Brian simulator

We propose and demonstrate a unified hierarchical method to measure n-point correlation functions that can be applied to driven, dissipative, or otherwise open or nonequilibrium quantum systems. In this method, the time evolution of the system is repeatedly interrupted by interacting an ancilla qubit with the system through a controlled operation, and measuring the ancilla immediately afterward. We discuss the robustness of this method as compared to other ancilla-based interferometric techniques (such as the Hadamard test), and highlight its advantages for near-term quantum simulations of open quantum systems...

Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD), yet strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we use simulations, a true IBD inference algorithm, and empirical data sets from different malaria transmission settings to investigate the extent of this bias and explore potential correction strategies. We analyze whole genome sequence data generated from 640 new and 3089 publicly available Plasmodium falciparum clinical isolates...

BACKGROUND: Identification of unsuspected nodal metastasis may occur at the time of operation for a stage I non-small cell lung cancer. Guidelines for this scenario are unclear. Our goal was to assess the cost-effectiveness of aborting the operation in an attempt to first provide neoadjuvant systemic therapy compared with upfront resection. METHODS: A computer simulation Markov model with a lifetime horizon was constructed to compare the costs and clinical outcomes, as measured by quality-adjusted life-years (QALYs), of upfront resection at the time of identification of unsuspected N2 mediastinal disease vs...

The 400 m and 1,500 m are track events that rely on different but important contributions from both the aerobic and anaerobic energy systems. The purpose of this study is to model men's and women's 400 m and 1,500 m championship performances to gain a deeper understanding of the key mechanical and physiological factors affecting running speed and bend running using high-resolution data from live competition (10 Hz). To investigate World-class athletes' instantaneous speeds, propulsive forces and aerobic and anaerobic energy, we model and simulate the performances of the men's and women's European Athletics 400 m champions, Matthew Hudson-Smith and Femke Bol, as well as the men's European Athletics 1,500 m champion, Jakob Ingebrigtsen, and the women's European Athletics U23 1,500 m champion, Gaia Sabbatini...

As ocean temperatures continue to rise, coral bleaching events around the globe are becoming stronger and more frequent. High-resolution temperature data is therefore critical for monitoring reef conditions to identify indicators of heat stress. Satellite and in situ measurements have historically been relied upon to study the thermal tolerances of coral reefs, but these data are quite limited in their spatial and temporal coverage. Ocean circulation models could provide an alternative or complement to these limited data, but a thorough evaluation against in situ measurements has yet to be conducted in any Pacific Islands region...

Adjusting for an unmeasured confounder is generally an intractable problem, but in the spatial setting it may be possible under certain conditions. We derive necessary conditions on the coherence between the exposure and the unmeasured confounder that ensure the effect of exposure is estimable. We specify our model and assumptions in the spectral domain to allow for different degrees of confounding at different spatial resolutions. One assumption that ensures identifiability is that confounding present at global scales dissipates at local scales...

Markerless motion capture has recently attracted significant interest in clinical gait analysis and human movement science. Its ease of use and potential to streamline motion capture recordings bear great potential for out-of-the-laboratory measurements in large cohorts. While previous studies have shown that markerless systems can achieve acceptable accuracy and reliability for kinematic parameters of gait, they also noted higher inter-trial variability of markerless data. Since increased inter-trial variability can have important implications for data post-processing and analysis, this study compared the inter-trial variability of simultaneously recorded markerless and marker-based data...

STATEMENT OF PROBLEM: New denture base acrylic resins have been introduced that are specifically formulated for microwave polymerization. Microwave polymerization is a time-efficient procedure, but few studies have evaluated how these new acrylic resin formulations compare with conventionally processed acrylic resins. PURPOSE: The purpose of this in vitro study was to compare the stiffness and strength of denture base acrylic resins formulated for microwave polymerization with conventionally processed acrylic resin...

BACKGROUND: Treatment variation from observational data has been used to estimate patient-specific treatment effects. Causal Forest Algorithms (CFAs) developed for this task have unknown properties when treatment effect heterogeneity from unmeasured patient factors influences treatment choice - essential heterogeneity. METHODS: We simulated eleven populations with identical treatment effect distributions based on patient factors. The populations varied in the extent that treatment effect heterogeneity influenced treatment choice...

As airborne methane surveys of oil and gas systems continue to discover large emissions that are missing from official estimates1-4 , the true scope of methane emissions from energy production has yet to be quantified. We integrate approximately one million aerial site measurements into regional emissions inventories for six regions in the USA, comprising 52% of onshore oil and 29% of gas production over 15 aerial campaigns. We construct complete emissions distributions for each, employing empirically grounded simulations to estimate small emissions...

G-protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by stimulating guanine nucleotide exchange in the Gα subunit1 . To visualize this mechanism, we developed a time-resolved cryo-EM approach that examines the progression of ensembles of pre-steady-state intermediates of a GPCR-G-protein complex. By monitoring the transitions of the stimulatory Gs protein in complex with the β2 -adrenergic receptor at short sequential time points after GTP addition, we identified the conformational trajectory underlying G-protein activation and functional dissociation from the receptor...

Avena sativa phototropin 1 light-oxygen-voltage 2 domain (AsLOV2) is a model protein of Per-Arnt-Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change begins with the unfolding of the N-terminal A'α helix in the dark state followed by the unfolding of the C-terminal Jα helix. The light state is characterized by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, β-sheets are identified as crucial components for mediating allosteric signal transmission between the two termini...

Gene fusions are found as cancer drivers in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential in cancer clinical diagnostics, prognostics, and for guiding therapeutic development. Most currently available methods for fusion transcript detection are compatible with Illumina RNA-seq involving highly accurate short read sequences. Recent advances in long read isoform sequencing enable the detection of fusion transcripts at unprecedented resolution in bulk and single cell samples...

Introduction: Several signaling pathways are activated during hypoxia to promote angiogenesis, leading to endothelial cell patterning, interaction, and downstream signaling. Understanding the mechanistic signaling differences between endothelial cells under normoxia and hypoxia and their response to different stimuli can guide therapies to modulate angiogenesis. We present a novel mechanistic model of interacting endothelial cells, including the main pathways involved in angiogenesis. Methods: We calibrate and fit the model parameters based on well-established modeling techniques that include structural and practical parameter identifiability, uncertainty quantification, and global sensitivity...

Species distribution models and maps from large-scale biodiversity data are necessary for conservation management. One current issue is that biodiversity data are prone to taxonomic misclassifications. Methods to account for these misclassifications in multi-species distribution models have assumed that the classification probabilities are constant throughout the study. In reality, classification probabilities are likely to vary with several covariates. Failure to account for such heterogeneity can lead to biased prediction of species distributions...

Certain animal species use the Earth's magnetic field (i.e., magnetoreception) alongside their other sensory modalities to navigate long distances that include continents and oceans. It is hypothesized that several animals use geomagnetic parameters, such as field intensity and inclination, to recognize specific locations or regions, potentially enabling migration without a pre-surveyed map. However, it is unknown how animals use geomagnetic information to generate guidance commands, or where in the world this type of strategy would maximize an animal's fitness...

Photovoltaic-coupled electrolysis (PV-E) and photoelectrochemical (PEC) water splitting are two options for storing solar energy as hydrogen. Understanding the requirements for achieving a positive energy balance over the lifetime of facilities using these technologies is important for ensuring sustainability. While neither technology has yet reached full commercialisation, they are also at very different technology readiness levels and scales of development. Here, we model the energy balance of standalone large-scale facilities to evaluate their energy return on energy invested (ERoEI) over time and energy payback time (EPBT)...

Protease-cleavable supramolecular oligopeptide nanofilaments are promising materials for targeted therapeutics and diagnostics. In these systems, single amino acid substitutions can have profound effects on the supramolecular structure and consequent proteolytic degradation, which are critical parameters for their intended applications. Herein, we describe changes to the self-assembly and proteolytic cleavage of iodine containing sequences for future translation into matrix metalloprotease (MMP-9)-activated supramolecular radio-imaging probes...

The performance of individual biomarkers in discriminating between two groups, typically the healthy and the diseased, may be limited. Thus, there is interest in developing statistical methodologies for biomarker combinations with the aim of improving upon the individual discriminatory performance. There is extensive literature referring to biomarker combinations under the two-class setting. However, the corresponding literature under a three-class setting is limited. In our study, we provide parametric and nonparametric methods that allow investigators to optimally combine biomarkers that seek to discriminate between three classes by minimizing the Euclidean distance from the receiver operating characteristic surface to the perfection corner...

Spiking neural network simulations are a central tool in Computational Neuroscience, Artificial Intelligence, and Neuromorphic Engineering research. A broad range of simulators and software frameworks for such simulations exist with different target application areas. Among these, PymoNNto is a recent Python-based toolbox for spiking neural network simulations that emphasizes the embedding of custom code in a modular and flexible way. While PymoNNto already supports GPU implementations, its backend relies on NumPy operations...