A very fast inference algorithm for finite-dimensional spin glasses: Belief Propagation on the dual lattice

Starting from a Cluster Variational Method, and inspired by the correctness of the paramagnetic Ansatz (at high temperatures in general, and at any temperature in the 2D Edwards-Anderson model) we propose a novel message passing algorithm --- the Dual algorithm --- to estimate the marginal probabilities of spin glasses on finite dimensional lattices. We show that in a wide range of temperatures our algorithm compares very well with Monte Carlo simulations, with the Double Loop algorithm and with exact calculation of the ground state of 2D systems with bimodal and Gaussian interactions. Moreover it is usually 100 times faster than other provably convergent methods, as the Double Loop algorithm.Comment: 23 pages, 12 figures. v2: improved introductio

High Vcmax, Jmax and photosynthetic rates of Sonoran Desert species : using nitrogen and specific leaf area traits as predictors in biochemical models

Dryland ecosystems largely control the inter-annual variability of the global carbon cycle. Unfortunately, there is a paucity of data on key biochemical parameters, such as maximum carboxylation velocity (Vcmax25) and electron transport rate (Jmax25), from species in these ecosystems which limits our capacity to model photosynthesis across ecological scales. We studied six dominant C3 shrub and tree species from the Sonoran Desert with different leaf traits and phenological strategies. We characterized Vcmax25 and Jmax25 for each species and assessed which traits or trait combinations were the best predictors of these parameters for biochemical models of photosynthesis. All species had high values of Vcmax25 and Jmax25, mostly explained by high leaf nitrogen content (Narea) and high nitrogen allocation to photosynthetic enzymes comparable to those reported for herbs and crop species but higher than those of shrubs and other functional types in world databases. We found that the high values of Vcmax25 and Jmax25, by increasing rates of photosynthetic reactions, enhance photosynthetic water and nitrogen-use efficiencies and may favor carbon gain under typical conditions in drylands. Our findings improve the parameterization of photosynthesis models, and provide novel implications to common findings of high Narea in dryland species

Non-Gaussian Stochastic Equivalent Linearization Method for Inelastic Nonlinear Systems with Softening Behaviour, under Seismic Ground Motions

A non-Gaussian stochastic equivalent linearization (NSEL) method for estimating the non-Gaussian response of inelastic non-linear structural systems subjected to seismic ground motions represented as nonstationary random processes is presented. Based on a model that represents the time evolution of the joint probability density function (PDF) of the structural response, mathematical expressions of equivalent linearization coefficients are derived. The displacement and velocity are assumed jointly Gaussian and the marginal PDF of the hysteretic component of the displacement is modeled by a mixed PDF which is Gaussian when the structural behavior is linear and turns into a bimodal PDF when the structural behavior is hysteretic. The proposed NSEL method is applied to calculate the response of hysteretic single-degree-of-freedom systems with different vibration periods and different design displacement ductility values. The results corresponding to the proposed method are compared with those calculated by means of Monte Carlo simulation, as well as by a Gaussian equivalent linearization method. It is verified that the NSEL approach proposed herein leads to maximum structural response standard deviations similar to those obtained with Monte Carlo technique. In addition, a brief discussion about the extension of the method to muti-degree-of-freedom systems is presented

Foliar C, N, and P stoichiometry characterize successful plant ecological strategies in the Sonoran Desert

Ecological processes are centered to water availability in drylands; however, less known nutrient stoichiometry can help explain much of their structure and ecological interactions. Here we look to the foliar stoichiometry of carbon (C), nitrogen (N), and phosphorus (P) of 38 dominant plant species from the Sonoran Desert, grouped in four different functional types to describe ecological characteristics and processes. We found that foliar N, C:N, C:P, and N:P stoichiometric ratios, but not P, were higher than those known to most other ecosystems and indicate P but not N limitations in leaves. Biological N fixers (BNF) had even higher leaf N concentrations, but bio-elemental concentrations and stoichiometry ratios were not different to other non-N-fixing legume species which underscores the need to understand the physiological mechanisms for high N, and to how costly BNF can succeed in P-limiting drylands environments. Stoichiometry ratios, and to lesser extent elemental concentrations, were able to characterize BNF and colonizing strategies in the Sonoran Desert, as well as explain leaf attribute differences, ecological processes, and biogeochemical niches in this dryland ecosystem, even when no direct reference is made to other water-limitation strategies

Replica Cluster Variational Method: the Replica Symmetric solution for the 2D random bond Ising model

We present and solve the Replica Symmetric equations in the context of the Replica Cluster Variational Method for the 2D random bond Ising model (including the 2D Edwards-Anderson spin glass model). First we solve a linearized version of these equations to obtain the phase diagrams of the model on the square and triangular lattices. In both cases the spin-glass transition temperatures and the tricritical point estimations improve largely over the Bethe predictions. Moreover, we show that this phase diagram is consistent with the behavior of inference algorithms on single instances of the problem. Finally, we present a method to consistently find approximate solutions to the equations in the glassy phase. The method is applied to the triangular lattice down to T=0, also in the presence of an external field.Comment: 22 pages, 11 figure

Genomic epidemiology of NDM-1-encoding plasmids in latin American clinical isolates reveals insights into the evolution of multidrug resistance

Bacteria that produce the broad-spectrum Carbapenem antibiotic NewDelhi Metallo-b-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistancemechanism.Although it is believed that theassociated resistancegenebla NDM-1 originated inAcinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we usedwhole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) aswell as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian dollmodel for the dissemination of blaNDM-1 in LatinAmerica,with P. rettgeri playing a central role in this process, andrevealnewinsights into the evolution and disseminationof plasmids carrying such antibiotic resistance genes

SIM Regional Supplementary Comparison : SIM.L-S6. Calibration of gauge blocks by mechanical comparison

This supplementary comparison concerns the calibration of gauge blocks by mechanical comparison, which is a technique of paramount importance as it is at the highest level in the traceability chain of length for most countries of the American Continent. This comparison is designed to support the submitted CMC claims of these countries. The measurand is the central length of several gauge blocks as defined in ISO 3650 and the circulated gauge blocks were used for two comparisons carried out in two stages: the first stage, SIM.L-K1:2007, Calibration of gauge blocks by optical interferometry (2007–2010); the gauge blocks were also measured by mechanical comparison for those NMI also participating in SIM.L-S6:2007; the second stage, SIM.L-S6:2007, Calibration of gauge blocks by mechanical comparison (2010–2011) for the participants that measured only by mechanical comparison. In this second comparison there were 16 participants, 14 from the Americas, and 2 invited NMIs from other regions. The circulation in the second stage had 10 participants.Fil: Viliesid, Miguel. Centro Nacional de Metrología (CENAM); MéxicoFil: Colín Castellanos, Carlos. Centro Nacional de Metrología (CENAM); MéxicoFil: Chávez, T. Centro Nacional de Metrología (CENAM); MéxicoFil: Chaudhary, K. P. National Physical Laboratory (NPL); IndiaFil: Dvořáček, Frantisek. Czech Metrology Institute (CMI); República ChecaFil: Stoup, John. National Institute of Standards and Technology (NIST); Estados UnidosFil: Santos Barros, Wellington. Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMetro); BrasilFil: Vaudagna, Leandro. Instituto Nacional de Tecnología Industrial (INTI); ArgentinaFil: Morales, Roberto. Laboratorio Nacional de Longitud (DICTUC); ChileFil: Acquarone, Alejandro. Laboratorio Tecnológico del Uruguay (LATU); UruguayFil: Carrasco, J. Servicio Nacional de Metrología (INDECOPI); PerúFil: Vega, M. Instituto Boliviano de Metrología (IBMetro); BoliviaFil: Salazar, M. Instituto Ecuatoriano de Normalización (INEN); EcuadorFil: Gil, V. Superintendencia de Industria y Comercio (SIC); ColombiaFil: Dimas, J. Centro Nacional de Metrología de Panamá (CENAMEP); PanamáFil: Reyes, E. Laboratorio Costarricense de Metrología (LACOMET); Costa RicaFil: Hamilton, F. Trinidad and Tobago Bureau of Standards (TTBS); Trinidad y TobagoFil: Reddock, T. Trinidad and Tobago Bureau of Standards (TTBS); Trinidad y TobagoFil: Durga, S. Bureau of Standards Jamaica (BSJ); JamaicaFil: Burton, T. Bureau of Standards Jamaica (BSJ); Jamaic

Diferentes estrategias en las dinámicas de flujo de savia y nicho hidrológico de árboles dominantes en el Desierto Sonorense posibilitan su coexistencia

Antecedentes: Las plantas en ecosistemas áridos exhiben adaptaciones a las sequías periódicas, más frecuentes e intensas por el cambio global. Conocer los atributos ecofisiológicos en las especies, ayudará a entender sus adaptaciones a las limitaciones de agua. En los ecosistemas del Noroeste de México coexisten árboles perennifolios y caducifolios, de los que poco se conocen sus adaptaciones hídricas y funcionales. Preguntas: ¿Cuáles son las diferencias en los atributos de resistencia a la sequía e hídricos, en árboles coexistentes de una comunidad semi-árida? ¿Es posible determinar mecanismos de coexistencia? Especies de estudio: Olneya tesota, Ipomoea arborescens y Jatropha cordata. Sitio y año de estudio: Matorral subtropical del Desierto Sonorense. Sonora, México, 2021. Métodos: Densidad de flujo de savia (Fd) medido continuamente utilizando sensores de disipación de calor, potenciales hídricos al amanecer (Ψpd), al mediodía (Ψmd) y conductancia estomática (gs), en el verano. Resultados: Olneya (perennifolia) mantuvo Fd durante todo el año, pero Ipomoea y Jatropha (deciduas) solo durante días húmedos del verano. La Fd máxima de Ipomoea y Jatropha (~1200 g cm-2 día-1) fue el doble que Olneya (600 g cm-2 día-1). Durante los períodos secos, los árboles deciduos disminuyeron Fd. Los potenciales hídricos y conductancia estomática permitieron diferenciar los nichos hidrológicos en tipos funcionales isohídricos (Ipomoea y Jatropha) y anisohídricos (Olneya). Conclusiones: Un gradiente decreciente de resistencia a la sequía se encontró entre Ipomoea, Jatropha y Olneya. Estas especies logran su coexistencia por sus nichos hidrológicos, caracterizados por flujos de savia, estrategias iso-anisohídricas, y profundidad de raíces

A putative design for the electromagnetic activation of split proteins for molecular and cellular manipulation

The ability to manipulate cellular function using an external stimulus is a powerful strategy for studying complex biological phenomena. One approach to modulate the function of the cellular environment is split proteins. In this method, a biologically active protein or an enzyme is fragmented so that it reassembles only upon a specific stimulus. Although many tools are available to induce these systems, nature has provided other mechanisms to expand the split protein toolbox. Here, we show a novel method for reconstituting split proteins using magnetic stimulation. We found that the electromagnetic perceptive gene (EPG) changes conformation due to magnetic field stimulation. By fusing split fragments of a certain protein to both termini of the EPG, the fragments can be reassembled into a functional protein under magnetic stimulation due to conformational change. We show this effect with three separate split proteins: NanoLuc, APEX2, and herpes simplex virus type-1 thymidine kinase. Our results show, for the first time, that reconstitution of split proteins can be achieved only with magnetic fields. We anticipate that this study will be a starting point for future magnetically inducible split protein designs for cellular perturbation and manipulation. With this technology, we can help expand the toolbox of the split protein platform and allow better elucidation of complex biological systems