pinecone/core-2020-05-10-deduplication huggingface dataset:
A quasi-static discontinuous Galerkin configurational force crack propagation method for brittle materials.

This paper presents a framework for r-adaptive quasi-static configurational force (CF) brittle crack propagation, cast within a discontinuous Galerkin (DG) symmetric interior penalty (SIPG) finite element scheme. Cracks are propagated in discrete steps, with a staggered algorithm, along element interfaces which align themselves with the predicted crack propagation direction. The key novelty of the work is the exploitation of the DG face stiffness terms existing along element interfaces to propagate a crack in a mesh independent r-adaptive quasi-static fashion, driven by the CF at the crack tip. This adds no new degrees of freedom to the data structure. Additionally as DG methods have element specific degrees of freedom, a geometry driven p-adaptive algorithm is also easily included allowing for more accurate solutions of the CF on a moving crack front. Further, for non-determinant systems, we introduce an average boundary condition that restrains rigid body motion leading to a determinant system. To the authors' knowledge this is first time such a boundary condition has been described. The proposed formulation is validated against, single and multiple crack problems with single-and mixed-mode cracks, demonstrating the predictive capabilities of the method
Weight-adjusted discontinuous Galerkin methods: matrix-valued weights
  and elastic wave propagation in heterogeneous media

Weight-adjusted inner products are easily invertible approximations to
weighted $L^2$ inner products. These approximations can be paired with a
discontinuous Galerkin (DG) discretization to produce a time-domain method for
wave propagation which is low storage, energy stable, and high order accurate
for arbitrary heterogeneous media and curvilinear meshes. In this work, we
extend weight-adjusted DG (WADG) methods to the case of matrix-valued weights,
with the linear elastic wave equation as an application. We present a DG
formulation of the symmetric form of the linear elastic wave equation, with
upwind-like dissipation incorporated through simple penalty fluxes. A
semi-discrete convergence analysis is given, and numerical results confirm the
stability and high order accuracy of WADG for several problems in elastic wave
propagation
FEMxDEM multiscale modeling: model performance enhancement, from Newton strategy to element loop parallelization

This paper presents a multiscale model based on a FEM×DEM approach, a method that couples discrete elements at the microscale and finite elements at the macroscale. FEM×DEM has proven to be an effective way to treat real-scale engineering problems by embedding constitutive laws numerically obtained using discrete elements into a standard finite element framework. This proposed paper focuses on some numerical open issues of the method. Given the nonlinearity of the problem, Newton's method is required. The standard full Newton method is modified by adopting operators different from the consistent tangent matrix and by developing ad-hoc solution strategies. The efficiency of several existing operators is compared, and a new and original strategy is proposed, which is shown to be numerically more efficient than the existing propositions. Furthermore, a shared memory parallelization framework using OpenMP directives is introduced. The combination of these enhancements allows to overcome the FEM×DEM computational limitations, thus making the approach competitive with classical FEM in terms of stability and computational cost.Peer reviewe
Two-scale topology optimization in computational material design: an integrated approach

In this work, a new strategy for solving multiscale topology optimization problems is presented. An alternate direction algorithm and a precomputed offline microstructure database (Computational Vademecum) are used to efficiently solve the problem. In addition, the influence of considering manufacturable constraints is examined. Then, the strategy is extended to solve the coupled problem of designing both the macroscopic and microscopic topologies. Full details of the\ud
algorithms and numerical examples to validate the methodology are provided.Peer ReviewedPostprint (published version
Accelerating isogeometric boundary element analysis for\ud
three-dimensional elastostatics problems through black-box fast multipole method with proper generalized decomposition.

The isogeometric approach to computational engineering analysis makes use of Non-Uniform Rational B-splines (NURBS) to discretise both the geometry and the analysis field variables, giving a higher fidelity geometric description and leading to improved convergence properties of the solution over conventional piecewise polynomial descriptions. Because of its boundary-only modelling, with no requirement for a volumetric NURBS geometric definition, the boundary element method is an ideal choice for isogeometric analysis of solids in 3-D. An isogeometric boundary element analysis (IGABEM) algorithm is presented for the solution of such problems in elasticity, and is accelerated using the black-box Fast Multipole Method (bbFMM). The bbFMM scheme is of O(n) complexity, giving a general kernel-independent separation that can be easily integrated into existing, conventional IGABEM codes with little modification. In the bbFMM scheme, an important process of obtaining a low rank approximation of M2L operators has been hitherto based on Singular Value Decomposition (SVD), which can be very time consuming for large 3-D problems, and this motivates the present work. We introduce the Proper Generalized Decomposition (PGD) method as an alternative approach, and this is demonstrated to enhance efficiency in comparison with schemes that rely on the SVD. In the worst case a factor of approximately 2 performance gain is achieved. Numerical examples show the performance gains that are achievable in comparison to standard IGABEM solutions, and demonstrate that solution accuracy is not affected. The results illustrate the potential of this numerical technique for solving arbitrary large scale elastostatics problems directly from CAD models
A Higher Order Equilibrium Finite Element Method

In this paper a mixed spectral element formulation is presented for planar,
linear elasticity. The degrees of freedom for the stress are integrated
traction components, i.e. surface force components. As a result the tractions
between elements are continuous. The formulation is based on minimization of
the complementary energy subject to the constraints that the stress field
should satisfy equilibrium of forces and moments. The Lagrange multiplier which
enforces equilibrium of forces is the displacement field and the Lagrange
multiplier which enforces equilibrium of moments is the rotation. The
formulation satisfies equilibrium of forces pointwise if the body forces are
piecewise polynomial. Equilibrium of moments is weakly satisfied. Results of
the method are given on orthogonal and curvilinear domains and an example with
a point singularity is given.Comment: 32 pages, 27 figures, Article accepted in International Journal for
  Numerical Methods in Engineerin
An adaptive cracking particle method providing explicit and accurate description of 3D crack surfaces.

Cracks in 3D have arbitrary shapes and therefore present difficulties for numerical modelling. A novel adaptive cracking particle method with explicit and accurate description of 3D cracks is described in this paper. In this meshless method, crack surfaces are described by a set of discontinuous segments which are associated with particles. This group of particles are assumed all to be “cracked” and split into two sub-particles with modified support domains. Compared to the original method where the spherical supports at particles are equally divided, the proposed method makes use of non-planar segments to account for changes in crack face direction. The orientations of those segments and the angular changes of cracks during crack propagation steps are recorded using triangular meshes. Supports of weight functions are modified according to those changes so that quasi-continuous crack surfaces can be obtained, avoiding the spurious cracking seen in earlier CPMs. An adaptive approach in 3D is then introduced to capture stress gradients around crack fronts. Several 3D crack problems with reference results have been tested to validate the proposed method with good agreement being achieved using the new method, showing it to be potentially a significant advance for 3D fracture predictions problems
Numerical convergence of nonlinear nonlocal continuum models to local
  elastodynamics

We quantify the numerical error and modeling error associated with replacing
a nonlinear nonlocal bond-based peridynamic model with a local elasticity model
or a linearized peridynamics model away from the fracture set. The nonlocal
model treated here is characterized by a double well potential and is a smooth
version of the peridynamic model introduced in n Silling (J Mech Phys Solids
48(1), 2000). The solutions of nonlinear peridynamics are shown to converge to
the solution of linear elastodynamics at a rate linear with respect to the
length scale $\epsilon$ of non local interaction. This rate also holds for the
convergence of solutions of the linearized peridynamic model to the solution of
the local elastodynamic model. For local linear Lagrange interpolation the
consistency error for the numerical approximation is found to depend on the
ratio between mesh size $h$ and $\epsilon$. More generally for local Lagrange
interpolation of order $p\geq 1$ the consistency error is of order
$h^p/\epsilon$. A new stability theory for the time discretization is provided
and an explicit generalization of the CFL condition on the time step and its
relation to mesh size $h$ is given. Numerical simulations are provided
illustrating the consistency error associated with the convergence of nonlinear
and linearized peridynamics to linear elastodynamics
A face-centred finite volume method for second-order elliptic problems

This work proposes a novel finite volume paradigm, the face-centred finite
volume (FCFV) method. Contrary to the popular vertex (VCFV) and cell (CCFV)
centred finite volume methods, the novel FCFV defines the solution on the mesh
faces (edges in 2D) to construct locally-conservative numerical schemes.
  The idea of the FCFV method stems from a hybridisable discontinuous Galerkin
(HDG) formulation with constant degree of approximation, thus inheriting the
convergence properties of the classical HDG. The resulting FCFV features a
global problem in terms of a piecewise constant function defined on the faces
of the mesh. The solution and its gradient in each element are then recovered
by solving a set of independent element-by-element problems.
  The mathematical formulation of FCFV for Poisson and Stokes equation is
derived and numerical evidence of optimal convergence in 2D and 3D is provided.
Numerical examples are presented to illustrate the accuracy, efficiency and
robustness of the proposed methodology. The results show that, contrary to
other FV methods, the accuracy of the FCFV method is not sensitive to mesh
distortion and stretching. In addition, the FCFV method shows its better
performance, accuracy and robustness using simplicial elements, facilitating
its application to problems involving complex geometries in 3D.Comment: 43 pages, 33 figures, 3 table
Time accurate consistently stabilized mesh-free methods for convection dominated problems

This is the pre-peer reviewed version of the following article: Huerta, A.; Fernandez, S. Time accurate consistently stabilized mesh-free methods for convection dominated problems. "International journal for numerical methods in engineering", Gener 2003, vol. 56, núm. 9, p. 1225-1242, which has been published in final form at http://www3.interscience.wiley.com/journal/102522343/abstractThe behaviour of high-order time stepping methods combined with mesh-free methods is studied for the transient convection-diffusion equation. Particle methods, such as the element-free Galerkin (EFG) method, allow to easily increase the order of consistency and, thus, to formulate high-order schemes in space and time. Moreover, second derivatives of the EFG shape functions can be constructed with a low extra cost and are well defined, even for linear interpolation. Thus, consistent stabilization schemes can be considered without loss in the convergence rates.Peer ReviewedPostprint (author’s final draft
Recovering lower bounds of the error by postprocessing implicit residual a posteriori error estimates

Classical residual type error estimators approximate the error flux around the elements and yield upper bounds of the exact (or reference) error. Lower bounds of the error are also needed in goal oriented adaptivity and for bounds on functional outputs. This work introduces a simple and cheap strategy to recover a lower bound estimate from standard upper bound estimates. This lower bound may also be used to assess the effectivity of the former estimate and to improve it.Peer ReviewedPostprint (author’s final draft
Hierarchic finite element bases on unstructured tetrahedral meshes

The problem of constructing hierarchic bases for finite element discretization of the spaces H1, H(curl), H(div) and L2 on tetrahedral elements is addressed. A simple and efficient approach to ensuring conformity of the approximations across element interfaces is described. Hierarchic bases of arbitrary polynomial order are presented. It is shown how these may be used to construct finite element approximations of arbitrary, non-uniform, local order approximation on unstructured meshes of curvilinear tetrahedral elements
Numerical modelling of void inclusions in porous media

This is the pre-peer reviewed version of the following article: Rodríguez, A.; Sarrate, J.; Huerta, A. Numerical modelling of void inclusions in porous media. "International journal for numerical methods in engineering", Gener 2004, vol. 59, núm. 4, p. 577-596, which has been published in final form at http://www3.interscience.wiley.com/journal/106570919/abstractNumerical modelling of porous flow in a low-permeability matrix with high-permeability inclusions is a challenging task because the large ratio of permeabilities ill-conditions the finite element system of equations. We propose a coupled model where Darcy flow is used for the porous matrix and potential flow is used for the inclusions. We discuss appropriate interface conditions in detail and show that the head drop in the inclusions can be prescribed in a very simple way. Algorithmic aspects are treated in full detail. Numerical examples show that this coupled approach precludes ill-conditioning and is more efficient than heterogeneous Darcy flow.Peer ReviewedPostprint (author’s final draft
First report of the ceftazidimase CTX-M-19 in South America

AbstractWe report the first detection of blaCTX-M-19 in South America, harboured in an Escherichia coli isolate obtained from a urine sample; such an isolate belonged to phylogenetic group A, ST603, and showed a ceftazidimase profile. blaCTX-M-19 was encoded in an approximately 100 kb IncI1/IncF conjugative plasmid, featuring pndAC and hok/sok addiction systems; the β-lactamase gene was flanked upstream by three tandem-like transposons (IS26, IS10 and ISEcp 1), inserted one inside the other, and downstream by IS903
Rapid identification of Stenotrophomonas maltophilia by peptide nucleic acid fluorescence in situ hybridization

AbstractThe objective of this study was to develop a novel peptide nucleic acid (PNA) probe for Stenotrophomonas maltophilia identification by fluorescence in situ hybridization (FISH). The probe was evaluated using 33 human and veterinary clinical S. maltophilia isolates and 45 reference strains representing common bacterial species in the respiratory tract. The probe displayed 100% sensitivity and 100% specificity on pure cultures and allowed detection in sputum from cystic fibrosis patients. The detection limit was 104 CFU/mL in spiked tracheal aspirate and bronchoalveolar lavage from healthy horses. Altogether the study shows that this species-specific PNA FISH probe facilitates rapid detection of S. maltophilia in biological specimens
Fusobacterium necrophorum, an emerging pathogen of otogenic and paranasal infections?

AbstractFusobacterium necrophorum is a rare causative agent of otitis and sinusitis. Most commonly known is the classic Lemièrre's syndrome of postanginal sepsis with suppurative thrombophlebitis of the jugular vein. We report five patients diagnosed recently with a complicated infection with F. necrophorum originating from otitis or sinusitis. Two patients recovered completely, one patient died due to complications of the infection, one patient retained a slight hemiparesis and one patient had permanent hearing loss. Diagnosis and management are discussed. A possible factor in the emergence of F. necrophorum is proposed
Emergence of KPC-producing Klebsiella pneumoniae in Uruguay: infection control and molecular characterization

AbstractWe describe the first outbreak of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP), the infection control measures adopted and the shift in resistance patterns of isolates during antibiotic treatment. The ST258 KPC-KP strain exhibited a multiresistant antibiotic phenotype including co-resistance to gentamycin, colistin and tigecycline intermediate susceptibility. Isolates before and after treatment had different behaviour concerning their antibiotic susceptibility and the population analysis profile study. A progressive increase in the aminoglycosides (acquiring amicacin resistance) and β-lactam MICs, and a decreased susceptibility to fosfomycin was observed throughout the administration of combined antimicrobial regimens including meropenem. A high meropenem resistance KPC-KP homogeneous population (MIC 256 Jg/mL), could arise from the meropenem heterogeneous low-level resistance KPC-KP population (MIC 8 Jg/mL), by the selective pressure of the prolonged meropenem therapy. The kpc gene was inserted in a Tn4401 isoform a, and no transconjugants were detected. The core measures adopted were successful to prevent evolution towards resistance dissemination
Epidemiology of Clostridium difficile infection in two tertiary-care hospitals in Perth, Western Australia: a cross-sectional study

AbstractThe epidemiology of Clostridium difficile infection (CDI) has changed over time and between countries. It is therefore essential to monitor the characteristics of patients at risk of infection and the circulating strains to recognize local and global trends, and improve patient management. From December 2011 to May 2012 we conducted a prospective, observational epidemiological study of patients with laboratory-confirmed CDI at two tertiary teaching hospitals in Perth, Western Australia to determine CDI incidence and risk factors in an Australian setting. The incidence of CDI varied from 5.2 to 8.1 cases/10 000 occupied bed days (OBDs) at one hospital and from 3.9 to 16.3/10 000 OBDs at the second hospital. In total, 80 patients with laboratory-confirmed CDI met eligibility criteria and consented to be in the study. More than half (53.8%) had hospital-onset disease, 28.8% had community-onset and healthcare facility-associated disease and 7.5% were community-associated infections according to the definitions used. Severe CDI was observed in 40.0% of these cases but the 30-day mortality rate for all cases was only 2.5%. Besides a shorter length of stay among cases of community-onset CDI, no characteristics were identified that were significantly associated with community-onset or severe CDI. From 70 isolates, 34 different ribotypes were identified. The predominant ribotypes were 014 (24.3%), 020 (5.7%), 056 (5.7%) and 070 (5.7%). Whereas this study suggests that the characteristics of CDI cases in Australia are not markedly different from those in other developed countries, the increase in CDI rate observed emphasizes the importance of surveillance
Multi-drug resistance and reduced susceptibility to ciprofloxacin among Salmonella enterica serovar Typhi isolates from the Middle East and Central Asia

AbstractTyphoid fever is common in developing countries, with an estimated 120 million infections and 700 000 annual deaths, worldwide. Fluoroquinolones have been the treatment of choice for infection with multidrug-resistant (MDR) Salmonella enterica serovar Typhi (S. Typhi). However, alarming reports of fluoroquinolone-resistance and failure of typhoid fever treatment have recently been published. To determine the proportion of S. Typhi isolates with reduced susceptibility to ciprofloxacin (RSC) from six countries in the Middle East and Central Asia, 968 S. Typhi isolates collected between 2002 and 2007 from Egypt, Uzbekistan, Pakistan, Qatar, Jordan and Iraq were tested for antibiotic susceptibility to five antibiotics using the disc-diffusion method. MDR was defined as resistance to amicillin, chloramphenicol and trimethoprim-sulfamethoxazole. The E-test was employed to determine the MIC of ciprofloxacin only. Nalidixic acid resistance was evaluated as a marker for RSC. Interpretations were made according to CLSI guidelines. MDR strains were considerably more prevalent in Iraq (83%) and Pakistan (52%) compared with the other countries studied (13–52%). Nearly all isolates were susceptible (99.7%) to ceftriaxone. RSC was detected in a total of 218 isolates (22%), mostly from Iraq (54/59, 92%), Uzbekistan (98/123, 80%), Qatar (23/43, 54%) and Pakistan (31/65, 47%). Many of these (21%) were also MDR. Use of nalidixic acid resistance as an indicator for RSC was 99% sensitive and 98% specific. This study reinforces the need for routine antimicrobial susceptibility surveillance of enteric fever isolates and close review of current therapeutic policies in the region
Genotyping of methicillin-resistant Staphylococcus aureus in the Sultan Qaboos University Hospital, Oman reveals the dominance of Panton–Valentine leucocidin-negative ST6-IV/t304 clone

AbstractThe objective of this study was to determine the prevalence and distribution of methicillin-resistant Staphylococcus aureus (MRSA) genotypes circulating at a tertiary hospital in the Sultanate of Oman. A total of 79 MRSA isolates were obtained from different clinical samples and investigated using antibiogram, pulsed-field gel electrophoresis (PFGE), staphylococcal chromosome cassette mec (SCCmec), Spa typing and multilocus sequence typing (MLST). The isolates were susceptible to linezolid, vancomycin, teicoplanin, tigecycline and mupirocin but were resistant to tetracycline (30.4%), erythromycin (26.6%), clindamycin (24.1%), trimethoprim (19.0%), ciprofloxacin (17.7%), fusidic acid (15.2%) and gentamicin (12.7%). Molecular typing revealed 19 PFGE patterns, 26 Spa types and 21 sequence types. SCCmec-IV (86.0%) was the dominant SCCmec type, followed by SCCmec-V (10.1%). SCCmec-III (2.5%) and SCCmec-II (1.3%) were less common. ST6-IV/t304 (n = 30) and ST1295-IV/t690 (n = 12) were the dominant genotypes followed by ST772-V/t657 (n = 5), ST30-IV/t019/t021 (n = 5), ST22-IV/t852 (n = 4), ST80-IV/t044 (n = 3) and 18 single genotypes that were isolated sporadically. On the basis of SCCmec typing and MLST, 91.2% of the isolates were classified as community-associated MRSA and 8.8% of the isolates (consisting of four ST22-IV/t852, one ST239-III/t632, one ST5-III/t311 and one ST5-II/t003) were classified as healthcare-associated MRSA. The study has revealed the dominance of a Panton–Valentine leucocidin-negative ST6-IV/t304 clone and provided insights into the distribution of antibiotic resistance in MRSA at the tertiary hospital in Oman. It also highlights the importance of surveillance in detecting the emergence of new MRSA clones in a healthcare facility