czech Science Foundation  (Project  GA22-06405S ) (JH)  Charles University Grant Agency  (project no. 1414120 ) (JN) We acknowledge the core facility CELLIM supported by the  Czech-BioImaging large RI  project ( LM2018129  funded by  MEYS CR ) for their support with obtaining scientific data presented in this paper.
CIISB research infrastructure project  LM2018127  funded by  MEYS CR  and  European Regional Development Fund-Project  " UP CIISB " (No. CZ. 02. 1. 01/0. 0/0. 0/18_046/0015974  are gratefully acknowledged for the financial support of the measurements at the  Proteomics Core Facility (CEITEC)  and at the  Josef Dadok National NMR Centre. Computational resources were supplied by the project "e -Infrastruktura CZ " (e- INFRA LM2018140 ) provided within the program Projects of  Large Research, Development and Innovations Infrastructures. We would like to thank  Bryjalab  members and  Mikołaj Nowak  ( Institut Curie ) for technical support.
Data and materials availability: All data needed for evaluation of the study (apart from raw mass spectrometry datasets) are present in the paper and/or in the Supplementary Material. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD034237 and PXD033548 for LC-MS analysis of DVL3 polyglutamylation and DVL3 interactome, respectively. Scripts to reproduce analyses are available at Zenodo https://doi. org/10. 5281/zenodo. 7370985. All reagents used are mentioned in Materials and Methods section or listed in supplementary material with corresponding source and/or RRID. Unique reagents generated in this study (plasmids, recombinant proteins) are available upon request.
ion searches were done against modified cRAP database (based on http://www. thegpm. org/crap) containing protein contaminants like keratin, trypsin etc. , and Match between runs was set among all analyzed samples. Protein abundance was assessed using protein intensities calculated by MaxQuant 74. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE 73  partner repository with the dataset identifier PXD033548. Protein intensities reported in proteinGroups. txt file (output of MaxQuant) were further processed using the software container environment (https://github. com/OmicsWorkflows), version 3. 7. 2a. Processing workflow is available upon request. Briefly, it covered: a) removal of decoy hits and contaminant protein groups, b) protein group intensities log2 transformation, c) LoessF normalization, d) imputation by the global minimum and e) differential expression using LIMMA statistical test.
Volcano plot was created in R version 3. 6. 1, using the log fold change and adjusted p-value reported by LIMMA. Proteins passing the threshold of log fold change >1 and adjusted p-value < 0. 05 were further processed by REPRINT with integrated CRAPOME and SAINTexpress tools. For the background list of contaminants, CC66 was used; SAINTexpress was run with the default settings only against the CRAPOME control. REPRINT output was further processed by ProHits-Viz web interface producing Dot Plots and Correlation heat maps using default settings. Scripts to reproduce analyses are available at Zenodo https://doi. org/10. 5281/zenodo. 7231808. UniProtKB protein database for Homo Sapiens (https://ftp. uniprot. org/pub/databases/uniprot/current_release/knowledgebase/reference_pr oteomes/Eukaryota/UP000005640/UP000005640_9606.
Other method-specific statistical operations are explained in corresponding method section. Scripts to reproduce analyses are available at Zenodo https://doi. org/10. 5281/zenodo. 7231808. Xenopus embryos The work with Xenopus laevis was carried out according to the Czech animal use and care law and approved by the local authorities and committees (Animal Care and Housing Approval: 45055/2020-MZE-18134, issued by Ministry of Agriculture of the Czech Republic; and Animal Experiments Approval: CZ 62760214, issued by State Veterinary Administration/Section for South Moravian Region). and analyzed for morphogenetic defects. Alternatively, five embryos (stage 26) were lysed before fixation in a 5x Laemmli loading buffer for the subsequent SDS-PAGE/WB analysis. As for the analysis of blastopore closure, the embryos were cultivated in 0.
Data Availability Statement The values of each metric and relative sediment flux are available in the supplementary material and are available along with code used to reproduce the analysis on Zenodo: https://doi. org/10. 5281/zenodo. 7706814. The Global Surface Water masks used to define the shorelines are available at https://developers. google. com/earth-engine/ datasets/catalog/JRC_GSW1_1_GlobalSurfaceWater?hl=en. ROAM, A fast R-based implementation of the Opening Angle Method, is available at http://github. com/lvulis/ROAM.
SIECs were screened as DNA-binding protein fusions (DB-SIECs) against a library of 12,000 Arabidopsis proteins (12k_space) and 500 additional proteins associated with hormone signalling  32. After removal of autoactivating DB-SIECs, we uncovered and verified 207 protein-protein interactions (PPI) between 156 Arabidopsis proteins and 33 SIECs (Fig. 1b  and Supplementary Data 2). 14 SIECs interacted with only one host protein, while 19 interacted with two or more host proteins (Fig. 1b, c ). 115 host proteins were targeted by only one SIEC, while 41 were targeted by more than one (Fig. 1d ). This partition pattern of SIEC targeting is consistent with previously observed pathogen effector-host protein interactions  11, 30. To confirm the quality of our dataset experimentally, we analysed six randomly selected interactions between SIECs and host proteins in independent co-immunoprecipitation assays in planta (Fig.
In both the DEGs and the interactome, enrichments for over 150 biological processes were over-represented (p < 0. 05) illustrating in both datasets the broad extent to which Si modulates host systems. Terms associated with more specific secondary metabolite biosynthesis such as glucosinolate were observed only for the DEGs, although this may reflect the increased depth of RNA sequencing vs. the less exhaustive Y2H screen. Overall, 20% (34/174) and 32% (59/183) of terms were linked to host defences or hormone signalling in the Si interactome and DEGs, respectively. This immune targeting by symbiotic Si is consistent with previous reports  25, 33, 34  and supports in addition to the robustness, the biological validity of the dataset.
To identify SHIPs in this study, we first integrated the SIEC interactome with the systematic portion of the Arabidopsis Interactome 1 (AI-1 MAIN ), and annotated hormone functions in this network using the Arabidopsis hormone database 2 (AHD2)  46, 47  and hormonerelated GO terms (Fig. 3a ). This revealed interactions of SIECs with Arabidopsis hormone proteins that we defined as direct SHIPs (1 st degree) and 2 nd degree SHIPs, i. e. SIEC-hormone protein interactions via hormone-un-annotated mediators  31  (Fig. 3a-c ). Of the 33 SIECs in our SIEC interactome (Figs. 1b  and 2e ), 20 formed 1 st degree SHIPs with 50 hormone-annotated targets, and 7 SIECs formed 2 nd degree SHIPs with 62 hormone proteins. 6 SIECs had no 1 st or 2 nd degree hormoneinteraction and their targets remained un-annotated (Fig.