Top-down systems biology modeling of host metabotype-microbiome associations in obese rodents

Covariation in the structural composition of the gut microbiome and the spectroscopically derived metabolic phenotype (metabotype) of a rodent model for obesity were investigated using a range of multivariate statistical tools. Urine and plasma samples from three strains of 10-week-old male Zucker rats (obese (fa/fa, n = 8), lean (fal-, n = 8) and lean (-/-, n = 8)) were characterized via high-resolution H-1 NMR spectroscopy, and in parallel, the fecal microbial composition was investigated using fluorescence in situ hydridization (FISH) and denaturing gradient gel electrophoresis (DGGE) methods. All three Zucker strains had different relative abundances of the dominant members of their intestinal microbiota (FISH), with the novel observation of a Halomonas and a Sphingomonas species being present in the (fa/fa) obese strain on the basis of DGGE data. The two functionally and phenotypically normal Zucker strains (fal- and -/-) were readily distinguished from the (fa/fa) obese rats on the basis of their metabotypes with relatively lower urinary hippurate and creatinine, relatively higher levels of urinary isoleucine, leucine and acetate and higher plasma LDL and VLDL levels typifying the (fa/fa) obese strain. Collectively, these data suggest a conditional host genetic involvement in selection of the microbial species in each host strain, and that both lean and obese animals could have specific metabolic phenotypes that are linked to their individual microbiomes.

Improved channel estimation in TDMA by reproduction with applications in GSM/GPRS under co-channel interference

Finding an estimate of the channel impulse response (CIR) by correlating a received known (training) sequence with the sent training sequence is commonplace. Where required, it is also common to truncate the longer correlation to a sub-set of correlation coefficients by finding the set of N sequential correlation coefficients with the maximum power. This paper presents a new approach to selecting the optimal set of N CIR coefficients from the correlation rather than relying on power. The algorithm reconstructs a set of predicted symbols using the training sequence and various sub-sets of the correlation to find the sub-set that results in the minimum mean squared error between the actual received symbols and the reconstructed symbols. The application of the algorithm is presented in the context of the TDMA based GSM/GPRS system to demonstrate an improvement in the system performance with the new algorithm and the results are presented in the paper. However, the application lends itself to any training sequence based communication system often found within wireless consumer electronic device(1).

Reversible addition of CO to coordinatively unsaturated high-spin iron(II) complexes

Several new coordinatively unsaturated iron(II) complexes of the types [Fe(EN-iPr)X2] (E = P, S, Se; X = Cl, Br) and [Fe(ON-iPr)2X]X containing bidentate EN ligands based on N-(2-pyridinyl)aminophosphines as well as oxo, thio, and seleno derivatives thereof were prepared and characterized by NMR spectroscopy and X-ray crystallography. Mössbauer spectroscopy and magnetization studies confirmed their high-spin nature with magnetic moments very close to 4.9 μB, reflecting the expected four unpaired d-electrons in all these compounds. Stable low-spin carbonyl complexes of the types [Fe(PN-iPr)2(CO)X]X (X = Cl, Br) and cis-CO,cis-Br-[Fe(PN-iPr)(CO)2X2] (X = Br) were obtained by reacting cis-Fe(CO)4X2 with the stronger PN donor ligands, but not with the weaker EN donor ligands (E = O, S, Se). Furthermore, the reactivity of [Fe(PN-iPr)X2] toward CO was investigated by IR spectroscopy. Whereas at room temperature no reaction took place, at −50 °C [Fe(PN-iPr)X2] added readily CO to form, depending on the nature of X, the mono- and dicarbonyl complexes [Fe(PN-iPr)(X)2(CO)] (X = Cl) and [Fe(PN-iPr)(CO)2X2] (X = Cl, Br), respectively. In the case of X = Br, two isomeric dicarbonyl complexes, namely, cis-CO,trans-Br-[Fe(PN-iPr)(CO)2Br2] (major species) and cis-CO,cis-Br-[Fe(PN-iPr)(CO)2Br2] (minor species), are formed. The addition of CO to [Fe(PN-iPr)X2] was investigated in detail by means of DFT/B3LYP calculations. This study strongly supports the experimental findings that at low temperature two isomeric low-spin dicarbonyl complexes are formed. For kinetic reasons cis,trans-[Fe(PN-iPr)(CO)2Br2] releases CO at elevated temperature, re-forming [Fe(PN-iPr)Br2], while the corresponding cis,cis isomer is stable under these conditions.

Nomi di parentela

Encyclopedia entry on "Kinship expressions and terms"

The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation

Objective: Proper interactions between the intestinal mucosa, gut microbiota and nutrient flow are required to establish homoeostasis of the host. Since the proximal part of the small intestine is the first region where these interactions occur, and since most of the nutrient absorption occurs in the jejunum, it is important to understand the dynamics of metabolic responses of the mucosa in this intestinal region.Design: Germ-free mice aged 8-10 weeks were conventionalised with faecal microbiota, and responses of the jejunal mucosa to bacterial colonisation were followed over a 30-day time course. Combined transcriptome, histology, (1)H NMR metabonomics and microbiota phylogenetic profiling analyses were used.Results: The jejunal mucosa showed a two-phase response to the colonising microbiota. The acute-phase response, which had already started 1 day after conventionalisation, involved repression of the cell cycle and parts of the basal metabolism. The secondary-phase response, which was consolidated during conventionalisation (days 4-30), was characterised by a metabolic shift from an oxidative energy supply to anabolic metabolism, as inferred from the tissue transcriptome and metabonome changes. Detailed transcriptome analysis identified tissue transcriptional signatures for the dynamic control of the metabolic reorientation in the jejunum. The molecular components identified in the response signatures have known roles in human metabolic disorders, including insulin sensitivity and type 2 diabetes mellitus.Conclusion: This study elucidates the dynamic jejunal response to the microbiota and supports a prominent role for the jejunum in metabolic control, including glucose and energy homoeostasis. The molecular signatures of this process may help to find risk markers in the declining insulin sensitivity seen in human type 2 diabetes mellitus, for instance.

System dynamics mapping of acute patient flows

Department of Health staff wished to use systems modelling to discuss acute patient flows with groups of NHS staff. The aim was to assess the usefulness of system dynamics (SD) in a healthcare context and to elicit proposals concerning ways of improving patient experience. Since time restrictions excluded simulation modelling, a hybrid approach using stock/flow symbols from SD was created. Initial interviews and hospital site visits generated a series of stock/flow maps. A ‘Conceptual Framework’ was then created to introduce the mapping symbols and to generate a series of questions about different patient paths and what might speed or slow patient flows. These materials formed the centre of three workshops for NHS staff. The participants were able to propose ideas for improving patient flows and the elicited data was subsequently employed to create a finalized suite of maps of a general acute hospital. The maps and ideas were communicated back to the Department of Health and subsequently assisted the work of the Modernization Agency.

Cooperative metal-ligand-induced properties of heteroleptic copper(I) xanthate/dithiocarbamate PPh3 complexes

Four new heteroleptic mononuclear complexes, [Cu(PPh3)2L1](1) {L1 = (C9H11O2CS2), [2-(4-methoxyphenyl)ethyl]xanthate}, [Cu(PPh3)2L2] (2) [L2 = (C6H7OCS2), benzylxanthate], [Cu(PPh3)2L3] (3) [L3 = (C5H9OCS2), (cyclobutylmethyl)xanthate] and [Cu(PPh3)2L4] (4) [L4 = (NC13H13NCS2), N-benzyl-N-(4-pyridylmethyl)dithiocarbamate], have been synthesized and characterized by using microanalysis, IR, UV/Vis, 1H, 13C and 31P NMR spectroscopy and X-ray crystallography; their photoluminescent behaviour and molecular electrical conductivity have been investigated. CuI possesses four-coordinate distorted tetrahedral geometry in all the complexes. All are weakly conducting and exhibit semiconductor behaviour in the studied 303363 K temperature range. Complex 4 shows striking luminescent behaviour emitting bluish green light at 480 nm in CH2Cl2 solution at room temperature

Design of delay-tolerant linear dispersion codes

In cooperative communication networks, owing to the nodes' arbitrary geographical locations and individual oscillators, the system is fundamentally asynchronous. This will damage some of the key properties of the space-time codes and can lead to substantial performance degradation. In this paper, we study the design of linear dispersion codes (LDCs) for such asynchronous cooperative communication networks. Firstly, the concept of conventional LDCs is extended to the delay-tolerant version and new design criteria are discussed. Then we propose a new design method to yield delay-tolerant LDCs that reach the optimal Jensen's upper bound on ergodic capacity as well as minimum average pairwise error probability. The proposed design employs stochastic gradient algorithm to approach a local optimum. Moreover, it is improved by using simulated annealing type optimization to increase the likelihood of the global optimum. The proposed method allows for flexible number of nodes, receive antennas, modulated symbols and flexible length of codewords. Simulation results confirm the performance of the newly-proposed delay-tolerant LDCs.

Power allocation strategies for distributed space-time codes in two-way relay networks

We study a two-way relay network (TWRN), where distributed space-time codes are constructed across multiple relay terminals in an amplify-and-forward mode. Each relay transmits a scaled linear combination of its received symbols and their conjugates,with the scaling factor chosen based on automatic gain control. We consider equal power allocation (EPA) across the relays, as well as the optimal power allocation (OPA) strategy given access to instantaneous channel state information (CSI). For EPA, we derive an upper bound on the pairwise-error-probability (PEP), from which we prove that full diversity is achieved in TWRNs. This result is in contrast to one-way relay networks, in which case a maximum diversity order of only unity can be obtained. When instantaneous CSI is available at the relays, we show that the OPA which minimizes the conditional PEP of the worse link can be cast as a generalized linear fractional program, which can be solved efficiently using the Dinkelback-type procedure.We also prove that, if the sum-power of the relay terminals is constrained, then the OPA will activate at most two relays.

Anisotropic model for granulated sea ice dynamics

A continuum model describing sea ice as a layer of granulated thick ice, consisting of many rigid, brittle floes, intersected by long and narrow regions of thinner ice, known as leads, is developed. We consider the evolution of mesoscale leads, formed under extension, whose lengths span many floes, so that the surrounding ice is treated as a granular plastic. The leads are sufficiently small with respect to basin scales of sea ice deformation that they may be modelled using a continuum approach. The model includes evolution equations for the orientational distribution of leads, their thickness and width expressed through second-rank tensors and terms requiring closures. The closing assumptions are constructed for the case of negligibly small lead ice thickness and the canonical deformation types of pure and simple shear, pure divergence and pure convergence. We present a new continuum-scale sea ice rheology that depends upon the isotropic, material rheology of sea ice, the orientational distribution of lead properties and the thick ice thickness. A new model of lead and thick ice interaction is presented that successfully describes a number of effects: (i) because of its brittle nature, thick ice does not thin under extension and (ii) the consideration of the thick sea ice as a granular material determines finite lead opening under pure shear, when granular dilation is unimportant.

Atlas of coronavirus replicase structure

The international response to SARS-CoV has produced an outstanding number of protein structures in a very short time. This review summarizes the findings of functional and structural studies including those derived from cryoelectron microscopy, small angle X-ray scattering, NMR spectroscopy, and X-ray crystallography, and incorporates bioinformatics predictions where no structural data is available. Structures that shed light on the function and biological roles of the proteins in viral replication and pathogenesis are highlighted. The high percentage of novel protein folds identified among SARS-CoV proteins is discussed.

Design of delay-tolerant space–time codes with limited feedback

In cooperative communication networks, owing to the nodes' arbitrary geographical locations and individual oscillators, the system is fundamentally asynchronous. Such a timing mismatch may cause rank deficiency of the conventional space-time codes and, thus, performance degradation. One efficient way to overcome such an issue is the delay-tolerant space-time codes (DT-STCs). The existing DT-STCs are designed assuming that the transmitter has no knowledge about the channels. In this paper, we show how the performance of DT-STCs can be improved by utilizing some feedback information. A general framework for designing DT-STC with limited feedback is first proposed, allowing for flexible system parameters such as the number of transmit/receive antennas, modulated symbols, and the length of codewords. Then, a new design method is proposed by combining Lloyd's algorithm and the stochastic gradient-descent algorithm to obtain optimal codebook of STCs, particularly for systems with linear minimum-mean-square-error receiver. Finally, simulation results confirm the performance of the newly designed DT-STCs with limited feedback.

Study of the carbon dioxide chemical fixation-activation by guanidines

Fixation of CO(2) is one of the most important priorities of the scientific community dedicated to reduce global warming. In this work, we propose new methods for the fixation of CO2 using the guanidine bases tetramethylguanidine (TMG) and 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]-pyrimidine (TBD). In order to understand the reactions occurring during the CO(2) fixation and release processes, we employed several experimental methods, including solution and solid-state NMR, FTIR, and coupled TGA-FTIR. Quantum mechanical NMR calculations were also carried out. Based on the results obtained, we concluded that CO(2) fixation with both TMG and TBD guanidines is a kinetically reversible process, and the corresponding fixation products have proved to be useful as transcarboxylating compounds. Afterward, CO(2) thermal releasing from this fixation product with TBD was found to be an interesting process for CO(2) capture and isolation purposes. (C) 2008 Elsevier Ltd. All rights reserved.

Rhenium chelate complexes with maltolate or kojate

Novel rhenium complexes containing the maltolate (mal) or kojate (koj) anions as chelating ligands have been synthesized: [ReOCl(mal)(2)] (1), [ReOCl(2)(mal)(PPh(3))] (2), [ReOBr(2)(mal)(PPh(3))] (3), [ReOCl2(koj)(PPh(3))] (4) and [ReOBr(2)(koj)(PPh(3))] (5). The products have been characterized by MR, (1)H, (13)C, and (31)P NMR spectroscopies and elemental analysis. The crystal and molecular structures of all complexes were determined. Complex I crystallizes monoclinic, space group C2/c, Z = 8. It contains two O, O`-bidentate maltolate ligands and one chloro ligand at the (ReO)(3+) unit, so that a distorted octahedral geometry is adopted by the six-coordinated rhenium(V) center. The chloro ligand occupies a cis position to the oxo ligand. Complexes 2 and 3 are isostructural and crystallize orthorhombic, space group Pbca and Z = 8. The isostructural complexes 4 and 5 crystallize monoclinic, space group P2(1)/n and Z = 4. In complexes 2-5, the (ReO)(3+) unit is coordinated by a monoanionic O,O-bidentate unit of the maltolate (2 and 3) or kojate (41 and 5) ligand, one triphenylphosphine and two halogeno ligands (Cl in 2 and 4; Br in 3 and 5), with the rhenium(V) center in a distorted octahedral environment. The halide ligands are in cis positions to each other. (c) 2008 Elsevier Ltd. All rights reserved.

Magnetic resonance study of a vanadium pentoxide gel

In this work we report results from continuous-wave (CW) and pulsed electron paramagnetic resonance (EPR) and proton nuclear magnetic resonance (NMR) studies of the vanadium pentoxide xerogel V2O5:nH(2)O (n approximate to 1.6). The low temperature CW-EPR spectrum shows hyperfine structure due to coupling of unpaired V4+ electron with the vanadium nucleus. The analysis of the spin Hamiltonian parameters suggests that the V4+ ions are located in tetragonally distorted octahedral sites. The transition temperature from the rigid-lattice low-temperature regime to the high temperature liquid-like regime was determined from the analysis of the temperature dependence of the hyperfine splitting and the V4+ motional correlation time. The Electron Spin Echo Envelope Modulation (ESEEM) data shows the signals resulting from the interaction of H-1 nuclei with V4+ ions. The modulation effect was observed only for field values in the center of the EPR absorption spectrum corresponding to the single crystals orientated perpendicular to the magnetic field direction. At least three protons are identified in the xerogel by our magnetic resonance experiments: (I) the OH groups in the equatorial plane, (ii) the bound water molecules in the axial V=O bond and (iii) the free mobile water molecules between the oxide layers. Proton NMR lineshapes and spin-lattice relaxation times were measured in the temperature range between 150 K and 323 K. Our analysis indicates that only a fraction of the xerogel protons contribute to the measured conductivity.