dataesr/scientific-paragraphs-categorization huggingface dataset:
In the asymmetric structures refined from MetaD simulations, only a single binding site in the cytoplasmic region remains competent to coordinate Mg 2+ , whereas in the NMA-generated structure, four binding sites remain within distance to bind Mg 2+. In the transmembrane region, the pore dimensions obtained by the HOLE program  (Smart et al. , 1996)  indicate that for all the NMA-and MetaD-generated structures, the pores contain narrow constrictions with diameters significantly smaller than the 2. 4 Å radius of hydrated Mg 2+  (Maguire and Cowan, 2002, Figure 4-figure supplement 4). This suggests that all the refined asymmetric structures are in fact non-conducting. Taken together, the general picture of our simulations does not provide a mechanistic link between symmetry break and channelopening.
05 ml/min during elution of the main peak. Measurements were run twice to obtain data from two sample-to-detector distances, 2 m and 11 m, yielding data in a q-range of 0. 0044 Å -1 to 0. 42 Å -1 with the neutron wavelength of 6 Å. The scattering intensity, I(q), was brought to absolute scale in units of cm -1 by normalizing to the direct beam intensity measured with an attenuator in place. All SANS data and metafiles are from ILL-DATA. 8-03-940 as in https://doi. ill. fr/105291/ ILL-DATA8-03-940. Pair distance, p(r), distributions were calculated by Bayesian indirect Fourier transformation at the bayesapp server  (Hansen, 2014)  (available from the genapp server at https://somo. chem. utk. edu/ bayesapp/). p(r)s and the corresponding I(q)s for PDB structures were calculated using CaPP (available at github.
The system was solvated with the MARTINI non-polarizable water and neutralized with 300mM NaCl comparable to the SANS experimental set-up. The equilibration was performed according to the CHARMM-GUI equilibration protocol using a minimization step followed by six equilibration steps with slow decrease in the positional restraint forces on both lipids and protein in each step  (Qi et al. , 2015). The GROMACS-5. 1. 4 software package (GROMACS, RRID:SCR_014565)  (Abraham et al. , 2015)  was used to simulate with a 20 fs time step. Temperature and semi-isotropic pressure were controlled at 303. 15K and 1bar using the stochastic velocity rescaling thermostat  (Bussi et al. , 2007)  and Parrinello-Rahman barostat  (Parrinello and Rahman, 1981). Electrostatic interactions were treated using the reaction field approach.
The cutoff of short-range distance for the electrostatic interactions was 1. 1nm. The potential shift Verlet scheme was used to cut off the Lennard-Jones potential at long ranges. Well-Tempered Metadynamics  (Barducci et al. , 2008)  simulations were performed with the PLUMED2. 3. 0 software (PLUMED 2, RRID:SCR_021952)  (Tribello et al. , 2014). A radius of gyration collective variable was applied on all backbone beads for the intracellular residues 170-190 and 220-250 of all five chains. The metadynamics parameters were set as follows: Gaussian width = 0. 05, Gaussian height = 2. 1, Gaussian deposition stride = 100, biasfactor = 15and an upper wall defined at a CV radius of gyration of 4. 0nm. The wall was defined as a harmonic restraint with a force constant = 10000, harmonic exponential power = 4, off-set = 0, and a rescaling factor of 1.
Multiple wall types and sizes were attempted, with lower walls causing too little dynamics for fitting with the experimental SANS data and higher walls causing individual monomers to bend unphysically and giving an unfeasible large sample space. Clustering of the simulation trajectory was performed using the KMeans clustering method  (Tiberti et al. , 2015). The software program BME (BME, RRID: SCR_021953) was used to reweight the MetaD trajectory to fit the experimental SANS data  (Bottaro et al. , 2020). The hyperparameter θ was determined based on a L-curve analysis (analogous to the procedure in normal mode analysis, see Figure  4 figure supplement 2) of S rel vs χ 2 , where θ is chosen where a natural kink is observed and any further decrease in χ 2 gives rise to an increasing larger penalty in S rel.
Spectral analysis and assignment were accomplished with CcpNmr Analysis (CCPN Analysis, RRID:SCR_016984)  (Vranken et al. , 2005)  and FLYA  (Schmidt and Güntert, 2012)  available from the CYANA program package (CYANA, RRID:SCR_014229). Relaxation experiments were based on a 1 H, 15 N 1 H-detected CP-HSQC experiment incorporating an appropriate relaxation delay  (Knight et al. , 2012). 38 and 33 residues spanning different regions of the proteins were used for the uniformly labelled sample in the presence and in the absence of Mg 2+ , respectively. The measurements of site-specific 15 N R 1ρ rates were performed at 107 kHz MAS, 19. 5T and 300 K or 280 K, using relaxation delays of 0. 05,  1, 5, 15, 50, 100, 200  ms under a spin-lock field of 15 kHz. Measurements of bulk 15 N R 1 were performed at 107 kHz MAS, 19.
Negative stain EM CorA was purified by SEC and diluted to 0. 1 μM in appropriate buffers containing 1 mM EDTA or 40 mM Mg 2+. Copper grids were neutralized with an Easiglow glow discharger (Agar Scientific). 3 μl of sample was applied to the grid and incubated for 30 s. The grid was blotted onto a filter paper from the edge, and 3 μL of 2% uranyal formate was added immediately and incubated for 30 s. The staining procedure was repeated two more times. After the final staining, the grid was left to dry for ten minutes. EM data were acquired on a Tecnai TEM (FEI, Thermo Fischer scientific) at Aarhus University, Denmark. The micrographs were processed by XMIPP to *. mcp files, and particle picking, 2D class averages and 3D model refinement was done in Relion 3. 0. Statistics for the 3D refinement are given in Table  1.
Data availability SANS data have been deposited in SASBDB under IDs SASDM42, SASDM52, SASDM62, SASDM72. EM data have been uploaded to the Electron Microscopy Data Bank under IDs EMD-13326 and EMD-13327. Activity (fluorescence) data have been uploaded to GitHub at https://github. com/Niels-Bohr-Institute-XNS-StructBiophys/CorAData (copy archived at swh:1:rev:94c6ed6e-fa9166781a36307eb7c6d05e125ffa2d). The Metadynamics simulations have been uploaded to GitHub at https://github. com/KULL-Centre/papers/tree/main/2021/CorA-Johansen-et-al (swh:1:rev:511f01bdf1c2b57d68654deee7f15ce019f65d7a). NMR data have been deposited in Biological Magnetic Resonance Data Bank under ID 50959. The following datasets were generated:.
Modeling of error estimates in the GRASP algorithm As mentioned in the introduction, in this work we make use of the GRASP (Generalized Retrieval of Atmosphere and Surface Properties) algorithm. It is a rigorous, versatile and open-source algorithm capable of providing information of the aerosol properties from measurements of different instruments and dynamic error estimates  (Dubovik et al. , 2011 (Dubovik et al. , , 2014 (Dubovik et al. , , 2021)). It is a flexible, generalized algorithm that relies on two independent modules: the forward model and the numerical inversion. The forward contains the full description of the physical model including various interactions of electromagnetic solar radiations, such as aerosol scattering, surface reflectance and gaseous absorption. The multiple scattering interactions in the atmosphere are accounted by solving the vector of radiative transfer equation.
5 degrees to ±180 degrees (Table  1 ). The detailed aerosol properties in the total atmospheric column provided by AERONET inversion of Sun/sky-scanning radiometers has been widely recognized as rather unique reliable data. For example, AERONET retrievals provided first reliable data about aerosol spectral absorption and other detailed aerosol optical characteristics (e. g. , see  Dubovik et al. , 2002b; Giles et al. , 2012, etc. ). These detailed data are of vital importance for evaluating the impact of aerosol on such important aspects as a climate change and diverse pollution effects, and can be reliable estimated nearly uniquely from remote sensing observations  (Kaufman et al. , 2002). Therefore, this retrieved aerosol information has been proven to be very useful for assessment of climate change dynamics in IPCC reports  (Boucher et al.
Considering these aspects, in present study, as a first step, make more detailed and extensive analysis of error variances and then, as a second step, we illustrate the usefulness of obtained non-diagonal elements. The performance of GRASP error variances estimated provided by Eqs. (25-27) is studied using a series of numerical tests. Figure  1  illustrates the general scheme of these test organization. First, as showed in Fig. 1 , the parameters a assumed for assumed detailed aerosol properties (dV (r i )/d ln r i , n(λ i ), k(λ i ), C sph and C V (h) in the case of lidar) are used to obtain the synthetic observations using the GRASP forward model. These synthetic observations include the spectral AOD, sky radiances and range corrected signals (RCS) of lidar. These data are used then in the inversion tests where the aerosol parameters and their errors are estimated from these synthetic observations using GRASP algorithm.
01 and maximum bias of ±0. 02, and ii) in radiances nominal bias of ±3% and maximum bias of ±5%. To evaluate the effects of biases, the above values were added to synthetic direct measurements of AOD and sky-radiance by AERONET like ground-based radiometer. These data were inverted by GRASP code and the retrieved values of aerosol parameters were compared to the values assumed in synthetic simulation as a 'truth'. In addition, the deviations of retrieved.
Acknowledgements. The authors acknowledge the support from the  H2020 Marie Skłodowska-Curie RISE Actions  (grant no. 778349 ) and the authors acknowledge the support from the  European Metrology Program for Innovation and Research (EMPIR)  within the joint research project  EMPIR 19ENV04 MAPP 'Metrology for aerosol optical properties '. The EMPIR is jointly funded by the  EMPIR participating countries within EURAMET  and the  European Union. T. Lapyonok  was supported from the  Chemical and Physical Properties  of the  Atmosphere  Project funded by the  French National Research Agency  through the  Programme d'Investissement d'Avenir  under contract  ANR-11-LABX-0 0 05-01 , the  Regional Council 'Hauts-de-France ', and the 'European  Funds for Regional Economic Development', from Research grant  (no.
2 to 7. 5 dB. In addition, the approximate path length through the device is 6 to 7 cm and therefore the propagation losses accumulate and add a further 1 to 3 dB which accounts for the remainder of the loss measured. The spectral ripple on the various flat states (green and red) have an amplitude of 2 to 3 dB, which is consistent with what we would expect from the back-to-back AWG. The approximate difference between the maximum and minimum throughput states is 38 dB. The short and long wavelength ends of the minimum throughput spectrum (purple) were impacted by the noise floor of the OSA (brown trace). The stability of the full BAPSS device was tested. The BAPSS was set for maximum throughput while maintaining a high degree of flatness (green trace), and the OSA set to record data every 5 minutes for nearly 12 hrs.
Note, that the TEC was not used to stabilize the PIC in these experiments, but the lab is stabilized by an air conditioning system to within ±0. 5 • C. After the experiment was setup, we departed the lab and waited 15 minutes before starting to acquire data to allow the setup to reach thermal equilibrium. The results are shown in the bottom panel of Fig. 9. The data are shown for the region of the spectrum where there was good signal-to-noise on the OSA (1450 to 1625 nm), to not conflate instabilities brought about by the OSA with the BAPSS. It can be seen that traces generated over the ∼ 12 hr period are highly overlapping with a scatter of <±0. 1 dB, demonstrating an extraordinary level of stability. The next set of tests involved the LFC. Figure  10  shows the results. The top left panel shows the LFC spectrum through the reference waveguide (blue) as well as the BAPSS device (orange, green, red and purple).
Data were also acquired with OSA resolutions of 0. 05 nm where the comb lines were separated, as shown in the middle panels of Fig. 10. The panel on the left looks similar to the low resolution scan in the top left panel, except that the traces are no longer lines, but rather shaded regions. This is because in the high resolution mode the modulation in the spectrum due to individual comb lines can be seen. The panel on the right shows the same spectrum but zoomed into only a 2 nm segment around 1600 nm. The lines are clearly separable in this plot. The results at high resolution were deemed to be consistent with the lower resolution data presented here. Finally, we tested the power handling capabilities of the device. To ensure we did not damage the device, we connected the LFC to the reference waveguide and took a spectrum.
Acknowledgments. This work was produced with support from the  Keck Institute for Space Studies. N. Cvetojevic  acknowledges the funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement CoG -683029). P. Gatkine is supported by  NASA  through the  NASA Hubble Fellowship  grant  HST-HF2-51478. 001-A  awarded by the  Space Telescope Science Institute , which is operated by the  Association of Universities for Research in Astronomy, Inc. , for  NASA , under contract  NAS5-26555. Gatkine also acknowledges the support from  David and Ellen Lee Postdoctoral Fellowship  at the  California Institute of Technology. Some of this research was carried out at the  Jet Propulsion Laboratory, California Institute of Technology , under a contract with the  National Aeronautics and Space Administration  ( 80NM0018D0004 ).
In their software Landscape Generator (LG),  van Strien et al. (2016)  addressed this limit of neutral landscape models, making it possible to generate artificial landscapes using the same parameters used to evaluate real landscapes. In LG, the user defines target values to control class-level landscape indices such as the number of patches, the total habitat amount and patch-level indices such as patch area, or patch maximum perimeter. In addition,  van Strien et al. (2016)  presented some potential improvements to increase the control over generated landscapes. Notably, they suggested integrating more landscape indices as user targets, such as the largest patch index. Moreover, they recognized that the computation time of LG needs to be improved. Indeed, LG relies on a multi-objective optimization algorithm which can take several hours to generate 50 × 50 pixels landscapes and increases exponentially with increasing landscape size, making it unsuited to generate large landscapes and large series of landscapes.
Although targets focus on composition and fragmentation, the spatial configuration of landscapes can be controlled with continuous environmental gradients. The main technical novelty of flsgen is the decomposition of landscape generation into two distinct processes: the identification of suitable landscape structures by solving a constraint satisfaction problem with a constraint programming (CP) solver, and the spatial landscape generation with a stochastic algorithm. This approach allows flsgen to generate landscapes with millions of cells, hundreds of patches and several land-use classes within seconds, which makes it suited for large-scale experiments and analysis. Flsgen is available as free and open-source software through a Java API, a commandline interface and an R package. structures; consequently, it is up to the user to specify how many solutions are desired.
| Distribution The software flsgen is distributed as open-source software under the GNU GPL3 licence. Source code and downloads are available on GitHub. The software can be used as a Java API, an R package or through a command-line interface (CLI). (1) NP i ≤ NP i ≤ NP i foralli ∈ 1, N ; (2) AREA i j ≤ AREA i j ≤ AREA i j foralli ∈ 1, N and forallj ∈ 1, NP i ; (3) CA i ≤ ∑ j ∈ [1,NPi] AREA i j ≤ CA i foralli ∈ 1, N ; (4) NPRO i ≤ ∑ j ∈ [1,NPi] AREA i j 2 ≤ NPRO i foralli ∈ 1, N ; (5) ∑ i ∈ [1,N] CA i ≤ L S. Java API (https://github. com/dimit ri-juste au/flsgen): The three components of fslgen were developed in Java. The Java API of flsgen is then its native API and offers a great flexibility. Notably, using flsgen from Java offers a full access to the Choco solver library, which makes it appropriate for advanced uses.
| Generating landscape series with fixed structure and varying spatial configurations Neutral landscapes series are useful to assess the impact of landscape spatial configuration on ecological processes or to evaluate spatially explicit models (e. g. fire spread simulation) with controlled datasets. However, for systematic analysis, it is necessary to ensure that landscape composition remains fixed while the spatial configuration is variable. In this use case, we illustrate how flsgen can be used to savanna and forest. Then we generated a landscape structure satisfying these targets with flsgen structure. Maintaining this structure fixed, we generated a landscape series with a varying landscape configuration through the terrain dependency parameter (see Section 2. 2) which varied from 0 to 1 with a step of 0.
01, resulting in 101 landscapes. A continuous environmental gradient was generated on-the-fly by flsgen with the diamond-square algorithm and a roughness parameter of 0. 2. A subset of the generated landscape is depicted in Figure  2. Finally, we evaluated the variation of spatial configuration in the landscape series through the edge density and disjunct core area density indices at the landscape level, using the landscapemetrics R package  (Hesselbarth et al. , 2019)  (see Figures  2  and 3 ).
In this special case, PC equals MESH divided by the landscape area. F I G U R E 4 (use case 3. 2) Subset of the 2,370 generated 500 × 500 landscapes with controlled effective MESH size (MESH) F I G U R E 5 (use case 3. 2) Relation between the probability of connectivity (PC) index and the effective MESH size (MESH) evaluated from 2,370 neutral landscapes of 500 × 500 pixels at 30 × 30 m resolution (22,500 ha) In this last use case, we illustrate how flsgen can be used to extract landscape structures from large real landscapes to recreate landscape composition patterns, with a focus on the forest cover of the main island of New Caledonia, which is a tropical archipelago in the South Pacific. First, we extracted 105 × 105 m New Caledonian forest cover data from the Copernicus Global Land Service database (Buchhorn et al.
Furthermore, the main difference between our approach and LG is that we focused on satisfying composition and fragmentation targets while controlling F I G U R E 6 (use case 3. 3) Open and closed forest cover in the main island of New Caledonia, at 105 × 105 m resolution. Data from the Copernicus global land service database F I G U R E 7 (use case 3. 3) Neutral landscape generated with flsgen recreating the landscape composition pattern of open and closed forest cover in the main island of New Caledonia (see Figure6). The new Caledonian digital elevation model was used as the continuous environmental gradient in flsgen, with a terrain dependency set to 0. 9. The 8-connectivity rule was used to extract the original landscape structure and to generate the neutral landscape Use cases computation time (landscape generation).
DATA AVA I L A B I L I T Y S TAT E M E N T The software package and its source code is available on Zenodo at https://doi. org/10. 5281/zenodo. 6386429 (Justeau-Allaire et al. , 2022a) and https://doi. org/10. 5281/zenodo. 6386420 (Justeau-Allaire et al. , 2022b). It is also available on GitHub at https:// github. com/dimit ri-juste au/flsgen and https://github. com/dimit ri-.
The calculation code A code developed by Sabetta and Pugliese in 1996 was used to generate the synthetic signals. It is based on the stochastic method; its principle is to build the spectrogram of the simulated signals by analogy with the spectrograms of a natural database. An existing code was adapted in order to generate synthetic motions, which are considered as signal inputs for structural seismic analysis. Further details about the operational procedure for this synthetic generation can be found in the technical note DEI/SARG/2005-035  (Rey and Berge, 2005). a-Northridge-01 earthquake record b-Cumulative absolute velocity of the Northridge-01 earthquake record Fig. 1  Example of the cumulative absolute velocity of the Northridge-01 earthquake record  (Anastasios and Elias, 2018). Vol.
Matlab procedure In this article, we present an overview of the Matlab procedure followed  (Matlab, 2019). The difficulty in understanding this procedure is related to the fact that the numerical data are extremely numerous and that some classification logic must therefore be kept in mind (Fig. 2 ). The program gathers all the procedures and permits, with seven magnitudes for three classes of soils and an epicentral distance, which varies from 0 to 100 Km with a step of 05 Km, to obtain a database of artificial earthquakes of 693 accelerograms.
Data assumed for the structures studied The six RCF buildings studied have the same plan views. The total dead and live loads on the floor slabs are assumed to be 5. 1 and 2. 5 kN/m 2 , respectively; for the roof slab, they are assumed to be 5. 8 and 1. 0 kN/m 2. The frames were designed according to reinforced concrete code BAEL 91  (BAEL, 1992)  and the Algerian seismic code RPA99/version2003 (RPA99, 2003), with the following parameters: zone of high seismicity: zone III, importance class group 2, soil type S3 (soft soil), quality factor Q=1, and viscous damping ration ξ=7 %. The analysis will be performed for the zone acceleration factor A=0. 25. A seismic behavior factor of R=5 was taken into consideration for RCF without any masonry infill.
CONCLUSION This study has proposed a theoretical relationship between the CAV and the structural performance point (S d ). The case studies represent the existing structural typology in Algeria (reinforced concrete frame structures). This typology of structure is taken into consideration in the present work through its ductility, which is defined by the ratio between the ultimate and elastic displacement. In order to study this typical and dominant typology in Algeria, six classes of ductility were tested numerically, and the capacity curve that reflects their behaviors was established. In order to find a correlation between the seismic demand and the performance point, the collection of a natural earthquake database is not easy, particularly in the case of Algeria. An artificial earthquake database was created to remedy this lack based on existing mathematical models of seismic attenuation.
Electromechanical Actuators An electromechanical actuator (EMA) includes components from multiple disciplines. There are mechanical parts (rod ends, bearings and rotary/linear conversion mechanisms, and a clutch), electrical parts (a motor, brake, and clutch), and electronic parts for power and control. The paper  [3]  presents an example of an EMA in detail and the different possible EMA architectures. Except for low-power and/or less safety-critical applications (flaps, slats, spoilers, and a trim horizontal stabilizer), the EMA technology is not mature enough yet for primary flight controls  [6]. This is essentially because of their lack of accumulated return of experience. The statistical database on components fault modes is poor  [8]. EMAs entail some concerns in terms of reliability, risk of failures due to the jamming in the mechanical transmission components, health monitoring (HM) and assessment, and thermal management.