Machine-learning of atomic-scale properties based on physical principles

We briefly summarize the kernel regression approach, as used recently in materials modelling, to fitting functions, particularly potential energy surfaces, and highlight how the linear algebra framework can be used to both predict and train from linear functionals of the potential energy, such as the total energy and atomic forces. We then give a detailed account of the Smooth Overlap of Atomic Positions (SOAP) representation and kernel, showing how it arises from an abstract representation of smooth atomic densities, and how it is related to several popular density-based representations of atomic structure. We also discuss recent generalisations that allow fine control of correlations between different atomic species, prediction and fitting of tensorial properties, and also how to construct structural kernels---applicable to comparing entire molecules or periodic systems---that go beyond an additive combination of local environments

Factors associated with mortality in HIV-infected and uninfected patients with pulmonary tuberculosis

<p>Abstract</p> <p>Background</p> <p>HIV has fuelled the TB epidemic in sub-Saharan Africa. Mortality in patients co-infected with TB and HIV is high. Managing factors influencing mortality in TB patients might help reducing it. This study investigates factors associated with mortality including patients' HIV sero-status, CD4 cell count, laboratory, nutritional and demographic characteristics in AFB smear positive pulmonary TB patients.</p> <p>Methods</p> <p>We studied 887 sputum smear positive PTB patients, between 18 and 65 years of age receiving standard 8 months anti-TB treatment. Demographic, anthropometric and laboratory data including HIV, CD4 and other tests were collected at baseline and at regular intervals. Patients were followed for a median period of 2.5 years.</p> <p>Results</p> <p>Of the 887 participants, 155 (17.5%) died, of whom 90.3% (140/155) were HIV-infected, a fatality of 29.7% (140/471) compared to 3.6% (15/416) among HIV-uninfected. HIV infection, age, low Karnofsky score, CD4 cell counts and hemoglobin, high viral load, and oral thrush were significantly associated with high mortality in all patients.</p> <p>Conclusion</p> <p>Mortality among HIV-infected TB patients is high despite the use of effective anti-TB therapy. Most deaths occur after successful completion of therapy, an indication that patients die from causes other than TB. HIV infection is the strongest independent predictor of mortality in this cohort.</p

Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation

Insulin, the primary hormone regulating the level of glucose in the bloodstream, modulates a variety of cellular and enzymatic processes in normal and diseased cells. Insulin signals are processed by a complex network of biochemical interactions which ultimately induce gene expression programs or other processes such as translation initiation. Surprisingly, despite the wealth of literature on insulin signaling, the relative importance of the components linking insulin with translation initiation remains unclear. We addressed this question by developing and interrogating a family of mathematical models of insulin induced translation initiation. The insulin network was modeled using mass-action kinetics within an ordinary differential equation (ODE) framework. A family of model parameters was estimated, starting from an initial best fit parameter set, using 24 experimental data sets taken from literature. The residual between model simulations and each of the experimental constraints were simultaneously minimized using multiobjective optimization. Interrogation of the model population, using sensitivity and robustness analysis, identified an insulin-dependent switch that controlled translation initiation. Our analysis suggested that without insulin, a balance between the pro-initiation activity of the GTP-binding protein Rheb and anti-initiation activity of PTEN controlled basal initiation. On the other hand, in the presence of insulin a combination of PI3K and Rheb activity controlled inducible initiation, where PI3K was only critical in the presence of insulin. Other well known regulatory mechanisms governing insulin action, for example IRS-1 negative feedback, modulated the relative importance of PI3K and Rheb but did not fundamentally change the signal flow

On the origin of selective nitrous oxide N-N bond cleavage by three-coordinate molybdenum(III) complexes

Reaction of Mo(N[R]Ar)(3) (R = Bu-t or (CD3)(2)CH3) with N2O gives rise exclusively to a 1: 1 mixture of nitride NMo(N[R]Ar)(3) and nitrosyl ONMo(N[R]Ar)(3), rather than the known oxo complex OMo(N[R]Ar)(3) and dinitro-en. Solution calorimetry measurements were used to determine the heat of reaction of Mo(N[R]Ar)3 with N2O and, independently, the heat of reaction of Mo(N[R]Ar)3 with NO. Derived from the latter measurements is an estimate (155.3 +/- 3.3 kcal . mol(-1)) of the molybdenum-nitrogen bond dissociation enthalpy for the terminal nitrido complex, NMo(N[R]Ar)(3). Comparison of the new calorimetry data with those obtained previously for oxo transfer to Mo(N[R]Ar)(3) shows that the nitrous oxide N-N bond cleavage reaction is under kinetic control. Stopped-flow kinetic measurements revealed the reaction to be first order in both Mo(N[R]Ar)(3) and N2O, consistent with a mechanism featuring post-rate-determining dinuclear N-N bond scission, but also consistent with cleavage of the N-N bond at a single metal center in a mechanism requiring the intermediacy of nitric oxide. The new 2-adamantyl-substituted molybdenum complex Mo(N[2-Ad]Ar)(3) was synthesized and found also to split N2O, resulting in a 1:1 mixture of nitrosyl and nitride products;,the reaction exhibited first-order kinetics and was found to be ca. 6 times slower than that for the tert-butyl-substituted derivative. Discussed in conjunction with studies of the 2-adamantyl derivative Mo(N[2-Ad]Ar)(3) is the role of ligand-imposed steric constraints on small-molecule, e.g. N-2 and N2O, activation reactivity. Bradley's chromium complex Cr((NPr2)-Pr-i)(3) was found to be competitive with Mo(N[R]Ar)(3) for NO binding, while on its own exhibiting no reaction with N2O. Competition experiments permitted determination of ratios of second-order rate constants for NO binding by the two molybdenum complexes and the chromium complex. Analysis of the product mixtures resulting from carrying out the N2O cleavage reactions with Cr((NPr2)-Pr-i)(3) present as an in situ NO scavenger rules out as dominant any mechanism involving the intermediacy of NO. Simplest and consistent with all the available data is a post-rate-determining bimetallic N-N scission process. Kinetic funneling of the reaction as indicated is taken to be governed by the properties of nitrous oxide as a ligand, coupled with the azophilic nature of three-coordinate molybdenum(III) complexes

Impaired Hypothalamic mTOR Activation in the Adult Rat Offspring Born to Mothers Fed a Low-Protein Diet

Several epidemiological and experimental studies have clearly established that maternal malnutrition induces a high risk of developing obesity and related metabolic diseases in the offspring. To determine if altered nutrient sensing might underlie this enhanced disease susceptibility, here we examined the effects of perinatal protein restriction on the activation of the nutrient sensor mTOR in response to acute variations in the nutritional status of the organism. Female Wistar rats were fed isocaloric diets containing either 17% protein (control) or 8% protein (PR) throughout pregnancy and lactation. At weaning offspring received standard chow and at 4 months of age the effects of fasting or fasting plus re-feeding on the phosphorylation levels of mTOR and its downstream target S6 ribosomal protein (rpS6) in the hypothalamus were assessed by immuno-fluorescence and western blot. Under ad libitum feeding conditions, PR rats exhibited decreased mTOR and rpS6 phosphorylation in the arcuate (ARC) and ventromedial (VMH) hypothalamic nuclei. Moreover, the phosphorylation of mTOR and rpS6 in these hypothalamic nuclei decreased with fasting in control but not in PR animals. Conversely, PR animals exhibited enhanced number of pmTOR imunostained cells in the paraventricular nucleus (PVN) and fasting decreased the activation of mTOR in the PVN of malnourished but not of control rats. These alterations occurred at a developmental stage at which perinatally-undernourished animals do not show yet obesity or glucose intolerance. Collectively, our observations suggest that altered hypothalamic nutrient sensing in response to an inadequate foetal and neonatal energetic environment is one of the basic mechanisms of the developmental programming of metabolic disorders and might play a causing role in the development of the metabolic syndrome induced by malnutrition during early life