dataesr/scientific-paragraphs-categorization huggingface dataset:
Study population This study includes all patients with newly-diagnosed and histologically confirmed GBM in 2008 (1 January-31 December). Histological diagnosis of GBM according to WHO 2007 classification  [27]  including glioblastoma, giant cell glioblastoma, and gliosarcoma, corresponding to ICD-O codes 9440/3, 9441/3, and 9442/3 respectively, were included. Exclusion criteria were previous surgery for GBM, spinal cord GBM, and patients from abroad or French overseas departments. A data card was used to retrospectively collect data on the oncological management [surgery, RT, and chemotherapy (CT)] and the followup care of these patients for the period 2008/01/01 to 2015/02/03. According to French neurosurgical guidelines, extent of RS should be evaluated with postoperative MRI. In our study, this information was reported from patient file.
Statistical analysis Statistical analysis was performed using SAS Enterprise Guide software, version 6. 1. The analysis included a descriptive part of the original data and the oncological treatments received by the patients. Survival was estimated by the Kaplan-Meier method and defined as the time from first surgery (corresponding to the histological diagnosis) to death or censored at the date of last follow-up. The log-rank test was used to compare survival curves among different strata. The assumption of proportional hazards was verified before survival curve comparisons. Univariate Cox regression model was used to estimate hazard ratios (HRs) of strata versus reference level and their 95% Wald confidence interval (CI). For continuous variables, log linearity was tested before HR estimations.
But none of them was a specific clinical trial or a real population-based study. Blumenthal et al. [35]  performed an interesting pooled analysis of individual patient data from four randomized trials for newly diagnosed GBM. A total of 2214 GBM patients were included in the four trials. All patients who were progression free 28 days after cycle 6 were included. The decision to continue temozolomide was per local practice and standards, and at the discretion of the treating physician. Of these, 624 qualified for analysis: 291 continued maintenance temozolomide until progression or up to 12 cycles, while 333 discontinued temozolomide after 6 cycles (these nearly equivalent numbers illustrate the difficulty of the question). First, as noted by the authors, this study is an unplanned retrospective meta-analysis of patients included in clinical trials spanning a decade.
Secondly, these patients were selected and were not representative of the population in the real world (age, percentage of complete RS, comorbidity, etc. ). Thirdly, whilst the percentage of approximately 30% of patients remained progression free at the end of the standard 6 cycles of temozolomide maintenance therapy is in accordance with data from clinical trials, it is high compared with data from population-based or real world studies. This could reflect the frequent selectivity of patients in inclusion in clinical trials. Fourthly, the pattern of patients free of progression after the 6th adjuvant temozolomide, includes in these randomized studies was different than ours, particularly in proportion of total RS (53. 7 vs. 42. 7%). This better prognostic factor is less frequent in real life population patients and participates to increase the heterogeneity  [30].
Background: The purpose of this systematic review was to appraise the empirical evidence pertaining to medical students and the integration of mindfulness and physical exercise regimens. Methods: A systematic review was undertaken. Five databases were used to survey the salient literature. Results: The initial search identified 353 potentially relevant articles of which 17 articles were considered for the final review. The findings indicated that the research was mainly conducted in the USA with some research originating from Europe, Canada, Jamaica, and India. In addition, a range of research designs were applied to measure or discuss the efficacy of the integrated intervention. Four key categories captured the essence of the results of our review, namely: (1) quality of evidence and research methods; (2) types of interventions; (3) measurement protocols; and (4) benefits of integrating mindfulness and physical exercises.
Given the lauded benefits of mind-body strategies in promoting health and ameliorating ill-health  [20, 21] , we were interested to find out what methods were being researched and to see if these methods had proven to be effective for medical students. This study preferentially employed a systematic review to determine the evidence, in both the quantitative and qualitative literature, regarding the use of mindfulness and physical exercises to enhance the wellbeing of medical students. Systematic reviews require the implementation of a detailed search strategy and aim to methodologically search relevant databases and determine the quality of evidence on a particular topic  [22]. This review option was preferred to a narrative review that may have a selection bias or a meta-analysis which requires a focus on the quantitative evidence to determine a summary effect size  [22].
Search Protocol A literature search was conducted in five databases: the three Ovid databases Embase (1980-Present), Medline (1946-Present) and PsycINFO (1806-Present), as well as Scopus and all segments of the Cochrane Library. Three researchers (MH, TJP, JH) collaborated to identify search terms and develop search strategies that would be both sensitive enough to retrieve all relevant studies, as well as studies specific to our research focus. The key concepts mindfulness/meditation, were combined with a range of exercise related terms and modalities. The keyword medic* was included to narrow the focus to medical students. Relevant subject headings specific to each database were combined with keywords to increase the scope of the searches, for example, see Table  1  for the medical subject headings and keywords used.
Types of Outcome Measures Outcome measures for our study were not defined ahead of time, but were identified as the outcomes reported in the included papers (outcomes being beneficial, harmful or uncertain). The final search strategies were run in all five databases and search results were imported and collated into EndNote, a reference management program  [25]. The articles were then reviewed by two researchers (MH, TJP) and duplicates were removed. The resulting studies were screened systematically by TJP and MH, first by title and then by abstract. After screening, the full texts were reviewed together by two researchers (TJP & MH) using precise inclusion and exclusion criteria as listed below: 1. Studies must have included an empirical study or a critical review of the area. 2. Only journal articles and conference abstracts (with sufficient data) were considered for review.
Search History and Results The initial search results from the five databases yielded a total of 353 articles (Figure  1 ). Seventy six duplicates were identified and in the next step we conducted a review of 277 titles and abstracts based on inclusion and exclusion criteria. The subsequent quota of articles resulted in the exclusion of 250 articles. A list of 31 articles was identified as potentially relevant by two researchers (MH, TJP). This was reduced to a final list of 17 refereed sources after appraisal of the full text. Table  3  shows the final collated list of 17 articles included in the evidence review, showing key study features such as methods, research design, key findings and conclusions.
For example, Tai Chi has been relatively well researched in the general literature heralding its benefits for students in higher education  [21] , although not specifically with medical students (a group purported to be at high risk of ill-health). In addition, the Webster et al  [21]  systematic review of Tai Chi practices in higher education reviewed articles not only in English but also in Chinese, and one of the findings was the greater number of articles in Chinese. Hence, a further search involving databases showing articles written in non-English languages may have created a greater research yield and may have included studies of Tai Chi and other mindfulness and physical exercise programmes being applied to medical students.
Measurement Protocols Two measurement protocols were identified in the literature reviewed, namely physiological measures and self-reported measures. For example, some of the physiological measures being employed included forced vital capacity, expiratory reserve volume, peak expiratory flow rate, and maximum voluntary ventilation  [48]. In addition, some of the self-reported measures included the Jefferson Scale of Physician Empathy, Cohen's Perceived Stress Scale, the Self-Compassion Scale, and the General Well Being Scale  [46, 47]. None of the reviewed studies integrated both physiological and self-reported data, which would have been useful assuming that the two tend to be complementary. Given the studies in this review reported on interventions that were aimed at heightening mindfulness  [36, 38] , including multiple data sources, as used in other studies  [61] , would have improved triangulation and the credibility of the results.
Quantification of N. meningitidis (bioluminescence imaging) Mice infected intranasally with bioluminescent N. meningitidis were anesthetized with a constant flow of 2. 5% isoflurane mixed with oxygen, using an XGI-8 anaesthesia induction chamber (Xenogen Corp. ). Bacterial infection images were acquired using an IVIS 100 system (Xenogen Corp. , Alameda, CA) according to the instructions of the manufacturer. Analysis and acquisition were performed using Living Image 4. 3. 1 software (Xenogen Corp. ). Images were acquired using a 1-min as previously described  [18]. An uninfected mouse under the same conditions of acquisition was used to subtract the background.
Antibodies and flow cytometry The second part of whole-lung homogenates were used to prepare single-cell suspensions were using treatment with collagenase IV (Sigma-Aldrich, St. Quentin Fallavier, France) and ACK (Ammonium-Chloride-Potassium) Lysing Buffer (Fisher Scientific, Graffenstaden, France) as previously described  [15, 20]. Analysis was then performed using a LSR Fortessa Flow Cytometer (BD Biosciences, San Jose, CA, USA) and the results analysed with FlowJo software (v10; Tree Star, Ashland OR, USA). The antibodies and the gating strategies used are depicted in the Additional file 1: Figure  S1.
2. B | Treatment planning and pretreatment QC preparation Treatment planning for H&N and prostate localizations were performed with Eclipse ® v13. 5 software (Varian Medical System, Palo Alto, CA, USA). For prostate treatment plans, a prescribed dose of 76 Gy with a fraction of 2 Gy was delivered. For H&N treatment plans, the prescribed dose ranged from 66 to 70 Gy (three dose levels corresponding to high-risk CTV (66-70 Gy), intermediate risk CTV (57-60 Gy), and low-risk CTV (54-56 Gy)) with a fraction of 2-2. 12 Gy. For each localization, the plan was delivered by two coplanar arcs, one clockwise, and one counterclockwise, with a 6 MV energy and a maximum dose rate of 600 UM/min which are the parameters usually used in our institution. For both AC and PDIP processes, the treatment plan was computed in the ArcCheck ® or EPID As 1200 ® image to obtain the planned dose or CU matrix (Fig.
2. D | Assessment of process sensitivity for various potential technical errors To assess the detection sensitivity of AC and PDIP processes, the following potential technical errors were simulated: • Collimator error (from 1°to 5°, increment of 1°) • Dose error (equal to +2% and +3%) • MLC opening error (equal to +0. 5 mm, +1 mm and +2 mm) These errors were inserted into five H&N and five prostate initial DICOM-RT treatment plans using a MATLAB 2017 ® routine (The MathWorks, Natick, MA, USA). A total of 10 error-free plans and 100 plans with errors were respectively computed for AC and then for PDIP (50 plans with a collimator error, 20 plans with a dose error, and 30 plans with an MLC opening error). The comparison of all the measurements was made with the error-free planned dose matrix.
Clinical Data Medical records were used to obtain the most relevant data about demographics, clinical, virological, and laboratory characteristics, and all the information was recorded at each institution using a standard database via an online form, as we have previously described  [27]. The LSM was assessed by transient elastography (FibroScan®, Echosens, Paris, France), with results expressed in kilopascals (kPa), and a range from 2. 5 to 75 kPa. Trained operators carried out the transient elastography. Representative measurements of liver stiffness were considered reliable when we obtained ten acquisitions with a success rate ≥60% (interquartile range <30%)  [28]. From these LSM values, patients were stratified according to LSM cutoffs previously described: <12. 5 kPa (non-cirrhosis,  [28] ), 12.
Next, the IMMUNOPREP Reagent System (Beckman Coulter, Galway, Ireland) was added to each sample using a Coulter MULTI-Q-PREP Lysing Workstation (Beckman Coulter, Miami, FL, USA) to lyse and fixate them. Fluorescence was measured with a Gallios™ flow cytometer (Beckman Coulter, Miami, FL, USA). The number of minimum events was 200,000 cells in the lymphocyte gate for each sample, and flow cytometry data were analyzed using the Kaluza™ software package (version 1. 5; Beckman Coulter, Miami, FL, USA). The flow cytometry gating strategy for regulatory T cells subsets is shown in Figure  1. were first gated on a forward scatter/side scatter (FSC-A/SSC-A) dot plot. The lymphocytes events were visualized using a CD3/CD4 dot plot and the CD4 + T cells were gated on a gate CD4 +. Cells on CD4 + are simultaneously displayed on both the CD127/CD25 dot plot and CD45RA histogram.
Statistical Analysis The statistical analysis was performed with the Statistical Package for the Social Sciences (SPSS) 21. 0 (SPSS INC, Chicago, IL, USA). Statistical significance was defined as p < 0. 05. All p-values were two-tailed. For the descriptive study, values were expressed as an absolute number (percentage) and median (25th; 75th percentile). Categorical data and proportions were analyzed using the chi-squared test or Fisher's exact test, as required. Kruskal-Wallis and Mann-Whitney tests were used to compare data among independent groups. We also used Generalized Linear Models (GLM), with a gamma distribution (log-link), for evaluating the adjusted association between LSM values and levels of biomarkers in peripheral blood. This test gives the arithmetic mean ratio (AMR) or the value by which the arithmetic mean of the primary outcome is multiplied.
Supplementary Materials: The following are available online http://www. mdpi. com/2073-4409/7/11/196/s1, Table  S1 : Characteristics of control groups and HIV/HCV co-infected patients. Funding: This study was supported by grants from Instituto de Salud Carlos III (ISCII; grant numbers grant numbers PI14/01094 and PI17/00657 to JB, PI14/01581 and PI17/00903 to JGG, PI14CIII/00011 and PI17CIII/00003 to SR, and PI17/01115 to JLJ), Ministerio de Sanidad, Servicios Sociales e Igualdad (grant number EC11-241), Comunidad de Madrid (B2017/BMD3703). The study was also funded by the RD16CIII/0002/0002, RD16/0025/0018, and RD16/0025/0017 projects as part of the Plan Nacional R + D + I and co-funded by ISCIII-Subdirección General de Evaluación and the Fondo Europeo de Desarrollo Regional (FEDER). J. B.
Acknowledgments: We want to acknowledge the patients in this study for their participation, and the  Spanish HIV HGM BioBank  integrated into the  Spanish AIDS Research Network (RIS)  and collaborating centers for the generous gifts of clinical samples used in this work. The  HIV BioBank , integrated in the  Spanish AIDS Research Network , is supported by the  Institute of Health Carlos III, ISCIII ,  Spanish Health Ministry  (Grant no  RD06/0006/0035  and  RD12/0017/0037 ) as part of the  State Plan for Scientific and Technical Research and Innovation  and cofinanced by  ISCIII-Sub-Directorate General for Research Assessment and Promotion  and.
This study is structured as follows: The PASTiS-57 sensor is presented in detail in Section 2. 1. Section 2. 2 describes the field data collection and analysis. Section 2. 3 elaborates on implementation of the sensor in DART, the set up of the synthetic canopy and how sensitivity analysis was conducted. Results are presented in Section 3 and discussed in Section 4. Section 5 summarises the results and lists implications for future sensor design.
PASTiS-57 Instrument The PASTiS-57 consists of a weather proof, battery powered datalogger with 6 photodiode-based sensors (Figure  1 ). The sensors are fixed to a viewing zenith angle of 57. 5 • , sensitive in the blue spectral region to minimise canopy multiple scattering and have different lengths of wire for sensor distribution around the data-logger. The logger is battery powered and can autonomously collect data at 1 min interval for up to four months. Intervals of 2 min and 5 min are also possible. Radiation is recorded with uncalibrated Digital Number (DN) in the interval 0-4000, whereas larger DNs are treated as unreliable due to saturation effects. The signal can be calibrated with dedicated Photosynthetically-Active Radiation (PAR) sensors  [25]. However, a more practical approach is to utilise the relative signal by installing one device above the canopy, which serves as reference for incoming radiation, and another device below the canopy, which represents the observations.
Reference Datasets Next to PASTiS-57 records, a multi-temporal campaign with a RIEGL VZ-400 Terrestrial Laser Scanning (TLS) (RIEGL LMS GmbH, Horn, Austria) was conducted at the Speulderbos site. This scanner has shown good results for monitoring phenology  [39]. The main advantage of TLS as a gap fraction sensor is its independence from illumination conditions  [42, 46, 47]. This results in high precision time series, i. e. , with low noise in the temporal domain. On the other side, partial hits lead to underestimation of gap fraction by these kind of sensors  [46, 48]. Partial hits result from objects that only partially cover the laser instantaneous field of view, but are registered as full interceptions by the waveform analysis methods of commercial suppliers to maximise point cloud density.
Phenological Model Fitting LSP can be modelled with logistic functions  [1, 9]. These mathematically simple models are fitted piecewise to time series of vegetation indices or LAI to describe the spring growth and autumn senescence periods  [39]. From these models LSP indicators like SOS and EOS can be derived. Here, a logistic model was used  [9, 39] : PAI(t) = U -L 1 + e -k(t-t m ) + L ( 5 ) where t is time (expressed as Day Of Year (DOY)), U the upper asymptote ( m 2 m -2 ), L the lower asymptote ( m 2 m -2 ), k the growth rate (d -1 ) and t m the inflection point, where k is maximal (DOY). The model was fitted with a non-linear least squares routine implemented in the nls function of the R stats package  [51, 52]. Separate sigmoids were estimated for the spring 2016 and autumn 2017 periods.
Acknowledgments: Data analysis was supported by the  Research and User Support (RUS) Service. The  RUS Service  is funded by the  European Commission , managed by the  European Space Agency , and operated by  CSSI  and its partners. The authors thank the  Dutch Forestry Service (Staatsbosbeheer)  for granting access to the site, and  Murat Üçer  and  Christiaan van der Tol  for access to the scaffold tower. The fieldwork design of this study was inspired by the M. Sc. thesis of Tom Schenkels (http://edepot. wur. nl/333531). Further thanks go to  Marcello Novani ,  Alvaro Lau Sarmiento  and  Mathieu Decuyper  for help during the fieldwork.
Data Analysis Optical AP signals were filtered using spatial averaging (kernel 2. 1 mm) and temporal averaging (kernel 3 ms). Optical ATs were determined by the time of maximal derivative during the AP upstroke and APD was determined as the difference between the time of 90% of repolarization and AT. APDs were measured from a small area (2. 8 mm × 2. 8 mm) at the origin of activation or the origin of breakthrough, on each surface and depending on the pacing location. For PF pacing, local endocardial APD was measured in a region distinct from all potential origins of activation mediated by PF. Dispersion of APD (µ) was measured as the difference between 5 and 95% confidence interval of normal sample distribution. Epicardial conduction velocities were analyzed using a published MATLAB program  (Doshi et al.
FUNDING This work was supported by  European Research Council  under the European Union's  Seventh Framework Programme  (FP/2007-2013; Grant Agreement N •  ERC-2012-ADG_20120314  to MM, RW, MiH, MéH, and OB), the  Leducq Foundation (Transatlantic Network of Excellence RHYTHM  to MM, MiH, EV, MéH, and OB), and the  French Government  as part of the  "Investments of the Future" program  managed by the  National Research Agency (ANR ; Grant No. ANR-10-IAHU04-LIRYC  to MM, RW, JB, MiH, EV, MéH, and OB).
RESULTS All transplant patients were subjected to general analyses, but only patients transplanted from MMDs are reported here. Between 2003 and 2013, 1115 patients up to age 18 years, presenting with ALL in CR1 or subsequent CR, were en-rolled in either the ALL SCT 2003 BFM Study (n = 705) or the ALL SCT 2007 I-BFM study (n = 410). Among these patients, 148 underwent HSCT from MMDs, 86 were enrolled in the 2003 BFM study, and the 62 remaining patients were enrolled in the international protocol. Data regarding patients treated on the ALL SCT 2003 BFM study and ALL SCT 2007 I-BFM study and transplanted from named MSDs and MUDs (as defined per protocol) were published by Peters et al. [8]  in 2015. We did not perform statistical comparisons between the cohort reported by Peters et al. and the cohort described here.
Obtaining significantly less transplant-associated early and late toxicity is also desired. Thus, we avoided TBI-based conditioning regimen for patients younger than age 2 years with MMDs. To further investigate the possibility of TBI-free conditioning regimen, we initiated a prospective randomized trial (Eudract no. 2012-003032-22, see also www. clinicaltrials. gov) to evaluate the outcome after TBI-versus chemotherapy-based conditioning regimens in patients over 4 years of age with ALL and MSDs or MUDs. All other patients (younger than 4 years and those with only MMDs, including T cell-replete posttransplant cyclophosphamide haploidentical HSCT patients) receive TBI-free conditioning regimens. In the present study we demonstrated the feasibility of allogeneic HSCT from alternative donors in both HRR and VHRR pediatric patients with ALL in CR after myeloablative conditioning.
Thus, alternative proteins are not identical to reference proteins  (36, 37). For example, AltMRVI1, an alternative protein of the MRVI1 gene present in the 3ЈUTR region of the MRVI1 mRNA, has been shown to interact with BRCA1  (36). Translation of altORFs in human mRNAs in addition to refORFs provides access to a large set of novel proteins whose functions have not been characterized, and that cannot be detected using conventional protein databases. Moreover, conventional bottom-up proteomics is not well suited for their analysis because these proteins are relatively small (between 2 and 20 kDa) and more often do not contain enzyme-cleavable sites. Thus, the number of enzymatically cleaved peptides generated is too small compared with those of reference proteins. Consequently, the probability of peptide and protein identification is poor, in the absence of low-mass protein enrichment steps.