bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative short echo time 1H MRSI of the peripheral edematous region of human brain tumors in the differentiation between glioblastoma, metastasis, and meningioma
Authors: Wijnen J.P. , Idema A.J.S. , Stawicki M. , Lagemaat M.W. , Wesseling P. , Wright A.J. , Scheenen T.W.J. , Heerschap A.
Published: June 2012

Purpose:

To assess metabolite levels in peritumoral edematous (PO) and surrounding apparently normal (SAN) brain regions of glioblastoma, metastasis, and meningioma in humans with 1H‐MRSI to find biomarkers that can discriminate between tumors and characterize infiltrative tumor growth.

Materials and Methods:

Magnetic resonance (MR) spectra (semi‐LASER MRSI, 30 msec echo time, 3T) were selected from regions of interest (ROIs) under MRI guidance, and after quality control of MR spectra. Statistical testing between patient groups was performed for mean metabolite ratios of an entire ROI and for the highest value within that ROI.

Results:

The highest ratios of the level of choline compounds and the sum of myo‐inositol and glycine over N‐acetylaspartate and creatine compounds were significantly increased in PO regions of glioblastoma versus that of metastasis and meningioma. In the SAN region of glioblastoma some of these ratios were increased. Differences were less prominent for metabolite levels averaged over entire ROIs.

Conclusion:

Specific metabolite ratios in PO and SAN regions can be used to discriminate glioblastoma from metastasis and meningioma. An analysis of these ratios averaged over entire ROIs and those with most abnormal values indicates that infiltrative tumor growth in glioblastoma is inhomogeneous and extends into the SAN region. J. Magn. Reson. Imaging 2012;36:1072–1082. © 2012 Wiley Periodicals, Inc.
The effect of co‐composted cabbage and ground phosphate rock on the early growth and P uptake of oilseed rape and perennial ryegrass
Authors: Walker Robin L. , Edwards Anthony C. , Maskell Phillip , Watson Christine A. , Rees Robert M. , Knox Oliver G.G. , Stockdale Elizabeth A.
Published: June 2012

Phosphorus (P) availability to crops in organic systems can be a major issue, with the use of readily available forms often restricted. One product that can be used in organically managed systems, that is also relatively easily accessible to growers, is phosphate rock, although its solubility and therefore crop availability is often poor. One possible approach to improve this situation is co‐composting phosphate rock with selected organic waste materials. Various ratios of phosphate rock and cabbage (Brassica oleracea L.) residues were co‐composted and the products tested at different rates of application. The effects were assessed over 12 weeks using oilseed rape (Brassica napus L.) and perennial ryegrass (Lolium perenne L.) as bioassay crops in a pot experiment. At harvest, estimates of P derived from cabbage and phosphate rock for the lowest of two rates of compost were ≈ 2 and 10 mg P pot–1 for oilseed rape, compared to 5 and 2 mg P pot–1 for perennial ryegrass, respectively. Roots tended to have higher P concentrations than shoots. The crops showed differences in their abilities to access various P sources, with oilseed rape effectively taking P from phosphate rock, whereas perennial ryegrass was more effective at accessing cabbage‐derived P (the main substrate in the compost). Oilseed rape was able to take up 20% of the total P applied as phosphate rock, whereas perennial ryegrass took up less than 5% of the total P applied from this material. Both pre‐ and post‐application solubilisation/transformation mechanisms were involved in supplying plant‐available P. Quantifying the relative contribution from individual P sources remains problematic even within this relatively simple system.
Effect of source–sink manipulation on accumulation of micronutrients and protein in wheat grains
Authors: Zhang Yinghua , Zhang Yongping , Liu Na , Su Da , Xue Qingwu , Stewart Bob A. , Wang Zhimin
Published: June 2012

The effect of source and sink manipulation on accumulation of micronutrients (Fe, Zn, Mn, Cu) and protein in wheat grains was studied in a field experiment and ear culture. The source and sink manipulation was obtained by reducing assimilate source (through defoliation and spike shading) or sink (through 50% spikelets removal) after anthesis in the field and by changing sucrose or NH4NO3 levels of the culture media in ear culture. In the field experiment, reducing source and sink generally increased Fe, Zn, Mn, Cu, and protein concentrations except defoliation which decreased Mn concentration. Grain yield as well as micronutrient and protein contents in grains were all reduced by reducing source and sink sizes, suggesting that the accumulation of micronutrients and protein in grains was restricted by source supply and sink capacity. In ear culture, the supply of 20 to 80 g L–1 sucrose increased grain weight and yield, but decreased grain Fe, Zn, Mn, Cu, and protein concentrations. The supply of 0.57 to 2.28 g L–1 NH4NO3 increased grain yield and the concentrations and contents of micronutrients and protein. All these results show that micronutrient and protein accumulation in grains can be affected by the source–sink relationship of carbohydrate and nitrogen. Adequate N supply can simultaneously increase grain yield and the accumulation of Fe, Zn, Mn, Cu, and protein.
An electronic micropenetrometer (EMP) for field measurements of biological soil crust stability
Authors: Laureen Drahorad Sylvie , Felix‐Henningsen Peter
Published: June 2012

Despite the importance of biological soil crusts (BSC) for ecosystem functions in arid and semiarid areas, little information on their mechanical stability is available. Goal of this study was to develop a micropenetrometer (EMP) that allows to determine BSC stability at high spatial resolutions. First results show that differences in BSC stability at 39 μm resolution can be detected and that cyanobacterial BSC has an average penetration resistance of 0.75 MPa.
Complex concentration dependence of SERS and UV–Vis absorption of glycine/Ag‐substrates because of glycine‐mediated Ag‐nanostructure modifications
Authors: Ojha Animesh K. , Donfack Patrice , Materny Arnulf
Published: June 2012

Complex concentration‐dependence of surface‐enhanced Raman scattering (SERS) and UV–Vis absorption of Ag‐nanoparticles (AgNPs) mixed with Gly has been observed. Surprisingly, with decreasing Gly concentration, a new band in UV–Vis absorption of AgNPs/Gly mixtures is found to red‐shift with increasing intensity, until a turning point at a critical concentration. Further diluting Gly, the new band blue‐shifts with decreasing intensity. Similarly, the SERS intensities of Gly bands at 615 and 905 cm–1 consistently increase with decreasing Gly concentrations, reaching maxima at the critical concentration. This agrees consistently with the variation in position and intensity of the new developing plasmon absorption band. Interestingly, transmission electron microscopy (TEM) revealed Gly‐induced modifications of AgNPs, including a reassembling and increasing aspect ratio with deceasing Gly concentration. The concentration‐dependent behavior of UV–Vis absorption, SERS, and TEM of AgNPs/Gly mixtures could be due to the complex nature of Gly‐AgNPs interaction depending on the molecular density, as supported by TEM images. Copyright © 2012 John Wiley & Sons, Ltd.
Computing Raman and infrared wavenumbers of nanostructures: application to silicon nanowires
Authors: Zörgiebel Felix , Kunstmann Jens , Nozaki Daijiro , Cuniberti Gianaurelio
Published: June 2012

The characterization of nanostructures with spectroscopic methods is a fundamental tool in nanoscience. For novel nanostructures, the interpretation of spectral features is a challenging task. To address this issue, we present the “Symmetry‐Filtered Molecular Dynamics (SFMD)” method to calculate Raman and infrared wavenumbers from molecular dynamics (MD) simulations, employing only the symmetry of the atomic structure. Explicit and expensive calculations of the electric polarizability or the dipole moment are not required. Therefore, our method can be easily used with any standard MD software. On the basis of the density functional tight‐binding method for the MD simulations, we apply our method to bulk silicon and small‐diameter hydrogen‐passivated silicon nanowires. For bulk silicon, we study the wavenumber shift of the Raman peak with temperature and obtain results that are in good agreement with experiments. We further show that thermal lattice expansion is a minor effect (22%) and that temperature‐driven anharmonic effects (78%) are the main contributions to that wavenumber shift. By analyzing the bond lengths of different silicon nanowires, we found that surface stress manifests as a 0.37% shortening of bonds only in the outermost silicon layer. We further analyzed the diameter‐dependent wavenumber shift of a Raman peak in silicon nanowires. We found that the main contribution to the wavenumber shift comes from the phonon confinement effect and surface stress leads to an additional shift of 9–22%. Our results indicate that our method is able to produce quantitative results that can be compared with experiments. We propose our method to be used for the understanding of Raman and infrared spectra of novel bulk and nanostructures. Copyright © 2012 John Wiley & Sons, Ltd.
A novel strategy for target profiling analysis of bioactive phenylethanoid glycosides in Plantago medicinal plants using ultra‐performance liquid chromatography coupled with tandem quadrupole mass spectrometry
Authors: Qi Meng , Xiong Aizhen , Geng Fang , Yang Li , Wang Zhengtao
Published: June 2012

Phenylethanoid glycosides are a group of phenolic compounds with diverse biological activities such as hypotensive, diuretic, and hypoglycemic effects. In this study, a target profiling analysis approach using ultra‐performance liquid chromatography coupled with tandem quadrupole mass spectrometry (MS) was established on the basis of parent ion scanning for m/z 161, the characteristic product ion for phenylethanoid glycosides. It was successfully employed to discriminate the chemical composition of phenylethanoid glycosides between Plantaginis Herba and Plantaginis Semen, two medicinal parts of Plantago plants, which are widely used as herbal medicine in China. Totally, 34 phenylethanoid glycosides were characterized and tentatively identified by their retention times, MS, and tandem quadrupole MS (MS/MS) data. Combined with chemometrics analysis of principal component analysis and orthogonal projection to latent structural discriminate analysis, eight of them, especially acteoside and plantamajoside, were picked out and contributed to the chemical distinction between Plantaginis Herba and Plantaginis Semen, which might be responsible for the differences in diuretic and hypotensive effects between the two medicinal parts. This new approach for target profiling provides not only a novel idea for specific analysis of active chemical constituents in the same type, but also a promising and reference method for quality evaluation of traditional Chinese medicines.
A novel thermodynamic state recursion method for description of nonideal nonlinear chromatographic process of frontal analysis
Authors: Liu Qian , OuYang Liangfei , Liang Heng , Li Nan , Geng Xindu
Published: June 2012

A novel thermodynamic state recursion (TSR) method, which is based on nonequilibrium thermodynamic path described by the Lagrangian–Eulerian representation, is presented to simulate the whole chromatographic process of frontal analysis using the spatial distribution of solute bands in time series like as a series of images. TSR differs from the current numerical methods using the partial differential equations in Eulerian representation. The novel method is used to simulate the nonideal, nonlinear hydrophobic interaction chromatography (HIC) processes of lysozyme and myoglobin under the discrete complex boundary conditions. The results show that the simulated breakthrough curves agree well with the experimental ones. The apparent diffusion coefficient and the Langmuir isotherm parameters of the two proteins in HIC are obtained by the state recursion inverse method. Due to its the time domain and Markov characteristics, TSR is applicable to the design and online control of the nonlinear multicolumn chromatographic systems.
Low‐molecular weight protein profiling of genetically modified maize using fast liquid chromatography electrospray ionization and time‐of‐flight mass spectrometry
Authors: Koc Anna , Cañuelo Ana , Garcia‐Reyes Juan F. , Molina‐Diaz Antonio , Trojanowicz Marek
Published: June 2012

In this work, the use of liquid chromatography coupled to electrospray time‐of‐flight mass spectrometry (LC‐TOFMS) has been evaluated for the profiling of relatively low‐molecular weight protein species in both genetically modified (GM) and non‐GM maize. The proposed approach consisted of a straightforward sample fractionation with different water and ethanol‐based buffer solutions followed by separation and detection of the protein species using liquid chromatography with a small particle size (1.8 μm) C18 column and electrospray‐time‐of‐flight mass spectrometry detection in the positive ionization mode. The fractionation of maize reference material containing different content of transgenic material (from 0 to 5% GM) led to five different fractions (albumins, globulins, zeins, zein‐like glutelins, and glutelins), all of them containing different protein species (from 2 to 52 different species in each fraction). Some relevant differences in the quantity and types of protein species were observed in the different fractions of the reference material (with different GM contents) tested, thus revealing the potential use of the proposed approach for fast protein profiling and to detect tentative GMO markers in maize.
Tris(hydroxymethyl)aminomethane‐functionalized agarose particles: Parameters affecting the binding of bovine serum albumin
Authors: Zhang Bin , Wang Ye , Gao Min , Gu Ming , Wang Changhai
Published: June 2012

A new protein adsorbent is introduced based on the coupling of the common buffer ion, tris(hydroxymethyl)aminomethane, to the agarose gel Sepharose HPfrom GEHealthcare Bio‐Sciences AB, Uppsala, Sweden. The article describes the synthesis of the new adsorbent and the use of BSA as a model in a binding study. By optimization of the coupling procedure, a maximum ligand density of 63.5 μmol/mL gel could be obtained. Adsorption equilibria were investigated in the pH range 5.0–8.0 and at salt concentrations of 0–0.4 mol/L. Binding of BSA under different conditions indicated that both electrostatic interaction and hydrogen bonding were involved in the adsorption process where the former played a major role.
C18 functionalized graphene oxide as a novel coating for solid‐phase microextraction
Authors: Xu Lili , Feng Juanjuan , Liang Xiaojing , Li Jubai , Jiang Shengxiang
Published: June 2012

A novel C18 functionalized graphene oxide (GO) coated solid‐phase microextraction fiber was prepared by a novel protocol. Based on the strong van der Waals interaction present in GO and abundant oxygenous groups in GO sheets, a simple layer‐by‐layer self‐assembly method was used in the preparation process and then C18 was successfully self‐assembled on GO via C‐O‐Si bonding. Coupled with gas chromatography, extraction performance of the fiber was tested with polycyclic aromatic hydrocarbons (PAHs) as model analytes. The fiber not only exhibited excellent extraction efficiency and selectivity, but also showed many advantages including high rigidity, long service life and well stability toward organic solvent, acidic and alkali solutions, and high temperature. The relative standard deviations for single‐fiber repeatability and fiber‐to‐fiber reproducibility were less than 7.26 and 17.25%, respectively. The detection limits to the PAHs were less than 0.08 μg L−1 and the calibration curves were linear in a wide range for all analytes. The as‐established Solid‐phase microextraction GC method was also successfully used for determination of PAHs in two real water samples.
Random‐access distributed fiber sensing
Authors: Zadok A. , Antman Y. , Primerov N. , Denisov A. , Sancho J. , Thevenaz L.
Published: June 2012

Optical sensing offers an attractive solution to the societal concern for prevention of natural and human‐generated threats and for efficient use of natural resources. The unprecedented properties of optical fibers make them ideal for implementing a ‘nervous system’ in structural health monitoring: they are small, low‐cost and electrically and chemically inert. In particular, the nonlinear interaction of stimulated Brillouin scattering allows for the distributed measurement of strain and temperature with tens of km range. In this work, a novel, radar‐inspired technique for random‐access Brillouin scattering‐based sensors is shown, making a significant step towards a real optical sensing nerve. The method selectively addresses each fiber segment as a distinct sensing element in a synaptic neuronal system. The measurement principle relies on phase‐coding of both the Brillouin pump and signal waves by a high‐rate, pseudo‐random bit sequence. Temperature measurements with 1 cm resolution are reported. The measurement range is scalable to several km.
Dual‐wavelength optical parametric oscillator using antiresonant ring interferometer
Authors: Esteban‐Martin A. , Ramaiah‐Badarla V. , Ebrahim‐Zadeh M.
Published: June 2012

A novel technique for coupling of two resonant optical cavities using an antiresonant ring (ARR) interferometer is reported. By deploying two synchronously‐pumped femtosecond optical parametric oscillators (OPOs), it is shown that the use of an ARR can provide an intracavity common path for the two oscillating fields, but without gain coupling between the two nonlinear media. The new technique permits the generation of two signal (idler) wavelengths, which can be independently and arbitrarily varied across the OPO tuning range. The absence of gain coupling also enables unrestricted and uninterrupted tuning through wavelength degeneracy at any arbitrary point within the OPO tuning range. It is shown that signal wavelength pairs tunable across 1500–1580 nm, corresponding to a frequency separation from ∼ 10 THz down to exact degeneracy, can be generated from the coupled OPOs, limited only by the reflectivity of the available mirrors.
A0001 in Friedreich ataxia: Biochemical characterization and effects in a clinical trial
Authors: Lynch David R. , Willi Steven M. , Wilson Robert B. , Cotticelli M. Grazia , Brigatti Karlla W. , Deutsch Eric C. , Kucheruk Olena , Shrader William , Rioux Patrice , Miller Guy , Hawi Amale , Sciascia Thomas
Published: June 2012

This study tested the ability of A0001 (α‐tocopheryl quinone; EPI‐A0001), a potent antioxidant, to improve in vitro measures, glucose metabolism, and neurological function in Friedreich ataxia. We used an in vitro study of protection from cell toxicity followed by a double‐blind, randomized, placebo‐controlled trial of 2 doses of A0001 in 31 adults with Friedreich ataxia. The primary clinical trial outcome was the Disposition Index, a measure of diabetic tendency, from a frequently sampled intravenous glucose tolerance test, evaluated 4 weeks into therapy. Secondary neurologic measures included the Friedreich Ataxia Rating Scale. A0001 potently inhibited cell death in Friedreich ataxia models in vitro. For the clinical trial, mean guanine‐adenine‐adenine repeat length was 699, and mean age was 31 years. Four weeks after treatment initiation, differences in changes in the Disposition Index between subjects treated with A0001 and placebo were not statistically significant. In contrast, a dose‐dependent improvement in the Friedreich Ataxia Rating Scale score was observed. Patients on placebo improved 2.0 rating scale points, whereas patients on low‐dose A0001 improved by 4.9 points (P = .04) and patients on a high dose improved by 6.1 points (P < .01). Although A0001 did not alter the Disposition Index, it caused a dose‐dependent improvement in neurologic function, as measured by the Friedreich Ataxia Rating Scale. Longer studies will assess the reproducibility and persistence of neurologic benefit. © 2012 Movement Disorder Society
An anisotropic damage–plasticity model for saturated quasi‐brittle materials
Authors: Hu D. W. , Zhou H. , Shao J. F.
Published: June 2012

This article is devoted to numerical modeling of anisotropic damage and plasticity in saturated quasi‐brittle materials such as rocks and concrete. The damaged materials are represented by an isotropic poroelastic matrix containing a number of families of microcracks. Based on previous works, a discrete thermodynamic approach is proposed. Each family of microcracks exhibits frictional sliding along crack surfaces as well as crack propagation. The frictional sliding is described by a Coulomb–Mohr‐type plastic criterion by taking into account the effect of fluid pressure through a generalized effective stress concept. The damage evolution is entirely controlled by and coupled with the frictional sliding. The effective elastic properties as well as Biot's coefficients of cracked porous materials are determined as functions of induced damage. The inelastic deformation due to frictional sliding is also taken into account. The procedure for the identification of the model's parameters is presented. The proposed model is finally applied to study both mechanical and poromechanical responses of a typical porous brittle rock in drained and undrained compression tests as well as in interstitial pressure controlled tests. The main features of material behaviors are well reproduced by the model. Copyright © 2012 John Wiley & Sons, Ltd.
Does pre‐entry licensing undermine the performance of subsequent independent activities? Evidence from the global aerospace industry, 1944–2000
Authors: Mulotte Louis , Dussauge Pierre , Mitchell Will
Published: June 2012

We study how firms' use of in‐licensing for their initial entry to a business domain can detract from the performance of their subsequent autonomous endeavors in the domain. We argue that in‐licensing produces high levels of causal ambiguity about factors that drive the performance achieved with the licensed product. In turn, the experience that firms gather through pre‐entry licensing is likely to generate superstitious learning and overconfidence that undermine the performance of licensees' subsequent independent operations. The biases will be particularly strong in the face of contextual dissimilarity. We find consistent evidence in a study of firms that entered the global aircraft industry between 1944 and 2000. The research helps advance the understanding of the benefits and costs of markets for technology. Copyright © 2012 John Wiley & Sons, Ltd.
Layered reasoning for randomized distributed algorithms
Authors: Swaminathan Mani , Katoen Joost-Pieter , Olderog Ernst-Rüdiger
Published: June 2012

This paper adopts the communication closed layer (CCL) concept of Elrad and Francez to the formal reasoning of randomized distributed algorithms. We do so by enriching probabilistic automata (PA) with a layered composition operator, an intermediate between parallel and sequential composition. Layered composition is used to establish probabilistic counterparts of the CCL laws that exploit independence and/or precedence conditions between the constituent PA. The probabilistic CCL laws enable partial order (po-) equivalence when layered composition is replaced by sequential composition. Such po-equivalence induces a purely syntactic partial-order state space reduction via layered separation in compositions of PA while preserving probabilistic next-free linear-time properties. The feasibility of such layered separation is demonstrated on a randomized mutual exclusion algorithm by Kushilevitz and Rabin, complementing an algebraic approach (for analyzing this algorithm) by McIver, Gonzalia, Cohen, and Morgan.
Characterisations of testing preorders for a finite probabilistic
π
-calculus
Authors: Deng Yuxin , Tiu Alwen
Published: June 2012

We consider two characterisations of the may and must testing preorders for a probabilistic extension of the finite
π
-calculus: one based on notions of probabilistic weak simulations, and the other on a probabilistic extension of a fragment of Milner–Parrow–Walker modal logic for the
π
-calculus. We base our notions of simulations on similar concepts used in previous work for probabilistic CSP. However, unlike the case with CSP (or other non-value-passing calculi), there are several possible definitions of simulation for the probabilistic
π
-calculus, which arise from different ways of scoping the name quantification. We show that in order to capture the testing preorders, one needs to use the “earliest” simulation relation (in analogy to the notion of early (bi)simulation in the non-probabilistic case). The key ideas in both characterisations are the notion of a “characteristic formula” of a probabilistic process, and the notion of a “characteristic test” for a formula. As in an earlier work on testing equivalence for the
π
-calculus by Boreale and De Nicola, we extend the language of the
π
-calculus with a mismatch operator, without which the formulation of a characteristic test will not be possible.
External and internal choice with event groups in Event-B
Authors: Butler Michael
Published: June 2012

Abrial’s Event-B formalism for refinement-based system development is influenced by Back’s action system approach. Morgan has defined a CSP-like failures-divergence semantics for action systems that distinguishes internal and external choice of actions. Morgan’s semantics has the characteristic that the choice between enabled actions is external while internal choice is represented less directly through nondeterministic effect of actions. Practical experience with Event-B has demonstrated the need to be able to represent both internal and external choice between enabled events more explicitly. In this paper, Morgan’s failures semantics for action systems is modified to allow both internal and external choice to be represented directly. This is achieved by grouping events so that external choice is between event groups and internal choice is within event groups. This leads to a refinement rule for preservation of choice between event groups while allowing for reduction of choice within event groups. We also provide a refinement rule for splitting event groups in order to increase external choice. The refinement rules are justified in terms of failures refinement.
On building cyclic and shared structures in Haskell
Authors: Bird Richard S.
Published: June 2012

We demonstrate how to build certain cyclic and other multi-linked structures in the lazy functional programming language Haskell. No explicit pointers are used in these constructions. Each task is accomplished by starting with a suitable specification and then calculating the required program.
Dijkstra, Floyd and Warshall meet Kleene
Authors: Höfner Peter , Möller Bernhard
Published: June 2012

Around 1960, Dijkstra, Floyd and Warshall published papers on algorithms for solving single-source and all-sources shortest path problems, respectively. These algorithms, nowadays named after their inventors, are well known and well established. This paper sheds an algebraic light on these algorithms. We combine the shortest path problems with Kleene algebra, also known as Conway’s regular algebra. This view yields a purely algebraic version of Dijkstra’s shortest path algorithm and the one by Floyd/Warshall. Moreover, the algebraic abstraction yields applications of these algorithms to structures different from graphs and pinpoints the mathematical requirements on the underlying cost algebra that ensure their correctness.
Architectural refinement and notions of intransitive noninterference
Authors: van der Meyden Ron
Published: June 2012

This paper deals with architectural designs that specify components of a system and the permitted flows of information between them. In the process of systems development, one might refine such a design by viewing a component as being composed of subcomponents, and specifying permitted flows of information between these subcomponents and others in the design. The paper studies the soundness of such refinements with respect to a spectrum of different semantics for information flow policies, including Goguen and Meseguer’s purge-based definition, Haigh and Young’s intransitive purge-based definition, and some more recent notions TA-security, TO-security and ITO-security defined by van der Meyden. It is shown that all these definitions support the soundness of architectural refinement, for both a state- and an action-observed model of systems. A notion of systems refinement in which the information content of observations is reduced is also studied. It is also shown that refinement preserves weak access control structure, an implementation mechanism that ensures TA-security.
Leptin and dementia over 32 years—The Prospective Population Study of Women
Authors: Gustafson Deborah R. , Bäckman Kristoffer , Lissner Lauren , Carlsson Lena , Waern Margda , Östling Svante , Guo Xinxin , Bengtsson Calle , Skoog Ingmar
Published: June 2012

Background

We have shown that high mid‐life central adiposity may increase the risk for dementia after 32 years. Leptin, an adipose tissue hormone, is correlated with adiposity measures and may contribute to a better etiological understanding of the relationship between high adiposity and dementia. We explored the relationship between serum leptin in mid‐life and dementia, which is a late‐life outcome.

Methods

A longitudinal cohort study, the Prospective Population Study of Women, in Gothenburg, Sweden, includes a representative sample of 1462 women followed from mid‐life ages of 38 to 60 years to late‐life ages of 70 to 92 years. Women were examined in 1968, 1974, 1980, 1992, and 2000 using neuropsychiatric, anthropometric, clinical, and other measurements. Serum leptin was measured on samples collected at the 1968 baseline examination, after storage at −20°C for 29 years. Cox proportional hazards regression models estimated incident dementia risk by baseline leptin. Logistic regression models related leptin levels to dementia among surviving participants 32 years later. All models were adjusted for multiple potential confounders.

Results

Mid‐life leptin was not related to dementia risk using Cox or logistic regression models. This was observed despite positive baseline correlations between leptin and adiposity measures, and given our previous report of high mid‐life waist‐to‐hip ratio being related to a twofold higher dementia risk.

Conclusions

Leptin is not a mid‐life marker of late‐life dementia risk in this population sample of Swedish women born between 1908 and 1930.
Generic top-down discrimination for sorting and partitioning in linear time
Authors: HENGLEIN FRITZ
Published: June 2012

We introduce the notion ofdiscriminationas a generalization of both sorting and partitioning, and show thatdiscriminators(discrimination functions) can be definedgenerically, by structural recursion on representations oforderingandequivalence relations. Discriminators improve the asymptotic performance of generic comparison-based sorting and partitioning, and can be implemented not to expose more information than the underlying ordering, respectively equivalence relation. For a large class of order and equivalence representations, including all standard orders for regular recursive first-order types, the discriminators execute in the worst-case linear time. The generic discriminators can be coded compactly using list comprehensions, with order and equivalence representations specified using Generalized Algebraic Data Types. We give some examples of the uses of discriminators, including the most-significant digit lexicographic sorting, type isomorphism with an associative-commutative operator, and database joins. Source code of discriminators and their applications in Haskell is included. We argue that built-in primitive types, notably pointers (references), should come with efficient discriminators, not just equality tests, since they facilitate the construction of discriminators for abstract types that are both highly efficient and representation-independent.
Strategic placement of localization devices (such as pilot points and anchors) in inverse modeling schemes
Authors: Yang Yarong , Over Matthew , Rubin Yoram
Published: June 2012

Localization schemes using devices such as pilot points or anchors (localization devices) are used in inversion schemes as a tool for gleaning information from measurements that can be used to constrain inversion schemes with the added benefit in the form of a potential for reduction in the number of parameters employed in the inversion scheme. This paper proposes and demonstrates a method for strategic placement of the localization devices. The method combines stochastic singular value decomposition with parameter rejection methods to produce a map of “intensity” scores which allows the inverse modeler to place the localization devices at locations defined by their probability for producing informative, probabilistic constraints on the statistical distributions of the target variables. We also show that the method can be used for selecting measurement locations when designing data acquisition campaigns. The method is demonstrated for the case of steady state flow in a heterogeneous conductivity field using MAD (method of anchored distributions). In summary, the proposed localization scheme intends to increase the information gleaned from measurements while reducing the associated computational costs associated with stochastic inversion.
Lake microbial communities are resilient after a whole-ecosystem disturbance
Authors: Shade Ashley , Read Jordan S , Youngblut Nicholas D , Fierer Noah , Knight Rob , Kratz Timothy K , Lottig Noah R , Roden Eric E , Stanley Emily H , Stombaugh Jesse , Whitaker Rachel J , Wu Chin H , McMahon Katherine D
Published: June 2012

Disturbances act as powerful structuring forces on ecosystems. To ask whether environmental microbial communities have capacity to recover after a large disturbance event, we conducted a whole-ecosystem manipulation, during which we imposed an intense disturbance on freshwater microbial communities by artificially mixing a temperate lake during peak summer thermal stratification. We employed environmental sensors and water chemistry analyses to evaluate the physical and chemical responses of the lake, and bar-coded 16S ribosomal RNA gene pyrosequencing and automated ribosomal intergenic spacer analysis (ARISA) to assess the bacterial community responses. The artificial mixing increased mean lake temperature from 14 to 20 °C for seven weeks after mixing ended, and exposed the microorganisms to very different environmental conditions, including increased hypolimnion oxygen and increased epilimnion carbon dioxide concentrations. Though overall ecosystem conditions remained altered (with hypolimnion temperatures elevated from 6 to 20 °C), bacterial communities returned to their pre-manipulation state as some environmental conditions, such as oxygen concentration, recovered. Recovery to pre-disturbance community composition and diversity was observed within 7 (epilimnion) and 11 (hypolimnion) days after mixing. Our results suggest that some microbial communities have capacity to recover after a major disturbance.
Functional responses of methanogenic archaea to syntrophic growth
Authors: Walker Christopher B , Redding-Johanson Alyssa M , Baidoo Edward E , Rajeev Lara , He Zhili , Hendrickson Erik L , Joachimiak Marcin P , Stolyar Sergey , Arkin Adam P , Leigh John A , Zhou Jizhong , Keasling Jay D , Mukhopadhyay Aindrila , Stahl David A
Published: June 2012

Methanococcus maripaludis grown syntrophically with Desulfovibrio vulgaris was compared with M. maripaludis monocultures grown under hydrogen limitation using transcriptional, proteomic and metabolite analyses. These measurements indicate a decrease in transcript abundance for energy-consuming biosynthetic functions in syntrophically grown M. maripaludis, with an increase in transcript abundance for genes involved in the energy-generating central pathway for methanogenesis. Compared with growth in monoculture under hydrogen limitation, the response of paralogous genes, such as those coding for hydrogenases, often diverged, with transcripts of one variant increasing in relative abundance, whereas the other was little changed or significantly decreased in abundance. A common theme was an apparent increase in transcripts for functions using H2 directly as reductant, versus those using the reduced deazaflavin (coenzyme F420). The greater importance of direct reduction by H2 was supported by improved syntrophic growth of a deletion mutant in an F420-dependent dehydrogenase of M. maripaludis. These data suggest that paralogous genes enable the methanogen to adapt to changing substrate availability, sustaining it under environmental conditions that are often near the thermodynamic threshold for growth. Additionally, the discovery of interspecies alanine transfer adds another metabolic dimension to this environmentally relevant mutualism.
Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes
Authors: Lenk Sabine , Moraru Cristina , Hahnke Sarah , Arnds Julia , Richter Michael , Kube Michael , Reinhardt Richard , Brinkhoff Thorsten , Harder Jens , Amann Rudolf , Mußmann Marc
Published: June 2012

Roseobacter clade bacteria (RCB) are abundant in marine bacterioplankton worldwide and central to pelagic sulfur cycling. Very little is known about their abundance and function in marine sediments. We investigated the abundance, diversity and sulfur oxidation potential of RCB in surface sediments of two tidal flats. Here, RCB accounted for up to 9.6% of all cells and exceeded abundances commonly known for pelagic RCB by 1000-fold as revealed by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA and sulfate thiohydrolase (SoxB) genes indicated diverse, possibly sulfur-oxidizing RCB related to sequences known from bacterioplankton and marine biofilms. To investigate the sulfur oxidation potential of RCB in sediments in more detail, we analyzed a metagenomic fragment from a RCB. This fragment encoded the reverse dissimilatory sulfite reductase (rDSR) pathway, which was not yet found in RCB, a novel type of sulfite dehydrogenase (SoeABC) and the Sox multi-enzyme complex including the SoxCD subunits. This was unexpected as soxCD and dsr genes were presumed to be mutually exclusive in sulfur-oxidizing prokaryotes. This unique gene arrangement would allow a metabolic flexibility beyond known sulfur-oxidizing pathways. We confirmed the presence of dsrA by geneFISH in closely related RCB from an enrichment culture. Our results show that RCB are an integral part of the microbial community in marine sediments, where they possibly oxidize inorganic and organic sulfur compounds in oxic and suboxic sediment layers.
Leukotriene A4 Hydrolase: Biology, Inhibitors and Clinical Applications
Authors: GRICE CHERYL A. , FOURIE ANNE M. , LEE-DUTRA ALICE
Published: June 2012

Leukotriene A4 hydrolase is a zinc-containing cytosolic enzyme with both hydrolase and aminopeptidase activity. LTA4H stereospecifically catalyzes the transformation of the unstable epoxide LTA4 to the potent pro-inflammatory mediator LTB4. Variations in the lta4h gene have been linked to susceptibility to multiple diseases including myocardial infarction, stroke and asthma. Pre-clinical animal models and human biomarker data have implicated LTB4 in inflammatory diseases. Several groups have now identified selective inhibitors of LTA4H, many of which were influenced by the disclosure of a protein crystal structure a decade ago. Clinical validation of LTA4H remains elusive despite the progression of inhibitors into pre-clinical and clinical development.
Syk Kinase Inhibitors
Authors: KAILA NEELU , RYAN MARK S. , THORARENSEN ATLI , SAIAH EDDINE
Published: June 2012

Diseases such as rheumatoid arthritis, asthma and chronic allergies are thought to be the result of chronic inflammatory processes and are the subject of intense research by academia and pharmaceutical companies. One of the major proteins targeted by this research is Syk kinase. Since Syk is uniquely positioned at the origins of multiple inflammatory pathways in many cell types, inhibition of the activity of this kinase promises to slow the debilitating effects of chronic inflammation. This review will present a discussion of what has been learned through the efforts on this field of research and report on the recent progress toward clinical drug development. Initially, the biologic role of Syk in generating inflammation will be considered and some of the major genetic and animal studies that have been performed to validate Syk as a target will be described. In the second section, the structural features of the enzyme and approaches taken for the design of inhibitors will be presented. The third section will review the inhibitors that have been designed and chemotypes that have proved effective at inhibiting Syk. And finally, the results of clinical trials are described.
Current sheet oscillations in the magnetic filament approach
Authors: Erkaev N. V. , Semenov V. S. , Biernat H. K.
Published: June 2012

Magnetic filament approach is applied for modeling of nonlinear “kink”-like flapping oscillations of thin magnetic flux tubes in the Earth’s magnetotail current sheet. A discrete approximation for the magnetic flux tube was derived on a basis of the Hamiltonian formulation of the problem. The obtained system of ordinary differential equations was integrated by method of Rosenbrock, which is suitable for stiff equations. The two-dimensional exact Kan’s solution of the Vlasov equations was used to set the background equilibrium conditions for magnetic field and plasma. Boundary conditions for the magnetic filament were found to be dependent on the ratio of the ionospheric conductivity and the Alfvén conductivity of the magnetic tube. It was shown that an enhancement of this ratio leads to the corresponding increase of the frequency of the flapping oscillations. For some special case of boundary conditions, when the magnetic perturbations vanish at the boundaries, the calculated frequency of the “kink”-like flapping oscillations is rather close to that predicted by the “double gradient” analytical model. For others cases, the obtained frequency of the flapping oscillations is somewhat larger than that from the “double gradient” theory. The frequency of the nonlinear flapping oscillations was found to be a decreasing function of the amplitude.
Shift of indirect to direct bandgap and optical response of LaAlO3 under pressure
Authors: Murtaza G. , Ahmad Iftikhar
Published: June 2012

The structural and optoelectronic properties of LaAlO3 under pressure have been investigated for the first time using the highly accurate all electrons full potential linearized augmented plane wave method. The calculated lattice parameter at zero pressure is found in excellent agreement with the experimental results. Furthermore, with the increase in the external pressure, the lattice constant as well as bonds length decreases in accordance with the experimental results. The compound at zero pressure is an indirect bandgap semiconductor, while interestingly the indirect nature shifts to direct one with the increase of the pressure. The bonding in the material is of mixed covalent and ionic nature. In optical properties, frequency dependent parameters such as real and imaginary parts of dielectric function, refractive index, reflectivity, optical conductivity, absorption coefficient, and sumrules are calculated under pressure.
Understanding of the retarded oxidation effects in silicon nanostructures
Authors: Krzeminski C. D. , Han X.-L. , Larrieu G.
Published: June 2012

In-depth understanding of the retarded oxidation phenomenon observed during the oxidation of silicon nanostructures is proposed. The wet thermal oxidation of various silicon nanostructures such as nanobeams, concave/convex nanorings, and nanowires exhibits an extremely different and complex behavior. Such effects have been investigated by the modeling of the mechanical stress generated during the oxidation process explaining the retarded regime. The model describes the oxidation kinetics of silicon nanowires while predicting reasonable and physical stress levels at the silicon/silicon dioxide interface by correctly taking into account the relaxation effects in silicon oxide through plastic flow.
A compressible wall model for large-eddy simulation with application to prediction of aerothermal quantities
Authors: Bocquet S. , Sagaut P. , Jouhaud J.
Published: June 2012

Large-eddy simulation (LES) of compressible flow with wall modelling is assessed on a quasi-isothermal and supersonic plane channel. The derivation of a quasi-analytical wall model based on empirical laws appears very difficult for combined physical effects like compressibility with pressure gradient. A wall model based on the compressible thin boundary layer equations constitutes a more general approach toward the simulation of multiphysical wall bounded flows with LES. In this work, such a wall model is derived and solved thanks to a new meshless method. An adequate scaling of the wall distance is introduced in the Van-Driest damping function of the wall model to handle compressibility effects. The choice of the proper wall distance scaling is shown to be crucial as soon as compressibility effects become significant. Additionally, some sources of error inherent to this wall-modelling approach are treated by appropriate corrections, and show non-negligible impact on the results. On a quasi-isothermal plane channel flow, the mean wall fluxes, primitive variable profiles and velocity fluctuations compare well to Direct Numerical Simulation (DNS) and empirical correlations for a wide range of Reynolds number. Then the DNS of supersonic isothermal-wall plane channel of Coleman at Mach = 1.5 and Mach = 3 are used as a more discriminant test case. The results agree well with the DNS data in terms of mean wall friction and wall heat flux. Finally, a specific analysis of the wall model accuracy is performed outside of the LES solver. This analysis allows to discriminate the error due to the wall model itself from the error due to the interaction between the wall model and the LES solver.