dataesr/scientific-paragraphs-categorization huggingface dataset:
Liver biopsies from patients infected with HCV are highlighted in red. infected and uninfected with HCC (see online supplementary table  S1 ). In four out of six donors, PTPRD expression was downregulated or even completely absent in tumour lesions compared with paired adjacent tissue samples (figure  5A ). To verify whether this downregulation was also specifically present in HCV-infected patients with HCC, we analysed PTPRD expression in paired tumour and adjacent liver tissue specimens. 17 In this data set of patients undergoing surgical resection of liver tumours, information for 46 patients with HCV-associated HCCs could be retrieved. In 30 out of 46 paired biopsies was PTPRD expression downregulated in tumour lesions compared with adjacent non-tumoural tissue (figure  5B ). This 30/46 ratio echoes the western blot results of paired HCC biopsies (figure  5A ), and the observed downregulation in tumour tissue was statistically significant ( p=0.
01, two-sided Wilcoxon signed-rank test) (figure  5B ). Next, we took advantage of the long-term clinical follow-up information provided in the database. Strikingly, when looking at all patients with HCC (n=82), those ranking in the highest 20 percentile levels of PTPRD expression in adjacent tissue (figure  4B ) had a higher long-term survival rate ( p=0. 048, log-rank test) (figure  5C ) and had less chance of recurrent liver cancer ( p=0. 02, log-rank test) (figure  5D ), irrespective of cancer aetiology. We confirmed the same trend of prognostic association in two additional independent cohorts with shorter patient follow-up (see online supplementary figures S5 and S6).
Figure5Dampened protein tyrosine phosphatase receptor delta (PTPRD) expression in liver biopsies is associated with a decreased patient survival and increased tumour recurrence after surgical resection. (A) PTPRD is impaired in tumour lesions of patients with hepatocellular carcinoma (HCC). Expression of PTPRD and actin was assessed in HCC lesions (T), and the corresponding paired adjacent tissue (A) of six patients with HCC by western blotting using specific antibodies. Patient codes are indicated. A random primary human hepatocytes (PHH) lysate served as positive control. (B) PTPRD is significantly ( p=0. 01, two-sided Wilcoxon signed-rank test) impaired in HCV-associated HCCs. The gene expression database of cohort A was analysed for PTPRD expression in paired liver biopsies from 46 patients infected with HCV.
Acknowledgements The authors thank  Dr Sébastien Pfeffer  ( UPR 9002 ,  IBMC ,  University of Strasbourg, France ) for providing small RNA sequencing data of HCVcc-infected Huh7. 5. 1 cells,  Dr Michel Tremblay  ( McGill University, Montreal, Canada ),  Dr Catherine Schuster  ( Inserm U1110, University of Strasbourg, France ) and  Luc Dupuis  ( Inserm U1118, University of Strasbourg, France ) for helpful discussions;  Sarah C. Durand  ( Inserm U1110, University of Strasbourg, France ) for isolation of primary human hepatocytes and excellent technical assistance. Moreover, they thank  Emilie Heuillard ,  Dr Eric Robinet  ( Inserm U1110, IHU, University Hospital Strasbourg ) and the  Biological Resource Centre (Centre de Ressources Biologiques (CRB) of the University Hospital Strasbourg, France)  for managing the biobank; Dr Frank Chisari  ( The Scripps Research Institute, La Jolla, California, USA ) for the Huh7.
Funding This work was supported by grants from the  Wilhelm Sander-Stiftung  ( Förderantrag 2010. 023. 1  to TFB), the  European Union  ( Interreg IV-Rhin Supérieur-FEDER-Hepato-Regio-Net  to TFB and MBZ; ERC-AdG-2014 HEPCIR to TFB;  EU H2020 HEPCAR  to TFB), the  French Cancer Agency  ( ARC IHU201301187  to TFB), the  University of Strasbourg  ( IdEx, Projet Attractivité 2014 ,  ANR , to JL) and from the  French ANRS  ( ECTZ4236 ,  ECTZ4446  to JL and AARS). NVR was funded by an  IdEx fellowship  from the  University of Strasbourg  (IdEx, Contrat Doctoral 2012,  ANR , to MBZ and TFB). This work has been published under the framework of the LABEX  ANR-10-LAB-28  and benefits from a funding from the state managed by the  French National Research Agency  as part of the investments for the future programme.
Acknowledgements We thank  D. Castro  and the referee P. Slane for their helpful comments on this paper. The  Fermi LAT Collaboration  acknowledges generous ongoing support from a number of agencies and institutes that have supported both the development and the operation of the LAT as well as scientific data analysis. These include the  National Aeronautics and Space Administration  and the  Department of Energy in the United States , the  Commissariat à l'Energie Atomique  and the  Centre National de la Recherche Scientifique / Institut National de Physique Nucléaire et de Physique des Particules in France , the  Agenzia Spaziale Italiana  and the  Istituto Nazionale di Fisica Nucleare in Italy , the  Ministry of Education, Culture, Sports, Science and Technology (MEXT) ,  High Energy Accelerator Research Organization (KEK)  and  Japan Aerospace Exploration Agency (JAXA) in Japan , and the  K.
Then, samples were transfer to RNeasy spin columns (RNeasy kit; Qiagen, Venlo, Netherlands) and centrifuged for 15 s at 8000 9 g, discarding the eluate. RNA was purified and concentrated in RNase-free water, following the protocol provided in the RNeasy kit (Qiagen). RNA yield was measured by absorbance at 260 nm (NanoDrop ND-100; Thermo Fisher Scientific, Waltham, Massachusetts, USA). RNA purity was assessed by examining A260/280 ratio with both samples exceeding a 1. 8 value. RNA extracts were sent to FPCM (Campus Cantoblanco, Madrid) to perform the RNA sequencing (RNA-seq). Bioinformatics analysis was performed by Era7 Bioinformatics (Granada, Spain) and FASTQ files collected after RNA-seq were analysed using CUFFDIFF 2. 2. 1 (Public domain). Annotation of genes was extracted from NCBI database.
METHODS Data of gastrectomies performed from May 2014 to October 2016, were extracted and analyzed. Basic characteristics of patients, surgical and clinical outcomes were reported. The technique for reconstruction (Parisi Technique) consists on a loop of bowel shifted up antecolic to directly perform the esophago-enteric anastomosis followed by a second loop, measured up to 40 cm starting from the esojejunostomy, fixed to the biliary limb to create an enteroenteric anastomosis. The continuity between the two anastomoses is interrupted.
Reported outcomes Descriptive information on characteristics of patients, details of procedures and tumor findings were reported. Operative results, data on the postoperative course and assessment of complications were based on the following primary outcomes: Estimated blood loss (EBL, mL), retrieved lymphnodes (No. ), hospital stay (d), resumption of a liquid and solid diet (POD), inhospital complications (No. , Type), 30 d readmission (No. ). Secondary outcomes included: the operative time (min), margin status (No. negative/total) and R assessment (No. R0 resections), intraoperative com plications and death (No. ), resumption of peristalsis (POD).
RESULTS Data of 55 consecutive patients underwent the robotic doubleloop reconstruction method (called Parisi technique) after performing a robotic total gastrectomy for gastric cancer were considered in the present study. Table  1  reported patients' characteristics. Mean age was 72. 56 ± 10. 67, 66. 04% of patients had one or more comorbidities and the mean BMI was 24. 42 ± 72. 56. Most tumors were in the middle third of the stomach (54. 54%). If the tumor is localized at the lower third of the stomach, usually we perform a BII subtotal gastrectomy, with a robotic intracorporeal anastomosis. However, in some selected cases we prefer to perform a total gastrectomy. In 12 of the reported cases, where the tumor was located in between the lower and the middle third of the stomach, we decided, after discussion with the patient, to perform a total than a subtotal gastrectomy for the following reasons: (1) some patients were less than 65 years old and we wanted to reduce the risk of recurrence on the residual limb (5 patients); (2) the lesion appeared to extensively involve the lower two thirds of the stomach (5 patients); and (3) in two cases with diffuse type, there was not only a main pre pyloric lesion but also a biopsy proven adenocarcinoma at the upper third.
Intravenous iodinated contrast was not administered. Data obtained from the CT-scan were used for attenuation correction of PET data and for fusion with attenuation-corrected PET images. PET data was reconstructed iteratively using the ordered-subset expectation maximization (OSEM) algorithm (2 iterations and 8 subsets in Angers and Brest; 2 iterations and 16 subsets in Paris; 4 iterations and 8 subsets in Saint Etienne).
FDG-PET/CT was considered false-positive in patients with a FDG-PET/CT interpreted as positive for possible malignancy who did not developed malignant disease during follow-up. FDG-PET/CT was considered true-negative in patients with a FDG-PET/CT interpreted as negative for malignancy who did not develop malignancy during follow-up. FDG-PET/CT was considered false-negative in patients with a FDG-PET/CT interpreted as negative for possible malignancy who developed a malignant disease during follow-up. Statistical analysis was performed using IBM SPSS Statistics software, version 19 installed on PC. The trial is registered with ClinicalTrials. gov, number NCT00964275.
Our study has strengths and limitations. Our sample size was somewhat limited, resulting in wide confidence intervals around estimated accuracy indices. However, our data represent the largest population of venous thromboembolism patients investigated using a FDG-PET/ CT. Moreover, our patient population was included in a multicenter, prospective, randomized trial, with a 24-month follow-up through outpatient clinic visits every six months. FDG-PET/ CT images were centrally reviewed at the main study site by a board-certified nuclear medicine physician, blinded from patients' history, initial FDG-PET/CT interpretation, and follow-up status but without specific reproducible interpretation criteria for a positive FDG-PET/CT. However, an interobserver agreement was not performed in this study which could limit the robustness of the results.
Data analysis The following data were recorded with a sampling frequency of 20 Hz: mask airflow (V′), mask pressure (Pm), tracheal pressure (Ptr), pressure in the Starling resistor (Ps) and total leak. The muscular pressure (Pmus) was exported from the ASL5000 software (IngMar Medical, Pittsburgh, USA) and was synchronized to the bench-recorded data for further analyses. For each 5-min period during which the inspiratory trigger and total leak level were unchanged, the number of autotriggered cycles and ineffective efforts were calculated by analyzing the Pm and Pmus curves. As leak flow follows the airway pressure, the distribution of leak values relates to that of the airway pressure. High leaks occurred at inspiratory phases when pressure support was applied; during the rest of time, a constant lower leak corresponding to the expiratory pressure persisted (i.
e. , the expiratory leak). The leak values during ventilatory cycles were thus not normally distributed. Consequently, the "critical leak" was presented as median (range, min-max values) of the 5-min period. Comparisons of "critical leaks" between devices for each diseased respiratory and UA conditions were performed using Kruskal-Wallis tests. Statistical analyses were performed with MedCalc (MedCalc Software, Mariakerke, Belgium).
Hull-mounted 75 kHz broadband ADCPs from Teledyne RD Instruments were used before spring 2010, and they were switched to 38 kHz Ocean Surveyor ADCPs thereafter. A total of 33 transects from the period of 2004-2016 are selected and analysed in this study. Among these transects, 25 cover the full 3-34°N range as indicated in Fig. 1  and eight shorter transects span from 24 to 34°N (Fig. 1b ). Seasonally, 10, 5, 10 and 8 transects are occupied in winter (January-February), spring (April-May), summer (June-August) and fall (October-December), respectively. The raw ship-board ADCP data are processed using the Common Ocean Data Access System available from http://currents. soest. hawaii. edu/docs. As in previous studies utilizing the ship-board ADCP data  [13] [14] [15] [16]  , we assume that the ship velocity, averaged at 5 m s À 1 , is much faster than evolving mesoscale and submesoscale features of our interest.
Acknowledgements We are grateful to the past and present captains and crews of  R/V Ryofu Maru  and  Keifu Maru , and staff of the  Marine Division, Japan Meteorological Agency , for their laudable long-term observational efforts. We thank  Jules Hummon  and  Eric Firing  for help with the processing and deciphering of the shipboard ADCP data, and  Lee Fu  and  Jinbo Wang  for their in-depth discussions. B. Q. and S. C. acknowledge support from  NASA SWOT and OSTST missions  ( NNX16AH66G  and  NNX13AE51E ). P. K. acknowledges support of  CNRS (France) ,  LabexMer  ( ANR-10-LABX-19-01 ), as well as of the  NASA-CNES SWOT mission.
Metabolomic assay Serum samples (100 μl) were assessed by ultra performance liquid chromatography (UPLC) and quadruple/time-of-flight mass spectrometry. The mass spectrometer was operated in both positive and negative electrospray ionization (ESI+/ESI -) mode. The UPLC-quadruple/time-offlight mass spectrometry ESI+ and ESIraw data were analyzed by the MarkerLynx Applications Manager version 4. 1 (Waters Corp. , Milford, MA, USA) and total ion chromatography was generated. To identify different metabolomic profile between MYC-high and MYC-low groups, multivariate analysis was performed using SIMCA-P software version 12. 0 (Umetrics AB, Umeå, Sweden). The unsupervised principal component analysis and supervised orthogonal partial least squares-discriminant analysis (OPLS-DA) models were constructed.
549 for ESI+, R2Y = 0. 931, Q2 = 0. 491 for ESI -, Figure  1e ). To elucidate the regulatory mechanism of MYC on lymphoma choline metabolism, cellular levels of choline, PC(16:0/22:6), LPC (16:0) and LPC(18:0) were assessed by UPLC-triple quadrupole mass spectrometry. Compared with untreated or negative control (CON siRNA-transfected) cells, 10058-F4-treated or MYC siRNAtransfected B-lymphoma cells displayed a significant decrease in cellular levels of choline and its phosphorylated derivatives (Figure  1f  and Supplementary Figure  S1B ). Together, these data indicated that MYC overexpression is related to aberrant choline metabolism.
The results showed that MYC enhances the gene and protein expression of PCYT1A (Figure  2b ). Putative potential conserved MYC binding site within the regulatory region of PCYT1A promoter were predicted using JASPAR database (http://jaspar. genereg. net/cgi-bin/jaspar_db. pl). Chromatin immunoprecipitation assay was conducted in DB cells to verify the physiological interaction of MYC with promoter region of PCYT1A. MYC was able to bind with PCYT1A and the binding activity declined upon treatment with 10058-F4 or transfection with MYC siRNA (Figure  2c ). Moreover, when luciferase reporter assay was performed on HEK-293T cells with MYC binding site mutation, the transcriptional activity of PCYT1A was no longer altered by MYC overexpression (Figure  2d ). To gain insight into the biological role of MYC-induced aberrant choline metabolism in B-cell lymphoma, DB and Ramos cells were either treated with MYC inhibitor 10058-F4 or transfected with MYC siRNA (Figure  2e , left panel).
ACKNOWLEDGEMENTS This study was supported, in part, by research funding from the  National Natural Science Foundation of China  ( 81325003 ,  81520108003 ,  81670716  and  81201863 ), the  Shanghai Commission of Science and Technology  ( 14430723400 ,  14140903100  and  16JC1405800 ), the  National Key Research and Development Program  ( 2016YFC0902800 ),  Shanghai Municipal Education Commission Gaofeng Clinical Medicine Grant Support  ( 20152206  and  20152208 ), Multi-center Clinical Research Project by  Shanghai Jiao Tong University School of Medicine  ( DLY201601 ),  SMC-Chen Xing Scholars Program ,  Chang Jiang Scholars Program ,  Innovation Fund Projects of Shanghai Jiao Tong University  ( BXJ201607 ),  Collaborative Innovation Center of Systems Biomedicine  and the  Samuel Waxman Cancer Research Foundation.
, 2016). Conceptual flow and transport modelling with travel-time distributions has been recently applied on the agricultural catchment scale to simulate atrazine and chloride transport  (Van der Velde et al. , 2010; Benettin et al. , 2013; Botter et al. , 2011; Harman, 2015). The novelty of this study lies in the inclusion of CSIA data in such modelling approaches. Finally, by comparing the model and the Rayleigh equation, this study investigates how to upscale sample-based CSIA information for degradation assessment on catchment scale. Overall, the main objectives of this study are to (i) analyse herbicide CSIA data from an agricultural catchment on different scales, (ii) develop a quantitative model using travel-time distributions for the interpretation of pesticide concentration and CSIA data on catchment scale, and (iii) evaluate the added value of this modelling approach for the assessment of pesticide transport and degradation on catchment scale.
Model performance of each parameter set was calibrated using a combined objective function (N comb ) that simultaneously evaluates the Nash-Sutcliffe coefficients for discharge (N Q ), concentrations (N C ), and δ 13 C values of S-metolachlor (N δ13C ; see Sect. S5 for a detailed description). In view of the relatively few field data, we opted for a threshold value for N comb of 0. 7 (based on preliminary model calibrations) defining equally suitable (i. e. behavioural) model results similar to the GLUE approach  (Beven, 2012). This criterion was used in 10 000 calibration runs to determine 10 000 behavioural parameter sets with the particle swarm optimization algorithm implemented in the open-source R package "HydroPSO" (Zambrano-Bigiarini and Rojas, 2013). www. hydrol-earth-syst-sci. net/21/5243/2017/ Hydrol.
In addition to testing of different model setups, we used our conceptual model to assess a field-integrated enrichment factor (ε C ). We propose that travel-time distribution modelling inherently accounts for dispersion and flow-path mixing  (Hrachowitz et al. , 2016)  and is thus able to mirror attenuation of potentially large isotope fractionation due to dispersion and mixing in open systems  (Abe and Hunkeler, 2006; Lutz et al. , 2013; van Breukelen and Prommer, 2008). In contrast, enrichment factors derived from field CSIA data via the Rayleigh equation (Eq. S2) are prone to underestimate the "true" enrichment factor in open systems  (Abe and Hunkeler, 2006; van Breukelen, 2007). Hence, conceptual traveltime-based models represent an alternative way of assessing field-integrated enrichment factors, which might improve in accuracy with increased temporal resolution of CSIA samples.
We made use of simulated (virtual) CSIA data to assure unbiased comparison of continuous time series. Assuming the same enrichment factor and initial isotopic signature of the applied product as in the best-fit simulation (i. e. ε C = -1. 13 ‰ and δ 13 C 0 = -32. 5 ‰, respectively), the Rayleigh equation approach gave an extent of degradation of D Rayleigh = 94. 1 % (Eq. S3) for the simulated δ 13 C value of -29. 4 ‰ on 17 July (i. e. best-fit simulation on the last day of field CSIA data). In comparison, based on the simulated concentrations of S-metolachlor and a conservative tracer at the catchment outlet (for the entire simulation period from 2004 to 2012), the actual extent of degradation on 17 July was D Sample = 99. 9 % (Eq. S4) in the best-fit simulation. Overall, the Rayleigh equation applied to (virtual) CSIA data from the catchment outlet underestimated the actual extent of degradation as occurred for the outlet sample (i.
g. following rainfall events). As CSIA measurements in this study were only possible after rainfall events and not during low-flow periods, we were not able to corroborate this model result. This implies that additional CSIA data at higher temporal resolution (ideally at the same resolution as concentration data) and at later times of the study period, especially during low-flow conditions, can yield a much clearer picture of pesticide transport and degradation. Such data might further improve the representation of pesticide degradation in models building on the conceptual model presented in this paper, and allow for the use of CSIA data as tracer for different flow paths on catchment scale. Depending on the study-compound properties, future modelling studies might include additional processes such as re-equilibration between pesticide in the dissolved and particulate phase.
Acknowledgements. This research has been financially supported by the  European Union  under the  7th Framework Programme  (project acronym CSI:ENVIRONMENT, contract number  PITN-GA-2010-264329 , and grant agreement no. 603629-ENV-2013-6. 2. 1-Globaqua ), and the  PhytoRET  project ( C. 21 ) of the  European INTERREG IV program Upper Rhine. Marie Lefrancq  was supported by a fellowship of the  Rhine-Meuse Water Agency. We acknowledge the help and support of  Matthias Gehre  and  Ursula Günther  ( Department of Isotope Biogeochemistry, UFZ Leipzig ) for the stable isotope measurements. Edited by: Bettina Schaefli Reviewed by:  Enrico Bertuzzo  and one anonymous referee.
In this paper we present a novel health monitoring method by estimating the heart rate and respiratory rate using an RGB camera. The heart rate and the respiratory rate are estimated from the photoplethysmography (PPG) and the respiratory motion. The method mainly operates by using the green spectrum of the RGB camera to generate a multivariate PPG signal to perform multivariate de-noising on the video signal to extract the resultant PPG signal. A periodicity based voting scheme (PVS) was used to measure the heart rate and respiratory rate from the estimated PPG signal. We evaluated our proposed method with a state of the art heart rate measuring method for two scenarios using the MAHNOB-HCI database and a self collected naturalistic environment database. The methods were furthermore evaluated for various scenarios at naturalistic environments such as a motion variance session and a skin tone variance session.
Experiment setup A series of experiments were conducted to evaluate the heart rate estimation of the proposed method along with the state of the art methods. The state of the art methods included the remote heart rate measuring methods proposed by Poh et al. [2], using BSS on RGB spectrum, de Haan et al. [14] , using chrominance space derived from the RGB spectrum, Lam et al. [9], using green spectrum based BSS method, Feng et al. [11] , using green and red differentiation operation, and Wang et al. [17] , using spatial-subspace rotation of the RGB spectrum for PPG signal estimation. All the methods were implemented in MATLAB and run on a personal computer with a 3. 4 GHz processor and 8 GB RAM. The experiments were carried out for two databases; Experiment 1, using publicly available MAHNOB-HCI database  [33]  and Experiment 2, using self-collected dataset at naturalistic environment.
Experiment 1: MAHNOB-HCI database is a multi-model database; we used the emotion elicitation experiment. During the experiment, we used 27 subjects of which 15 were female, and 12 were male of age 19 to 40 years old (mean of 26. 06 and standard deviation of 4. 39). We used the data, recorded with a AVI compression using a 24 bit RGB camera of 61 fps (frames processed per second) at a resolution of 780 × 580. The camera was positioned in front of the subject at a distance of 0. 4 meters. The ground truth for the heart rate measurement was extracted from the ECG signal of channel 34 of the sensor attached to the upper left corner of the chest, under clavicle bone. We also used the MAHNOB-HCI database to validate the respiratory rate estimation. Here the ground truth for the respiratory rate measurement was extracted from the respiratory belt connected to channel 45.