dataesr/scientific-paragraphs-categorization huggingface dataset:
01) (Fig. 2B ). It is noteworthy that EB1 expression level was not modulated by MTA treatment (Supplementary Fig. 2A ), strongly suggesting that EB1 proteins were delocalized at the microtubule plus-ends. We then evaluated the impact of KCN and tiron on EB1 localization in A549 cells. Interestingly, their simultaneous combination with MTAs prevented drug-induced EB1 delocalization (Fig. 2B ). For instance, the impact of vincristine on EB1 comet length was limited to 30 % when combined with KCN and totally suppressed by tiron. These results were similarly obtained in U87-MG and SK-N-SH cells (Supplementary Fig. 2B , 2C and data not shown). It should be noticed that treatment with tiron alone increased the length of EB1decorated plus-end of microtubules by 23 % in A549 cells (Fig. 2B ) and by 13 % in U87-MG cells (Supplementary Fig.
2C ), strengthening the link between intracellular ROS levels and EB1 ability to accumulate at microtubule plusends. To further confirm these unexpected results, we measured EB1 comet length in wt and ρ (-) SK-N-SH cells. Consistently with the 29 ± 3 % decrease in basal mitochondrial O 2. -levels (Fig. 1C ), comet length was increased in ρ (-) SK-N-SH cells to 2. 8 ± 0. 2 µm (Fig. 2C ), as compared with the parental wt cells (1. 7 ± 0. 1 µm; p<0. 001). We also quantified the median number of EB1 comets per cell, that increased from 160 ± 10 in wtSK-N-SH cells to more than 270 ± 22 in ρ (-) cells suggesting that number of growth microtubules increased (data not shown). Vincristine treatment (for 6 h), which was highly effective in wtSK-N-SH cells, caused a complete disappearance of EB1 accumulation at microtubule plusends in 88 % of the cell population (data not shown).
ROS-mediated EB1 phosphorylation is involved in MTA activities. To investigate whether EB1 phosphorylation play a role in MTA activity, we performed EB1 immunoprecipitation from MTA-treated A549 cells (for 6 h). We showed that 6 h-treatment of vincristine, paclitaxel and patupilone increased EB1 phosphorylation 1. 7, 2. 5 and 3. 2 times, respectively (Fig. 4A , left and right panels). We revealed thus that patupilone-mediated EB1 phosphorylation was governed by ROS, since it was suppressed by a simultaneous combination with tiron (Fig. 4A , right panel). These data were validated in U87-MG cells exposed to vincristine (Supplementary Fig. 3 ). In agreement with results obtained in U87-MG cells, vincristine decreased EB1 comet length by 60 % in wtEB1-GFP transfected U87-MG cells (Table  1 ).
8 ± 0. 1 µm and 2. 6 ± 0. 9 µm for vincristine and the combination respectively; p>0. 05) (Fig. 6A ). Same results were obtained in U87-MG cells (Supplementary Fig. 4B ). Lastly, we showed that GSK3β was involved in both pro-apoptotic and anti-migratory activities of MTAs. For instance, SB216763 reduced 2. 0 and 1. 9 times A549 cell death induced by a 48 h-treatment with vincristine and patupilone respectively (p<0. 01; Fig. 6B ). Likewise, we showed that combination of MTAs with SB216763 resulted in a total suppression of the anti-migratory effect of vincristine and patupilone (Fig. 6C ). Of note, we also analyzed AMPK activity, that appeared not to be involved in MTA activities (data not shown). Altogether, our results highlight a pivotal role for the ROS-modulated Akt/GSK3β pathway that, via EB1 phosphorylation and accumulation to microtubule plus-ends, governs MTA efficacy.
Indirect immunofluorescence analysis Cells were grown on 8-well chamber slides (Labtek, Thermo Scientific, Roskilde, Denmark), precoated for 1 hour with fibronectin (10 μg/ml) for U87-MG or with type I collagen (30µg/ml) for SK-N-SH (Sigma Aldrich), to be treated for 6 hours with MTAs and inhibitors. As previously described  [32] , cells were incubated with the anti-EB1 (clone 5; BD Biosciences, San Jose, CA) and α-tubulin (clone DM1A; Sigma Aldrich) primary antibodies, and then with Alexa488 or 568-conjugated secondary antibodies (Molecular Probes). Staining was observed using either a Leica DM-IRBE microscope or a Leica TCS SP5 confocal laser-scanning microscope (Leica, Heidelberg, Germany). Images were acquired using Metamoph software or the Leica Confocal software, and were processed using Image J software.
Western blot analysis Cells were lysed after 6 hours treatment in RIPA buffer (Tris-HCl 50mM pH 8. 0, NaCl 250mM, Triton-X100 0. 1 %) with a cocktail of proteases and phosphatases inhibitors (Sigma-Aldrich) added freshly. Protein concentrations were determined using the Bio-Rad Protein Assay (Bio-Rad laboratories, France). Proteins were separated by SDS-PAGE and electrotransferred onto a nitrocellulose membrane. Primary antibodies used were directed against EB1 (clone 5; BD Biosciences), α-tubulin (clone DM1A, Sigma Aldrich), Ser 473 phospho-Akt, total Akt, Ser 9 phospho-GSK3β (Cell Signaling, Boston, USA), total GSK3β (Life Technologies). Peroxydase-conjugated secondary antibodies (Jackson Immunoresearch, Baltimore, USA) and chemiluminescence detection kit (Millipore) were used for visualization, and signal quantification was done with Image J software.
Fluorescent time-lapse video microscopy Time-lapse acquisitions for microtubule dynamics experiments (wtEB1-GFP, T166A-GFP and S155A-GFP U87-MG cells) were performed with a Leica DM-IRBE equipped with a 60X / NA 1. 49 objective lens. Thirtyone images per cell were acquired at 2-s intervals using a digital camera (CCD camera Coolsnap FX; Princeton Instruments). Analysis of microtubule dynamics was performed using the manual tracking personalized plug-in for Image J software. Position of EB1 comets was detected by thresholding a filtered image and the centroids of individual comets were followed over time. www. impactjournals. com/oncotarget Changes in length exceeding 0. 067 µm were considered as growth events. Catastrophe frequency was calculated for each individual comet tracked, and corresponds to the inverse of the total length of growth.
ACKNOWLEDGEMENTS This work has been carried out thanks to the support of  INCa-DGOS-Inserm 6038  (siric label), and  A*MIDEX  project (n°ANR- 11-IDEX-0001-02 ) funded by the " Investissements d'Avenir" French Government program , managed by the  ANR. Amandine Rovini  received an  ARC foundation (Association pour la Recherche contre le Cancer)  fellowship. The authors wish to thank  Charles Prevot  for flow cytometry analysis.
Abstract (max 250 words): While the mutational status in gastrointestinal stromal tumors (GIST) can predict the response to treatment with tyrosine kinase inhibitors, the role of tumor genotype as a prognostic factor remains controversial. The ConticaGIST study sought to determine the pathologic and molecular factors associated with the disease-free survival (DFS) in patients with the operable, imatinib-naive GIST. Clinicopathological and molecular data from 1056 patients with localized GIST who underwent surgery with curative intention (R0/R1) and were registered in the European ConticaGIST database were prospectively obtained and reviewed. Risk of tumor recurrence was stratified using the modified NIH criteria. The median follow-up was 52 months. On testing for potential prognostic parameters, primary non-gastric site, size >10cm, mitotic index >10 mitoses per 50 high power field, and the KIT exon 9 duplication [hazard ratio (HR) 1.
Moreover, in the last years the potential role of mutational status as a prognostic factor has been examined in a number of retrospective studies. In particular, it has been shown that deletions of KIT exon 11, especially those involving codon 557 and/or codon 558 (designated as KITdel-inc557/558) are associated with malignant behavior  [11] [12] [13] [14]. Conversely, KIT/PDGFRA WT GIST and most PDGFRA-mutated GIST generally have a lower potential for malignancy  [2, 15]. However, the available data are still insufficient to be incorporated into routine clinical risk assessment. In the present study, we assess the role of the tumor KIT and PDGFRA genotype along with key prognostic factors for DFS in localized, operable GIST in the largest so far data set from 1056 patients registered in the European ConticaGIST database.
Patients We assessed the information from patients that were included in the ConticaGIST registry (https://conticagist. sarcomabcb. org) and diagnosed between January 1985 and April 2012 in 13 contributing institutions from four European countries. The majority of cases, i. e. all those diagnosed from 2001, were studied prospectively (83% of all). Each patient was assigned a registry code prior data transfer to ensure data anonymization. The study was approved by Ethics Boards of participating institutions. A small subset (n=127) of the present cohort has been previously published  [16]. Only patients with primary GIST diagnosis who underwent surgery with curative intent (R0 or R1) were eligible. Pre-or postoperatively, the patients were not treated with any chemotherapeutic agents, including imatinib, until disease recurrence.
From 1625 patients with data transferred from the pooled series, 559 did not fulfill these eligibility criteria and were excluded from the study. Due to the small number of patients, we have also excluded 10 pediatric GIST (age of diagnosis <18). Finally, a total of 1056 patients were included for further analysis. DFS, defined as the duration from surgery to relapse (local recurrence or metastasis) or last follow-up, was used for prognosis evaluation. Relapse was determined based on routine imaging assessment and/or biopsy. The follow-up was updated on January 15 th , 2014. If patients were relapse free at the time of the last follow-up, they were censored for a disease recurrence.
Statistical analysis For univariate analysis, the Chi-square or Fisher exact tests and Mann Whitney test were used to compare categorical and continuous variables, respectively. Survival analysis was performed with the Kaplan-Meyer method and survival between groups was compared using the log-rank test. Univariate and multivariate Cox proportional hazards models were used to determine associations between variables of interest (tumor size, MI, tumor rupture and tumor genotype) and DFS. The strengths of associations were summarized with hazard ratio (HR) and corresponding 95% confidence interval (CI). The value of p<0. 05 was interpreted as statistically significant. Analyses were carried out with STATISTICA v. 12 software package (StatSoft Inc).
Clinicopathological characteristics Information about primary tumor size, MI, anatomical site and mutational status were available from 996, 974, 1050 and 1056 patients, respectively (Table  1 ). The DFS data was available from 998 patients. The majority of tumors were localized in the stomach (55. 6%), followed by small intestine (28. 1%), duodenum (5. 8%), colon and rectum (5. 5%). The median tumor size was 6. 0 cm (mean 7. 4 ± 5. 3 cm, range 0. 2-40 cm), and 20. 6% of tumors were >10 cm at initial diagnosis. The median number of mitoses was 4 per 50 HPF (mean 13 ± 27/50 HPF, range 0-300/50 HPF), with a mitotic rate >5/50 HPF documented in 38. 8% of cases. Perioperative tumor rupture was recorded in 6. 3% of patients. Using the modified NIH classification, the risk of relapse could be assessed in 957 cases; 7.
Study design and serum samples The LITHE have previously been thoroughly described by Kremer et al. [19]  and Smolen et al. [18]  (clinicalTrials. gov identifier: NCT00106535). The study is a 2-year phase III, multicenter, randomized, 3-arm, placebo-controlled, and parallel group trial in patients with moderate to severely active RA who had an inadequate response to MTX. The sub-study of LITHE consisted of serum samples from a 1-year, double-blinded treatment study, where 704 patients were randomized 1:1:1 to one of three treatment groups: 4-mg/kg, 8-mg/kg TCZ, or placebo (PBO) in combination with a stable dosage of MTX (10-25 mg/week). TCZ and PBO were given intravenously over 4 weeks. The end point of the biomarker sub-study was response rate, according to the American college of rheumatology criteria, for 50% improvement (ACR50).
" Sensitivity and specificity, including AUCs, were used to determine the optimal cut-off values derived from receiver-operator curve (ROC) analyses at highest likelihood ratio. Odds ratios were calculated using these cut-off values. Difference between responder and non-responder groups (Fig. 2 ) was investigated by Student's t-test. All statistical analyses were performed using SAS software version 9. 1. 3 and MedCalc version 12. 3. 0. Graphing was performed using Prism Graphpad version 5. 03.
Acknowledgment The study was supported by the  Danish Research foundation. We would like to acknowledge the work of our skilled and diligent technicians, especially  Kathrine Marcher-Mikkelsen ,  Maibritt Andersen ,  Emeric Chassaing , and  Sedi Tavallaee , as well as the  Head of Synarc laboratories in Lyon ,  Tanja Schubert. Samples  from the LITHE study were kindly donated by  Roche-Genentech. We acknowledge that the clinical data was attained from patients who volunteered in the study and collected and supervised by the  ACTEMRA group.
Data collection In total, 106 images of 9 prostate cancer patients were analyzed. All patients were instructed to follow a dietary protocol in order to have a full bladder and an empty air-free rectum at the time of the planning CT acquisition and during treatment. The planning CT data was acquired using a General Electrics Light Speed scanner. The treatment system was an ELEKTA Synergy linear accelerator (LINAC) equipped with CBCT imaging. During CT (CBCT) acquisition, the peak-voltage, X-ray tube current and exposure time were 120 kVp (120 kVp), 300 mA (40 mA or 64 mA) and 1000 ms (40 ms), respectively. For clinical requirements, the prostate CTV was manually delineated on each planning CT scan by a radiation oncologist (this step is always required in clinical practice for treatment planning).
Registration Algorithm Although the context is not strictly monomodal image registration, the relationship between the intensities on the CT image and those on the CBCT image is given by a linear equation. Hence the normalized-cross correlation metric was chosen as a suitable advanced cost function. The similarity between images was intensity-based, allowing registration to be fully automatic. Optimization was performed with the regular step gradient method. Transformations were rigid (six degrees of freedom, allowing translations and rotations). Linear interpolation was used in all our experiments. Three resolution levels were used. For this study, all the data processing and visualization were performed on a Linux computer with distribution openSUSE 11. 4 x86 64, with an Intel Dual Core i5-560M 2.
66 GHz processor, 3MB L2 cache, 4 threads, and 8GB RAM. For our implementation, the following open-source software, based on C++, was used: • the Insight Toolkit ITK  [9] , freely available at www. itk. org, • the ITK-based Command Line Image Toolkit clitk, freely available at http://www. creatis. insa-lyon. fr/rio/clitk. The software versions used were ITK 3. 20. 1, CMake 2. 8. 3 and gcc 4. 5. 1.
Impact of rectal distension on local RR quality We investigated in which cases local RR with 8-mm margin failed. Figure  2  illustrates the impact of the variation of rectal filling between the images to be registered on the quality of local RR with 8-mm margin. We observed with our database that if the F factor as defined in Eq. 1 is lower than or equal to 112. 6, registrations were all successful. All failed registrations appeared for values of F higher than 147. 6. The range of F values obtained was from 0. 2 to 406. 6. Fig. 2 : Plot of (blue) the cumulative number of failed registrations and (red) its derivative, i. e. the failure frequency, obtained with local RR with 8-mm margin, against the CBCT scans arranged in order of increasing F number.
12/1 000  [24]. In another study that analysed data from four regions in Italy, the HZ incidence in adults aged ≥50 years was 6. 6/1 000, and 9. 4% and 7. 2% of the patients had PHN at 1 month and 3 month, respectively  [25]. Another study that analysed data from 1999 to 2005 reported a mean annual number of 4 503 HZ hospitalisations and 543 dayhospitalisations; 62% of patients were >65 years  [26]. In the perspective of a VZV vaccine to prevent and reduce the severity of HZ becoming available in Europe, it was decided to obtain baseline data on the occurrence of PHN in a multicenter, longitudinal, prospective, observational study involving general practitioners (GPs) throughout Italy, the HER. O. E. S. Study -HERpes zoster Outcome: Epidemiological Study. The primary objective was to assess the percentage of patients with HZ that have HZ-associated chronic pain and its duration.
Study objectives The co-primary objectives of the six-month study were: to assess the percentage of patients with HZ who developed HZ-associated chronic pain and how long the pain lasted. to collect disease management data from diagnosis to resolution of the acute symptoms, and data on the management of HZ-related pain. The secondary objectives were to assess quality of life (QoL) in the patients with HZ/PHN using the SF-12 instrument and to assess HZ-related pain intensity using a visual analogue scale (VAS). We also recorded the presence of clinical variables that have been identified as risk factors for HZ and assessed the patients' care pathway and their disease progression during the study period.
The scores ranged from 0 (lowest level of health) to 100 (highest level of health)  [29]. A score of <50 indicates a below-average health status. The level of pain was assessed using a visual analogue scale (VAS) for the worst pain felt during the previous two weeks, with scores ranging from 0 ('no pain') to 10 ('worst pain imaginable'). A VAS score of ≥3 was considered to be correlated with pain interfering with activities of daily living  [30]. At each follow-up visit the presence of HZ-associated pain, the level of pain using the VAS and quality of life (QoL) scales were assessed. In addition, data on the clinical evolution and the health care resources used were collected. The presence of allodynia, itching, paresthesia and malaise were all assessed by the physicians during the clinical examination at corresponding study visit.
Statistical analyses The descriptive analyses were performed with SAS (Statistical Analysis System), V9. 2. The recorded or derived variables were summarized as frequencies (absolute or relative) or means or medians with their associated distribution (number of observations, mean, standard deviation, median, minimum, maximum). For all clinically-relevant variables, 95% confidence intervals (CIs) were calculated. Analyses were stratified on gender, age group (50-59, 60-69 and ≥70), and presence of pain at the respective visit. Variables present at the initial visit associated (p = 0. 25) with PHN at 3-months in univariate analyses were included in a multivariate regression model to identify PHN predictive factors (p ≤ 0. 05). The fit of the final model was assessed using the Hosmer and Lemeshow goodness-of-fit test.
Patient population A total of 108 of the 147 GPs who accepted to participate in the study included at least one patient. These 108 GPs were from 21 local health units localized in 12 Italian regions. Their regional distribution was similar to the national distribution (data not shown). They enrolled 435 patients with a new diagnosis of HZ from 27 March 2009 to 5 July 2010 of whom 413 were included in the study (Figure  1 ). The majority of the GPs (72. 2%) respected the time windows for all their patients' follow-up visits. The patients were aged 67. 9 ± 10. 7 years old and 64. 2% were women (Table  2 ). Almost half (46. 7%) of the study population were aged ≥70 years. The majority (81. 4%) lived with their family; about 25% were working. Most patients (90. 3%) had been followed by their GP for >5 years with a mean of 8.
2% and 13. 6% of patients at the 3-and 6-month visits, respectively; we cannot exclude that patients who suffered more from pain were more likely to complete the VAS score. The percentage of patients with PHN reported in retrospective database studies ranged from 6. 9% to 32%  [21, 25, 33, [37] [38] [39]. Retrospective studies using International Classification of Disease (ICD) codes to extract data from databases do not always provide a reliable estimate of HZ and PHN incidences because of possible miscoding and under-coding. Additionally, the absence of a specific ICD code for PHN makes database extraction less reliable for this endpoint. The prospective design of our study, including three follow-up visits, enabled a better diagnosis of PHN than retrospective studies. Nevertheless, even if the actual estimates were different, the studies also generally reported an age-related increase in the percentage of patients with HZ-associated pain.
The percentage of patients with PHN observed in HEROES was lower than the 40% assumed for the sample size estimation. Although we recruited fewer than the original target of 500 patients, we had data for the planned 400 patients needed to estimate the percentages of patients with PHN at 3 and 6 months with good precision. PHN can last for several months to several years but in this study we followed the patients for six months. This may have led to an underestimation of the true clinical burden of PHN. In this study, general practitioners recruited the participants. In Italy patients need to be referred for specialist care by their general practitioner, and even when they use private healthcare to consult a specialist directly, they have to report to their general practitioner for reimbursement of prescriptions via the national health system.
Acknowledgements The authors take full responsibility for the contents of this manuscript but would like to thank  Margaret Haugh ,  MediCom Consult  (supported by  Sanofi Pasteur MSD ) for her assistance in the preparation of the manuscript. The authors would like to thank all the study investigators: local health unit (LHU) of Asti:  G. De Maria ,  C. Torello ,  C. Nuti ;  LHU of Bologna :  A. Guerra , L.
, the resulting datasets are rich and complex. Currently there exists no single standard procedure for performing reproducible cohort-wide analysis while tackling systems-level heterogeneity and noise in multiple samples. Recently, we developed a platform (FLAME) for automated analysis of high-dimensional flow data  [7]. Each cell population (henceforth simply called population) in a sample is modeled by FLAME as a cluster of points with similar fluorescence intensities in the multi-dimensional space of markers. FLAME's heavy-tailed and asymmetric distributions are especially appropriate for flow data, since rare and interesting subpopulations tend to be tails connected to larger populations  [8]. Notably, the field of computational cytomics has witnessed rapid growth in the past few years, as reviewed by Lugli et al  [3].
In recent years, researchers have also started multiplexing many staining panels to overcome limits on the numbers of markers that can be accurately measured together using commercial cytometers  [4]. While the resulting data are more enriched, it can also produce a large number of distinct features from every panel of markers. Currently there exists no technique for systematic integration of such features across panels into meta-features for the common underlying sample. As part of JCM analysis, we introduce a new technique to combine both univariate and multivariate JCM features across multiplexed panels to construct enriched meta-features (or feature-sets), and use these to improve sample classification. Using simulation as well as several real-world benchmark datasets, we found that key performance attributes such as classification accuracy and running time of JCM are quite favorable compared to other methods.