Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes

Background: Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to find novel carbapenemases and other resistance genes not yet described in clinical strains. Our aim was therefore to investigate the microbiota and antibiotic resistome of hospital effluent collected from the city of Mumbai, India, with a special focus on identifying novel carbapenemases. Results: Shotgun metagenomics revealed a total of 112 different mobile antibiotic resistance gene types, conferring resistance against almost all classes of antibiotics. Beta-lactamase genes, including encoding clinically important carbapenemases, such as NDM, VIM, IMP, KPC, and OXA-48, were abundant. NDM (0.9% relative abundance to 16S rRNA genes) was the most common carbapenemase gene, followed by OXA-58 (0.84% relative abundance to 16S rRNA genes). Among the investigated mobile genetic elements, class 1 integrons (11% relative abundance to 16S rRNA genes) were the most abundant. The genus Acinetobacter accounted for as many as 30% of the total 16S rRNA reads, with A. baumannii accounting for an estimated 2.5%. High throughput sequencing of amplified integron gene cassettes identified a novel functional variant of an IMP-type (proposed IMP-81) carbapenemase gene (eight aa substitutions) along with recently described novel resistance genes like sul4 and bla RSA1. Using a computational hidden Markov model, we detected 27 unique metallo-beta-lactamase (MBL) genes in the shotgun data, of which nine were novel subclass B1 genes, one novel subclass B2, and 10 novel subclass B3 genes. Six of the seven novel MBL genes were functional when expressed in Escherichia coli. Conclusion: By exploring hospital wastewater from India, our understanding of the diversity of carbapenemases has been extended. The study also demonstrates that the microbiota of hospital wastewater can serve as a reservoir of novel resistance genes, including previously uncharacterized carbapenemases with the potential to spread further

Deformed Quantum Cohomology and (0,2) Mirror Symmetry

We compute instanton corrections to correlators in the genus-zero topological subsector of a (0,2) supersymmetric gauged linear sigma model with target space P1xP1, whose left-moving fermions couple to a deformation of the tangent bundle. We then deduce the theory's chiral ring from these correlators, which reduces in the limit of zero deformation to the (2,2) ring. Finally, we compare our results with the computations carried out by Adams et al.[ABS04] and Katz and Sharpe[KS06]. We find immediate agreement with the latter and an interesting puzzle in completely matching the chiral ring of the former.Comment: AMSLatex, 30 pages, one eps figure. V4: typos corrected, final version appearing in JHE

F-theory on Genus-One Fibrations

We argue that M-theory compactified on an arbitrary genus-one fibration, that is, an elliptic fibration which need not have a section, always has an F-theory limit when the area of the genus-one fiber approaches zero. Such genus-one fibrations can be easily constructed as toric hypersurfaces, and various $SU(5)\times U(1)^n$ and $E_6$ models are presented as examples. To each genus-one fibration one can associate a $\tau$-function on the base as well as an $SL(2,\mathbb{Z})$ representation which together define the IIB axio-dilaton and 7-brane content of the theory. The set of genus-one fibrations with the same $\tau$-function and $SL(2,\mathbb{Z})$ representation, known as the Tate-Shafarevich group, supplies an important degree of freedom in the corresponding F-theory model which has not been studied carefully until now. Six-dimensional anomaly cancellation as well as Witten's zero-mode count on wrapped branes both imply corrections to the usual F-theory dictionary for some of these models. In particular, neutral hypermultiplets which are localized at codimension-two fibers can arise. (All previous known examples of localized hypermultiplets were charged under the gauge group of the theory.) Finally, in the absence of a section some novel monodromies of Kodaira fibers are allowed which lead to new breaking patterns of non-Abelian gauge groups.Comment: 53 pages, 9 figures, 6 tables. v2: references adde

Non-Perturbative Superpotentials in F-theory and String Duality

We use open-closed string duality between F-theory on K3xK3 and type II strings on CY manifolds without branes to study non-perturbative superpotentials in generalized flux compactifications. On the F-theory side we obtain the full flux potential including D3-instanton contributions and show that it leads to an explicit and simple realization of the three ingredients of the KKLT model for stringy dS vacua. The D3-instanton contribution is highly non-trivial, can be systematically computed including the determinant factors and demonstrates that a particular flux lifts very effectively zero modes on the instanton. On the closed string side, we propose a generalization of the Gukov-Vafa-Witten superpotential for type II strings on generalized CY manifolds, depending on all moduli multiplets.Comment: 49 pages, harvmac, 1 figure; references & figures adde

F-Theory and the Mordell-Weil Group of Elliptically-Fibered Calabi-Yau Threefolds

The Mordell-Weil group of an elliptically fibered Calabi-Yau threefold X contains information about the abelian sector of the six-dimensional theory obtained by compactifying F-theory on X. After examining features of the abelian anomaly coefficient matrix and U(1) charge quantization conditions of general F-theory vacua, we study Calabi-Yau threefolds with Mordell-Weil rank-one as a first step towards understanding the features of the Mordell-Weil group of threefolds in more detail. In particular, we generate an interesting class of F-theory models with U(1) gauge symmetry that have matter with both charges 1 and 2. The anomaly equations --- which relate the Neron-Tate height of a section to intersection numbers between the section and fibral rational curves of the manifold --- serve as an important tool in our analysis.Comment: 29 pages + appendices, 5 figures; v2: minor correction

Mortality in GOLD stages of COPD and its dependence on symptoms of chronic bronchitis

BACKGROUND: The GOLD classification of COPD severity introduces a stage 0 (at risk) comprising individuals with productive cough and normal lung function. The aims of this study were to investigate total mortality risks in GOLD stages 0–4 with special focus on stage 0, and furthermore to assess the influence of symptoms of chronic bronchitis on mortality risks in GOLD stages 1–4. METHOD: Between 1974 and 1992, a total of 22 044 middle-aged individuals participated in a health screening, which included a spirometry as well as recording of respiratory symptoms and smoking habits. Individuals with comorbidity at baseline (diabetes, stroke, cancer, angina pectoris, or heart infarction) were excluded from the analyses. Hazard ratios (HR 95% CI) of total mortality were analyzed in GOLD stages 0–4 with individuals with normal lung function and without symptoms of chronic bronchitis as a reference group. HR:s in smoking individuals with symptoms of chronic bronchitis within the stages 1–4 were calculated with individuals with the same GOLD stage but without symptoms of chronic bronchitis as reference. RESULTS: The number of deaths was 3674 for men and 832 for women based on 352 324 and 150 050 person-years respectively. The proportion of smokers among men was 50% and among women 40%. Self reported comorbidity was present in 4.6% of the men and 6.6% of the women. Among smoking men, Stage 0 was associated with an increased mortality risk, HR; 1.65 (1.32–2.08), of similar magnitude as in stage 2, HR; 1.41 (1.31–1.70). The hazard ratio in stage 0 was significantly higher than in stage 1 HR; 1.13 (0.98–1.29). Among male smokers with stage 1; HR: 2.04 (1.34–3.11), and among female smokers with stage 2 disease; HR: 3.16 (1.38–7.23), increased HR:s were found in individuals with symptoms of chronic bronchitis as compared to those without symptoms of chronic bronchitis. CONCLUSION: Symptoms fulfilling the definition of chronic bronchitis were associated with an increased mortality risk among male smokers with normal pulmonary function (stage 0) and also with an increased risk of death among smoking individuals with mild to moderate COPD (stage 1 and 2)

Anomaly Equations and Intersection Theory

Six-dimensional supergravity theories with N=(1,0) supersymmetry must satisfy anomaly equations. These equations come from demanding the cancellation of gravitational, gauge and mixed anomalies. The anomaly equations have implications for the geometrical data of Calabi-Yau threefolds, since F-theory compactified on an elliptically fibered Calabi-Yau threefold with a section generates a consistent six-dimensional N=(1,0) supergravity theory. In this paper, we show that the anomaly equations can be summarized by three intersection theory identities. In the process we also identify the geometric counterpart of the anomaly coefficients---in particular, those of the abelian gauge groups---that govern the low-energy dynamics of the theory. We discuss the results in the context of investigating string universality in six dimensions.Comment: 29 pages + appendices, 8 figures; v2: minor corrections, references added; v3: minor corrections, reference adde

Structure in 6D and 4D N=1 supergravity theories from F-theory

We explore some aspects of 4D supergravity theories and F-theory vacua that are parallel to structures in the space of 6D theories. The spectrum and topological terms in 4D supergravity theories correspond to topological data of F-theory geometry, just as in six dimensions. In particular, topological axion-curvature squared couplings appear in 4D theories; these couplings are characterized by vectors in the dual to the lattice of axion shift symmetries associated with string charges. These terms are analogous to the Green-Schwarz terms of 6D supergravity theories, though in 4D the terms are not generally linked with anomalies. We outline the correspondence between F-theory topology and data of the corresponding 4D supergravity theories. The correspondence of geometry with structure in the low-energy action illuminates topological aspects of heterotic-F-theory duality in 4D as well as in 6D. The existence of an F-theory realization also places geometrical constraints on the 4D supergravity theory in the large-volume limit.Comment: 63 page

Explicit de Sitter Flux Vacua for Global String Models with Chiral Matter

We address the open question of performing an explicit stabilisation of all closed string moduli (including dilaton, complex structure and Kaehler moduli) in fluxed type IIB Calabi-Yau compactifications with chiral matter. Using toric geometry we construct Calabi-Yau manifolds with del Pezzo singularities. D-branes located at such singularities can support the Standard Model gauge group and matter content. In order to control complex structure moduli stabilisation we consider Calabi-Yau manifolds which exhibit a discrete symmetry that reduces the effective number of complex structure moduli. We calculate the corresponding periods in the symplectic basis of invariant three-cycles and find explicit flux vacua for concrete examples. We compute the values of the flux superpotential and the string coupling at these vacua. Starting from these explicit complex structure solutions, we obtain AdS and dS minima where the Kaehler moduli are stabilised by a mixture of D-terms, non-perturbative and perturbative alpha'-corrections as in the LARGE Volume Scenario. In the considered example the visible sector lives at a dP_6 singularity which can be higgsed to the phenomenologically interesting class of models at the dP_3 singularity.Comment: 49 pages, 5 figures; v2: references adde

A Calabi-Yau Database: Threefolds Constructed from the Kreuzer-Skarke List

Kreuzer and Skarke famously produced the largest known database of Calabi-Yau threefolds by providing a complete construction of all 473,800,776 reflexive polyhedra that exist in four dimensions [1]. These polyhedra describe the singular limits of ambient toric varieties in which Calabi-Yau threefolds can exist as hypersurfaces. In this paper, we review how to extract topological and geometric information about Calabi-Yau threefolds using the toric construction, and we provide, in a companion online database (see http://​nuweb1.​neu.​edu/​cydatabase), a detailed inventory of these quantities which are of interest to physicists. Many of the singular ambient spaces described by the Kreuzer-Skarke list can be smoothed out into multiple distinct toric ambient spaces describing different Calabi-Yau threefolds. We provide a list of the different Calabi-Yau threefolds which can be obtained from each polytope, up to current computational limits. We then give the details of a variety of quantities associated to each of these Calabi-Yau such as Chern classes, intersection numbers, and the Kähler and Mori cones, in addition to the Hodge data. This data forms a useful starting point for a number of physical applications of the Kreuzer-Skarke list