dataesr/scientific-paragraphs-categorization huggingface dataset:
Data preprocessing and normalization To standardize and further compare the datasets, we applied a series of quality control criteria. (i) We restricted the analysis to peptides mapped in the Ensembl canonical transcripts, resulting in 12,427 canonical phospho-modified proteins. According to Ensembl, the canonical transcripts correspond to the longest Consensus CDS (CCDS) model in each gene  (Pruitt et al, 2009). (ii) The quantified changes of peptides with the same set of modifications but different sequences were merged into one single entry, therefore increasing the conditional coverage. On those cases where more than one quantified peptide contains the same set of modifications for the same condition, their ratios were averaged. (iii) The conditional ratios between technical replicates were averaged, while remaining separated for biological replicates.
Kinase activity validation using RPPA data We compared the predictions based on the collected quantitative phosphoproteomic data with the antibody-based kinase activities from a previous study  (Hill et al, 2016). We used the BT20 cell line as reference, showing the most responsive quantitative profiles after EGF receptor stimulation. We scaled the antibody-based measurements to make them comparable across conditions and antibodies. We quantile-normalized per antibody to assure equal final distributions. Next, we standardized each individual combination of cell line, inhibitor, stimulus, and time point by calculating the z-score of each of the measurements based on the mean and standard deviation of the unstimulated conditions. Replicates were averaged. The final dataset contains 26 quantifications reporting changes in regulatory phosphosites in kinases.
7), and a SpectraX LED light source. Image analysis was performed using MATLAB or CellProfiler  (Carpenter et al, 2006). Briefly, a low-pass Gaussian filter was first applied to each image. The local background value of each pixel was then determined by searching for a surrounding ring area, with the outer and inner radii of the ring being 10 and 5 times the approximate nuclear radius, respectively. The lowest 5 th percentile value of the ring area was used as the background intensity of the center pixel. Cell nuclei were identified using fluorescent DAPI images as masks. When needed, cytoplasmic mask consisted of a ring around the nucleus. The MATLAB function regionprops was then used to label each nucleus and to retrieve the xy coordinates of all pixels in specific nuclei. The level of immunofluorescence staining in each cell was calculated as the average value of the intensities from each pixel of the specific nucleus.
PCA based on kinase activity profiles To restrict the analysis to consistently estimated kinases, only those inferred in at least 75% of the perturbations were considered. Conditions displaying extreme redundancies were also excluded, reducing the matrix of kinase activities to 58 kinases and 387 conditions. For the 7. 43% of the matrix containing missing values, the data were imputed using the regularized iterative PCA algorithm implemented in the imputePCA function contained in the R package missMDA. Using the resulting complete matrix, principal components analysis (PCA) was performed using the rda function in the R package vegan without any additional scaling. The expected (baseline) percent variance in each PC stemming from noise in data was estimated using the stringent "broken stick" method and the relaxed average eigenvalue (Kaiser-Guttman criterion)  (Jackson, 1993).
Co-regulation between driver kinases and effector complexes We first quantified the phospho-regulation of stable human complexes [from the CORUM database  (Ruepp et al, 2010) ] in each condition. We limited the complex redundancy by subsetting the interactions in which only one copy of the homologous protein complexes is included. For each of the 1,331 complexes and for each condition, we compared the distribution of absolute changes in phosphosite abundance in the complex against all phosphosites using the Kolmogorov-Smirnov (KS) test. The resulting P-values were log-transformed and signed based on the average fold change of all sites in the complex. We then fitted a linear regression to estimate those responses in protein complex phosphorylation that correlate with changes in kinase activity across conditions.
LC-MS/MS data processing Raw data files were converted to mzXML and searched using Comet version 2015. 01 against the human SwissProt database including reviewed isoforms (April 2015; 42,121 entries) allowing for binary (all or none) labeling of lysine (+8. 0142) and arginine (+10. 0083), and variable oxidation of methionine, protein N-terminal acetylation, and phosphorylation of serine, threonine, and tyrosine residues. Carbamidomethylation of cysteines was set as a fixed modification. Trypsin (KR|P) fully digested was selected allowing for up to two missed cleavages. Precursor mass tolerance was set to 50 ppm and fragment ion tolerance to 1. 0005 Daltons. Search results were filtered using Percolator to reach a 1% false discovery rate at the PSM level. Peak area heavy/light ratios were calculated using an in-house quantification algorithm.
Phosphosite assignment was performed using an in-house implementation of Ascore, and sites with Ascore ≥ 13 were considered localized (P = 0. 05). Phosphopeptides in the database with multiple non-localized instances spanning the same sequence were only considered to correspond to the minimum number of phosphosites that explain the data. Finally, the dataset was additionally filtered to reach a site-adjusted false discovery rate of 1%.
Acknowledgements We thank all the groups involved in generating the phosphoproteomics data for their invaluable public resource. We thank  Jeff Johnson ,  Brandon Invergo , and  Inigo Martincorena  for critical reading of the manuscript,  Omar Wagih  and  Francesco Ioirio  for their help on implementing some of the methods, and  Julio Saez-Rodríguez ,  John Marioni , and the rest of the group at the  EMBL-EBI  for their insightful comments. PB acknowledges support from an  HFSP   CDA award  ( CDA00069/2013 ) and  ERC   Starting Grant  ( ERC-2014-STG 638884-PhosFunc ). JV acknowledges support from a  Howard Temin Pathway to Independence Award in Cancer Research  ( NIH K99/R00 CA140789 ) and an  Ellison Medical Foundation   New Scholar Award  ( AG-NS-0953-12 ). MJ and SDMS are supported by the  Medical Research Council (MRC)  ( MCA652-5PZ600 ).
This experimental approach allowed both the determination of the crystal structure under the electric field and an evaluation of the dynamic ferroelectric response  (Wooldridge et al. , 2012). Electric fields are often applied to plate-shaped crystals via metallic contacts that are deposited on the sides of the plate. In this case X-ray diffraction data can be collected in reflection geometry with the X-ray beam transmitted through the top contact. Although it is easier to apply the electric field this way, this experimental geometry is far from ideal from a diffraction point of view. Firstly, only a limited number of Bragg nodes can be accessed and accurately measured; secondly, the rather small penetration depth of X-ray radiation increases the contribution from near surface zones of the crystal.
172 mm pixel size) with a 0. 1 angular step. The experimental diffraction setup with the electric cell is shown in Fig. 1. In order to transform the considerable volumes of data (Tb per experiment) into a usable and interpretable form (e. g. reciprocal space maps and crystallographic projections), the following procedure was adopted. The raw Pilatus 2M frames were preprocessed with the SNBL Toolbox  (Dyadkin et al. , 2016) ; the orientation matrix and reciprocal space maps were reconstructed with the CrysAlis software  (Rigaku, 2015)  with the diffracted intensities distributed in a volume near Bragg nodes of the cubic lattice. The position of every volume element (voxel) is given by the scattering vector pointing to the center of the voxel. The length of the scattering vector is defined by the corresponding Bragg angle 2 with its orientation fixed by two angles, ' and !.
Acknowledgements The authors would like to thank the  EPSRC  for funding staff and equipment, the  ESRF  for provision of beamtime on BM28 (XMaS), and SNBL for the beamtime at BM01. DC, IB and TV also acknowledge support of the grant of the  Russian Science Foundation  under the project  14-22-00136. SG acknowledges the funding of the  German Federal Ministry of Education and Research (BMBF Bundesministerium fu ¨r Bildung und Forschung  grant No. 05K13PSA ).
This technique may also permit dengue envelope sequencing for deeper molecular epidemiology analysis from RNA purified from RDTs. This could greatly increase availability of dengue epidemiological data from previously inaccessible tropical areas by facilitating dengue confirmation tests and strain identification to aid surveillance and public health interventions. This will also be of considerable importance if dengue vaccines are introduced. In addition, negative dengue RDTs could also be evaluated for PCR for other viruses causing similar clinical syndromes, such as chikungunya and zika viruses, to aid in differential diagnosis. As RDTs become increasingly used for a diversity of diseases, further exploration to look at what 'added value' could be extracted could be important for public health.
Acknowledgments We are very grateful to the patients and to Ass. Prof. Bounthaphany Bounxouei  the Director of  Mahosot Hospital ,  Dr Rattanaphone Phetsouvanh , Director of the  Microbiology Laboratory , the staff of the  Infectious Disease Center and the Microbiology Laboratory, Director and staff of Salavan Provincial Hospital, Ass. Prof. Chanphomma Vongsamphan , the Director of  Department of Health Care ,  Ministry of Health , and  Prof. Eksavang Vongvichit ,  Minister of Health, Lao PDR  for their very kind help and support.
Recombinant novirhabdoviruses express large amount of recombinant HA antigens We next evaluated the amount of HA antigen comparatively to that of an UV-inactivated purified influenza A/PR/8/34 parental strain virus. Serial dilutions of purified rVHSV-HA, rIHNV-HA (both produced in EPC cells) and influenza A/PR/8/34 viruses (produced in MDCK) were analyzed on SDS-PAGE. Following a Western blot assay using an anti-HA mAb (H36-26), the amount of HA antigens inserted in the recombinant virus envelopes was evaluated using the image processing program ImageJ (National Institute of Health, USA; http://rsb. info. nih. gov/ij/) (Fig  5 ). The quantities of recombinant HA antigens in recombinant Adjuvanted recombinant novirhabdovirus-HA platforms induce a neutralizing immune response against HA A/PR/8/34 in BALB/c mice Six-weeks old BALB/c mice were immunized subcutaneously with three doses, at two-week intervals, with purified recombinant novirhabdovirus platforms with adjuvant (Experiment #1) following the protocols depicted in Fig 6.
Mice were randomly divided into groups of 8 as shown in Fig 6B (except for 2 groups with 7 mice as explained in materials and methods). Two groups were immunized with either rIHNV-HA or rVHSV-HA and two groups were immunized with rIHNV-HA and rVHSV-HA in alternation. The rational for the latest groups was to  In order to assess the level of heterosubtypic protection induced by immunization with the recombinant novirhabdovirus-HA platforms, we performed NAB assays against another H1N1 influenza virus (A/WSN/33) or a H3N2 influenza virus (A/Udorn/1/2004). Equivalent amounts of serum were pooled together in a single mix to evaluate immune response of the whole group. None of the groups showed any detectable neutralizing immune response against heterosubtypic influenza viruses (detection limit 1:10), highlighting the specificity of the immune response induce by recombinant novirhabdovirus-HA (data not shown).
Recombinant viruses displayed the same morphology as wild-type viruses and were produced at similar titers as those previously observed for rVHSV bearing WNV E-derived antigen, approximately a log lower compared to rVHSV-WT  [10]. The genetic stability of the recombinant virus genomes was confirmed by sequencing analysis after four passages in fish cells (data not shown). We next demonstrated the efficient expression and incorporation of HA at the surface of the virus particle and their immunogenic and protective potential in mice. Whether the mice were immunized subcutaneously with Freund's adjuvant or intramuscularly without any adjuvant, all mice vaccinated on a three dose schedule were fully protected against a lethal challenge with the parental strain of influenza H1N1. Neutralizing antibody titers measured at day 21 (experiment #2 without adjuvant), after the second boost of vaccination ranged from 1:40 to 1:1280, suggesting that two boosts might be sufficient to induce a complete protection (Fig  8C ).
Acknowledgments We thank members of the animal facilities ( Infectiologie Expérimentale des Rongeurs et Poissons, INRA ) for taking care of experimental mice and for their precious help. We also thank  Dr Nicolas Bertho  for his kind gift of  H1N1 A/PR/8/34  influenza virus and  Dr Jonathan Yewdell  for the anti-HA antibody ( H36-26 ). We also thank  Dr Christophe Chevalier  and  Dr Bruno Da Costa  for advices and for providing influenza  H1N1 A/ WSN/33  and  H3N2 A/Udorn/1/ 2004  aliquots.
A(H5N1) serological surveys in humans During 2006-2010, six confirmed A(H5N1)-infected human cases were identified in five villages of five Cambodian provinces. Teams from IPC, the Cambodian Communicable Disease Control Department (Ministry of Health) and from the World Health Organization (WHO) conducted serological investigations in humans within a one-kilometer radius area approximately four to ten weeks after confirmation of the human A(H5N1) index cases. The objective was to interview and sample all villagers using a standardized questionnaire to collect demographic, poultry exposure and environmental exposure data for the three months preceding symptom onset in index cases. For children aged <12 years old, parents or guardians were interviewed. We used major social events such as Khmer or Lunar New Year, or Water Festival as temporal markers to help respondents recall past activities  [3].
Statistical analysis Statistical analyses were conducted using Stata software (StataCorp, College Station, TX, USA). All tests were twotailed and statistical significance level was set at p < 0. 05. For statistical comparisons, we used Chi 2 or Fisher Exact tests for proportions, Student test for means and Kruskal-Wallis test for medians. Conditional logistic regression models and Wald Chi 2 test were used in bivariate and multivariate analyses to calculate maximum likelihood estimates for the matched odds ratios (OR) and 95 % confidence intervals (CI). All variables showing association at p < 0. 20 with serology in bivariate analysis were included in the multivariate model using a backward process. Three multivariate models were constructed with regards to the age of seropositive cases: (1) one model for all ages; (2) one for subjects aged less than 20 years; and (3) one model for subjects aged ≥20 years.
Factors associated with A(H5N1) infections to human In total 35 cases and 115 matched control subjects were enrolled in the case-control studies (pooled data for 2006, 2007 and 2009 excluding military recruits). Bivariate analysis using conditional logistic regression for matched case-control analysis identified variables significantly associated with seropositivity at a <20 % level (Table  3 ), which were included in the multivariate analyses. Among subjects of all ages, the following exposures were more frequently reported by cases positive by A(H5N1) serology compared to matched controls: having a poultry cage or nesting area located under or right next to the house (77. 8 % vs 52. 9 %; p = 0. 060); swimming in ponds also accessed by poultry (40 % vs 30. 4 %; p = 0. 099); swimming in ponds also accessed by wild birds (47.
Acknowledgments. A large part of this paper was written while Thomas Ourmières-Bonafos was supported by a public grant as part of the "Investissement d'avenir" project, reference ANR-11-LABX-0056-LMH, LabEx LMH. Now, Thomas Ourmières-Bonafos is supported by the ANR "Défi des savoirs (DS10) 2017" programm, reference ANR-17-CE29-0004, project molQED. The initial version of the paper was significantly reworked following referee's suggestions. We are very grateful to her/him for very constructive criticisms which resulted in a significant improvement of the text and in the inclusion of several additional results.
Balaji est soutenu par le Cooperative Institute for Modeling the Earth System, Princeton Université, sous le prix NA18OAR4320123 de la National Oceanic and Atmospheric Administration, US Department of Commerce, et par l'aide d'État française Make Our Planet Great Again gérée par l'Agence Nationale de Recherche dans le cadre du programme « Investissements d'avenir » avec la référence ANR-17-MPGA-0009. Les déclarations, constatations, conclusions et recommandations sont celles des auteurs et ne reflètent pas nécessairement les vues de l'Université de Princeton, de la National Oceanic and Atmospheric Administration, du Department of Commerce américain ou de l' Agence Nationale de Recherche française. Les auteurs déclarent n'avoir aucun intérêt concurrent.
Remerciements Je remercie  Ghislain de Marsily ,  Fabien Paulot , et  Raphael Dussin pour leur lecture soigneuse des versions initiales de cet article ce qui a permis d'améliorer considérablement le manuscrit. Je remercie l'Académie des sciences et les organisateurs du colloque « Face au changement climatique , le champ des possibles » en janvier 2020, de m'avoir accordé l'opportunité d'y participer et de contribuer à ce numéro spécial.
FinancementV. Balaji est soutenu par le Cooperative Institute for Modeling the Earth System, Princeton Université, sous le prix NA18OAR4320123 de la National Oceanic and Atmospheric Administration, US Department of Commerce, et par l'aide d'État française Make Our Planet Great Again gérée par l'Agence Nationale de Recherche dans le cadre du programme « Investissements d'avenir » avec la référence ANR-17-MPGA-0009. Les déclarations, constatations, conclusions et recommandations sont celles des auteurs et ne reflètent pas nécessairement les vues de l'Université de Princeton, de la National Oceanic and Atmospheric Administration, du Department of Commerce américain ou de l' Agence Nationale de Recherche française. Les auteurs déclarent n'avoir aucun intérêt concurrent.
Par ailleurs, la bibliométrie s'appuie de plus en plus sur des outils libres et interconnectés : CrossRef, HAL, IdRef et Orcid sont autant de briques vers une bibliométrie non dépendante des données commerciales. Ainsi la bibliométrie, en utilisant des données ouvertes et en soutenant les politiques de sciences ouverte, s'intègre dans le mouvement global de l'ouverture des données et des sciences. On l'a vu, le suivi bibliométrique à l'UPSaclay s'appuie presque exclusivement sur Bibliolabs. La direction des bibliothèques consacre pour son fonctionnement 2 à 3 ETP, répartis sur 5 à 6 personnes environ, qui assurent des missions de développement et maintenance, de suivi des évolutions fonctionnelles, et de mise à jour ou enrichissement des différents référentiels sur lesquels il s'appuie. Cependant, les possibilités offertes par une base de données collectant des données bibliométriques reliées aux structures de l'établissement dépassent la simple évaluation d'impact, même si cette évaluation reste appréciée par la communauté.
Présentation et discussion des résultats Afin de tester nos hypothèses relatives à l'impact de l'application de la RA en techniques boursières TechBourse AR sur la performance des apprenants quant à la maîtrise des connaissances, la compréhension des concepts et la capacité d'analyse en matière de techniques boursières, nous avons procédé à un test de ces hypothèses à partir des résultats du post-test qu'ont subi le groupe témoin et le groupe expérimental à la fin de la formation. Nous avons mobilisé pour cela la méthode statistique ANCOVA (analyse des covariances) sous le logiciel SPSS afin de détecter la présence ou l'absence de différences significatives entre les performances des deux groupes sur le plan des trois niveaux taxonomiques (connaissance, compréhension et analyse). 2021 -Revue internationale des technologies en pédagogie universitaire, 18(2) ritpu.
Test de performance aux trois niveaux taxonomiques (connaissance, compréhension et analyse) Le test d'ANCOVA sous SPSS nous a fourni les différents résultats suivants. -Il y a d'abord une nette différence entre les moyennes des deux groupes (tableau 2) en faveur du groupe expérimental au seuil de signification de 0,05 (7,392 sur une échelle de 10 contre 5,886) après que l'effet du pré-test ait été éliminé (avant ce traitement, les moyennes étaient respectivement de 7,43 et 5,85). -Nous constatons également à la suite du test des effets inter-sujets (tableau 3) que la valeur de F est égale à 35,570 et que le niveau de signification avoisine 0 (nettement inférieur au seuil de 0,05). SPSS nous fournit, par ailleurs, une valeur Eta 2 = 0,597 (tableau 3), l'effet de cette variance est donc notable.
Ce domaine interdisciplinaire, partage l'apprentissage automatique avec l'intelligence artificielle, mais mise également sur l'expertise humaine pour analyser des quantités importantes de données et en extraire des connaissances qu'un humain tout seul ne pourrait pas voir, ce qui en fait une discipline de prédilection pour la médecine. La science des données est au carrefour de l'expertise, des techniques informatiques et mathématiques (Fig. 7 ). Le but de la fouille des données et d'extraire des connaissances à partir des bases de données disponibles. Cela correspond en pratique à l'utilisation de techniques exploratoires dans le but de découvrir des relations au sein des données étudiées (règles, corrélations, dépendances) après les avoir nettoyées et prétraitées (Fig. 8 ).
L'apprentissage automatique (Machine Learning) Les méthodes d'apprentissage automatique sont une des approches les plus importantes de l'intelligence artificielle. L'apprentissage automatique est au coeur de la science des données. Selon le professeur Tom Mitchell  [6] , l'apprentissage automatique consiste à créer des programmes informatiques qui s'améliorent avec l'expérience. Dans ce contexte, la tâche est de construire un algorithme basé sur les données disponibles et de prédire une classe à la sortie. Par exemple, dans la reconnaissance d'image, le but de l'algorithme sera de reconnaître un foie sur une image d'IRM avec le meilleur pourcentage possible de réussite (score de précision). Pour arriver à ce résultat, les principales composantes de l'apprentissage automatique sont : • une base de données, • une fonction de perte ou fonction d'objectif (la définition du but pour l'agent), • un modèle (ou, comment l'on va représenter le problème), • une méthode d'optimisation (comment on va faire l'apprentissage).
Une sorte de reformulation de la liste ci-dessous (section 1, l'agent rationnel), sauf que l'environnement est encadré sur une base de données et le planning qui n'est pas forcement nécessaire dans ce contexte où chaque donnée est prise de façon indépendante par rapport aux autres (on exclut notamment de cette remarque les tâches d'apprentissage par renforcement qui -même si bien définies comme un genre d'apprentissage automatique -sont plutôt pertinent au schéma de l'agent rationnel généralisé. Aussi, les « actions » à prendre son spécifiquement de choisir une étiquette à placer sur chaque entrée (perception d'une donnée). Avec les différentes combinaisons de cette recette, lorsque la base de données est annotée par des experts, c'est-à-dire que nous avons déjà une étiquette pour entraîner l'algorithme, on parle d'apprentissage supervisé (voir Figure  9 ).