dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments: We thank  J. Chang ,  C. Doughty , and  M. Clauss  for constructive comments and feedback on a previous version of the manuscript,  Y. Hui  for providing MODIS data,  F. Maignan ,  M. Peaucelle , and  N. Viovy  for the assistance with ORCHIDEE,  P. Stevenson  for help with fruit production, and  L. Santini  for the help with linear mixed-effects model setup. F. B. was supported by  European Union 's  Horizon 2020 research and innovation program  under the  Marie Sklodowska-Curie grant  # 845265.
Deep regional geothermal heat flow Over continents, heat flow data are generally obtained from temperature profiles measured in boreholes with a few hundreds of m depth; in particular, heat flow maps of France  [Lucazeau and Vasseur, 1982, Bonte and Guillou-Frottier, 2006]  show that the area of southern Languedoc is characterized by a regional heat flow of 80 to 90 mW•m -2. An essential condition for obtaining significant heat flow data is to avoid areas where heat convection occurs through active water flow; this precludes the use of such temperature profiles in karstic areas. However in most sedimentary basins, the oil industry has been drilling very deep boreholes for hydrocarbon exploration, reaching depths (several km) where active hydraulic fluxes are certainly much smaller; bottom hole temperatures (BHT) are recorded during well-log acquisition, being imposed more by technical purposes than by scientific ones.
Acknowledgments This work was initiated following discussions with  Michel Bakalowicz ,  Francis Lucazeau ,  Véronique Leonardi  and  Hervé Jourde. The development of the mathematical model received assistance from  Pierre Genthon. The possible importance of the gravitational potential was pointed out by  Patrick Lachassagne  and resulted in discussions with  Patrick Goblet ,  Emmanuel Ledoux  and  Ghislain de Marsily. The author apologizes for committing a basic error in a previous version of the manuscript while omitting the influence of pressure in the energy budget. Most of the data come from the collections of  CERGA (Centre pour l'Enseignement et la Recherche en Geosciences et Applications ) which has been recording and storing most of the hydrogeological studies on the Lez karstic system; the help of  Josè Gravellec ,  Pierre Bérard ,  Jean Pierre Faillat  and  Jean Christophe Marechal  is gratefully acknowledged.
, 2020]  and the Eastern Corbières aquifer, both located to the West of Montpellier. These aquifers are instrumented with salinity, temperature and groundwater level data loggers to assess the seawater intrusion, as part of a research project conducted by the French Geological Survey (BRGM). The outlets, namely the Vise submarine spring in the Thau lagoon, at 30 m bsl, and Fontestramar coastal spring, at +4 m above sea level (asl) are monitored, as well as boreholes and surface flow upstream swallow holes. The study on the Thau karst is currently ongoing. Over the last 50 years, the Thau karst aquifer was subject to seven brackish water intrusions via the submarine spring of La Vise. These events, called inversac, took place in  1967 , 1983 , 1993 , 2008 , 2010 , 2014 and 2021 -2022 [Ladouche et al.
Scalability of parallel solvers for problems with high heterogeneities relies on adaptive coarse spaces built from generalized eigenvalue problems in the subdomains. The corresponding theory is powerful and flexible but the development of an efficient parallel implementation is challenging. We report here on recent advances in adaptive coarse spaces and on their open source implementations in domain specific languages such as FreeFem, focusing on a new domain decomposition for saddle point formulations with some numerical tests. Résumé. L'extensibilité des solveurs parallèles pour les problèmes à forte hétérogénéité repose sur des espaces grossiers adaptatifs construits à partir de problèmes de valeurs propres généralisés dans les sousdomaines. La théorie correspondante est puissante et flexible mais le développement d'une implémentation parallèle efficace est un défi.
It implies a huge effort in algorithmic development. Scientific computing is only one illustration of this general need in computer science. Visualization, data storage, mesh generation, operating systems, languages,. must be designed with parallelism in mind. For computational fluid dynamics simulation codes as well, parallelism is nowdays "a has to have". For developers, it means integrating in their codes more and more complex tools such as parallel mesh generation, graph partitioners (e. g. , METIS or Scotch) for mesh decomposition, parallel linear solvers (e. g. , PETSc, Trilinos, MUMPS, PARDISO, SuperLU DIST, parallel multigrid or domain decomposition (DD)r science tools such as OpenMP for shared parallelism and/or MPI (Message Passing Interface) for distributed parallelism as well as OpenCL or Cuda for taking advantage of GPUs.
g. , Comsol are now well established to easily handle multiphysics simulations as well as parallelism. We focus here on FreeFEM since it will be used in the sequel for the implementation and test of a new DD method for saddle point problem. Specifically a FreeFEM script is very close to the mathematical variational formulation of the equations. This allows non-computational experts to solve non-trivial PDEs on parallel computers through a user friendly language. This is one of the reasons why it can be used for both teaching and prototyping, in academia as well as in industry. As an example, it was used in  [1]  for performing large-scale hydrodynamic stability analysis, see Figure  1  or also Figure  2  taken from  [2]  as an example of parallel computations made with the DSL FreeFem. In this paper, we focus on linear solvers based on DD methods for solving large-scale saddle point problems.
Libraries for large-scale computations We have thus a strong set of mathematical techniques that enable to build efficient DD methods. But it comes at the expense of some difficulties since the implementation of these methods is not so easy due to the need to have access to the variational formulation to build the local matrices (A Neu i ) 1≤i ≤N in the generalized eigenvalue problem for computing the coarse space, see  (8). Also, an efficient parallel implementation needs a careful organization of the code and the use of the message passing interface MPI on distributed memory machines. This motivated the development of open source implementation of the GenEO coarse space: • the C++/MPI library hpddm  [52]  either as an autonomous library or interfaced with FreeFem  [53]  or PETSc  [54]. The library also provides access to the GCRODR method  [24]  useful when solving linear systems with multiple right-hand sides.
• the FreeFem DD library ffddm  [55]  • a Dune solver as described in  [56]  It is worth noticing that the access to the variational formulation is made easy if one makes use of domain specific languages or libraries such as FreeFem  [53] , Dune  [57]  or Firedrake  [58]. It facilitates the encapsulation of two-level methods. The resulting scripts are then quite compact and do not require writing of MPI lines of code although they enable the parallel solving of all kinds of equations with the above mentioned methods.
Also, the tests were performed with FreeFem scripts using the standalone ffddm  [55]  framework. The integration of the method in the C++/MPI library hpddm  [52]  could lead to faster codes and a more general diffusion of the saddle point preconditioner. In a different setting, the design of adaptive coarse space is strongly connected to multiscale finite element (MFE) methods (see e. g. ,  [34, 59, 60]  and references therein) and this work could be used in designing MFE or Reduced Order Methods for saddle point problems.
La investigación fue aprobada por el Comité de Ética en Investigación de la Escuela de Enfermería de Ribeirão Preto de la Universidad de São Paulo de número 66095517. 4. 0000. 5393, 074/2017. Se han respetado todos los preceptos éticos según la Resolución de Brasil. Financiación Coordenacão de Aperfeicoamento de Pessoal de Nível Supe- rior (CAPES) beca m'sster en el periodo 10/2016 a 01/2018 número 1657273. Esta investigación también fue financiada por el Consejo Nacional de Desarrollo Científico y Tec- nológico (CNPq) Beca de Productividad en Investigación 1D Beca 317384/2021-0, CNPq n • 26/2021, proceso número 402515/2022-6.
g. ycf3, rps12, rpl20, rpl2, ndhB, ndhD, clpP and others). By contrast, rrn16 and some tRNAs (e. g. trnG-UCC; trnV-UAC; trnA-UGC; trnR-ACG, trnL-UAA) are believed to be transcribed primarily by PEP  (Kanamaru et al. , 2001; Legen et al. , 2002; Ishizaki et al. , 2005; Williams-Carrier et al. , 2014) , but these RNAs appeared not to be significantly enriched in the pTAC12 RIP-chip experiments. The small enrichment peaks of latter genes could be a result of signal saturation caused by high RNA abundance in the supernatants. A summary of the pTAC12 RIP-chip data is provided in Table  S3. The RIP-chip data were validated by slot blot hybridization assays using the same coimmunoprecipitation conditions as for RIP-chip assays (Fig. 4b ). From the set of tested sequences, most of the highly enriched RNAs in the RIP-chip assays (psbA, psaAB, rps12, rpl2 and petB) were confirmed by the slot-blot data; psbB, rps14 and psbE coimmunoprecipitated with ZmpTAC12 to a relative moderate degree (c.
50%). Consistently with the RIP-chip data, several tRNAs showed little or no enrichment. Taken together, these data provide support for the hypothesis that ZmpTAC12 associates with a subset of PEP-derived transcripts, either directly or indirectly through its association with PEP. In an attempt toward delineating plastid DNA loci associated with pTAC12 (and potentially loci of high PEP-activity), DNAs were extracted from the immunoprecipitation pellet and supernatant and subjected to DIP-chip analyses. In this assay, DNAs were fragmented including the restriction enzymes AluI and Eco-RI before immunoprecipitation. Additionally, stromal extracts were treated with ribonucleases, and alkali hydrolysis was included to remove RNA after the immunoprecipitation. The signal ratio of the two DNA populations (pellet and supernatant) was calculated in order to reflect the enrichment of respective DNA segments precipitated by the pTAC12 antibodies (Fig.
Acknowledgements We thank  Rosalind Williams-Carrier  for assistance in RIP/DIPchip experiments, and  Susan Belcher  and  Susanne Klug  for technical support. We would like to thank  Prof. Takashi Shiina  for the kind donation of pTAC3 antibodies, respectively. This work is funded by the  DFG  grants  PF323-4 (T. P. ), Mi373/15-1  (M. M. ), and  PF667-4  (J. P. ) and by  National Science Foundation  grant to A. B. ( IOS-0922560 ).
Acknowledgments The results presented in this paper have not been published previously in whole or in part. This project was supported by grants from the  Mexican Council of Science and Technology (CONACyT)  ( 101030 ,  181267 ,  235855  to NAB and  229524  to NAB and FJ) and from the  National University of Mexico  ( IN223915  to NAB). RRR is a graduate student in the  Biomedical Science Ph. D. Program at Universidad Nacional Autónoma de México  and is supported by a scholarship from  CONACyT-Mexico.
Methods Electrode implantation. Participants were eight patients (four female, age range 18-36 years) with pharmacologically intractable epilepsy undergoing a work up to determine eligibility for surgical therapy of the epilepsy at the SEIN (Stichting Epilepsie Instellingen Nederland)-VU Medical Center epilepsy surgery programme, Amsterdam, Netherlands. Patients were implanted with depth electrodes for 7-10 days for chronic seizure recording to localize the seizure focus for possible surgical resection  13, 44. All surgeries were performed by J. C. B. The Medical Ethics Committee at the VU Medical Center approved the studies. Written informed consent was obtained from all patients before participation. The electrode locations were based entirely and exclusively on clinical criteria (patient data of any kind necessary to determine a resection with highest probability to render the patient seizure free).
Each electrode consisted of eight microwires from which we recorded single-and multi-unit activity and a ninth microwire that served as a local reference. The signal from the microwires was recorded using a 64-channel Neuralynx system, filtered between 1 and 9,000 Hz, sampled at 32 KHz. On average, each patient was implanted with 34 ± 12 microwires. Participants sat in their hospital room and performed the experimental sessions on a laptop computer. All patients participated in the two types of experimental sessions described below. Spike detection and sorting. Spike detection and sorting were performed with wave_clus  45. Briefly, the data were band pass filtered between 300 and 3,000 Hz and spikes were then detected with an automatic amplitude threshold. Spike sorting was performed with a wavelet transform that extracted the relevant features of the spike waveform.
Images were presented for 1,000 ms, followed by an inter-stimulus interval of 500 ms. Each image was repeated eight times in a randomized order. Between 7 and 51 images were used in the screening sessions depending on the time span the patient was available. After the presentation of each image the patients performed a simple yes/no task, for example, 'Did the picture contain a human face'? The exact question depended on the picture set. This task ensured that patients attended to the stimuli. Data from the screening sessions were rapidly analysed to determine which images were the 'preferred' images of the neurons. A neuron's 'preferred' images were defined as those that elicited a significant (paired t-test, Po0. 05) response during the stimulus presentation period (0-1,000 ms after stimulus onset) compared with the preceding ISI ( À 500 to 0 ms before stimulus onset).
Acknowledgements We are grateful to  Benedikt Zoefel  for his help in obtaining some of the data reported here, and to the entire staff of the  EMU of the VUmc  for their help during these recordings. In particular we would like to thank  Peterjan Ris  and  Hanneke Ronner  for their technical assistance, and  Demetrios Velis  for invaluable help with planning the patient workup and implantation design. We are also grateful to  Ruud Joosten  for his help in setting up the recordings and  C. J. Stam  for his help with obtaining ethics approval. We thank  K. Diba ,  M. Mehta ,  B. Poucet ,  C. J. Stam  and  R. VanRullen  for helpful comments on the manuscript. This work was supported by grants from the  Fyssen foundation , the  Universite 0 Paul Sabatier, Toulouse, France (BQR, 2009 and Appel a' Projets de Recherche Labellise 's, 2013) and the  French Agence Nationale de la Recherche  ( ANR-JCJC ) to L.
R. , and the  European Research Council  ( ERC Grant  Agreement no. 339490 ) and  Neuroscience Campus Amsterdam proof  of concept funding to P. R. E. v. D, L. D and J. C. R were funded by the  Dutch Epilepsy Foundation  (grant  08-08  to L. D. and J. C. R. , and grant  09-09  to E. v. D and J. C. R).
Cell attachment assay Thirty minutes, 1 hour and 2 hours after plating, calvaria cells were washed twice with PBS to rinse off unattached cells, fixed with 3. 7% PFA and stained with 4&rsquo;6-diamidino-2-phenylindole (DAPI, Chemicon, Temecula, CA, 0,1μg/ml). Cells were examined with a Zeiss AxioObserver fluorescent videomicroscope (Zeiss, Le Pecq, France) and images acquired with the AxioCam camera using the AxioVision software (Zeiss, version 4. 8. 1. 0). The nuclei were then counted using the Image J software (http://rsb. info. nih. gov/ij).
Ki67 positive and negative nuclei were then counted in 10 fields per coverslips (n = 6 coverslips/genotype/time-point) using Image J. To take into account the difference in growth kinetics, the data were normalized to 1000 DAPI-labelled nuclei in the bar graph. In other dishes, a colorimetric immunoassay was used based on the measurement of BrdU (pyrimidine analogue 5-bromo-2'-deoxyuridine) incorporation (Cell proliferation ELISA BrdU kit, Roche Diagnostic GmbH, Mannheim, Germany). Apoptosis was assayed by fluorescent transferase-mediated dUTP nick-end labeling (TUNEL) assay using the ApoTag PLUS Fluorescein In Situ Apoptosis Detection kit (Serologicals, Norcross, GA, USA). As a positive control, some wells were incubated with 10 -8 M dexamethasone overnight prior to the assay.
Immunolabelling For immunolabeling, cells were grown on 10-mm-diameter glass coverslips for 10 days, then fixed with 3. 7% PFA and permeabilized in methanol. Cultures were labeled overnight at 4°C in a humid chamber with an anti-mouse OPN primary monoclonal antibody (Santa Cruz, Dallas, USA, ref sc-21742) diluted 1:100 in PBS with 10% goat serum (labeling buffer). After washes in PBS, the cells were incubated for 1. 5 hour at room temperature with a mixture of Alexa 488-labeled goat anti-mouse secondary antibody and 4&rsquo;6-diamidino-2-phenylindole (DAPI, Chemicon, Temecula, CA, 1 μg/ml) in labeling buffer. After rinsing, cells were examined with a Zeiss AxioObserver fluorescent videomicroscope and images acquired with the AxioCam camera using the AxioVision software.
Osteopontin immunoassay After 6, 14 and 17 days of culture, ELISA was performed to measure OPN in cell lysate and culture medium using the DuoSet mouse Osteopontin ELISA Development System (R&D Systems, Minneapolis, MN, USA) according to the manufacturer's instructions. Cells were collected in a lysis buffer composed of PBS with 0. 5% Nonidet 40 and 1% protease inhibition cocktail (PIC, Sigma), 1μl/ml triton (Sigma) and 1,8 mg/ml iodometacin (Sigma). Each sample was run in duplicate in the assays. Data were corrected for fresh culture medium or fresh lysis.
Statistical analysis The STATISTICA software (version 8. 2; StataCorp, College Station, TX) was used for statistical analysis. Quantitative data are presented as mean±SD (except for Ki67 labeling, as mentioned), from one experiments in a series of two to three repeats, done with distinct cell isolates and giving the same results. Inter-group differences were tested with the non-parametric Mann-Whitney U-test for all experiments except Ki67 labeling. For the latter, the total numbers of positive and negative cells for each day in each genotype were plotted in a contingency table and assessed for homogeneity with a χ 2 test.
This work was funded by the  French "Institut National de la Santé et de la Recherche Médicale" (INSERM)  and by the  French Ministry of Research  (PhD fellowship to GB). WB and LJ gratefully acknowledge scholarship funding by the  Rhône-Alpes Region  ( Cible Program ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
As a consequence nationally and internationally accepted dietary indices have been developed to measure diet quality, each having specific principles and approaches in its concept and calculation. The Healthy Eating Index-2010 (HEI) is based on dietary guidelines summarized in the United States Department of Agriculture Food Guide Pyramid  [6]. The Mediterranean Diet Score (MDS) is based on the adherence to the Mediterranean diet  [7]. The Diet Quality Index (DQI) evaluates the adherence to Flemish food-based dietary guidelines  [8]. The HEI and the DQI are calculated by comparing the participants' dietary intake with prior defined guidelines, while the MDS uses collected data to obtain genderspecific median component intakes. In cross-sectional research, the HEI was negatively associated with overweight and obesity  [9, 10] , but weakly with blood lipids  [11] [12] [13].
Subjects This study is based on data collected by the Flemish Policy Research Centre Sport, Physical Activity and Health  [27]. One of the aims of this Research Centre was to examine the relationship between health behavior, physical health, mental health and physical fitness among an adult population. Therefore 46 Flemish municipalities were randomly selected by the National Institute of Statistics. Within those municipalities, a random sample of men and women between 18 and 75 years old was selected in 2002. The sample can be considered as sufficiently representative for geographic distribution, age, gender and educational level. The first test moment took place during 2002-2004, the second during 2012-2014. Of the original 1569 volunteers who participated in 2002-2004, 652 returned for retesting in 2012-2014.
Dietary assessment Participants completed a three-day diet record, in which they recorded all foods and drinks during two weekdays and one weekend day  [28]. Participants were asked to weigh the amount of foods and drinks consumed if possible. Otherwise they were inquired to estimate the amount of foods and drinks consumed by using standard household measures. Information about the diet record was included in the three-day record booklet. The diet records were analyzed using Becel Nutrition software (Unilever Co. ; Rotterdam, The Netherlands). Total energy intake (in kcal/day), consumption of food groups (in g/day), macronutrients (in g/day) and micronutrients (in mg/day or μg/day) were calculated.
Statistical analysis SPSS 21. 0 (SPSS Inc. Chicago, IL) statistics software was used for data analysis. A drop-out analysis was performed by comparing baseline results between the follow-up group and the group that only participated in 2002-2004 using an independent samples t-test. A paired samples t-test was used to examine if there are any differences in parameters between the two test moments. Differences in actual smokers between the two test moments were investigated using the chi-square test. Residual change scores of the dietary indices (HEI, MDS and DQI), anthropometric parameters (WC and BMI), blood lipids (TC, HDL cholesterol, LDL cholesterol, ratio total/HDL cholesterol, triglycerides), smoking and VO 2peak between the two test periods were calculated. Residual change scores were created by regressing the follow-up measures onto their respective baseline measures.
Both crosssectionally but even more longitudinally the differences in approach and calculation may have an influence on the associations with fitness components. Since the gender-specific median of the MDS was calculated separately for the data gathered in 2002-2004 and 2012-2014, the value of the median might be different between the two time points. This has important implications when change scores are calculated. Men (N = 373) Women (N = 197) Model 1 Model 2 Model 1 Model 2 β R 2 β R 2 β R 2 β R 2 The results of the present study are only partly in agreement with cross-sectional studies. Cross-sectional research showed that a low HEI was associated with overweight and obesity in a sample of both men and women  [9] , while in the present study only an association with anthropometric parameters was found in men.
Peptides eluting from the capillary tip were introduced into the a linear ion trap mass spectrometer (LXQ, Thermo Finnigan, San Jose, CA, USA) equipped with a nanoelectrospray source operating with a capillary voltage of 1. 8 kV and at a temperature of 200 °C, and performing a full scan and precursor selection in the range of m/z 300-1700. MS/MS spectra were recorded using dynamic exclusion of previously analysed precursors for 45 sec with a repeat of 1 and a repeat duration of 2. MS/MS data were evaluated using the TuboSequest algorithm of the Bioworks 3. 1 software (Thermo Electron Corporation) and searches were performed against the SwissProt database for Triticum. Data on Sequest was filtered using Xcorr score thresholds of ≥2 for 1 + peptides, Xcorr ≥ 2. 5 for 2 + peptides, and Xcorr ≥ 3 for 3 + peptides with Rsp ≤ 5 and Sp ≥ 350.