A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

Building Risk Prediction Models for Type 2 Diabetes Using Machine Learning Techniques

Introduction

As one of the most prevalent chronic diseases in the United States, diabetes, especially type 2 diabetes, affects the health of millions of people and puts an enormous financial burden on the US economy. We aimed to develop predictive models to identify risk factors for type 2 diabetes, which could help facilitate early diagnosis and intervention and also reduce medical costs.

Methods

We analyzed cross-sectional data on 138,146 participants, including 20,467 with type 2 diabetes, from the 2014 Behavioral Risk Factor Surveillance System. We built several machine learning models for predicting type 2 diabetes, including support vector machine, decision tree, logistic regression, random forest, neural network, and Gaussian Naive Bayes classifiers. We used univariable and multivariable weighted logistic regression models to investigate the associations of potential risk factors with type 2 diabetes.

Results

All predictive models for type 2 diabetes achieved a high area under the curve (AUC), ranging from 0.7182 to 0.7949. Although the neural network model had the highest accuracy (82.4%), specificity (90.2%), and AUC (0.7949), the decision tree model had the highest sensitivity (51.6%) for type 2 diabetes. We found that people who slept 9 or more hours per day (adjusted odds ratio [aOR] = 1.13, 95% confidence interval [CI], 1.03–1.25) or had checkup frequency of less than 1 year (aOR = 2.31, 95% CI, 1.86–2.85) had higher risk for type 2 diabetes.

Conclusion

Of the 8 predictive models, the neural network model gave the best model performance with the highest AUC value; however, the decision tree model is preferred for initial screening for type 2 diabetes because it had the highest sensitivity and, therefore, detection rate. We confirmed previously reported risk factors and also identified sleeping time and frequency of checkup as 2 new potential risk factors related to type 2 diabetes.

[INFLUENCE OF CHRONIC IMMOBILIZATION STRESS DURING PREGNANCY ON MORPHOFUNCTIONAL STATE OF THE LIVER IN FEMALE RATS DURING POSTPARTUM PERIOD]

Morphofunctional state of the liver (in particular, indexes of carbohydrate, protein, and fat metabolism, structural elements and condition of vascular endothelium of the liver) in female rats subjected to immobilization stress during pregnancy, has been studied. Morphological changes in the liver include discomplexation of beam-radial structure, pyknosis of hepatocyte nucleus, increased regeneration activity of parenchyma, and increased stromal parenchymal index. Functional disorders are manifested by development of dysproteinemia, hyperlipidemia, hyperglycemia, and increased activity of organo-specific liver enzymes. It testifies to risk of fibrosis and diffuse nodular cirrhosis development in the animals, as well as diabetes mellitus of type II in the future.

[THE INFLUENCE OF UNBALANCED NUTRITION OF PREGNANT RATS ON THE CONTENT OF BIOGENIC ELEMENTS IN THE ENAMEL AND BLOOD SERUM OF THEIR OFFSPRING]

Malnutrition of pregnant women can slow down dental tissue development in offspring, cause growth of tooth decay and other disruptions, associated with changes amount of biogenic elements (BE), which are received into child in the womb body. The aim of this study-determination of the BE in the enamel and blood serum of mother rats, who had unbalanced nutrition with excess or lack of nutrients during the pregnancy. The content of Ca, Mg, Cu, Fe, P and Zn was studied in 129 species 1- and 2-month offspring. Reduction of BE in the enamel and blood serum mote often exist and more raised in pups, whose prenatal development took place under a shortage of nutrients. The direction of content changes of BE in pups and their degree of intensity are not identical in the enamel and blood serum. Certain pattern was identified between the content in the enamel and blood serum only two elements- Ca (direct correlation) and Fe (negative correlation). Irregularities of BE imbalance in the enamel during mothers' unbalanced nutrition at the time of pregnancy threaten by negative effects in terms of growth various pathological conditions and diseases of dentition apparatus their offspring in later life.

An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics

Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome. By extending the PeptideClassifier concept of unambiguous peptides for prokaryotes, close to 95% of the identifiable peptides imply one distinct protein, largely simplifying downstream analysis. Searching a comprehensive Bartonella henselae proteomics data set against such an iPtgxDB allowed us to unambiguously identify novel ORFs uniquely predicted by each resource, including lipoproteins, differentially expressed and membrane-localized proteins, novel start sites and wrongly annotated pseudogenes. Most novelties were confirmed by targeted, parallel reaction monitoring mass spectrometry, including unique ORFs and single amino acid variations (SAAVs) identified in a re-sequenced laboratory strain that are not present in its reference genome. We demonstrate the general applicability of our strategy for genomes with varying GC content and distinct taxonomic origin. We release iPtgxDBs for B. henselae, Bradyrhizobium diazoefficiens and Escherichia coli and the software to generate both proteogenomics search databases and integrated annotation files that can be viewed in a genome browser for any prokaryote.

Fourier-transform spectroscopy and potential construction of the (2)(1)Π state in KCs

The paper presents an empirical pointwise potential energy curve (PEC) of the (2)(1)Π state of the KCs molecule constructed by applying the Inverted Perturbation Approach routine. The experimental term values in the energy range E(v', J') ∈ [15 407; 16 579] cm(-1) involved in the fit were based on Fourier-Transform spectroscopy data obtained with 0.01 cm(-1) accuracy from the laser-induced (2)(1)Π → X(1)Σ(+) fluorescence spectra. Buffer gas Ar was used to facilitate the appearance of rotation relaxation lines in the spectra, thus enlarging the (2)(1)Π data set and allowing determination of the Λ-splitting constants. The data set included vibrational v' ∈ [0, 28] and rotational J' ∈ [7, 274] quantum numbers covering about 67% of the potential well. The present PEC reproduces the overall set of data included in the fit with a standard deviation of 0.5 cm(-1). The obtained value of the Λ-doubling constant q = + 1.8 × 10(-6) cm(-1) for J' > 50 and v' ∈ [0, 6] is in an excellent agreement with q = + 1.84 × 10(-6) cm(-1) reported in Kim, Lee, and Stolyarov [J. Mol. Spectrosc. 256, 57-67 (2009)].

edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology

The edgeR package, an R-based tool within the Bioconductor project, offers a flexible statistical framework for detection of changes in abundance based on counts. In this chapter, we illustrate the use of edgeR on a human embryonic stem cell dataset, in particular for RNA-seq and ChIP-seq data. We focus on a step-by-step statistical analysis of differential expression, going from raw data to a list of putative differentially expressed genes and give examples of integrative analysis using the ChIP-seq data. We emphasize data quality spot checks and the use of positive controls throughout the process and give practical recommendations for reproducible research.

Fourier-transform spectroscopy of (4)1Σ+ → A1Σ+ - b3Π, A1Σ+ - b3Π → X1Σ+, and (1)3Δ1→b3Π(0±) transitions in KCs and deperturbation treatment of A1Σ+ and b3Π states

High resolution Fourier-transform spectroscopy data of term values in the spin-orbit (SO) coupled first excited A(1)Σ(+) and b(3)Π states in KCs were obtained from (4)(1)Σ(+) → A(1)Σ(+) - b(3)Π, A(1)Σ(+) - b(3)Π → X(1)Σ(+), and (1)(3)Δ1→b(3)Π(0(±)) spectra of laser-induced fluorescence (LIF). About 3000 new rovibronic term values of the A(1)Σ(+) and b(3)Π(Ω) states were obtained with an uncertainty about 0.01 cm(-1) and added to the previously obtained 3439 term values in Kruzins et al. [Phys. Rev. A 81, 042509 (2010)] and 30 term values of the b(3)Π(0(+)) state levels below the A(1)Σ(+) state in Tamanis et al. [Phys. Rev. A 82, 032506 (2010)]. The data field was extended considerably, going down to vibrational level v(b) = 0 and up in energy to 13,814 cm(-1), as compared to previously achieved v(b) = 14 and E = 13,250 cm(-1). Overall 6431 e-symmetry term values of (39)K(133)Cs were included in 4 × 4 coupled-channel deperturbation analysis. The analytical Morse-Long-Range (MLR) function yielded empirical diabatic potentials for the A(1)Σ(+) and b(3)Π(0(+)) states while the morphing of the SO ab initio points [J. T. Kim et al., J. Mol. Spectrosc. 256, 57 (2009)] provided the empirical diagonal and off-diagonal SO functions. Overall 98.5% of the fitted term values were reproduced with a rms (root mean square) uncertainty of 0.004 cm(-1). The reliability of the model is proved by a good agreement of predicted and measured term values of the (41)K(133)Cs isotopologue, as well as of measured and calculated intensities of (4)(1)Σ(+) → A(1)Σ(+) - b(3)Π LIF progressions. Direct-potential-fit of low-lying v(b) levels of the b(3)Π(0(-)) component yielded the MLR potential which represents the 204 f-symmetry experimental term values with a rms uncertainty of 0.002 cm(-1). The Ω-doubling of the b(3)Π0 sub-state demonstrates a pronounced vb-dependent increase.

Fourier-transform spectroscopy and description of low-lying energy levels in the B(1)(1)Π state of RbCs

The Fourier transform spectrometer with resolution of 0.03 cm(-1) was applied to disperse the diode laser induced B(1)(1)Π → X(1)Σ(+) fluorescence spectra of the RbCs molecule in a heat pipe. The presence of buffer gas (Ar) produced in the spectra the dense pattern of collision-induced rotation relaxation lines, thus enlarging the B(1)(1)Π data set, allowing to determine the Λ-splitting constants and to reveal numerous local perturbations. In total, 2664 term values for (85)Rb(133)Cs and (87)Rb(133)Cs in the energy range from 13,770 to 15,200 cm(-1) were obtained with accuracy about 0.01 cm(-1). A pointwise potential energy curve (PEC) based on inverted perturbation approach was constructed in the R-range from 3.35 to 9.00 Å for less perturbed vibrational levels v' ε [0, 35] and compared with ab initio calculations. The data included in the fit were reproduced by present PEC with standard deviation (sd) 0.95 cm(-1). More systematic over rotational levels J(') ε [6, 228] data set was obtained for v' ε [0, 2]. These data were reproduced by the obtained PEC with sd of 0.08 cm(-1). The energy of PEC's minimum Te = 13,746.65 cm(-1), as well as other main molecular constants were determined.

B1(1)Π state of KCs: high-resolution spectroscopy and description of low-lying energy levels

The diode laser induced B(1)(1)Π → X(1)Σ(+) fluorescence spectra of the KCs molecule were recorded by Fourier-transform spectrometer with resolution of 0.03 cm(-1). Buffer gas Ar was used to facilitate appearance of rotation relaxation lines in the spectra, thus enlarging the B(1)(1)Π dataset, allowing one to determine the Λ-splitting constants and to reveal numerous local perturbations. A dataset was systematically obtained for B(1)(1)Π vibrational levels ν(') ∈ [0; 5] nonuniformly covering rotational levels with J(') ∈ [7; 233]. For ν(') ∈ [0; 3], the less-perturbed data of f-components were included in the fit. A pointwise potential energy curve (PEC) based on the inverted perturbation approach, as well as the Dunham coefficients, was obtained and compared with ab initio calculations; in particular, the energy of the PEC's minimum T(e) = 14,044.918(6) cm(-1) was determined. Both approaches allowed us to reproduce the vast majority of data used in the fit with accuracy of 0.02 cm(-1). Tentative molecular constants for several vibrational levels of the near lying C(3)(1)Σ(+) state were estimated.

Experimental and theoretical studies of Λ doublings and permanent electric dipoles in the low-lying Π1 states of NaCs

We present experimental data on the electric permanent dipole moments d(v',J') and lambda splittings (q factors) in the quasidegenerate (3) 1pi(e/f) state of the NaCs molecule over a wide range of the vibrational (v') and rotational (J') quantum numbers by using the combination of dc Stark mixing and electric radio frequency-optical double resonance methods. Within the experimental (3) 1pi state v' ranged from v' = 0 to 34, q values exhibited a pronounced decrease from 7.91x10(-6) to 0.47x10(-6) cm(-1), while absolute value(d) values varied between 8.0 and 5.0 D. Experimental evaluation yielded small d values about 1 D for D2 1pi state v' < 3 levels. The experiment is supported by ab initio electronic structure calculations performed for the (1-3) 1pi states of NaCs by means of the many-body multipartitioning perturbation theory of potential energy curves, permanent dipole, and angular coupling matrix elements for the lowest singlet states. The predicted d values reproduce their experimental counterparts within the measurement errors while theoretical q factors reproduce the measured v' dependence being, however, systematically overestimated by ca. 1x10(-6) cm(-1). The present NaCs data are compared with those of the NaK and NaRb molecules.

Photoassociative production and trapping of ultracold KRb molecules

We have produced ultracold heteronuclear KRb molecules by the process of photoassociation in a two-species magneto-optical trap. Following decay of the photoassociated KRb*, the molecules are detected using two-photon ionization and time-of-flight mass spectroscopy of KRb+. A portion of the metastable triplet molecules thus formed are magnetically trapped. Photoassociative spectra down to 91 cm(-1) below the K(4s)+Rb(5p(1/2)) asymptote have been obtained. We have made assignments to all eight of the attractive Hund's case (c) KRb* potential curves in this spectral region.

The adaptive imbalance in base excision-repair enzymes generates microsatellite instability in chronic inflammation

Chronic infection and associated inflammation are key contributors to human carcinogenesis. Ulcerative colitis (UC) is an oxyradical overload disease and is characterized by free radical stress and colon cancer proneness. Here we examined tissues from noncancerous colons of ulcerative colitis patients to determine (a) the activity of two base excision-repair enzymes, AAG, the major 3-methyladenine DNA glycosylase, and APE1, the major apurinic site endonuclease; and (b) the prevalence of microsatellite instability (MSI). AAG and APE1 were significantly increased in UC colon epithelium undergoing elevated inflammation and MSI was positively correlated with their imbalanced enzymatic activities. These latter results were supported by mechanistic studies using yeast and human cell models in which overexpression of AAG and/or APE1 was associated with frameshift mutations and MSI. Our results are consistent with the hypothesis that the adaptive and imbalanced increase in AAG and APE1 is a novel mechanism contributing to MSI in patients with UC and may extend to chronic inflammatory or other diseases with MSI of unknown etiology.

The adaptive imbalance in base excision-repair enzymes generates microsatellite instability in chronic inflammation

Chronic infection and associated inflammation are key contributors to human carcinogenesis. Ulcerative colitis (UC) is an oxyradical overload disease and is characterized by free radical stress and colon cancer proneness. Here we examined tissues from noncancerous colons of ulcerative colitis patients to determine (a) the activity of two base excision-repair enzymes, AAG, the major 3-methyladenine DNA glycosylase, and APE1, the major apurinic site endonuclease; and (b) the prevalence of microsatellite instability (MSI). AAG and APE1 were significantly increased in UC colon epithelium undergoing elevated inflammation and MSI was positively correlated with their imbalanced enzymatic activities. These latter results were supported by mechanistic studies using yeast and human cell models in which overexpression of AAG and/or APE1 was associated with frameshift mutations and MSI. Our results are consistent with the hypothesis that the adaptive and imbalanced increase in AAG and APE1 is a novel mechanism contributing to MSI in patients with UC and may extend to chronic inflammatory or other diseases with MSI of unknown etiology.