dataesr/scientific-paragraphs-categorization huggingface dataset:
Playa del Faro In March 2018, the pH changed from 8 in offshore samples to 7. 5 nearshore, reaching 7. 16 and 7. 13 during December 2018 130 and June 2019, respectively (Fig. 2 ). Similarly, high AT and DIC were measured throughout Playa del Faro. In March 2018, the ocean data obtained in the furthest coast station of Playa del Faro reached typical values of 2132 µmol kg -1 and 2418 µmol kg -1 , respectively for CT and AT (supplementary material 2). As we approached the shore, both factors increased to values that exceeded 3100 µmol kg -1 , following an inverse distribution observed with salinity, with an increase in the CT:AT ratio close to 1:1, indicating an important contribution of bicarbonate along the area (Fig. 3a, b ). In December 2018, the anomaly increased 135 to over 3500 µmol kg -1 in both parameters.
As a direct consequence of the low pH values, although compensated by the high https://doi. org/10. 5194/bg-2020-232 Preprint. Discussion started: 3 August 2020 c Author(s) 2020. CC BY 4. 0 License. CT, AT and dissolved calcium contents (determined by ICP-MS, data not presented), the calcite and aragonite saturation states were also affected. It was observed that the area nearest to the shore presented saturation values of calcite and aragonite that were below 1. 5 (Fig. 3c, d ).
Acknowledgements This research received a grant from the  Fundación Biodiversidad of the Ministerio para la Transición Ecológica of the Spanish Government  and help from the  Ministerio de Economía y Competitividad  through  ATOPFe  project ( CTM2017-83476 ). We 290 thank the researchers, the officers and crew of the  R/V Ángeles Alvariño  from  Instituto Español de Oceanografía (IEO)  for their help during the sampling process. Also, we want to thank  Adrián Castro  for his help during the water sample analysis in the laboratory of QUIMA group (ULPGC) and  Enrique Lozano-Bilbao  from the  University of La Laguna  for his comments and feedback. Finally, we very much appreciate all the help offered by the Fuencaliente town hall ( La Palma ). The authors declare that they have no conflict of interest.
Methods The French multicentre study "FLUPROSTIC" (NCT01501630) was a prospective integrated clinical and economic national multicentre study comparing NaF, FCH and DW-MRI in detecting bone metastasis in PCa patients with first BCR. The medical objective was to compare the diagnostic performance and the impact on patient management of these three imaging modalities in this indication. It was completed by a cost effectiveness analysis using real treatment costs of trial patients. The FLUPROSTIC trial was conducted in accordance with the Declaration of Helsinki and approved by a national review board (IDRCB 2011-A01041-40). All patients provided written informed consent. The study design, inclusion/exclusion criteria, follow-up and standard of truth (SOT) for bone metastasis that were applied in this study are summarized in Additional file 1.
Costs Real treatment costs (updated to 2016 Euros (€)) were calculated for each patient included in the trial for the year following his inclusion. The costs of inpatients and outpatients were established based on activity logs completed by hospital practitioners, by considering the diagnosis-related group, healthcare common procedure coding system and ambulatory payment classification codes. The costs of out-of-hospital care (biology, imaging and medical consultations) were based on activity logs completed by the referring physician. Inpatients, outpatients and ambulatory care costs were calculated according to the data of the French National Study of health costs  [25]. The costs of pharmaceuticals were based on prices listed by the French Public Welfare Agency  [26]. The treatment costs that were used are summarized in Table  2.
Statistical analysis The data were analysed using R software. The heemod package  [28]  was used to calculate the transition probabilities from annual rates, run the Markov model, calculate the incremental cost-effectiveness ratio (ICER) and perform deterministic and probabilistic sensitivity analyses. The patient-based diagnostic performances of the three imaging modalities were compared by using the Cochran Q test with McNemar chi-square as a post hoc test. The agreement between the on-site and central readings for bone metastases was assessed for the 3 imaging modalities using Cohen's kappa coefficient. The economic evaluation followed the CHEERS recommendations  [29].
Base case: population and performance of imaging modalities Of the 59 patients with biochemical recurrence enrolled in the FLUPROSTIC trial, 4 were excluded because the SOT could not be determined. The data of 55 BCR patients prospectively included between December 2011 and August 2014 were thus analysed. At least one bone metastasis was found in 7/55 (12. 7%) patients (Table  3 ).
Acknowledgements The authors want to thank  Mrs. Zakia Idir ,  AP-HP , and  Prof. Eric Vicaut  of  URC Lariboisière  for monitoring this study. They pay tribute  Dr. Laure Michaud ,  Dr. Caroline Rousseau  and all clinicians for referring their patients and acknowledge their confidence. Dr. Gauthé  specially thanks  Dr. Jérôme Frenkiel ,  Dr. Pierre Rufat ,  Dr. Odile Talvard  and  Ms. Jessica Weinstein  for help in collecting cost data.
Acknowledgments The authors would like to thank  GRSDT  and  MESRS (PNE), Algeria ,  Drs. Ouided Abdelaziz ,  Imed Mennai ,  Miss Benouchen Djamila ,  Mrs Maya Medjmedj , and  Professor Hocine Ali -khoudja for English revision from  Brothers Mentouri University of Constantine 1, Algeria. Authors are also thankful to  Dicle University Science and Technology Research and Application Center  for opening its facilities.
g. , La Chimba and Chañaral flood), and volcanic eruptions (e. g. , Chaitén Volcano), which can also be projected on these kinds of models. In order to depict the impact of the 1730 event in the Valparaíso region, tsunami propagation and inundation were modeled using the well-known tsunami modeling software Geoclaw  [27, 28]. The modeled earthquake scenario was obtained from  [1] , with an estimated moment magnitude between Mw 9. 1 and Mw 9. 3. High resolution topography and bathymetry were used, and tsunami wave heights and flow depths for the finest grid were stored every 10 s in order to generate high resolution videos to be projected on the Valparaíso and Viña del Mar mock-ups, as shown in (Figure  4 ). The maximum tsunami flow depth for Valparaíso and Viña del Mar obtained from the simulation are shown in Figure  5.
onemi. gov. cl/visor-chilepreparado/ accessed on 12 April 2020. ), in the downtown of Viña del Mar, there are 10 established security areas to gather people in case of a tsunami, all of them located over 30 m. a. s. l. , and 25 evacuation routes are recommended, some of them having paths longer than 2. 5 km from the origin to the assembly areas, as shown in (Figure  7 ). Simulations of the downtown's pedestrian tsunami evacuation  [31]  were done using an agent-based model developed with the PARI-AGENT software, coupling evacuation and tsunami flooding parameters  [32]. The tsunami inundation was previously modeled with the aid of STOC-ML software  [33] , using a worst-case earthquake scenario similar to the 1730 event. Results obtained showed that the estimated tsunami arrival time was about 15 min, and the maximum flow depth was 5 m.
CIGIDEN mounted an exhibition with TsunamiLab and projection mapping of tsunami inundation on the Valparaíso terrain relief mock-up where the 1730 tsunami inundation was projected, as described in Section 3. 1 and shown in Figure  4. Scientific talks were given by researchers of diverse universities, and the aim of the presentations was to explain the general concepts of tsunamis, also emphasizing the importance of scientific research and its connection with decision makers and society at large. While these activities took place at schools in Viña del Mar and Valparaíso, the public exhibition was mounted near La Matriz Church Square, inviting citizens and children to interact with researchers and the different modules. A broad scientific talk (Figure  8 ) was introduced by experts who have greatly contributed to the study of paleotsunamis and tsunami hazard.
Study setting and patients The data of all women diagnosed with endometriosis and referred for FP from July 2015 to October 2018 were extracted from the prospectively maintained database of Tenon University Hospital. Inclusion criteria for FP were: i) age < 40 years, ii) endometriosis with ovarian cysts with and without deep endometriosis (DE), and iii) alteration of ovarian reserve (antral follicle count (AFC) < 10 and/or anti-Mullerian hormone (AMH) level < 2). Indications for FP were systematically validated by a multidisciplinary committee.
Conclusion Our results highlight that FP procedures are feasible and effective for patients with endometriosis, even if several cycles will be required for most patients. Antagonist and PPOS protocols are associated with similar outcome in terms of number of retrieved and vitrified oocytes with a medico-economic analysis in favor of PPOS protocols. We suggest that data should be collected on a continuous basis to further clarify indications for FP in the context of endometriosis, taking both the economic burden and success rates into consideration.
But in pig n˚3 and 4, TP was modified to account for changes to the tumor depth and diameter, based on the preoperative CT-scan acquired at day 14 post-implantation (D14), 30 minutes before the treatment. This modification was required because of a rapid increase in tumor volume and change in tumor coordinates between D10 and D14. In the fifth minipig, TP was performed directly on a CT scan that was acquired as close to the treatment as possible, 30 minutes before the 165 Ho injection, at D14 (Table  1 ). Performing the CT-scan as close to the treatment as possible meant that the planning was performed with the most up-to-date information regarding the tumor's size, shape and position. For the CT-acquisition, contrast product was used to easily differentiate the tumor from healthy tissue. Tumor segmentation was then performed with the open-source software, 3D Slicer.
2 of the Avizo software (Thermo Fisher). The segmentation was performed only on few slides and an interpolation procedure was then performed in order to obtain a Region Of Interest (ROI) around all the tumor. Using this ROI, the tumor volume was calculated in mm 3 , again with Avizo v 9. 2. The day of 165 Ho injection (D14), pre-and post-operative CT acquisitions were performed. Pre-operative CT was done to obtain the coordinates of the tumor which are necessary for preparing the TP and finding the location of injections inside the tumor. Post-operative CT was acquired to observe the distribution of injected Ho inside the tumor. The injected 165 Ho distribution was visible through CT-scan imaging thanks to the high relative density of Ho compared to normal tissue and bone. Ho CT-scan calibration curve were determined prior to the study.
Transcriptome assembly and analysis Sequence processing and analysis were carried out in CyVerse's Discovery Environment using the High-Performance Computing applications  [38]. The Illumina BCL output files were converted to FASTQ-sanger file format and sequence quality trimming was performed using Trimmomatic  [39] , with a minimum phred quality score >20 over the length of the reads. The trimmed reads were then quality checked using the FASTQC tool. The processed and trimmed reads were used to construct de novo transcriptomes using the Trinity assembler v2. 0. 6  [40]  on CyVerse's Atmosphere cloud computing platform, using a minimum overlap value of 25 and a minimum contig length of 400 nucleotides (nt). Raw sequence reads and assembled transcriptomes are available from NCBI Bioproject numbers PRJNA561766 (G.
polynesiensis) and PRNJA561774 (G. pacificus). The transcriptomes were annotated using BLAST+ for blastx searches (E-value � 1e-4), followed by conserved domain mapping and gene ontology assignment using Blast2GO v. 4. 1. 9 [41]. The Core Eukaryotic Genes Mapping Approach (CEGMA)  [42]  and Benchmarking Universal Single Copy Orthologs (BUSCO V3. 0. 2)  [43]  were used to analyze the comprehensiveness of the gene catalogues. HMMER  [44]  was used for the identification of contigs containing conserved PKS domains (KS, KR, ACP, AT, DH, ER, TE) using an in-house HMM database and an E-value cutoff of �10e-10. Functional prediction of sequences was further analyzed by Pfam  [45]  and conserved domain searches  [46]  were used for identification of conserved amino acid residues and functional prediction of PKS and NRPS/PKS transcripts.
g. , Symbiodinium 50. 5%-56. 4% [53] ) and fucoxanthin containing dinoflagellates (e. g. , Karenia brevis 52. 4%,  [29] ) have lower GC content. BLASTx searches found 51. 8% of G. polynesiensis contigs and 51. 1% of G. pacificus contigs with significant similarity to sequences in the Genbank non-redundant database (E value < 10 -4 ). To assess the completeness of the transcriptome assemblies, we found 84. 7% and 84. 3% complete copies of 248 ultra-conserved core eukaryotic genes using CEGMA in G. polynesiensis and G. pacificus, respectively. BUSCO analysis revealed 81. 2% (G. polynesiensis) and 82. 3% (G. pacificus) of 303 highly conserved single-copy orthologs in the assemblies.
Polyketide synthases Because of the high sequence conservation within active sites, PKSs are most often identified by the presence of KS domains. HMMER and conserved domain searches found 107 KS domain containing contigs in the G. polynesiensis transcriptome. Of these 98 possessed a single KS domain while 9 sequences contained multiple KS domains in 1 to 7 modules. G. pacificus possessed a similar number of KS domains (103) but in contrast to G. polynesiensis, only four were found in multidomain sequences and these contained only single or partial modules (a complete list of all KS contigs is presented in S1 and S2 Tables). The number of KS transcripts and multidomain PKSs is presented in Table  1 , in comparison with those found in previously reported transcriptomes from two low-toxicity, MTX producing species G.
Peroxisome targeting signals (PTS) are recognized by peroxin (Pex) proteins for import to the peroxisome. The most common is PTS1, a tripeptide consensus sequence (S/A/C)-(K/R/H)-(L/M) found at the C-terminal end of peroxisomal proteins that are imported by Pex5. A less common motif, PTS2 [(R/K)-(L/V/ I)-X 5 -(H/Q)-(L/A)], is found at the N-terminal region of proteins recognized by the importer Pex7. Both manual inspection and analysis using the PTS Predictor algorithm (http://www. peroxisomedb. org) indicated the absence of these canonical PTS sequences in the N-and Cterminal ends of all single-domain KS proteins. The DeepLoc algorithm does not look explicitly for these motifs, but rather conducts neural network analysis using a training set of 13,858 proteins with experimentally confirmed intracellular localization from the Uniprot database, including 154 peroxisome matrix and membrane proteins  [60].
To better evaluate the validity the Deeploc algorithm's assignment of KSs to the peroxisome, we searched for known peroxisomal proteins in the transcriptomes of G. polynesiensis and G. pacificus in order to characterize their PTS motifs. An inventory of peroxisomal metabolic pathways present in dinoflagellates (Prorocentrum minimum) and other alveolates has been recently published  [61]. These include the beta oxidation of fatty acids, catabolism of purines, detoxification of reactive oxygen species, photorespiration, and the glyoxylate cycle, which uses acetyl-CoA from the breakdown of fatty acids as a carbon source for the synthesis of succinate. To identify peroxisomal proteins in our Gambierdiscus transcriptomes we searched for genes in this inventory by text search of Blast2Go annotations and by blasting Prorocentrum minimum sequences present in the inventory against our Gambierdiscus databases.
The K. brevis contig (Kbcon-tig10632) with identical domain structure had 49% identity and 61% similarity with G. polynesiensis TB92contig47444. Sequences with the same architecture were also recently reported from Ostreopsis spp. [32]  but were absent from Symbiodinium isolates reported in  [31]. However, S. microadriaticum PKS N (Genbank Acession No. OLQ14315. 1), has partial  The only other NRPK/PKS sequences found in the Gambierdiscus transcriptomes (A-KR-PP-leu rpt; Table  3 ) lack a KS domain and were therefore not included in the KS-based phylgeny. This sequence was found in both Gambierdiscus species. A similar sequence found in S. microadriadicum (Genbank Acession No. OLQ09666. 1) is listed as a HSC70 interacting protein because of an upstream heat shock binding motif, absent from the Gambierdiscus sequences.
An exception is one sequence present in both G. polynesiensis and G. pacificus with a modified active site, LCAGN. Since the tyrosine (Y) is a critical residue for catalytic activity  [64] , the role of these sequences in PKS activity is uncertain. The PKS KR domains differed from the Type II fatty acid synthase KR (fabG) in these species (MUR4contig31717, Genbank Accession No. MT165603; TB92contig14168, Genbank Accession No. MT165604), which possessed the conserved active site YxxxK, specifically YGASK in both species. Both fabG sequences possessed a signal peptide consistent with plastid localization. All other standalone KR domains lacked signal peptides, transit peptides or peroxisome targeting signals when analyzed by signal or target. Deeploc assigned several to the peroxisome, but like in the KS domains, PTS motifs were absent, making the basis of the assignment uncertain.
Several multidomain sequences containing KR domains but lacking KS domains were found (Table  3 ), including an ER-KR sequence present in both species, ER-KR-PP-TE in G. polynesiensis, and AT-DH-KR[ER]KR-PP-TE in G. pacificus, which is 83% identical to G. polynesiensis contig3790 module 7, but missing the KS domain. Methyl transferase containing sequences with the structure MT-KR were present in both species, with similarity to lovastatin nonaketide synthase in Symbiodinium microadriaticum (Accession number OLP87649. 1). G. polynesiensis expressed double (KR-KR) and triple KR sequences (KR-KR-KR) absent from G. pacificus. Acyl Transferase (AT). The number of trans-AT contigs far exceeded the number of cis-AT domains in both species: G. polynesiensis expressed 3 cis-AT and 28 trans-AT domains, while G.
C-terminal peroxisome targeting signal PTS1, (S/A/C)-(K/R/H)-(L/M), and N-terminal PST2 targeting signal (R/K)-(L/V/I)-X5-(H/Q)-(L/A) were found in candidate peroxisomal proteins in Gambierdiscus. Mito-mitochondrial; Cyto-cytoplasm. Genbank accession numbers for Gambierdiscus spp. peroxisome sequences are presented in S5 Table.
Acknowledgements We thank the operational team (statisticians, data manager and CRAs), with  K. Le Malicot ,  C. Choine ,  C Fuchey ,  F. Guiliani ,  N. Lasmi ,  G. Arnould ,  N. Guiet ,  M. Maury-Negre ,  H. Fattouh ,  N. Le Provost ,  L Gaba , and  C. Girault  for editing support and  Bayer France  for financial support.
Objective: The application of sentinel lymph node biopsy (SLNB) in elderly patients with early breast cancer remains somewhat controversial. This study aimed to establish individualized nomograms to predict survival outcomes of elderly patients with and without SLNB and find out which patients could avoid SLNB. Methods: A total of 39,962 ≥70-year-old patients diagnosed with T1-T2 breast cancer in 2010-2015 were included from the Surveillance, Epidemiology, and End Results (SEER) program and were divided into the training set (n = 29,971) and the validation set (n = 9,991). Axillary surgery was not specified in the SEER database, and we defined removing one to five lymph nodes as SLNB. Survival analysis was performed using the Kaplan-Meier plot and log-rank test. Multivariate Cox analysis was utilized to identify risk factors for overall survival (OS) and breast-cancer-specific survival (BCSS).
Database and Patient Selection This retrospective study extracted data from the SEER program, which collects the information of cancer patients of 18 cancer registries and covers ∼27. 8% of the US population  (17). The SEER database 8. 3. 6 was queried for ≥70-year-old women who were diagnosed with T1-T2 (American Joint Committee on Cancer seventh edition, AJCC T, 7th ed) primary breast cancer as their only cancer or first of subsequent cancers from 2010 to 2015. This study was reviewed and approved by the institutional review board of our institution, and informed consent was exempt because all records of the database are anonymous and open to the public. Variables involved in this study were demographic characteristics (age at diagnosis, race, marital status, and benign or borderline tumor history), disease characteristics [lateral, tumor location, histology, grade, subtype (ER, PR, and HER2 status), and T and N stage], treatment characteristics (breast surgery type, chemotherapy, and radiotherapy), and survival status (survival time and cause of death).
Age at diagnosis was transformed into categorical variables (70-74, 75-79, 80-84, and ≥85). Based on the code information in SEER, we divided tumor location into three groups (outer quadrant and axillary tail, inner quadrant, and others). Histology was categorized into five groups according to the latest classification of the World Health Organization  (18) : no special type (NST); invasive lobular carcinoma (ILC); favorable (tubular/mucinous/papillary); metaplastic; and others (histological types other than the above four types). The "number of regional lymph nodes examined" code was used to distinguish between SLNB and non-SLNB. The SEER database does not specify the type of axillary surgery, so based on the AJCC definition of a standard ALND (at least six lymph nodes removed)  (19) , we defined that one to five lymph nodes examined were categorized as the SLNB group.
Statistical Analysis All eligible patients were randomly assigned 3:1 into two cohorts: the training set for survival analysis and construction of nomograms and the validation set for external validation. Categorical characteristics were compared using Pearson chisquare test, and continuous characteristics were compared using Student t-test. The outcomes of this study were breast-cancer-specific survival (BCSS) and overall survival (OS). BCSS was defined as the time from the date of diagnosis to the date of death attributed to breast cancer using cause-specific death classification in the SEER database. OS was defined as the time from the date of diagnosis to death due to any causes. The Kaplan-Meier plot and log-rank test were utilized to compare OS and BCSS between different groups. Univariate and multivariate COX proportional hazards regression models were utilized to detect independent risk factors.
Firstly, since some detailed information was not reported in SEER, there may be some potential confounding factors that we did not take into consideration, such as multigene signature assessment, endocrine therapy, targeted therapy, and comorbidities (cardiovascular disease, diabetes mellitus, and other chronic diseases). As a result, the benefit of omitting SLNB in elderly patients may be underestimated because they are often faced with significant comorbidities and cannot tolerate aggressive complications of surgery, but standard adjuvant systemic therapy could compensate for the risk of no SLNB. The second was the inherent limitation of a retrospective study based on the SEER dataset. Since no variable in the current SEER database clearly specifies the type of lymph node surgery, we categorized removing one to five lymph nodes as SLNB according to the AJCC definition as other researchers did  (31).