Hot new directions for quasi-Monte Carlo research in step with applications

This article provides an overview of some interfaces between the theory of quasi-Monte Carlo (QMC) methods and applications. We summarize three QMC theoretical settings: first order QMC methods in the unit cube $[0,1]^s$ and in $\mathbb{R}^s$, and higher order QMC methods in the unit cube. One important feature is that their error bounds can be independent of the dimension $s$ under appropriate conditions on the function spaces. Another important feature is that good parameters for these QMC methods can be obtained by fast efficient algorithms even when $s$ is large. We outline three different applications and explain how they can tap into the different QMC theory. We also discuss three cost saving strategies that can be combined with QMC in these applications. Many of these recent QMC theory and methods are developed not in isolation, but in close connection with applications

Environmental Health Disparities: A Framework Integrating Psychosocial and Environmental Concepts

Although it is often acknowledged that social and environmental factors interact to produce racial and ethnic environmental health disparities, it is still unclear how this occurs. Despite continued controversy, the environmental justice movement has provided some insight by suggesting that disadvantaged communities face greater likelihood of exposure to ambient hazards. The exposure–disease paradigm has long suggested that differential “vulnerability” may modify the effects of toxicants on biological systems. However, relatively little work has been done to specify whether racial and ethnic minorities may have greater vulnerability than do majority populations and, further, what these vulnerabilities may be. We suggest that psychosocial stress may be the vulnerability factor that links social conditions with environmental hazards. Psychosocial stress can lead to acute and chronic changes in the functioning of body systems (e.g., immune) and also lead directly to illness. In this article we present a multidisciplinary framework integrating these ideas. We also argue that residential segregation leads to differential experiences of community stress, exposure to pollutants, and access to community resources. When not counterbalanced by resources, stressors may lead to heightened vulnerability to environmental hazards

The Schro¨\ddot{o}dinger-Poisson equations as the large-N limit of the Newtonian N-body system: applications to the large scale dark matter dynamics

In this paper it is argued how the dynamics of the classical Newtonian N-body system can be described in terms of the Schr$\ddot{o}$dinger-Poisson equations in the large $N$ limit. This result is based on the stochastic quantization introduced by Nelson, and on the Calogero conjecture. According to the Calogero conjecture, the emerging effective Planck constant is computed in terms of the parameters of the N-body system as $\hbar \sim M^{5/3} G^{1/2} (N/)^{1/6}$, where is $G$ the gravitational constant, $N$ and $M$ are the number and the mass of the bodies, and $$ is their average density. The relevance of this result in the context of large scale structure formation is discussed. In particular, this finding gives a further argument in support of the validity of the Schr$\ddot{o}$dinger method as numerical double of the N-body simulations of dark matter dynamics at large cosmological scales.Comment: Accepted for publication in the Euro. Phys. J.

Derivation of a biomass proxy for dynamic analysis of whole genome metabolic models

A whole genome metabolic model (GEM) is essentially a reconstruction of a network of enzyme-enabled chemical reactions representing the metabolism of an organism, based on information present in its genome. Such models have been designed so that flux balance analysis (FBA) can be applied in order to analyse metabolism under steady state. For this purpose, a biomassfunctionisaddedtothesemodelsasanoverallindicatorofthemodel’s viability. Our objective is to develop dynamic models based on these FBA models in order to observe new and complex behaviours, including transient behaviour. There is however a major challenge in that the biomass function does not operate under dynamic simulation. An appropriate biomass function would enable the estimation under dynamic simulation of the growth of both wildtype and genetically modified bacteria under different, possibly dynamically changing growth conditions. Using data analytics techniques, we have developed a dynamic biomass function which acts as a faithful proxy for the FBA equivalent for a reduced GEM for E. coli. This involved consolidating data for reaction rates and metabolite concentrations generated under dynamic simulation with gold standard target data for biomass obtained by steady state analysis using FBA. It also led to a number of interesting insights regarding biomass fluxes for pairs of conditions. These findings were reproduced in our dynamic proxy function

Unravelling the rate of action of hits in the Leishmania donovani box using standard drugs amphotericin B and miltefosine

In recent years, the neglected diseases drug discovery community has elected phenotypic screening as the key approach for the identification of novel hit compounds. However, when this approach is applied, important questions related to the mode of action for these compounds remain unanswered. One of such questions is related to the rate of action, a useful piece of information when facing the challenge of prioritising the most promising hit compounds. In the present work, compounds of the "Leishmania donovani box" were evaluated using a rate of action assay adapted from a replicative intracellular high content assay recently developed. The potency of each compound was determined every 24 hours up to 96 hours, and standard drugs amphotericin B and miltefosine were used as references to group these compounds according to their rate of action. Independently of this biological assessment, compounds were also clustered according to their minimal chemical scaffold. Comparison of the results showed a complete correlation between the chemical scaffold and the biological group for the vast majority of compounds, demonstrating how the assay was able to bring information on the rate of action for each chemical series, a property directly linked to the mode of action. Overall, the assay here described permitted us to evaluate the rate of action of the "Leishmania donovani box" using two of the currently available drugs as references and, also, to propose a number of fast-acting chemical scaffolds present in the box as starting points for future drug discovery projects to the wider scientific community. The results here presented validate the use of this assay for the determination of the rate of action early in the discovery process, to assist in the prioritisation of hit compounds

Perceived Devaluation and STI Testing Uptake among a Cohort of Street-involved Youth in a Canadian Setting

Perceived devaluation has been shown to have adverse effects on the mental and physical health outcomes of people who use drugs. However, the impact of perceived devaluation on sexually transmitted infections (STI) testing uptake among street-involved youth, who face multiple and intersecting stigmas due to their association with drug use and risky sexual practices, has not been fully characterized. Data were obtained between December 2013 and November 2014 from a cohort of street-involved youth who use illicit drugs aged 14–26 in Vancouver, British Columbia. Multivariable generalized estimating equations were constructed to assess the independent relationship between perceived devaluation and STI testing uptake. Among 300 street-involved youth, 87.0% reported a high perceived devaluation score at baseline. In the multivariable analysis, high perceived devaluation was negatively associated with STI testing uptake after adjustment for potential confounders (Adjusted Odds Ratio = 0.38, 95% Confidence Interval 0.15–0.98). Perceived devaluation was high among street-involved youth in our sample and appears to have adverse effects on STI testing uptake. HIV prevention and care programs should be examined and improved to better meet the special needs of street-involved youth in non-stigmatizing ways

The Validity of d′ Measures

Subliminal perception occurs when prime stimuli that participants claim not to be aware of nevertheless influence subsequent processing of a target. This claim, however, critically depends on correct methods to assess prime awareness. Typically, d′ (“d prime”) tasks administered after a priming task are used to establish that people are unable to discriminate between different primes. Here, we show that such d′ tasks are influenced by the nature of the target, by attentional factors, and by the delay between stimulus presentation and response. Our results suggest that the standard d′ task is not a straightforward measure of prime visibility. We discuss the implications of our findings for subliminal perception research

Vision First? The Development of Primary Visual Cortical Networks Is More Rapid Than the Development of Primary Motor Networks in Humans

The development of cortical functions and the capacity of the mature brain to learn are largely determined by the establishment and maintenance of neocortical networks. Here we address the human development of long-range connectivity in primary visual and motor cortices, using well-established behavioral measures - a Contour Integration test and a Finger-tapping task - that have been shown to be related to these specific primary areas, and the long-range neural connectivity within those. Possible confounding factors, such as different task requirements (complexity, cognitive load) are eliminated by using these tasks in a learning paradigm. We find that there is a temporal lag between the developmental timing of primary sensory vs. motor areas with an advantage of visual development; we also confirm that human development is very slow in both cases, and that there is a retained capacity for practice induced plastic changes in adults. This pattern of results seems to point to human-specific development of the “canonical circuits” of primary sensory and motor cortices, probably reflecting the ecological requirements of human life

Neural Correlates of Ongoing Conscious Experience: Both Task-Unrelatedness and Stimulus-Independence Are Related to Default Network Activity

The default mode network (DMN) is a set of brain regions that consistently shows higher activity at rest compared to tasks requiring sustained focused attention toward externally presented stimuli. The cognitive processes that the DMN possibly underlies remain a matter of debate. It has alternately been proposed that DMN activity reflects unfocused attention toward external stimuli or the occurrence of internally generated thoughts. The present study aimed at clarifying this issue by investigating the neural correlates of the various kinds of conscious experiences that can occur during task performance. Four classes of conscious experiences (i.e., being fully focused on the task, distractions by irrelevant sensations/perceptions, interfering thoughts related to the appraisal of the task, and mind-wandering) that varied along two dimensions (“task-relatedness” and “stimulus-dependency”) were sampled using thought-probes while the participants performed a go/no-go task. Analyses performed on the intervals preceding each probe according to the reported subjective experience revealed that both dimensions are relevant to explain activity in several regions of the DMN, namely the medial prefrontal cortex, posterior cingulate cortex/precuneus, and posterior inferior parietal lobe. Notably, an additive effect of the two dimensions was demonstrated for midline DMN regions. On the other hand, lateral temporal regions (also part of the DMN) were specifically related to stimulus-independent reports. These results suggest that midline DMN regions underlie cognitive processes that are active during both internal thoughts and external unfocused attention. They also strengthen the view that the DMN can be fractionated into different subcomponents and reveal the necessity to consider both the stimulus-dependent and the task-related dimensions of conscious experiences when studying the possible functional roles of the DMN

Histone acetylation controls the inactive X chromosome replication dynamics

In mammals, dosage compensation between male and female cells is achieved by inactivating one female X chromosome (Xi). Late replication of Xi was proposed to be involved in the maintenance of its silenced state. Here, we show a highly synchronous replication of the Xi within 1 to 2 h during early-mid S-phase by following DNA replication in living mammalian cells with green fluorescent protein-tagged replication proteins. The Xi was replicated before or concomitant with perinuclear or perinucleolar facultative heterochromatin and before constitutive heterochromatin. Ectopic expression of the X-inactive-specific transcript (Xist) gene from an autosome imposed the same synchronous replication pattern. We used mutations and chemical inhibition affecting different epigenetic marks as well as inducible Xist expression and we demonstrate that histone hypoacetylation has a key role in controlling Xi replication. The epigenetically controlled, highly coordinated replication of the Xi is reminiscent of embryonic genome replication in flies and frogs before genome activation and might be a common feature of transcriptionally silent chromatin