dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements The authors acknowledge all the members of the  Molecular Diagnosis and Risk Stratification of Sepsis consortium  for the participation in the data collection and especially acknowledge  Friso M. de Beer, M. D. ; Lieuwe D. J. Bos, Ph. D. ; Gerie J. Glas ,  M. D. ; Roosmarijn T. M. van Hooijdonk, M. D. , Ph. D. ;  Janneke Horn, M. D. , Ph. D. ; Laura R. A. Schouten , M. D. ;  Marleen Straat , M. D. ;  Luuk Wieske, M. D. , Ph. D. ; Esther Witteveen, M. D. ( Department of Intensive Care, Academic Medical Center, University of Amsterdam, The Netherlands ),  Arie J. Hoogendijk, Ph. D. ; Mischa A. Huson ,  M. D. ; Maryse A. Wiewel ,  M. D. ( Center for Experimental and Molecular Medicine, and Center of Infection and Immunity Amsterdam (CINIMA) ,  Amsterdam University Medical Centers , location  Academic Medical Center ,  University of Amsterdam, Amsterdam, The Netherlands ),  Peter M.
Design and patients This clinical trial was approved by both the Ethics Committee CPP EST I (Dijon, France, EudraCT N°: 2015-000213-42) and the Drug Safety Agency (ANSM). All the study procedures were performed in accordance with the provisions of the Declaration of Helsinki and the Good Clinical Practice guidelines. The study was also registered at www. clinicaltrial. gov (Study ID: NCT02851394). The current single-center, prospective, randomized, double-blind study was conducted at Dijon University Hospital, Burgundy, France, between October 2015 and October 2016. Patients requiring scheduled or non-urgent surgery for valve disease, aorta disease, atrial myxoma, or coronary artery bypass graft via medial sternotomy were included in the study. The exclusion criteria were patients who underwent redo surgery following previous sternotomy and patients with a known hypersensitivity to any of the products used in the present study.
The catheter was purged with 10 mL of 0. 5% levobupivacaine. On admission to the ICU, the patients were given either a bolus of tramadol as a local infusion at a dose of 2 mg/kg or 0. 9% saline via a syringe filled to 10 mL. The syringe was prepared and sterilized by the pharmacy following the attribution of the batch using Tenalea randomization software. The bolus was administrated by the ICU nurse, who was blind to the allocated syringe. Once the bolus had been given, the wound catheter was linked to an elastomeric pump (Multirate Infusor LV 5 7 12 mL/h, Baxter) filled with 0. 125% levobupivacaine. The portable diffuser administered the local anesthetic at a rate of 12 mL/h until extubation, and then at a rate of 7 mL/h for the first 48 hrs following extubation. After this period, the catheter was removed.
Data collection The clinical data, including the patients' daily consumption of morphine, were recorded, with the initial titration recorded at extubation H0, then at H+6 hrs, H+24 hrs, and H+48 hrs. The time between the titration and the first bolus delivered by the PCA was also recorded. Data concerning the static and dynamic pain, as evaluated using the VAS, were collected at extubation, at H+6 hrs, and then every 12 hrs for the first 48 hrs following extubation. The type and the total dose of rescue analgesia were also recorded during the first 48 hrs. The level of sedation was evaluated using the Ramsay scale at H+6 hrs following extubation, and then every 12 hrs for 48 hrs. The arterial blood gasses were measured at H+6 hrs after extubation, and then once per day over the 2 days following the surgery.
Data sharing statement Will individual participant data be available? Yes. What data in particular will be shared? All the individual participant data collected during the trial will be shared following deidentification. What other documents will be available? The study protocol. When will data be available? Immediately following publication. No end date. With whom? Researchers who provide a methodologically sound proposal. For what types of analyses? To achieve the aims of the approved proposal. By what mechanism will data be made available? Proposals should be directed to mohamedomar. ellouze@chu-dijon. fr. To gain access, data requestors will need to sign a data access agreement.
That initial review indicated that the literature is equivocal about the most effective strategies to communicate scientific uncertainties and that, on the whole, there is a lack of empirical data in the literature on which to base a working model. In EFSA's own publication on best practice in risk communication 'When food is cooking up a stormproven recipes for risk communications'  (EFSA, 2017) , which was developed with national partners, the advice to communicators is only of a general nature. Therefore, the Scientific Committee recommended that EFSA should initiate research activities to explore best practices and develop further guidance in areas where this would benefit implementation of the Uncertainty Analysis GD, and the communication of uncertainties in scientific assessments targeted at different audiences.
Further support will be provided by establishing an online resource of 'frequently asked questions' ('FAQs') including entries on key concepts and expressions for communicating uncertainty, including the interpretation of probability expressions (see  Section 3. 1). This will be useful to assessors and communicators at EFSA as well as providing supporting information for interested members of the target audiences. These FAQs will be made available publicly on EFSA's website. The authors recognise the limited type and number of example assessments used in Section 3. 2. A proposal in the implementation of the Uncertainty Analysis GD is the creation of a database of examples, which will grow over time and assist assessors when dealing with similar types of Confidence Assessors sometimes use qualitative expressions of confidence (e.
55 61 MERS-CoV vaccines are in the early stages of development,  55 62 63  with one candidate vaccine in phase I clinical trials (NCT02670187). 64 Neutralising monoclonal antibodies have been designed to target the MERS-CoV spike protein,  53 65  with ChAdOx1 and modified vaccinia Ankara vectors also strong vaccine candidates,  60 66  but none have yet advanced to clinical trials. To accelerate the process, the Coalition for Epidemic Preparedness Innovation has recently launched a call for proposals for the development of a human MERS-CoV vaccine in order to engage with developers interested in supporting these efforts. 67.
Serological assays Serology is not widely performed for diagnosing acute MERS-CoV infection; however, it has been a useful tool BMJ Global Health to determine the extent of infection around clusters and in seroepidemiological studies in animals and humans. Seroconversion typically occurs during the second and third week after symptom onset; data suggest that low antibody titre in the second week or delayed seroconversion is more closely associated with mortality than high viral load. 71 74 MERS-CoV seroconversion may not be observed for some patients, notably with mild or asymptomatic infection, and can show cross-reactivity with antibodies to other coronaviruses. 42 69 erological methods for the detection of antibodies against MERS-CoV include ELISA, IIFT and neutralisation tests. MERS-CoV serological assays can employ commercial reagents or proprietary monoclonal antibodies as capture agents.
Acknowledgements We gratefully acknowledge input to the roadmap from all those who attended the FAO-OIE-WHO Global Technical Meeting on MERS-CoV in September 2017. The opinions expressed in this article are those of the authors and do not necessarily reflect those of the institutions or organisations with which they are affiliated. Editorial assistance for later drafts was provided by  Rachel Wright, PhD , funded by FIND, according to Good Publication Practice guidelines. Contributors CK-C contributed insight into the diagnostic needs for outbreak pathogens. LTM provided the background research for the manuscript. AC, CJO and MDVK contributed to drafting the manuscript. All authors reviewed, edited and approved the final version of the manuscript. funding Publication of this article was funded by FIND.
endTB monitoring procedures and follow-up The endTB observational study captures routine clinical data for study participants who are treated under the supervision of the NTPs or local implementing partners at each site. No additional interventions or procedures are undertaken as part of the observational study. Figure  1  illustrates the process-flow from pre-enrollment, to enrollment and follow-up, to the final outcome and analysis. The decision to start patients on a bedaquiline-or delamanid-containing regimen was made by responsible physicians according to indications in WHO interim guidance for the use of bedaquiline  [7]  and delamanid  [8] ; in some countries an expert committee or "consilium" participated in decision-making. Use of bedaquiline or delamanid was not affected in any way by participation in the observational study.
Protection of human subjects and ethical approval This study was approved by the Partners Healthcare Human Research Committee (Boston, MA, USA), the MSF Ethics Review Board (Geneva, Switzerland), IRD Institutional Review Board (Karachi, Pakistan) and in all 17 enrolling countries by local ethics committees or IRBs. The study is registered on clinicaltrials. gov (NCT03259269). Patients started on treatment with bedaquiline or delamanid were invited to enroll in the observational study. Informed consent was solicited from patients (or assent from the patient and consent from a guardian in the case of minors, as defined by local legal requirements). During this process, study staff clearly communicated potential risks in the appropriate language. Those who did not consent to their data being used for research still received treatment with bedaquiline or delamanid per national and site protocols.
Data collection and management This study involved collection of data only, without experimental interventions or additional patient encounters with research staff outside of routine treatment visits. Local and central research staff ensured that data collection and reporting followed study protocols through site monitoring visits and regular local review of documentation. Standardized forms capture routine clinical, sociodemographic, microbiological, clinical laboratory results, and treatment records of TB and comorbidities and safety data. Local research staff performed site level quality checks of paper-based forms. Most data were directly collected into standardized forms (Additional file 2) and then entered into the endTB electronic medical record (EMR). Based on an open-source system called 'Bahmni' (https://www.
bahmni. org), the endTB EMR (Database MySQL) was developed with an independent software company. It was designed to capture and harmonize detailed longitudinal patient-level data across all 17 countries. The endTB EMR is freely available for use by other MDR-TB programs or projects (install and set up: https://github. com/ endtb/endtb-config; https://github. com/endtb/endtb-config/wiki/Deployment-Steps). Continuous quality control and quality assurance (QA) are achieved through automated range checks at data entry, real-time data reviews at each study site, periodic source-data verification, and a system of monthly data quality checks at central level. The queries generated by the central QA are sent to site staff who review, confirm entered data or make appropriate corrections to site EMRs and report to the central site for resolution of each query.
Pharmacovigilance As a part of endTB, a pharmacovigilance (PV) database is maintained and hosted by a single PV unit based in Geneva, Switzerland. The PV unit was established to ensure that safety information is properly reported to improve medical practices. The reporting aims to ensure the safety of patients treated with regimens containing new TB drugs and to disseminate relevant safety information to appropriate stakeholders in a timely manner. This includes: Reporting of Serious Adverse Events (SAE) within 24 h of physician knowledge [Serious adverse event is an untoward medical occurrence that, at any severity level: results in death; requires hospitalization or prolongation of hospitalization; results in persistent or significant disability/ incapacity; is life-threatening; is a congenital anomaly or a birth defect; is otherwise medically significant]; and Periodic reporting of non-serious adverse events (AE) of clinical significance including: AEs of special interest, AEs recorded as having led to a treatment change/interruption, and AEs otherwise judged to be clinically significant by the treating physician.
To address this, we have tracked informed consent acceptance at each site and will conduct sensitivity analyses that consider various scenarios accounting for study refusal. Lastly, the intervention was not part of the study and was not randomized. Confounding by indication is likely to have occurred in the use and duration of bedaquiline and/or delamanid and companion drugs. In the design phase of this study, we collected data on the myriad of time-varying factors that could influence regimen prescription, and we will adjust for them in the analysis phase using appropriate statistical methods.
Additional, important questions about the optimization of regimens containing these-and repurposed-drugs and especially about all-oral regimens were also anticipated by the endTB project. The endTB trial (Clinicaltrials. gov identifier: NCT02754765) planned at the same time as the endTB observational study, explores these optimization questions, which are better suited to randomized studies. Although the endTB trial design was finalized prior to accumulation of safety and effectiveness results in the endTB observational study,  [17, 18]  ongoing evaluation of the assumptions that guided the trial sample size and revision of the control regimen composition have been informed by the endTB observational study. While clinical trials are "the preferred source of evidence for measuring the effects of interventions" in the GRADE process for WHO Guideline development  [19] , observational studies of MDR-TB treatment continue to provide critical evidence that shapes our understanding of the best way to treat MDR-TB  [20, 21].
Observational studies, particularly of patients treated under programmatic conditions, can have a number of potential pitfalls which we have tried to address in the design and implementation of the endTB observational study. Generating high quality evidence in programmatic conditions is challenging particularly for NTPs who are chronically underfunded for both clinical care and data reporting  [22]. This is further complicated in MDR-TB treatment, which requires complex treatment regimens over a long period requiring comprehensive patient support  [23]. Patients receiving these treatments often experience AEs that must be detected, managed and recorded. The endTB observational study brought additional resources for data collection, provided clinical guidance, and support for adverse event monitoring, reporting, and management.
Even though national guidelines may clearly stipulate the type of AE screening that should be done for all MDR-TB patients, the costs of the tests may not be covered by the NTP; if patients cannot raise funds for the tests, they are often not performed  [29, 30]. In endTB, project funds were used to cover screening tests recommended by the NTP but not paid for by the health system, to ensure uniformity in screening and patient safety. In many countries this was necessary not only for new screening tests related to bedaquiline and delamanid, such as ECG, but also standard screening tests for AEs-such as hearing loss, electrolyte wasting, and peripheral neuropathy-that are commonly linked to other drugs. The endTB observational study will therefore collect data on serious and non-serious AEs, related to new and conventional MDR-TB drugs, at a scale and detail unprecedented for a programmatic setting.
Acknowledgements We would like to acknowledge the support of all our implementing local partners, the National TB Programmes in all participating countries, the  Bedaquiline Donation Programme  (a partnership between  USAID  and  Janssen Therapeutics of Johnson & Johnson) , which helped provide bedaquiline to patients free of cost,  Otsuka Pharmaceutical  for their donation of delamanid treatments at the start of the endTB Project. We also acknowledge many global organizations including GFATM,  GDF  and  WHO  for working in parallel together to improve access to, and evidence for, high -quality treatment for RR/MDR-TB. Finally, we would like to thank all our country project teams and our patients for participating in this study and contributing to global evidence.
6 and 14. 3 • C, respectively, mean daytime VPD 0. 39 kPa, mean annual rainfall 1879 mm and mean daytime PPFD 633 μmol m -2 s -1 during 2007-13. More information on meteorological conditions at both Arboretum and Nyungwe was provided by  Mujawamariya et al. (2018). In addition, a weather station (VP-3, PYR and ECRN-100, Decagon Device, Inc. , Pullman, WA, USA) recorded air temperature, relative humidity, solar radiation and precipitation at another open place by the Arboretum office during the last quarter of the study. These data were used for comparisons with leaf temperature measurements (see below). Seven Tiny Tags (Model Tinytag Plus 2, Gemini Data Loggers Ltd, Chichester, UK) recorded air temperature and relative humidity at 1. 8 m in plots with different radiation regimes (six plots with different overstorey canopy transmission plus one open plot; see below) during 15 successive days in March 2016.
For the third plant, photosynthesis was only measured at 410 μmol mol -1. Measurements were conducted within a few minutes after clamping onto the leaf or changing CO 2 concentration, without waiting for stomatal conductance to respond to respond to altered environmental conditions. Data of A n in shaded plots (and the derived V cmax and J max values) are thus representative for photosynthesis during sunflecks and do not reflect values where both photosynthesis and stomata have fully responded to the high measurement radiation. The stomatal conductance data point reported is that measured at 410 μmol mol -1 CO 2 concentration. The photosynthesis model by  Farquhar et al. (1980) , with modifications of photosynthetic temperature dependencies by  Bernacchi et al. (2001) , was parameterized using the one-point method  (De Kauwe et al.
Out of these non-N elements, only data for phosphorus are reported. The iWUE determined based on carbon isotope data was calculated as the difference between the ambient CO 2 concentration and intracellular CO 2 concentration times 1. 6 to account for the difference in stomatal conductance of water vapor compared with CO 2. Ambient CO 2 was assumed to be 402 μmol mol -1 , and intercellular CO 2 was calculated using equations in  Farquhar et al. (1989).
Wood density of dry wood was determined based on measurements of mass and volume on a piece of a dry stem without bark from each plant. In addition, eight plants per species which were not included in the main experiment were harvested in April 2015 to determine the initial biomass of different plant parts at the beginning of the experiment. The mean total initial dry mass ranged from 5 g to 14 g in the six species (Table  S1  available as Supplementary Data at Tree Physiology Online).
Data The data provided here two different omics approaches to contribute to the understanding of the impact of sub-optimal temperature growth conditions on A. thaliana responses. The raw data include information about differential gene expression and cell wall protein abundance in five wild A. thaliana ecotypes. All the LC-MS/MS proteomics data have been deposited at PROTICdb (http://moulon. inra. fr/ protic/wallomics). The RNAseq data are available at NCBI short read archive (https://www. ncbi. nlm. nih. gov/sra, BioProject PRJNA344545). The transcriptomic and proteomic quantification datasets in rosettes and floral stems are provided in two Supplementary files including: Supplementary file 1: Quantitative cell wall proteomics data: proteins were extracted from purified cell walls of A. thaliana rosettes or floral stems after growth at 22 C or 15 C by saline solutions (CaCl 2 0.
Value of the Data The data provide a first level of molecular description at the transcriptomics and the cell wall proteomics levels of four newly-identified A. thaliana altitudinal ecotypes from the Pyrenees mountains. The datasets include RNAseq and cell wall proteomics quantitative analyses of two organs (rosettes and stems) of five A. thaliana ecotypes at two growth temperatures. The data can be used to study the impact of sub-optimal temperature growth conditions on A. thaliana ecotypes responses. analyses. The rosettes and floral stems were collected just before bolting (stage 5. 10  [3] ) and at the first flower stage of development (stage 6  [3] ), respectively. The same biological triplicates were used to prepare samples for both transcriptomics and cell wall proteomics analyses.
Identification of proteins by LC-MS/MS The identification of proteins extracted from cell walls was performed by LC-MS/MS at the PAPPSO proteomics platform (pappso. inra. fr/) after tryptic digestion in solution as described  [6]. Parameters for MS data processing in the X!Tandem software (JACKHAMMER, 2013. 6. 15, www. thegpm. org/tandem/) and the X!Tandem Pipeline 3. 3. 4 [7]  are detailed in Ref. [8]. Trypsin digestion was declared with no possible miscleavage. Only proteins identified with at least two different specific peptides in the same sample and found in at least two biological replicates were validated. Furthermore, quantification was performed on peptides with standard deviation retention times lower than 20 s.
Bioinformatics annotation of proteins and quantification The prediction of sub-cellular localization of proteins was performed with the ProtAnnDB tool (http://www. polebio. lrsv. ups-tlse. fr/ProtAnnDB/, [9]. A protein was considered as a cell wall protein (CWP) if two bioinformatics programs predicted it as secreted, no intracellular retention signal was found and no more than one trans-membrane domain was predicted as described in Ref. [10]. Quantification was only operated for CWPs using the MassChroQ 2. 2. 12 software (http://pappso. inra. fr/ bioinfo/masschroq/,  [11] ) and it was done as in Ref. [12]. Briefly, a background noise was used to replace missing data in order to facilitate the statistical analysis. This step was done differently to distinguish between validated (identification with at least two specific peptides in at least two of the three biological replicates of the ecotype/temperature combination), non-validated proteins (identification of only one specific peptide and/or in only one biological replicate) and undetectable proteins (no peptide identified in this combination).
RNA sequencing (RNAseq) Protocols used for the transcriptomic analysis have been detailed in Ref. [12]. The RNAseq data have been obtained at the Get-PlaGe platform (https://get. genotoul. fr/). Short pair-end sequencing reads generated from the Illumina platform (https://ng6. toulouse. inra. fr/) were trimmed based on the quality scores (limit: 0. 05), end ambiguity (maximum allowed number of ambiguities: 2) and adaptor sequences, using the commercial CLC Genomic Workbench 8. 0 software (CLC bio, Aarhus, Denmark). The online CLC protocol for trimming and assembly has been followed (https://www. qiagenbioinformatics. com/). The reads shorter than 50 bp after trimming were discarded. The TAIR 10 database has been used for the assembly process (https://www. arabidopsis. org/). The calculation of gene expression level (RPKM) has been obtained with the CLC software (settings: minimum mapped read length fraction¼0.