dataesr/scientific-paragraphs-categorization huggingface dataset:
3A ). The analysis of real protein data could benefit from our analysis in several ways. First, the understanding of the relationship between the couplings and the contact map obtained here indicates that the pressures λ ij (Eq. [2] ) are excellent estimators of contacts (Fig. 2A ), and may outperform the usual scores, F (AP C) ij (Eq. [10] ). The use of λ ij allows one to both keep track of the sign of the couplings (and avoid false positives corresponding to pressures originating from negative design, see above) and increase signal-to-noise ratio, by removing noise in the inferred couplings not aligned along the Miyazawa-Jernigan energy matrix. In real proteins, the physico-chemical properties of amino acids suggest the existence of different classes of contacts, whose energetics could be inferred from large-scale analysis of databases and used to define class templates E.
Among those let us cite the detection of homology. Current protein databases, such as PFAM, classify query sequences into families based on Hidden Markov Model profiles, an extension of independent-site models capable of taking into account deletions and insertions  [36]. It is an open problem to understand whether couplingbased models, exploiting covariation, could, contrary to HMM, recognize sequences with low homology in a reliable and computationally tractable way. Another very important issue is the estimation of fitness landscapes, or fitness changes in responses to one or more mutations  [37, 38]. Covariation-based models have been recently introduced to predict escape paths of pathogens (virus or bacteria) from drugs or vaccines in this context  [18]. Lattice proteins offer a unique benchmark to understand deeply and quantitatively and, ultimately, improve those approaches.
When relaxation towards an equilibrium or steady state is exponential at large times, one usually considers that the associated relaxation time τ, i. e. , the inverse of that decay rate, is the longest characteristic time in the system. However that need not be true, and in particular other times such as the lifetime of an infinitesimal perturbation can be much longer. In the present work we demonstrate that this paradoxical property can arise even in quite simple systems such as a chain of reactions obeying mass action kinetics. By mathematical analysis of simple reaction networks, we pin-point the reason why the standard relaxation time does not provide relevant information on the potentially long transient times of typical infinitesimal perturbations. Overall, we consider four characteristic times and study their behavior in both simple chains and in more complex reaction networks taken from the publicly available database "Biomodels".
Focusing further on those models that have been manually curated, we are left with only a handful of cases. The reason is that measuring kinetic constants of enzymes is a very difficult task so almost always when building a kinetic model the modeler has to use indirect methods to overcome the problem of dealing with many unknown parameters. We studied four of these models, published respectively in  [10] [11] [12] [13]. For each of those four kinetic models, we first downloaded its SBML specification  [9]  from the repository and exported the ordinary differential equations into Python code that can be processed. Once in our format, we determined the steady state of the network of reactions and we then computed the matrices J (c) and J (t). The associated leading eigenvectors and eigenvalues were obtained using the inverse power method, thereby providing the values of τ c and τ t.
METHODS The recommendations given in table 1 relate to the grading system currently suggested by the European Society of Cardiology (ESC) and the American Heart Association, and was based on paediatric data only (class, level of evidence). The grading and voting process within the writing group is outlined in this issue. 11 Computerised searches of the PubMed/ MEDLINE bibliographic database from 1990 to June 2015 were conducted. The developer searched using the terms 'paediatric pulmonary hypertension', 'congenital heart disease', 'pulmonary arterial hypertension', 'vasoreactivity in pulmonary hypertension', 'cavopulmonary anastomosis pulmonary hypertension', 'Fontan circulation and pulmonary vascular disease', 'operability in congenital heart disease in children', 'nitric oxide in pulmonary hypertension in children', 'Eisenmenger syndrome and pulmonary hypertension'.
Iron supplementation has been shown to improve symptoms and secondary organ failure in adult Eisenmenger patients. 18 19 62 ] [65] [66] [67] [68]  Bosentan has been shown to improve exercise tolerance and oxygen saturation after Fontan surgery. 69 Sildenafil improved max. oxygen consumption (VO 2 max. ) and pulmonary blood flow in patients with Fontan circulation. Another randomised crossover study showed that sildenafil therapy improved exercise tolerance and ventilatory efficiency in Fontan patients. 64 Data on the use of riociguat or selexipag in Fontan patients are currently lacking. A subgroup analysis of 35 patients with postoperative PAH-CHD treated with riociguat in the PATENT trial has been published. 41 Upcoming results from an international registry (COMPERA-KIDS) will enhance our knowledge of medical treatment for the different settings of PAH-CHD.
Reporting In EU/EEA countries, the Member States' Coordinating Competent Bodies have nominated national operational contact points for HIV/AIDS surveillance to work on reporting surveillance data to the joint ECDC/WHO database for HIV/AIDS surveillance. For non-EU/EEA countries, nominations for national HIV/AIDS surveillance focal points were received directly by the WHO Regional Office via the respective ministries of health. Data are submitted through a web-based platform to a joint database of The European Surveillance System (TESSy). Three types of data are collected: HIV (casebased and aggregate), AIDS (case-based and aggregate) and number of HIV tests performed (aggregate). Data are uploaded directly by the reporting country into the database. When uploading data, a built-in set of validation rules ensures the verification of the data within the database.
Individual country datasets Data were uploaded, validated and approved in the joint database for HIV/AIDS surveillance by the reporting countries. Once the data were submitted, individual datasets were validated. Seventeen countries uploaded datasets containing only 2013 data for HIV, whereas the remainder uploaded data concerning longer periods. Two countries (Kazakhstan and Ukraine) reported aggregated HIV data compared with four countries in 2012. Eighteen countries uploaded datasets containing only 2013 data for AIDS. Ukraine reported aggregated AIDS data for the years 2004 to 2013. All other countries reported case-based AIDS data. Reporting of aggregated HIV and AIDS data has an impact on the data presentation and analysis and the epidemiological overview of HIV/AIDS in Europe because fewer variables are available from the aggregated datasets, hence reducing the amount of data that can be presented in certain tables and figures.
For this purpose, we use the data from 21 weather stations of the Soil Moisture Observing System -Meteorological Automatic Network Integrated Application (SMOSMA-NIA) network  (Calvet et al. , 2007)  in southern France. The soil temperature and the soil moisture probes are buried in the enclosure around each weather station. Most of these stations are located in agricultural areas. However, the vegetation cover in the enclosure around the stations consists of grass. Along the Atlantic-Mediterranean transect formed by the SMOSMANIA network (Fig. 1 ), the grassland cover fraction ranges between 10 and 40 %  (Zakharova et al. , 2012). Various mineral soil types can be found along this transect, ranging from sand to clay and silt loam (see Supplement 1). During the installation of the probes, we collected soil samples which were used to determine soil characteristics: soil texture, soil gravel content, soil organic matter and bulk density.
The SMOSMANIA data The SMOSMANIA network was developed by  Calvet et al. (2007)  in southern France. The main purposes of SMOS-MANIA are to (1) validate satellite-derived soil moisture products  (Parrens et al. , 2012) ; (2) assess land surface models used in hydrological models  (Draper et al. , 2011)  and in meteorological models  (Albergel et al. , 2010) ; and (3) monitor the impact of climate change on water resources and droughts  (Laanaia et al. , 2016). The station network forms a transect between the Atlantic coast and the Mediterranean sea (Fig. 1 ). It consists of preexisting automatic weather stations operated by Météo-France, upgraded with four soil moisture probes at four depths: 0. 05, 0. 10, 0. 20 and 0. 30 m. Twelve SMOSMANIA stations were activated in 2006 in southwestern France.
, 2008). We revised the calibration in order to avoid spurious high soil moisture values during intense precipitation events. Logistics curves were used (see Supplement 1) instead of exponential curves in the previous version of the data set. The observations from the soil moisture (48) and from the temperature (48) probes are automatically recorded every 12 min. The data are available to the research community through the International Soil Moisture Network web site (https://ismn. geo. tuwien. ac. at/). Figure  2  shows soil temperature time series in wet conditions at various soil depths for a station presenting an intermediate value of λ sat (Table  2 ) and of soil texture (see Fig. S1. 1 in Supplement 1). The impact of recording temperature with a resolution of 0. 1 • C is clearly visible at all depths as this causes a leveling of the curves.
This data sorting procedure is described in Supplement 2. Given that three soil temperatures T i (i ranging from 1 to 3) are measured at depths z 1 = -0. 05 m, z 2 = -0. 10 m and z 3 = -0. 20 m, the soil diffusivity D hi at z i = z 2 = -0. 10 m can be obtained by solving the one-dimensional heat equation, using a finite-difference method based on the implicit Crank-Nicolson scheme  (Crank and Nicolson, 1996). When three soil depths are considered (z i-1 , z i , z i+1 ), the change in soil temperature T i at depth z i , from time t n-1 to time t n , within the time interval t = t n -t n-1 , can be written as T n i -T n-1 i t = D h i 1 2 γ n i+1 -γ n i z m + 1 2 γ n-1 i+1 -γ n-1 i z m , with γ n i = T n i -T n i-1 z i , z m = z i + z i+1 2 and z i = z i -z i-1. (5) In this study, z i = -0. 05 m, z i+1 = -0.
Prospects for using soil temperature profiles Using standard soil moisture and soil temperature observations is a way to investigate soil thermal properties over a large variety of soils, as the access to such data is facilitated by online databases  (Dorigo et al. , 2011). A limitation of the data set we used, however, is that soil temperature observations (T i ) are recorded with a resolution of T i = 0. 1 • C only (see Sect. 2. 1). This low resolution affects the accuracy of the soil thermal diffusivity estimates. In order to limit the impact of this effect, a data filtering technique is used (see Supplement 5) and D h is retrieved with a precision of 18 %. It can be noticed that if T i data were recorded with a resolution of 0. 03 • C (which corresponds to the typical uncertainty of PT100 probes), D h could be retrieved with a precision of about 5 % in the conditions of Eq.
Conclusions An attempt was made to use routine soil temperature and soil moisture observations of a network of automatic weather stations to retrieve instantaneous values of the soil thermal conductivity at a depth of 0. 10 m. The data from the SMOSMA-NIA network, in southern France, are used. First, the thermal diffusivity is derived from consecutive measurements of the soil temperature. The λ values are then derived from the thermal diffusivity retrievals and from the volumetric heat capacity calculated using measured soil properties. The relationship between the λ estimates and the measured soil moisture at a depth of 0. 10 m permits the retrieval of λ sat for 14 stations. The  Lu et al. (2007)  empirical λ model is then used to retrieve the quartz volumetric content by reverse modeling.
Acknowledgements. We thank  Xinhua Xiao  ( NC State University Soil Physics, Raleigh, USA ),  Tusheng Ren  ( China Agricultural University, Beijing, China ) and a third anonymous referee for their review of the manuscript and for their fruitful comments. We thank  Aaron Boone  ( CNRM, Toulouse, France ) for his helpful comments. We thank our  Météo-France colleagues  for their support in collecting and archiving the SMOSMANIA data:  Catherine Bienaimé ,  Marc Bailleul ,  Laurent Brunier ,  Anna Chaumont ,  Jacques Couzinier ,  Mathieu Créau ,  Philippe Gillodes ,  Sandrine Girres ,  Michel Gouverneur ,  Maryvonne Kerdoncuff ,  Matthieu Lacan ,  Pierre Lantuejoul ,  Dominique Paulais ,  Fabienne Simon ,  Dominique Simonpietri ,  Marie-Hélène Théron  and  Marie Yardin. Edited by: A. Cerdà Reviewed by:  T.
Imaging Photographs were taken using a Zeiss SteREO Discovery V16 microscope system and Zen software, and in most instances, incident light and transmitted light were used simultaneously. All of the images were digitally stacked photomicrographic composites of approximately 40 individual focal planes obtained using the free software CombineZP for better illustration of the three-dimensional structures. The figures were prepared with CorelDraw X4 and Adobe Photoshop CS3.
Acknowledgments: We are grateful to  D. Azar ,  C. Weirauch ,  V. N. Makarkin ,  D. Badano ,  C. A. Tauber ,  A. G. Ponomarenko , and  Y. Z. Yao  for helpful discussions;  M. Li ,  Y. R. Huang ,  Q. Q. Zhang ,  D. R. Zheng ,  N. Jia , and  G. de Ploëg  for specimen preparation;  D. H. Yang  for reconstructions; and  M. Clapham  and one anonymous reviewer for careful comments that improved this manuscript. Funding: This research was supported by the  National Basic Research Program of China  ( 2012CB821900 ), the  National Natural Science Foundation of China  ( 41572010 ), and the  Chinese Academy of Sciences (CAS) President 's  International Fellowship Initiative  (2011t2z04). B. W. was also supported by the  Youth Innovation Promotion Association of CAS  (no. 2011224 ) and a  Research Fellowship  from the  Alexander von Humboldt Foundation.
The index of novelty preference was calculated as the time spent in the new compartment/(time spent in the new compartment + time spent in the familiar compartment) × 100. Light intensity into the boxes was about 0. 20 lux. Before starting the experiments, we verified the absence of spontaneous preference for one of the compartments in a separate group of mice (data not shown). Anxiety. Anxiety was evaluated in the EPM and LDB tests. % of time spent in the EPM open arms and in their extremities (as complementary anxiety detection factor  (Cruz et al. 1994 )) and total distance moved were measured for 10 min. The light in the testing room was set up at 20 lux. For LDB test, % of time spent in the light side was measured for 5 min. The EPM was elevated 50 cm from the floor, and consisted of two 'open arms', i.
Neuronal activity was recorded in real time using Spike2 software (Cambridge Electronic Design, Cambridge, UK), which was also used to analyze neurons offline. In each mouse, all presumed 5-HT neurons were recorded for 2 min to determine the means ± SEM of 1) firing rate and 2) number of DRN 5-HT neurons per track in WT and α5 -/-mice. The last neuron was tested to determine the change in firing rate in response to the intraperitoneal administration of nicotine on DRN 5-HT neuronal activity for 1 min after approximately 10 min of stabilization. Microdialysis 5-HT microdialysis. Concentric dialysis probes were made of cuprophan fibers (active length of 1. 0 mm, outer diameter 0. 30 mm). Mice were anaesthetized with chloral hydrate (40mg/kg, i. p. ), placed on a stereotaxic frame and implanted with a probe bilaterally into the dorsal hippocampus (Coordinates from Bregma (in mm): anterior = +1.
After 2 hours of balancing perfusion, 4 samples were collected to determine basal values over 60 min. Then, animals received an i. p. systemic administration of 0. 9% NaCl and 4 samples were collected before i. p. systemic administration of 0. 5 mg/kg of nicotine. Responses to nicotine administration were determined over a 120 -min period (8 samples). At the end of the day, mice were killed by an overdose of chloral hydrate. Brains were removed and stored at +4°C in 2% formalin for 1 week. Brains were then cut using a Kryomat apparatus that maintained them at -25°C to provide 40-μm sections. Each section was photographed using a digital camera, and the implantation site was identified according to the mouse brain atlas. Only mice with probe confined in the dorsal hippocampus were used for subsequent data analysis DA microdialysis.
2012). Discovery HS-F5 column (150 mm × 2. 1 mm, 3 µm) (Sigma-Aldrich, Milan, Italy) was used for chromatographic separations. The HPLC analyses were carried out using an elution profile composed of a first isocratic step water (formic acid 0. 1%): acetonitrile (ACN) 95:5 for 1. 5 min and then to 30% of ACN over 6 min to separate DA from other analytes at 25 • C. The column was washed with 90% of ACN for 2. 5 min followed by the equilibration of the column for 5 min with 5% ACN. The flow rate was 0. 3 ml/min. The chromatograms were integrated using Agilent Mass Hunter software. DA detection limit was 0. 05 nM. At the end of each experiment, the animals were killed by rapid decapitation, brains were removed from the skull and the positions of the microdialysis probes were verified by visual inspection of the fresh tissue or the frozen brain during cut at the cryostat.
Statistical analysis Data were analyzed with Statistica (StatSoft, Inc. , France). Differences in behavioural and electrophysiological phenotypes between WT and α5 -/-mice were analyzed with unpaired Student's t-tests. Two-way ANOVAs were used to analyze the data for novelty preference (genotype as between-and environment as within-subject factors). Microdialysis data were analyzed with one or two-way repeated measures ANOVAs, (genotype and nicotine dose as between-and time as within-subject factors); paired and unpaired Student's ttests were used for genotype or drug treatment comparisons. For comparison between GFP, α5WT and α5SNP vectorized groups, data were analyzed using one-way ANOVAs (group as between-subject factor). Significant main effects (p<0. 05) were further analyzed using LSD Fisher post-hoc tests.
This work was supported by the  Institut Pasteur ,  Centre National de la Recherche Scientifique   UMR 3571& 7102 ,  Agence Nationale pour la Recherche, Fondation pour Neuropole de Recherche Francilien of Ile de France ,  National Cancer Institute INCa BIO-SILC programme, Ecole des Neurosciences de Paris ,  EU   FP7 ERANET Neuron NICO-GENE network, LabEx BIOPSY  funded by  ANR ,  Italian Ministry of Health   RF2009-154961. We thank  M. Soudant  for lentivirus production,  C. Morel  for sharing vectorized mice and  B. Forget  for comments on the work and manuscript.
Volumetric scanning. In this stage the experimental data are acquired and their digitalization is performed. Segmentation. The process of segmentation is used in order to segment a voxel set into two categories: material voxels versus empty space. Layered texture generation. This is the stage where the surface modelling is performed. Digital restoration. The surface flattening and unrolling can be interpreted as an isometric mapping (i. e. it preserve distances, which minimises text distortion in the parchment) from 3D to 2D images. To solve these problems different approaches were proposed. One of the most promising is described by Seales and colleagues  6, 8. The authors have developed software that integrates functions of flattening and unrolling based on mass-spring surface simulation.
A priori it is not possible to know the letters aspect and even whether the text is present in the analysed portion of rolls. In principle the text could be destroyed or could not appear due to the wrong position in the papyrus foil. We performed semi-manually procedure to reveal the hidden text based on computed algorithms exploiting Matlab ® codes ImageJ macros and different available commercial computer software. Once the phase contrast tomography provided the 3D volume of the bookrolls, to reveal the Greek text hidden inside, a multistep procedure has been settled: 1. Accurate optimization of the range of grey-levels has been done to individuate the inner structure of papyri with preserving all information about text. 2. Selection of areas with packaging of sheets with similar orientation.
Acknowledgements The authors wish to thank  Luigi Nicolais  (CNR),  Glenn Most  ( SNS, Pisa ),  Daniel Koger  ( Lindsey Wilson College, Kentucky, US ),  G. Neville Greaves  ( University of Cambridge, UK ) for valuable discussions and revisions of the present study, the  ESRF Directorate  for having granted the beamtime, the  Biblioteca Nazionale 'Vittorio Emanuele III' of Naples , for lending us the samples (in particular, the officers  Sofia Maresca  and  Vincenzo Boni ),  Eugenio Amendola  ( CNR-IPCB ), for valuable assistance in the preparation of the containers for the samples,  Carlo Ionta  for technical assistance in data-analysis,  Luigi Verolino  ( University of Naples Federico II ) and  Gaetano Campi  ( CNR-IC ), for preliminary discussions.
I. INTRODUCTION While the Large Hadron Collider (LHC) has just begun its second period of data taking, its first run has been an experimental success with many new measurements at an energy regime unexplored beforehand. In particular, the search for new phenomena has been given a boost with the discovery of a new particle, the celebrated Higgs boson  [1, 2]. Theoretically, however, we are still in the dark, as most searches performed at the LHC seem to be consistent with the Standard Model (SM) predictions. This includes the measurements of the Higgs couplings  [3] , the searches for new physics at the energy frontier with the ATLAS and CMS experiments and at the luminosity frontier with the LHCb experiment  1. In the absence of new physics signals, the naturalness argument that motivates the possible observation of new dynamics at the TeV scale seems slightly less appealing as a guiding principle (see Ref.
Next, we apply a detector response emulator to the simulation results by means of the Delphes 3 program  [54] , that internally relies on the anti-k T jet algorithm  [55]  as implemented in the FastJet software  [56]  for object reconstruction. For each of the recasted analyses, the Delphes configuration has been consistently tuned to match the setup depicted in the experimental documentation  [42]. Finally, we have used the MadAnalysis 5 framework  [57, 58]  to calculate the signal efficiencies for the different search strategies, and to derive 95% confidence level (CL) exclusions with the CLs method  [59]. As most of the LHC analyses under consideration rely on a proper description of the jet properties, we have merged event samples containing up to one extra jet compared to the Born process and accounted for the possible double-counting arising from radiation that could be described both at the level of the matrix element and at the level of the parton showering by means of the Mangano (MLM) scheme  [60, 61].
ACKNOWLEDGMENTS The authors are extremely grateful to  David Cohen , the administrator of the  ATLAS-Technion grid  project for his extensive support. His personal support, and assignment of resources have greatly facilitated in the progress of this work. We also thank  Monica d'Onofrio  and  Tomasso Lari  procedure mentioned in Section III. 1. The MadAnalysis 5 implementation of the analysis can be obtained from Inspire [68].