Assessing and Interpreting the Within-Body Biogeography of Human Microbiome Diversity

A human body hosts a relatively independent microbiome including five major regional biomes (i.e., airway, oral, gut, skin, and urogenital). Each of them may possess different regional characteristics with important implications to our health and diseases (i.e., so-termed microbiome associated diseases). Nevertheless, these regional microbiomes are connected with each other through diffusions and migrations. Here, we investigate the within-body (intra-individual) distribution feature of microbiome diversity via diversity area relationship (DAR) modeling, which, to the best of our knowledge, has not been systematically studied previously. We utilized the Hill numbers for measuring alpha and beta-diversities and built 1,200 within-body DAR models with to date the most comprehensive human microbiome datasets of 18 sites from the human microbiome project (HMP) cohort. We established the intra-DAR profile (z-q pattern: the diversity scaling parameter z of the power law (PL) at diversity order q = 0–3), intra-PDO (pair-wise diversity overlap) profile (g-q), and intra-MAD (maximal accrual diversity) profile (Dmax-q) for the within-body biogeography of the human microbiome. These profiles constitute the “maps” of the within-body biogeography, and offer important insights on the within-body distribution of the human microbiome. Furthermore, we investigated the heterogeneity among individuals in their biogeography parameters and found that there is not an “average Joe” that can represent majority of individuals in a cohort or population. For example, we found that most individuals in the HMP cohort have relatively lower maximal accrual diversity (MAD) or in the “long tail” of the so-termed power law distribution. In the meantime, there are a small number of individuals in the cohort who possess disproportionally higher MAD values. These findings may have important implications for personalized medicine of the human microbiome associated diseases in practice, besides their theoretical significance in microbiome research such as establishing the baseline for the conservation of human microbiome

Semen Microbiome Biogeography: An Analysis Based on a Chinese Population Study

Investigating inter-subject heterogeneity (or spatial distribution) of human semen microbiome diversity is of important significance. Theoretically, the spatial distribution of biodiversity constitutes the core of microbiome biogeography. Practically, the inter-subject heterogeneity is crucial for understanding the normal (healthy) flora of semen microbiotas as well as their possible changes associated with abnormal fertility. In this article, we analyze the scaling (changes) of semen microbiome diversity across individuals with DAR (diversity-area relationship) analysis, a recent extension to classic SAR (species-area relationship) law in biogeography and ecology. Specifically, the unit of “area” is individual subject, and the microbial diversity in seminal fluid of an individual (area) is assessed via metagenomic DNA sequencing technique and measured in the Hill numbers. The DAR models were then fitted to the accrued diversity across different number of individuals (area size). We further tested the difference in DAR parameters among the healthy, subnormal, and abnormal microbiome samples in terms of their fertility status based on a cross-sectional study of a Chinese cohort. Given that no statistically significant differences in the DAR parameters were detected among the three groups, we built unified DAR models for semen microbiome by combining the healthy, subnormal, and abnormal groups. The model parameters were used to (i) estimate the microbiome diversity scaling in a population (cohort), and construct the so-termed DAR profile; (ii) predict/construct the maximal accrual diversity (MAD) profile in a population; (iii) estimate the pair-wise diversity overlap (PDO) between two individuals and construct the PDO profile; (iv) assess the ratio of individual diversity to population (RIP) accrual diversity. The last item (RIP) is a new concept we propose in this study, which is essentially a ratio of local diversity to regional or global diversity (LRD/LGD), applicable to general biodiversity investigation beyond human microbiome

The Optimized Transport Scheme of Empty and Heavy Containers with Novel Genetic Algorithm

To design the transport scheme of empty and heavy containers reasonably, a model with objective maximizing the route benefits is proposed. The model considered two factors: (1) the fluctuation of cargo transport demand and the switching of different voyages; (2) the optimal transport scheme of empty and heavy containers in slack and brisk seasons and the handover process of these two seasons. In order to solve this model, a novel GA is developed. With this model and algorithm, the optimal transport scheme of empty and heavy containers is put forward, and the optimization allocation of resources can be realized. The case study about China-Europe route proves that this model can improve the liner company's benefits effectively

Emissive Platinum(II) Cages with Reverse Fluorescence Resonance Energy Transfer for Multiple Sensing

It is quite challenging to realize fluorescence resonance energy transfer (FRET) between two chromophores with specific positions and directions. Herein, through the self-assembly of two carefully selected fluorescent ligands via metal-coordination interactions, we prepared two tetragonal prismatic platinum(II) cages with a reverse FRET process between their faces and pillars. Bearing different responses to external stimuli, these two emissive ligands are able to tune the FRET process, thus making the cages sensitive to solvents, pressure, and temperature. First, these cages could distinguish structurally similar alcohols such as n-butanol, t-butanol, and i-butanol. Furthermore, they showed decreased emission with bathochromic shifts under high pressure. Finally, they exhibited a remarkable ratiometric response to temperature over a wide range (223–353 K) with high sensitivity. For example, by plotting the ratio of the maximum emission (I600/I480) of metallacage 4b against the temperature, the slope reaches 0.072, which is among the highest values for ratiometric fluorescent thermometers reported so far. This work not only offers a strategy to manipulate the FRET efficiency in emissive supramolecular coordination complexes but also paves the way for the future design and preparation of smart emissive materials with external stimuli responsiveness

Quantifying the human vaginal community state types (CSTs) with the species specificity index

The five community state types (CSTs) first identified by Ravel et al. (2011) offered a powerful scheme to classify the states of human vaginal microbial communities (HVMC). The classification is a significant advance because it devised an effective handle to deal with the enormous inter-subject heterogeneity and/or intra-subject temporal variability, the quantification of which is extremely difficult but of critical importance such as the understanding of BV (bacterial vaginosis) etiology. Indeed, arguably the most plausible ecological hypothesis for interpreting the BV etiology heavily depends on the CST classification (Gajer et al., 2012; Ma, Forney & Ravel, 2012; Ravel et al., 2011). Nevertheless, the current form of CSTs is still qualitative and lacks a quantitative criterion to determine the CSTs. In this article, we develop a quantitative tool that can reliably distinguish the CSTs by applying the species specificity of Mariadassou, Pichon & Ebert (2015) and the specificity aggregation index (SAI) we propose in this study. The new tool accurately characterized the classifications of the five CSTs with both 400-crosssectional cohort (Ravel et al., 2011) and 32-longitudinal cohort (Gajer et al., 2012) studies originally utilized to develop the CST scheme. Furthermore, it offers a mechanistic interpretation of the original CST scheme by invoking the paradigm of specificity continuum for species adaptation and distribution. The advances we made may not only facilitate the accurate applications of the CST scheme, but also offer hints towards an effective tool for microbiome typing such as classifying gut enterotypes

Data_Sheet_1_Semen Microbiome Biogeography: An Analysis Based on a Chinese Population Study.PDF

Investigating inter-subject heterogeneity (or spatial distribution) of human semen microbiome diversity is of important significance. Theoretically, the spatial distribution of biodiversity constitutes the core of microbiome biogeography. Practically, the inter-subject heterogeneity is crucial for understanding the normal (healthy) flora of semen microbiotas as well as their possible changes associated with abnormal fertility. In this article, we analyze the scaling (changes) of semen microbiome diversity across individuals with DAR (diversity-area relationship) analysis, a recent extension to classic SAR (species-area relationship) law in biogeography and ecology. Specifically, the unit of “area” is individual subject, and the microbial diversity in seminal fluid of an individual (area) is assessed via metagenomic DNA sequencing technique and measured in the Hill numbers. The DAR models were then fitted to the accrued diversity across different number of individuals (area size). We further tested the difference in DAR parameters among the healthy, subnormal, and abnormal microbiome samples in terms of their fertility status based on a cross-sectional study of a Chinese cohort. Given that no statistically significant differences in the DAR parameters were detected among the three groups, we built unified DAR models for semen microbiome by combining the healthy, subnormal, and abnormal groups. The model parameters were used to (i) estimate the microbiome diversity scaling in a population (cohort), and construct the so-termed DAR profile; (ii) predict/construct the maximal accrual diversity (MAD) profile in a population; (iii) estimate the pair-wise diversity overlap (PDO) between two individuals and construct the PDO profile; (iv) assess the ratio of individual diversity to population (RIP) accrual diversity. The last item (RIP) is a new concept we propose in this study, which is essentially a ratio of local diversity to regional or global diversity (LRD/LGD), applicable to general biodiversity investigation beyond human microbiome.</p

Adaptive fuzzy dynamic surface control for unknown time delay nonlinear systems preceded by unknown asymmetric hysteresis

In this paper, a fuzzy approximator based adaptive dynamic surface control scheme is proposed for a class of unknown time delay nonlinear systems preceded by asymmetric hysteresis nonlinearities. The features of the proposed method are: 1) by combining the approximated property of the fuzzy logic systems (FLSs) with the Finite Covering Lemma, the Krasovskii functionals are disposed of, achieving the L∞ norm of the tracking error by using the initializing technique; 2) the assumptions on the time-delay functions are removed due to the use of the Finite Covering Lemma and the FLSs; 3) the proposed adaptive fuzzy dynamic surface control scheme can also compensate the asymmetric shifted Prandtl Ishlinskii (ASPI) hysteresis without constructing the inverse of the ASPI model with the density function of ASPI model being unknown and estimated on-line to compensate the hysteresis. It is proved that all the signals in the closed-loop system are ultimately uniformly bounded and can be made arbitrarily small. Simulation results show the validity of the proposed method

Adaptive output-feedback inverse control for a class of time delay nonlinear hysteretic systems via fuzzy approximeter

In this paper, an fuzzy approximator based output feedback adaptive dynamic surface inverse control (DSIC) scheme is proposed for a class of time-delay systems preceded by unknown asymmetric hysteresis. The main advantages are as follows: 1) by combining the Finite Covering Lemma with fuzzy logic systems (FLSs), a novel time-delay function approx-imator is proposed with the benefits of the assumptions of the conservative upper bound functions on the time-delay functions are removed and the Krasovskii functionals are not required when deal with time delays. Also, the time delay functions extends to a more general one with states variables and time-delay variables being coupled; 2) by using the proposed initial technique, the Lnorm of the tracking error is obtained; 3) by constructing the inverse of the asymmetric hysteresis and approximating the unknown time-delay functions, both time delays and asymmetric hysteresis phenomena in the actuators are mitigated simultaneously when only the output of the system is available. It is proved that all the signals in the closed-loop systems are semi-globally ultimately uniformly bounded (SUUG). Simulation results show the validity of the proposed scheme