T-dualising the Deformed and Resolved Conifold

In a previous paper we used T-duality to construct a new type of 1/4-BPS solution describing a pair of NS5-branes intersecting in 1+3 dimensions and localised in all other directions except for a single transverse circle. This led to an explicit solution to a sourced Monge--Ampere equation, of which there are few known examples. In this paper we refine this formalism and apply it to two important generalisations: the resolved and deformed conifolds. In doing so we construct two new solutions describing, respectively, a pair of NS5-branes separated in a transverse direction and a pair of NS5-branes with smooth `diamond' profile. We show how the parameter of the resolved conifold (size of the S^2) maps to a transverse separation of the NS5-branes, while the modulus of the deformed conifold (size of the S^3) maps to the deformation parameter of the diamond web.Comment: 57 pages, 1 figure; v2: typos fixe

Plasmon excitations in homogeneous neutron star matter

We study the possible collective plasma modes which can affect neutron-star thermodynamics and different elementary processes in the baryonic density range between nuclear saturation ($\rho_0$) and $3\rho_0$. In this region, the expected constituents of neutron-star matter are mainly neutrons, protons, electrons and muons ($npe\mu$ matter), under the constraint of beta equilibrium. The elementary plasma excitations of the $pe\mu$ three-fluid medium are studied in the RPA framework. We emphasize the relevance of the Coulomb interaction among the three species, in particular the interplay of the electron and muon screening in suppressing the possible proton plasma mode, which is converted into a sound-like mode. The Coulomb interaction alone is able to produce a variety of excitation branches and the full spectral function shows a rich structure at different energy. The genuine plasmon mode is pushed at high energy and it contains mainly an electron component with a substantial muon component, which increases with density. The plasmon is undamped for not too large momentum and is expected to be hardly affected by the nuclear interaction. All the other branches, which fall below the plasmon, are damped or over-damped.Comment: misprint corrected in Eq. (1

Final report on a field study of soil-to-plant transfer of radioactive caesium, strontium and zinc in tropical Northern Australia to the IAEA/FAO/IUR CRP on classification of soils systems on the basis of transfer factors of radionuclides from soil to reference plants.

Soil-to-plant radionuclide transfer factors for cesium (134Cs), strontium (85Sr) and zinc (65Zn) into sorghum and mung plants grown in tropical Australia have been determined over a four-year study period. The crops were grown on two types of red earth soils. Transfer factors for Cs and Sr are not substantially different from the expected values based on previous studies, reported in the general literature and compiled in the IUR database, mainly performed within temperate climates. In contrast, the values for zinc (Zn) are more than an order of magnitude greater than anticipated. Most of the radioactivity added to the soils has been retained in the top 5 cm of both soils. There has been a general decline in soil-to-plant transfer of Cs and Zn as time has increased

Linear Sigma Models with Torsion

Gauged linear sigma models with (0,2) supersymmetry allow a larger choice of couplings than models with (2,2) supersymmetry. We use this freedom to find a fully linear construction of torsional heterotic compactifications, including models with branes. As a non-compact example, we describe a family of metrics which correspond to deformations of the heterotic conifold by turning on H-flux. We then describe compact models which are gauge-invariant only at the quantum level. Our construction gives a generalization of symplectic reduction. The resulting spaces are non-Kahler analogues of familiar toric spaces like complex projective space. Perturbatively conformal models can be constructed by considering intersections.Comment: 40 pages, LaTeX, 1 figure; references added; a new section on supersymmetry added; quantization condition revisite

The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing

Peer reviewedPublisher PD

Variable responses of human microbiomes to dietary supplementation with resistant starch

Abstract Background The fermentation of dietary fiber to various organic acids is a beneficial function provided by the microbiota in the human large intestine. In particular, butyric acid contributes to host health by facilitating maintenance of epithelial integrity, regulating inflammation, and influencing gene expression in colonocytes. We sought to increase the concentration of butyrate in 20 healthy young adults through dietary supplementation with resistant starch (unmodified potato starch—resistant starch (RS) type 2). Methods Fecal samples were collected from individuals to characterize butyrate concentration via liquid chromatography and composition of the microbiota via surveys of 16S rRNA-encoding gene sequences from the Illumina MiSeq platform. Random Forest and LEfSe analyses were used to associate responses in butyrate production to features of the microbiota. Results RS supplementation increased fecal butyrate concentrations in this cohort from 8 to 12 mmol/kg wet feces, but responses varied widely between individuals. Individuals could be categorized into three groups based upon butyrate concentrations before and during RS: enhanced, high, and low (n = 11, 3, and 6, respectively). Fecal butyrate increased by 67 % in the enhanced group (from 9 to 15 mmol/kg), while it remained ≥11 mmol/kg in the high group and ≤8 mmol/kg in the low group. Microbiota analyses revealed that the relative abundance of RS-degrading organisms—Bifidobacterium adolescentis or Ruminococcus bromii—increased from ~2 to 9 % in the enhanced and high groups, but remained at ~1.5 % in the low group. The lack of increase in RS-degrading bacteria in the low group may explain why there was no increase in fecal butyrate in response to RS. The microbiota of individuals in the high group were characterized by an elevated abundance of the butyrogenic microbe Eubacterium rectale (~6 % in high vs. 3 % in enhanced and low groups) throughout the study. Conclusions We document the heterogeneous responses in butyrate concentrations upon RS supplementation and identify characteristic of the microbiota that appear to underlie this variation. This study complements and extends other studies that call for personalized approaches to manage beneficial functions provided by gut microbiomes.http://deepblue.lib.umich.edu/bitstream/2027.42/134598/1/40168_2016_Article_178.pd

Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens

<p>Abstract</p> <p>Background</p> <p>The influence of diet on intestinal microflora has been investigated mainly using conventional microbiological approaches. Although these studies have advanced knowledge on human intestinal microflora, it is imperative that new methods are applied to facilitate scientific progress. Culture-independent molecular fingerprinting method of Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis (PCR-DGGE) has been used to study microbial communities in a variety of environmental samples. However, these protocols must be optimized prior to their application in order to enhance the quality and accuracy of downstream analyses. In this study, the relative efficacy of four commercial DNA extraction kits (Mobio Ultra Clean^®Fecal DNA Isolation Kit, M; QIAamp^®DNA Stool Mini Kit, Q; FastDNA^®SPIN Kit, FSp; FastDNA^®SPIN Kit for Soil, FSo) were evaluated. Further, PCR-DGGE technique was also assessed for its feasibility in detecting differences in human intestinal bacterial fingerprint profiles.</p> <p>Method</p> <p>Total DNA was extracted from varying weights of human fecal specimens using four different kits, followed by PCR amplification of bacterial 16S rRNA genes, and DGGE separation of the amplicons.</p> <p>Results</p> <p>Regardless of kit, maximum DNA yield was obtained using 10 to 50 mg (wet wt) of fecal specimens and similar DGGE profiles were obtained. However, kits FSp and FSo extracted significantly larger amounts of DNA per g dry fecal specimens and produced more bands on their DGGE profiles than kits M and Q due to their use of bead-containing lysing matrix and vigorous shaking step. DGGE of 16S rRNA gene PCR products was suitable for capturing the profiles of human intestinal microbial community and enabled rapid comparative assessment of inter- and intra-subject differences.</p> <p>Conclusion</p> <p>We conclude that extraction kits that incorporated bead-containing lysing matrix and vigorous shaking produced high quality DNA from human fecal specimens (10 to 50 mg, wet wt) that can be resolved as bacterial community fingerprints using PCR-DGGE technique. Subsequently, PCR-DGGE technique can be applied for studying variations in human intestinal microbial communities.</p

Heterotic T-folds with a small number of neutral moduli

We discuss non-geometric supersymmetric heterotic string models in D=4, in the framework of the free fermionic construction. We perform a systematic scan of models with four a priori left-right asymmetric Z_2 projections and shifts. We analyze some 2^{20} models, identifying 18 inequivalent classes and addressing variants generated by discrete torsions. They do not contain geometrical or trivial neutral moduli, apart from the dilaton. However, we show the existence of flat directions in the form of exactly marginal deformations and identify patterns of symmetry breaking where product gauge groups, realized at level one, are broken to their diagonal at higher level. We also describe an "inverse Gepner map" from Heterotic to Type II models that could be used, in certain non geometric settings, to define "effective" topological invariants.Comment: 37 page