Mapping the landscape of metabolic goals of a cell

Genome-scale flux balance models of metabolism provide testable predictions of all metabolic rates in an organism, by assuming that the cell is optimizing a metabolic goal known as the objective function. We introduce an efficient inverse flux balance analysis (invFBA) approach, based on linear programming duality, to characterize the space of possible objective functions compatible with measured fluxes. After testing our algorithm on simulated E. coli data and time-dependent S. oneidensis fluxes inferred from gene expression, we apply our inverse approach to flux measurements in long-term evolved E. coli strains, revealing objective functions that provide insight into metabolic adaptation trajectories.MURI W911NF-12-1-0390 - Army Research Office (US); MURI W911NF-12-1-0390 - Army Research Office (US); 5R01GM089978-02 - National Institutes of Health (US); IIS-1237022 - National Science Foundation (US); DE-SC0012627 - U.S. Department of Energy; HR0011-15-C-0091 - Defense Sciences Office, DARPA; National Institutes of Health; R01GM103502; 5R01DE024468; 1457695 - National Science Foundatio

Structure propagation for zero-shot learning

The key of zero-shot learning (ZSL) is how to find the information transfer model for bridging the gap between images and semantic information (texts or attributes). Existing ZSL methods usually construct the compatibility function between images and class labels with the consideration of the relevance on the semantic classes (the manifold structure of semantic classes). However, the relationship of image classes (the manifold structure of image classes) is also very important for the compatibility model construction. It is difficult to capture the relationship among image classes due to unseen classes, so that the manifold structure of image classes often is ignored in ZSL. To complement each other between the manifold structure of image classes and that of semantic classes information, we propose structure propagation (SP) for improving the performance of ZSL for classification. SP can jointly consider the manifold structure of image classes and that of semantic classes for approximating to the intrinsic structure of object classes. Moreover, the SP can describe the constrain condition between the compatibility function and these manifold structures for balancing the influence of the structure propagation iteration. The SP solution provides not only unseen class labels but also the relationship of two manifold structures that encode the positive transfer in structure propagation. Experimental results demonstrate that SP can attain the promising results on the AwA, CUB, Dogs and SUN databases

Ripple modulated electronic structure of a 3D topological insulator

3D topological insulators, similar to the Dirac material graphene, host linearly dispersing states with unique properties and a strong potential for applications. A key, missing element in realizing some of the more exotic states in topological insulators is the ability to manipulate local electronic properties. Analogy with graphene suggests a possible avenue via a topographic route by the formation of superlattice structures such as a moir\'e patterns or ripples, which can induce controlled potential variations. However, while the charge and lattice degrees of freedom are intimately coupled in graphene, it is not clear a priori how a physical buckling or ripples might influence the electronic structure of topological insulators. Here we use Fourier transform scanning tunneling spectroscopy to determine the effects of a one-dimensional periodic buckling on the electronic properties of Bi2Te3. By tracking the spatial variations of the scattering vector of the interference patterns as well as features associated with bulk density of states, we show that the buckling creates a periodic potential modulation, which in turn modulates the surface and the bulk states. The strong correlation between the topographic ripples and electronic structure indicates that while doping alone is insufficient to create predetermined potential landscapes, creating ripples provides a path to controlling the potential seen by the Dirac electrons on a local scale. Such rippled features may be engineered by strain in thin films and may find use in future applications of topological insulators.Comment: Nature Communications (accepted

Estimation of colorectal adenoma recurrence with dependent censoring

<p>Abstract</p> <p>Background</p> <p>Due to early colonoscopy for some participants, interval-censored observations can be introduced into the data of a colorectal polyp prevention trial. The censoring could be dependent of risk of recurrence if the reasons of having early colonoscopy are associated with recurrence. This can complicate estimation of the recurrence rate.</p> <p>Methods</p> <p>We propose to use midpoint imputation to convert interval-censored data problems to right censored data problems. To adjust for potential dependent censoring, we use information from auxiliary variables to define risk groups to perform the weighted Kaplan-Meier estimation to the midpoint imputed data. The risk groups are defined using two risk scores derived from two working proportional hazards models with the auxiliary variables as the covariates. One is for the recurrence time and the other is for the censoring time. The method described here is explored by simulation and illustrated with an example from a colorectal polyp prevention trial.</p> <p>Results</p> <p>We first show that midpoint imputation under an assumption of independent censoring will produce an unbiased estimate of recurrence rate at the end of the trial, which is often the main interest of a colorectal polyp prevention trial, and then show in simulations that the weighted Kaplan-Meier method using the information from auxiliary variables based on the midpoint imputed data can improve efficiency in a situation with independent censoring and reduce bias in a situation with dependent censoring compared to the conventional methods, while estimating the recurrence rate at the end of the trial.</p> <p>Conclusion</p> <p>The research in this paper uses midpoint imputation to handle interval-censored observations and then uses the information from auxiliary variables to adjust for dependent censoring by incorporating them into the weighted Kaplan-Meier estimation. This approach can handle a situation with multiple auxiliary variables by deriving two risk scores from two working PH models. Although the idea of this approach might appear simple, the results do show that the weighted Kaplan-Meier approach can gain efficiency and reduce bias due to dependent censoring.</p

Strong Anisotropy in Spin Suceptibility of Superfluid 3He-B Film Caused by Surface Bound States

Spin susceptibility of superfluid 3He-B film with specular surfaces is calculated. It is shown that, when the magnetic field is applied in a direction perpendiculr to the film, the suseptibility is significantly enhanced by the contribution from the surface bound states. No such enhancement is found for the magnetic field parallel to the film. A simplified model with spatially constant order parameter is used to elucidate the magnetic properties of the surface bound states. The Majorana nature of the zero energy bound state is also mentioned.Comment: 4 pages, 4 figure

Temperature and Frequency Dependence of Complex Conductance of Ultrathin YBa2Cu3O7-x Films: A Study of Vortex-Antivortex Pair Unbinding

We have studied the temperature dependencies of the complex sheet conductance of 1-3 unit cell (UC) thick YBa2Cu3O7-x films sandwiched between semiconducting Pr0.6Y0.4Ba2Cu3O7-x layers at high frequencies. Experiments have been carried out in a frequency range between: 2 - 30 MHz with one-spiral coil technique, 100 MHz - 1 GHz frequency range with a new technique using the spiral coil cavity and at 30 GHz by aid of a resonant cavity technique. The real and imaginary parts of the mutual-inductance between a coil and a film were measured and converted to complex conductivity by aid of the inversion procedure. We have found a quadratic temperature dependence of the kinetic inductance, L_k^-1(T), at low temperatures independent of frequency, with a break in slope at T^dc_BKT, the maximum of real part of conductance and a large shift of the break temperature and the maximum position to higher temperatures with increasing frequency. We obtain from these data the universal ratio T^dc_BKT/L_k^-1(T^dc_BKT) = 25, 25, and 17 nHK for 1-, 2- and 3UC films, respectively in close agreement with theoretical prediction of 12 nHK for vortex-antivortex unbinding transition. The activated temperature dependence of the vortex diffusion constant was observed and discussed in the framework of vortex-antivortex pair pinning. PACS numbers: 74.80.Dm, 74.25.Nf, 74.72.Bk, 74.76.BzComment: PDF file, 10 pages, 6 figures, to be published in J. Low Temp. Phys.; Proc. of NATO ARW: VORTEX 200

Urinary biomarker concentrations of captan, chlormequat, chlorpyrifos and cypermethrin in UK adults and children living near agricultural land

There is limited information on the exposure to pesticides experienced by UK residents living near agricultural land. This study aimed to investigate their pesticide exposure in relation to spray events. Farmers treating crops with captan, chlormequat, chlorpyrifos or cypermethrin provided spray event information. Adults and children residing ≤100 m from sprayed fields provided first-morning void urine samples during and outwith the spray season. Selected samples (1–2 days after a spray event and at other times (background samples)) were analysed and creatinine adjusted. Generalised Linear Mixed Models were used to investigate if urinary biomarkers of these pesticides were elevated after spray events. The final data set for statistical analysis contained 1518 urine samples from 140 participants, consisting of 523 spray event and 995 background samples which were analysed for pesticide urinary biomarkers. For captan and cypermethrin, the proportion of values below the limit of detection was greater than 80%, with no difference between spray event and background samples. For chlormequat and chlorpyrifos, the geometric mean urinary biomarker concentrations following spray events were 15.4 μg/g creatinine and 2.5 μg/g creatinine, respectively, compared with 16.5 μg/g creatinine and 3.0 μg/g creatinine for background samples within the spraying season. Outwith the spraying season, concentrations for chlorpyrifos were the same as those within spraying season backgrounds, but for chlormequat, lower concentrations were observed outwith the spraying season (12.3 μg/g creatinine). Overall, we observed no evidence indicative of additional urinary pesticide biomarker excretion as a result of spray events, suggesting that sources other than local spraying are responsible for the relatively low urinary pesticide biomarkers detected in the study population

Dental and periodontal status of 12-year-old Dai school children in Yunnan Province, China: a cross-sectional study

published_or_final_versio

Evolution of edge states in topological superfluids during the quantum phase transition

The quantum phase transition between topological and non-topological insulators or between fully gapped superfluids/superconductors can occur without closing the gap. We consider the evolution of the Majorana edge states on the surface of topological superconductor during transition to the topologically trivial superconductor on example of non-interacting Hamiltonian describing the spin-triplet superfluid 3He-B. In conventional situation when the gap is nullified at the transition, the spectrum of Majorana fermions shrinks and vanishes after the transition to the trivial state. If the topological transition occurs without the gap closing, the Majorana fermion spectrum disappears by escaping to ultraviolet, where Green's function approaches zero. This demonstrates the close connection between the topological transition without closing the gap and zeroes in the Green's function. Similar connection takes place in interacting systems where zeroes may occur due to interaction.Comment: 5 pages, 2 figures, JETP Letters style, version submitted to JETP Letter

Molecular layer-by-layer re-stacking of MoS2–In2Se3 by electrostatic means: assembly of a new layered photocatalyst

2D-layered transition metal chalcogenides are useful semiconductors for a wide range of opto-electronic applications. Their similarity as layered structures offers exciting possibility to modify their electronic properties by creating new heterojunction assemblies from layer-by-layer restacking of individual monolayer sheets, however, the lack of specific interaction between these layers could induce phase segregation. Here, we employed a chemical method using n-BuLi to exfoliate MoS2 and In2Se3 into their monolayer-containing colloids in solution. The bulky Se atoms can be selectively leached from In2Se3 during Li treatment which gives positively charged surface monolayers in neutral pH whereas the strong polarization of Mo–S with moderate S leaching gives a negatively charged surface. Specific interlayer electrostatic attraction during their selective assembly gives a controllable atomic AB-type of layer stacking as supported by EXAFS, STEM with super-EDX mapping, TAS/TRPL and DFT calculations. Using this simple but inexpensive bottom-up solution method, a new photocatalyst assembled from layers for photo water splitting can be tailor-made with high activity