dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We are grateful to  S. Jørgensen  and  C. Colding  for assistance in the early stages of the project and to  Yasuko Antoku  and  Kasper Nørskov Kragh  for immunofluorescence analysis assistance. We thank  Ursula Sauder  and  Vesna Oliveri  for electron microscopy expert technical assistance. We thank  Brian Larsen  for his help in Comet assay and  Heike Ilona Rösner  for useful scientific discussions and advice. We also thank  Sung-Bao Lee  for help in setting up MNase assay. We thank  Montpellier Ressources Imagerie  ( MRI ) for assistance with FLIM-FRET microscopy. C. S. S. , M. S. , and D. W. are funded by The  Novo Nordisk Foundation  (to C. S. S. ), The  Danish Cancer Society  (to C. S. S. ), The  Lundbeck Foundation  (to C. S. S. ), and The  Danish Medical Research Council  (to C.
S. S. ),  Swiss National Science Foundation  (to D. W. ), and  Villum Foundation  (to M. S. ). B. F. is funded by  FNRS Belgium  and P. J. G. and J. J. B. are funded by  Cancer Research UK  (grant  C303/ A14301 ). F. I. and E. J. were supported by grants from  French Plan-Cancer  ( EPIG2013-13 ),  Labex EpiGenMed , and  SIRIC Montpellier Cancer. F. I. was supported by a PhD fellowship from the  French Ligue Contre le Cancer and Fondation pour la Recherche Médicale. D. L. was supported by a  Cancéropole GSO-Emergence  grant ( 2014-E17 ) and  CNRS.
The existence of other acquired resistance mechanisms has not been studied in these patients. The AURA 3 clinical trial  [43]  compared osimertinib vs. platinum-based chemotherapy plus pemetrexed in patients with EGFR p. Thr790Met mutated tumors who had disease progression after first generation EGFR-TKI. The median PFS was significantly longer with osimertinib compared to chemotherapy (10. 1 vs. 4. 4 months, respectively) and the ORR was also increased (71% vs. 31%). Osimertinib is now recommended as second line therapy for patients with EGFR p. Thr790Met mutated tumors. To confirm the efficacy of osimertinib as a second line treatment, the ASTRIS phase III clinical trial (NCT02474355) is currently in progress and includes patients with advanced or metastatic EGFR p. Thr790Met mutation-positive NSCLC that have progressed after treatment with EGFR-TKIs therapy.
Osimertinib is now recommended as second line therapy for patients with EGFR p. Thr790Met mutated tumors. To confirm the efficacy of osimertinib as a second line treatment, the ASTRIS phase III clinical trial (NCT02474355) is currently in progress and includes patients with advanced or metastatic EGFR p. Thr790Met mutation-positive NSCLC that have progressed after treatment with EGFR-TKIs therapy. Unfortunately, as described for the other EGFR-TKIs, resistances to osimertinib ultimately develop after a median PFS of 9. 6 months  [42]. Mechanisms involved in this resistance are not fully understood and appeared to be as heterogeneous as those described for first and second-generation EGFR-TKIs. Osimertinib resistance can be divided into EGFR dependent and EGFR independent mechanisms. The first resistance mechanism identified in patients was the tertiary EGFR mutation p.
The ASCEND-4 phase III clinical trial compared ceritinib vs. platinum-based chemotherapy for first-line therapy of ALK-rearranged NSCLC. The median PFS was significantly increased in the ceritinib group compared with chemotherapy group (16. 6 vs. 8. 1 months, respectively)  [51]. Moreover, ceritinib significantly improves PFS of patients with crizotinib-refractory ALK-rearranged NSCLC  [69]. In the same way, the 12-month event-free survival rate was significantly increased with alectinib compared with crizotinib in the first line treatment of ALK-rearranged NSCLC (68. 4% vs. 48. 7%, respectively). Unlike crizotinib and ceritinib, alectinib is also effective in central nervous system progression  [70]. Lorlatinib is the third-generation ALK and ROS1 inhibitor. A phase-3 clinical trial (NCT03052608) is now recruiting patients to compare lorlatinib and crizotinib in the first line treatment of advanced ALK-rearranged NSCLC.
Then, NGS data can be included in the molecular report. What can we expect from NGS data? We recently showed in a large series of lung cancer patients that besides allowing the identification of EGFR, KRAS, and BRAF mutations, NGS identified a potential driver in 36% of patients (FGFR, ERBB2, AKT, MAP2K1, STK11. )  [14, [94] [95] [96]. Numerous experimental drugs are under development  [97] , and a large molecular characterization could be mandatory in the coming years. Many different panels are being developed, including more genes, tumor mutation load (TML), MSI status determination, and fusions. These comprehensive panels will bring answers and questions. Large NGS panels drive more information and more questions when variants of unknown significance VUS, of unknown predictive value, of predictive value in another cancer type are identified in genes that are potential driver  [98].
The link between detection and clinics is not always easy, however international databases help to provide information for each variant identified, combining the functional effect on proteins and response to treatment. Methods for high-throughput functional evaluation are being developed and could offer a fast and accurate improvement for data interpretation  [99]. The increase in the number of genes in panels raises different problems-technical issues: panel validation, quality assessment and quality control may be tough; clinical issues: the management of VUS, the comprehensive analysis of network of mutations, and the management of incidental findings. Notably, it is now possible to perform a somatic exome in clinical routine. Genetic counseling should be mandatory before somatic exome sequencing in patients with lung cancer so patients may be advised on the possibility of incidental findings and the options for future management and eventually family planning (Figure  2 ).
patients. If NGS provides a wider analysis, results are available within a week. To shorten delays for hotspot alterations, prescreening with mutant specific probes can be part of the testing pipeline in order to provide a quick answer for first line treatment. Then, NGS data can be included in the molecular report. What can we expect from NGS data? We recently showed in a large series of lung cancer patients that besides allowing the identification of EGFR, KRAS, and BRAF mutations, NGS identified a potential driver in 36% of patients (FGFR, ERBB2, AKT, MAP2K1, STK11…)  [14, [94] [95] [96]. Numerous experimental drugs are under development  [97] , and a large molecular characterization could be mandatory in the coming years. Many different panels are being developed, including more genes, tumor mutation load (TML), MSI status determination, and fusions.
These comprehensive panels will bring answers and questions. Large NGS panels drive more information and more questions when variants of unknown significance VUS, of unknown predictive value, of predictive value in another cancer type are identified in genes that are potential driver  [98]. The link between detection and clinics is not always easy, however international databases help to provide information for each variant identified, combining the functional effect on proteins and response to treatment. Methods for high-throughput functional evaluation are being developed and could offer a fast and accurate improvement for data interpretation  [99]. The increase in the number of genes in panels raises different problems-technical issues: panel validation, quality assessment and quality control may be tough; clinical issues: the management of VUS, the comprehensive analysis of network of mutations, and the management of incidental findings.
The records were also reviewed for epidemiologic data and clinical presentation. The laboratory tests at diagnosis were collected, before any treatment, including the lymphocyte count (number/mm 3 ) and platelet count (number/mm 3 ). We calculated the PLR by dividing the absolute count of platelets to that of lymphocytes at diagnosis (when both expressed in number/mm 3 ). All patients were classified according to the Binet system at diagnosis. For all patients, three survival end points were defined. First, duration of watchful waiting was defined as the time from diagnosis until the start of chemotherapy or death. Second, postdiagnosis survival (or overall survival [OS]) was defined as the duration from diagnosis until death. Third, postchemotherapy survival was defined as the duration from the start of chemotherapy until death.
All three end points were reported in number of days. Patients who were lost to follow-up or who did not suffer any of the events for a given end point at last follow-up were censored for that end point. Continuous variables were summarized by their medians and ranges. Categorical variables were summarized by number and percentage of patients within each category. SPSS Statistics version 20. 0 (IBM Corporation, NY, USA) and XlStat version 2017. 1 (Addinsoft, Paris, France) were used for statistical analysis. All continuous variables were analyzed as such and not categorized. Univariable Cox regression models were computed while considering duration of watchful waiting, postdiagnosis survival and postchemotherapy survival as dependent variables, and demographic, laboratory and disease characteristics as independent variables.
Results • The data of 100 patients with CLL were reviewed for this study. • The PLR correlated only to watchful waiting in the univariable analysis (HR = 0. 48 [0. 32-0. 73]; p = 0. 018). • In the multivariable analysis, the duration of watchful waiting was determined by Binet staging and lymphocyte count (p < 0. 001). • The postdiagnosis survival was determined by age (p = 0. 002) and lymphocyte count (p = 0. 010). • The postchemotherapy survival was found to be solely determined by age (HRa = 1. 13 [1. 04-1. 22]; p = 0. 003). • However, both postdiagnosis survival and postchemotherapy survival were not found to be related to PLR.
The nearby Herbig Be star HD 100546 is known to be a laboratory for the study of protoplanets and their relation with the circumstellar disk, that is carved by at least two gaps. We observed the HD 100546 environment with high contrast imaging exploiting several different observing modes of SPHERE, including data sets with/without coronagraphs, dual band imaging, integral field spectroscopy and polarimetry. The picture emerging from these different data sets is complex. Flux-conservative algorithms images clearly show the disk up to 200 au. More aggressive algorithms reveal several rings and warped arms that are seen overlapping the main disk. The bright parts of this ring are found out to lie at considerable height over the disk mid-plane at about 30 au. Our images demonstrate that the brightest wings close to the star in the near side of the disk are a unique structure, corresponding to the outer edge of the intermediate disk at ∼ 40 au.
(2017) ;  Rameau et al. (2017) ;  Currie et al. (2017) , all based on GPI data sets, debate on the presence of both the planets and the impact of the reduction methods on them. HD 100546 is located in the Sco-Cen complex. In this analysis we consider a stellar mass of M * =2. 4M  (Brittain et al. 2014) , and apparent magnitudes of J=6. 42, H=5. 96, and K=5. 42  (Cutri et al. 2003) , as well as L =4. 52 and M =4. 13 as in  Quanz et al. (2015). For the disk, we assume an inclination i=42 •  (Ardila et al. 2007; Pineda et al. 2014)  and P A=146 •  (Pineda et al. 2014). In this paper, we present the results of a two year observational campaign on this star, based on observations in direct imaging with VLT/SPHERE, the new high-contrast and high-resolution instrument dedicated to exoplanet and disk imaging, that includes both pupil tracking and polarimetric observations.
2014) , and Principal Component Analysis (PCA,  Soummer et al. 2012; Amara & Quanz 2012). These procedures are available at the SPHERE DC through the SpeCal software  (Galicher et al. 2018). For IFS, the cADI is based on a median combination of the images, while the PCA is evaluated on the whole image at the same time; no exclusion zones are considered. For IRDIS, no spatial filtering was applied to the data beforehand. We performed several reduction and, verified that both disk and wide companions (see Appendix A) are detected using the alternate methods. We also confirm that these detections are robust across a range of algorithm parameter space (e. g. varying numbers of principal components from 2 to 5). In classical ADI, SpeCal averages the cube of frames over the angular dimension for each spectral channel to remove the speckle contamination.
The resulting RDI images are shown in Fig. 9. The residuals clearly show the presence of the two wings, that are even more evident when applying to this model the ADI method. To show this, we constructed a data cube (x, y, lambda, time) made of the sum of the disk model and of the reference image used in our RDI analysis, that is the data set of HD 95086. This datacube was then processed by the same ADI routine used for the original HD 100546 datacube. In this case, the two bright wings visible in all the images in Fig. 3  can be reproduced only by assuming a much thicker disk, with a value of H ∼ 30 au at r ∼ 40 au. This is because the bright wings visible in the ADI images, that correspond to the edge of the disk, are described by an ellipse whose center is far from the star. A similar result has been found for several disks, a classical example being HD 97048  (Ginski et al.
Detection limits Two candidate companions around HD 100546 have been proposed over the years  (Quanz et al. 2013; Brittain et al. 2014; Quanz et al. 2015; Currie et al. 2015). We investigated IFS and IRDIS images to find signatures of the already proposed candidate companions or new signatures. None of the IFS images shows evidence of new candidate companions above threshold while in the IRDIS images seven objects were identified as background stars (see Appendix A). To properly discuss our data, we should consider the detection limits for point sources on our data. The IRDIS 5σ detection limits for point sources were obtained through the SpeCal software  (Galicher et al. 2018 ): it estimates the noise level σ as the azimuthal standard deviation of the flux in the reduced image inside FWHM/2 wide annuli at increasing separations, and rescales it as function of the stellar flux derived from the off-axis PSF images, taking into account the transmission of the neutral density filter used to avoid the star image saturation.
g. monochromatic PCA with low number of modes) is more suitable. We considered the HD 95086 data set mentioned above to show what will be the expected contrast limit in absence of the disk (red dash-dotted line in Fig. 10  In this Figure, we also show the H magnitudes of the two candidate companions around HD 100546 from  Currie et al. (2015)  using GPI: the impact of the disk on the contrast limit for IFS images is not negligible at separation of both CCc (∼ 2. 2 mag) and CCb (∼ 1. 5 mag). We note here that CCc with a contrast of 7. 12 mag should be nominally visible in the IFS May 2015 and May 2016 data sets, where the contrast limits at the candidate separation are 7. 3 mag and 7. 8 mag, respectively. CCb (∆H = 13. 44, r ∼ 0. 47 ), instead, is below the detection limit in the H band. However it would be above the detection limit if we consider the limits applicable to a star without a luminous disk.
CCc No obvious point-like structure is visible at the expected position of CCc in any of our IFS and IRDIS data sets  in all epochs. Using a different reduction approach,  Garufi et al. (2016)  identified a bright knot in the SE arm (r ∼ 0. 120 ± 0. 016 , P A ∼ 165 ± 6 • ) at least in H band for the May 2015 data. On one hand, one could try to associate CCc with this knot, as it may lie at/just inside the disk cavity and is counterclockwise from the position noted by  Currie et al. (2015) , as expected for an orbiting object predicted from  Brittain et al. (2013). On the other hand, these results do not establish CCc as a companion since there are equally compelling alternatives. We detect bright, elongated emission at a similar location in all our IFS and IRDIS H2H3 data set, suggesting confusion between bright disk emission and that of any point source.
In the following discussion we use a not aggressive monochromatic PCA approach with only one component over the whole IFS FoV simultaneously, and over the inner circle of 0. 8 for IRDIS one. Moreover, we exploit the very wide spectral range simultaneously offered by the SPHERE IRDIFS_EXT set up (from 0. 95 up to 2. 2 µm). All IRDIS K1K2 datas ets show a clear diffuse emission on top of the Northern wing (as already noticed by  Garufi et al. 2016  for the 2015 data sets) that is compatible with the CCb detections in L and M band using NACO. In order to obtain a more precise characterization of this feature, we focused on the two best IRDIFS_EXT data sets and we found out that the position of this source varies a little between the two epochs, as shown in Table  2. From the disk velocity retrieved from spectroastrometric analysis of different molecules (see e.
2015)  and located at about 28 mas (∼ 0. 7λ/D) from the expected position of the source detected at longer wavelengths. trast limits in the corresponding area of CCb, while in the H2H3 filter we only detect a very weak diffuse emission at its location; (b) what we see in the IRDIS data at positions corresponding to CCb could be simply a bright structure of the disk; (c) we are not subtracting the disk contribution to the flux. Similar to what discussed above, the self subtraction on extended sources is not negligible even with this not aggressive reduction method and it is difficult to estimate because it depends on the specific distribution of light than cannot be easily modelled. This implies that the ADI technique alters the photometry of the extended object. What we can conclude is simply that the structure seen in our K1K2 images is compatible with an extended object whose apparent magnitude is brighter than what is expected for a point source at the same location and is com-patible, within the uncertainties, with the flux observed at longer wavelengths.
Acknowledgements. The authors thank the anonymous referee for a very constructive referee report that improved the initial manuscript. The authors thank the  ESO Paranal Staff  for support for conducting the observations. The authors thank  Sascha Quanz ,  Adriana Pohl  and  Tomas Stolker  for the very useful comments that improved a lot the quality of the paper. E. S. , R. G. , D. M. , S. D. and  R. U. C. acknowledge support from the  "Progetti Premiali" funding scheme of the Italian Ministry of Education, University, and Research. E. R. is supported by the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Skłodowska-Curie  grant agreement No  664931. This work has been supported by the project  PRIN-INAF 2016 The Cradle of Life -GENESIS-SKA (General Conditions in Early Planetary Systems  for the rise of life with SKA).
The authors acknowledge financial support from the  Programme National de Planétologie (PNP)  and the  Programme National de Physique Stellaire (PNPS)  of  CNRS-INSU. This work has also been supported by a grant from the  French Labex OSUG@2020  (Investissements d'avenir - ANR10 LABX56 ). The project is supported by  CNRS , by the  Agence Nationale de la Recherche  ( ANR-14-CE33-0018 ). This work is partly based on data products produced at the  SPHERE Data Centre hosted at OSUG/IPAG, Grenoble. We thank  P. Delorme  and  E. Lagadec  ( SPHERE Data Centre ) for their efficient help during the data reduction process. SPHERE is an instrument designed and built by a consortium consisting of  IPAG (Grenoble, France ),  MPIA (Heidelberg, Germany) ,  LAM (Marseille, France), LESIA (Paris, France), Laboratoire Lagrange (Nice, France), INAF Osservatorio Astronomico di Padova (Italy) ,  Observatoire de Genève (Switzerland) ,  ETH Zurich (Switzerland) ,  NOVA (Netherlands) ,  ONERA (France)  and  ASTRON (Netherlands)  in collaboration with  ESO.
Introduction: Gastric Carcinoid Tumors (GCT) are very rare in general population, but some studies evidenced a higher incidence among bariatric surgery patients. Laparoscopic Sleeve Gastrectomy (LSG) is a widely accepted procedure for the surgical treatment of morbid obesity. LSG acts both in reducing food intake and interfering with hormonal balance in the gut-brain axis. In these patients, incidental GCT diagnosis can occur both during pre-bariatric surgery investigation and during post-operative follow-up. Methods: We retrospectively analyzed the database of obesity patients submitted to LSG in two different centers to find out incidence of GCT in patients treated by surgery from May 2013 to March 2018. Results: From the 560 obese consecutive patients underwent LSG, we recorded two cases of patients with GCT (0.
Methods We retrospectively analyzed the database of obesity patients submitted to LSG in two different centers (Surgical Obesity Center (CCO), Clinique Saint Michel, Toulon, France, and Surgical Division of University of L'Aquila) to find out incidence of GCT in patients treated by surgery from May 2013 to March 2018. Indications and pre-intervention procedures in bariatric surgery patients followed the Guidelines of American Society for Metabolic and Bariatric Surgery  [5]. This study has been registered on the Research Registry with the Unique Identifying Number 4149.
When evaluating new therapeutic strategies, it is important to weigh the risk and benefit for high-risk patients, such as those with visceral organ metastases. To this end, we carried out prespecified analyses in the phase III PALOMA-3 and PALOMA-2 studies and compared the efficacy and safety of palbociclib plus ET in patients with visceral versus nonvisceral metastases. These studies enrolled patients with varying degrees of ET responsiveness: premenopausal and postmenopausal women with resistance to prior ET in PALOMA-3, and postmenopausal women still treatment naive for advanced disease in PALOMA-2. Because the prevalence of visceral involvement is higher in patients who progressed on prior ET compared with patients naive to ET in the ABC setting, we first analyzed the PALOMA-3 data and then carried out the same analyses for PALOMA-2.
Patients and study designs This analysis includes data from the phase III PALOMA-2 and PALOMA-3 trials. Patients with symptomatic visceral spread who were at risk of life-threatening complications were excluded from both studies  [12, 13]. Patients remained on treatment until disease progression, unacceptable toxicity, or consent withdrawal  [12, 13]. Detailed descriptions of study methodology have been described elsewhere  [12, 13] , and are highlighted in further detail in supplementary Table  S1 , available at Annals of Oncology online. Both studies were approved by institutional review boards or ethics committees at participating sites and carried out in accordance with the International Harmonisation Good Clinical Practice guidelines and provisions of the Declaration of Helsinki.