bluuebunny/crossref_metadata_2025 huggingface dataset:
Diminished cage effect in solid p-H2: Infrared absorption of CH3S observed from photolysis in situ of CH3SH, CH3SCH3, or CH3SSCH3 isolated in p-H2 matrices
Authors: Bahou Mohammed , Lee Yuan-Pern
Published: October 2010

We report the infrared absorption spectrum of the methylthio (or thiomethoxy) radical, CH3S (X E23/2), produced via photodissociation in situ of three precursors CH3SH, CH3SCH3, and CH3SSCH3 isolated in solid p-H2. The common absorption features observed with similar intensity ratios in each experiment are assigned to CH3S. The wavenumbers of these features agree satisfactorily with those predicted with a spin-vibronic Hamiltonian accounting for the anharmonic effects and the Jahn–Teller effects to the quartic term [A. V. Marenich and J. E. Boggs, J. Chem. Theory Comput. 1, 1162 (2005)]. In addition to an absorption line at 724.2 cm−1, corresponding to a transition of 31 previously determined to be 727 cm−1 from fluorescence spectra of gaseous CH3S, we identified fundamental transitions 61(a1) at 771.1, 61(e) at 1056.6, 51(a1) at 1400.0, 41(a1) at 2898.4 cm−1, and several combination and overtone transitions. In contrast, photolysis of CH3SSCH3 isolated in solid Ar produces mainly H2CS, CH3SH, and CS2, but no CH3S. These results demonstrate the feasibility of using photolysis in situ of precursors isolated in solid p-H2 to produce free radicals by taking advantage of the diminished cage effect of the matrix.
Multiband reflectometry system for density profile measurement with high temporal resolution on JET tokamak
Authors: Sirinelli A. , Alper B. , Bottereau C. , Clairet F. , Cupido L. , Fessey J. , Hogben C. , Meneses L. , Sandford G. , Walsh M. J. , Contributors JET-EFDA
Published: October 2010

A new system has been installed on the JET tokamak consisting of six independent fast-sweeping reflectometers covering four bands between 44 and 150 GHz and using orthogonal polarizations. It has been designed to measure density profiles from the plasma edge to the center, launching microwaves through 40 m of oversized corrugated waveguides. It has routinely produced density profiles with a maximum repetition rate of one profile every 15 μs and up to 100 000 profiles per pulse.
Fast ion charge exchange spectroscopy adapted for tangential viewing geometry in LHD
Authors: Ito T. , Osakabe M. , Ida K. , Yoshinuma M. , Kobayashi M. , Goto M. , Murakami S. , Isobe M. , Kobayashi S. , Toi K. , Ogawa K. , Takeiri Y. , Okamura S.
Published: October 2010

A tangential Fast Ion Charge eXchange Spectroscopy is newly applied on a Large Helical Device (LHD) for co/countercirculating fast ions, which are produced by high energy tangential negative-ion based neutral beam injection. With this new observation geometry, both the tangential-neutral beam (NB) and a low-energy radial-NB based on positive ions can be utilized as probe beams of the measurement. We have successfully observed Doppler-shifted H-alpha lights due to the charge exchange process between the probing NB and circulating hydrogen ions of around 100 keV in LHD plasmas.
A comprehensive theoretical investigation of the electronic states of Ca2 up to the Ca(4s2 S1)+Ca(4s5p P1) dissociation limit
Authors: Bouissou Thomas , Durand Gérard , Heitz Marie-Catherine , Spiegelman Fernand
Published: October 2010

A theoretical survey of the electronic structure of Ca2 is presented using two-electron pseudopotentials complemented by core-polarization operators on Ca atoms and multireference configuration interaction/quasidegenerate perturbation theory (MRCI/QDPT) treatment of molecular excited states. The spectroscopic constants of 70 electronic states up to 30 000 cm−1 above the ground state are determined. This implies all Ca2 states dissociating up to the Ca(4s2 S1)+Ca(4s5p P3,1) dissociation limits. All spin states (singlet, triplet, and quintet) are investigated. The work emphasizes the variety of interactions implying singly valence and lowest Rydberg excited states, doubly excited states generated by atom pairs P3(4s4p)+P3(4s4p), or P3(4s4p)+D3(4s3d), 4p3d double excitations asymptotically localized on a single-atom. Zwitterionic Ca++Ca− configurations are evidenced and shown to induce specific electronic patterns in Σ1g+, Σ3g+, Σ1u+, Σ3u+, Π1g, Π3g, Π1u, and Π3u symmetry manifolds. They also provide insight for qualitative features (barriers) found for the lower electronic states already investigated in previous publications by other authors.
Scaling the energy conversion rate from magnetic field reconnection to different bodies
Authors: Mozer F. S. , Hull A.
Published: October 2010

Magnetic field reconnection is often invoked to explain electromagnetic energy conversion in planetary magnetospheres, stellar coronae, and other astrophysical objects. Because of the huge dynamic range of magnetic fields in these bodies, it is important to understand energy conversion as a function of magnetic field strength and related parameters. It is conjectured theoretically and shown experimentally that the energy conversion rate per unit area in reconnection scales as the cube of an appropriately weighted magnetic field strength divided by the square root of an appropriately weighted density. With this functional dependence, the energy release in flares on the Sun, the large and rapid variation of the magnetic flux in the tail of Mercury, and the apparent absence of reconnection on Jupiter and Saturn, may be understood. Electric fields at the perihelion of the Solar Probe Plus mission may be tens of V/m.
Deformation-induced accelerated dynamics in polymer glasses
Authors: Warren Mya , Rottler Jörg
Published: October 2010

Molecular dynamics simulations are used to investigate the effects of deformation on the segmental dynamics in an aging polymer glass. Individual particle trajectories are decomposed into a series of discontinuous hops, from which we obtain the full distribution of relaxation times and displacements under three deformation protocols: step stress (creep), step strain, and constant strain rate deformation. As in experiments, the dynamics can be accelerated by several orders of magnitude during deformation, and the history dependence is entirely erased during yield (mechanical rejuvenation). Aging can be explained as a result of the long tails in the relaxation time distribution of the glass, and similarly, mechanical rejuvenation is understood through the observed narrowing of this distribution during yield. Although the relaxation time distributions under deformation are highly protocol specific, in each case they may be described by a universal acceleration factor that depends only on the strain.
Vibrational dynamics, intermolecular interactions, and compound formation in GeH4–H2 under pressure
Authors: Strobel Timothy A. , Chen Xiao-Jia , Somayazulu Maddury , Hemley Russell J.
Published: October 2010

Optical microscopy, spectroscopic and x-ray diffraction studies at high-pressure are used to investigate intermolecular interactions in binary mixtures of germane (GeH4)+hydrogen (H2). The measurements reveal the formation of a new molecular compound, with the approximate stoichiometry GeH4(H2)2, when the constituents are compressed above 7.5 GPa. Raman and infrared spectroscopic measurements show multiple H2 vibrons substantially softened from bulk solid hydrogen. With increasing pressure, the frequencies of several Raman and infrared H2 vibrons decrease, indicating anomalous attractive interaction for closed-shell, nonpolar molecules. Synchrotron powder x-ray diffraction measurements show that the compound has a structure based on face-centered cubic (fcc) with GeH4 molecules occupying fcc sites and H2 molecules likely distributed between Oh and Td sites. Above ca. 17 GPa, GeH4 molecules in the compound become unstable with respect to decomposition products (Ge+H2), however, the compound can be preserved metastably to ca. 27 GPa for time-scales of the order of several hours.
Thin-sample limit for time-resolved terahertz spectroscopy
Authors: Schins Juleon M.
Published: October 2010

The retrieval of the primary (subpicosecond) photoproducts in small-band two-dimensional time-domain terahertz spectroscopy has succeeded only in a few model systems, due to the complicated correlation between the two time parameters. We show that the nature of the primary photoproducts is revealed upon differentiating the measured time-domain spectra with respect to the pump-probe delay. An analytical treatment is given in the thin-sample limit, which distinguishes unambiguously between excitons and free charge carriers. This treatment gives a fair description of the data even for thick samples, including the subpicosecond timescale.
The ultralow driven current ultraviolet-blue light-emitting diode based on n-ZnO nanowires/i-polymer/p-GaN heterojunction
Authors: Guo Zhen , Zhang Hong , Zhao Dongxu , Liu Yichun , Yao Bin , Li Binghui , Zhang Zhenzhong , Shen Dezhen
Published: October 2010

Under the ultralow driven current of 25 μA an ultraviolet (UV)-blue electroluminescence (EL) with a weak defect-related emission could be obtained for the n type (n-) ZnO nanowires (NWs)/insulating (i-) polymer/p-type (p-) GaN light-emitting diode (LED). The i-MgO layer was also explored as a carrier blocking layer for the comparison. For the i-polymer inserted LED the EL emission peak was located at 400 nm, by analyzing the spectra it is believed that the emission includes several compound originations from both ZnO and GaN. The flexible carrier blocking layer, such as i-polymer, could effectively confine the radiative recombination zone.
Position controlled nanowires for infrared single photon emission
Authors: Dorenbos S. N. , Sasakura H. , van Kouwen M. P. , Akopian N. , Adachi S. , Namekata N. , Jo M. , Motohisa J. , Kobayashi Y. , Tomioka K. , Fukui T. , Inoue S. , Kumano H. , Natarajan C. M. , Hadfield R. H. , Zijlstra T. , Klapwijk T. M. , Zwiller V. , Suemune I.
Published: October 2010

We report the experimental demonstration of single-photon and cascaded photon pair emission in the infrared, originating from a single InAsP quantum dot embedded in a standing InP nanowire. A regular array of nanowires is fabricated by epitaxial growth on an electron-beam patterned substrate. Photoluminescence spectra taken on single quantum dots show narrow emission lines. Superconducting single photon detectors, which have a higher sensitivity than avalanche photodiodes in the infrared, enable us to measure auto and cross correlations. Clear antibunching is observed [g(2)(0)=0.12] and we show a biexciton–exciton cascade, which can be used to create entangled photon pairs.
Measuring the two-photon absorption cross sections of thiol-capped CdTe quantum dots in living cells
Authors: Zheng Shen , Chen Ji-Yao , Wang Pei-Nan , Yang Wu-Li , Zhou Lu-Wei
Published: October 2010

A modality to measure the two-photon absorption cross sections (TPACSs) of thiol-capped CdTe quantum dots (QDs) in living cells was established. The photoluminescence (PL) quantum yield (Φ) of cellular QDs was measured by the established relationship of Φ versus PL lifetime of cellular QDs. Then the local concentration of cellular QDs with the determined Φ in the measured region was obtained by the calibration curve of the PL intensity versus the QD aqueous concentration. The TPACSs of cellular QDs were gotten finally according to the measured PL intensity with the method of two-photon induced PL.
Role of electronic structure and oxygen defects in driving ferromagnetism in nondoped bulk CeO2
Authors: Singhal R. K. , Kumari P. , Samariya A. , Kumar Sudhish , Sharma S. C. , Xing Y. T. , Saitovitch Elisa B.
Published: October 2010

This article reports on reversible manipulation of room temperature ferromagnetism (RTFM) in nondoped bulk CeO2. The magnetization measurements establish that paramagnetic CeO2 is driven to a ferromagnetic state, without change in structure, when vacuum annealed at 600 °C. The Ce ions transform from 4+ to 3+ state, accompanied by evolution of oxygen vacancies (VO) during the RTFM transition, as determined by x-ray photoemission. The F+ centers (the electrons in singly occupied oxygen vacancies) play key role in the exchange mechanism. The transition shows complete reversibility where the RTFM is removed by removing the vacancies through re-heating the vacuum-annealed CeO2 in air.
Melting, thermal expansion, and the Lindemann rule for elemental substances
Authors: Granato A. V. , Joncich D. M. , Khonik V. A.
Published: October 2010

An interpretation of a long-standing problem—the Lindemann melting rule—has been suggested within the framework of the interstitialcy theory. Melting is considered to be due to the rapid generation of thermodynamically equilibrium defects—dumbbell interstitials, which drastically decrease the shear modulus at the melting point. An analytical expression for the relationship between the thermal expansion coefficient and melting temperature coinciding with the Lindemann melting rule has been derived. The obtained results agree with available data on elemental substances. A correlation between the melting temperature and shear modulus has been discovered and explained within the framework of the same approach.
A miniaturized power source using electron stimulated impact ionization field emission
Authors: Ghosh N. , Kang W. P. , Davidson J. L.
Published: October 2010

This paper reports the fabrication and characterization of miniaturized monolithic lateral field emission power cell (FEPC) comprising of carbon nanotube (CNT) emitters and an integrated metallic anode. Electron stimulation impact ionization on FEPC CNT cathode was activated by an integrated electron beam emitter. Field emission behavior with and without the activation of the electron beam was characterized in diode configuration. The emission current of the FEPC increased with the activation of the electron beam. At this operating condition, ten times current amplification and 1.4 μW of power was generated. Results demonstrate the feasibility of power generation using electron stimulated impact ionization.
Totally solution-processed ferroelectric-gate thin-film transistor
Authors: Miyasako Takaaki , Trinh Bui Nguyen Quoc , Onoue Masatoshi , Kaneda Toshihiko , Tue Phan Trong , Tokumitsu Eisuke , Shimoda Tatsuya
Published: October 2010

We have fabricated inorganic ferroelectric-gate thin film transistors (FGTs) using only a chemical solution deposition (CSD) process. All layers, including the channel [indium-tin-oxide (ITO)], ferroelectric-gate insulator [Pb(Zr,Ti)O3], gate electrode (LaNiO3) and source/drain electrodes (ITO), were formed by the CSD process. The fabricated FGT exhibited typical n-channel transistor operation with good saturation in drain current and drain voltage (ID-VD) characteristics. The obtained on/off current ratio, memory window, and subthreshold voltage swing were about 107, 2.5 V, and 420 mV/decade, respectively.
Three-dimensional simulation of efficiency enhancement in free-electron laser with prebunched electron beam
Authors: Chitsazi Mahboobeh , Maraghechi B. , Rouhani M. H.
Published: October 2010

The effect of prebunching of the electron beam and tapering of the wiggler amplitude on the harmonic upconversion in free-electron laser amplifier is studied in three dimensions. A set of coupled nonlinear first-order differential equations that describe the three-dimensional simulation of the system is solved numerically. This set of equation describes self-consistently the longitudinal spatial dependence of radiation waists, curvatures, and amplitudes together with the evaluation of the electron beam. The analysis is related to extreme ultraviolet and x-ray emission. In addition to uniform beam, prebunched electron beam has also been studied. The effect of sinusoidal distribution of entry times for the electron beam on the evolution of radiation is compared with uniform distribution. It is shown that prebunching reduces the saturation length substantially. For efficiency enhancement, the wiggler is set to decrease linearly when the radiation of the third harmonic saturates. The optimum starting point and the slope of tapering of the amplitude of the wiggler are found by a successive run of the code. It was found that tapering can increase the saturated power of the third harmonic considerably.
Photoassisted Kelvin probe force microscopy at GaN surfaces: The role of polarity
Authors: Wei J. D. , Li S. F. , Atamuratov A. , Wehmann H.-H. , Waag A.
Published: October 2010

The behavior of GaN surfaces during photoassisted Kelvin probe force microscopy is demonstrated to be strongly dependant on surface polarity. The surface photovoltage of GaN surfaces illuminated with above-band gap light is analyzed as a function of time and light intensity. Distinct differences between Ga-polar and N-polar surfaces could be identified, attributed to photoinduced chemisorption of oxygen during illumination. These differences can be used for a contactless, nondestructive, and easy-performable analysis of the polarity of GaN surfaces.
David Hutchins in Australia 1914 - 1915: the Penultimate Chapter in the Career of an Imperial Forester
Authors: Roche Michael
Published: October 2010

David Hutchins, after a distinguished career in forestry in India and Africa, visited Australia as part of the British Association for the Advancement of Science tour in 1914. This paper reconstructs Hutchins' tour and considers how it prepared him for writing a controversial report published in 1916 as Discussion on Australian Forestry. Reactions to the report are also considered. The place that Hutchins occupies in the Australian forest history literature is reassessed, particularly the interplay between his preconceived ideas and local experiences. Discussion on Australian Forestry is interpreted as the last major, though not unequivocal, success in his long career in forestry.
Whole-genome sequencing and microarray analysis of ex vivo
Plasmodium vivax
reveal selective pressure on putative drug resistance genes
Authors: Dharia Neekesh V. , Bright A. Taylor , Westenberger Scott J. , Barnes S. Whitney , Batalov Serge , Kuhen Kelli , Borboa Rachel , Federe Glenn C. , McClean Colleen M. , Vinetz Joseph M. , Neyra Victor , Llanos-Cuentas Alejandro , Barnwell John W. , Walker John R. , Winzeler Elizabeth A.
Published: October 2010

Plasmodium vivax
causes 25–40% of malaria cases worldwide, yet research on this human malaria parasite has been neglected. Nevertheless, the recent publication of the
P. vivax
reference genome now allows genomics and systems biology approaches to be applied to this pathogen. We show here that whole-genome analysis of the parasite can be achieved directly from ex vivo-isolated parasites, without the need for in vitro propagation. A single isolate of
P. vivax
obtained from a febrile patient with clinical malaria from Peru was subjected to whole-genome sequencing (30× coverage). This analysis revealed over 18,261 single-nucleotide polymorphisms (SNPs), 6,257 of which were further validated using a tiling microarray. Within core chromosomal genes we find that one SNP per every 985 bases of coding sequence distinguishes this recent Peruvian isolate, designated IQ07, from the reference Salvador I strain obtained in 1972. This full-genome sequence of an uncultured
P. vivax
isolate shows that the same regions with low numbers of aligned sequencing reads are also highly variable by genomic microarray analysis. Finally, we show that the genes containing the largest ratio of nonsynonymous-to-synonymous SNPs include two AP2 transcription factors and the
P. vivax
multidrug resistance-associated protein (PvMRP1), an ABC transporter shown to be associated with quinoline and antifolate tolerance in
Plasmodium falciparum
. This analysis provides a data set for comparative analysis with important potential for identifying markers for global parasite diversity and drug resistance mapping studies.
A biochemical mechanism for the oncogenic potential of the p110β catalytic subunit of phosphoinositide 3-kinase
Authors: Dbouk Hashem A. , Pang Huan , Fiser Andras , Backer Jonathan M.
Published: October 2010

Class I PI3-kinases signal downstream of receptor tyrosine kinases and G protein-coupled receptors and have been implicated in tumorigenesis. Although the oncogenic potential of the PI3-kinase subunit p110α requires its mutational activation, other p110 isoforms can induce transformation when overexpressed in the wild-type state. In wild-type p110α, N345 in the C2 domain forms hydrogen bonds with D560 and N564 in the inter-SH2 (iSH2) domain of p85, and mutations of p110α or p85 that disrupt this interface lead to increased basal activity and transformation. Sequence analysis reveals that N345 in p110α aligns with K342 in p110β. This difference makes wild-type p110β analogous to a previously described oncogenic mutant, p110α-N345K. We now show that p110β is inhibited by p85 to a lesser extent than p110α and is not differentially inhibited by wild-type p85 versus p85 mutants that disrupt the C2–iSH2 domain interface. Similar results were seen in soft agar and focus-formation assays, where p110β was similar to p110α-N345K in transforming potential. Inhibition of p110β by p85 was enhanced by a K342N mutation in p110β, which led to decreased activity in vitro, decreased basal Akt and ribosomal protein S6 kinase (S6K1) activation, and decreased transformation in NIH 3T3 cells. Moreover, unlike wild-type p110β, p110β-K342N was differentially regulated by wild-type and mutant p85, suggesting that the inhibitory C2–iSH2 interface is functional in this mutant. This study shows that the enhanced transforming potential of p110β is the result of its decreased inhibition by p85, due to the disruption of an inhibitory C2–iSH2 domain interface.
Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance
Authors: Hare Stephen , Vos Ann M. , Clayton Reginald F. , Thuring Jan W. , Cummings Maxwell D. , Cherepanov Peter
Published: October 2010

The development of HIV integrase (IN) strand transfer inhibitors (INSTIs) and our understanding of viral resistance to these molecules have been hampered by a paucity of available structural data. We recently reported cocrystal structures of the prototype foamy virus (PFV) intasome with raltegravir and elvitegravir, establishing the general INSTI binding mode. We now present an expanded set of cocrystal structures containing PFV intasomes complexed with first- and second-generation INSTIs at resolutions of up to 2.5 Å. Importantly, the improved resolution allowed us to refine the complete coordination spheres of the catalytic metal cations within the INSTI-bound intasome active site. We show that like the Q148H/G140S and N155H HIV-1 IN variants, the analogous S217H and N224H PFV INs display reduced sensitivity to raltegravir in vitro. Crystal structures of the mutant PFV intasomes in INSTI-free and -bound forms revealed that the amino acid substitutions necessitate considerable conformational rearrangements within the IN active site to accommodate an INSTI, thus explaining their adverse effects on raltegravir antiviral activity. Furthermore, our structures predict physical proximity and an interaction between HIV-1 IN mutant residues His148 and Ser/Ala140, rationalizing the coevolution of Q148H and G140S/A mutations in drug-resistant viral strains.
Germ-line elimination of electric charge on pre–T-cell receptor (TCR) impairs autonomous signaling for β-selection and TCR repertoire formation
Authors: Ishikawa Eri , Miyake Yasunobu , Hara Hiromitsu , Saito Takashi , Yamasaki Sho
Published: October 2010

The pre–T-cell receptor (TCR) is crucial for the early T-cell development, but the ligand for pre-TCR remains unidentified. We recently proposed a model that pre-TCR complexes oligomerize spontaneously through interactions of the pre-TCRα chain. To investigate the mechanism underlying this ligand-independent signaling in vivo, we established knock-in mice that express a pre-TCRα mutant lacking charged amino acids (D
22
R
24
R
102
R
117
to A
22
A
24
A
102
A
117
; 4A). CD4
+
CD8
+
thymocyte number was significantly reduced in invariant pre-TCRα (pTα
4A/4A
) mice, whereas CD4
−
CD8
−
thymocytes were unaffected. The percentages of double-negative 3 (DN3) cells and γδ T cells were increased in the pTα
4A/4A
thymus, indicating that β-selection is impaired in pTα
4A/4A
mice. Pre-TCR–mediated tyrosine phosphorylation and clonal expansion into double-positive thymocytes were also defective in the knock-in mice. Pre-TCR was expressed at higher levels on pTα
4A/4A
cell surfaces than on those of the wild type, suggesting that the charged residues in pTα are critical for autonomous engagement and subsequent internalization of pre-TCR. Pre-TCR–mediated allelic exclusion of the TCRβ gene was also inhibited in pTα
4A/4A
mice, and thereby, dual TCRβs were expressed on pTα
4A/4A
T cells. Furthermore, the TCRβ chain variable region (Vβ) repertoire of mature T cells was significantly altered in pTα
4A/4A
mice. These results suggest that charged residues of pTα are critical for β-selection, allelic exclusion, and TCRβ repertoire formation.
Morphological characteristics and plant development.
Authors: Robinson J. C. , Galán Saúco V.
Published: October 2010

This chapter describes the morphological characteristics and development of banana plants (Musa), focusing on the root system, rhizome, suckers, leaves, pseudostems, inflorescence, bunch, and fruit.
Climatic requirements and problems.
Authors: Robinson J. C. , Galán Saúco V.
Published: October 2010

This chapter describes the general climatic requirements of banana (Musa), showing that banana is primarily a crop of the humid tropical lowlands characterized by less than 10° latitude, less than 100 m altitude, not less than 19°C mean minimum temperature and more than 100 mm rain every month. Four distinct zones which differ widely in their climates but in which bananas are successfully grown commercially are described, i.e. the humid tropics (Guapiles, Costa Rica), hot, semi-arid tropics (Kununurra, Western Australia), warm, arid subtropics (Carnarvon, Western Australia) and cool subtropics (Kiepersol, South Africa). The effect of rainfall, or the lack of it, on physiological, pathological and management aspects of banana growing is discussed. Some problems in banana-growing regions outside the humid tropics due to hot and cold weather and other climatic problems (hail, wind, drought, flood and radiation and lightning) are described.
Phenological and physiological responses.
Authors: Robinson J. C. , Galán Saúco V.
Published: October 2010

This chapter describes the developmental phases of a ratoon banana (Musa) plant (Cavendish subgroup), i.e. the vegetative phase, characterized externally by the emergence of leaves, and the reproductive phase, easily identified by emergence of the bunch. The seasonal influences of temperature on development cycles of the banana plant in the tropics and subtropics ('phenological responses') and the specific effects of climatic factors (temperature, vapour pressure deficit, light, water stress and wind) on the assimilation (photosynthesis), transpiration and dry matter accumulation of banana plants ('physiological responses') are discussed. The most important phenological parameters are described: (i) planting to harvest duration for different planting dates and localities; (ii) Leaf emergence rates; (iii) primary root extension rates; and (iv) variations in flower emergence to harvest duration. The main phenological differences between bananas in a humid, tropical locality (Honduras), a cool, subtropical locality (South Africa) and a Mediterranean locality (Israel) are summarized.
Systems of cultivating bananas and product certifications.
Authors: Robinson J. C. , Galán Saúco V.
Published: October 2010

This paper describes the four systems of banana (Musa) cultivation, i.e. the traditional and conventional, integrated, organic and protected. Different certification schemes that consider the internal and external quality of the product, as well as the social and environmental aspects of the cultivation system, are provided. The certification process which verifies that a product, a service or an organization fulfils a given number of rules is discussed and the procedure for obtaining ISO certification, which is given by different organizations in different countries, is enumerated.
Water requirements and irrigation.
Authors: Robinson J. C. , Galán Saúco V.
Published: October 2010

An account is given on the different properties of irrigation systems needed to fulfill the water requirements of bananas and plantains. Topics covered include: irrigation systems (flood or furrow irrigation, overcanopy sprinklers, undercanopy sprinklers, microjet or microspinners, and drip irrigation); irrigation scheduling; and irrigation depths for plantains.
Ripening, biochemistry and uses.
Authors: Robinson J. C. , Galán Saúco V.
Published: October 2010

This chapter describes the pre-climacteric, climacteric, ripening and eat-ripe stages of banana and plantain (Musa) fruits, as well as the biochemical characteristics of their fruits during ripening in terms of water, carbohydrate, pigment, aromatic compound, phenolic, pectin, lipid protein, organic acid and vitamin contents. The nutritional value, uses and processing of these fruits are summarized. Some preconditions that must be satisfied in order for a banana processing industry to be successful are mentioned.
Psychiatric Disorders and Unmet Needs in Australian Police Cells
Authors: Baksheev Gennady N. , Thomas Stuart D. M. , Ogloff James R. P.
Published: October 2010

Objective: To determine the prevalence of current psychiatric disorders and unmet needs in a sample of police cell detainees in Victoria.

Method: A cross-sectional descriptive study was conducted, including data linkage with the Victoria Police database and the Victorian Psychiatric Case Register. In Melbourne, Australia, 150 detainees were recruited from two busy metropolitan police stations. Outcome measures included estimated rates of psychiatric disorders, using the Structured Clinical Interview for DSM-IV-TR, and individual needs, using the Camberwell Assessment of Need – Forensic Version.

Results: One quarter (n = 32, 25.4%) of detainees had a prior admission to a psychiatric hospital, and three quarters met current criteria for a diagnosable mental disorder. The most common disorders were substance dependence (n = 81, 54%) and mood disorders (n = 60, 40%). A third met diagnostic criteria for both a mental illness and a substance use disorder. The odds of being classified with mood (OR = 10.1), anxiety (OR = 2.2), psychotic (OR = 15.4) and substance use disorders (OR = 26.3) were all significantly higher in the current sample as compared with the general population. Detainees with a mental illness identified significantly more needs and significantly more unmet needs (e.g. psychological distress) than those who did not rate as having a current mental illness.

Conclusions: There remains a pressing need to evaluate standardized screening tools for mental illnesses in police cells to provide timely access to assessment and treatment services. The need for functional interagency collaborations are highlighted and discussed.
Statistical distribution of amino acid sequences: a proof of Darwinian evolution
Authors: Eitner Krystian , Koch Uwe , Gawęda Tomasz , Marciniak Jędrzej
Published: October 2010

Motivation: The article presents results of the listing of the quantity of amino acids, dipeptides and tripeptides for all proteins available in the UNIPROT–TREMBL database and the listing for selected species and enzymes. UNIPROT–TREMBL contains protein sequences associated with computationally generated annotations and large-scale functional characterization. Due to the distinct metabolic pathways of amino acid syntheses and their physicochemical properties, the quantities of subpeptides in proteins vary. We have proved that the distribution of amino acids, dipeptides and tripeptides is statistical which confirms that the evolutionary biodiversity development model is subject to the theory of independent events. It seems interesting that certain short peptide combinations occur relatively rarely or even not at all. First, it confirms the Darwinian theory of evolution and second, it opens up opportunities for designing pharmaceuticals among rarely represented short peptide combinations. Furthermore, an innovative approach to the mass analysis of bioinformatic data is presented.

Contact:  eitner@amu.edu.pl

Supplementary information:  Supplementary data are available at Bioinformatics online.
SPHINX—an algorithm for taxonomic binning of metagenomic sequences
Authors: Mohammed Monzoorul Haque , Ghosh Tarini Shankar , Singh Nitin Kumar , Mande Sharmila S.
Published: October 2010

Motivation: Compared with composition-based binning algorithms, the binning accuracy and specificity of alignment-based binning algorithms is significantly higher. However, being alignment-based, the latter class of algorithms require enormous amount of time and computing resources for binning huge metagenomic datasets. The motivation was to develop a binning approach that can analyze metagenomic datasets as rapidly as composition-based approaches, but nevertheless has the accuracy and specificity of alignment-based algorithms. This article describes a hybrid binning approach (SPHINX) that achieves high binning efficiency by utilizing the principles of both ‘composition’- and ‘alignment’-based binning algorithms.

Results: Validation results with simulated sequence datasets indicate that SPHINX is able to analyze metagenomic sequences as rapidly as composition-based algorithms. Furthermore, the binning efficiency (in terms of accuracy and specificity of assignments) of SPHINX is observed to be comparable with results obtained using alignment-based algorithms.

Availability: A web server for the SPHINX algorithm is available at http://metagenomics.atc.tcs.com/SPHINX/.

Contact:  sharmila@atc.tcs.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Adaptations for economical bipedal running: the effect of limb structure on three-dimensional joint mechanics
Authors: Rubenson Jonas , Lloyd David G. , Heliams Denham B. , Besier Thor F. , Fournier Paul A.
Published: October 2010

The purpose of this study was to examine the mechanical adaptations linked to economical locomotion in cursorial bipeds. We addressed this question by comparing mass-matched humans and avian bipeds (ostriches), which exhibit marked differences in limb structure and running economy. We hypothesized that the nearly 50 per cent lower energy cost of running in ostriches is a result of: (i) lower limb-swing mechanical power, (ii) greater stance-phase storage and release of elastic energy, and (iii) lower total muscle power output. To test these hypotheses, we used three-dimensional joint mechanical measurements and a simple model to estimate the elastic and muscle contributions to joint work and power. Contradictory to our first hypothesis, we found that ostriches and humans generate the same amounts of mechanical power to swing the limbs at a similar self-selected running speed, indicating that limb swing probably does not contribute to the difference in energy cost of running between these species. In contrast, we estimated that ostriches generate 120 per cent more stance-phase mechanical joint power via release of elastic energy compared with humans. This elastic mechanical power occurs nearly exclusively at the tarsometatarso-phalangeal joint, demonstrating a shift of mechanical power generation to distal joints compared with humans. We also estimated that positive muscle fibre power is 35 per cent lower in ostriches compared with humans, and is accounted for primarily by higher capacity for storage and release of elastic energy. Furthermore, our analysis revealed much larger frontal and internal/external rotation joint loads during ostrich running than in humans. Together, these findings support the hypothesis that a primary limb structure specialization linked to economical running in cursorial species is an elevated storage and release of elastic energy in tendon. In the ostrich, energy-saving specializations may also include passive frontal and internal/external rotation load-bearing mechanisms.
Disease transmission in territorial populations: the small-world network of Serengeti lions
Authors: Craft Meggan E. , Volz Erik , Packer Craig , Meyers Lauren Ancel
Published: October 2010

Territoriality in animal populations creates spatial structure that is thought to naturally buffer disease invasion. Often, however, territorial populations also include highly mobile, non-residential individuals that potentially serve as disease superspreaders. Using long-term data from the Serengeti Lion Project, we characterize the contact network structure of a territorial wildlife population and address the epidemiological impact of nomadic individuals. As expected, pride contacts are dominated by interactions with neighbouring prides and interspersed by encounters with nomads as they wander throughout the ecosystem. Yet the pride–pride network also includes occasional long-range contacts between prides, making it surprisingly
small world
and vulnerable to epidemics, even without nomads. While nomads increase both the local and global connectivity of the network, their epidemiological impact is marginal, particularly for diseases with short infectious periods like canine distemper virus. Thus, territoriality in Serengeti lions may be less protective and non-residents less important for disease transmission than previously considered.
Molecular typing of Staphylococcus aureus bloodstream isolates from geriatric patients attending a long-term care Spanish hospital
Authors: Argudín M. Angeles , Mendoza M. Carmen , Vázquez Fernando , Guerra Beatriz , Rodicio M. Rosario
Published: October 2010

AllStaphylococcus aureusisolates (n=31) that caused bacteraemia in a Spanish geriatric hospital during 1996–2006 were analysed by a simple, rapid and inexpensive PCR technique based on variations in thehsdS1andhsdS2genes encoding the sequence recognition subunits of the Sau1 restriction–modification (RM) system. An equal number of isolates collected from surgical wounds over the same time period (control group) were similarly characterized. The RM test allocated 75 % of the isolates to the six major clonal complexes (CC1, CC5, CC8, CC22, CC30 and CC45) for which it was developed. However, recognition of minor CCs and precise identification of the circulating clones required more powerful and comprehensive techniques such asspatyping and multilocus sequence typing (MLST), which are more demanding and expensive. The RM test is not intended to replacespaor MLST typing, but may be of use when time, technical and/or financial resources are limited. Overall, nine and seven CCs were detected in bloodstream and wound isolates, respectively. In both groups, CC5 was the most frequent (35.5 % each), followed by CC45 or CC8 (22.6 and 32.3 % of bloodstream and wound isolates, respectively). The frequency of meticillin resistance was lower in bloodstream (16.1 %) than in wound (51.6 %) isolates (P=0.0025). Among the former, sequence type (ST) 5-staphylococcal cassette chromosomemec(SCCmec) II, ST5-SCCmecIV, ST45-SCCmecIV and ST125-SCCmecIV (now dominant in Spanish hospitals) clones were found. Among the wound isolates, nine meticillin-resistant clones were represented, with three of them (ST125-SCCmecIII, ST125-SCCmecV and ST14-SCCmecV) being newly described.
Q fever: the neglected biothreat agent
Authors: Oyston P. C. F. , Davies C.
Published: October 2010

Coxiella burnetiiis the causative agent of Q fever, a disease with a spectrum of presentations from the mild to fatal, including chronic sequelae. Since its discovery in 1935, it has been shown to infect a wide range of hosts, including humans. A recent outbreak in Europe reminds us that this is still a significant pathogen of concern, very transmissible and with a very low infectious dose. For these reasons it has also featured regularly on various threat lists, as it may be considered by the unscrupulous for use as a bioweapon. As an intracellular pathogen, it has remained an enigmatic organism due to the inability to culture it on laboratory media. As a result, interactions with the host have been difficult to elucidate and we still have a very limited understanding of the molecular mechanisms of virulence. However, two recent developments will open up our understanding ofC. burnetii: the first axenic growth medium capable of supporting cell-free growth, and the production of the first isogenic mutant. We are approaching an exciting time for expanding our knowledge of this organism in the next few years.
A case of infection caused by the basidiomycete Phellinus undulatus
Authors: Williamson Deborah , Pandey Sushil , Taylor Susan , Rogers Karen , Storey Louanne , Marshall Mark R. , Holland David
Published: October 2010

We present a case of soft tissue infection caused by the basidiomycetePhellinus undulatus. To our knowledge, this is the first reported case of human infection caused by this fungus. Definitive identification was only possible through molecular analysis as the isolate failed to produce any distinct morphological featuresin vitro.
Txe, an endoribonuclease of the enterococcal Axe–Txe toxin–antitoxin system, cleaves mRNA and inhibits protein synthesis
Authors: Halvorsen Elizabeth M. , Williams Julia J. , Bhimani Azra J. , Billings Emily A. , Hergenrother Paul J.
Published: October 2010

Theaxe–txeoperon encodes a toxin–antitoxin (TA) pair, Axe–Txe, that was initially identified on the multidrug-resistance plasmid pRUM inEnterococcus faecium. InEscherichia coli, expression of the Txe toxin is known to inhibit cell growth, and co-expression of the antitoxin, Axe, counteracts the toxic effect of Txe. Here, we report the nucleotide sequence of pS177, a 39 kb multidrug-resistant plasmid isolated from vancomycin-resistantEnt. faecium, which harbours theaxe–txeoperon and thevanAgene cluster. RT-PCR analysis revealed that theaxe–txetranscript is produced by strain S177 as well as by other vancomycin-resistant enteroccoci. Moreover, we determine the mechanism by which the Txe protein exerts its toxic activity. Txe inhibits protein synthesis inE. coliwithout affecting DNA or RNA synthesis, and inhibits protein synthesis in a cell-free system. Usingin vivoprimer extension analysis, we demonstrate that Txe preferentially cleaves single-stranded mRNA at the first base after an AUG start codon. We conclude that Txe is an endoribonuclease which cleaves mRNA and inhibits protein synthesis.
Central cannabinoid receptors modulate acquisition of eyeblink conditioning
Authors: Steinmetz Adam B. , Freeman John H.
Published: October 2010

Delay eyeblink conditioning is established by paired presentations of a conditioned stimulus (CS) such as a tone or light, and an unconditioned stimulus (US) that elicits the blink reflex. Conditioned stimulus information is projected from the basilar pontine nuclei to the cerebellar interpositus nucleus and cortex. The cerebellar cortex, particularly the molecular layer, contains a high density of cannabinoid receptors (CB1R). The CB1Rs are located on the axon terminals of parallel fibers, stellate cells, and basket cells where they inhibit neurotransmitter release. The present study examined the effects of a CB1R agonist WIN55,212-2 and antagonist SR141716A on the acquisition of delay eyeblink conditioning in rats. Rats were given subcutaneous administration of 1, 2, or 3 mg/kg of WIN55,212-2 or 1, 3, or 5 mg/kg of SR141716A before each day of acquisition training (10 sessions). Dose-dependent impairments in acquisition were found for WIN55,212-2 and SR141716A, with no effects on spontaneous or nonassociative blinking. However, the magnitude of impairment was greater for WIN55,212-2 than SR141716A. Dose-dependent impairments in conditioned blink response (CR) amplitude and timing were found with WIN55,212-2 but not with SR141716A. The findings support the hypothesis that CB1Rs in the cerebellar cortex play an important role in plasticity mechanisms underlying eyeblink conditioning.
Low Oleic Acid-Derived Repression of Jasmonic Acid-Inducible Defense Responses Requires the WRKY50 and WRKY51 Proteins
Authors: Gao Qing-Ming , Venugopal Srivathsa , Navarre Duroy , Kachroo Aardra
Published: October 2010

Signaling induced upon a reduction in oleic acid (18:1) levels simultaneously up-regulates salicylic acid (SA)-mediated responses and inhibits jasmonic acid (JA)-inducible defenses, resulting in enhanced resistance to biotrophs but increased susceptibility to necrotrophs. SA and the signaling component Enhanced Disease Susceptibility1 function redundantly in this low-18:1-derived pathway to induce SA signaling but do not function in the repression of JA responses. We show that repression of JA-mediated signaling under low-18:1 conditions is mediated via the WRKY50 and WRKY51 proteins. Knockout mutations in WRKY50 and WRKY51 lowered SA levels but did not restore pathogenesis-related gene expression or pathogen resistance to basal levels in the low-18:1-containing Arabidopsis (Arabidopsis thaliana) mutant, suppressor of SA insensitivity2 (ssi2). In contrast, both JA-inducible PDF1.2 (defensin) expression and basal resistance to Botrytis cinerea were restored. Simultaneous mutations in both WRKY genes (ssi2 wrky50 wrky51) did not further enhance the JA or Botrytis-related responses. The ssi2 wrky50 and ssi2 wrky51 plants contained high levels of reactive oxygen species and exhibited enhanced cell death, the same as ssi2 plants. This suggested that high reactive oxygen species levels or increased cell death were not responsible for the enhanced susceptibility of ssi2 plants to B. cinerea. Exogenous SA inhibited JA-inducible PDF1.2 expression in the wild type but not in wrky50 or wrky51 mutant plants. These results show that the WRKY50 and WRKY51 proteins mediate both SA- and low-18:1-dependent repression of JA signaling.
Role and contribution of formal models to governing: a heuristic
Authors: Türke Ralf‐Eckhard
Published: October 2010

Purpose

The paper aims to investigate the link between models and system results. It looks at fundamental principles underlying social activities and strives to understand the logical role of models in social governing. Based on these a heuristic is assembled enabling the recognition of the specific contribution formal models can provide for social contexts and also for recognizing the limitations that apply.

Design/methodology/approach

The heuristic is developed based on first principles of systems theory and cybernetics with particular consideration of managerial cybernetics. It starts with the assumption that human cognition roots in an autopoietic process from which individual “realities” andWeltanschauungenevolve. Interaction then leads human actors to adopt social system notions through which they initiate and constantly reconcile the implementation of their commonly aspired purposes. With system structures, it is referred to how actors relate to each other in governing – which is a key to learning about what models can contribute. Therefore, the concept of system structure is derived from interaction and rooted in the social system notion distinguishing aspects of structural capacity that pre‐condition the implementation of desired social outcomes. Subsequently, a logical anatomy of system notions is revealed and expressed with a set of invariant systemic topics necessary when being addressed in governing.

Findings

The paper finds a heuristic for identifying the contribution formal models provide to the governance of social systems and recognition of the benefits and limitations specific models provide to governing. Conclusions are drawn on the pre‐conditions securing sustained organizational development through the application of formal models.

Originality/value

The heuristic assembled in this paper facilitates the harmonization and alignment of models in governance settings. The recognition of the role of models in social governing is identified as a logical pre‐condition of sustainable governance. The heuristic presented facilitates assessing and optimizing governing structures with respect to those pre‐conditions.