bluuebunny/crossref_metadata_2025 huggingface dataset:
Gyrokinetic simulation tests of quasilinear and tracer transport
Authors: Waltz R. E. , Casati A. , Staebler G. M.
Published: July 2009

A nonlinear gyrokinetic simulation code is used to test the quasilinear transport approximation (QLTA) with simulated nonlinear spectral (potential field) intensity. Two common forms of the QLTA are defined. The first uses the linear mode spectrum (mQLTA) and the second uses the complete frequency spectrum (fQLTA) for the nonlinear spectral intensity. The mQLTA is tested via two-step linear then nonlinear simulations convoluting a quasilinear weight with a nonlinear field intensity spectral weight to get the quasilinear transport in comparison with the actual nonlinear transport. The fQLTA is tested via one-step simulations that have ion and electron “plasma species” at full densities and “tracer species” at negligible densities (and making no contribution to the Poisson field solve equation). If the tracer and plasma gyrokinetic equations are identical, then so are their respective energy and particle diffusivities. Comparing tracer and plasma (actual) diffusivities, when the tracer equation nonlinearity is deleted, provides a quantifiable test of the fQLTA form. The mQLTA preserves ambipolarity but the two-step test includes only the leading linear normal modes at each wave number. The one-step test of the fQLTA subsumes all normal modes but precludes ambipolar particle flow. The mQLTA and fQLTA quasilinear weights (per normal mode) are shown to be identical for a commonly used (but unphysical) mode frequency line width model. In successful cases, quasilinear diffusivities are typically 1.4–1.8 (1.2–1.4) larger than actual diffusivities for mQLTA (fQLTA). The QLTA is expected to make best predictions in the ratios of energy and particle flows. Electron to ion energy flow ratios are well approximated but both forms of the QLTA appear to breakdown most evidently for ratios of particle to energy flows in cases with strongly pinched (and impractically large) particle flows. An example of the so-called passive tracer diffusivity, which includes only linear and nonlinear E×B motion, is given for comparison with actual diffusivities.
Quantitative prediction of gas-phase O17 nuclear magnetic shielding constants
Authors: Auer Alexander A.
Published: July 2009

Benchmark calculations of O17 NMR chemical shifts for a series of 19 molecules with 22 chemical shifts are presented. This includes calculations at the HF-SCF, DFT (BP86 and B3-LYP), MP2, CCSD(T), and for a special case full CCSDT level of theory using basis sets of quadruple zeta quality and better. The effects of the quality of the geometry, electron correlation, basis set, and the inclusion of zero-point vibrational and temperature corrections are discussed in detail and the results are compared to gas-phase experimental values. Mean and standard deviations are 6 and 24 ppm for HF-SCF, −20 and 14 ppm for BP86, −20 and 13 ppm for B3-LYP, and 26 and 12 ppm for MP2. Results at the CCSD(T)/pz3d2f level of theory using geometries optimized at the CCSD(T)/cc-pVTZ level of theory exhibit a mean deviation of 16 ppm and a standard deviation of 6 ppm. A mean deviation of 6 ppm and a standard deviation of 4 ppm are obtained if these values are corrected for zero-point vibrational and temperature effects.
Collisional model of quasilinear transport driven by toroidal electrostatic ion temperature gradient modes
Authors: Pusztai I. , Fülöp T. , Candy J. , Hastie R. J.
Published: July 2009

The stability of ion temperature gradient (ITG) modes and the quasilinear fluxes driven by them are analyzed in weakly collisional tokamak plasmas using a semianalytical model based on an approximate solution of the gyrokinetic equation, where collisions are modeled by a Lorentz operator. Although the frequencies and growth rates of ITG modes far from threshold are only very weakly sensitive to the collisionality, the a/LTi threshold for stability is affected significantly by electron-ion collisions. The decrease in collisionality destabilizes the ITG mode driving an inward particle flux, which leads to the steepening of the density profile. Closed analytical expressions for the electron and ion density and temperature responses have been derived without expansion in the smallness of the magnetic drift frequencies. The results have been compared with gyrokinetic simulations with GYRO and illustrated by showing the scalings of the eigenvalues and quasilinear fluxes with collisionality, temperature scale length, and magnetic shear.
An electrical evaluation method for the silicidation of silicon nanowires
Authors: Tang X. , Reckinger N. , Bayot V. , Flandre D. , Dubois E. , Yarekha D. A. , Larrieu G. , Lecestre A. , Ratajczak J. , Breil N. , Passi V. , Raskin J.-P.
Published: July 2009

Physical and electrical properties of PtSi nanowires (NWs) fabricated on a silicon-on-insulator wafer are investigated. The Si consumption rule in NW silicidation is consistent with that of planar process. The cross-sectional area ratio between PtSi NW and Si NW is about 1.5:1. An electrical method is used to evaluate the silicidation degree of NWs. According to the dependence of the current passing through the NW on the backside substrate voltage, we can determine whether the Si NW is fully or partially silicided. The electrical evaluation results are in agreement with transmission electron microscopy inspections.
Numerically exact quantum dynamics for indistinguishable particles: The multilayer multiconfiguration time-dependent Hartree theory in second quantization representation
Authors: Wang Haobin , Thoss Michael
Published: July 2009

A new theory is proposed to accurately simulate quantum dynamics in systems of identical particles. It is based on the second quantization formalism of many-body quantum theory, in which the Fock space is represented by occupation-number states. Within this representation the overall Fock space can be formally decomposed into smaller subspaces, and the wave function can be expressed as a multilayer multiconfiguration Hartree expansion involving subvectors in these subspaces. The theory unifies the multilayer multiconfiguration time-dependent Hartree theory for both distinguishable and indistinguishable particles. Specific formulations are given for systems of identical fermions, bosons, and combinations thereof. Practical implementations are discussed, especially for the case of fermions, to include the operator algebra that enforces the symmetry of identical particles. The theory is illustrated by a numerical example on vibrationally coupled electron transport.
Ambipolar transport in solution-deposited pentacene transistors enhanced by molecular engineering of device contacts
Authors: Saudari Sangameshwar Rao , Frail Paul R. , Kagan Cherie R.
Published: July 2009

We report ambipolar transport in bottom gold contact, pentacene field-effect transistors (FETs) fabricated by spin-coating and thermally converting its precursor on a benzocyclobutene/SiO2 gate dielectric with chemically modified source and drain electrodes. A wide range of aliphatic and aromatic self-assembled thiolate monolayers were used to derivatize the electrodes and all enhanced electron and hole currents, yet did not affect the observable thin film morphology. Hole and electron mobilities of 0.1–0.5 and 0.05–0.1 cm2/V s are achieved, though the threshold for electron transport was >80 V. These ambipolar FETs are used to demonstrate inverters with gains of up to 94.
Nonlinear optical switching behavior of Au nanocubes and nano-octahedra investigated by femtosecond Z-scan measurements
Authors: Lee Yih Hong , Yan Yongli , Polavarapu Lakshminarayana , Xu Qing-Hua
Published: July 2009

Two types of gold nanoparticles, nanocubes and nano-octahedra were prepared and their nonlinear absorption properties were investigated by using femtosecond open aperture Z-scan experiments. Both nanocubes and nano-octahedra exhibited a shift from saturable absorption (SA) to reverse saturable absorption (RSA) at higher excitation intensities. The SA behavior was ascribed to ground state plasmon band bleaching and RSA was ascribed to excited state absorption and two-photon absorption of these materials. The competition of different processes is responsible for the observed switching behavior.
Spin reorientation transitions in Pt/Co/Pt films under low dose Ga+ ion irradiation
Authors: Jaworowicz J. , Maziewski A. , Mazalski P. , Kisielewski M. , Sveklo I. , Tekielak M. , Zablotskii V. , Ferré J. , Vernier N. , Mougin A. , Henschke A. , Fassbender J.
Published: July 2009

An elegant route for tuning the magnetic anisotropy of ultrathin Co films by Ga+ ion irradiation is presented. The magnetic anisotropy of a Pt/Co(2.6 nm)/Pt film is first changed from in-plane to out-of-plane by uniform low dose Ga+ ion irradiation at 30 keV. When increasing the dose, a second spin reorientation transition toward the sample plane is also evidenced. This could be a way to design magnetic nanowires with perpendicular anisotropy, embedded in an in-plane magnetized environment, either by irradiation through a mask or focused ion beam. Tentative explanations on the origin of these two successive spin reorientations are proposed.
Efficient Large-Scale Synthesis of CAT811, a Potent Calpain Inhibitor of Interest in the Treatment of Cataracts
Authors: Jones Matthew A. , Coxon James M. , McNabb Stephen B. , Mehrtens Janna M. , Alexander Nathan A. , Jones Seth , Chen Hongyuan , Buisan Clémence , Abell Andrew D.
Published: July 2009

A high-yielding, short, and scalable synthesis of a potent calpain 2 inhibitor (CAT811) is reported. The key step in the sequence involves an intramolecular macrocyclization of a 6-iodonorleucine residue to the side chain of tyrosine.
Naturally Occurring Nitrogen–Sulfur Compounds. The Benzothiazole Alkaloids
Authors: Le Bozec Lucille , Moody Christopher J.
Published: July 2009

Several alkaloids contain both nitrogen and sulfur, and a subset of these interesting terrestrial and marine natural products – the benzothiazoles – forms the subject of the present short review. Benzothiazole alkaloids are relatively rare in Nature, but they range in structural complexity from benzothiazole itself and simple derivatives thereof, through the well-known firefly luciferin, to more complex molecules such as the thiazo-rifamycins and the dercitin-kuanoniamine family. Although the biosynthesis of benzothiazoles has not been studied in many cases, the evidence suggests that they are derived from cysteine addition to benzoquinone derivatives followed by ring contraction of the resulting benzothiazine adducts. The review also highlights the fact that little synthetic work has been done on benzothiazole-containing natural products.
The Absolute Configurations of Haliclonacyclamines A and B Determined by X-Ray Crystallographic Analysis
Authors: Mudianta I. Wayan , Garson Mary J. , Bernhardt Paul V.
Published: July 2009

X-Ray crystallography establishes that the marine alkaloids (–)-haliclonacyclamine A 1 and (+)-haliclonacyclamine B 2 each have the configuration C2 (R), C3 (R), C7 (R), and C9 (R). The alkaloids appear to be enantiomerically pure; this provides an insight into the stereochemical consequences of the biosynthetic pathway leading to these bioactive 3-alkylpiperidine alkaloids.
A Total Synthesis of the Marine Alkaloid Ningalin B from (S)-Proline
Authors: Hasse Katrin , Willis Anthony C. , Banwell Martin G.
Published: July 2009

The title alkaloid 1 has been synthesized from (S)-proline (2) using a sequence of reactions involving oxidative bromination (of 2), N-alkylation, Suzuki–Miyaura cross-coupling, and bromination steps.
SN2 Substitution Reactions at the Amide Nitrogen in the Anomeric Mutagens, N-Acyloxy-N-alkoxyamides
Authors: Cavanagh Katie L. , Glover Stephen A. , Price Helen L. , Schumacher Rhiannon R.
Published: July 2009

N-Acyloxy-N-alkoxyamides 1a are unusual anomeric amides that are pyramidal at the nitrogen because of bis oxyl substitution. Through this configuration, they lose most of their amide character and resemble α-haloketones in reactivity. They are susceptible to SN2 reactions at nitrogen, a process that is responsible for their mutagenic behaviour. Kinetic studies have been carried out with the nucleophile N-methylaniline that show that, like SN2 reactions at carbon centres, the rate constant for SN2 displacement of carboxylate is lowered by branching β to the nitrogen centre, or bulky groups on the alkoxyl side chain. Branching or bulky groups on the carboxylate leaving group, however, do not impact on the rate of substitution, which is mostly controlled by the pKA of the departing carboxylate group. These results are in line with computed properties for the model reaction of ammonia with N-acetoxy-N-methoxyacetamide but are in contrast to the role of steric effects on their mutagenicity.
The Effect of Unsaturation on the Formation of Self-Assembled Gels from Fatty Acid L-Serine Amides and their Cytotoxicity Towards Caco-2 Cancer Cells
Authors: Lim Li Yun Grace , Su Yingying , Braet Filip , Thordarson Pall
Published: July 2009

A series of saturated and unsaturated fatty acid l-serines 3 were synthesized and their ability to form self-assembled gels was investigated. The saturated (lauroyl 3a and steraoyl 3b) and monounsaturated (oleoyl 3c) fatty acid l-serines form gels in both water and organic solvent, whereas the diunsaturated linoleyl-l-serine 3d does not form gels in these solvents, indicating that unsaturation adversely affects the gelation process. Cytotoxicity studies on these compounds with Caco-2 cancer cells in vitro show that these gels are only moderately cytotoxic at concentrations up to 0.5 mM, making them a promising candidate for applications such as drug delivery.
Islamic architecture as a reflection of functionalism and interactionism: conceptual origins in culture and sociology
Authors: Al-Qahtany Hani Mohammad
Published: July 2009

What kind of society does Islamic architecture reflect? What are the basic units and forms of Islamic society associated with Islamic architecture, and what kinds of relationships existed among its individuals? Is Islamic society a ‘uniform society’ or a ‘multi-layered society’? These fundamental questions are at the centre of this study. This paper explores the basic intellectual, social and environmental aspects that have shaped Islamic architecture. It explores these aspects as reflected in the building forms of Muslim societies. Functionalism and interactionism are two major schools of modern sociology. As a social phenomenon, Islamic architecture is examined in the light of these two schools. The urban fabric of the traditional Islamic city as an example of functionalism in architecture is examined with reference to the ruined city of Sāmarrāʾ, in Iraq; and examples of Ottoman architecture are considered as models of interactionism in city planning and architecture. The works of three major figures in contemporary Arab thought, Muḥammad Abed Al-Jabri and ꜤAbdullah Al- ꜤArawī from Morocco, and Mohammad Al-Anṣārī from Bahrain, are considered in this paper. Their thoughts and views are used as vehicles to test some innate features of Islamic architecture. The influence of language and the desert, two exceptionally important factors that have shaped the culture of Muslim societies and its manifestation in architecture, is also explored. The findings of this paper, although still at a preliminary stage, reiterate the major concepts of the medieval Arab scholar Ibn Khaldūn, in his Muqaddimah, in an architectural context.
The nucleolar RNA methyltransferase Misu (NSun2) is required for mitotic spindle stability
Authors: Hussain Shobbir , Benavente Sandra Blanco , Nascimento Elisabete , Dragoni Ilaria , Kurowski Agata , Gillich Astrid , Humphreys Peter , Frye Michaela
Published: July 2009

Myc-induced SUN domain–containing protein (Misu or NSun2) is a nucleolar RNA methyltransferase important for c-Myc–induced proliferation in skin, but the mechanisms by which Misu contributes to cell cycle progression are unknown. In this study, we demonstrate that Misu translocates from the nucleoli in interphase to the spindle in mitosis as an RNA–protein complex that includes 18S ribosomal RNA. Functionally, depletion of Misu caused multiple mitotic defects, including formation of unstructured spindles, multipolar spindles, and chromosome missegregation, leading to aneuploidy and cell death. The presence of both RNA and Misu is required for correct spindle assembly, and this process is independent of active translation. Misu might mediate its function at the spindle by recruiting nucleolar and spindle-associated protein (NuSAP), an essential microtubule-stabilizing and bundling protein. We further identify NuSAP as a novel direct target gene of c-Myc. Collectively, our results suggest a novel mechanism by which c-Myc promotes proliferation by stabilizing the mitotic spindle in fast-dividing cells via Misu and NuSAP.
Ca2+ signaling evoked by activation of Na+ channels and Na+/Ca2+ exchangers is required for GABA-induced NG2 cell migration
Authors: Tong Xiao-ping , Li Xiang-yao , Zhou Bing , Shen Wanhua , Zhang Zhi-jun , Xu Tian-le , Duan Shumin
Published: July 2009

NG2 cells originate from various brain regions and migrate to their destinations during early development. These cells express voltage-gated Na+ channels but fail to produce typical action potentials. The physiological role of Na+ channels in these cells is unclear. We found that GABA induces membrane depolarization and Ca2+ elevation in NG2 cells, a process requiring activation of GABAA receptors, Na+ channels, and Na+/Ca2+ exchangers (NCXs), but not Ca2+ channels. We have identified a persistent Na+ current in these cells that may underlie the GABA-induced pathway of prolonged Na+ elevation, which in turn triggers Ca2+ influx via NCXs. This unique Ca2+ signaling pathway is further shown to be involved in the migration of NG2 cells. Thus, GABAergic signaling mediated by sequential activation of GABAA receptors, noninactivating Na+ channels, and NCXs may play an important role in the development and function of NG2 glial cells in the brain.
The Drosophila afadin homologue Canoe regulates linkage of the actin cytoskeleton to adherens junctions during apical constriction
Authors: Sawyer Jessica K. , Harris Nathan J. , Slep Kevin C. , Gaul Ulrike , Peifer Mark
Published: July 2009

Cadherin-based adherens junctions (AJs) mediate cell adhesion and regulate cell shape change. The nectin–afadin complex also localizes to AJs and links to the cytoskeleton. Mammalian afadin has been suggested to be essential for adhesion and polarity establishment, but its mechanism of action is unclear. In contrast, Drosophila melanogaster’s afadin homologue Canoe (Cno) has suggested roles in signal transduction during morphogenesis. We completely removed Cno from embryos, testing these hypotheses. Surprisingly, Cno is not essential for AJ assembly or for AJ maintenance in many tissues. However, morphogenesis is impaired from the start. Apical constriction of mesodermal cells initiates but is not completed. The actomyosin cytoskeleton disconnects from AJs, uncoupling actomyosin constriction and cell shape change. Cno has multiple direct interactions with AJ proteins, but is not a core part of the cadherin–catenin complex. Instead, Cno localizes to AJs by a Rap1- and actin-dependent mechanism. These data suggest that Cno regulates linkage between AJs and the actin cytoskeleton during morphogenesis.
Predictors of survival after aortic valve replacement in patients with low‐flow and high‐gradient aortic stenosis
Authors: Ding Wen‐Hong , Lam Yat‐Yin , Duncan Alison , Li Wei , Lim Eric , Kaya Mehmet G. , Chung Robin , Pepper John R. , Henein Michael Y.
Published: July 2009

Aims

To identify predictors of survival following aortic valve replacement (AVR) in patients with low‐flow and high‐gradient aortic stenosis (AS).

Methods and results

Eighty‐six patients (aged 71 ± 10 years) with severe AS [aortic valve mean pressure gradient >40 mmHg or valve area <1.0 cm2] and left ventricular (LV) dysfunction [ejection fraction (EF) <50%] underwent AVR. Cox proportional hazards were used to identify independent clinical and echocardiographic predictors of mortality. Operative (30‐day) mortality was 10%. Peri‐operative mortality was associated with lower mean LVEF, higher mitral E:A ratio, peak systolic pulmonary artery pressure (PSPAP), and serum creatinine (by 12%, 2.3, 28 mmHg, and 74 mmol/L, respectively, all P < 0.001), NYHA class III–IV (100 vs. 65%), concomitant CABG (89 vs. 55%), urgent surgery (78 vs. 35%), and longer bypass‐time (by 28 min, all P < 0.05). Mortality at 4 years was 17%. Univariate predictors [hazard ratio (HR)] of 4‐year mortality were: lower EF (HR 0.68 per % increase, P < 0.001), presence of restrictive LV filling (HR: 3.52, P < 0.001), raised PSPAP (HR: 1.07, P < 0.001), and CABG (HR: 4.93, P = 0.037). However, only low EF (<40%, HR 0.74, P = 0.030), the presence of restrictive filling (HR 1.77, P = 0.033), and raised PSPAP (>45 mmHg, HR 2.71, P = 0.010) remained as independent predictors after multivariate analysis.

Conclusion

The severity of pre‐operative systolic and diastolic LV dysfunction is the major predictor of mortality following AVR for low‐flow and high‐gradient AS.
Spring Dead Spot of Bermudagrass: A Challenge for Researchers and Turfgrass Managers
Authors: Tredway Lane P. , Tomaso-Peterson Maria , Perry Hunter , Walker Nathan R.
Published: July 2009

Spring dead spot is a destructive disease of bermudagrass turf in climates where the host is exposed to freezing temperatures during winter dormancy. The disease is the result of a complex interaction between a dormant host plant, fungal pathogens in the genus Ophiosphaerella, and environmental conditions. Although progress has been made in our understanding of the individual factors that determine spring dead spot development, we must begin to understand how factors interact to influence the disease. This knowledge will facilitate the development of effective and integrated management plans for spring dead spot in bermudagrass turf.

Accepted for publication 8 May 2009. Published 10 July 2009.
Multilocus Sequence Typing Reveals Two Evolutionary Lineages of Acidovorax avenae subsp. citrulli
Authors: Feng Jianjun , Schuenzel Erin L. , Li Jianqiang , Schaad Norman W.
Published: July 2009

Acidovorax avenae subsp. citrulli, causal agent of bacterial fruit blotch, has caused considerable damage to the watermelon and melon industry in China and the United States. Understanding the emergence and spread of this pathogen is important for controlling the disease. To build a fingerprinting database for reliable identification and tracking of strains of A. avenae subsp. citrulli, a multilocus sequence typing (MLST) scheme was developed using seven conserved loci. The study included 8 original strains from the 1978 description of A. avenae subsp. citrulli, 51 from China, and 34 from worldwide collections. Two major clonal complexes (CCs), CC1 and CC2, were identified within A. avenae subsp. citrulli; 48 strains typed as CC1 and 45 as CC2. All eight original 1978 strains isolated from watermelon and melon grouped in CC1. CC2 strains were predominant in the worldwide collection and all but five were isolated from watermelon. In China, a major seed producer for melon and watermelon, the predominant strains were CC1 and were found nearly equally on melon and watermelon.
Analysis of Nonlinear Relationships in Dual Epidemics, and Its Application to the Management of Grapevine Downy and Powdery Mildews
Authors: Savary Serge , Delbac Lionel , Rochas Amélie , Taisant Guillaume , Willocquet Laetitia
Published: July 2009

Dual epidemics are defined as epidemics developing on two or several plant organs in the course of a cropping season. Agricultural pathosystems where such epidemics develop are often very important, because the harvestable part is one of the organs affected. These epidemics also are often difficult to manage, because the linkage between epidemiological components occurring on different organs is poorly understood, and because prediction of the risk toward the harvestable organs is difficult. In the case of downy mildew (DM) and powdery mildew (PM) of grapevine, nonlinear modeling and logistic regression indicated nonlinearity in the foliage–cluster relationships. Nonlinear modeling enabled the parameterization of a transmission coefficient that numerically links the two components, leaves and clusters, in DM and PM epidemics. Logistic regression analysis yielded a series of probabilistic models that enabled predicting preset levels of cluster infection risks based on DM and PM severities on the foliage at successive crop stages. The usefulness of this framework for tactical decision-making for disease control is discussed.
Morphological, Genetic, and Pathogenic Characterization of Colletotrichum acutatum, the Cause of Anthracnose of Almond in Australia
Authors: McKay Suzanne F. , Freeman Stanley , Minz Dror , Maymon Marcel , Sedgley Margaret , Collins Graham C. , Scott Eileen S.
Published: July 2009

Almond anthracnose was reported for the first time in Australia in 1998 and has since been observed in all of the major almond-growing regions. The organism causing anthracnose was confirmed as Colletotrichum acutatum using taxon-specific polymerase chain reaction (PCR). Three main morphotypes of C. acutatum from almond in Australia were identified (namely, pink, orange, and cream colony color) and the optimum temperature for mycelial growth of representative isolates was 25°C. Australian isolates of C. acutatum were more similar morphologically to the pink subpopulation of C. acutatum from California than to the gray Californian subpopulation and the isolates of Colletotrichum from Israel. Inter-simple-sequence-repeat (ISSR) PCR analysis revealed that the majority of Australian isolates shared an identical banding pattern whereas Australian isolates of C. acutatum from almond were distinct from isolates of the pink and gray subpopulations of C. acutatum from almond in California and of Colletotrichum spp. from almond in Israel. Sequence analysis of the internally transcribed spacer (ITS1-2) ribosomal DNA region of representative isolates differed from the results of ISSR-PCR in that polymorphisms were revealed among isolates, indicating that some genetic variation may be present. Pathogenicity experiments on detached leaves and fruit revealed pathogenic variation among representative isolates of C. acutatum from almond in Australia, California, and Israel; however, all isolates tested caused disease. Distinct subgroups among Australian isolates of C. acutatum from almond were not supported on the basis of morphology, mycelial growth rates, ISSR-PCR, and pathogenicity.
Neurochemical Changes in the Aging Process: Implications in Medication in the Elderly
Authors: Anyanwu Ebere C.
Published: July 2009

Aging is an inevitable process in human development, which follows a time course thatcan be delayed, or hastened, by lifestyles, diseases and events. The factors that affectthe aging process can be delayed, but not prevented. This paper evaluates theneurochemical changes in the aging process and their relevance in the modality ofelderly medication. For clarity and understanding of the relevant neurobiochemicalprocess and effects, the neuroanatomical, physiological, and neurobehavioral changesare reviewed as they relate to medication in the elderly.
Adult versus adolescent onset of smoking: how are mood disorders and other risk factors involved?
Authors: Ajdacic‐Gross Vladeta , Landolt Karin , Angst Jules , Gamma Alex , Merikangas Kathleen R. , Gutzwiller Felix , Rössler Wulf
Published: July 2009

Aims  To examine the strength of association between smoking and mood disorders and the association between smoking and its traditional risk factors, comparing those who started smoking in adolescence with those who started smoking in early adulthood.

Design and participants  The analyses relied on prospective data from the Zurich Study. This longitudinal community study started in 1979 with a stratified sample of 591 participants aged 20/21 years, weighted towards those with mental disorders. Follow‐up interviews were conducted at ages 23, 28, 30, 35 and 41.

Measurements  In this analysis the adult versus adolescent onset of smoking was regressed on the cumulative prevalence of mood disorders, personality characteristics measured by the Freiburg Personality Inventory, common risk factors such as parental smoking, conduct and school problems, troubles with the family and basic socio‐demographic variables (sex, education).

Findings  In the Zurich Study cohort we found that 61.6% were former or current smokers, of whom 87% started smoking before the age of 20 and 13% after the age of 20. Adolescent onset of smoking was associated strongly with later major depression, dysthymia or bipolar disorders and, furthermore, with parental smoking, extroverted personality and discipline problems and rebelliousness in youth. However, only depression and dysthymia were associated with adult onset smoking and other risk factors associated with smoking were not so associated in this group.

Conclusions  Correlates of smoking onset in adolescence are mainly not applicable to the onset of smoking in young adulthood. Smoking onset beyond adolescence is an open research issue.
General scaling rules of the hysteretic water retention function based on Mualem’s domain theory
Authors: Mualem Y. , Beriozkin A.
Published: July 2009

Based on the domain theory of hysteresis, the present study rigorously derives a unified scaling transformation for predicting the wetting scanning retention function, θw(ψ), following any sequence of wetting and drying processes, from the measured main wetting curve. It is proved theoretically that a shape‐similarity exists among the different wetting curves of a given soil. Each wetting scanning curve and the main wetting curve are described by the same normalized equation, over the common interval of ψ values. This shape‐similarity is a direct result of the Mualem domain theory. On this basis, a general unique equation is formulated for prediction of all wetting scanning curves, of all orders, which is compatible with the Mualem dependent, as well as independent, domain theory. On the same theoretical basis, it is proved that no similarity exists among the drying scanning curves. Thus, the use of the scaling transformation for prediction of the drying scans is subjected to inconsistency with the physical principles underlying the dependent domain theory. As a result, scaling in this case would inevitably lead to inaccuracies in the calculated drying curves. A significant step forward has been made in the present study, from Mualem’s dependent domain model (1984) with its implicit predictive formulae of the drying scanning curves. A unique explicit equation was theoretically derived, applicable for describing the drying scanning curves of all orders. This unique equation of the drying scanning curves, together with the general single equation of the wetting scanning curves, provided closure of all theoretical wetting and drying scans within the main hysteresis loop. Consequently, the retention function following any sequence of successive wetting and drying processes can be predicted by these two equations determined by the measured boundary curves.
Accumulation and solubility of metals during leaf litter decomposition in non‐polluted and polluted soil
Authors: Scheid S. , Günthardt‐Goerg M. S. , Schulin R. , Nowack B.
Published: July 2009

The decomposition of alder (Alnus glutinosa) and poplar (Populus tremula) leaf litter placed in direct contact with non‐polluted and metal‐polluted soil was investigated over 25 months in a controlled model‐ecosystem experiment using the litterbag method. In addition to mass loss, we monitored the total and soluble concentrations of carbon, Cu, Zn, Cd and Pb. Leaves from trees grown on polluted soil had larger initial Zn, Cd and dissolved organic carbon concentrations. Neither the origin of the leaves (from trees grown on non‐polluted or polluted soil) nor the placement of the leaves in polluted or unpolluted soil affected the decomposition process. Total metal contents increased in leaves placed on polluted soil over time. The solubility of metals in the leaf litter decreased over time, indicating that leaves acted as a temporary pool for metals from the soil in direct contact with the leaves. The sorbed metals were strongly bound in the litter even after two years of decomposition. The strong binding and thus reduced bioavailability of the metals provides an explanation for why they had no observable effects on litter decomposition.
Responses of ethylene and methane consumption to temperature and pH in temperate volcanic forest soils
Authors: Xu X. , Inubushi K.
Published: July 2009

There is limited knowledge about the consumption and interaction of methane (CH4) and ethylene (C2H4) in forest soils under disturbances of temperature and acidification. Temperate volcanic forest topsoils (0‐5 cm) sampled under different tree species (e.g. Pinus sylvestris, Cryptomeria japonica and Quercus serrata) were used to study the capacities for CH4 and C2H4 consumption and their sensitivity to temperature and pH. We also studied the responses of soil nitrogen (N) transformations to temperature and relationships to consumption of both CH4 and C2H4. The C2H4 consumption rates increased with temperature up to 35oC, whereas the optimum temperature for CH4 consumption rates was approximately 25oC. Both Q10 values and activation energies for CH4 consumption rates over the range 5 to 25oC were larger than corresponding values for C2H4 consumption rates. The rates of nitrous oxide (N2O) and nitric oxide (NO) evolution and net N mineralization in the soils increased exponentially with temperature up to 35oC, with relatively large Q10 values and activation energies for NO evolution. In these forest topsoils, rates of CH4 and C2H4 consumption at pH < 4.0 were negligible, and the pH optimum for both consumptions varied from 5.5 to 6.2. Most of the tested forest soils had an optimum pH for CH4 and C2H4 consumption that was above natural pH values, which indicated that soil acidification would inhibit CH4 and C2H4 consumption in situ. There was a high rate of net C2H4 evolution from forest soils acidified experimentally to pH < 4.0, particularly from Cryptomeria japonica forest soil, and 67% of the variation in C2H4 evolution rates could be accounted for by the increase in soil water‐soluble organic carbon concentrations. Previous studies have shown that addition of C2H4 in headspace gases can inhibit atmospheric CH4 consumption in such forest soils. Hence, the evolution of C2H4 from temperate volcanic forest soils at decreasing pH can exacerbate inhibition of the soil atmospheric CH4 consumption in situ.
Landscape‐level vegetation recovery from herbivory: progress after four decades of invasive red deer control
Authors: Tanentzap Andrew J. , Burrows Larry E. , Lee William G. , Nugent Graham , Maxwell Jane M. , Coomes David A.
Published: July 2009

1.  Ungulates have reached such high densities in some natural ecosystems that culling is frequently used to reduce their impacts on vegetation. However, much is still unknown about the outcomes of landscape‐level control, in part because monitoring vegetation recovery requires decades.

2.
 We report long‐term vegetation changes in permanent plots located in forest, shrubland and grassland communities across a mountain range in southern New Zealand. We test whether c. 92% reduction in the population of invasive non‐indigenous red deer Cervus elaphus since 1964 has led to the recovery of deer‐preferred species.

3.  Tree seedlings, saplings and the number of seedlings per adult tree increased over time. There was lower recruitment, however, of highly palatable forest species compared with less palatable species, and the recruitment of saplings was lower in browsed forest plots compared with deer exclosures.

4.
 The total number of occurrences and absolute number of palatable species per plot increased over time in shrublands and grasslands respectively. The height of both shrublands and palatable grassland snow tussocks Chionochloa spp. increased, although the occurrences of most individual species remained unchanged over time.

5.  Vegetation recovery at our site in response to long‐term and significant herbivore reductions may be limited by several factors, including the slow growth rates of New Zealand species, density‐dependent diet switching by deer, altered successional trajectories and below‐ground processes.

6.
 Synthesis and applications. Our results suggest that after nearly four decades, even low densities of introduced herbivores may restrict ecosystem recovery, and therefore, restoring herbivore‐disturbed ecosystems by solely manipulating herbivore population numbers may require a long‐term perspective. Management strategies can accelerate recovery by protecting existing palatable plants within deer‐exclosures, and planting or seeding palatable species within these refugia. However, in addition to increasing seed sources, restoration may only become apparent following large‐scale disturbance events and canopy turnover.
Taking into account phylogenetic and divergence‐time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae
Authors: Smith Stephen A.
Published: July 2009

Aim  To examine the biogeographical history of the angiosperm clade Caprifolieae (Caprifoliaceae) using parametric biogeographical reconstruction methods. The existing parametric method was extended to evaluate biogeographical reconstructions over the distribution of dated phylogenies. This method provides a framework for reconstructing large‐scale biogeography with parametric methods, while accounting for uncertainty in the phylogenetic relationships and divergence time.

Location  Asia, Europe and North America.

Methods  The biogeographical history of the major lineages of Caprifolieae was reconstructed over the posterior distribution of dated trees generated from Bayesian divergence‐time analyses. Results from a model with no geological constraints were compared with those from one where movement is disallowed across the North Atlantic after the Eocene. The most plausible scenarios were segregated at each node to test whether particular scenarios were reconstructed for particular divergence times. The parametric biogeographical method was also extended to estimate connectivity between areas so that the probability of dispersal between the major areas of the Northern Hemisphere could be explored.

Results  Phylogenetic results for Caprifolieae agreed with previous estimates using smaller sampling, but uncertainty remained despite efforts to resolve the relationships of the four genera within this clade using multiple markers. In addition to topological uncertainty, there were few fossils available for calibrations, resulting in large confidence intervals for divergence times. Divergence‐time analyses put the diversification of Caprifolieae at between 36 and 51 Ma and showed that Caprifolieae probably originated in Asia, with multiple movements into Europe and western and eastern North America.

Main conclusions  Newly developed parametric methods for biogeographical reconstruction incorporate more data and better models. Here, the parametric biogeographical reconstruction method has been extended to allow for topological and divergence‐time uncertainty. The analyses of Caprifolieae demonstrated that biogeographical hypotheses can be explored even where there are large confidence intervals on divergence times and uncertainty in topology. These results add to the growing evidence that Asia was an important source of Northern Hemisphere diversity throughout the Cenozoic.
Implementation of Clinical Supervision: educational preparation and subsequent diary accounts of the practicalities involved, from an Australian mental heath nursing innovation
Authors: WHITE E. , WINSTANLEY J.
Published: July 2009

Accessible summary

Clinical Supervision (CS) has shown promise as a positive contribution to the clinical governance agenda in health service provision.

Educational preparation and first‐hand testimony of the issues faced by mental health nursing staff engaged as supervisors in the implementation of CS arrangements in Queensland, Australia, are reported.

Several challenges emerge from the diary accounts of their experience that may confront Clinical Supervision policy makers, educators, managers and clinicians, anywhere in the world, with immediate effect.

Set against the backdrop of several inquiry reports about mental health service provision in Australia, the privately experienced cost of working and coping in contemporary mental health settings, remains poorly understood. Clinical Supervision, a structured staff support arrangement, has shown promise as a positive contribution to the clinical governance agenda and is now found reflected in central policy themes elsewhere in the world. However, the concept of Clinical Supervision remains underdeveloped in Australia. The background to a novel randomized controlled trial, currently in progress in Queensland, Australia, is reported elsewhere. This paper reports on the educational preparation for, and subsequent first‐hand testimony of the issues faced by, front‐line mental health nursing staff engaged in the implementation of Clinical Supervision, under the auspices of the randomized controlled trial. It is argued here that, in advance of quantitative findings becoming available, several challenges emerge from their supplementary and contemporaneous diary accounts of their experience that may confront Clinical Supervision policy makers, educators, managers and clinicians, anywhere in the world, with immediate effect.
The GLABRA2 homeodomain protein directly regulates CESA5 and XTH17 gene expression in Arabidopsis roots
Authors: Tominaga‐Wada Rumi , Iwata Mineko , Sugiyama Junji , Kotake Toshihisa , Ishida Tetsuya , Yokoyama Ryusuke , Nishitani Kazuhiko , Okada Kiyotaka , Wada Takuji
Published: July 2009

Arabidopsis root hair formation is determined by the patterning genes CAPRICE (CPC), GLABRA3 (GL3), WEREWOLF (WER) and GLABRA2 (GL2), but little is known about the later changes in cell wall material during root hair formation. A combined Fourier‐transform infrared microspectroscopy–principal components analysis (FTIR‐PCA) method was used to detect subtle differences in the cell wall material between wild‐type and root hair mutants in Arabidopsis. Among several root hair mutants, only the gl2 mutation affected root cell wall polysaccharides. Five of the 10 genes encoding cellulose synthase (CESA1–10) and 4 of 33 xyloglucan endotransglucosylase (XTH1–33) genes in Arabidopsis are expressed in the root, but only CESA5 and XTH17 were affected by the gl2 mutation. The L1‐box sequence located in the promoter region of these genes was recognized by the GL2 protein. These results indicate that GL2 directly regulates cell wall‐related gene expression during root development.
A new HLA‐B*5124 variant, B*512402 allele, identified by sequence‐based typing
Authors: Kim K. W. , Kwon O. J. , Kwon S.‐Y. , Cho N. S. , Oh D. J.
Published: July 2009

A novel human leukocyte antigen‐B allele, officially named B*512402, was identified in a Korean bone marrow donor. The B*512402 allele shows two nucleotide substitutions compared with B*512401 in exon 3 at codons 135 (GCG → GCC) and 138 (ACC → ACG) without any amino acid substitution.
S‐genotyping of Eastern European almond cultivars: identification and characterization of new (S36–S39) self‐incompatibility ribonuclease alleles
Authors: Halász J. , Fodor Á. , Pedryc A. , Hegedűs A.
Published: July 2009

With 3 figures and 2 tables

Consensus polymerase chain reaction (PCR) primers amplifying the first and second intron regions of the S‐RNase gene and DNA sequencing as well as fruit set analysis after controlled pollinations were used for S‐genotyping of Eastern European almond cultivars. Complete S‐genotypes have been proposed for 19 accessions, and partial S‐genotypes have been proposed for three additional accessions. Based on DNA sequences and fruit set analysis, two novel cross‐incompatibility groups have been proposed: group XXI (S11S31H) including ‘Szigetcsépi 55’ (3/9) and ‘Eriane’ and group XXII (S36S37) for ‘Nikitskyi’ and ‘Óriás kagyló’ (4/4). Four new alleles were identified, S36 (FJ529211), S37 (FJ529212), S38 (FJ529213) and S39 (FJ529214). The combination of consensus PCR primers amplifying the first and second intron regions could reliably discriminate the S‐RNase alleles identified in this study from those described previously. Our results supply long‐awaited information on almond S‐allele diversity from regions between the main cultivation centres and the centre of origin of this species.
The ‘I’ in personalized genetics: 2008 Ian Constable lecture
Authors: Mackey David A
Published: July 2009

Abstract

The completion of the Human Genome Project heralded a new era in human genetic testing to predict individuals at risk from many common diseases. DNA markers can also be used to track one's ancestry. Eye diseases such as age‐related macular degeneration and glaucoma have been important examples of the success of genome‐wide association studies. Resource‐strapped genetic services have been limited in providing DNA testing for many well‐established hereditary diseases. Thus, several direct‐to‐consumer genetic services have arisen to fill the gap. However, there is a major need for research into interpreting the results of such tests of up to one million DNA markers. Studies of population, family and twins sharing common diseases help us clarify the significance of gene–disease associations. However, as identical twins show us, for some conditions our genes do not absolutely determine our destiny and environmental factors interact with our genetic profile.
Recurrence of treated ciliary body melanoma following trabeculectomy
Authors: Tay Eugene , Cree Ian A , Hungerford John , Franks Wendy
Published: July 2009

Abstract

A 69‐year‐old man was treated for a right ciliary body melanoma with plaque radiotherapy. One year later, he had uncomplicated cataract extraction but developed prolonged postoperative inflammation and secondary glaucoma. The tumour remained unchanged on yearly ultrasound B scans but intraocular pressures became uncontrolled despite maximal medical therapy. After radiotherapy, he underwent trabeculectomy with 5‐fluorouracil and revision with mitomycin C 2 years later. The melanoma recurred with extrascleral extension under the trabeculectomy bleb 14 years after plaque radiotherapy and 5 years after trabeculectomy surgery. Enucleation was performed and histological analysis showed a ring melanoma involving the root of the iris, filling the trabecular meshwork and extending into the anterior chamber. The predominant cell type was epithelioid with large nuclei and prominent nucleoli. Trabeculectomy surgery may increase the risk of extrascleral extension of ciliary body melanoma even after apparently successful plaque radiotherapy and long‐term local tumour control.