Measuring acute effects of subanesthetic ketamine on cerebrovascular hemodynamics in humans using TD-fNIRS.

Quantifying neural activity in natural conditions (i.e. conditions comparable to the standard clinical patient experience) during the administration of psychedelics may further our scientific understanding of the effects and mechanisms of action. This data may facilitate the discovery of novel biomarkers enabling more personalized treatments and improved patient outcomes. In this single-blind, placebo-controlled study with a non-randomized design, we use time-domain functional near-infrared spectroscopy (TD-fNIRS) to measure acute brain dynamics after intramuscular subanesthetic ketamine (0.75 mg/kg) and placebo (saline) administration in healthy participants (n = 15, 8 females, 7 males, age 32.4 ± 7.5 years) in a clinical setting. We found that the ketamine administration caused an altered state of consciousness and changes in systemic physiology (e.g. increase in pulse rate and electrodermal activity). Furthermore, ketamine led to a brain-wide reduction in the fractional amplitude of low frequency fluctuations, and a decrease in the global brain connectivity of the prefrontal region. Lastly, we provide preliminary evidence that a combination of neural and physiological metrics may serve as predictors of subjective mystical experiences and reductions in depressive symptomatology. Overall, our study demonstrated the successful application of fNIRS neuroimaging to study the physiological effects of the psychoactive substance ketamine in humans, and can be regarded as an important step toward larger scale clinical fNIRS studies that can quantify the impact of psychedelics on the brain in standard clinical settings.

A Data-Driven Approach to Classifying Daily Continuous Glucose Monitoring (CGM) Time Series.

According to the World Health Organization, about 422 million people worldwide have type 1 or type 2 diabetes (T1D, T2D), with the latter accounting for 90-95% of cases. Safe and effective treatment of patients with diabetes requires accurate and frequent monitoring of their blood sugar levels. Continuous glucose monitoring (CGM) is a monitoring technology developed to address this need, and its use among U.S. T1D patients has increased from 6% in 2011 to 38% in 2018 and continues to increase worldwide in both T1D and T2D. This paper presents a data-driven approach to determine Ω, a finite set of representative daily profiles (motifs) such that almost any daily CGM profile generated by a patient can be matched to one of the motifs in Ω. The training data set (9741 profiles) was used to identify 8 candidate sets of motifs, while the validation data set (14 175 profiles) was used to select the final set Ω. The robustness of Ω was established by using it to successfully classify (match against a representative daily profile in Ω) 99.0% of 42 595 daily CGM profiles in the testing data set. All data sets contained daily CGM profiles from six studies involving T1D and T2D patients using a variety of treatment modes, including daily insulin injections, insulin pumps, or artificial pancreas (AP). The classified profiles can be used in predictive modeling, decision support, and automated control systems (e.g., AP).

Solvent-Solvent Correlations across Graphene: The Effect of Image Charges.

Wetting experiments show pure graphene to be weakly hydrophilic, but its contact angle (CA) also reflects the character of the supporting material. Measurements and molecular dynamics simulations on suspended and supported graphene often reveal a CA reduction due to the presence of the supporting substrate. A similar reduction is consistently observed when graphene is wetted from both sides. The effect has been attributed to transparency to molecular interactions across the graphene sheet; however, the possibility of substrate-induced graphene polarization has also been considered. Computer simulations of CA on graphene have so far been determined by ignoring the material's conducting properties. We improve the graphene model by incorporating its conductivity according to the constant applied potential molecular dynamics. Using this method, we compare the wettabilities of suspended graphene and graphene supported by water by measuring the CA of cylindrical water drops on the sheets. The inclusion of graphene conductivity and concomitant polarization effects leads to a lower CA on suspended graphene, but the CA reduction is significantly bigger when the sheets are also wetted from the opposite side. The stronger adhesion is accompanied by a profound change in the correlations among water molecules across the sheet. While partial charges on water molecules interacting across an insulator sheet attract charges of the opposite sign, apparent attraction among like charges is manifested across the conducting graphene. The change is associated with graphene polarization, as the image charges inside the conductor attract equally signed partial charges of water molecules on both sides of the sheet. Additionally, using a nonpolar liquid (diiodomethane), we affirm a detectable wetting translucency when liquid-liquid forces are dominated by dispersive interactions. Our findings are important for predictive modeling toward a variety of applications including sensors, fuel cell membranes, water filtration, and graphene-based electrode materials in high-performance supercapacitors.

Anisotropic structure and dynamics of water under static electric fields.

We study the structure and dynamics of water subject to a range of static external electric fields, using molecular dynamics simulations. In particular, we monitor the changes in hydrogen bond kinetics, reorientation dynamics, and translational motions of water molecules. We find that water molecules translate and rotate slower in electric fields because the tendency to reinstate the aligned orientation reduces the probability of finding a new hydrogen bond partner and hence increases the probability of reforming already ruptured bonds. Furthermore, dipolar alignment of water molecules with the field results in structural and dynamic anisotropies even though the angularly averaged metrics indicate only minor structural changes. Through comparison of selected nonpolarizable and polarizable water models, we find that the electric field effects are stronger in polarizable water models, where field-enhanced dipole moments and thus more stable hydrogen bonds lead to slower switching of hydrogen bond partners and reduced translational mobility, compared to a nonpolarizable water model.

BioMiCo: a supervised Bayesian model for inference of microbial community structure.

BACKGROUND: Microbiome samples often represent mixtures of communities, where each community is composed of overlapping assemblages of species. Such mixtures are complex, the number of species is huge and abundance information for many species is often sparse. Classical methods have a limited value for identifying complex features within such data. RESULTS: Here, we describe a novel hierarchical model for Bayesian inference of microbial communities (BioMiCo). The model takes abundance data derived from environmental DNA, and models the composition of each sample by a two-level hierarchy of mixture distributions constrained by Dirichlet priors. BioMiCo is supervised, using known features for samples and appropriate prior constraints to overcome the challenges posed by many variables, sparse data, and large numbers of rare species. The model is trained on a portion of the data, where it learns how assemblages of species are mixed to form communities and how assemblages are related to the known features of each sample. Training yields a model that can predict the features of new samples. We used BioMiCo to build models for three serially sampled datasets and tested their predictive accuracy across different time points. The first model was trained to predict both body site (hand, mouth, and gut) and individual human host. It was able to reliably distinguish these features across different time points. The second was trained on vaginal microbiomes to predict both the Nugent score and individual human host. We found that women having normal and elevated Nugent scores had distinct microbiome structures that persisted over time, with additional structure within women having elevated scores. The third was trained for the purpose of assessing seasonal transitions in a coastal bacterial community. Application of this model to a high-resolution time series permitted us to track the rate and time of community succession and accurately predict known ecosystem-level events. CONCLUSION: BioMiCo provides a framework for learning the structure of microbial communities and for making predictions based on microbial assemblages. By training on carefully chosen features (abiotic or biotic), BioMiCo can be used to understand and predict transitions between complex communities composed of hundreds of microbial species.

BiomeNet: a Bayesian model for inference of metabolic divergence among microbial communities.

Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function. Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework. Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic subnetworks among microbial communities. To infer the structure of community-level metabolic interactions, BiomeNet applies a mixed-membership modelling framework to enzyme abundance information. The basic idea is that the mixture components of the model (metabolic reactions, subnetworks, and networks) are shared across all groups (microbiome samples), but the mixture proportions vary from group to group. Through this framework, the model can capture nested structures within the data. BiomeNet is unique in modeling each metagenome sample as a mixture of complex metabolic systems (metabosystems). The metabosystems are composed of mixtures of tightly connected metabolic subnetworks. BiomeNet differs from other unsupervised methods by allowing researchers to discriminate groups of samples through the metabolic patterns it discovers in the data, and by providing a framework for interpreting them. We describe a collapsed Gibbs sampler for inference of the mixture weights under BiomeNet, and we use simulation to validate the inference algorithm. Application of BiomeNet to human gut metagenomes revealed a metabosystem with greater prevalence among inflammatory bowel disease (IBD) patients. Based on the discriminatory subnetworks for this metabosystem, we inferred that the community is likely to be closely associated with the human gut epithelium, resistant to dietary interventions, and interfere with human uptake of an antioxidant connected to IBD. Because this metabosystem has a greater capacity to exploit host-associated glycans, we speculate that IBD-associated communities might arise from opportunist growth of bacteria that can circumvent the host's nutrient-based mechanism for bacterial partner selection.