dataesr/scientific-paragraphs-categorization huggingface dataset:
Usage Notes Often, when developing new tools for NTA, they are restricted to a limited number of datasets usually generated in one laboratory. These datasets rarely represent the actual diversity in potential future datasets that should be processed using these tools. In this data descriptor, we present a dataset which covers a wide range of instruments and instrumental/analysis conditions. Additionally, the dataset in this study provides three different levels of chemical complexity (i. e. the number of potential chemical constituents) in blank, drinking water, and river water, respectively. Such a dataset can be used for the assessment of the impact of method transfer on the explored chemical space of the samples as well as the quality of the generated spectra. The records made available with this data descriptor constitute a valuable resource for the future development of NTA algorithms and workflows, for example by providing a collection of successfully identified compounds and retention time indices obtained over a wide range of instruments and analytical conditions.
Schulze, Denice van Herwerden, Ian Allan, Lubertus Bijlsma, Nestor Etxebarria, et al. Interlaboratory mass spectrometry dataset based on passive sampling of drinking water for non-target analysis. Scientific Data , Nature Publishing Group, 2021, 8 (1), pp. 223. 10. 1038/s41597-021-01002w. hal-03325586Inter-laboratory mass spectrometry dataset based on passive sampling of drinking water for non-target analysisBastian Schulze et al. #.
Additional consent provisions for collections and use of participant data and biological specimens {26b} We will take advantage of the existing "Immunology" research program declared by CHU Nantes to set up the "POLYCOR" biocollection. Biological samples will be collected and stored if the patient has signed the biocollection informed consent. In this informed consent form, it is noted that the samples may be used for other scientific research. This biocollection will be a biological and longitudinal follow-up of patients with diagnosis of COVID-19, to assess immune changes and host-virus interactions. Ethic authorization is already granted, and the preanalytical steps are already implemented and efficient.
Explanation for the choice of comparators {6b} POLYCOR project has the aim to define the optimal XAV-19 dose to administrate to moderate COVID-19 pneumonia patients, and to evaluate its safety and efficacy. ❖ All sexually active male subjects must agree to use an adequate method of contraception throughout the study period and for 90 days after the last dose of study drug and agree to no sperm donation until the end of the study, or for 90 days after the last dose of XAV-19, whichever is longer French regulatory authorities (ANSM), thus, has given their scientific recommendation to conduct the first part of the study (phase 2a) as a first-in-human study, with sequential enrolment to check for safety. Dose levels selected in the first-in-human assessment of XAV-19 are based on 3 datasets:   [14].
The estimated dose to reach this target is 2 mg/Kg. Based on these 3 datasets, the Pharmacologically Active Dose (PAD) Standard of Care SOC for Group 2 of phase 2a would be 2 mg/kg infused on day 1 and on day 5 for a batch of XAV-19 presenting the IC 50 of 2. 5 μg/mL in the ELISA Spike/ACE2 neutralization assay. It is meant to maintain trough levels of XAV-19 above 25 μg/mL over several days. This dosing is lower than the dose already administered in human in the previous clinical experience demonstrating safety with LIS1 (5 daily administrations of 8 mg/kg, thus a total of 40 mg/kg), thus lower than a dosing which might reach a dose limiting toxicity. In other words, this dosing (two administrations of 2 mg/kg) presents a 10-fold safety factor for the first administration of XAV-19, as compared with previous experience with glyco-humanized swine IgG.
Interventions description {11a} Phase 2a will enroll 16 subjects in one of the two dose-level groups: group 1 with dose level defined according to the neutralization titer of the XAV-19 batch (first estimation being 0. 5 mg/kg) and group 2 as 4 times higher than group 1 (estimated 2. 0 mg/kg). If a patient does not receive the full treatment or has not been followed for 8 days, then he/she will be replaced within the limit of 20 patients in total. Each subject will receive two infusions of XAV-19 or placebo separated by an interval of 4 days (administrations on day 1 and day 5). More precisely, after enrollment of the first two patients in the low dose group (one patient treated and one patient placebo), data will be obtained after first (day 1) and second (day 5) infusions to collect any severe adverse events that might have occurred, especially in the first 48 h following each infusion.
DSMC will have to review immediately safety data of the first 2 patients (based on day 8 information) and provide advice on continuing enrolment of the 6 last patients of group 1 (low dose). DSMC statement, and sponsor decision with regard to study continuation will be immediately communicated to ANSM. If there is no signal of severe intolerance by day 8 of enrollment of the first two patients, the rest of the group will be enrolled with the same process of review of tolerance. When the final patient of group 1 has been enrolled, day 8 safety data of all 8 patients from this low-dose cohort will have to be reviewed by the DSMC to advise of starting high-dose group (group 2). DSMC statement and sponsor decision with regard to study continuation will be immediately communicated to ANSM. At any time during the phase 2a study, if a serious adverse event occurs, this will be communicated to the DSMC and the sponsor and coordinating investigator will have the responsibility to decide whether DSMC must meet to advise on study conduct.
The same sequential XAV-19 administrations will apply for the second group dosed at 2 mg/kg, with safety steps and DSMC data review. At the end of phase 2a and as requested by the French regulatory authorities (ANSM), an amendment will be made to the protocol to continue the study in phase 2b. The phase 2b (DFD) will be a double-blinded, placebocontrolled randomized study to assess clinical benefit and safety of the phase 2a selected dose of XAV-19 in 352 hospitalized adults with COVID-19-associated moderate pneumonia. Patients will be randomized to either XAV-19 or placebo in a 1:1 ratio and will receive 2 consecutive doses 4 days apart (day 1 and day 5). Obviously, during this 2b study, the DSMC will regularly meet as defined in the DSMC charter. During the phase 2b study, if the proportion of patients requiring invasive mechanical ventilation after inclusion increases to 30~50% (analyzed by incremental groups of 50 patients), the DSMC will be requested to review data without discontinuation of the study.
The primary reason for discontinuation must be recorded in the appropriate section of the e-CRF and all efforts made to complete and report the observations as thoroughly as possible. If a patient fails to return for a scheduled visit/followup, attempts should be made to contact the patient to identify reason for not returning. Likewise, if a patient declares their wish to discontinue from the study, e. g. , for personal reasons, all efforts should be made to establish that the cause is not due to an AE (bearing in mind the patient is not obliged to their reasons). A definitive or temporary discontinuation of all or part of the study may be decided by ANSM, the Ethics Committee, the Sponsor after Data and Safety Monitoring Committee (DSMC) opinion. In any case: -A written confirmation of this early discontinuation of the study shall be sent to the coordinating investigator of the study (specifying the reasons for the early discontinuation).
Sequence generation {16a} Randomization will be performed and balanced by blocks. The software used for the randomization is SAS version 9. 4. In terms of the ratio, for phase 2a, the first 2 patients in each cohort will have a ratio of 1:1, and if all goes well, the remaining 6 patients in the 2 cohorts will have a ratio of 1:5 (1 placebo for 5 doses of XAV-19). For the phase 2b, it will be carried out in a 1:1 ratio.
Procedure for unblinding if needed {17b} Under normal circumstances, blind should not be broken until all patients have completed the study and the database is locked. In the current study, the investigator does not need to know the treatment arm of the patient in case of adverse event, as the treatment will be symptomatic and not adapted to the arm. The blind will be broken only by the pharmacovigilant team for safety purposes and transmission. This will be done according to the internal sponsor's procedure.
Data collection and management Plans for assessment and collections of outcomes-description of the parameters for evaluating efficacy {18a} All examinations will be performed by the investigator or a qualified member of the investigational staff. Firstly, he will make a full physical examination which includes the following assessments: cardiovascular, head-earnose-throat, eyes, gastro-intestinal, general appearance, lymph nodes, musculoskeletal, neurological, respiratory, skin, and mucous membranes. Body weight and height will be measured. Any abnormalities present at inclusion, or subsequent changes, will be documented in the appropriate sections of the eCRF. Any clinically significant abnormalities persisting at the end of the study will be followed by the investigator until resolution or until reaching a clinically stable endpoint.
Data management {19} For each patient, a case report form (CRF) is created which includes the data necessary to ensure compliance with the protocol and all data necessary for the statistical analysis and to identify major protocol deviations. Data collection is done directly by the investigator or clinical research associate in charge of the study, using an electronic CRF (eCRF) developed by the Sponsor Department of the CHU Nantes with ENNOV Clinical. The data are encoded to keep the identities of the patients confidential.
Confidentiality {27} Data collected during the study will be processed electronically in compliance with the requirements of the CNIL (compliance with the French Reference Methodology MR001). The CNIL is an independent French administrative regulatory body whose mission is to ensure that data privacy law is applied to the collection, storage, and use of personal data. Plans for collection, laboratory evaluation, and storage of biological specimens for genetic or molecular analysis in this trial/future use {33} For the pharmacokinetics analysis, blood samples will be collected at each draw for specific analysis as described below according to the study schedule. These analyses will be run under Good Laboratory Practices conditions. In the phase 2a, all patients included in the study will have pharmacokinetic samples taken.
Categorical variables will be summarized by percent and continuous variable by means and standard error, and medians and interquartile range. For the phase 2b, categorical variables will be summarized by percent and continuous variable by means and standard error, and medians and interquartile range. Survival rate and duration of oxygen therapy will be compared between the two groups for the primary endpoints. For the secondary endpoint, quantitative endpoint will be compared using linear mixed model and qualitative data with logistic mixed model to take into account stratification factors. Time data's will be analyzed using survival model. Fine and Gray method will be used to take into account competing risk.
Plans to give access to the full protocol, participant-level data, and statistical code {31c} According to French law, the results of the study will be published on the website of the regulatory authority. Data sharing will be between the investigators only. However, the datasets analyzed during the current study will be available from the corresponding author on reasonable request. Furthermore, the sponsor will enter the study results in the European Union database as soon as the main publication from the research is released, in order to preserve intellectual property.
Adverse event reporting and harms {22} All patients will be closely monitored during both study phases for overall biological and clinical safety data (e. g. , infections or malignancies) and any drugs toxicity. According to regulation, each AE reported by the patient or identified by the investigator must be collected and reported to sponsor, as soon as he is aware, if it meets to seriousness criteria from inclusion of the subject, to the end of the participation. As a routine precaution, patients enrolled in this trial must be observed for at least 2 h post infusion of study drugs. Patients will be assessed for signs or symptoms of any infusion reactions (e. g. , hypotension, hypoxia, tachycardia, fever, nausea, fatigue, headache, myalgia, and malaise).
Acknowledgements This study is supported by  Public Investment Bank , also known as BPI France in the framework of the " Investment for the Future" programme (Programme d'Investissements d'Avenir ). Thanks to all the  Clinical Pharmacology Department (Nantes University Hospital)  for their support for this protocol. Thanks to the POLYCOR study group:  Eric Dailly ,  Thomas Guimard ,  Cécile Braudeau ,  Denis Malvy ,  Jean-François Faucher ,  Gabriela Illes Hajnal ,  Marc-Olivier Vareil ,  Mariam Roncato-Saberam ,  Laurent Vacher ,  Charlotte Biron ,  Maeva Lefebvre ,  Géraldine Paul Le Turnier ,  Deschanvres ,  Raphael Lecomte ,  Marie Chauveau ,  Anne-sophie Lecompte ,  Matthieu Grégoire ,  Ronan Bellouard ,  Guillaume Deslandes ,  Zineb Ouazene ,  Diane Bollens ,  Thibault Chiarabani ,  Jessica Krause-Le Garrec ,  Agathe Becker ,  Pierre Chauvelot ,  Anne Conrad ,  Tristan Ferry ,  Patrick Miailhes ,  Cécile Pouderoux ,  Sandrine Roux ,  Claire Triffault-Fillit.
LIS1 is an experimental lymphodepleting polyclonal swine antibody pro- duced by the glyco-humanized GH-pAb platform of Xenothera Laboratory. It is currently in clinical de- velopment in kidney transplant patients in EU (EUDRACT 2019-000917-35). So far, the maximal dose that has been reached in the escalating dose arm and found acceptable by the DSMC (which recommended pursuing the trial at this dose) is five daily administrations of 8 mg/kg, i. e. , a cumulated dose of 40 mg/kg. Therefore, in this first-in-human trial with XAV-19, we have proposed that the cumulative dose stays inferior to the maximal LIS1 dose administered. 2) Published clinical experience gained with use of convalescent plasma (CP) containing anti-COVID-19 neutralizing antibodies, having evidenced improvement of clinical symptoms.
Behavioral data Statistical analyses were performed with SAS Enterprise Guide software, Version 5. 1 (Copyright © 2012 SAS Institute Inc. , Cary, NC, USA) and with MATLAB 7. 5 (The MathWorks, Natick, MA, USA). Generalized Linear Mixed Models (GLMMs) were performed in the SAS software. In all models, all fixed effects were allowed to vary between subjects in the random part of the model. In the modified version of the Stroop task, the number of blocks varied between participants due to the availability of the MR scanner as mentioned above (see Design and experimental procedure). In order to analyze the effect of timeon-task on accuracy and log-transformed RT, we grouped the data in 5 successive bins, from beginning to the end of the task. The GLMM analysis was performed on both accuracy and RT where the main factors (time bins, congruency) and their interactions were modeled as fixed effects.
fMRI data 2. 5. 2. 1. Imaging acquisition parameters. Functional, resting-state and anatomical scans were performed with a Achieva 3T scanner (Philips Healthcare, Eindhoven, The Netherlands) equipped with a 32-channel phased array head coil. Functional and resting-state scans T2-weighted echo-planar images were acquired with the following parameters: echo time (TE) = 27 ms, repetition time (TR) = 2250 ms, flip angle (FA) = 85 °, 41 slices acquired in an ascending order, slice thickness = 3 mm, field of view (FOV) = 123 × 123 mm 2 , acquisition matrix = 80 × 80 (reconstruction 80 2 ). Each functional scan (lasting 2 runs of the task respectively) included 280 vol (acquisition time 10 min and 30 s) while the restingstate scan consisted of 164 vol (acquisition time 6 min and 9 s). A 3D heavily T1-weighted structural image was also recorded at the end of the MRI session.
fMRI preprocessing and analysis. BrainVoyager QX 2. 8. (Brain Innovation BV, Maastricht, Netherlands) was used to preprocess and analyze the functional neuroimaging data acquired during the Missing Number task (see Fig. 1 B ). The preprocessing of the functional data consisted of the following steps: slice time correction, temporal filtering (high-pass, cutoff: 2 cycles; analysis was also performed with 4 cycles, leading to identical GLM results) and motion correction. Since the structural image was acquired in the end of the experiment, motion correction was performed by aligning volumes from all runs to the first volume of the last run in a given session. Co-registration parameters were calculated only between the last functional run and structural image. Prior to the motion correction procedure we first confirmed that the participants' in-scanner motion did not differ between experimental conditions.
𝑁+1 , with C sh corresponding to the vector of shuffled correlation coefficients and C to the actual correlation coefficient obtained on non-shuffled data. Since the reward contrast ( ΔBOLD REWARD ) highlighted not only motivation-related regions but also the task-related ( ΔBOLD Task ) areas that were modulated by reward, we identified a set of regions-of-interest (ROI) that have been classically associated to reward and motivation processing (Neurosynth. org meta-analyses for terms "reward " and "motivation ", including 922 and 189 published datasets respectively; see Supplementary Fig. 2B  The coordinates of these ROIs (Talairach coordinates;  Mai et al. , 2008 )  were taken as the center of a 5 mm radius sphere per ROI using the Talairach coordinate-to-spherical VOI plugin in BrainVoyager QX 2.
Regions of interest (ROIs) were defined using the Harvard-Oxford atlas of cortical and subcortical areas combined with the AAL atlas of cerebellar areas. We computed the ROI-to-ROI connectivity matrices by correlating averaged BOLD time series between each pair of ROIs. These correlation coefficients were Fisher-transformed and submitted to a second-level GLM. The model included a between-subject factor SESSION, indicating whether the functional data corresponded to the FATIGUE or CONTROL session and a within-subject factor ΔMFI CTR-FAT.
83; BA19: 10. 63; BA37: 10. 72; see Fig. 4  B and Supplementary Table  S4 ). ). Eventrelated map is thresholded at voxel-p < 0. 001, uncorrected and p < 0. 05, clusterlevel corrected. Block-based map was computed with more liberal threshold ( p < 0. 005). In both maps, ventral visual processing stream / FFG activity is decreased in fatigue compared to control condition. Unthresholded data is available from NeuroVault at https://identifiers. org/neurovault. image:512326 (cuerelated) and https://identifiers. org/neurovault. image:512327 (block design). In order to confirm the results of the cue-related analysis we revisited the block-based analysis under a more liberal threshold (voxelp < 0. 005), finding the same fatigue-induced hypoactivity of the ventral visual stream (see right image in Fig.
, 2018)  and diffusion MRI  (Heidemann et al. , 2010) , but at the expense of longer scan durations. More recently, a novel simultaneous multi-slab, diffusion-weighted sequence was proposed to perform diffusion MRI in vivo at the submillimeter resolution at 3T  (Setsompop et al. , 2018). However, a trade-off must be made to choose between the target diffusion sensitization magnitude and the target spatial resolution. In addition, the specific localization of the brainstem next to the petrous bones, with an important air-tissue interface causing major susceptibility artifacts, and its predisposition to movement induced by the pulsation of blood in posterior fossa arteries are all reasons that make the acquisition of very high-resolution MRI data of the brainstem extremely difficult in vivo.
The choice of a volume-versus-surface coil was motivated by the need for a homogeneous excitation profile over the large field of view of the brainstem despite a reduced signal-to-noise ratio with volume coils. The B1 field homogeneity also comes with a constant noise model over the field of view, which is also recommended for the noise removal of diffusion-weighted MRI data. The imaging protocol included anatomical and diffusion scans. Anatomical images were acquired using a 3D T2-weighted spin-echo sequence with isotropic spatial resolution of 100 µm and 185 µm, matrix 500x512; 800 slices, TR/TE=500/20 ms, and a total scan time of 35h33min. A single-shell High Angular Resolution Diffusion Imaging (HARDI) dataset was acquired using a conventional 2D Pulsed-Gradient Spin-Echo (PGSE) sequence.
The b-value, characterizing the gradients used to measure diffusion, was chosen to 4500 s/mm 2 to compensate for post-mortem loss of contrast. Diffusion data were acquired along 400 directions uniformly distributed over a sphere and split into 12 blocks of 31 directions and one of 28 due to memory limitation of the MRI system and to limit heating of the specimen, which is prone to induce artifacts. For each block, two b=0 images (without diffusion ponderation) were acquired. Scanning parameters were as follows: isotropic spatial resolution of 300µm; TR/TE= 9000/24. 6ms; Δ/δ= 14. 4/4. 3ms; matrix size: 167x163; 250 slices; and a total scan time of 5 days and 18 hours. The diffusion tensor was calculated for each voxel using a weighted least-squares approach to generate various tensor derived scalar maps including fractional anisotropy (FA), mean diffusivity (MD), and color-encoded direction (CED -RGB code) maps.
Microstructural and connectivity data obtained from the HARDI acquisition were not used in the frame of the current study focused on anatomical structures, but they will be investigated in another study. Preprocessing of anatomical and diffusion MRI dataset was done using the freely available Ginkgo ToolBox  (Poupon, n. d. )  providing a set of processing tools to correct for imaging artifacts and a set of tools to specifically process diffusion MRI data. Anatomical and diffusion MRI datasets were processed at their original resolutions (100µm and 185µm for the anatomy and 300µm for diffusion respectively). First, the 185µm resolution anatomical MRI dataset and the 300µm diffusion MRI dataset at b=0s/mm² were matched to the highest resolution anatomical dataset (at 100µm), using the 3D affine registration Ginkgo tool relying on the optimization of a mutual information criterion optimized using coarse-to-fine strategy and involving a Nelder-Mead simplex algorithm  (Wells et al.
, 1996). No intensity correction was applied to the anatomical scan to avoid any modification of the raw dataset intensity to be manually segmented. The 12 Diffusion MRI datasets were corrected for noise using the Non Local Means filter of the Ginkgo toolbox assuming a Rician noise model (related to the single-channel transmit-receive coil used to perform the acquisitions)  (Wiest-Daesslé et al. , 2008). The diffusion MRI acquisitions were performed using a multi-shot PGSE sequence and a high number of shots (33 shots), which allowed to reduce the geometrical distortions related to susceptibility effects or eddy currents to a level which does not require the application of any dedicated correction and, thus, preventing the use of any resampling of the data. Lastly, rotationally invariant DTI maps including the apparent diffusion coefficient (ADC), the fractional anisotropy (FA), the transverse (Dparallel) and longitudinal (Dperpendicular) diffusion coefficients were computed with a further color-encoded direction map (CED) using a robust fit to ensure the positiveness of the solution  (Fillard et al.