dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2017 [126] ). And a third discrepancy is the global temperatures in the mesopause region  (110-130 km) , much colder than what Martian ground-to-thermosphere GCMs predict  (Medvedev et al. , 2015 [96] ; González-Galindo et al. , 2017  [55] ). Still we rely on GCM predictions to design space instrumentation and aerobraking maneuvers, and to complete the disperse map of measurements. Datasets like the Mars Climate Database  (Millour et al. , 2015 [98] ) and Mars-GRAM  (Justh et al. , 2011 [65] ),  based on GCMs simulations, are under continuous validation from new missions, and TGO will supply a new and unique dataset with a focus on the day-night transition and a wide range of local times at high latitudes which are novel and valuable for model validation purposes. The latitude and local time coverage expected for 2018 are shown in Figure  2.
These two methods are completely independent and both have been applied previously to solar occultations measurements in the Venus atmosphere by SPICAM/SOIR on Venus Express; their agreement within noise limits confirmed the values obtained and served as a mutual validation  (Piccialli et al. , 2015 [109] ;  Mahieux et al. , 2015 [91] ). Further, the combination of the thermal profiles with those obtained in the lower atmosphere during the nadir mapping with TIRVIM at 15 µm will characterize the thermal regime from the ground to the thermosphere, although not with a perfect 1-D description but rather as a statistical combination of spatially and temporally comparable data. The impact of all these results on the extension of existing databases of composition, temperature and aerosol loading at high altitudes will be very significant and represent the first benefit from this mission for our understanding of the Mars upper atmosphere.
NOMAD and ACS IR channels Figure  7  shows such a calculation in the IR, specifically in the 2. 5-2. 9 µm region for an arbitrary reference atmosphere extracted from the Mars Climate Database. The line-by-line transmittances were convolved with an approximate instrumental response at 0. 15 cm-1 resolution, to mimic the NOMAD SO signal, as was done by  Vandaele et al. , 2015 [132]  in similar transmittance calculations but at tangent heights below 50 km. Using a conservative estimation of the SNR of 2500 for the SO channel  (Robert et al. , 2016 [112] ), consistent with the NESR value shown in Table  1 , all the spectral features visible in figure  7 , even at 170 km altitude (about 0. 05 nbar in this reference atmosphere), should be detected in the SO signal. Since the ACS MIR has a spectral resolution about 3 times better than the SO channel but a lower sensitivity by about the same factor, the same conclusion applies to the solar occultation with ACS/MIR.
, 2006 [100] ;  Määttänen et al. , 2013 [86] ). An interesting result from the combination of SPICAM UV and IR solar occultations during the Northern winter, obtained by  Fedorova et al. (2014)   [36] , is the identification of a bi-modal distribution of particles on Mars at tropospheric altitudes  (10-40 km). The coarser mode, with particle radius near 1 µm was consistent with many previous atmospheric dust observations, and seemed to contain both dust and H 2 O ice particles, with 0. 7 and 1. 2 µm radii, respectively. But their UV data were essential to identify the fine mode, with radius smaller than 0. 1 µm and reaching altitudes up to about 60-70 km in such a data sample. In summary, the UVIS channel may extend significantly the upper atmospheric dataset of aerosols, clarifying the population and variability of small particles during periods of large dust storms and other episodes, and if combined with a concomitant IR sounding and microphysical models, clarify the nature of the aerosol layers.
Ultraviolet mapping with UVIS The continuous UV mapping in nadir will supply a useful dataset to study airglow. The nightglow signals will be weaker than the limb components and than solar occultation detections but the accumulation of data may reveal the emissions and permit analysis of the spatial and temporal variations. One notable example is the NO nightglow, detected in the limb but not in nadir by SPICAM  (Bertaux et al. , 2005 [5] ). This is an emission of large interest as it is associated to downwelling of atomic species (O 3 P and N 4 S) from the global interhemispheric circulation during solstices  (Bertaux et al. , 2005[5] ,  Stiepen et al. , 2015 [125] ). However, there are discrepancies between models and simulations at equatorial latitudes, where such emissions are expected to be much weaker  (Gagné et al.
ESA, on the other hand, has performed only one aerobraking campaign, during the last phase of the Venus Express mission. These operations permitted successful retrievals of density profiles which revealed wave phenomena in polar regions (Müller-Wodarg et al. , 2016  [102] ) and permitted comparisons with atmospheric reference models  (Bruinsma et al. , 2015 [13] ). The aerobraking phase of Exomars TGO will supply an additional source of information on the still highly incomplete dataset of in-situ thermospheric densities and temperatures available to date. A large interest in the TGO dataset comes from the combination of three factors: a wide latitudinal coverage, an extended investigation in time, and a focus on the lower thermospheric altitudes. Starting with the last one, the expected altitude range of the periapsis is  km, with some seasons at higher altitudes [150-160km], as shown in Figure  13.
The part of the orbit when the spacecraft will be below 200km altitude will cover around 40 deg in latitude, until TGO orbit achieves its final circular shape at 400 km above the planet's surface. It will have a periodicity of 1 Martian day (sol) at the beginning and 2 h at the end of the aerobraking experiment. One of the open problems whose study could benefit from the TGO aerobraking data is the propagation of gravity waves. Previous analysis using extended aerobraking datasets from MGS and Mars Odyssey suggest that such a propagation is possible up to the lower thermosphere, and might be filtered by tidal activity  (Withers et al. , 2006 [139] ). Also non-migrating tides were detected in the aerobraking data  (Wang et al. , 2006 [135] ,  Fritts et al. , 2006 [41] ), together with smaller scale perturbations without a clear oscillatory shape and which remain unexplained.
Also, these observations shall permit to complete the daily cycle of minor species (chemistry & dynamics) outside the specific local times of the terminator at each latitude. Specific emission from solar fluorescence and airglow data would permit to study the upper atmosphere physics behind them, and perhaps to derive information about the thermal structure in the vertical. After detection of specific areas on the planet where trace gases are found, a vertical sounding capability above such areas would be of large interest, if their emission in a limb geometry permit to gain insight into their vertical distribution. These observations would also extend in time the current database of Mars limb observations to date (OMEGA, PFS and SPICAM on Mars Express, TES on MGS, and MCS and CRISM on board MRO).
Mars Express instruments OMEGA, SPICAM and PFS have been extremely successful studying the upper atmosphere using both emission and absorption data  (Titov et al. , 2017 [130] ). Mars Express offers the opportunity to perform correlated observations and cross-validation with TGO instruments, and with both the nominal observation modes and the possible additional modes discussed above. The very different orbits offer chances to complement each other in areas like daily cycles of dust and ice  (Giuranna et al. , 2017 [51] ). Also, new tools for exploitation of Mars Express data are under development, with the goal to apply them to Exomars TGO instruments, opening the door for optimal exploitation of both datasets (http://www. upwards-mars. eu/). These tools include synergistic retrieval schemes combining two spectral ranges and/or different instruments  (Robert et al.
Acknowledgements The  IAA/CSIC  team has been supported by the  European Union 's  Horizon 2020 Programme  ( H2020-Compet-08-2014 ) under grant agreement  UPWARDS-633127 , by  CSIC  Proyecto Intramural 201450E022 and by the  Plan Nacional del Espacio   ESP2015-65064-C2-1-P (MINECO/FEDER ). This research was partly supported by the  SCOOP/BRAIN program  of the  Belgian Science Policy Office (BELSPO). We acknowledge the work of  Sabrina Guilbon  during her Master internship at LATMOS on the development of the technique to compare the slant profiles of SPICAM and the LMD GCM. M. R. P. thanks  UKSA  for support under grant  ST/I003061/1  and  ST/P001262/1. C. F. W. acknowledges funding support from the  UK Space Agency. Work by A. K. , D. J. MC. and D. M. K. at the  Jet Propulsion Laboratory, California Institute of Technology  was performed under a contract with the  National Aeronautics and Space Administration.
International collaborations among birth cohorts to better understand asthma and allergies have increased in the last years. However, differences in definitions and methods preclude direct pooling of original individual participant data. We harmonized data from 14 birth cohorts, with three to 20 follow-ups, from nine European countries, as part of the Mechanisms of the Development of Asthma and Allergies (MeDALL) project. The harmonization process followed six steps: 137 reference definitions. The inferential equivalence of 3,551 cohort variables to their corresponding reference definition was classified as complete, partial and impossible for 70%, 15% and 15% of the variables, respectively. A harmonized database was delivered. In birth cohorts of asthma and allergies, the harmonization of data for pooled analyses is feasible and may achieve high inferential comparability.
Over 130 birth cohorts with data on asthma and allergy have been initiated in the world over the past 30 years (1). The information gathered by these birth cohorts has already significantly advanced in our understanding of allergy and asthma, particularly during the first years of life (2). However, this data is usually in an isolated, independent database. Although the assessment methods of the data vary, the majority of the birth cohorts followed rigorous methodology, and the resultant data is relatively readily available in electronic format. cohorts and produced a large number of joint studies that have frequently used metaanalysis based on cohort original data (1,  12, 13). Though few studies have integrated data from different birth cohorts in single pooled analysis  (7, 14) , a formal reproducible approach for data harmonization has not been reported.
Harmonization process The harmonization process was adapted from the DataSHaPER project (15) and followed six steps (see Figure  1 ). Step 1: organization of the harmonization panel, formed by the harmonization coordinators and cohort experts. The harmonization coordinators were in charge of organizing all the process, contacting each cohort, and ensuring active participation of the cohort experts. These included, for each birth cohort, a principal investigator and a statistician or data manager very familiar with the cohort database. Step 2: Identification of candidate variables. The cohort experts identified relevant variables for ongoing and future research objectives within MeDALL. From the identified variables, the harmonization coordinators pre-selected those for which (i) an agreed reference definition was likely to be found or produced by expert consensus, and (ii) enough data was available to provide sufficient power for the envisioned analyses (i.
Most questions (candidate variables) were collected at several periods (e. g. , wheezing in last 12 months) and they were considered as many times as they appeared. Then each principal investigator assessed the compatibility (inferential equivalence) of their own variables to the corresponding reference definitions by means of assessing the meaning, format, and data collection procedure of each variable (general pairing rules). Three qualification categories (complete, partial, and impossible) were used, adapted from the ones proposed in the DataSHaPER project (15, 21). A variable was classified as complete if the meaning, format, and standard operating procedures used for data collection allowed the complete construction of the reference definition. A partial qualification was given if the meaning, format, and standard operating procedures used for the data collection allowed the construction of the reference definition, but with an unavoidable loss of information.
The rules for discussion were made explicit and agreed by the harmonization panel at the beginning of the workshop e. g. a maximum of ten minutes was assigned for the discussion of a reference definition; if no consensus was reached during that time the proposed reference definition was excluded from the harmonization process and its variable(s) from the final database. Notes were taken during the workshop by different participants and checked by the harmonization coordinators for a post workshop quality control. The final agreed reference definitions can be found in the Web Table  2. Step 6: Data preparation and delivery. Each cohort provided the harmonized variables following the decisions agreed on during the workshop to the knowledge management portal. The MeDALL partner Biomax, a bioinformatics company with experience in systems medicine  (24, 41, 42) , provided dedicated technological support during all the steps.
Biomax developed a knowledge management portal for the project (https://ssl. biomax. de/medall) that stores, manages, structures, and provides project- specific knowledge, allowing flexible data harmonization and integration. After the harmonization process, all the data was integrated in the portal where different algorithmic checks were performed to ensure data quality. Cleaning rules included checks for completeness (e. g. , were data available for all participants?), availability of required data (e. g. , were all variables provided as defined in the metadata?), data type check (e. g. , float, thesaurus), consistency checks of the collected data across follow-up periods (e. g. , if a "yes" answer occurred to "doctor diagnosis of asthma ever" then the same question in the following examinations were set to "yes"), and outlier detection.
Strengths and limitations Strengths of the present work are the very rigorous process applied, which allows others to reproduce the approach, the use of a technological support (the MeDALL knowledge management portal) that includes all reference definitions, variables, and codification, and all the expert knowledge used in order to take decisions. Existing long term collaboration of most birth cohorts starting with the GA 2 LEN initiative (3, 4), and continued through the ENRIECO (8) and CHICOS  (10)   (details available from Biomax upon request), thus supporting the reproducibility of our approach. We encountered several limitations while harmonizing the MeDALL data. First, the cross-cultural differences have been challenging occasionally, with some of the symptom definitions reflecting the subtle differences between the languages involved in this large European collaboration (e.
g. wheezing in German cannot be translated directly but is translated in three words: Giemen, Pfeifen, Brummen). Second, the cohorts were heterogeneous regarding the spectrum and assessment methods of environmental and psychosocial exposures. For instance, some of the cohorts had more detailed questions on indoor environment than others  (26-31, 33, 36, 38)  while others focused on psychological factors  (26) (27) (28) (30) (31) (32). Of note, some exposures and diseases could not be harmonized due to the large heterogeneity or lack of data. Thus the new common database after the MeDALL harmonization work does not yet include all but a large set of all core variables on asthma and allergy and on the most prevalent exposures and risk factors. Third, we did not assess the influence of using harmonized variables on the validity of previous studies using the same variables, which is an area deserving attention in future research.
shows the distribution of final inferential equivalence classification according to the five variable dimensions mentioned above. The symptoms dimension was the closest to the overall classification with 73% of the variables in this dimension classified as complete, 13% as partial, and 14% as impossible. The proportion of variables classified as complete was high (79%) in the environmental exposures dimension and low in the treatment (57%) and physical activity (29%) dimensions. Almost 60% of variables in the physical activity dimension were classified as impossible. Final classifications for all included variables are available in Web Figures 1 to 14. All variables, and their inferential equivalence classifications, have been integrated in the final MeDALL database in Downloaded from https://academic.
40 to 0. 50) (data on agreement by dimension and for each individual variable is available from the authors upon request). (Table2here)DISCUSSIONMain findingsThe present MeDALL harmonization study shows that harmonization of databases from different European asthma and allergy birth cohorts is feasible and successful following and adapting the steps reported by the DataSHaPER (15, 21) group. After six months of preparation and a four-day workshop we have agreed on 137 reference definitions and classified their inferential equivalence to 3,551 cohort variables. More than two thirds of the harmonized variables were classified as complete and the remaining 30 per cent were either partial, or impossible. Downloaded from https://academic. oup. com/aje/advance-article-abstract/doi/10. 1093/aje/kwy242/5142391 by Danish Regions user on 13 November 2018.
All the networks were symmetrized (non-directed links), by keeping only the highest score when two actors evaluated their relationship differently. We then conducted a longitudinal study of the mean scores of the variables (equivalent to the density for the symmetric networks), before analysing the interdependencies between the different variables, in order to identify those that lead the actors to collaborate. For this purpose, we have applied the quadratic assignment procedure (QAP), using the social network analysis software, Ucinet  (Borgatti et al. 2002) , which makes it possible to test whether the association between two networks is statistically significant. More precisely, we apply the logistic regression quadratic assignment procedure (LR-QAP), which consists of a multiple logistic regression of a dependent variable (here the collaborative network) on independent variables (here TGP, networks of friendships and networks of political relationships, and the group).
However, our study has some limitations. First, the method used for selecting the subpopulations restricted us to choosing among the active members of the programme. Analysing the networks of all the participants would have provided explanatory data on the mechanisms of exclusion of certain groups of actors. A second limitation is related to the collection of relational data. Due to the local conditions, we were not able to administer the questionnaires to all the actors in the identified subpopulations, which forced us to infer, from more qualitative data, the existence of a number of relations and to abandon the directed nature of the linkages, reducing the scope of structural analysis. Finally, the longitudinal network analysis was carried out a posteriori, creating biases related to the difficulty of the actors to remember perfectly these past relationships, even though they can identify with accuracy the main three phases on the basis of which we have structured our research.
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores.
Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker.
33 Tinker beneted from the availability of this low cost but powerful type of hardware. It led to a GPU version of the code denoted Tinker-OpenMM. 34 The code is based both on Tinker and on the OpenMM library (now version 7 (ref. 35)) which pioneered the use of GPUs with polarizable force elds. Tinker-OpenMM offers a 200-fold acceleration compared to a regular single core CPU computation giving access to accurate free energy simulations. However, when one considers the need for biophysical simulations, this acceleration remains not sufficient. The purpose of the present work is to push the scalability improvements of Tinker through new algorithms to explore strategies enabling a 1000-fold and more speedup. These new developments aim towards modern "big Iron" petascale supercomputers using distributed memory and the code design also offers consequent speedups on laboratory clusters and on multicore desktop stations.
The philosophy here is to build a highly scalable double precision code, fully compatible and consistent with the canonical reference Tinker and Tinker-OpenMM codes. As the new code remains a part of the Tinker package, it is designed to keep its user-friendliness offered to both developers and users but also to provide an extended access to larger scale/longer timescale MD simulations on any type of CPU platforms. The incentive to produce such a reference double precision code is guided by the will to also perform scalable hybrid QM/MM MD simulations where rounding errors must be eliminated. This will bring us not to cut any corners in our numerical implementation with the key mantra that one should not scale at any cost, as the algorithms developed in this interdisciplinary project should be based on solid mathematical grounds.
The paper is organized as follows. First, we will present the newly developed extension of 3D spatial decomposition and memory distribution to polarizable point dipole models that is at the heart of Tinker-HP for short-range interactions. Then we will detail the handling of long-range electrostatic and polarization interactions with a new framework coupling Smooth Particle Ewald to Krylov iterative and non iterative polarization solvers. We will then introduce the possibilities of the soware and show benchmarks for selected applications in the context of the AMOEBA PFF. 24, 36 Finally, we will present functionalities of Tinker-HP that go beyond MD simulations in periodic boundary conditions as we conclude by drawing some perspectives about evolutions of the code towards next HPC platforms.