dataesr/scientific-paragraphs-categorization huggingface dataset:
All samples were also systematically assessed for cellular ectopia (misplaced neurons). Neuroanatomical data (Supplementary Table  16 ) were analyzed using a Student two-tailed equal variance test. Further details of methods are given in the Supplementary Note. Genome Reference Consortium (GRCm38) and GENCODE annotation updates informed by the strain assemblies. Updates indicate known GRC issues solved based on C57BL/6NJ de novo assembly. GENCODE update is based on comparative Augustus predictions with 75% novel introns and includes annotation and predictions which occur on chromosomes 1-12.
Acknowledgements This work was supported by the  Medical Research Council  [ MR/L007428/1 ],  BBSRC  [ BB/M000281/1 ] and the  Wellcome Trust. DJA is supported by  Cancer Research-UK  and the  Wellcome Trust. MKS is supported by a research grant from  FONDECYT  No. 1171004  and the  European Commission  ( EUFP7 BLUEPRINT grant HEALTH-F5-2011-282510 ). DTO work was supported by  Cancer Research UK  ( 20412 ), the  Wellcome Trust  ( 202878/A/16/Z ), the  European Research Council  ( 615584 ). PF was supported by the  Wellcome Trust  (grant numbers  WT108749/Z/15/Z ,  WT098051 ,  WT202878/B/16/Z ), the  National Human Genome Research Institute  ( U41HG007234 ) and the  European Molecular Biology Laboratory. The research leading to these results has received funding from the  European Union 's  Seventh Framework Programme  ( FP7/2007-2013)  under grant agreement  HEALTH-F4-2010-241504  (EURATRANS).
Data availability Statement The genome sequencing reads are available from the European Nucleotide Archive and the assemblies are part of NCBI BioProject PRJNA310854 (Supplementary Table  22 ). The genome assemblies and annotation are available via the Ensembl genome browser, and the UCSC genome browser. Sequence accessions for the three immune related loci on Chr11 are available from the European Nucleotide Archive (Supplementary Table  23 ).
Several public domain micromagnetic simulation packages such as OOMMF, MuMax3 and Fidimag already offer implementations of different DMI terms. It is therefore highly desirable to propose a so-called micromagnetic standard problem that would allow one to benchmark and test the different software packages in a similar way as is done for ferromagnetic materials without DMI. Here, we provide a sequence of well-defined and increasingly complex computational problems for magnetic materials with DMI. Our test problems include 1D, 2D and 3D domains, spin wave dynamics in the presence of DMI, and validation of the analytical and numerical solutions including uniform magnetisation, edge tilting, spin waves and skyrmion formation. This set of problems can be used by developers and users of new micromagnetic simulation codes for testing and validation and hence establishing scientific credibility.
[11, 12, 21, 22]  The former two are named according to the domain wall-like rotation sense of the spins. The fixed chirality of spins imposed by the DMI causes skyrmions to have different properties from structures such as magnetic bubbles  [23] [24] [25]  or vortices  [26] [27] [28]. In addition, the antisymmetric nature of the DMI has an influence on the dynamics of excitations such as spin waves, making them dependent on their propagation direction in the material. In this paper, we define a set of micromagnetic standard problems for systems with different DMI mechanisms. This set of problems is aimed at verifying the implementation of the DMI by comparing the numerical solutions from different software with semi-analytical results from published studies  [29, 30]  where possible. In this context, we test these problems using three opensource micromagnetic codes, OOMMF,  [31]  MuMax3  [32]  and Fidimag.
29 , which is valid when the system has a large anisotropy and reads sin Θ = ± ∆ ξ. ( 12 ) Depending on the chirality of the system, which can be observed from the simulations, we fix the condition Θ(0) = arcsin(∓∆/ξ) and vary dΘ(0)/dx until finding a solution that satisfies Θ(L) = arcsin(±∆/ξ). The upper sign + refers to the interfacial case and the bottom signto the bulk DMI case. In Fig. 1a  and b  we compare results from the theory and simulations of the one dimensional problem, for systems with interfacial (C nv ) and bulk (T ) DMI, respectively. For every case we use permalloy-like parameters to test the problem, as specified in Table  I. This material has associated an exchange length of L ex = 2A/(µ 0 M 2 s ) ≈ 5. 3 nm and a helical length of L D = 4πA/|D| ≈ 54. 5 nm. Simulations were performed with the finite difference OOMMF, Fidimag and MuMax3 software.
In Ref. 34  an approximate solution is provided as an ansatz for the Ψ angle, which is based on a linear dependence on z. Although this approximation qualitatively describes the effects observed from the simulations, a more accurate solution would be possible to obtain by taking the general case Θ = Θ(r, z) and Ψ = Ψ(φ, z), but it generates a non-trivial set of non-linear equations to be minimised. Because of the consistent skyrmion size across z it is likely that the dependence on z in the Θ angle only appears as a weak term or a constant, which differentiates the solution from that of the two-dimensional model. Testing this problem using the OOMMF code we obtain equivalent results with the same skyrmion radius size. In the case of MuMax3, we had to use a slightly different mesh discretisation, since the software only accepts an even number of cells, which we adjusted to get a similar sample size.
Results from MuMax3 simulations produce a skyrmion with larger radii compared to Fidimag and OOMMF, with magnitudes of approximately 15. 9 nm close to z = 0 and 15. 6 nm at the cylinder caps. Nevertheless, the tendencies of the radial profiles of the magnetisation are still close to the ones obtained with the other codes. Details of these simulations are provided in Section S5 of the Supplementary Material. Although a cylinder system is also suitable for finite element code simulations, a cuboid geometry is more natural to a finite difference discretisation. Hence, we performed a similar study using a cuboid with periodic boundary conditions. In general results on this geometry are equivalent to the cylinder but with two main differences: the periodicity removes the effects at the boundaries and the skyrmion is slightly larger in radius.
In Fig. 5  we observe the presence of extra modes with a smaller intensity signal. These modes can be filtered by setting an exponential damping towards the boundaries of the stripe  [55]  to avoid the reflection of spin waves. In the codes provided in the manuscript we implemented functions for the damping with a simple exponential profile that can be used to only obtain the main branch from the spectrum. Using the OOMMF and MuMax3 codes for simulating spin waves in systems with DMI produced equivalent results to Fig. 5. With OOMMF simulations we obtained a minimum at k = -0. 1001 nm -1 and f = 12. 1796 GHz, while simulations performed with MuMax3 produce values of k = -0. 1014 nm -1 and f = 12. 5232 GHz, which is a slightly better approximation. Results for OOMMF and MuMax3 simulations, and details about the numerical interpolation to the curves are shown in Section S7 of the Supplementary Material.
Simulations in this study have been performed using codes based on the finite difference numerical technique. Since many of the problems are compared with semianalytical calculations the results can be also applied to finite element code simulations. Some finite element computations with our non-publicly available software Finmag are shown in Section S8 of the Supplementary Material. In addition, we compared our data with the results from a non-public finite-element code developed by R. Hertel, which is an entirely rewritten successor of the TetraMag software  [56, 57]. These results are also shown in Section S8, where we obtained an excellent quantitative agreement. With this set of problems we intend to cover the functionality of the DMI interaction implemented in a micromagnetic code by testing boundary conditions, energy minimisation, which can be achieved using LLG dynamics or minimisation algorithms such as the conjugate gradient method, and spin dynamics.
Overall, the micromagnetic codes used in our testings significantly agree with expected solutions and comparisons with the theory, thus our results substantiate studies based on micromagnetic simulations with the three codes we have tested. We hope this systematic analysis helps to promote the publication of codes in simulation based studies for their corresponding validation and reproducibility, and serve as a basis for more effective development of new simulation software. For the realisation of some of the problems, we have implemented new DMI modules for MuMax3  [58]  and OOMMF  [58] [59] [60] [61]  that take advantage of the computer softwares framework, such as GPU implementation in MuMax3 or the robustness of OOMMF. We have used the Jupyter OOMMF (JOOMMF) interface to drive OOMMF and analyse data.
, 2003; Andreeva & Lindgren, 2005; Andreeva et al. , 2007). Specific patterns of the reflectivity time spectra at various grazing angles and Bragg maxima of the reflectivity from periodic multilayers have been effectively used for the description of the magnetization depth-profiles in the investigated samples (see, for example,  Ro ¨hlsberger et al. , 2003; S ´le ˛zak et al. , 2010; Andreeva et al. , 2015). For the data analysis the program package REFTIM has been developed and uploaded to the ESRF scientific software web site  (Andreeva, 2008; Andreeva et al. , 2016b). The recent development of SMS at the nuclear resonance beamline ID18 of the ESRF allows for acquiring the conventional energy-domain, i. e. Mo ¨ssbauer reflectivity spectra, which give a more understandable and clear picture of hyperfine interactions.
Therefore, even with H ext as high as 3 T the complete ferromagnetic alignment is still not attained. The fit of the NRR curves (Fig. 7 ) has been performed jointly with the fit of the Mo ¨ssbauer reflectivity spectra  [Figs. 8(a)   and 8(b) ]. The program package REFTIM has been modified to REFSPC specifically for these studies  (Andreeva et al. , 2016b). The spin-flop state at H ext = 0. 15 T reveals itself in the case of H ext k k by the presence of only the second and fifth lines in the Mo ¨ssbauer reflectivity spectra, measured near the critical angle of total external reflection (Fig. 8a ). The similar 'two' lines spectrum appears when H ext is perpendicular to the scattering plane but only at an external field of 3 T. The Mo ¨ssbauer reflectivity spectra, measured at the 'magnetic' maximum (Fig.
Conclusions The specific features of the Mo ¨ssbauer reflectivity spectra measured for various grazing angles with a synchrotron Mo ¨ssbauer source and pure -polarized radiation in the conventional energy scale at different grazing angles have been thoroughly analyzed and explained. The full set of the experimental data, obtained for the [Fe/Cr] 30 multilayer for various values and orientations of the applied magnetic field, has been fitted by the program package REFSPC specially developed for this task. The magnetization profiles and hyperfine field value distributions have been recovered for each magnitude of the applied external field. The performed Mo ¨ssbauer reflectivity experiment with the SMS at the ESRF demonstrates the high efficiency of such investigations for the analysis and understanding of the multilayer structure and magnetization profiles.
METHODOLOGY In this study, we use finite element models (FEMs) to investigate the effect of ocean load on the vertical deformation and the state of stress within a basaltic ocean island volcano. We develop axisymmetric elastic models of a volcanic edifice overlying an elastic lithosphere following the work of  Galgana et al. (2011)  and using the COMSOL Multiphysics software. All our models have similar physical parameters (Table  1 ) and are loaded gravitationally with body forces and initial lithostatic stresses (Table  2 , no ocean load). The boundary condition applied at the base of the lithosphere balance the loading of the lithostatically-prestressed lithosphere (-g. ρ lith. T l ) and simulates buoyant restoring forces (g. ρ asth. w) in response to the lithosphere subsidence within a denser asthenosphere (Table  2 ;  Watts, 2001).
ACKNOWLEDGMENTS We would like to thank  Nicole Richter  for her help in improving the content of the manuscript. We are grateful for the insightful critiques provided by  Marco Neri ,  Alessandro Tibaldi , associate editor  Laura Becerril Carretero  and chief editor  Valerio Acocella. Data supporting this manuscript are available through the main author. This is LPI contribution 2111. This work represents LMV/ClerVolc contribution # 291.
e. , partial observation), when some individuals are detected but not sampled during a field session and as a result are assigned an unknown ("U") infection state on a given occasion. First, we evaluated how increasing infection state uncertainty (i. e. , increasing the proportion of U individuals) affected bias and precision of eco-epidemiological parameter estimates. This knowledge is essential to assess the reliability of MECMR approaches when the percentage of reliably sampled individuals in a free-ranging population is low, and therefore data on infection states are scarce. We gradually increased uncertainty by decreasing the probability of assigning each infection state by an equal amount in the simulated data set ("homogeneity" scenario, Figure  1A ). We expected bias and precision to increase and decrease, respectively, with increasing state uncertainty.
Simulations Data Sets and Input Parameter Values For all analyses, we considered variation in the level of uncertainty ranging between 20% and 90% and increased this level by 10% at each iteration. We set the number of occasions, corresponding for instance to years of observation, equal to five to mimic the conditions of most eco-epidemiological CMR studies, which are typically based on a few years of data collection during a disease outbreak [e. g. (11, 25) ]. For each level of uncertainty, we simulated 1000 data sets. For this, we first simulated the "true states" of individuals by applying for each individual the survival and infection processes captured by the matrix of the biological process SIR_Model (1) from the first detection occasion until the last one. Second, we considered the encounter histories of individuals by applying the observation process described by the matrices Obs1 (2) and Obs2 (3), for each individual alive along the sampling period.
R Programming Code We used R. 3. 5. 0. (  33 ) for all analyses. We used the R package "TMB" 1. 7. 13  (34)  to fit MECMR models to simulated data and perform maximum likelihood estimation. This study is the first application of the TMB package to MECMR models to our knowledge. Because in this package models are directly formulated in C++, TMB speeded up the optimization process substantially, making the analyses 100 times faster than the native R code based on a benchmarking analysis.
FUNDING SB and LM were supported by the  Deutsche Forschungsgemeinschaft during the initial phase of project development (DFG  grants  EA 5/3-1 ,  KR4266/2-1 ). For the robustness analysis and simulation experiments, SB was funded by a grant of the  Leibniz Association  (grant  SAW K79/2017 ) and LM and OG by the  French National Research Agency  (grant  ANR-16-CE02-0007 ).
The 2020 upgrade of the LHCb detector will vastly increase the rate of collisions the online system needs to process in software in order to filter events in real-time. 30 million collisions per second will pass through a selection chain where each step is executed conditional to its prior acceptance. The Kalman filter is a process of the event reconstruction that, due to its time characteristics and early execution in the selection chain, consumes 40% of the whole reconstruction time in the current trigger software. This makes it a time-critical component as the LHCb trigger evolves into a full software trigger in the upgrade. The algorithm Cross Kalman allows performance tests across a variety of architectures, including multi and many-core platforms, and has been successfully integrated and validated in the LHCb codebase.
Since its inception, it has successfully been applied to a range of applications including space tracking  [4]  and meteorology  [5]. In high-energy physics experiments, the Kalman filter is a fundamental part of the reconstruction of particle trajectories coming from particle collisions. In LHCb, the Kalman filter consumes 40% of the reconstruction time, rendering it a critical component in the reconstruction. In order to cope with the increase in data rate, the software in the LHCb reconstruction is being updated to current hardware standards. Cross Kalman is a cross-architecture Kalman filter optimized for a variety of SIMD processors  [6]   [7]. It is optimized for low-rank Kalman filters on multi and many-core processors, and we have successfully integrated it in the LHCb reconstruction software.
It also serves as a self-contained package to evaluate different architectures in the context of the LHCb upgrade. In this paper, we focus on the evaluation of modern Intel R platforms, including Xeon Phi TM and Xeon R Scalable Processors. Our software takes into account features like the support of the AVX-512F ISA extension and high bandwidth MCDRAM. We evaluate the scalability and price performance of Cross Kalman in all platforms. In addition, we evaluate our Kalman filter integrated in the multithreaded LHCb framework Gaudi  [8]. We show the ability of Cross Kalman to scale to all considered configurations, and draw conclusions over the platforms under analysis.
A vectorized Kalman filter In the LHCb software level trigger, particle trajectory reconstruction (track reconstruction) involves a complex selection chain where the trajectory of each particle is determined in several steps, due to the various subdetectors that compose the LHCb tracker  [9]. Several of these stages involve simplified fits, in the form of square root fits or simplified Kalman filters. In contrast, Cross Kalman performs a fit in three steps: For each track, a fit is performed in the forward direction, followed by the backward direction, and finally a smoother is applied to average both states  [10]. Additionally, a track is composed of two kind of nodes. Signal nodes are produced by detector signals, whereas virtual reference nodes are placed at certain positions in the track in order to determine track parameters up-front for later stages of the reconstruction.
Since the execution of nodes in different tracks is independent, we execute them in a horizontally parallel scheme. We allow for a configurable lane width, which makes our scheduler scale to the considered SIMD platforms. The LHCb Kalman filter needs to be processed in the backward direction as well. Our scheduler guarantees this requirement trivially by traversing the scheduled object in the reverse direction. The data structure that we use in our application is Array of Structures of Array (AOSOA). This data structure has been shown to work well with SIMD architectures  [11] , as it maximizes locality. In Cross Kalman, the data is assumed to be already in this format in the order we require to process it. This assumption is safe, as the schedule can be generated prior to populating these data structures (cf.
Integration Our software has been integrated and validated in the Gaudi framework. Following the preand post-condition requirements of the current Kalman filter application TrackMasterFitter (TMF), we have developed TrackVectorFitter (TVF) as a SIMD aware drop-in replacement for TMF. TVF implements the design of Cross Kalman, with the necessary code modifications and data adaptations. In order to minimize the impact of data transposition, we generate the static schedule prior to any data generation. This way, memory references are populated as the Cross Kalman filter would expect them. Then, the data is populated in-place. This method improves the data generation performance, and allows for future optimizations by vectorizing the methods for data generation. Additionally, the output data is required to adhere to Gaudi's data layout for the processes that follow in the selection chain after the Kalman filter.
Acknowledgements The authors would like to thank the High-Throughput Computing Collaboration at  CERN  openlab for fruitful discussions through the process of designing and writing the presented software. Thanks to  C. Potterat  for his contributions on the validation of the software. Thanks to  F. Lemaitre  for his contribution of the vectorized transposition code. In addition, thanks to  W. Hulsbergen  and  R. Aaij  for the mathematical discussions and data structure design. Finally, thanks to  A. Riscos Núñez  for his guidance and support.
The Versatile Arc Discharge and Laser Ion Source (VADLIS) is a recently established ion source for the CERN-ISOLDE radioactive ion beam facility. It offers either electron-impact ionization (VADIS-mode) or resonance laser ionization (RILIS-mode). The choice of operating mode depends on the element of interest or the required beam purity. Particle-in-cell simulations using the VSim software show that the ion extraction efficiency of the VADLIS in RILIS-mode can be improved if it is equipped with an insulated extractor plate, to which an optimal voltage can be applied. This enables optimization of the RILIS-mode ion extraction independently of the electron density. Experiments have been performed using a prototype VADLIS with an adjustable extractor plate voltage for the generation of gallium ion beams at the off-line separator as well as magnesium, molybdenum and mercury ion beams at ISOLDE.
The CPO software  [9]  has been used in the past to demonstrate the impact of the so called 'active' volume in the overall efficiency of the ion source. A model describing the dependance between efficiency and the active volume was then inferred from experimental results over a wide range of operational parameters. More details can be found in  [4, 10]. Recently it was demonstrated that the VADIS cavity could be used as an effective laser-atom interaction region provided that the lasers can be transmitted through the 1. 5 mm diameter exit aperture of the anode  [1]. In this case the ion source is operated in so-called RILIS-mode, with the source magnet and the anode voltage optimized for laser-ion survival and extraction, whilst keeping the anode voltage below the required value for electron impact ionization to occur.
Even though the VADIS operation mode can also benefit from these modifications, the enhancement in extraction efficiency was observed to be not as significant as for the RILIS-mode. We demonstrate that the source can perform as a standard VADIS with no loss of performance or drop in lifetime. The particle-in-cell software VSim  [15, 16]  is used to study improved RILIS-mode extraction characteristics. VSim is also used to simulate the ion extraction time profile which shows good agreement with experimental results. In the outlook we discuss the prospects of this modified VADLIS as the new standard configuration, and suggest further modifications for improved ion source flexibility, diagnostics and performance.