dataesr/scientific-paragraphs-categorization huggingface dataset:
The model GCbedstress (fifth and sixth in the two rankings) ranks highest when only ice caps are considered. The average deviation of 3 ± 17 % indeed suggests a very high www. the-cryosphere. net/11/949/2017/ The Cryosphere, 11, 949-970, 2017 model performance. However, it has to be noted that the result is based on one test case only (Table  2 ). For the models considering more ice caps, the results are heterogeneous and difficult to interpret, as models showing small IQRs show large bias, and vice versa (Table  4 ). The model GCneuralnet is found at the other end of the ranking (penultimate and last ranks respectively). The average deviation of -39 ± 52 % highlights both the large bias and large spread of the estimates. Obviously, the performance of approaches based on ANNs are highly dependent on the data set used for algorithm training.
With the initiation of the Glacier Thickness Database  (Gärtner-Roer et al. , 2014; WGMS, 2016) , the first steps towards a freely accessible, global database of ice thickness measurements have been undertaken. We anticipate that this effort, together with a second phase of ITMIX targeting at how to best integrate sparse thickness measurements to improve model performance, will foster the development of improved ice thickness estimation approaches. To summarize, in order to improve available thickness estimates for glacier and ice caps, we make the following recommendations: -Ensemble methods comprising a variety of independent, physically based approaches should be considered. This is likely to be a more effective strategy than focusing on one individual approach. -Models should be extended to take observational uncertainty into account.
The Bayesian framework used by  Brinkerhoff et al. (2016) , for example, showed promising results in this respect. -The increasing availability of surface ice flow velocity data (e. g. Scambos et al. , 2016)  should be exploited. In this context, the previously mentioned necessity of accounting for observational uncertainty is crucial. -The way individual models treat ice divides has to be improved. This is important when addressing ice caps and glacier complexes and to ensure consistency between subsurface topographies of adjacent ice masses. -Efforts for centralizing available ice thickness measurements should be strengthened. Initiatives such as the GlaThiDa database launched by the World Glacier Monitoring Service are essential for new generations of ice thickness models to be developed and validated.
Acknowledgements. ITMIX was made possible by the  International Association of Cryospheric Sciences (IACS). We are indebted to the  European Space Agency 's project Glaciers_cci as well as to  Elisa Bjerre ,  Emiliano Cimoli ,  Gwenn Flowers ,  Marco Marcer ,  Geir Moholdt ,  Johnny Sanders ,  Marius Schäfer ,  Konrad Schindler ,  Tazio Strozzi , and  Christoph Vogel  for providing data necessary for the experiment. D. Farinotti  acknowledges support from the  Swiss National Science Foundation (SNSF). M. Morlighem  and  C. Girard  were funded by the  National Aeronautics and Space Administration, Cryospheric Sciences Program , grant  NNX15AD55G. P. W. Leclercq  was funded by the  European Research Council  under the European Union's  Seventh Framework Programme  (FP/2007-2013)/ ERC  grant agreement no.
320816. J. A. Dowdeswell  acknowledges the  UK Natural Environment Research Council for supporting the airborne radio-echo sounding surveys of the three Arctic ice caps included in the experiment (grants  GR3/4663 ,  GR3/9958 ,  GR3/12469 , and  NE/K004999/1 ). A. Rabatel  and  O. Sanchez  acknowledge the contribution of Labex OSUG@2020 (Investissements d'avenir - ANR10 LABX56 ) and the  VIP_Mont-Blanc project  ( ANR-14-CE03-0006-03 ). F. Gillet-Chaulet  and  C. Mosbeux  acknowledge support from  French National Research Agency (ANR)  under the  SUMER (Blanc SIMI 6) 2012  project  ANR-12BS06-0018. The constructive comments by  Shin Sugiyama  and an anonymous referee helped to improve the manuscript. Edited by:  A. Vieli  Reviewed by:  S. Sugiyama  and one anonymous referee.
Software-Defined Networking (SDN) is among the emerging network architecture paradigms in the last few years. Originally designed for wired networks, SDN has known a phenomenal success both in academia and industry. SDN is based on: (i) a physical separation between the control plane and the data plane, and (ii) a logically centralized control and intelligence in a software controller. OpenFlow  [3]  is the most utilized standard for the communication between the control plane and data plane. It defines two kinds of networks equipment: OpenFlow controllers, which centralize all the network control functions and OpenFlow vStwichs, which only perform data packet forwarding functions. Each vSwitch has a flow table that contains controller flow entries. The controller handles the vSwitchs by formulating flow rules and installing corresponding entries in the flow table.
Communication interfaces: Currently there are neither standardized SDN interfaces for directly integrating SDN into HetVNets, nor an ad-hoc (no IPoriented) version of OpenFlow protocol compatible with security applications features of HetVNet. Thus, we propose to use a customized version of OpenFlow protocol adapted to HetVNet scenarios as southbound API to communicate between the control plane and the data plane and to use a customized interface as Northbound API to communicate between the control plane and applications  [4].
Overview The remainder of the paper is structured as follows. Section 2 describes the numerical algorithms that are employed for performing interpolation and differentiation in a 'field-aligned' fashion. Section 3 details the field-aligned semi-Lagrangian scheme in the simplified setting of the constant advection equation in 2D, and provides a rigorous proof of unconditional stability, together with an extensive error analysis. Section 4 presents a simplified gyrokinetic model in cylindrical geometry (screw pinch), which is implemented in Selalib (semi-Lagrangian library) and verified against an analytical solution. Section 5 presents a gyrokinetic model in toroidal geometry (circular Tokamak), which is implemented in the Gysela code and benchmarked against a standard (not aligned) version of the same code.
Algorithm 2 describes the second solution, which is effectively used in the Gysela code. In the Selalib code (Sect. 4) we do not need to evaluate z derivatives of the electric potential φ(r, θ, z), as in the equations everything is expressed in terms of derivatives in the poloidal plane (r, θ) or along the parallel direction b. To evaluate the electric field along b, we use for example a finite difference formula of order 6, which reads (after setting z = R 0 ϕ 123 Input : g, Output : dg/dϕ for j = 0, N ϕ do η(i = * , j) ← spline coefficients for g(i = * , j) for j = 0, N ϕ do for i = 0, N θ do for k = -d, d +1 do θ + k ← fieldline θ (θ i , ϕ j + , j + k); θ - k ← fieldline θ (θ i , ϕ j -, j + k); u + k ← 1D spline interpolation along θ at θ + k using η(i = * , j + k); u - k ← 1D spline interpolation along θ at θ - k using η(i = * , j + k); u + ← 1D Lagrange interpolation using values (u + k ) k=-d,d+1 ; u -← 1D Lagrange interpolation using values (u - k ) k=-d,d+1 ; dg dϕ (i, j) ← u + +u - 2 Algorithm 2: Derivatives along ϕ with aligned scheme and z = R 0 ϕ) b • ∇φ(r i , θ j , z k ) b z (r i ) z 3 =-3 w φ(r i , fieldline θ (θ j , z k , k + ), z k+ ), with coefficients w 0 = 0, w 1 = -w -1 = 3 4 , w 2 = -w -2 = - 3 20 , w 3 = -w -3 = 1 60 , where φ(r i , fieldline θ (θ j , z k , k + ), z k+ ) is obtained by interpolation (for example cubic splines) from the values φ(r i , θ l , z k+ ), l = 0,.
Acknowledgements Open access funding provided by  Max Planck Society. The authors are grateful to  Edoardo Zoni  for carefully reading our manuscript and pointing out some typos and mistakes, which we have corrected; we also acknowledge his help with the streamline plots in Fig. 5. This work has been carried out within the framework of the  EUROfusion Consortium  and has received funding from the  Euratom  research and training programme 2014-2018 under Grant Agreement No. 633053. The views and opinions expressed herein do not necessarily reflect those of the  European Commission.
We study the impact of dimension-six operators of the standard model effective field theory relevant for vector-boson fusion and associated Higgs boson production at the LHC. We present predictions at the next-to-leading order accuracy in QCD that include matching to parton showers and that rely on fully automated simulations. We show the importance of the subsequent reduction of the theoretical uncertainties in improving the possible discrimination between effective field theory and standard model results, and we demonstrate that the range of the Wilson coefficient values allowed by a global fit to LEP and LHC Run I data can be further constrained by LHC Run II future results.
Introduction The LHC Run I and early Run II data have not yet put forward any strong evidence of physics beyond the standard model (SM) and limits on new states have instead been pushed to higher and higher energies. As a consequence, the effective field theory (EFT) extension of the SM (SMEFT) has become increasingly relevant. The SMEFT is built from the SM symmetries and degrees of freedom (including the Higgs sector) by adding new operators of dimension higher than four to the SM Lagrangian. Being a tool to parameterise the search for new anomalous interactions, it is fully complementary to direct searches for new particles. Interpreting data in the context of the SMEFT hence allows us to be sensitive to new physics beyond the current energy reach of the LHC in a modelindependent way. The formulation of the effective Lagrangian restricted to operators of dimension of at most six relies on the definition of a complete and non-redundant operator basis  [1] [2] [3]  and should additionally include the translations among the possible choices  [4].
Higgs production in association with a vector boson Higgs-boson production in association with a vector boson is an excellent probe for new physics, as the momentum transfer in the process is directly sensitive to the Lorentz structure appearing in the interaction vertices  [53]. The use of differential information at the LHC Run I has therefore enhanced the sensitivity of Higgs data to possible new physics effects  [39]. Those Run I studies have, however, relied on predictions evaluated at the LO accuracy in QCD. With the improved capabilities of the LHC Run II, NLO QCD effects become more relevant and more precise predictions are in order. To showcase our NLO simulation setup for associated VH production, we study various differential distributions in the p p → H W + → b b + + / E (17) channel, where / E stands for the final-state missing energy.
Conclusions We have presented FeynRules and UFO implementations of dimension-six SMEFT operators affecting electroweak Higgs-boson production, which can be used for NLO(QCD)+PS accurate Monte Carlo event generation within the MG5 aMC framework. We have considered five SILH basis operators and have accounted for all field redefinitions that are necessary to canonically normalise the theory. Moreover, the ensuing modifications of both the gauge couplings and the relationships between the electroweak inputs and the derived parameters have also been included. We have showcased the strength of our approach by simulating both associated VH and VBF Higgsboson production at the 13 TeV LHC, selecting a pair of benchmark scenarios informed both by recent limits from global fits to the LEP and LHC Run I data and by theoretical motivations originating from integrating out certain popular ultraviolet realisations.
Acknowledgements We would like to express a special thanks to  Fabio Maltoni  for useful discussions. We moreover acknowledge the organisers of the 2015 ' Les Houches-Physics at TeV  colliders' workshop and the  Mainz Institute for Theoretical Physics  for their hospitality and support during the completion of this work. CD is a  Durham International Junior Research Fellow. BF and KMa have been supported by the  Theory-LHC-France initiative of the CNRS  ( INP/IN2P3 ) and KMi and VS by the  Science and Technology Facilities Council  (Grant number  ST/J000477/1 ).
Bacteriophages are the most abundant viruses on earth and display an impressive genetic as well as morphologic diversity. Among those, the most common order of phages is the Caudovirales, whose viral particles packages linear double stranded DNA (dsDNA). In this study we investigated how the information gathered by high throughput sequencing technologies can be used to determine the DNA termini and packaging mechanisms of dsDNA phages. The wet-lab procedures traditionally used for this purpose rely on the identification and cloning of restriction fragment which can be delicate and cumbersome. Here, we developed a theoretical and statistical framework to analyze DNA termini and phage packaging mechanisms using next-generation sequencing data. Our methods, implemented in the PhageTerm software, work with sequencing reads in fastq format and the corresponding assembled phage genome.
Phage de novo assembly To find the termini of an unknown phage, the first step consisted of a de novo assembly using NGS raw data. To validate that the assembly did not alter the result of the software, we assembled the 5 reference phages using spades  23  with standard options. Assemblers will frequently introduce mistakes at the edges of contigs due to the presence of low abundance reads that do not correspond to the actual phage sequence. This can usually be seen as a drop in coverage at the contig ends. Phage assembly genome are available in the Sourceforge deposit (https://sourceforge. net/projects/phageterm).
Nucleotide sequence accession numbers The complete genome sequences of phiCD24-1, phiCD111, phiCD146, phiCD481-1, phiCD505, phiCD506, phiMMP01 and phiMMP03 were deposited in European Nucleotide Archive under the accession no. LN681534, LN681535, LN681536, LN681538, LN681539, LN681540, LN681541, LN681542. The de novo assemblies performed on reference phages are available at Sourceforge (https://sourceforge. net/projects/phageterm). Phages used in this study are described in Table  S1. The raw reads data of all phages was deposited in sequence reads archives (SRA) under the accession SRP093616 (Table  S2 ).
Software implementation PhageTerm is a standalone program designed for biologists which purpose is to perform termini and packaging mode analysis for any bacteriophage of interest. PhageTerm is written in Python 2. 7, the source code and documentation are freely available at https://sourceforge. net/projects/phageterm under a GPL license (GPL 3. 0). PhageTerm is compatible on three operating systems (Linux, Mac OS X, and Windows) in command line (require Python 2. 7. X with the following library: matplotlib 1. 3. 1, numpy 1. 9. 2, pandas 0. 19. 1, sklearn 0. 18. 1, scipy 0. 18. 1, statsmodels 0. 6. 1 and reportlab 3. 3. 0. ). For direct graphical interface operation, a Galaxy wrapper version is also available at https://galaxy. pasteur. fr.
For 3' cos phage, HK97  5  was sequenced. The PhageTerm software was able to determine the exact characteristics of lambda and HK97: the nature of the termini (Figure  1B ), the cos mode of packaging and the length of their cohesive sequence (Table  1 ). Phage Efm1 from Enterococci was described as a 3' cos phage  27  , and was also accurately recognized by PhageTerm. Among Clostridium phages that we sequenced, PhiCD481-1 and PhiCD506 also matched the theoretical description of cos phages with 3' overhangs (Figure  2B ).
DTR Phages with direct terminal repeats are expected to have one nice peak in each orientation, and the forward peak should be to the left of the reverse peak. The region in between the peaks should show twice the average sequence coverage (Figure  2C ). Because of their terminal redundancy, DTR phages will typically be attributed a random first base by DNA assemblers. A typical example of this is phage T7, a podoviridae that has exact short direct terminal repeats of 160 bases  25. The PhageTerm software was able to determine the exact characteristics of T7: nature of its termini (Figure  1B ), the termini positions and the exact length of its direct terminal repeats (Table  1 ).
Note that the signal obtained to determine the position of the pac site is C+1 time weaker than that for cos phages (Figure  S3 ). This phenomenon is amplified by the fact that the cleavage position of the terminase at pac sites can be imprecise, leading to several possible termini. As an example of this packaging mechanism we sequenced phage P1, a myoviridae enterobacteria phage. The PhageTerm software was able to determine the exact characteristics of P1: nature of the termini (Figure  2D ), the pac mode of packaging and an estimation of the number of concatemers. Other phages have been described to package their genome through a headful packaging mechanisms but with no preferred packaging signal. The packaged phage genomes are circularly permuted with random termini. No signal can be recovered for this type of phage.
We sequenced phage Mu as the father of this category. The PhageTerm software results are in line with those expected: no significant peak in the value of X were found (Figure  1B ), but a high number of hybrid inserts were detected (Figure  3 ). The host termini of Mu are asymmetric, a short fragment at one side (~50) and a long one at the other side (~2000bp). Unfortunately, the short read length provided by illumina sequencing does not allow to determining these fragment sizes easily and systematically.
Clostridium difficile Phages difficile is currently the principal cause of antibiotic-induced infectious diarrhea in humans  28. Most C. difficile isolates analyzed to date carry one or several prophages, however only a few of them have been fully characterized. The packaging mode of four phages included in this study have been determined experimentally in our using the ligation-digestion method and could be used to compare the results we obtain with the software. PhageTerm determined PhiCD481-1 and PhiCD506 to be cos phages, and found 13nt 3' overhangs identical for both phages (Table  S1 ). These phages also showed the expected decrease in coverage between the termini of 3'cos phages (Figure  2B ). PhiCD146, PhiMMP01 and PhiMMP03 were found to be pac phages. PhiCD211 was found to have direct terminal repeat of 378 bp.
SRA Phages To test the versatility and robustness of the PhageTerm software on data generated by others, we have fetched the raw sequencing data of six phages (T3, T7, HP1, Efm1, Slur09 and PBES-2) from the sequence read archive (SRA). Among these phages, four have known termini and packaging mode (T7, T3, HP1 and Efm1) detailed in table  S1. The PhageTerm software was able to identify the right termini and packaging mode for T3 and T7 along with an exact short DTR of respectively 160 and 231 bases. For phage Efm1 and PBES-2, the PhageTerm software found cohesive sequence of 9 bases and direct repeats of 443 bases, respectively.
Important note on sequencing library preparation methods The methods described here rely on the random fragmentation of the phage DNA and the availability of DNA termini to adapter ligation. As a consequence methods that rely on transposases to ligate the adapters, such as Nextera, should not produce suitable data for PhageTerm and similar strategies  29. We confirmed this by analyzing the data of phage HP1 and Slur09 that we retrieved from SRA. These phages were sequenced using illumina nextera kits which lead to the loss of the termini sequence. As expected no termini could be detected when using the data generated for these two phages.
In a recent publication by Rashid, J. et al. 30  analyzing termini and packaging of C. difficile phages, researchers inferred packaging mechanism by looking at homologies between the terminase of newly sequenced phages and that of phages with known packaging mechanisms. This strategy only provides very partial and uncertain information about packaging mode and no information on termini type and sequences. Recently, another study made available a procedure to analyze whole genomes, physical ends and packaging strategies of phages using a pre-existing software  31. This procedure can be very time consuming and contains numerous steps requiring bioinformatic skills, including the installation of the Phamerator program  32  and the management of the related SQL databases. The heavy and unwieldy procedures available to phage scientists motivated our efforts to develop PhageTerm, an easy-to-use program that consolidates in a single straightforward analysis numerous highly valuable pieces of information about phage termini and packaging mode.
CONCLUSIONS PhageTerm provides a rapid and reliable analysis of NGS data to determine phage termini and packaging mode, provided that data is generated following some simple rules: (i) random fragmentation should always be used when preparing sequencing libraries. (ii) Paired-end sequencing should be used to obtain a more complete characterization of the termini. The broad availability of phage termini information will in the future enable to shed light on the diversity of packaging mechanisms in nature. The PhageTerm software will also attempt to assign termini type even when these do not correspond to known phage packaging mechanism. As such the software might help in the identification of novel packaging strategies. We encourage the phage community to contact us in the case of such discovery and we will be happy to update the software to better take into account any novel class.
AKNOWLEDGMENTS The authors would like to thank  Laurence Van Melderen  and  Ariane Toussaint  for providing strain RH8816,  Erica Lieberman  from  Eligo Bioscience  for providing the sequencing data for phage HK97 and  Laurent Debarbieux  for providing phage T4 as well as useful discussions. We also acknowledge the  Plate-forme Genomics  and the center of informatics for Biology, especially  Christiane Bouchier ,  Laurence Ma ,  Eric Deveau ,  Fabien Mareuil  and  Olivia Doppelt-Azeroual  for their help and support with sequencing and Galaxy integration. This work was supported by a discovery grant from the  Natural Sciences and Engineering Research Council of Canada  ( NSERC  # 341450-2010 ), the  Agence Nationale de la Recherche  (" CloSTARn ",  ANR-13-JSV3-0005-01 ) and the french Government's  Investissement d'Avenir program ;  Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'  [ ANR-10-LABX-62-IBEID ].
AVAILABILITY AND REQUIREMENTS Project name: PhageTerm Project home page: https://sourceforge. net/projects/phageterm Operating system(s): Platform independent Programming language: Python Other requirements: matplotlib 1. 3. 1, numpy 1. 9. 2, pandas 0. 19. 1, sklearn 0. 18. 1, scipy 0. 18. 1, statsmodels 0. 6. 1, reportlab 3. 3. 0. License: General Public License version 3. 0 (GPL3. 0) Any restrictions to use by non-academics: No.
Mechanical test After the creation of the molds, the samples were placed at 4 °C overnight to be tested the following day. Prior to the test, the samples were left at ambient temperature for 30 min. Tibiae were then placed axially in custom loading fixtures and pre-cycled using a sinusoidal waveform between -0. 5 N and -2 N for 30 cycles at 0. 5 Hz. The destructive test was conducted immediately after pre-cycling by compressing the tibia at a rate of 0. 03 mm/s until failure using an electromagnetic testing machine (Bose Corporation, Eden Prairie, MN: 5500). Load-displacement data were recorded at 60 Hz (WinTest® Digital Control System) and test curves were analyzed to determine stiffness and ultimate force. However, as all the ligaments were cut, this should not have a major impact. Another limitation is that we assumed from a statistical result on low effectives that there were no differences between each right and left limb.