dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements. We are grateful to the anonymous referee who provided very useful criticism and suggestions. Funding for the TESS mission is provided by  NASA's Science Mission Directorate. We acknowledge the use of public TESS data from pipelines at the  TESS Science Office and at the TESS Science Processing Operations Center. Resources supporting this work were provided by the  NASA   High-End Computing (HEC) Program  through the  NASA Advanced Supercomputing (NAS) Division at Ames Research Center  for the production of the SPOC data products. This paper includes data collected by the TESS mission that are publicly available from the  Mikulski Archive for Space Telescopes (MAST). We acknowledge funding from the  French National Research Agency (ANR)  under contract number  ANR-18-CE31-0019  (SPlaSH).
SH acknowl-edges CNES funding through the grant  837319. This work was also supported by  FCT -Fundação para a Ciência e a Tecnologia  through national funds and by  FEDER  through  COMPETE2020 -Programa Operacional  Competitividade e Internacionalização by these grants:  UID/FIS/04434/2019 ;  UIDB/04434/2020 ;  UIDP/04434/2020; PTDC/FIS-AST/32113/2017 & POCI-01-0145-FEDER-032113; PTDC/FIS-AST/28953/2017 & POCI-01-0145-FEDER-028953; PTDC/FIS-AST/28987/2017 & POCI-01-0145-FEDER-028987. PC thanks the  LSSTC Data Science Fellowship Program , which is funded by  LSSTC, NSF  Cybertraining Grant # 1829740 , the  Brinson Foundation , and the  Moore Foundation ; her participation in the program has benefited this work. This work has been carried out within the framework of the  NCCR PlanetS  supported by.
Although DXA just provides an 'areal' density, this remains the most common technique of assessing bone strength clinically. BMD thresholds also contribute, but less than in adults, to the diagnosis of osteoporosis in children  (58, 72). In children, aBMD data require adjustment for body size to avoid misinterpretation from size artefacts, by using lumbar spine BMAD and total body less head  (73). The ISCD definitions of osteoporosis in children are mainly based on the presence of fractures  (74). Hip structural analysis (HSA)  (75, 76) , has been developed to derive other parameters related to bone strength, for example by calculating femoral neck width  (77). Finite element analysis has also been applied to hip DXA images, which may provide additional information on fracture risk  (78). In addition, current DXA devices enable specific morphological features to be assessed such as vertebral fractures and osteophytes.
Standardization of the analytes is ongoing, but assay results may differ between providers. BTMs are easily measured in mice using ELISA or commercially available assays. In an ovariectomized mouse (as a model of osteoporosis) OC and CTX provided conclusive outcomes on bone turnover when compared to µCT imaging  (267, 268). Although serum BTMs hold the benefit of allowing multiple tests to be taken from one animal over a time course, it should be considered when planning an experiment whether more useful data can be gained by qPCR or western blot of bone tissue post mortem. Bone formation (osteocalcin, alkaline phosphatase) and resorption markers (TRAP) are measured ex vivo through immunoassays in whole-mount, dissected tissues and on histological sections. For in vivo studies Alizarin Red and Calcein can be used to measure bone formation as well as the use of transgenic lines for osteocalcin, and TRAP line labelling osteoclasts  (205, 269).
ACKNOWLEDGMENTS This publication is based upon work from  COST Action GEMSTONE  ( CA18139 ), supported by  COST (European Cooperation in Science and Technology). COST  is a funding agency for research and innovation networks. Our Actions help connect research initiatives across Europe and enable scientists to grow their ideas by sharing them with their peers. This boosts their research, career and innovation. (www. cost. eu). The Graphical Abstract and Figure 3 are created with  BioRender (www. BioRender. com).
Patient selection We conducted a retrospective multicentric matched case control study (NCT03565601) in 4 French tertiary care centers (Nancy, Lille, Dijon, and Metz). Study protocol was validated by the local ethics committee of Nancy University Hospital. Among the 2106 patients who had been screened for anti-Ro52 antibodies by immunoblot between January 2010 and December 2018 in immunology departments, patients with a new diagnosis of CTD and anti-Ro52 antibodies screening at the time of diagnosis were included (Fig. 1 ). All subjects were enrolled after providing informed consent. Then, two groups were retrospectively formed according to the presence (case) or not (control) of anti-Ro52 antibodies at diagnosis. An unbiased 1:1 matching on CTD types was performed.
Data collection and definition A standardized case report form captured demographic, clinical and laboratory features at the time of CTD diagnosis, 6 months after initial evaluation and at the time of the last follow-up. Specific treatments and relapses were also recorded. ILD presence at CTD diagnosis was defined by the identification of ILD signs on high-resolution computerized tomography (HRCT) interpreted by thoracic radiologists. HRCT patterns of ILD were determined based on conclusions of radiologists and/or clinicians in medical records. ILD severity at CTD diagnosis was assessed by NYHA dyspnea classification, pulmonary function testsforced vital capacity (FVC), forced expiratory volume in the first second (FEV1) and diffusing capacity of the lung for carbon monoxide (DLCO) predicted values percentagesand 6 min walk test (6MWT).
The table of inertia determined the number of axes to be retained. The hierarchical cluster analysis was performed on the number of dimensions retained in the MCA. The semi-partial R-square and the cubic clustering criterion were used to define the number of clusters to be selected. A description of the clusters was carried out to define profiles for each of them. Alpha risk was 5% for all analysis. Statistical analyses were performed using SAS 9. 4 software (SAS Institute).
Hierarchical clustering analysis in CTD patients with anti-Ro52 antibodies Twenty-eight binary variables were selected for hierarchical clustering analysis according to their clinical relevance. One hundred and four anti-Ro52 positive CTD patients with complete data for the 28 selected variables were included for the MCA. We performed MCA on the first 4 dimensions (cumulatively explaining 40. 3% of the variance; online supplementary Fig. 1 ) and then hierarchical clustering to identify clusters (Fig. 2 ). The hierarchical tree suggested a partition into 6 clusters. Twenty-two variables were discriminant for the hierarchical cluster analysis. Patients' characteristics among the 6 identified clusters were described in online supplementary Table  2. In the first cluster, patients were older at the time of diagnosis and no muscular involvement was reported.
To standardize anti-Ro52 antibodies detection in all centers, we only included CTD patients, for whom an immunoblot technique was used, resulting in an obvious selection bias towards CTD with muscular manifestations. The association of anti-Ro52 antibodies with vascular manifestations, more relapses and more immunosuppressive drugs used were lost in multivariate analysis, thus we cannot exclude potential confounders. In our cohort, data was collected retrospectively according to defined   precise evaluation points (time of diagnosis, 6 months after initial evaluation) for appropriate comparisons of functional NYHA class and pulmonary function tests data. This resulted in some missing data. Immunoblot technique lacks inter-test reproducibility and false positive results are common  [31]. However, the prevalence of anti-Ro52 antibodies in CTD was very similar in previous studies  [32].
Materials and methods: The institutional review board approved this retrospective study conducted on 138 women from the population of a previous prospective multicenter study, with 69 consecutive patients with benign or high-risk lesions and 69 randomized patients with breast cancer, all confirmed at pathology. Four radiologists (two senior and two junior) blinded to the clinical, mammographic and pathological data independently reviewed the MLO DM-DBT views, the CC DM-DBT views and the MLO + CC DM-DBT views using the American College of Radiology Breast Imaging-Reporting and Data System criteria for index lesion characterization. Areas under the receiver were calculated and compared for each reader and imaging protocol. Results: No significant differences in breast cancer characterization were observed between single MLO and CC views for all the readers.
The added value of a second view was statistically significant for characterization in pooled data and for junior readers but not for senior readers (p ranging from 0. 15 to 0. 57 depending on the view and the senior reader). Finally, in 4 breast cancer cases, lesions were only detectable on the CC DM-DBT view in two cases and on the MLO DM-DBT view in the two other cases. Conclusion: Our results support the use of two-view DM-DBT for breast lesion characterization when the readers are inexperienced. There is no significant difference between CC and MLO views when diagnosis is performed with one view.
Patient population A prospective multicentric research project focused on assessing the value of DBT in breast cancer diagnosis and staging was conducted between May 2012 and May 2014 among 424 women from seven different French institutions. These women were over 40 years old, with lesions categorized as Breast Imaging Reporting and Data Systems (BI-RADS) 4 or 5 lesions and no previous breast surgery history. Fifty-eight of the patients had been included in a previously published study on local tumor staging  [19, 20]. The suspected breast lesions were diagnosed on the basis of mammographic and/or DBT, ultrasound (US) or MRI findings obtained during the diagnostic or screening examinations. Exclusion criteria were women with previous breast surgery, highrisk women included in an MRI breast cancer screening program, pregnant women and those unwilling to give consent.
Bilateral DM and DBT images were performed in both CC and MLO views. Lesions were diagnosed by pathologic assessment of imageguided biopsies. In patients with benign lesions, a follow-up of at least 1 year without progression of the lesion was included in the protocol. We retrospectively excluded patients with incomplete data (missing DBT or DM views or lost at follow-up) and those whose data could not be anonymized upon inclusion. Among the patients of the current study, all women with benign lesions -including high-risk or B3 lesions composed of atypical ductal hyperplasia, lobular neoplasia (including the subcategories lobular carcinoma in situ and atypical lobular hyperplasia), flat epithelial atypia, radial scar and papillary lesions, and phyllode tumor  [21]  -were eventually analyzed (69 patients) and 69 other patients with breast cancer were randomized in order to match the number of benign cases (Fig.
00-0. 20 indicating poor agreement; 0. 21-0. 40, fair agreement; 0. 41-0. 60, moderate agreement; 0. 61-0. 80, substantial agreement; and 0. 81-1. 00, almost perfect agreement. Statistical significance was set at p ≤ 0. 05. Analyses were performed using SAS version 9. 4 (SAS Institute, Cary, NC, USA).
As the quasi-3D format of DBT reduces the confounding effect of tissue overlap, malignancy should always be a diagnostic consideration for abnormalities that are only or more visible on one-view DBT  [26]. Our study had some limitations. First, synthetic 2D images were not available since the generation of such images reconstructed from DBT data has only become technically possible after completion of our data collection. These images could have allowed comparison of DBT views without DM. The fact that our study relied on the combination of DBT and DM for each projection prevented us from specifically assessing the performances of DBT alone. Second, a selection bias was likely induced by the readers being aware that there were only a few normal exams due to the inclusion criteria, while the interpretation of the DM-DBT view could have produced distorted ROC results.
This bias was nevertheless equivalent for all modalities, thereby minimizing its impact on our primary outcome. Finally, our data were derived from a single DBT vendor and the DBT images were acquired with a narrow sweep angle (15 • ). Consequently, our results cannot be applicable to other DBT manufacturers, particularly to those that acquire images with a wider acquisition angle, because of the impact of the angular range on the visualization of calcifications, masses, and architectural distortion  [32]. In conclusion, our results support the use of two-view digital breast tomosynthesis for the characterization of breast lesions, particularly when the readers are inexperienced. Moreover, in about 5% of the cases, abnormality could only be identified on one of the two DM-DBT projections. No significant differences were observed between CC and MLO views when a single view was performed for diagnosis.
Purpose: To describe the sociodemographic, medical and management characteristics of patients using intravitreal (IVT) anti-vascular endothelial growth factors (VEGF) in France. Methods: An observational study was conducted in patients treated with IVT ranibizumab or aflibercept, aged 18 years or older using the French National Health Insurance Databases covering 99% of the French population. Patients currently treated in 2018 were included in a cross-sectional approach to describe treatment history over the previous 6 years. Patients newly treated between 2014 and 2018 were included in a longitudinal approach to describe treatment management during up to 6 years of follow-up. Sociodemographic characteristics and medical history were described in both populations. The analyses were performed at the patient level, as no distinction between the eyes could be made.
e. one monthly injection for three consecutive months) followed by a flexible maintenance regimen for ranibizumab or for aflibercept via (i) a bimonthly injection, the rest of the first year, and (ii) a flexible maintenance regimen protocol, after the first year. A loading phase of 5 months is recommended for the initial treatment of DME with aflibercept. For myopic CNV, less frequent injections might be sufficient  (European Medicine Agency 2009 , 2012; Sayanagi et al. 2019). In practice, the wide variability in patient response to IVT anti-VEGF and the clinical burden may lead to the development of alternative injection strategies to reduce the number of injections needed to maintain or improve visual acuity  (Fung et al. 2007; Oubraham et al. 2011; Semoun et al. 2017). This study, conducted on almost the entire French population using national medico-administrative databases, aimed to describe the characteristics and management modalities of patients treated with IVT anti-VEGF (i) in a crosssectional manner among patients currently treated in 2018 benefiting from a 6-year history and (ii) prospectively among patients newly treated between 2014 and 2018, followed up to 6 years.
Data source The French National Health Insurance Databases ("Syst eme National des Donn ees de Sant e"-SNDS) were used to identify patients with IVT anti-VEGF dispensations between 01-01-2012 and 12-31-2018. The SNDS contains anonymous and individual data on all reimbursed health expenses for 99% of the French population (i. e. over 66 million inhabitants), including medicines (Anatomical Therapeutic Classification-ATC codes), outpatient medical and nursing care prescribed or performed by healthcare professionals, and out-of-hospital laboratory tests (without results). Medical indications for outpatient reimbursements are not available, but the patient's status for 100% reimbursement for care related to a serious and costly long-term disease (e. g. cardiovascular diseases, diabetes, cancer etc.
) is recorded and coded according to International Classification of Diseases, 10th revision-ICD-10, along with the date of the onset of the disease. The SNDS also contains sociodemographic data such as age, sex, area of residence (ZIP code), affiliation to complementary universal health insurance, corresponding to free access to healthcare for people with an annual income <50% of the poverty threshold (attributed to 5. 6 million inhabitants under 65 years of age) and deprivation index, corresponding to an index of the participant's area of residence calculated from socio-economic data  (Rey et al. 2009 ). This information is chain-linked via a unique and anonymous individual identifier to the national hospital database, which covers all admissions and discharges from public and private hospitals and contains information about hospitalization stays: admission and discharge dates, ICD-10 coded diagnoses, care and surgical procedures, expensive drugs or medical devices provided.
Study populations and observation periods Patients aged 18 years or older who received at least one IVT anti-VEGF (i. e. pegaptanib-ATC code S01LA03, ranibizumab-S01LA04, aflibercept-S01LA05, bevacizumab-L01XC07) dispensation between 01-01-2012 and 12-31-2018 were initially identified using the SNDS databases. Intravitreal (IVT) bevacizumab users were not included because this drug is rarely prescribed (e. g. 158 patients treated in 2018) and used only in hospitals in France.
Statistical analysis The analyses were conducted at the patient level, as no distinction between the eyes could be made. The data were analysed descriptively. Qualitative variables were summed up using effectives and percentages in each category and quantitative variables by mean (standard deviation) or median (interquartile range). For newly treated patients, characteristics related to IVT anti-VEGF use during follow-up were first evaluated in the total sample of initiators. Sensitivity analyses were conducted to assess potential differences according to the molecule initiated and the year of initiation. Additional sensitivity analyses were conducted (i) to exclude patients with only one dispensation during follow-up when describing treatment interruptions and (ii) to assess possible variations in the number of IVT anti-VEGF dispensations and eye monitoring examinations according to the occurrence of a treatment interruption during the first year.
Finally, a sub-analysis was conducted among newly treated patients to assess sociodemographic and management characteristics according to likely or possible treatment indications. For patients who had multiple episodes of IVT anti-VEGF initiation during the study period, only the first episode was considered in analyses summarizing the results for the entire study period. Descriptions in the second year of treatment were made among patients with at least two years of follow-up. The data were computed using SAS guide version 7. 15.
In fact, pro-active strategies, which generally induce more injections in real-world conditions  (Oubraham et al. 2011 ) than reactive strategies, are most often considered the therapeutic regimen of choice by learned societies  (Hufendiek et al. 2018). Several recent observational studies on the use of IVT anti-VEGF for the treatment of nAMD in other countries, based on large databases, have been published. Among 30 106 patients newly treated with IVT anti-VEGF between 2009 and 2016 recorded in the US Retina electronic database, the mean number of injections was 6. 0 in the first year and 4. 9 in the second year  (Kiss et al. 2020 ). Among 8328 patients registered in the Swedish Macular Registry, newly treated with IVT anti-VEGF between 2012 and 2014, the mean number of injections at 12 months was 6.
All IVT anti-VEGF dispensations are registered in the SNDS database and the dispensing date is a good approximation of the injection date (the median duration between dispensing and injection dates was 5 days, results not shown) because of specific protocols required in France e509 for the prescription and dispensing of these costly molecules. This study also has several limitations. First, this study did not aim to describe management characteristics according to IVT anti-VEGF indication, as this information was not directly available in the databases. Although significant efforts were made to estimate the likely or possible indications of IVT anti-VEGF treatments, some misclassification cannot be excluded. Nevertheless, nAMD is the most frequent indication and the overall results largely reflect the management of this disease.
Second, these data do not enable to distinguish the IVT anti-VEGF dispensations related to each treated eye, which may have led to an overestimation of the number of injections per treated eye and an underestimation of the intervals between injections per treated eye in the case of bilateral disease with staggered treated eyes. In our study, about 16% of newly treated patients had received more than one unitary box within a timeframe of 3 weeks several times during the first two years (results not shown). This indicator, which could help to estimate the proportion of patients with bilateral disease, suggests that this would only concern a minority of newly treated patients, at least in the first two years of treatment. Third, the SNDS databases are lacking in clinical data to identify potential outcome factors (e.
Projected Leaf Area and SC The projected leaf area (PLA) of a photographed rosette was determined using the software ImageJ  (Schneider et al. , 2012). Five plants per genotype and treatment were followed during the 15 days of experimentation. SC (mmol/m 2 /s) was measured using a leaf porometer (Model SC-1, Decagon Devices Inc. , Pullman, WA, USA). Measurements were taken daily after an illumination period of 5 h. Two measurements were taken per plant (i. e. , two leaves per plant), and 10 plants per genotype and per condition were used.
In the atesl3. 03 mutant, the induction of AtESL3. 07 expression took place later than in Col-0 in the SD phase instead of the MD phase. In atesl3. 07/esl1 mutant, the reduction of the expression of its tandem gene AtESL3. 08/ERD6 was emphasized during the EM phase. In the atesl3. 05/esl3 mutant, no significant differences in the expression of AtESL genes were found when compared to those of the wild genotype. To determine whether the content of soluble sugars was affected in the mutant lines, glucose, fructose, and sucrose contents were measured in the leaves of WW, WD, and RW plants. No differences in sugar content could be detected in atesl3. 03, atesl3. 05/esl3, and atesl3. 07/esl1 mutants as well as for fructose (data not shown) and sucrose content in the mutant atesl1. 02/erdl6 (Supplementary Figure  4 ).
08/ERD6 were evolving in opposite ways. In fact, the gene expression data analysis from Genevestigator databases showed that ESL3. 07/ESL1 is highly induced by ABA treatment, whereas ESL3. 08/ERD6 is strongly repressed. According to these data,  Yamada et al. (2010)  have shown that the expression of ESL3. 08/ERD6 is reduced in leaves and roots after ABA treatment. These results corroborate the idea of a differential regulation by ABA and water deficit of these two tandem duplicated genes and highlight the possible mechanisms of sub-functionalization. In the SD phase (WC from 90 to 86%), although FW and PLA decreased, TW stayed stable and DW still increased as in WW plants (Figure  2 ). The osmotic pressure (Table  1 ) rose in parallel with a strong increase of glucose and sucrose content (Figure  4 ).