dataesr/scientific-paragraphs-categorization huggingface dataset:
identification of cancer-specific genes and 3) estimation of the prognostic value of each gene. The Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset15  , which constitutes 1230 cases of clinically annotated ER+ luminal breast cancer patients with long-term survival information, was used to investigate the prognostication potential of the DHT-induced gene set. Analyses were performed in R using survival and SigCheck. Statistical analyses were performed by Kaplan-Meier log-rank, Kruskal-Wallis (pairwise comparisons), and survival p-value log-rank tests where appropriate. Immunohistochemistry. Standard immunohistochemical techniques were employed using the following primary antibodies: Ki67 (MIB-1, 1:400; DAKO #M7240); BrdU (BU209, 1:300; DAKO #M0744), AR (N-20, 1:1000, Santa Cruz #SC-816); ERα (1D5, 1:300; DAKO #M7047); GFP(7.
Acknowledgements. The authors thank  C. Hoffmann ,  N. Dean  and the teams supporting them for consenting and recruiting tissue donors; as well as tissue donors themselves. We also thank  A. Welm  for PDX model provision;  J. Robinson ,  M. Pickering ,  Z. Kikhtyak , and  N. Ryan  for experimental assistance; and our institutional animal care facilities and genomics cores. This work was supported by grants from the  National Health and Medical Research Council of Australia  (W. D. T, J. S. C. , T. E. H. , E. L. , L. A. S. , E. E. , S. N. B. , C. P. , A. S. ; ID 1084416, ID 1130077; K. M. C; ID 1093801), the  National Breast Cancer Foundation  (NBCF; W. D. T. ;  ID PS-15-041; C. E. C. ; ID ECF-17-002 ) and a  Movember and National Breast Cancer Foundation Collaboration Initiative  grant ( MNBCF-17-012  to W.
2 ) 2 identification of cancer-specific genes and 3) estimation of the prognostic value of each gene. The Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset15  , which constitutes 1230 cases of clinically annotated ER+ luminal breast cancer patients with long-term survival information, was used to investigate the prognostication potential of the DHT-induced gene set. Analyses were performed in R using survival and SigCheck. Statistical analyses were performed by Kaplan-Meier log-rank, Kruskal-Wallis (pairwise comparisons), and survival p-value log-rank tests where appropriate. Immunohistochemistry. Standard immunohistochemical techniques were employed using the following primary antibodies: Ki67 (MIB-1, 1:400; DAKO #M7240); BrdU (BU209, 1:300; DAKO #M0744), AR (N-20, 1:1000, Santa Cruz #SC-816); ERα (1D5, 1:300; DAKO #M7047); GFP(7.
1 ). The displayed average is refreshed on the screen every 4 s. The CI value measured in this way will hereafter be called "CI Starling-24. 4 ". We also extracted raw data from our recordings by the Starling device. In a post-hoc analysis, we changed the averaging time to 8 s, instead of 24. This duration was the shortest possible time that could be achieved, according to the technological limitations of the currently available device. We judged this interval as appropriate for estimating the effects of the 15-s EEXPO. The refreshing delay was reduced to one second, instead of 4. The CI value obtained in this way will be called "CI Starling 8. 1 " (Fig. 1 ).
Transpulmonary thermodilution and pulse contour analysis measurements The PiCCO2 device measures CI through transpulmonary thermodilution, which is performed by injecting three 15-mL boluses of cold saline in the superior vena cava  [19, 20] , and through pulse contour analysis (CI pulse ), which is calibrated by transpulmonary thermodilution  [21]. The value of CI pulse provided by pulse contour analysis is averaged over 12 s, with values that are refreshed every second. CI pulse was continuously recorded by the PiCCOWin software (Pulsion Medical Systems).
Other measurements In addition to arterial pressure, heart rate and CI, we measured central venous pressure at end-expiration. Respiratory variables such as positive end-expiratory pressure, plateau pressure, respiratory rate and tidal volume (Vt) were also collected. Intra-abdominal pressure was measured through the bladder pressure as previously described  [22]. Arterial, central venous and airway pressures were continuously recorded by data acquisition software (HEM-3. 5, Notocord, Croissy-sur-Seine, France).
Statistical analysis Based on a previous study by our group  [11] , to detect an increase in CI of at least 5% measured by the Starling device, expecting a baseline value of 3. 1 L/min/m 2 , we estimated that 42 pairs of measurements were required. This assessment was performed taking into account an α risk of 5% and a β risk of 20%, estimating that half of the patients would be preload responders. The minimal change of 5% was chosen, because it corresponds to the best threshold of EEXPO-induced CI changes that detects preload responsiveness  [14]. It is compatible with the least significant change of CI pulse  [25]. Data are summarized as mean ± SD or median [interquartile range, IQR] as appropriate. The normality of distribution was evaluated visually. Pairwise comparisons of data were done with the paired Student's t test or Wilcoxon test.
∆CI Starling-24. 4 and ∆CI Starling-8. 1 , both for EEXPO and PLR. Radial limits of agreement < 30° are considered to indicate good trending ability. Statistical significance was set at a p value < 0. 05 and statistical analysis was performed with MedCalc software 19. 1 (Mariakerke, Belgium) and R 3. 5. 2 statistical software with lme4, MethodCompare and irr packages  [30].
Background: The feasibility of segmental resection for early-stage non-small cell lung cancer (NSCLC) is still controversial. This study aimed to compare survival outcomes following lobectomy and segmental resection in patients with pathological T1cN0M0 (tumor size 21-30 mm) NSCLC. Methods: Patients diagnosed between 1998 and 2016 with pathological stage IA NSCLC and with tumors measuring 21-30 mm were extracted from the Surveillance, Epidemiology, and End Results (SEER) database. The observational outcomes were cancer-specific survival (CSS) and overall survival (OS) at 5 years. Univariate survival analysis was carried out to identify potential prognostic factors of prolonged survival. Cox proportional hazards model was used to adjust for confounding factors. Additionally, pairwise comparisons were conducted between lobectomy and segmental resection for CSS and OS, and forest plots were drawn.
On the contrary, in a Surveillance, Epidemiology, and End Results (SEER) data analysis of patients with pathological stage I NSCLC, the subgroup analysis for tumors measuring 21-30 mm as defined under the 7th edition staging system (T1b) demonstrated that lobectomy was associated with significantly better OS  (10). Therefore, the optimal the extent of surgical resection for stage T1cN0M0 (>20-30 mm) NSCLC, as defined by the 8th edition staging proposal, is still unclear. In this study, we used data from the SEER database to evaluate whether lobectomy confers a survival advantage over anatomic segmental resection in patients with pathological T1cN0M0 (21-30 mm) NSCLC. And we present the following article in accordance with the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) reporting checklist (available at http://dx.
Patient selection Data of patients who underwent segmental resection (surgery of primary site code: 22) and lobectomy (surgery of primary site codes: 30 and 33) for primary lung cancer between 1998 and 2016 were obtained from the SEER 18 Regs Custom Data (with additional treatment fields). Patients aged <18 years, with additional synchronous malignancies, diagnosed with pulmonary neuroendocrine tumors or melanoma (i. e. , carcinoid, large cell neuroendocrine tumor, small cell lung cancer), who received neoadjuvant or intraoperative therapy, or who had incomplete clinicopathological or follow-up information, were excluded. In addition, since this study focused on patients with stage IA NSCLC with a tumor size of >20-30 mm,patients with nodal involvement, distant metastases, or a tumor size ≤20 mm or >30 mm were also excluded from the final analysis.
Ethical statement The study was conducted in accordance with the Declaration of Helsinki (as revised in 2013). This retrospective study based on the SEER database was approved by the Surveillance Research Program in National Cancer Institute's Division of Cancer Control and Population Sciences (DCCPS) (No. 12101-Nov2018), and was also approved by the institutional review at the Sun Yatsen University Cancer Center (No. B2018-011). Because of the retrospective nature of the research, the requirement for informed consent was waived.
graphpad. com/) and compared using the log-rank test. Subsequently, the potential prognostic factors (P<0. 05) for CSS and OS that were identified in the univariate analyses were included in the Cox proportional hazards models. Forest plots were drawn using the "forestplot" package in R software (version 3. 5. 3, https://www. r-project. org/). All statistical analyses were conducted with SPSS software (version 24, IBM, NY, USA; https://www. ibm. com/), with a two-sided P value <0. 05 set as the threshold for statistical significance.
Patient characteristics A total of 9,580 patients with stage IA NSCLC with a tumor size of 21-30 mm who met the inclusion criteria were identified from the SEER database. The clinicopathological variables of the lobectomy group (9,180, 95. 8%) and the segmental resection group (400, 4. 2%) were compared (Table  1 ). Segmental resections were more likely to be performed in patients with older age (≥60: 86. 5%), smaller tumor size (21-25 mm: 64. 8%), or left-sided tumors (48. 8%); moreover, segmental resections became more popular in the later part of the study period (2008-2016: 52. 5%). More lymph nodes were removed in the lobectomy group than in the segmental resection group (median: 8. 8 vs. 4. 4, P<0. 001). A higher proportion of patients in the segmental resection group received radiation after surgery (3.
Therefore, a number of studies have focused on comparing oncological outcomes between lobectomy and segmental resection but have excluded wedge resections for stage IA NSCLC  (2, 3, 9). A number of recent studies, which include retrospective propensity-score matched analyses and the SEER database analyses, have demonstrated that patients who undergo anatomical segmental resection may achieve outcomes comparable to those of patients who undergo lobectomy for stage IA NSCLC of ≤20 mm (2). However, there has been little research that has assessed the potential of segmental resection for stage IA NSCLC with tumors measuring >20-30 mm, perhaps because patients with cT1c (>20-30 mm) NSCLC have been reported to have a worse prognosis and higher risk of lymph node metastasis than those with cT1a-1b (≤20 mm) NSCLC  (3, 9, 13, 14).
Therefore, we hypothesized that a larger extent of lung resection (lobectomy) may be required to obtain the  sufficient margins and to examine more lymph nodes in this specific population  (1, 15). In 2011, Whitson et al. used the SEER database to compare survival after segmental resection versus lobectomy in patients diagnosed with pathological stage I adenocarcinoma (ADC) or squamous cell carcinoma (SCC) between 1998 and 2007  (10). After stratifying the patients by tumor size, they found that lobectomy was associated with more favorable CSS and OS for tumors measuring 21-30 mm, which is corroborated by the results of our study  (10). A more recent National Cancer Database (NCDB) study that reviewed 143,040 patients with cT1-3N0M0 NSCLC concluded that the survival advantage offered by lobectomy over segmental resection in patients with ADC >10 mm and SCC >15 mm (both categories encompass the size of interest of 21-30 mm in our study) could be confirmed in multivariate Cox regression models and subgroup analyses  (16).
More recently, Chan et al. observed no differences in OS or RFS based on a comparison of segmental resection and An additional advantage of lobectomy, compared to segmental resection, is that it allows the interlobar/hilar lymph nodes (N1) and mediastinal lymph nodes (N2) to be fully assessed to obtain more accurate pathological staging and possibly favorable survival  (9, 11, 17). In the present study, for patients with pathological stage IA (21-30 mm) NSCLC, a survival benefit was observed when the number of dissected lymph nodes was ≥3, and the lobectomy group had consistent survival advantages compared to the segmental resection group when the patients were stratified by the number of dissected lymph nodes (<3 vs. ≥3). These findings support those of another SEER database study that compared segmental resection and lobectomy in patients with stage I (≤30 mm) NSCLC divided into three subgroups according to the analogous number of lymph nodes removed (0/1-3/>3)  (11).
5% vs. 1. 6%, P=0. 004). Moreover, multivariate Cox regression analysis indicated that radiation after surgery for pathological stage IA (21-30 mm) NSCLC was associated with a worse OS, and the results from Qu et al. 's study support these findings  (11). Although the SEER database contains no detailed information on the indication for postoperative radiotherapy in early-stage NSCLC, we hypothesized that radiation oncologist might have recommended this multimodal therapy for cases with positive surgical margins, pathological high-risk factors, a lack of lymph node assessment, or local recurrence  (6). Consequently, the present study provides further support that maintaining a safe surgical margin and implementing extended lymph node removal are important oncological principles in surgery for node-negative early-stage NSCLC.
This population-based study had several limitations, and its results should be interpreted with caution. First, this retrospective study cohort is abstracted from a national database and the years of diagnosis spans 19 years; this inevitably caused selection bias and attrition bias. Second, many studies have reported a high rate of local recurrence in patients who undergo segmental resection rather than lobectomy, which may result in poorer survival. However, information on disease recurrence status and RFS are not recorded in the SEER database. Third, there was a lack of information on comorbidities, physical status, QoL, and pulmonary function, which made it challenging to establish whether patients treated with segmental resection could also tolerate lobectomy; thus, selection bias might have affected the survival analyses.
Fourth, several recent investigations have emphasized the value of the consolidation-to-tumor ratio (≤0. 25 or ≤0. 5) and pathological subtypes (micropapillary, solid, lepidic etc. ) as important factors in choosing the surgical procedure. The lack of radiological and pathological data on the SEER database forced us to extract cases only on the basis of a tumor size measuring 21-30 mm, and thus enrolling some part-solid nodules and high-risk subtypes was inevitable. The current results should be further verified through RCTs that factor in the consolidation-to-tumor ratio and pathological examination. Finally, the large range of subgroup sizes rendered any direct comparison between them difficult. Even the results in our study that reached statistical significance cannot preclude the possibility of group size imbalance which should also be considered when interpreting and drawing conclusions from these results.
1 s per scan) and a selected ion monitoring (SIM) mode, with a dwell time of 0. 2 s for each selected ion as shown in Table  1. Compounds from baking extracts were identified by analyzing the pure standards, performing mass spectral matches with the Wiley 8 and NIST 08 mass spectra databases, and comparison with the Van der Dool retention indices measured on the DB-Wax column. Chromatographic peak areas for each compound were calculated by extracting the quantifier ions from the SIM mode acquisition data using Quan Browser, Xcalibur 2. 1. 0 SP1, Build 1160 (Thermo Scientific, Waltham, MA, USA). Calibration curves for each compound were built using the ratio of the chromatogram peak areas (analyte vs dIS) plotted against the corresponding concentration. d4-pyrazine was used for 3-methylbutanal, pyrazine, 2-methylpyrazine, 2,5-dimethylpyrazine and 2,6-dimethylpyrazine whereas d4-furfural was used for acetic acid, furfural, 5-methylfurfural, furfuryl alcohol and 5-hydroxymethylfurfural.
Performance of the quantitative TD-GC-MS analysis The performance characteristics of the TD-GC-MS method outlined above are summarized in Table  4. The ratios (A/dIS) of the analytical blanks were low (0. 00010-0. 0175). These values were used as intercepts. Good linearity was observed throughout the concentration range, and the linearity range was defined as that between LOQ and the upper concentration. LOD and LOQ were calculated in ng for the 10 analytes. LOQ ranged from 0. 041 ng (2,5-dimethylpyrazine) to 11. 5 ng (3-methylbutanal) which was very satisfactory. The data thus obtained were not very comparable to those found in the literature where LOD and LOQ were expressed as concentrations, but a comparison could be made for furfural: the present method produced an LOQ which was 10 times lower than that obtained using a TD-GC-MS/MS method developed for e-cigarette aerosol by  Aszyk et al.
Preliminary results of such approach for polycrystalline materials have been presented in  Kowalczyk-Gajewska (2011)  without comparison with experimental data. The above models are able to capture the material response at the level of the RVE. To simulate the response of a structure under various loading conditions, mean-field models can be on the one hand embedded into a finite element (FE) software. Segurado et al. (2012)  implemented the viscoplastic self-consistent (VPSC) scheme  (Molinari et al. (1987) ,  Lebensohn and Tomé (1993) ) in a user-defined material UMAT subroutine. The authors validated the model using uniaxial tension and simple shear of a FCC AA6116 Al alloy. Texture evolutions were accurately predicted. Nevertheless, the elastic strain within each grain was not accessible.
So recently, an elastic-plastic self-consistent (EPSC) scheme was implemented in a finite element software by  Zecevic et al. (2017). In that case, the scale transition in each grain is carried out so the elastic strain development within individual grains is accessible. The integration of the EPSC equations was performed explicitly for each time increment. But an implicit FE software was used to carry out compression and cyclic loading on various alloys: AA6022 T4 aluminium alloy, DP590 steel and α-Ti. Note that kinematic hardening was accounted for to better describe cyclic loadings. Recently,  Zecevic and Knezevic (2019)  developed an implicit integration procedure of the EPSC model in ABAQUS software. They considered cup drawing of an AA6022 T4 sheet. One can also mention the work of  Msolli et al.
(2016)  who also coupled FE calculations and an elastic-viscoplastic mean field approach to simulate cup drawing. They considered the forming process of AISI 304L austenitic steel taking into account phase transformation. The tangent additive interaction law coupled with a Mori-Tanaka scheme was implemented in ABAQUS software. On the other hand, full-field finite element simulations of polycrystals subjected to cyclic loading can also be found in the literature. For instance,  Cruzado et al. (2018)  modeled the elastic-plastic behavior of IN718 alloy under uniaxial cyclic deformation tests with fully reversed deformation R ε = -1. They considered FE calculations of a RVE containing 300 grains. The crystal behavior was based on crystal plasticity model and kinematic hardening was introduced at the level of the slip system.
A dedicated Python program has been developed to detect positions where a rapid change in the brightness profile is observed. Measurements are repeated many times on each image and on several parts of the sample. One example of measurements made on a microsection is shown in Fig. 2b  In order to identify the substrate behavior, the copper present on both sides has been etched so that the gauge section of the sample is only made of the substrate material, as represented on Figure  1a. surements made on the microsection. The mean thickness over several images is reported in Table  1. cycles within the elastic domain to evaluate the in-plane elastic behavior. The tensile machine is an Instron E3000 equipped with a 1 kN load cell. Longitudinal and transversal strains have been captured by digital image correlation using VIC2D software.
EVPSC implementation The EVPSC scheme has been developed with a structure similar to the VPSC software of  Lebensohn and Tomé (1993). An evolutionary algorithm (EA), similar to the one presented in Frydrych (  2017  N hri = 20, maximal number of generations N gen = 200 and probability of mutation P mut = 0. 1. In addition the algorithm stops if the minimum mean standard deviation among fitness values of the HRIs is lower than 0. 001. In order to perform the EA optimization with a reasonable computational cost, the measured texture of Fig. 5  has been discretized into 100 orientations using the ATEX software,  Beausir and Fundenberger (2017). Next in the paper, when the parameters are identified, predictions of the behavior are obtained for 1000 grain orientations. It has been checked that for the overall behavior, no significant difference was observed when adopting 100 or 1000 orientations.
In  Read et al. (2004)  for instance, similar small value of Young's modulus (i. e. ca. 80 GPa) was measured. In order to reproduce the measured Young's modulus, we decided to apply in the simulations the reduced stiffness tensor, namely A e g = µA e0 g (20) where A e0 g is the tensor of cubic symmetry specified with use of literature data (19), while µ is a reduction parameter accounting for the effect of grain boundaries. In order to obtain the predictions consistent with experiments, µ = 0. 615 has been assumed. Note that the elastic anisotropy factor of A e g and A e0 g is the same. The motivation behind the relation (  20 ) is to keep the formulation as simple as possible and in the same time consistent with experimental measurements. Another possibility which was also tested, was to assume isotropic elastic stiffness of single crystal based on the measured values of the Young's modulus and Poisson's ratio.
e. Segurado et al. (2012)  or  Zecevic and Lebensohn (2020)  for copper also), leads to similar results. In addition, the developed EVPSC software is able to provide results also for larger values of n. For example, predictions conducted with reference parameters provided in Table  3  and n = 2 × 8 = 16 were obtained without numerical difficulties for amplitude Ampl. 1. On overall, the numerical efficiency of the code is comparable in this respect with the classical VPSC code, since as concerns the non-linear viscoplastic part of the response and the update of the local crystal plasticity variables similar procedures are used. Fig. 10a  shows the resulting longitudinal stress-strain curves for the first and 50th cycles. A comparison against the experimental data of Fig. 4  is also demonstrated.
Acknowledgments The authors thank for the support of Agence Nationale de Recherche through the program Labcom ANR-14-LAB7-0003-01 for the creation of the labcom LEMCI and Région Grand Est with the grant " soutien aux jeunes chercheurs" for Gautier Girard. The financial support of Metz Métropole, of Département de la Moselle, of CIMULEC, SYSTRONIC and CSI SUD OUEST through the NIT foundation is also acknowledged. The support of J. Guyon, O. Perroud, J. Slowensky of LEM3 for texture and EBSD measurements and for helpful discussions.