Boosting Monte Carlo simulations of spin glasses using autoregressive neural networks

The autoregressive neural networks are emerging as a powerful computational tool to solve relevant problems in classical and quantum mechanics. One of their appealing functionalities is that, after they have learned a probability distribution from a dataset, they allow exact and efficient sampling of typical system configurations. Here we employ a neural autoregressive distribution estimator (NADE) to boost Markov chain Monte Carlo (MCMC) simulations of a paradigmatic classical model of spin-glass theory, namely the two-dimensional Edwards-Anderson Hamiltonian. We show that a NADE can be trained to accurately mimic the Boltzmann distribution using unsupervised learning from system configurations generated using standard MCMC algorithms. The trained NADE is then employed as smart proposal distribution for the Metropolis-Hastings algorithm. This allows us to perform efficient MCMC simulations, which provide unbiased results even if the expectation value corresponding to the probability distribution learned by the NADE is not exact. Notably, we implement a sequential tempering procedure, whereby a NADE trained at a higher temperature is iteratively employed as proposal distribution in a MCMC simulation run at a slightly lower temperature. This allows one to efficiently simulate the spin-glass model even in the low-temperature regime, avoiding the divergent correlation times that plague MCMC simulations driven by local-update algorithms. Furthermore, we show that the NADE-driven simulations quickly sample ground-state configurations, paving the way to their future utilization to tackle binary optimization problems.Comment: 13 pages, 14 figure

The Role of Diversity in the Energetics of Plant Communities

Author Institution: Biological Research Laboratories, Syracuse UniversityCommunity organization, which is determined in an environmental matrix that varies in space, time, and resource quality, is an important determinant of fitnesses of constituent populations, [n addition, the fitnesses of individual populations are important determinants of community properties. Changes in species richness and equitability during plant succession indicate that comparative fitnesses of co-occuring populations, as measured by their abilities to contribute to energy flow, become more similar as succession proceeds. The rate of species invasion diminishes with greater diversity, and a smaller proportion of the flora is subject to extinction in a given time period. Community diversity, population fitness, environmental heterogeneity, and population and community stability are members of a complex feedback loop which couples each to the others

Reduction in jejunal fluid absorption in vivo through distension and cholinergic stimulation not attributable to enterocyte secretion

Jejunal fluid absorption in vivo was reduced by distension and by hydrostatic pressure and further declined on adding E. coli STa enterotoxin but no net fluid secretion was detected. Luminal atropine reduced pressure mediated reductions in fluid absorption to normal values but intravenous hexamethonium was without effect. A neural component to inhibition of absorption by pressure (though not stretch) may be mediated by axon reflexes within cholinergic neurons.Perfusion of cholinergic compounds also reduced net fluid absorption but did not cause secretion. In order to show that these actions were not secretory processes stimulated by cholinergic compounds that offset normal rates of absorption, these compounds were tested for their ability to cause net secretion in loops that were perfused with solutions in which choline substituted for sodium ion. In addition, these perfusates additionally contained E. coli STa enterotoxin or EIPA (ethyl-isopropyl-amiloride) to minimize absorption.In these circumstances, where it might be expected to do so if it were acting through a secretory rather than an absorptive mechanism, carbachol did not cause net fluid secretion. Cholinergic stimulation and pressure induced distension are thought to reduce net fluid absorption through inducing secretion but are found only to reduce fluid absorption.In conclusion, distension and cholinergic stimulation of the small intestine are two further circumstances in which fluid secretion is assumed to explain their action on fluid movement, as required by the enterocyte secretion model of secretion but, which like STa enterotoxin, instead are only able to reduce fluid absorption. This casts further doubt on the widespread validity of the enterocyte secretion model for fluid appearance in the lumen in diarrhoeal diseases

Sodium bicarbonate improves 4 km time trial cycling performance when individualised to time to peak blood bicarbonate in trained male cyclists

The aim of this study was to investigate the effects of sodium bicarbonate (NaHCO3) on 4 km cycling time trial (TT) performance when individualised to a predetermined time to peak blood bicarbonate (HCO3−). Eleven male trained cyclists volunteered for this study (height 1.82 ± 0.80 m, body mass (BM) 86.4 ± 12.9 kg, age 32 ± 9 years, peak power output (PPO) 382 ± 22 W). Two trials were initially conducted to identify time to peak HCO3− following both 0.2 g.kg−1 BM (SBC2) and 0.3 g.kg−1 BM (SBC3) NaHCO3. Thereafter, on three separate occasions using a randomised, double-blind, crossover design, participants completed a 4 km TT following ingestion of either SBC2, SBC3, or a taste-matched placebo (PLA) containing 0.07 g.kg−1 BM sodium chloride (NaCl) at the predetermined individual time to peak HCO3−. Both SBC2 (−8.3 ± 3.5 s; p < 0.001, d = 0.64) and SBC3 (−8.6 ± 5.4 s; p = 0.003, d = 0.66) reduced the time to complete the 4 km TT, with no difference between SBC conditions (mean differ- ence = 0.2 ± 0.2 s; p = 0.87, d = 0.02). These findings suggest trained cyclists may benefit from individualising NaHCO3 ingestion to time to peak HCO3− to enhance 4 km TT performance

Determinants of curvature constant (W’) of the power duration relationship under normoxia and hypoxia: the effect of pre-exercise alkalosis

Purpose This study investigated the effect of induced alkalosis on the curvature constant (W’) of the power-duration relationship under normoxic and hypoxic conditions. Methods Eleven trained cyclists (mean ± SD) Age: 32 ± 7.2 years; body mass (bm): 77.0 ± 9.2 kg; VO2peak: 59.2 ± 6.8 ml·kg−1·min−1 completed seven laboratory visits which involved the determination of individual time to peak alkalosis following sodium bicarbonate (NaHCO3) ingestion, an environment specific ramp test (e.g. normoxia and hypoxia) and four x 3 min critical power (CP) tests under different experimental conditions. Participants completed four trials: alkalosis normoxia (ALN); placebo normoxia (PLN); alkalosis hypoxia (ALH); and placebo hypoxia (PLH). Pre-exercise administration of 0.3 g.kg−1 BM of NaHCO3 was used to induce alkalosis. Environmental conditions were set at either normobaric hypoxia (FiO2: 14.5%) or normoxia (FiO2: 20.93%). Results An increase in W’ was observed with pre-exercise alkalosis under both normoxic (PLN: 15.1 ± 6.2 kJ vs. ALN: 17.4 ± 5.1 kJ; P = 0.006) and hypoxic conditions (ALN: 15.2 ± 4.9 kJ vs. ALN: 17.9 ± 5.2 kJ; P < 0.001). Pre-exercise alkalosis resulted in a larger reduction in bicarbonate ion (HCO3 −) concentrations during exercise in both environmental conditions (p < 0.001) and a greater blood lactate accumulation under hypoxia (P = 0.012). Conclusion Pre-exercise alkalosis substantially increased W’ and, therefore, may determine tolerance to exercise above CP under normoxic and hypoxic conditions. This may be due to NaHCO3 increasing HCO3 − buffering capacity to delay exercise-induced acidosis, which may, therefore, enhance anaerobic energy contribution

Evaluation of black carbon estimations in global aerosol models

We evaluate black carbon (BC) model predictions from the AeroCom model intercomparison project by considering the diversity among year 2000 model simulations and comparing model predictions with available measurements. These model-measurement intercomparisons include BC surface and aircraft concentrations, aerosol absorption optical depth (AAOD) retrievals from AERONET and Ozone Monitoring Instrument (OMI) and BC column estimations based on AERONET. In regions other than Asia, most models are biased high compared to surface concentration measurements. However compared with (column) AAOD or BC burden retreivals, the models are generally biased low. The average ratio of model to retrieved AAOD is less than 0.7 in South American and 0.6 in African biomass burning regions; both of these regions lack surface concentration measurements. In Asia the average model to observed ratio is 0.7 for AAOD and 0.5 for BC surface concentrations. Compared with aircraft measurements over the Americas at latitudes between 0 and 50N, the average model is a factor of 8 larger than observed, and most models exceed the measured BC standard deviation in the mid to upper troposphere. At higher latitudes the average model to aircraft BC ratio is 0.4 and models underestimate the observed BC loading in the lower and middle troposphere associated with springtime Arctic haze. Low model bias for AAOD but overestimation of surface and upper atmospheric BC concentrations at lower latitudes suggests that most models are underestimating BC absorption and should improve estimates for refractive index, particle size, and optical effects of BC coating. Retrieval uncertainties and/or differences with model diagnostic treatment may also contribute to the model-measurement disparity. Largest AeroCom model diversity occurred in northern Eurasia and the remote Arctic, regions influenced by anthropogenic sources. Changing emissions, aging, removal, or optical properties within a single model generated a smaller change in model predictions than the range represented by the full set of AeroCom models. Upper tropospheric concentrations of BC mass from the aircraft measurements are suggested to provide a unique new benchmark to test scavenging and vertical dispersion of BC in global models

Postrelease survival, vertical and horizontal movements, and thermal habitats of five species of pelagic sharks in the central Pacific Ocean

From 2001 to 2006, 71 pop-up satellite archival tags (PSATs) were deployed on five species of pelagic shark (blue shark [Prionace glauca]; shortfin mako [Isurus oxyrinchus]; silky shark [Carcharhinus falciformis]; oceanic whitetip shark [C. longimanus]; and bigeye thresher [Alopias superciliosus]) in the central Pacific Ocean to determine species-specific movement patterns and survival rates after release from longline fishing gear. Only a single postrelease mortality could be unequivocally documented: a male blue shark which succumbed seven days after release. Meta-analysis of published reports and the current study (n=78 reporting PSATs) indicated that the summary effect of postrelease mortality for blue sharks was 15% (95% CI, 8.5–25.1%) and suggested that catch-and-release in longline fisheries can be a viable management tool to protect parental biomass in shark populations. Pelagic sharks displayed species-specific depth and temperature ranges, although with significant individual temporal and spatial variability in vertical movement patterns, which were also punctuated by stochastic events (e.g., El Niño-Southern Oscillation). Pelagic species can be separated into three broad groups based on daytime temperature preferences by using the unweighted pair-group method with arithmetic averaging clustering on a Kolmogorov-Smirnov Dmax distance matrix: 1) epipelagic species (silky and oceanic whitetip sharks), which spent >95% of their time at temperatures within 2°C of sea surface temperature; 2) mesopelagic-I species (blue sharks and shortfin makos, which spent 95% of their time at temperatures from 9.7° to 26.9°C and from 9.4° to 25.0°C, respectively; and 3) mesopelagic-II species (bigeye threshers), which spent 95% of their time at temperatures from 6.7° to 21.2°C. Distinct thermal niche partitioning based on body size and latitude was also evident within epipelagic species

Prevalence of mixed genotype hepatitis C virus infections in the UK as determined by genotype‐specific PCR and deep sequencing

The incidence of mixed genotype hepatitis C virus infections in the UK is largely unknown. As the efficacy of direct acting antivirals is variable across different genotypes, treatment regimens are tailored to the infecting genotype, which may pose issues for the treatment of underlying genotypes within undiagnosed mixed genotype HCV infections. There is therefore a need to accurately diagnose mixed genotype infections prior to treatment. PCR-based diagnostic tools were developed to screen for the occurrence of mixed genotype infections caused by the most common UK genotypes, 1a and 3, in a cohort of 506 individuals diagnosed with either of these genotypes. The overall prevalence rate of mixed infection was 3.8% however this rate was unevenly distributed, with 6.7% of individuals diagnosed with genotype 3 harbouring genotype 1a strains and only 0.8% of samples from genotype 1a patients harbouring genotype 3 (p&lt;0.05). Mixed infection samples consisted of a major and a minor genotype, with the latter constituting less than 21% of the total viral load and, in 67% of cases, less than 1% of the viral load. Analysis of a subset of the cohort by Illumina PCR-next generation sequencing resulted in a much greater incidence rate than obtained by PCR. This may have occurred due to the non-quantitative nature of the technique and despite the designation of false positive thresholds based on negative controls