A Generic Communications Module for Cooperative 3D Visualization and Modelling over the Internet: the Collaborative API

Cooperative three-dimensional visualization and modeling applications allow a distributed group of users to work together with a model they share. To implement this kind of applications the underlying communications system must provide reliable and ordered multicast of users interactions. Due to the high complexity that characterizes the models, network bandwidth requirements have limited their use to intranets or in a few cases to very high-speed Internet connections. In this paper we present a communications module that solves this problem. The library exposed, which is called Collaborative API, supports the creation of very efficient cooperative 3D visualization and modeling applications by optimizing the use of the network resources. The Collaborative API, implements a new communications architecture: the dynamic client/server. The communications module presented in this paper is illustrated by two examples of applications that use it to provide cooperative 3D visualization over the Internet

Efficacy of DNA amplification in tissue biopsy samples to improve the detection of invasive fungal disease

AbstractThe performance of a pan-fungal PCR-based technique was evaluated to assess the aetiology of invasive fungal diseases (IFDs). A total of 89 formalin-fixed paraffin-embedded biopsy samples from 84 patients with proven IFD were studied. Culture of tissue was performed in 68 (81%) patients. The sensitivities of the PCR-based technique and microbiological culture of tissues were 89% and 56%, respectively (p <0.01). According to PCR results, Aspergillus species accounted for 67%, Candida species for 13%, zygomycetes for 11%, and rare and emerging fungi for 9%. Aspergillus species were significantly associated with lung samples (79.6%, p <0.01), Mucorales were associated with skin/subcutaneous samples, and Candida species were associated with gastrointestinal samples. Regarding biopsy samples with Aspergillus species, Aspergillus fumigatus DNA was detected in 43 of 50 (86%), and Aspergillus flavus in six of 50 (12%). PCR was positive in 24 of 30 (80%) cases with negative culture. In nine of the 84 patients, the PCR technique failed to amplify the DNA. Six also had negative cultures, and in the remaining three cases culture was positive (Rhizopus microsporus, Rhizopus arrhizus, and Sakseneae vasiformis), suggesting that the PCR technique was not as effective in amplifying the DNA of some species of Zygomycetes. In five cases, there was no correlation between culture results and those obtained with DNA amplification, indicating the possibility of a mixed infection or the presence of colonizer/contaminant microorganisms. In summary, PCR-based techniques for DNA amplification should be implemented in histopathology and microbiology departments, as they appear to be complementary to conventional methods for IFD detection

Topological Color Codes and Two-Body Quantum Lattice Hamiltonians

Topological color codes are among the stabilizer codes with remarkable properties from quantum information perspective. In this paper we construct a four-valent lattice, the so called ruby lattice, governed by a 2-body Hamiltonian. In a particular regime of coupling constants, degenerate perturbation theory implies that the low energy spectrum of the model can be described by a many-body effective Hamiltonian, which encodes the color code as its ground state subspace. The gauge symmetry $\mathbf{Z}_{2}\times\mathbf{Z}_{2}$ of color code could already be realized by identifying three distinct plaquette operators on the lattice. Plaquettes are extended to closed strings or string-net structures. Non-contractible closed strings winding the space commute with Hamiltonian but not always with each other giving rise to exact topological degeneracy of the model. Connection to 2-colexes can be established at the non-perturbative level. The particular structure of the 2-body Hamiltonian provides a fruitful interpretation in terms of mapping to bosons coupled to effective spins. We show that high energy excitations of the model have fermionic statistics. They form three families of high energy excitations each of one color. Furthermore, we show that they belong to a particular family of topological charges. Also, we use Jordan-Wigner transformation in order to test the integrability of the model via introducing of Majorana fermions. The four-valent structure of the lattice prevents to reduce the fermionized Hamiltonian into a quadratic form due to interacting gauge fields. We also propose another construction for 2-body Hamiltonian based on the connection between color codes and cluster states. We discuss this latter approach along the construction based on the ruby lattice.Comment: 56 pages, 16 figures, published version

Dynamical properties of liquid Al near melting. An orbital-free molecular dynamics study

The static and dynamic structure of liquid Al is studied using the orbital free ab-initio molecular dynamics method. Two thermodynamic states along the coexistence line are considered, namely T = 943 K and 1323 K for which X-ray and neutron scattering data are available. A new kinetic energy functional, which fulfills a number of physically relevant conditions is employed, along with a local first principles pseudopotential. In addition to a comparison with experiment, we also compare our ab-initio results with those obtained from conventional molecular dynamics simulations using effective interionic pair potentials derived from second order pseudopotential perturbation theory.Comment: 15 pages, 12 figures, 2 tables, submitted to PR

Brief Research Report: Virus-Specific Humoral Immunity at Admission Predicts the Development of Respiratory Failure in Unvaccinated SARS-CoV-2 Patients

Erratum for Brief Research Report: Virus-Specific Humoral Immunity at Admission Predicts the Development of Respiratory Failure in Unvaccinated SARS-CoV-2 Patients. Tajuelo A, Carretero O, García-Ríos E, López-Siles M, Cano O, Vázquez M, Más V, Rodríguez-Goncer I, Lalueza A, López-Medrano F, Juan RS, Fernández-Ruiz M, Aguado JM, McConnell MJ, Pérez-Romero P. Front Immunol. 2022 Apr 25;13:878812. doi: 10.3389/fimmu.2022.878812. eCollection 2022. PMID: 35547738 Free PMC article.Introduction: There is robust evidence indicating that the SARS-CoV-2-specific humoral response is associated with protection against severe disease. However, relatively little data exist regarding how the humoral immune response at the time of hospital admission correlates with disease severity in unimmunized patients. Our goal was toidentify variables of the humoral response that could potentially serve as prognostic markers for COVID-19 progressionin unvaccinated SARS-CoV-2 patients. Methods: A prospective cross-sectional study was carried out in a cohort of 160 unimmunized, adult COVID-19 patients from the Hospital Universitario 12Octubre. Participants were classified into four clinical groups based on disease severity: non-survivors with respiratory failure (RF), RF survivors, patients requiring oxygen therapy and those not receiving oxygen therapy. Serum samples were taken on admission and IgM, IgG, IgG subclass antibody titers were determined by ELISA, and neutralizing antibody titersusing a surrogate neutralization assay. The differences in the antibody titers between groups and the association between the clinical and analytical characteristics of the patients and the antibody titers were analyzed. Results: Patients that developed RF and survived had IgM titers that were 2-fold higher than non-survivors (p = 0.001), higher levels of total IgG than those who developed RF and succumbed to infection (p< 0.001), and than patients who required oxygen therapy (p< 0.05), and had 5-fold higher IgG1 titers than RF non-survivors (p< 0.001) and those who needed oxygen therapy (p< 0.001), and 2-fold higher than patients that did not require oxygen therapy during admission (p< 0.05). In contrast, RF non-survivorshad the lowest neutralizing antibodylevels, which were significantly lower compared those with RF that survived (p = 0.03). A positive correlation was found between IgM, total IgG, IgG1 and IgG3 titers and neutralizing antibody titers in the total cohort (p ≤ 0.0036). Conclusions: We demonstrate that patients with RF that survived infection had significantly higher IgM, IgG, IgG1 and neutralizing titers compared to patients with RF that succumb to infection, suggesting that using humoral response variables could be used as a prognostic marker for guiding the clinical management of unimmunized patients admitted to the hospital for SARS-CoV-2 infection.This work was supported by Mutua Madrileña Foundation (2020/0056) “Plan Nacional de I+D+I” and Instituto de Salud Carlos III (COVID-19 Research Call COV20/00181 and COV20_00679), Subdirección General de Redes y Centros de Investigación Cooperativa, Spanish Ministry of Science and Innovation, Spanish Network for Research in Infectious Diseases (REIPI RD16/0016) - co-financed by the European Development Regional Fund (EDRF) and the European Social Fund (ESF) "A way to achieve Europe- The ESF invests in your future". Red de Enfermedades Infecciosas (CIBERINFEC), CB21/13/00079. EG-R is supported by the Sara Borrell Program (CD18CIII/00007), MLS is supported by the Sara Borrell Program (CD17CIIII/00017), Instituto de Salud Carlos III, Ministerio de Ciencia, Innovación y Universidades., and AT is supported by the Garantía Juvenil Program of the Comunidad Autonoma de Madrid. IRG holds a research training contract “Río Hortega” (CM19/00163) and MFR a research contract “Miguel Servet” (CP18/00073), both from the Instituto de Salud Carlos III, Spanish Ministry of Science and Innovation.S

Tensor network states and geometry

Tensor network states are used to approximate ground states of local Hamiltonians on a lattice in D spatial dimensions. Different types of tensor network states can be seen to generate different geometries. Matrix product states (MPS) in D=1 dimensions, as well as projected entangled pair states (PEPS) in D>1 dimensions, reproduce the D-dimensional physical geometry of the lattice model; in contrast, the multi-scale entanglement renormalization ansatz (MERA) generates a (D+1)-dimensional holographic geometry. Here we focus on homogeneous tensor networks, where all the tensors in the network are copies of the same tensor, and argue that certain structural properties of the resulting many-body states are preconditioned by the geometry of the tensor network and are therefore largely independent of the choice of variational parameters. Indeed, the asymptotic decay of correlations in homogeneous MPS and MERA for D=1 systems is seen to be determined by the structure of geodesics in the physical and holographic geometries, respectively; whereas the asymptotic scaling of entanglement entropy is seen to always obey a simple boundary law -- that is, again in the relevant geometry. This geometrical interpretation offers a simple and unifying framework to understand the structural properties of, and helps clarify the relation between, different tensor network states. In addition, it has recently motivated the branching MERA, a generalization of the MERA capable of reproducing violations of the entropic boundary law in D>1 dimensions.Comment: 18 pages, 18 figure

Factors associated with the development of septic shock in patients with candidemia: A post hoc analysis from two prospective cohorts

Background: Almost one third of the patients with candidemia develop septic shock. The understanding why some patients do and others do not develop septic shock is very limited. The objective of this study was to identify variables associated with septic shock development in a large population of patients with candidemia. Methods: A post hoc analysis was performed on two prospective, multicenter cohort of patients with candidemia from 12 hospitals in Spain and Italy. All episodes occurring from September 2016 to February 2018 were analyzed to assess variables associated with septic shock development defined according to The Third International Consensus Definition for Sepsis and Septic Shock (Sepsis-3). Results: Of 317 candidemic patients, 99 (31.2%) presented septic shock attributable to candidemia. Multivariate logistic regression analysis identifies the following factors associated with septic shock development: age > 50 years (OR 2.57, 95% CI 1.03-6.41, p = 0.04), abdominal source of the infection (OR 2.18, 95% CI 1.04-4.55, p = 0.04), and admission to a general ward at the time of candidemia onset (OR 0.21, 95% CI, 0.12-0.44, p = 0.001). Septic shock development was independently associated with a greater risk of 30-day mortality (OR 2.14, 95% CI 1.08-4.24, p = 0.02). Conclusions: Age and abdominal source of the infection are the most important factors significantly associated with the development of septic shock in patients with candidemia. Our findings suggest that host factors and source of the infection may be more important for development of septic shock than intrinsic virulence factors of organisms