Centro de Supercomputación de Galicia

We develop a quantum Monte Carlo procedure, in the valence bond basis, to measure the Renyi entanglement entropy of a many-body ground state as the expectation value of a unitary Swap operator acting on two copies of the system. An improved estimator involving the ratio of Swap operators for different subregions enables convergence of the entropy in a simulation time polynomial in the system size. We demonstrate convergence of the Renyi entropy to exact results for a Heisenberg chain. Finally, we calculate the scaling of the Renyi entropy in the two-dimensional Heisenberg model and confirm that the Néel ground state obeys the expected area law for systems up to linear size L=32.

OBJECTIVE: Detecting and grading of diabetic retinopathy (DR) by means of digital retinal images sent via the Internet. RESEARCH DESIGN AND METHODS: Four nonstereoscopic digital retinal images (45 degrees field each) of 126 eye fundus images from 70 diabetic patients were obtained with a nonmydriatic camera at two peripheral units. The images were sent via the Internet using a web-based system to a reference center, where they were diagnosed and graded by one ophthalmologist. These results were compared with those obtained by two other ophthalmologists, one at each peripheral unit, after direct examination of the patients. A modified severity scale of Airlie House was used for grading DR in all cases. Agreement between observers was assessed using unweighted kappa for categorical data and the intraclass correlation coefficient (ICC) for continuous data. RESULTS: Presence of DR was detected in 69 eyes (55%). All eyes with DR (69 of 69, 100%) were correctly identified (kappa = 1) by inspecting the digital images. In 118 eyes (118 of 126, 94%), 57 with no DR and 61 with DR, there was an agreement between the gradation made after the direct examination and the gradation made after the inspection of the images (ICC = 0.92). In eight eyes with DR (8 of 126, 6%), there was disagreement in the grading made with both techniques. CONCLUSIONS: Inspection of digital retinal images sent via the Internet allowed diagnosis and grading of DR. The presence or absence of DR was correctly assessed by inspection of the images in all instances. We also found agreement, in most cases, between retinopathy gradation made from the images and the gradation made by direct examination of the eyes. These findings suggest that this technique is suitable for screening procedures.

Abstract This article examines the drivers of environmental proactivity in the service sector. Hypotheses were tested using multiple hierarchical regression analysis with data from a sample of 41 managers in Spanish environmental consulting companies. Results show statistically significant relationships between (1) managers’ attitude towards sustainable development, (2) positive short‐term firm performance and (3) the strategic attitude of environmental consulting firms and the adoption of proactive environmental strategies by the studied companies. This article is pioneering in the analysis of drivers of corporate proactive environmental strategies in the consultancy sector. The findings have practical implications for policy‐makers, investors and other agents interested in a better management of the environment. Economic incentives such as subsidies to environmental training programmes for managers can induce changes in cognitive components of managers’ attitudes. Education policies could also affect managers’ attitudes towards the environment. Companies may also encourage attitude change by providing their managers with financial assistance to receive environmental training. External assistance to develop a strategic attitude could be an interesting policy to encourage voluntary environmental initiatives. Finally, fiscal deductions, tax breaks or subsidies to those companies interested in managing the environment can be effective incentives for those firms facing a weak short‐term financial situation. Copyright © 2014 John Wiley & Sons, Ltd and ERP Environment

Abstract AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms ( J. Comput. Chem . 2018 , 39 , 1922). This release features a number of new capabilities: rare‐event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond‐order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin

Fourth-generation assays for the simultaneous detection of human immunodeficiency virus (HIV) antigen and antibody that were available on the international market until now have antigen detection modules with relatively poor sensitivity and produce a higher rate of false-positive results than third-generation enzyme immunoassays (EIAs). The new Cobas Core HIV Combi EIA with an improved sensitivity for HIV p24 antigen was compared to alternative fourth- and third-generation assays, the p24 antigen test, and HIV type 1 (HIV-1) RNA reverse transcriptase PCR (RT-PCR). A total of 94 seroconversion panels (n = 709 sera), samples from the acute phase of infection after seroconversion (n = 32), anti-HIV-1-positive specimens (n = 730) from patients in different stages of the disease, 462 subtyped samples from different geographical locations, anti-HIV-2-positive sera (n = 302), dilutions of cell culture supernatants (n = 62) from cells infected with different HIV-1 subtypes, selected performance panels from Boston Biomedica Inc., 7,579 unselected samples from blood donors, 303 unselected daily routine samples, 997 specimens from hospitalized patients, and potentially interfering samples (n = 1,222) were tested with Cobas Core HIV Combi EIA. The new assay showed a sensitivity comparable to that of the Abbott HIV-1 AG Monoclonal A for early detection of HIV infection in seroconversion panels. The mean time delay of Cobas Core HIV Combi EIA (last negative sample plus 1 day) in comparison to that for HIV-1 RT-PCR for 87 panels tested with both methods was 2.75 days. The diagnostic window was reduced with Cobas Core HIV Combi EIA by between 3.6 and 5.7 days from that for third-generation assays. The specificities of Cobas Core HIV Combi EIA in blood donors were 99.84 and 99.85% (after repeated testing). Overall, 30 repeatedly reactive false-positive results out of 10,031 HIV-negative samples were obtained with Cobas Core HIV Combi EIA. Our results show that a fourth-generation assay with improved specificity such as Cobas Core HIV Combi EIA is suitable for blood donor screening because of its low number of false positives and because it detects HIV p24 antigen with a sensitivity comparable to that of single-antigen assays.

We calculate the nonequilibrium electronic transport properties of a one-dimensional interacting chain at half filling, coupled to noninteracting leads. The interacting chain is initially in a Mott insulator state that is driven out of equilibrium by applying a strong bias voltage between the leads. For bias voltages above a certain threshold we observe the breakdown of the Mott insulator state and the establishment of a steady-state electronic current through the system. Based on extensive time-dependent density-matrix renormalization-group simulations, we show that this steady-state current always has the same functional dependence on voltage, independent of the microscopic details of the model and we relate the value of the threshold to the Lieb-Wu gap. We frame our results in terms of the Landau-Zener dielectric breakdown picture. Finally, we also discuss the real-time evolution of the current, and characterize the current-carrying state resulting from the breakdown of the Mott insulator by computing the double occupancy, the spin structure factor, and the entanglement entropy.

BACKGROUND AND OBJECTIVES: A photochemical treatment process (PCT) utilizing amotosalen and UVA light (INTERCEPT(™) Blood System) has been developed for inactivation of viruses, bacteria, parasites and leucocytes that can contaminate blood components intended for transfusion. The objective of this study was to further characterize the safety profile of INTERCEPT-treated platelet components (PCT-PLT) administered across a broad patient population. MATERIALS AND METHODS: This open-label, observational haemovigilance programme of PCT-PLT transfusions was conducted in 21 centres in 11 countries. All transfusions were monitored for adverse events within 24 h post-transfusion and for serious adverse events (SAEs) up to 7 days post-transfusion. All adverse events were assessed for severity (Grade 0-4), and causal relationship to PCT-PLT transfusion. RESULTS: Over the course of 7 years in the study centres, 4067 patients received 19,175 PCT-PLT transfusions. Adverse events were infrequent, and most were of Grade 1 severity. On a per-transfusion basis, 123 (0.6%) were classified an acute transfusion reaction (ATR) defined as an adverse event related to the transfusion. Among these ATRs, the most common were chills (77, 0.4%) and urticaria (41, 0.2%). Fourteen SAEs were reported, of which 2 were attributed to platelet transfusion (<0.1%). No case of transfusion-related acute lung injury, transfusion-associated graft-versus-host disease, transfusion-transmitted infection or death was attributed to the transfusion of PCT-PLT. CONCLUSION: This longitudinal haemovigilance safety programme to monitor PCT-PLT transfusions demonstrated a low rate of ATRs, and a safety profile consistent with that previously reported for conventional platelet components.

The impact of discrete doping in junctionless gate all-around n-type silicon nanowire transistors is studied using 3-D nonequilibrium Green's functions simulations. The studied devices have a 20 nm long gate and cross sections of 4.2 × 4.2 and 6.2 × 6.2 nm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The average doping concentration is 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">20</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> . The dopant distributions are randomly generated and modeled in a fully atomistic way. Phonon scattering, elastic and inelastic, is also included in the simulations. We show that junctionless nanowire transistors have a much higher subthreshold variability than their inversion mode counterparts for the equivalent geometry and doping level.

State-of-the-art climate models project a substantial decline in precipitation for the Mediterranean region in the future1. Supporting this notion, several studies based on observed precipitation data spanning recent decades have suggested a decrease in Mediterranean precipitation2–4, with some attributing a large fraction of this change to anthropogenic influences3,5. Conversely, certain researchers have underlined that Mediterranean precipitation exhibits considerable spatiotemporal variability driven by atmospheric circulation patterns6,7 maintaining stationarity over the long term8,9. These conflicting perspectives underscore the need for a comprehensive assessment of precipitation changes in this region, given the profound social, economic and environmental implications. Here we show that Mediterranean precipitation has largely remained stationary from 1871 to 2020, albeit with significant multi-decadal and interannual variability. This conclusion is based on the most comprehensive dataset available for the region, encompassing over 23,000 stations across 27 countries. While trends can be identified for some periods and subregions, our findings attribute these trends primarily to atmospheric dynamics, which would be mostly linked to internal variability. Furthermore, our assessment reconciles the observed precipitation trends with Coupled Model Intercomparison Project Phase 6 model simulations, neither of which indicate a prevailing past precipitation trend in the region. The implications of our results extend to environmental, agricultural and water resources planning in one of the world’s prominent climate change hotspots10. Our assessment of a 27-country weather station dataset in the Mediterranean region revealed long-term stability in precipitation over 150 years, along with substantial short-term variability on annual to decadal scales driven by atmospheric circulation; these findings align with the precipitation trends seen in CMIP6 models.

An efficient implementation of the density-gradient (DG) approach for the finite element and finite difference methods and its application in drift-diffusion (D-D) simulations is described in detail. The new, second-order differential (SOD) scheme is compatible with relatively coarse grids even for large density variations thus applicable to device simulations with complex 3-D geometries. Test simulations of a 1-D metal-oxide semiconductor diode demonstrate that the DG approach discretized using our SOD scheme can be accurately calibrated against Schrödinger-Poisson calculations exhibiting lower discretization error than the previous schemes when using coarse grids and the same results for very fine meshes. 3-D test D-D simulations using the finite element method are performed on two devices: a 10 nm gate length double gate metal-oxide-semiconductor field-effect transistor (MOSFET) and a 40 nm gate length Tri-Gate fin field-effect transistor (FinFET). In 3-D D-D simulations, the SOD scheme is able to converge to physical solutions at high voltages even if the previous schemes fail when using the same mesh and equivalent conditions. The quantum corrected D-D simulations using the SOD scheme also converge with an atomistic mesh used for the 10 nm double gate MOSFET saving computational resources and can be accurately calibrated against the results from non-equilibrium Green's functions approach. Finally, the simulated I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> -V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> characteristics for the 40 nm gate length Tri-Gate are in an excellent agreement with experimental data.

A new software, called tsscds2018, has been developed to discover reaction mechanisms and solve the kinetics in a fully automated fashion. The program employs algorithms based on Graph Theory to find transition state (TS) geometries from accelerated semiempirical dynamics simulations carried out with MOPAC2016. Then, the TSs are connected to the corresponding minima and the reaction network is obtained. Kinetic data like populations vs time or the abundancies of each product can also be obtained with our program thanks to a Kinetic Monte Carlo routine. Highly accurate ab initio potential energy diagrams and kinetics can also be obtained using an interface with Gaussian09. The source code is available on the following site: http://forge.cesga.es/wiki/g/tsscds/HomePage © 2018 Wiley Periodicals, Inc.

Data from citizen scientists reveal a worrying growth in light pollution over the past decade.

BACKGROUND: The number of allergic reactions to A. simplex reported in Spain has increased dramatically in the last decade. Nevertheless, there have been no studies of the prevalence of and possible risk factors for IgE sensitization to this parasite, possibly because suitably specific diagnostic methods have only recently become available. The objective was to investigate the prevalence of and risk factors for IgE sensitization to A. simplex in Galicia, a region of northwestern Spain with a population of about 3 million and high average fish consumption (78.5 g/person per day). METHODS: The study was performed with a random sample of 2801 healthy blood donors distributed in 53 geographic areas, proportional to the density of donors. IgE sensitization to A. simplex was tested by a capture ELISA method that has proved to be the most specific method currently available. RESULTS: The results showed a total of only 12 positive subjects, of whom five also showed IgG1 sensitization. All positive subjects and 101 randomly selected seronegative subjects were then included in a case-control study of risk factors for sensitization to A. simplex, based on a telephone interview about fish consumption (especially raw and undercooked fish). All seropositive subjects (but only 25% of seronegative subjects) reported consumption of undercooked fish or homemade raw-fish products. CONCLUSIONS: Our results strongly suggest that sensitization to A. simplex is caused only by live larvae, and not by allergens contained in fish tissues, and that ingestion of homemade boquerones (anchovies [Engraulis encrasicholus] in vinegar), and to a much lesser extent of undercooked fish, are the main risk factors for IgE sensitization to Anisakis in this region.

Protein aggregation is associated with an increasing number of human disorders and premature aging. Moreover, it is a central concern in the manufacturing of recombinant proteins for biotechnological and therapeutic applications. Nevertheless, the unique architecture of protein aggregates is also exploited by nature for functional purposes, from bacteria to humans. The relevance of this process in health and disease has boosted the interest in understanding and controlling aggregation, with the concomitant development of a myriad of algorithms aimed to predict aggregation propensities. However, most of these programs are blind to the protein environment and, in particular, to the influence of the pH. Here, we developed an empirical equation to model the pH-dependent aggregation of intrinsically disordered proteins (IDPs) based on the assumption that both the global protein charge and lipophilicity depend on the solution pH. Upon its parametrization with a model IDP, this simple phenomenological approach showed unprecedented accuracy in predicting the dependence of the aggregation of both pathogenic and functional amyloidogenic IDPs on the pH. The algorithm might be useful for diverse applications, from large-scale analysis of IDPs aggregation properties to the design of novel reversible nanofibrillar materials.

An efficient parallel implementation of the Fast Multipole Method (FMM) combined with the fast Fourier transform (FFT) is presented in this paper. The good scaling properties of the FMM-FFT, combined with a smart parallelization strategy, has been shown to be very effective when using large parallel supercomputers. A challenging problem with more than 150 million unknowns has been solved, demonstrating that the proposed implementation of the FMM-FFT constitutes a real alternative to the more frequently used multilevel approaches, such as the Multilevel FMM (MLFMA). Even more importantly, we have achieved a high efficiency with 1,024 parallel processors, which indeed constitutes one of the better scalability results ever reached for a rigorous integral-equation electromagnetic solver.

MOTIVATION: The theoretical possibility of determining the state and parameters of a dynamic model by measuring its outputs is given by its structural identifiability and its observability. These properties should be analysed before attempting to calibrate a model, but their a priori analysis can be challenging, requiring symbolic calculations that often have a high computational cost. In recent years, a number of software tools have been developed for this task, mostly in the systems biology community. These tools have vastly different features and capabilities, and a critical assessment of their performance is still lacking. RESULTS: Here, we present a comprehensive study of the computational resources available for analysing structural identifiability. We consider 13 software tools developed in 7 programming languages and evaluate their performance using a set of 25 case studies created from 21 models. Our results reveal their strengths and weaknesses, provide guidelines for choosing the most appropriate tool for a given problem and highlight opportunities for future developments. AVAILABILITY AND IMPLEMENTATION: https://github.com/Xabo-RB/Benchmarking_files.

We present a direct comparison of the recently proposed valence bond entanglement entropy and the von Neumann entanglement entropy on spin-1/2 Heisenberg systems using quantum Monte Carlo and density-matrix renormalization group simulations. For one-dimensional chains we show that the valence bond entropy can be either less or greater than the von Neumann entropy; hence, it cannot provide a bound on the latter. On ladder geometries, simulations with up to seven legs are sufficient to indicate that the von Neumann entropy in two dimensions obeys an area law, even though the valence bond entanglement entropy has a multiplicative logarithmic correction.

Data movement between the main memory and the processor is a key contributor to execution time and energy consumption in memory-intensive applications. This data movement bottleneck can be alleviated using Processing-in-Memory (PiM). One category of PiM is Processing-using-Memory (PuM), in which computation takes place inside the memory array by exploiting intrinsic analog properties of the memory device. PuM yields high performance and energy efficiency, but existing PuM techniques support a limited range of operations. As a result, current PuM architectures cannot efficiently perform some complex operations (e.g., multiplication, division, exponentiation) without large increases in chip area and design complexity. To overcome these limitations of existing PuM architectures, we introduce pLUTo (processing-using-memory with lookup table (LUT) operations), a DRAM-based PuM architecture that leverages the high storage density of DRAM to enable the massively parallel storing and querying of lookup tables (LUTs). The key idea of pLUTo is to replace complex operations with low-cost, bulk memory reads (i.e., LUT queries) instead of relying on complex extra logic. We evaluate pLUTo across 11 real-world workloads that showcase the limitations of prior PuM approaches and show that our solution outperforms optimized CPU and GPU base-lines by an average of $713 \times$ and $1.2 \times$, respectively, while simultaneously reducing energy consumption by an average of $1855 \times$ and $39.5 \times$. Across these workloads, pLUTo outperforms state-of-the-art PiM architectures by an average of $18.3 \times$. We also show that different versions of pLUTo provide different levels of flexibility and performance at different additional DRAM area overheads (between 10.2% and 23.1%). pLUTo’s source code and all scripts required to reproduce the results of this paper are openly and fully available at https://github.com/CMU-SAFARI/pLUTo.

BACKGROUND: The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and common carp (Cyprinus carpio) to obtain accurate estimates of the effective size for commercial populations. METHODS: Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. RESULTS: Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. CONCLUSIONS: Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes.

Using plasma chemistry, carbon was extracted from charcoal paint samples collected from megalithic monuments in north-west Iberia. Nine accelerator mass spectrometric radiocarbon dates on these paints establish their age to be within 1000 14 C years of each other, centred at approximately 5000 BP. These radiocarbon ages for megalithic paintings fall within the proposed time period for north-west Iberian megalithic culture. Multiple layers of paint on some stones show that more than one painting episode occurred.