bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrated kinetic simulation of laser-plasma interactions, fast-electron generation, and transport in fast ignition
Authors: Kemp A. J. , Cohen B. I. , Divol L.
Published: March 2010

We present new results on the physics of short-pulse laser-matter interaction of kilojoule-picosecond pulses at full spatial and temporal scale using a new approach that combines a three-dimensional collisional electromagnetic particle-in-cell code with a magnetohydrodynamic-hybrid model of high-density plasma. In the latter, collisions damp out plasma waves, and an Ohm’s law with electron inertia effects neglected determines the electric field. In addition to yielding orders of magnitude in speed-up while avoiding numerical instabilities, this allows us to model the whole problem in a single unified framework: the laser-plasma interaction at subcritical densities, energy deposition at relativistic critical densities, and fast- electron transport in solid densities. Key questions such as the multipicosecond temporal evolution of the laser energy conversion into hot electrons, the impact of return currents on the laser-plasma interaction, and the effect of self-generated electric and magnetic fields on electron transport will be addressed. We will report applications to current experiments.
Quantum fields on star graphs with bound states at the vertex
Authors: Bellazzini B. , Mintchev M. , Sorba P.
Published: March 2010

We investigate the propagation of a massless scalar field on a star graph, modeling the junction of n quantum wires. The vertex of the graph is represented by a pointlike impurity (defect), characterized by a one-body scattering matrix. The general case of off-critical scattering matrix with bound and/or antibound states is considered. We demonstrate that the contribution of these states to the scalar field is fixed by causality (local commutativity), which is the key point of our investigation. Two different regimes of the theory emerge at this stage. If bound sates are absent, the energy is conserved and the theory admits unitary time evolution. The behavior changes if bound states are present because each such state generates a kind of damped harmonic oscillator in the spectrum of the field. These oscillators lead to the breakdown of time-translation invariance. In both regimes we investigate in this framework the electromagnetic conductance of the Luttinger liquid on the quantum wire junction. We derive an explicit expression for the conductance in terms of the scattering matrix and show that antibound and bound states have a different impact, giving rise to oscillations with exponentially damped and growing amplitudes, respectively.
Gas temperature and electron density profiles in an argon dc microdischarge measured by optical emission spectroscopy
Authors: Belostotskiy Sergey G. , Ouk Tola , Donnelly Vincent M. , Economou Demetre J. , Sadeghi Nader
Published: March 2010

Optical emisssion spectroscopy was employed to study a high pressure (100 s of Torr), slot-type (600 μm interelectrode gap), argon dc microdischarge, with added traces of nitrogen. Spatially resolved gas temperature profiles were obtained by analyzing rovibrational bands of the N2 first positive system. The gas temperature peaked near the cathode and increased with current. The contribution of Stark broadening to the hydrogen Hβ emission lineshape was used to extract the electron density. The axial distribution of electron density as well as visual observation revealed that the microdischarge positive column was highly constricted. The electron density near the sheath edge increased with both pressure and current.
Influence of the surface potential on electrical properties of AlxGa1−xN/GaN heterostructures with different Al-content: Effect of growth method
Authors: Köhler K. , Müller S. , Aidam R. , Waltereit P. , Pletschen W. , Kirste L. , Menner H. P. , Bronner W. , Leuther A. , Quay R. , Mikulla M. , Ambacher O. , Granzner R. , Schwierz F. , Buchheim C. , Goldhahn R.
Published: March 2010

The influence of the growth method on the surface potential and thus on the sheet carrier concentration of GaN capped AlxGa1−xN/GaN heterostructures was evaluated. Nominally undoped low pressure metal-organic vapor-phase (MOVPE) and plasma-assisted molecular beam epitaxial (PA-MBE) grown structures with an Al-content between 12% and 30% yield carrier concentrations from 3.6×1012 to 1.2×1013 cm−2. A difference of the concentrations for a fixed Al-content was found between the different epitaxial techniques. This result indicates unambiguously different surface potentials determined quantitatively from the carrier concentration, and is verified in addition by the results of photoreflectance spectroscopy. The GaN surface potentials of MOVPE and PA-MBE grown samples amounts to (0.26±0.04) and (0.61±0.10) eV irrespective of the Al-content of the barrier layer. After device fabrication, we find that due to the identical surface potential defined by the Ni Schottky gate, the threshold voltage for a given Al-content is the same for samples grown with different techniques. Thus, the interplay between epitaxy and process technology defines the threshold voltage.
A noncharge-sheet channel potential and drain current model for dynamic-depletion silicon-on-insulator metal-oxide-semiconductor field-effect transistors
Authors: Zhang Jian , Zhang Lining , He Jin , Chan Mansun
Published: March 2010

This paper presents a noncharge-sheet channel potential and drain current model for long-channel dynamic-depletion (DD) silicon-on-insulator (SOI) metal-oxide-semiconductor field-effect transistors (MOSFETs). Based on the Poisson–Boltzmann equation, an analytical solution of the channel potentials in the front, back silicon/oxide and substrate/oxide interfaces is developed. It is a universal solution which predicts the channel potential accurately in all cases from accumulation to strong inversion. A unified noncharge-sheet drain current expression is derived from the three-interface analysis based on the universal channel potential solution. The proposed model shows excellent agreements with two-dimensional numerical simulations with varying geometrical structures at different device operation regions. This model provides a useful tool to study the device physics and develop a complete compact model for DD SOI MOSFET.
Development of analytically capable time-of-flight mass spectrometer with continuous ion introduction
Authors: Hárs György , Dobos Gábor
Published: March 2010

The present article describes the results and findings explored in the course of the development of the analytically capable prototype of continuous time-of-flight (CTOF) mass spectrometer. Currently marketed pulsed TOF (PTOF) instruments use ion introduction with a 10 ns or so pulse width, followed by a waiting period roughly 100 μs. Accordingly, the sample is under excitation in 10−4 part of the total measuring time. This very low duty cycle severely limits the sensitivity of the PTOF method. A possible approach to deal with this problem is to use linear sinusoidal dual modulation technique (CTOF) as described in this article. This way the sensitivity of the method is increased, due to the 50% duty cycle of the excitation. All other types of TOF spectrometer use secondary electron multiplier (SEM) for detection, which unfortunately discriminates in amplification in favor of the lighter ions. This discrimination effect is especially undesirable in a mass spectrometric method, which targets high mass range. In CTOF method, SEM is replaced with Faraday cup detector, thus eliminating the mass discrimination effect. Omitting SEM is made possible by the high ion intensity and the very slow ion detection with some hundred hertz detection bandwidth. The electrometer electronics of the Faraday cup detector operates with amplification 1010 V/A. The primary ion beam is highly monoenergetic due to the construction of the ion gun, which made possible to omit any electrostatic mirror configuration for bunching the ions. The measurement is controlled by a personal computer and the intelligent signal generator Type Tabor WW 2571, which uses the direct digital synthesis technique for making arbitrary wave forms. The data are collected by a Labjack interface board, and the fast Fourier transformation is performed by the software. Noble gas mixture has been used to test the analytical capabilities of the prototype setup. Measurement presented proves the results of the mathematical calculations as well as the future potentiality for use in chemical analysis of gaseous mixtures.
Relaxor behavior of (Ba,Bi)(Ti,Al)O3 ferroelectric ceramic
Authors: Cui Lei , Hou Yu-Dong , Wang Sai , Wang Chao , Zhu Man-Kang
Published: March 2010

Perovskite type (Ba0.9Bi0.1)(Ti0.9Al0.1)O3 (BBTA) ceramics have been prepared through solid state reaction route. The room temperature x-ray diffraction study suggests that BBTA ceramics have single phase tetragonal symmetry with space group P4mm. In contrast to the sharp dielectric transition of pure BaTiO3, a broad dielectric anomaly coupled with the shift in dielectric maxima toward a higher temperature with increasing frequency has been observed in BBTA. The quantitative characterization based on empirical parameters (ΔTm, γ, ΔTrelax, and ΔTdiffuse(1 kHz)) confirms its relaxor nature. The dielectric relaxation which follows the Vogel–Fulcher relationship with Eα=0.011 eV, Tf=356 K, and f0=1.38×1010 Hz, further supports spin-glass-like characteristics. In this system, the relaxor behavior can be attributed to the dynamic response of the polar clusters induced by the combined substitutions of Bi3+ and Al3+ on the Ba2+ and Ti4+ site. Moreover, the curie temperature of BBTA shows the decreasing trend compared to that of pure BaTiO3, which doesn't follow the normal Vegard's law, confirming that no BiAlO3 sublattice formed in BBTA. All these features indicate that BBTA is a promising candidate for lead-free relaxors.
Distribution and abundance of the south-eastern form of the greater long-eared bat Nyctophilus timoriensis.
Authors: Turbill C. , Ellis M.
Published: March 2010

In south-eastern Australia, the greater long-eared bat (Nyctophilus timoriensis) has been rarely captured and is considered uncommon, although large areas within its range have received little survey effort. We collate existing capture records and present new data on N. timoriensis captures from recent fauna inventory surveys across the western slopes and plains of New South Wales (NSW). From 1628 trap nights at 39 study areas, 118 N. timoriensis were captured out of a total of 8266 bats. In larger remnants in the Brigalow Belt South Bioregion, N. timoriensis was captured at a rate of 0.1 to 0.6 per trap night and made up 7 to 9% of bat captures. This was approximately an order of magnitude greater than in other study areas throughout western NSW. There were no captures from the Darling Riverine Plains Bioregion. These surveys show that the large vegetation remnants of Goonoo, Pilliga West and Pilliga East study areas are a distinct stronghold in the distribution of the south-eastern form of N. timoriensis.
Daytime behaviour of the grey-headed flying fox Pteropus poliocephalus Temminck (Pteropodidae: Megachiroptera) at an autumn/winter roost.
Authors: Connell K. A. , Munro U. , Torpy F. R.
Published: March 2010

The grey-headed flying fox (Pteropus poliocephalus Temminck) is a threatened large fruit bat endemic to Australia. It roosts in large colonies in rainforest patches, mangroves, open forest, riparian woodland and, as native habitat is reduced, increasingly in vegetation within urban environments. The general biology, ecology and behaviour of this bat remain largely unknown, which makes it difficult to effectively monitor, protect and manage this species. The current study provides baseline information on the daytime behaviour of P. poliocephalus in an autumn/winter roost in urban Sydney, Australia, between April and August 2003. The most common daytime behaviours expressed by the flying foxes were sleeping (most common), grooming, mating/courtship, and wing spreading (least common). Behaviours differed significantly between times of day and seasons (autumn and winter). Active behaviours (i.e., grooming, mating/courtship, wing spreading) occurred mainly in the morning, while sleeping predominated in the afternoon. Mating/courtship and wing spreading were significantly higher in April (reproductive period) than in winter (non-reproductive period). Grooming was the only behaviour that showed no significant variation between sample periods. These results provide important baseline data for future comparative studies on the behaviours of flying foxes from urban and ?natural? camps, and the development of management strategies for this species.
Effects of landscape, habitat and fire and the distribution of the white-footed dunnart Sminthopsis leucopus (Marsupialia: Dasyuridae) in the Eastern Otways, Victoria.
Authors: Wilson B. A. , Aberton J. G.
Published: March 2010

Conservation and planning for threatened species requires knowledge of the species? spatial distribution, prefered habitat and response to disturbance factors such as fire. The white-footed dunnart (Sminthopsis leucopus) is currently listed as ?Vulnerable? due to its patchy distribution, the low density of populations and extinction threats. Studies of the species have been limited, and the aims of this study were to investigate the spatial distribution with relationship to landscape, habitat and fire factors. The study was undertaken in the Eastern Otway Ranges, southern Victoria where the species was recorded at 42 sites (44% of survey sites). The sites were all located within 10 km of the coast, and located in vegetation ranging from sclerophyll communities (forest, woodland and heathland) to coastal shrublands dominated by sedges and grasses. Logistic regression models were generated for species occurrence and predictor variables. The most parsimonious model was selected and although there was an association between presence of S. leucopus with landsystem and altitude, support for the models was not strong. The relationship with altitude was negative, indicating a preference for lower elevations. Models developed for other fauna species have identified landscape variables as being strongly predictive of occurrence, indicating that variables other than those investigated may be more suitable in predicting occurrence of S. leucopus at a landscape level. S. leucopus was recorded at a high percentage of sites 6-15 years post-fire age, and at maximal relative abundance at 4-9 years, providing evidence that it prefers mid succession habitats.
Latrine use by the short-beaked echidna Tachyglossus aculeatus.
Authors: Sprent J. A. , Andersen N. A. , Nicol S. C.
Published: March 2010

Radio-tracking the short-beaked echidnas (Tachyglossus aculeatus) in southern Tasmania revealed that they have latrines under windrows piled up during land clearing, under a single log lying amongst thick braken, and under a sandstone overhang. The latrine area is usually about 25 cm diameter and clear of vegetation and sticks. Some are less than 1 m apart. Scats may be visible on the surface or burried 5 - 10 cm, and contain up to 2 kg of scats.The latrine first observed in 2002 was still in use in 2005.
Coordination chemistry of dimethylgold(III) and methylmercury(II). Synthesis, 1H N.M.R. and structural studies of Poly(pyrazol-1-yl)borate complexes
Authors: Canty AJ , Minchin NJ , Patrick JM , White AH
Published: March 2010

Dimethylgold(III) and methylmercury(II)
form complexes Me2AuL and MeHgL where L
are poly-(pyrazol-1-yl)borate ligands [HB(pz)3]-
and [B(pz)4]-. The structure of Me,Au{HB(pz)3} has
been determined by single-crystal X-ray diffraction at 295 K and refined by least-squares
methods to R 0.056 for 2194 independent 'observed' reflections. This complex
has square-planar coordination for the gold atom involving two coordinated
pyrazole rings and one uncoordinated ring, in contrast to the isoelectronic cation [Me2Au{(pz)3CH)]+
which has square planar coordination with a weak axial Au . .N
interaction. Variable temperature 1H n.m.r. spectra in CD2Cl2
indicate presence of rapid equilibria between
pyrazole ring environments at ambient temperature and, for the MeHgII
complexes, down to -90�C. For the Me2AuIII complexes
spectra at -90�C indicate presence of pyrazole ring environments in ratios 2 :
1 (L = [HB(pz)3]-) and 2 : 1 : 1 (L = [B(pz)4]-). Crystal data for Me2Au{HB(pz)3}: rhombohedral,
space group R3c, a 17.98(1) �, α
117.98(5)�, Z 18.
Antibiotics as ligands. The coordinating ability of deprotonated cycloserine towards transition metals
Authors: Forghieri F , Preti C , Tosi G , Zannini P
Published: March 2010

We report the complexes of
the deprotonated cycloserine
(ccs) ligand, 4-aminoisoxazolidin-3-one, with the
metal ions chromium(III), manganese(II), iron(II), iron(III), cobalt(II),
nicke1(II), zinc(II), zirconium(IV), palladium(II), silver(I), cadmium(II), osmium(III),
platinum(II) and mercury(II). The tentative structures of the complexes have
been assigned on the basis of analytical, spectral(u.v.-
visible, i.r. and far i.r.)
and magnetic data, and of thermal analyses (t.g. and d.t.g.). These complexes appear to contain ccs as an uninegative bidentate
ligand forming five-membered rings in which the O- and the NH2
groups bind to the metals. The ligand field parameters have been evaluated and
are in keeping with the proposed structures; they confirm the presence of
oxygen-and nitrogen-containing chromophores.
Studies in the cycloproparene series: Halogenation and dehydrohalogenation of some 1a,9b-dihydrocyclopropa[l]phenanthrenes
Authors: Halton B , Officer DL
Published: March 2010

Dehydrohalogenation of (1α,1aβ,9aβ)-1-chloro-1a,9b-dihydrocyclopropa
[l]phenanthrene (4b) yields products by way of the
corresponding dibenzobicyclohepta-2,4,6-triene (5b) whilst under solvolytic conditions
the 7-t-butoxydibenzocyclohepta-1,3,5-triene (llb) is
formed by cyclopropyl-allyl ring expansion. When
subjected to bromination the cyclopropaphenanthrenes
(4a,c) yield halophen-anthrenes(14a) and (15c) by
cleavage of an external bond of the cyclopropane
ring.
Studies on gibberellin synthesis. Preparation of advanced intermediates based on 1 H-2,10a-ethanophenanthrene
Authors: Mander LN , Urech R
Published: March 2010

The phenanthrenone
(6) was converted into 1H-2,10a-ethanophenanthrene (16) by means of an acid-induced
cyclization of α-diazoketone (14). Protection
and hydrogenation of (16), followed by reductive methylation of the resulting
tetracyclic ester (20) gave the corresponding dihydro
derivatives(22) or (23), potential precursors to gibberellic
acid (8).
Structure odour studies with nitrogen derivatives of diterpene-derived acetals
Authors: Grant PK , Prasad JS , Rowan DD
Published: March 2010

The nitrogen derivatives
(6) and (7) of the perfumery acetals (2) and (3) have been synthesized from manool (1) by the Beckmann rearrangement of the oxime (10). The azo derivative (18),possessing
the bridged ring system of the acetals, was synthesized by an intramolecular
Lewis-acid catalysed cyclization of the tosylhydrazone
(17).
The crystal and molecular structure of zinc(II) monoglycerolate
Authors: Hambley TW , Snow MR
Published: March 2010

An X-ray crystallographic
analysis of zinc(II) monoglycerolate has been carried
out. The crystals are monoclinic, space group P21/c with a 8.110(1), b 6.404(1), c 8.714(2)�
β 93.44(1)�. The structure was refined by full-matrix least-squares
techniques to an R factor (on 519F) of 0.019. The analysis reveals that the
zinc atoms bridge the glycerolate molecules forming
polymeric sheets lying parallel to the bc plane. Only aliphatic hydrogens are disposed into the
space between the layers, a fact consistent with the lubricity and hydrophobic
nature of the solid complex and the observed facile lamellar cleavage
perpendicular to the a axis.
Crystal structure of ammonium Bis(thiocyanato)argentate(I) (a redetermination)
Authors: Hall SR , Mills NK , White AH
Published: March 2010

The crystal structure of
the title compound, (NH4)Ag(SCN)2, has been redetermined at 295(1) K. Crystals are monoclinic, P21/n,
a 7.207(4), b 23.84(1), c 4.014(4) �,
β 95.24(7)�, Z 4. The structure comprises two-dimensional polymeric anion
layers parallel to ac, interleaved by
N. . .H hydrogen-bonded ammonium cations. The silver atom is pseudo-tetrahedrally four-coordinated by terminal and triply
bridging S thiocyanate groups (Ag-S, 2.469(4);
2.609-2.773(5) �). The structure was refined
to a residual of 0.051 for 550 'observed' reflections.
Synthetic approaches tb mycorrhizin A and gilmicolin. II. Early introduction of a C3 side chain into a benzofuranol precursor
Authors: Brown RFC , Edwards GL , Jones CM , Rae ID , Teo PYT
Published: March 2010

An attempt to modify the
previously reported synthesis of the tricyclic system (1) of mycorrhizin A (2) and gilmicolin
(3) by very early
introduction of a C3 side chain is described. However, both
6-(2-acetoxypropyl)-7a-methoxy-2,2-dimethylbenzofuran-4,7(2H,7aH)-dione
(21) and the
corresponding 6-allyl compound (24) fail
to add cyclopentadiene as required for protection of
the enedione
system
in the original scheme.
DNA as a universal substrate for chemical kinetics
Authors: Soloveichik David , Seelig Georg , Winfree Erik
Published: March 2010

Molecular programming aims to systematically engineer molecular and chemical systems of autonomous function and ever-increasing complexity. A key goal is to develop embedded control circuitry within a chemical system to direct molecular events. Here we show that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions. By using strand displacement reactions as a primitive, we construct reaction cascades with effectively unimolecular and bimolecular kinetics. Our construction allows individual reactions to be coupled in arbitrary ways such that reactants can participate in multiple reactions simultaneously, reproducing the desired dynamical properties. Thus arbitrary systems of chemical equations can be compiled into real chemical systems. We illustrate our method on the Lotka–Volterra oscillator, a limit-cycle oscillator, a chaotic system, and systems implementing feedback digital logic and algorithmic behavior.
Self-organization of grafted polyelectrolyte layers via the coupling of chemical equilibrium and physical interactions
Authors: Tagliazucchi Mario , de la Cruz Mónica Olvera , Szleifer Igal
Published: March 2010

The competition between chemical equilibrium, for example protonation, and physical interactions determines the molecular organization and functionality of biological and synthetic systems. Charge regulation by displacement of acid-base equilibrium induced by changes in the local environment provides a feedback mechanism that controls the balance between electrostatic, van der Waals, steric interactions and molecular organization. Which strategies do responsive systems follow to globally optimize chemical equilibrium and physical interactions? We address this question by theoretically studying model layers of end-grafted polyacids. These layers spontaneously form self-assembled aggregates, presenting domains of controlled local pH and whose morphologies can be manipulated by the composition of the solution in contact with the film. Charge regulation stabilizes micellar domains over a wide range of pH by reducing the local charge in the aggregate at the cost of chemical free energy and gaining in hydrophobic interactions. This balance determines the boundaries between different aggregate morphologies. We show that a qualitatively new form of organization arises from the coupling between physical interactions and protonation equilibrium. This optimization strategy presents itself with polyelectrolytes coexisting in two different and well-defined protonation states. Our results underline the need of considering the coupling between chemical equilibrium and physical interactions due to their highly nonadditive behavior. The predictions provide guidelines for the creation of responsive polymer layers presenting self-organized patterns with functional properties and they give insights for the understanding of competing interactions in highly inhomogeneous and constrained environments such as those relevant in nanotechnology and those responsible for biological cells function.
Academetron, automaton, phantom: uncanny digital pedagogies
Authors: Bayne Siân
Published: March 2010

This paper explores the possibility of an uncanny digital pedagogy. Drawing on theories of the uncanny from psychoanalysis, cultural studies and educational philosophy, it considers how being online defamiliarises teaching, asking us to question and consider anew established academic
practices and conventions. It touches on recent thinking on higher education as troublesome, anxiety-inducing and 'strange', viewing online learning and teaching practices through the lens of an uncanny which is productively disruptive in its challenging of the 'certainties' of place, body,
time and text. Uncanny pedagogies are seen as a generative way of working with the new ontologies of the digital.
S(t)imulating learning: pedagogy, subjectivity and teacher education in online environments
Authors: Saltmarsh Sue , Sutherland-Smith Wendy
Published: March 2010

Australian higher education increasingly relies on flexible modes of delivery as a means of attracting and retaining students in a highly competitive global education market. While education is among those disciplines that have been most actively involved in the shift from face-to-face
to online learning and teaching, the transition for many teacher educators is fraught with tensions and contradictions. For some, teaching online is seen as primarily a cost-cutting exercise on the part of universities, and has little to do with improving the quality of student learning. For
others, the online environment offers multiple pedagogic possibilities that have yet to be fully explored. Yet others consider online environments as problematic, posing challenges to pedagogic and peer relationships that are generally seen as integral to 'good' teaching. This paper draws
on an empirical study of teacher education faculties in five Australian universities, and analyses excerpts from interviews about learning and teaching with teacher educators, educational designers and faculty management. We argue that understanding how teacher educators constitute learner
and teacher subjectivities through their beliefs about and approaches to pedagogy is crucial to the future of online tertiary education. In particular, we consider how teacher educators' attitudes toward and approaches to online learning and teaching are predicated on their perceived subject
positions as either 'stimulating' or 'simulating' particular kinds of learning interactions.
Changelings and shape shifters? Identity play and pedagogical positioning of staff in immersive virtual worlds
Authors: Savin-Baden Maggi
Published: March 2010

This paper presents a study that used narrative inquiry to explore staff experiences of learning and teaching in immersive worlds. The findings introduced issues relating to identity play, the relationship between pedagogy and play and the ways in which learning, play and fun were managed
(or not). At the same time there was a sense of imposed or created values systems that introduced questions and challenges about what learning became or meant in these spaces. The issues identified by this small scale study may offer some purchase on concerns which appear to be emerging with
the digitisation of our lives.
Being online: social presence as subjectivity in online learning
Authors: Kehrwald Benjamin
Published: March 2010

This article discusses the relationship between social presence and subjectivity in online learning environments. Drawing from views of subjectivity synthesised by de Sousa and an exploratory study into online social presence (by Kehrwald), the presentation identifies the links between
various forms of subjectivity and the operation of social presence. The conclusions highlight the benefits of explicitly associating subjectivity with social presence in online learning and some of the key implications for online learning practice.
Theoretical accounts of spatial learning: A neurobiological view (commentary on Pearce, 2009)
Authors: Jeffery Kathryn J.
Published: March 2010

Theories of learning have historically taken, as their starting point, the assumption that learning processes have universal applicability. This position has been argued on grounds of parsimony, but has received two significant challenges: first, from the observation that some kinds of learning, such as spatial learning, seem to obey different rules from others, and second, that some kinds of learning take place in processing modules that are separate from each other. These challenges arose in the behavioural literature but have since received considerable support from neurobiological studies, particularly single neuron studies of spatial learning, confirming that there are indeed separable (albeit highly intercommunicating) processing modules in the brain, which may not always interact (within or between themselves) according to classic associative principles. On the basis of these neurobiological data, reviewed here, it is argued that rather than assuming universality of associative rules, it is more parsimonious to assume sets of locally operating rules, each specialized for a particular domain. By this view, although almost all learning is associative in one way or another, the behavioural-level characterization of the rules governing learning may vary depending on which neural modules are involved in a given behaviour. Neurobiological studies, in tandem with behavioural studies, can help reveal the nature of these modules and the local rules by which they interact.
Case-Crossover Study of Burkholderia cepacia Complex Bloodstream Infection
Associated with Contaminated Intravenous Bromopride
Authors: Martins Ianick Souto , Pellegrino Flávia Lúcia Piffano Costa , Freitas Andrea d'Avila , da Silva Santos Marisa , Ferraiuoli Giovanna lanini d'Alemeida , Vasques Màrcia Regina Guimarães , Amorim Efigenia Lourdes Teixeira , Oliveira Sandra , Nouér Simone Aranha , Cardoso Fernando Luiz Lopes , Mascarenhas Luiz Affonso , Magalhães Ana Cristina Gouveia , Cleinman Isabella Barbosa , Figueiredo Agnes Marie Sá , Moreira Beatriz Meurer
Published: March 2010

Objective.

To investigate an outbreak of healthcare-associated
Burkholderia cepacia complex (BCC) primary
bloodstream infections (BCC-BSI).

Design and Setting.

Case-crossover study in a public hospital, a university hospital and a
private hospital in Rio de Janeiro, Brazil, from March 2006 to May
2006.

Patients.

Twenty-five patients with BCC-BSI.

Design.

After determining the date BCC-BSI symptoms started for each patient, 3
time intervals of data collection were defined, each one with a duration of 3
days: the case period, starting just before BCC-BSI symptoms onset; the control
period, starting 6 days before BCC-BSI symptoms onset; and the washout period,
comprising the 3 days between the case period and the control period. Exposures
evaluated were intravascular solutions and invasive devices and procedures.
Potential risk factors were identified by using the McNemar
χ2 adjusted test. Cultures of samples of potentially
contaminated solutions were performed. BCC strain typing was performed by
pulsed-field gel electrophoresis using
Spel.

Results.

The statistical analysis revealed that the use of bromopride and dipyrone
was associated with BCC-BSI. A total of 21 clinical isolates from 17 (68%) of
the 25 patients and an isolate obtained from the bromopride vial were available
for strain typing. Six pulsotypes were detected. A predominant pulsotype (A)
accounted for 11 isolates obtained from 11 patients (65%) in the 3 study
hospitals.

Conclusion.

Our investigation, using a case-crossover design, of an outbreak of
BCC-BSI infections concluded it was polyclonal but likely caused by infusion of
contaminated bromopride. The epidemiological finding was validated by
microbiological analysis. After recall of contaminated bromopride vials by the
manufacturer, the outbreak was controlled.
Statistical expression deconvolution from mixed tissue samples
Authors: Clarke Jennifer , Seo Pearl , Clarke Bertrand
Published: March 2010

Motivation: Global expression patterns within cells are used for purposes ranging from the identification of disease biomarkers to basic understanding of cellular processes. Unfortunately, tissue samples used in cancer studies are usually composed of multiple cell types and the non-cancerous portions can significantly affect expression profiles. This severely limits the conclusions that can be made about the specificity of gene expression in the cell-type of interest. However, statistical analysis can be used to identify differentially expressed genes that are related to the biological question being studied.

Results: We propose a statistical approach to expression deconvolution from mixed tissue samples in which the proportion of each component cell type is unknown. Our method estimates the proportion of each component in a mixed tissue sample; this estimate can be used to provide estimates of gene expression from each component. We demonstrate our technique on xenograft samples from breast cancer research and publicly available experimental datasets found in the National Center for Biotechnology Information Gene Expression Omnibus repository.

Availability: R code (http://www.r-project.org/) for estimating sample proportions is freely available to non-commercial users and available at http://www.med.miami.edu/medicine/x2691.xml

Contact:  jclarke@med.miami.edu
An extended IUPAC nomenclature code for polymorphic nucleic acids
Authors: Johnson Andrew D.
Published: March 2010

The International Union of Pure and Applied Chemistry (IUPAC) code specified nearly 25 years ago provides a nomenclature for incompletely specified nucleic acids. However, no system currently exists that allows for the informatics representation of the relative abundance at polymorphic nucleic acids (e.g. single nucleotide polymorphisms) in a single specified character, or a string of characters. Here, I propose such an information code as a natural extension to the IUPAC nomenclature code, and present some potential uses and limitations to such a code. The primary anticipated use of this extended nomenclature code is to assist in the representation of the rapidly growing space of information in human genetic variation.

Contact:  johnsonad2@nhlbi.nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Can recreational scuba divers alter natural gross sedimentation rate? A case study from a Mediterranean deep cave
Authors: Di Franco Antonio , Ferruzza Gaetano , Baiata Pasquale , Chemello Renato , Milazzo Marco
Published: March 2010

Di Franco, A., Ferruzza, G., Baiata, P., Chemello, R., and Milazzo, M. 2010. Can recreational scuba divers alter natural gross sedimentation rate? A case study from a Mediterranean deep cave. – ICES Journal of Marine Science, 67: 871–874. Submarine caves are environments with features distinguishing them from other littoral habitats but, despite their ecological importance, their response to anthropogenic disturbance has been seldom verified. One potential threat affecting natural communities within caves is represented by recreational scuba diving. Divers' disturbance within marine caves is mainly related to physical contacts and increased sediment resuspension potentially affecting sessile organisms. The aim was to assess the potential effect of recreational divers' frequentation on the natural gross sedimentation rate (GSR) in a Mediterranean deep-water cave. To achieve this, sediment traps were deployed along a scuba trail before, during, and after the peak season for tourist-related diving. No effects of divers' frequentation were evident in terms of alteration of natural GSR, but findings will need to be validated for other caves to asses whether potential disturbance depends on frequentation levels and/or cave characteristics, i.e. sediment grain size or cave depth.
Genetic variation and spatial autocorrelation among young-of-the-year red snapper (Lutjanus campechanus) in the northern Gulf of Mexico
Authors: Saillant Eric , Bradfield S. Coleen , Gold John R.
Published: March 2010

Saillant, E., Bradfield, S. C., and Gold, J. R. 2010. Genetic variation and spatial autocorrelation among young-of-the-year red snapper (Lutjanus campechanus) in the northern Gulf of Mexico. – ICES Journal of Marine Science, 67: 1240–1250. Temporal and spatial genetic variations at 18 nuclear-encoded microsatellites were assayed among age-0 Gulf red snapper (Lutjanus campechanus), sampled from the 2004 and 2005 cohorts in each of five regions in the northern Gulf of Mexico (Gulf) and from a mixed-age group sampled off northwest Florida. Hierarchical analysis of molecular variance revealed genetic heterogeneity among habitat patches within regions, but not among regions. A significant, positive spatial autocorrelation of microsatellite genotypes among fish sampled within the geographic range 50–100 km was detected. Bayesian coalescent analysis of historical demography indicated a decline of nearly an order of magnitude in the effective population size for red snapper across the area surveyed. The highest posterior probability for the current effective population size was 2163, approximately four orders of magnitude smaller than the estimates of red snapper census size. The results of the study demonstrate that spatial genetic structuring among young-of-the-year red snapper in the Gulf occurs at small geographic scales and is consistent with a metapopulation stock-structure model of partially connected populations. This accentuates the importance of maintaining healthy local spawning populations of red snapper in all regions across the northern Gulf.
Identification of Genomic Regions Controlling Adult-Plant Stripe Rust Resistance in Chinese Landrace Pingyuan 50 Through Bulked Segregant Analysis
Authors: Lan Caixia , Liang Shanshan , Zhou Xiangchun , Zhou Gang , Lu Qinglin , Xia Xianchun , He Zhonghu
Published: March 2010

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most widespread and destructive wheat diseases worldwide. Growing resistant cultivars with adult-plant resistance (APR) is an effective approach for the control of the disease. In this study, 540 simple sequence repeat markers were screened to map quantitative trait loci (QTL) for APR to stripe rust in a doubled haploid (DH) population of 137 lines derived from the cross Pingyuan 50 × Mingxian 169. The DH lines were planted in randomized complete blocks with three replicates in Gansu and Sichuan provinces during the 2005–06, 2006–07, and 2007–08 cropping seasons, providing data for four environments. Artificial inoculations were carried out in Gansu and Sichuan with the prevalent Chinese race CYR32. Broad-sense heritability of resistance to stripe rust for maximum disease severity was 0.91, based on the mean value averaged across four environments. Inclusive composite interval mapping detected three QTL for APR to stripe rust on chromosomes 2BS, 5AL, and 6BS, designated QYr.caas-2BS, QYr.caas-5AL, and QYr.caas-6BS, respectively, separately explaining from 4.5 to 19.9% of the phenotypic variation. QYr.caas-5AL, different from QTL previously reported, was flanked by microsatellite markers Xwmc410 and Xbarc261, and accounted for 5.0 to 19.9% of phenotypic variance. Molecular markers closely linked to the QTL could be used in marker-assisted selection for APR to stripe rust in wheat breeding programs.
Population Genetic Analyses of Fusarium asiaticum Populations from Barley Suggest a Recent Shift Favoring 3ADON Producers in Southern China
Authors: Zhang H. , Zhang Z. , van der Lee T. , Chen W. Q. , Xu J. , Xu J. S. , Yang L. , Yu D. , Waalwijk C. , Feng J.
Published: March 2010

Fusarium asiaticum is the predominant causal agent of Fusarium head blight (FHB) in southern China. The genetic diversity was assessed by analyzing 448 single-spore F. asiaticum isolates from 18 sampling sites that were 10 to 2,000 km apart, using seven highly informative variable number of tandem repeat (VNTR) markers. This analysis showed a significant degree of population subdivision (P < 0.001) among populations from upper, middle, and lower valleys of the Yangtze River, with little gene flow (Nm = 1.210). We observed a strong association between this genetic population subdivision and the mycotoxin produced. Our results show that the dramatic cline in trichothecene chemotypes may be explained by a recent and significant invasion of 3-acetyldeoxynivalenol (3ADON) producers in FHB pathogen composition in the middle valley. Using Bayesian statistics, we found a biased gene flow from 3ADON to nivalenol (NIV) populations. In addition, we observed significant genetic differentiation and linkage disequilibrium between NIV- and 3ADON-producing isolates at the same sampling sites. The impact of the changed agronomy and trade of cereal commodities on the spread of the new Fusarium population and the consequent increase of FHB observed in southern China are discussed.
Evaluation of Resistance to Rhabdocline Needlecast in Douglas Fir Variety Shuswap, with Quantitative Polymerase Chain Reaction
Authors: Catal M. , Adams G. C. , Fulbright D. W.
Published: March 2010

A quantitative polymerase chain reaction assay was developed that could detect DNA of Rhabdocline pseudotsugae and R. oblonga among DNA of Douglas fir needles to a limit as low as three copies of target DNA. Differential infection rates of two varieties (seed sources) of Douglas fir interplanted in a field were studied in relation to staggered bud breaks. Infection of Douglas fir var. San Isabel corresponded to ascospore release times for Rhabdocline spp., whereas infection of var. Shuswap Lake did not occur throughout the spore release period during 2 years of study, despite abundant inoculum and adequate moisture during bud break. Rhabdocline spp. DNA was never detected in Shuswap Lake and disease symptoms were not observed in any year. We provide evidence that Shuswap Lake is resistant and probably immune to Rhabdocline spp. infection and Rhabdocline needlecast under Michigan conditions.
Diversity and Biogeography of Sooty Blotch and Flyspeck Fungi on Apple in the Eastern and Midwestern United States
Authors: Díaz Arias María M. , Batzer Jean C. , Harrington Thomas C. , Wong Amy Wang , Bost Steven C. , Cooley Daniel R. , Ellis Michael A. , Hartman John R. , Rosenberger David A. , Sundin George W. , Sutton Turner B. , Travis James W. , Wheeler Michael J. , Yoder Keith S. , Gleason Mark L.
Published: March 2010

Sooty blotch and flyspeck (SBFS) fungi on apple fruit were sampled from nine orchards in four midwestern U.S. states during 2000 and 30 orchards in 10 eastern U.S. states during 2005 in order to estimate taxonomic diversity and discern patterns of geographic distribution. Forty apple fruit per orchard were arbitrarily sampled and colonies of each mycelial phenotype were counted on each apple. Representative colonies were isolated, cultures were purified, and DNA was extracted. For representative isolates, the internal transcribed spacer (ITS) and large subunit (LSU) regions of ribosomal DNA were amplified and sequenced. In total, 60 SBFS putative species were identified based on ITS sequences and morphological characteristics; 30 of these were discovered in the 2005 survey. Modified Koch's postulates were fulfilled for all 60 species in an Iowa orchard; colonies resulting from inoculation of apple fruit were matched to the original isolates on the basis of mycelial type and ITS sequence. Parsimony analysis for LSU sequences from both surveys revealed that 58 putative SBFS species were members of the Dothideomycetes, 52 were members of the Capnodiales, and 36 were members of the Mycosphaerellaceae. The number of SBFS species per orchard varied from 2 to 15. Number of SBFS species and values of the Margalef and Shannon indexes were significantly (P < 0.05) lower in 21 orchards that had received conventional fungicide sprays during the fruit maturation period than in 14 unsprayed orchards. Several SBFS species, including Schizothyrium pomi, Peltaster fructicola, and Pseudocercosporella sp. RH1, were nearly ubiquitous, whereas other species, such as Stomiopeltis sp. RS5.2, Phialophora sessilis, and Geastrumia polystigmatis, were found only within restricted geographic regions. The results document that the SBFS complex is far more taxonomically diverse than previously recognized and provide strong evidence that SBFS species differ in geographic distribution. To achieve more efficient management of SBFS, it may be necessary to understand the environmental biology of key SBFS species in each geographic region.
Transmission Competency of Single-Female Xiphinema index Lines for Grapevine fanleaf virus
Authors: Demangeat Gérard , Komar Véronique , Van-Ghelder Cyril , Voisin Roger , Lemaire Olivier , Esmenjaud Daniel , Fuchs Marc
Published: March 2010

Grapevine fanleaf virus (GFLV) is vectored specifically from grapevine to grapevine by the ectoparasitic nematode Xiphinema index. Limited information is available on the vector competency of X. index populations from diverse geographical origins. We determined the transmissibility of two GFLV strains showing 4.6% amino acid divergence within their coat protein (e.g., strains F13 and GHu) by seven clonal lines of X. index developed from seven distinct populations from the Mediterranean basin (Cyprus, southern France, Israel, Italy, and Spain), northern France, and California. X. index lines derived from single adult females were produced on fig (Ficus carica) plants to obtain genetically homogenous aviruliferous clones. A comparative reproductive rate analysis on Vitis rupestris du Lot and V. vinifera cv. Cabernet Sauvignon showed significant differences among clones, with the single-female Cyprus line showing the highest rate (30-fold the initial population) and the Spain and California lines showing the lowest rate (10-fold increase), regardless of the grapevine genotype. However, there was no differential vector competency among the seven X. index lines for GFLV strains F13 and GHu. The implications of our findings for the dynamic of GFLV transmission in vineyards and screening of Vitis spp. for resistance to GFLV are discussed.
Phloem Cytochemical Modification and Gene Expression Following the Recovery of Apple Plants from Apple Proliferation Disease
Authors: Musetti R. , Paolacci A. , Ciaffi M. , Tanzarella O. A. , Polizzotto R. , Tubaro F. , Mizzau M. , Ermacora P. , Badiani M. , Osler R.
Published: March 2010

Recovery of apple trees from apple proliferation was studied by combining ultrastructural, cytochemical, and gene expression analyses to possibly reveal changes linked to recovery-associated resistance. When compared with either healthy or visibly diseased plants, recovered apple trees showed abnormal callose and phloem-protein accumulation in their leaf phloem. Although cytochemical localization detected Ca2+ ions in the phloem of all the three plant groups, Ca2+ concentration was remarkably higher in the phloem cytosol of recovered trees. The expression patterns of five genes encoding callose synthase and of four genes encoding phloem proteins were analyzed by quantitative real-time reverse transcription-polymerase chain reaction. In comparison to both healthy and diseased plants, four of the above nine genes were remarkably up-regulated in recovered trees. As in infected apple trees, phytoplasma disappear from the crown during winter, but persist in the roots, and it is suggested that callose synthesis/deposition and phloem-protein plugging of the sieve tubes would form physical barriers preventing the recolonization of the crown during the following spring. Since callose deposition and phloem-protein aggregation are both Ca2+-dependent processes, the present results suggest that an inward flux of Ca2+ across the phloem plasma membrane could act as a signal for activating defense reactions leading to recovery in phytoplasma-infected apple trees.