dataesr/scientific-paragraphs-categorization huggingface dataset:
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Comparison (through meta-analysis) between patients included and excluded from analyses. Supplemental material Supplemental material BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance placed on this supplemental material which has been supplied by the author(s) BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Ann Rheum Dis Ann Rheum Dis Ann Rheum Dis placed on this supplemental material which has been supplied by the author(s) Ann Rheum Dis Ann Rheum Dis REFLEX -NCT00468546/ NCT02097745 Supplementary Included (n=5,792) a yes no Excluded (n=2,322) The protocol did include week 104 assessment of radiographic score.
Also, very difficult to match visit date with visit number. Difference (95%CI) b IMAGE -NCT00299104 n Estimate (95%CI) yes n No Estimate (95%CI) Only safety data was provided ClinicalStudy-Baselines features RAPID 1 -NCT00152386 yes yes DataRequest 5 -data from UCB Female (%) Age (yrs) RAPID 2 -NCT00160602/ NCT00175877 5,792 79% (77 to 81) 2,322 yes 5,792 51. 4 (50. 5 to 52. 4) 2,320 79% (76 to 81) 52. 8 (51. 6 to 54. 0) yes 0% (-2. 2 to 2. 6) 1. 3 (0. 5 to 2. 0) C-OPERA -NCT01451203 Disease duration (yrs) 5,102 5. 6 (4. 5 to 6. 7) 2,086 The Sponsor was Astellas. Data 5. 6 (4. 5 to 6. 7) 0. 03 (-0. 18 to 0. 23) RF positive (%) 5,666 no 84% (80 to 88) 2,212 no not available in the Sharing Data 82% (76 to 87) 4% (-0. 3 to 7. 5) DAS28CRP3V CRP (mg/dl) 5,781 5,781 4. 98 (4. 83 to 5. 13) 2,260 2.
4V-near-remission 5,792 19 (15 to 22) 2,017 12 (9 to 16) -8 (-6 to -11) The YODA c. Assessed with numeric rating scale (0 to 10) and not with visual analogue scale (0 to 10cm) GO BEFORE -NCT00264537 yes yes Non-remission 5,792 58 (52 to 64) 2,017 76 (72 to 81) 20 (16 to 24) project 3 -data from Johnson d. All trials used Sharp van der Heijde mTSS (0 to 448) except in the LITHE trial, in which Genant mTSS (0 to 202) was used instead. NCT00264550 yes yes GO FORWARD - & Johnson GO FURTHER -NCT00973479 yes yes ATTRACT -NCT00269867 The radiographic data was yes no provided too late (after change in the platform has occurred) ClinicalStudy- ASPIRE -NCT00236028 The Sponsor was Centocor. Data DataRequest 4 -data from no no not available in the Sharing Data Platform , et al. Ferreira RJO , et al. Ferreira RJO Ann Rheum Dis Ann Rheum Dis :1 0 2020; :1 0 2020; -11.
-11. doi: 10. 1136/annrheumdis-2020-217171 doi: 10. 1136/annrheumdis-2020-217171 Roche LITHE -NCT00106535 yes yes FUNCTION -NCT01007435 yes yes BREVACTA -NCT01232569 yes no Only 1y data was provided ACT-RAY -NCT00810199 no no Tested discontinuation of therapy in the 2 nd year of trial. SAMURAI -NCT00144508 yes no Only 1y data was provided SURPRISE -NCT01120366 The Sponsor was "SURPRISE no no Study Group". Data not available in the Sharing Data Platform. Linked with ACT-RAY study. , et al. Ferreira RJO , et al. Ferreira RJO , et al. Ferreira RJO Ann Rheum Dis Ann Rheum Dis Ann Rheum Dis 2020; 2020; 2020; -11. :1 0 -11. :1 0 :1 0 doi: 10. 1136/annrheumdis-2020-217171 doi: 10. 1136/annrheumdis-2020-217171 1 -https://www. abbvie. com/our-science/clinical-trials/clinical-trials-data-and-information-sharing/data-and-informationsharing-with-qualified-researchers.
5% vs. 3. 8%, p =0. 03) and the TIMI criteria (2. 8% vs. 2. 2%, p =0. 03)  (25). However, a limited number of patients with stage >3b CKD (glomerular filtration rate (GFR) < 45 mL/min or dialysis) were included (21%), and dialysis patients were excluded. Moreover, CKD is associated with an increased rate of bleeding events; therefore, the particular ratio of thrombotic and bleeding risk in CKD patients is likely to differ from patients without CKD and remains to be determined  (26) (27) (28). Frequently, CKD patients do not receive up-todate management in relation to both therapeutic nihilism and the paucity of data regarding new therapies  (29). To fill this gap in evidence, we designed the TicagRelor Or Clopidogrel in severe or terminal chronic kidney patients Undergoing PERcutaneous coronary intervention for acute coronary syndrome (TROUPER) trial to compare the efficacy of ticagrelor and clopidogrel in ACS patients with stage ≥3b CKD intended for an invasive strategy.
Study design The TROUPER study is a prospective, multicenter, randomized, controlled, openlabel, 2 parallel-group study. The study design was recorded in clinicaltrial. gov (database: NCT03357874). The overall study design is summarized in Figure  1. This study includes 20 centers in France. Patients with ACS with or without ST segment elevation intended for an invasive strategy will be eligible. They will be included if all inclusion criteria are met and in the absence of non-inclusion criteria after an informed consent is signed. Following inclusion, patients will be randomized in a 1:1 ratio to receive clopidogrel or ticagrelor. In the control group, patients will receive a 600 mg loading dose of clopidogrel after randomization followed by a 75 mg od regimen for 1 year after PCI. In the ticagrelor group, patients will receive a 180 mg loading dose of ticagrelor after randomization followed by a 90 mg bid for 1 year.
Statistical analysis The data will be analyzed using SPSS version 17. 0 software (IBM) or a later version. All tests will be two-sided. Statistical significance is defined as p<0. 05. The methodology will be based on the Consolidated Standards of Reporting Trials Statement  (45). The full analysis population (including subjects who will be at least evaluated at baseline and randomized) will be used in the primary analysis. In this intention-to-treat analysis, all patients will remain in the group to which they were allocated. The per-protocol population (including all subjects who will be randomized and will not have major protocol deviations) will be used in the secondary analysis to assess the robustness of the results. No interim analysis is planned. The time from randomization to the first occurrence of a MACE during the 1-year follow-up will be compared between the 2 groups using a two-sided log-rank test.
Adverse events (AEs) will be summarized by frequency and proportion. The characteristics of AEs, the maximum grade, the incidence of deaths and the primary cause of death will be summarized. The results of scheduled assessments will be described. An independent Clinical Endpoints Committee (CEC), blinded to the treatment, will adjudicate all death, recurrent ischemia, MI, stroke, recurrent and all BARC bleeds. Primary analyses will be conducted on CEC-adjudicated endpoints. monitoring will be conducted under the auspices of an independent, external data monitoring committee (DMC) assigned to this study. The primary endpoint analysis and all other key efficacy and safety analyses will be conducted using the two-sided log-rank test from a time-to-first event analysis, unless otherwise specified.
The TROUPER study will help to unveil the potential interest of ticagrelor in CKD patients and analyze safety issues, including bleedings. The net clinical benefit (combining ischemic and bleeding events) will be assessed. The determination of the optimal P2Y12-ADP receptor inhibitor in ACS patients with stage 3b, 4 and 5 CKD or under chronic hemodialysis is critical to improve their clinical outcome. The TROUPER trial will provide critical data in this regard, which could help physicians decide the optimal therapy this population and update the guidelines.
| Strengths of the study Strengths of our study are that we have measures of maternal metabolic parameters at three time points in pregnancy, enabling us to look at longitudinal associations. Data were collected in nine European countries, increasing the external validity of our findings. Importantly, the mechanistic path analysis adds substantial insights on how some of the metabolic parameters during pregnancy in women with obesity could affect neonatal adiposity, although we cannot assert on causality and our model should be tested in clinical trials.
This study was funded by the European Union 7th Framework (FP7/ 2007-2013) under Grant Agreement no. 242187. Additional funding was provided by the Netherlands Organisation for Health Research and Development (ZonMw) (grant 200310013), in the Netherlands. In Poland, additional funding was obtained from Polish Ministry of Science (grants 2203/7, PR/2011/2). In Denmark, additional funding was provided by Odense University Free Research Fund. In Spain, additional funding was provided by CAIBER 1527-B-226. The study sponsors were not involved in the design of the study; the collection, analysis, and interpretation of data; writing the report; or the decision to submit the report for publication.
Data collection and processing CPETs were performed on a cycle ergometer before and after CR using an individualised ramp protocol to achieve patient's voluntary exhaustion within 8 to 12 min of ramp duration. CPET raw data was processed in the core laboratory (Uni Bern) using MATLAB software (R2017, The MathWorks1, United States). To reduce a potential systematic bias for centres, all ventilatory thresholds (VT 1 and VT 2 ) were visually determined by one single investigator (TM), a sports scientist with extensive experience in setting ventilatory thresholds in healthy people as well as cardiac patients. The investigator was blinded to patient characteristics and centre. Interrater reliability was determined in a random subset of 200 CPETs, in which thresholds were determined by a second experienced investigator (MW) blinded also to patients and centres as well as to thresholds set by the other investigator.
The black-lipped pearl oyster (Pinctada margaritifera) is extensively farmed in French Polynesia to produce black pearls. For a sustainable management of marine resources, studying interactions between organisms and environment, and the associated factors and processes that will impact their life cycle and thus modulate population dynamics is a major research priority. Here, we describe black-lipped pearl oyster energy acquisition and use, and its control by temperature and food concentration within the Dynamic Energy Budget (DEB) theory framework. The model parametrization was based on literature data and a specific laboratory experiment. Model validation was carried out thanks to historical in-situ datasets and a dedicated field survey. Three theoretical environmental scenarios were built to investigate the response of the pearl oyster to environmental variations.
DEB theory  (Kooijman, 2010)  offers a framework that describes the metabolic organization underlying the physiological functions of an organism in a fluctuating environment. Based on a restricted number of assumptions, written out as mathematical formulas, this theory allows the description of growth, development and reproduction throughout an organism's life cycle, as a function of available food and temperature. Its application is challenging because the state variables and parameters are abstract quantities that are not directly observable. Recent developments allow estimating all parameters of a DEB model using standard empirical datasets  (Marques et al. , 2018). Such calibrated DEB models have already been useful to predict the effects of global change, and better understand species geographical patterns, environmental stressors effects, bio-production optimization and management of exploited resources (e.
g. Desforges et al. , 2017; Molnár et al. , 2011; Muller et al. , 2019). Here, DEB theory was applied to assess the pearl oyster's life cycle sensitivity to the spatial and temporal variations of temperature and food, with a particular emphasis on growth, reproduction, and larval development. The parameters were estimated using a wide range of datasets provided by the literature and supplemented by a specific laboratory experiment  (Sangare et al. , 2019). The model was then validated using data specifically acquired for this study, as well as independent historical in situ data from three contrasted environments. Finally, a sensitivity analysis was performed to investigate how life history traits can vary within a wide range of environmental conditions known to occur (or that may potentially occur) in French Polynesian atoll lagoons.
Material and methods An approach combining in situ monitoring, laboratory experiment and modelling (with observation, calibration, validation and application), was used for our objectives. We provide here a short overview of our method before developing it in the next sections. A recent development, specifically "the AmP project", was used to fully calibrate the model  (Marques et al. , 2018). A field survey took place in the lagoon of Ahe (Tuamotu, French Polynesia) where oyster's reproduction, growth and environmental data were monitored simultaneously. The collected data were used jointly with literature data to validate the model ability to describe oyster's life history traits in three contrasted environments across the French Polynesian latitudes (Ahe, Takapoto and Gambier). Then, scenarios of food and temperature fluctuations were implemented to investigate the theoretical pearl oyster's response to environmental variations.
Field work: adult growth, reproduction and environment data in Ahe atoll Chlorophyll a (chl-a) concentration, as a proxy for food availability, and temperature were monitored during a six months field survey (February to August 2017) at 2 different sampling stations (Figure  1 ) assumed to be environmentally contrasted  (Thomas et al. , 2012). All measuring devices were placed at a depth of 5 m, directly on the rearing lines where the animals sampled were attached (see below). SMATCH ® probes measurements accuracy was controlled by comparing with direct measurement of chl-a every 6 weeks. Water samples (500 ml) were taken and filtered on GF/F Whatman filters (ca. 0. 7 µm pore size). Chl-a was extracted from phytoplankton cells during 8h in the dark in 6 ml of ethanol 70%. Concentration of chla was then quantified by chl-a fluorescence determined using a Trilogy ® fluorimeter calibrated with chl-a standard (Sigma) and equipped with the appropriates optical filters  (Welschmeyer, 1994).
Model parameters estimation The "AmP" procedure was applied with MATLAB ® (R2017b) to infer the DEB model parameters  (Marques et al. , 2018). This method uses experimental and field observations at different life stages and calibrates the parameters thanks to a Nelder-Mead numerical optimization that minimizes the difference between observed and predicted values, based on a weighted least-squares criterion. Initial values of the parameters were set following  Thomas et al. , (2011) and Fournier, (2011). Thirty datasets from the literature were used for model calibration ranging from length or age at different life stages, to respiration rate at different conditions of food and temperature  (Sangare et al. , 2019). The list of input data extracted from the literature is available at The parameter Xk, a component of the law governing ingestion, is the only parameter of the P.
Model validation To assess the accuracy of the model simulations and its generalization to other French Polynesian atoll lagoons, modelled description of the pearl oyster life cycle was tested on four in situ datasets of growth and reproduction at different life stages and in contrasted environments (Table  1 ). These datasets were all independent from those used for model parametrization. The agreement between field observations and model simulations was evaluated by linear regression between the samples' mean value of observations (X) and the mean value of individual simulations (Y), which was tested against the Y=X model at the alpha error threshold of 5%. The R² coefficient of determination allowed us to evaluate how much of the variance was explained by the model.
margaritifera growth and reproduction were investigated within the range 0. 05 to 1 µgChl-a l -1. In French Polynesian atoll lagoon, chl-a concentrations range from 0. 1 to 0. 7 µgChl-a l -1 with extreme values of 0. 05 µgChl-a l -1 in the open ocean and 1. 2 µgChl-a l -1 in Mataiva atoll  (Andréfouët et al. , 2001; Delesalle and Sournia, 1992). Independently of the atoll mean annual concentration, important variations of the planktonic ecosystem may occur at different time-scales and have been mostly related to grazing pressure  (Delesalle et al. , 2001; Fournier, 2011; Sakka et al. , 1999; Thomas et al. , 2010). Basic spectral analysis ("Fast Fourier transform" function from MATLAB ® R2107b) on food concentrations time series provided by the 4 validation datasets (see above) were performed, for further representation of food variations.
Parameterization Parameters values are summarized in During the model parameterization, the scaled functional response was assumed to be equal to 0. 3 and 0. 1 for in situ data representing the austral summer and winter respectively. The functional response for the ad libitum experimental data sets was set to 0. 9 instead of the possible maximum f = 1 because it was rather unclear how optimal the nutritional value of the cultivated phytoplankton used for the rearing was for the needs of the animals.
Model validation Dataset 1 In the case of larval rearing with cultured algae (Figure  4  A), the value of the half-saturation coefficient, Xk, corresponded to that calibrated for larvae experimentally: 0. 6 μgChl-a l -1 (Table  2 ). For in situ rearing, not supplied with cultured algae (Figure  4  B, C and D), the half-saturation parameter was calibrated at 0. 2 μgChla l -1 to obtain a better fit between simulations and observations. Despite a slight underestimation of the growth rate after day 11 for the rearing in mesocosm (Figure  4  C), the simulation fits were highly significant, with R 2 equal to 0. 995; 0. 937; 0. 943 0. 967 respectively for the simulations A, B, C and D with p-values < 0. 0001.
Dataset 2 Simulations compared with the validation dataset 2 are presented in Figure  5. Here, the half saturation coefficients were adjusted at 0. 7 mg POM l -1 for the age group 1 and 0. 5 mg POM l -1 for age group 2 and 3 to obtain better fits. This way R 2 were equal to 0. 864 and 0. 884 respectively for the age group 1 and 2 with p-values < 0. 0001 and simulations for age group 3 gave an R 2 equal to 0. 373 with a p-value of 0. 015. Pouvreau et al. , (2000a)  suggested from their study respectively 1, 2 and 4 spawning events for the age group 1, 2 and 3 represented by blue arrows on the Figure  5. These conclusions are not confirmed by the new simulations that suggested for each age group one spawning event per individual during the year of survey (marked by drops in the thin lines on Figure  5 ).
Dataset 3 Simulations of shell length and dry flesh mass evolution in Gambier Islands are compared with the validation dataset 3 in Figure  6. Here, the value of the halfsaturation coefficient, Xk, was readjusted at 0. 1 μgChl-a l -1 to improve the fits. The Gametogenesis occurred when food availability allowed it and spawning took place asynchronously the whole year (Figure  7 ). No massive spawning event could be clearly identified during the field survey. Here, the model did not accurately reproduce GamSI variations, with R 2 equals to 0. 057 and 0. 125 and p-value equals to 0. 1841 and 0. 1679 respectively to the Figure for adults and larvae respectively. The temperature from 24 to 30°C and food availability from 0. 1 to 0. 9 µg Chl-a l -1 is represented by rectangles on the Figure  9  to highlight the range of French Polynesian atoll lagoon conditions  (Delesalle and Sournia, 1992).
Within these ranges, we predicted a possible theoretic PLD from 10 to 70 days (Figure  9  A), 2 to 14 spawning events a year for a 13 cm shell length oyster (Figure  9 B ) and a commercial size was reached at 12 to 40 months after egg fertilization (Figure  9 C ). According to the dataset 2, Gambier Islands experienced annually a mean food of 0. 19 µgChl-a l -1 , a mean temperature of 25. 5 °C and a half saturation coefficient (Xk) suitable for validation equal to 0. 1 µgChl-a l -1. In these conditions a 13 cm shell length oyster would be able to spawn six times a year and the fertilized eggs would reach a commercial size after 23 months (not shown). Up north, in Ahe atoll, the dataset 4 framed food and temperature at 0. 21 µgChl-a l -1 and 28. 5 °C respectively with a Xk equal to 0. 2 µgChl-a l -1.
Thus, a 13 cm shell length oyster could reproduce 5 times a year and fertilized eggs would reach a commercial size after 24 months. Similarly, for the value of Xk = 0. 2 µgChl-a l -1 which was reported in situ for larvae in Ahe (Dataset 1), PLD would range between10 to 20 days in the northern Tuamotu archipelago (not shown) when respectively released in austral summer (30°C) and winter (27 °C). No larvae datasets were available to assess Xk in Gambier Island, thus under the assumption that the half saturation coefficient does not differ between locations, the PLD in Gambier would range from 17 to 27 days depending on whether spawning occurred in the summer (28. 5 °C) or winter (23. 5 °C).
Simulation 3: sensitivity to phytoplankton biomass stability The preliminary spectral analysis of the environmental conditions of the validation datasets (datasets 1; 2; 3 and 4) did not reveal any periodic signal in food variations (not shown). The absence of a regular time interval between food-rich and starvation periods suggested that fluctuation can be approximated by random variation in the field. Here, only results for oscillations that ranged from 0. 1 to 1 µgChl-a l -1 around the reference value of 0. 2 µgChl-a l -1 are represented. Changing the reference food concentration had qualitatively no impact on the general pattern of the life history traits. Indeed, the shape of the isoclines would just be redrawn around the horizontal line defined by the chosen reference value (Figure  11 , dotted lines = reference value of 0.
Critical examination of the new DEB model calibration The new DEB calibration for P. margaritifera leads to one single model with primary parameters applicable all along the life cycle. Compared to previous DEB models applied to P. margaritifera that described separately larvae and adult phases  (Fournier, 2011; Thomas et al. , 2011) , the new full life cycle calibration brings together a wide range of datasets ranging from simple age at birth to respiration curve at different food level and temperature. By considering all life stages in a single model, this new DEB model for P. margaritifera is more suitable for future ecotoxicological, physiological or biophysical ecology investigation. This is also a first step towards integrated population and ecosystem dynamic models. Compared to the larval and adult phase DEB models  (Fournier, 2011; Thomas et al.
gigas, Xk integrates all variations related to the trophic environment. This includes food sources, variations of food nutritive quality, different selection of the filtered particles and variability in assimilation efficiency according to the particles actually ingested. As such, the presence of a food source that is poorly or not captured by the chlorophyll-a might explain the disagreement between observations and simulations of weight  (Picoche et al. , 2014). It is known for other bivalves  (Sauriau and Kang, 2000)  that filtration, selection, and ingestion capacities depend on life stage or on prey sizes. Overall, high values correspond to poor trophic quality or low appetence for the available food. From there, the model suggests that cultivated micro-algae are less appropriate to feed pearl oysters than in situ species (Validation dataset 1) and in situ phytoplankton is more palatable for growing oysters (Validation dataset 2).