dataesr/scientific-paragraphs-categorization huggingface dataset:
cgl. ucsf. edu/chimera/). AMMOS2 minimization improved the binding energies for all used protein-ligand complexes. Chimera minimization improved the binding ener-gies for 14 out of the 21 protein-ligand complexes (Figure  S2  in Supplementary data). In all our tested proteins containing metal ions, the metal ions remained stable during the AMMOS2 minimization (see for illustration Figure  S3  in Supplementary data). We analyzed in more details the water displacement due to protein flexibility in cases 1 and 3 for the best-energy pose of the isoquinolinesulfonyl inhibitor H8 docked into cAMPdependent protein kinase. We found five water molecules placed close to the ligand and 12 water molecules within a radius of 6 Å of the bound ligand in the crystal structure of the complex (Protein Data Bank PDB ID 1YDS).
2. Protein-ligand interaction energies (in kcal/mol) before and after minimization with AMMOS2 for the best docking pose with a different number of water molecules in the binding pocket for trypsin (A), cAMP-dependent protein kinase (B) and neuraminidase (C). C0 notes the energy of the docked complex before minimization, C1 to C5 correspond to the five cases of protein flexibility. The PDB ID of the proteins are given. Table  1. Distances between the oxygen atom of water molecules W1-W5 and key ligand atoms and protein residues after AMMOS2 minimization compared to their X-ray positions in the PDB 1YDS complex Regarding the speed of performance, AMMOS2 typically requires <1 min for 1 ligand and full protein flexibility computation for a protein of typical length (350 residues). AM-MOS2 performed refinement of 1000 ligands in 25 min for case 1 and of 5000 ligands in 90 min for case 3 for a protein containing 356 amino acid residues.
AMMOS2 method AMMOS2 performs molecular mechanics of proteinligand complexes based on the program AMMP  (36). The web server parameters are optimized such as to handle a large number of ligands. AMMOS2 employs the program PREAMMP to convert the input protein and ligand files to AMMP format and performs AMMP autolink. AMMP uses a fast multipole algorithm for the efficient calculation of long-range forces thereby allowing evaluation of nonbonded terms without the use of a cutoff radius and increasing the speed, making calculations comparable to a standard treatment with an 8-10 Å radius cutoff  (36). The sp4 AMMP force field  (36)  is developed on the basis of the UFF (Universal Force Field) potential set  (41)  and the AMBER partial charges  (42). Our minimization procedure involves 2 × 500 iterations with conjugate gradient optimization.
Implementation AMMOS2 consists of several programs developed in C and Python, and makes use of the open source programs AMMP and PREAMMP. AMMOS routines written in C ensure the transformation of the input protein and ligands files to a specific ammp format, the rules for the five flexibility cases and at the end of the process they generate the protein in PDB format and the small molecules in mol2 format. The automatization of the procedure described in Figure  1  is accomplished via a Python script. The web server relies on a cluster provided by the RPBS (Ressource Parisienne en Bioinformatique Structurale) platform that has been running since 2009 with about 60 000 connections per year in average. RPBS ensures control program's execution on the server side (storage and resources quota, jobs tracking, etc.
The protein PDB files subjected for AMMMOS2 web server minimization were protonated with Chimera 1. 10. 2. The ligands docked with AutoDock4. 2 were subjected to energy minimization with AMMOS2 web server with their initial protonation. The pre-docked ligands for speed performance assessment were generated using virtual screening with the web server MTiOpenScreen for a protein receptor containing 356 amino acid residues (PDB ID: 1YDR). Screening of the diverse chemical compound collection Diverse-lib was performed in a binding site of dimensions 18 × 18 × 18 Å resulted in 2991 poses for 997 compounds. The top ranked 2000 poses were taken for AMMOS2 minimization.
The controller most often takes the form of a PC, or a workstation running database and control software. There are several different frequencies for RFID system, which can be used. Generally, there is the low-frequency band (from 125 KHz to 134 KHz), the high-frequency band (13. 56 MHz), the ultra-high frequency band (from 860 MHz to 960 MHz) and the microwaves frequency band (2. 45GHz or 5. 8GHz)  [6]. The microwaves frequency bands are popular than other RFID bands in many areas because of their high readable range, fast reading speed, large information storage capability and low cost. In 1968, the Russian physicist Victor G. Veselago has introduced an artificial material which has a negative permeability and permittivity values and this material is called metamaterial  [7]. Metamaterial structure consists of thin wire elements to generate negative permittivity and Split Ring Resonators (SRRs) to produce negative permeability.
2015). The considered timescales for an accurate description of these phenomena range from seconds for atmospheric extreme events to minutes or hours for GWs, days for PWs, seasons and up to tens of years for longterm mean trend studies. The observations cover areas extending over Europe and outlying regions, including polar and equatorial regions which have very different climate. The altitude range covers the troposphere, stratosphere, mesosphere, lower thermosphere and ionosphere. Data will be collected over the long term to monitor atmospheric extreme events and atmospheric parameters related to climate change. One of the main applications is the use of these data to improve the weather forecasting models up to timescales of weeks. ARISE also represents a relevant network for the remote observation of atmospheric extreme events including meteorological events and large-scale disturbances such as sudden stratospheric warmings.
The last part is dedicated to show the interest of ARISE data for future assimilation in weather forecasting and climate models. Perspectives for next project steps are presented in the last section. This paper mainly reviews the ARISE results obtained in the first step of the project (EU FP7 program). Following these results, ARISE work is continuing in the framework of the EU H2020 program. The objectives of the ARISE project are to provide 3D atmospheric observations in the different atmospheric layers to improve the modeling of the general global atmospheric circulation and develop related products and services. The ARISE objectives focus on the main following topics: • improving the representation of GWs and PWs in stratosphere resolving climate models to estimate the impact of stratospheric climate forcing on the troposphere and developing methods to parameterize GWs in the perspective of future assimilation in weather forecasting models, • determining the evolution of the atmospheric disturbances in relation to climate change by providing observations of climate-related phenomena over large time periods, in order to better understand the processes involved and to characterize their evolution in relation to climate change, • developing tools for future applications based on the quasi-real-time description of an atmospheric extreme event for civil applications.
ARISE Network The ARISE project integrates different atmospheric observation networks and satellite observations to recover the vertical structure of the unresolved atmospheric motions and disturbances with unprecedented spatial-temporal resolution and coverage. The ARISE station network (Fig. 2 ) includes complementary infrastructures listed in this article. The IMS infrasound network developed for the verification of the CTBT (http://www. ctbto. org) providing continuous infrasound measurements is unique by its global and homogeneous coverage as well as its data quality. It is larger and much more sensitive than Fig. 2  The ARISE observation network any previously operated infrasound network. Once complete, the network will include 60 stations uniformly distributed across the globe. Today, more than 80% of this network is operational.
Monochromatic laser pulses are sent vertically into the atmosphere, and a temporal analysis of the backscattered light provides information about the vertical structure and composition of the atmosphere. Rayleigh lidars are well adapted to the study of PWs, GWs and tides in the upper stratosphere and mesosphere as well as their interaction to induce mesospheric inversions. The Haute-Provence lidar database is the longest temperature series and allowed one of the first detections of the cooling of the upper stratosphere and mesosphere  (Ramaswamy et al. 2001). Now it is a key instrument to ensure inter-satellite adjustment like AMSU series  (Keckhut et al. 2011). A Rayleigh-Doppler wind lidar was developed by  Chanin et al. (1989)  to measure the horizontal wind in the stratosphere and in the upper troposphere.
Furthermore, other technologies associated with ARISE or identified to be of relevance to the project include new lidar systems (ALOMAR), MST radars (MAARSY) and meteor radars (SKiYMET) as new observation techniques highlighting a novel possibility to observe high-altitude dynamics. Ionospheric Doppler sounding observations are used for studying the coupling between the atmosphere and the ionosphere. EISCAT (European Incoherent Scatter Scientific Association) radar measurements complement ionospheric observations. ARISE also includes multi-technology sites at Haute-Provence, France, Andøya Space Center, Norway, and La Reunion Island, France, which are relevant ARISE reference stations. The first ARISE multi-technology site at the Observatoire de Haute-Provence (OHP, 43. 93°N, 5. 71°E, France) where a NDACC lidar is in operation provided high-quality data during the first 1-year observation campaign.
As for the temperature, larger differences are noted during the winter months. On longer timescales (October 2012-July 2013), the standard deviation of the mean difference in temperature exceeds 5 K between 40 and 60 km altitude. Significant differences in the zonal wind are also observed (Fig. 4 , bottom). The largest deviations appear in winter when the variability from large-scale PWs dominates over the general circulation and SSW occurs (Le  Pichon et al. 2015). The current ARISE data set can be used as a benchmark to assess future upgrades in assimilation systems and as a comparator for model forecasts. As the ARISE network data coverage increases spatially and the number and diversity of remote sounding techniques increases, additional and more large-scale comparison will be possible.
The periodogram, obtained using 14 years of data recorded at the IS26 station, displays the PW activity at periods of several days. There is no apparent trend in the PW activity. The data series could be too small or trend effects too weak or masked by other processes for such observation. However, strong differences appear from one year to another in the PW structure. Another way to characterize PWs is to analyze their effect on microbaroms measured in the infrasound stations. The ocean swell which forms a quasi-permanent infrasound noise   (1991) (1992) (1993) (1994) (1995) (1996) (1997) (1998) (1999) (2000) (2001) (2002) (2003) (2004) (2005). Each line corresponds to one ensemble member. (From Le  Pichon et al. 2015)  observed everywhere in the world is the driving force materializing their activity; infrasound waves generated at the ocean interface are propagating over thousands of kilometers in the atmospheric wave guide between ground, stratosphere and thermosphere.
Their amplitude is modulated by the PWs with a maximum of activity in winter  (Blanc et al. 2010). Figure  7  (bottom) shows several years of PWs observed in this way. Activity is larger in winter, and shows fluctuations in amplitude and azimuth in the range 70°-120°at timescales of weeks. The structure of these fluctuations is also variable from one year to another. These infrasound data can be interesting for the long-term characterization of tides, for the study of satellite long time series. Tides induce bias in satellite observations such as advanced microwave sounding unit (AMSU) series  (Keckhut et al. 2015). Ground-based instruments are needed to calibrate successive satellite instruments when overlap periods are missing  (Keckhut et al. 2011).
g. ,  Le Pichon et al. 2012). Coupled with realistic station noise and analysis products from ECMWF, simulations predict the minimum detectable amplitude at a reference distance of 1 km away from the source  (Tailpied et al. 2013). The detection capability methodology was calibrated using different events including the 2013 Chelyabinsk meteorite which generated a large airburst with an equivalent yield of 500 kT of TNT equivalent, detected at global scale. Figure  8  displays the global detection capability map and the infrasound signals recorded at several stations. It is the most energetic event recorded by the infrasound component of the CTBT-IMS network, globally detected by 20 out of 42 operational stations (Le  Pichon et al. 2013; Pilger et al. 2015). Meteor entries will be included in the ARISE database as these observations provide new benchmark for future studies on exploding fireballs and help advance the development of monitoring procedures to identify potentially dangerous exploding near-Earth objects.
2011). Therefore, polar lows represent a hazard for all maritime and coastal activities (fishing, oil drilling, etc. ) and population. Examples of infrasound measurements in Norway and Svalbard from turbulent convection produced by a polar low outbreak have already been reported in the Norwegian/ Barents Sea  (Orbaek and Naustvik 1995). Systematic long-range infrasound measurements of polar low-in high-latitude regions are taken in the framework of ARISE. These analyses will use the recently installed IMS infrasound station IS37 and other infrasound arrays in Scandinavia which are ideally located to characterize the source mechanism involved in the generation of the signals. Compared with satellite observations (infrared imagery, microwave observations, etc. ), the added value of infrasound data for polar low monitoring and short-term forecasting is investigated.
2013) , represent a significant tool for a future global volcano monitoring. Figure  13  presents an example of eruption chronology that can be inferred from remote infrasound observations (640 km) from the Sarychev Peak (Kuril Islands). A good   (Matoza et al. 2011a)  correlation between the explosion origin times inferred by infrasound data and those inferred by satellite data is found. Moreover, it appears that infrasound data can construct the eruption chronology with greater temporal resolution than is possible with satellite data alone. Satellite imagery technique provides relevant information on ash plume dispersion triggered by strong eruptions. However, cloud cover can hide eruption plumes and therefore strongly limit the capability of this technique. The cloud coverage over one active volcanic zone in Southeast Asia often exceeds 0.
Comparison Between Lidar and Satellite Observations Rayleigh lidar data provide accurate and altitude-resolved GW energy profiles but are only available at about 10 locations in the world. A global view of the GW field can only be determined using satellite data. The GPS radio occultation (RO) temperature profiling technique, featuring high vertical resolution and global coverage, represents a powerful means for studying the sources and climatology of GWs. Operational since April 2006, the COSMIC GPS RO system provides 1500-2000 occultations per day with sampling density maximizing at mid-latitudes. The GPS RO temperature observations cover the altitude range between about 8 and 35 km, with the highest accuracy (\ 0. 5 K) in the lower stratosphere and a vertical resolution of 0. 2-1. 4 km.
The mesospheric winds measured during the SSW are different from the Whole Atmosphere Community Climate Model (WACCM) (bottom left panel) showing the limitation of models in describing the wind in the mesosphere where no nudging is applied. The meteor radar data show a divergence in the momentum flux at 90 km altitude 6 days prior to the SSW onset of January 7, 2013 (as determined from the timing of the stratospheric zonal wind reversal). During this time, a maximum eastward forcing of * ? 145 ± 60 ms -1 d -1 was measured. As the SSW evolves, GW forcing turns westward, reaching a minimum of * -240 ± 70 m s -1 d -1 * 18 days after the SSW onset  (de Wit et al. 2014 (de Wit et al. , 2015)). GW precursor activity was also observed by lidar and satellite, up to one week in advance in the temperature and wind fields of the upper stratosphere, as shown in Fig.
Characterization of Tropospheric and Stratospheric Gravity Wave Variability An important driver of the stratospheric variability is severe weather. When GWs produced by convection from thunderstorms propagate vertically into the stratosphere, their cumulative effects may disturb the general atmospheric circulation. Valuable information for climate studies has been derived from the analysis of archived GW data recorded in tropical infrasound stations where activity is very intense. Lidar network provides GWinduced fluctuations in the wind profiles which are needed to fully retrieve the structure of these disturbances in the stratosphere and mesosphere. Mountain waves can also be characterized. Global satellite observations of the MA GW momentum fluxes clearly reveal that the activity induced by convection systems is not homogeneously distributed throughout the atmosphere as currently assumed by most GW parameterizations in climate models.
In particular, the eruption chronology can be inferred from remote infrasound observations (hundreds of km from the source) with greater temporal resolution and larger observation periods than is possible with satellite data alone. ARISE provides the eruption notifications including confidence index representative on propagation conditions and additional analysis results. In a further stage, infrasound signal parameters characterizing the intensity of the eruptions (Volcanic Explosivity Index) and the amount of ash injected into the atmosphere, as well as ash height, will be explored. Such studies interest several VAACs (including VAAC Toulouse) and the IAVWOPSG. In parallel, volcanoes are repetitive infrasound sources which can be used for remote sensing of the atmosphere when the source parameters are well determined.
The infrasound data recorded during over more than ten years at some stations also present a potential to monitor long-term mean trends of weather events. The long-term evolution of convection in Africa presents a large environmental interest as it is related to precipitation as rain. ARISE integrates operational infrastructures dedicated to long-term atmospheric monitoring (IMS infrasound network for CTBT verification, NDACC lidar network), complemented by observatories (OHP, OPAR, ASC, Esrange), national infrastructures (i. e. , forming the European infrasound network), and such observations are ongoing. The provided long-duration database will be used for weather, climate and extreme event studies.
Acknowledgements This work was mainly performed during the course of the ARISE design study (http:// arise-project. eu)funded by the  European Union 's 7th  Framework Programme for Research and Technological Development  under Grant Agreement No. 284387. ARISE is now funded by the  European Union 's  Horizon 2020 Research and Innovation Programme  under Grant Agreement No. 653980. We thank the  ARISE advisory board  ( Guy Brasseur ,  Adrian Simmons ,  Geir Braathen ,  Philippe Husson ) for relevant recommendations and the  CTBTO  for its support in the infrasound topic. We also thank the ARISE2 partners for their support to ARISE and strong motivation. Open Access This article is distributed under the terms of the Creative Commons Attribution 4. 0 International License (http://creativecommons.
Note that we cannot just let p ^ be the function computed by /eth program: it may happen that the fcth program does not define any lower semicomputable semimea sure. (It may compute a function which is not total or a function that sometimes decreases in the second argument or a function whose sum is greater than  1. )  The bug can be fixed using the following: L e m m a. Every program P computing a function of two natural arguments and taking rational values (and possibly the value -oo) can be algorithmically trans formed into a program P' having the following properties. The program P' defines a lower semicomputable semimeasure. If the program P itself defines a lower semi computable semimeasure, then P' defines the same semimeasure.
Acknowledgments In the beginning of the 1980s Kolmogorov (with the assistance of  A. Semenov ) initiated a seminar at the  Mathematics and Mechanics Department of Moscow State (Lomonosov) University called  "Description and computation complexity"; now the seminar (still active) is known as the "Kolmogorov seminar". The authors are deeply grateful to their colleagues working in this seminar, including  A. Zvonkin ,.
Marina Feigelman  who made a drawing for its cover,  Olga Lehtonen  who performed the cover design, and  Victor Shuvalov  who helped a lot with typesetting. The authors were supported by the  International Science Foundation (Soros foundation) ,  STINT (Sweden) ,  Russian Fund for Basic Research  ( 01-01-00493a ,  01-01-01028- a,  06-01-00122- a,  09-01-00709- a,  12-01-00864- a),  CNRS , and  ANR (France ,  ANR-08-EMER-008 NAFIT  and  ANR-15-CE40-0016-01 RaCAF  grants). The book was made possible by the generous support of our colleagues, in cluding  Bruno Bauwens ,.
FLUOLE-2 program FLUOLE-2  [4]  is a benchmark-type experiment dedicated to neutron attenuation analysis with the aim of improving the TRIPOLI-4 ®  [1]  Monte Carlo code validation. This two-year program has been developed by CEA (Commissariat à l'Energie Atomique et aux Energies Alternatives), with the financial support of EDF, to be representative of 900 and 1450 MWe Pressurized Water Reactors. In this perspective, different stainless steel structures have been designed and appropriately positioned inside the EOLE facility  [5]. In FLUOLE-2 program, a set of dosimeters were irradiated and the activity was measured. Calculated activity of each dosimeter was obtained with a specific calculation scheme based on TRIPOLI-4 ® Monte Carlo code, and DARWIN/PEPIN2 depletion code.
Applications: general For the numerical application, 8 dosimeters have been selected from the FLUOLE-2 analysis result database. These dosimeters were irradiated in the same position from the core  [4]. The analysis of 8 dosimeters shows relatively good agreement between calculated and measured activity values, as presented in Table  1. Average C/M values for all dosimeters grouped by type are similar to those results. Numerical applications have the objective to show that it is possible to enhance the target value using sometimes unsatisfying results, and running ESTIMA program with calculated and measured results. This improvement consists of a significant reduction of the variance associated to the target value. The ||CVniv3|| matrix is filled as described in chapter 3: experimental uncertainties are given by measurement laboratory, and calculation uncertainties are derived through feedback on PWR uncertainty analysis.