bluuebunny/crossref_metadata_2025 huggingface dataset:
Controlling embryonic stem cell proliferation and pluripotency: the role of PI3K- and GSK-3-dependent signalling
Authors: Welham Melanie J. , Kingham Emmajayne , Sanchez-Ripoll Yolanda , Kumpfmueller Benjamin , Storm Michael , Bone Heather
Published: March 2011

ESCs (embryonic stem cells) are derived from the inner cell mass of pre-implantation embryos and are pluripotent, meaning they can differentiate into all of the cells that make up the adult organism. This property of pluripotency makes ESCs attractive as a model system for studying early development and for the generation of specific cell types for use in regenerative medicine and drug screening. In order to harness their potential, the molecular mechanisms regulating ESC pluripotency, proliferation and differentiation (i.e. cell fate) need to be understood so that pluripotency can be maintained during expansion, while differentiation to specific lineages can be induced accurately when required. The present review focuses on the potential roles that PI3K (phosphoinositide 3-kinase) and GSK-3 (glycogen synthase kinase 3)-dependent signalling play in the co-ordination and integration of mouse ESC pluripotency and proliferation and contrast this with our understanding of their functions in human ESCs.
Viruses and the human DEAD-box helicase DDX3: inhibition or exploitation?
Authors: Schröder Martina
Published: March 2011

Human DDX3 is a DEAD (Asp-Glu-Ala-Asp)-box RNA helicase that appears to be a prime target for viral manipulation. While two viruses that manifest major global health threats, HIV and HCV (hepatitis C virus), utilize DDX3 for their replication, other viruses inhibit DDX3's newly identified function in innate antiviral signalling. This review discusses the role of DDX3 in antiviral immunity and its inhibition or exploitation by different viruses.
Allocating sex in road-killed possums using PCR
Authors: Russell Tracey C. , Neaves Linda E. , Herbert Catherine A.
Published: March 2011

Road-killed animals are a readily available but often overlooked source of specimens and data. Determining the sex of road-killed possums is often difficult due to the severe damage carcasses sustain on impact with vehicles. Consequently, valuable information is lost. To assess the potential application of genetic techniques to address this problem, tissue biopsies (n = 47) taken from road-killed possums were sexed via PCR, through the simultaneous use of W- (G6PD) and Y-linked (SRY) primers. Comparisons with animals of known sex were used to validate the accuracy of this method, with 100% (n = 19) of samples correctly identified in a blind test. This methodology can provide researchers with valuable, additional data for road-kill studies where assigning sex in the field is not possible.
The design and testing of linen thread weak-links in brushtail possum radio-collars
Authors: Cawthen Lisa , Munks Sarah
Published: March 2011

Linen thread was built into radio-collars as a weak-link to trial its effectiveness at ensuring that radio-collars did not remain indefinitely on animals if they were not recaptured. Eighty percent of collars with weak-links broke or degraded, resulting in the collars dropping off within 12–45 days. This method may be useful for short-term studies of some species of mammal that are difficult to recapture in order to remove collars.
A capture technique for free-ranging eastern grey kangaroos (Macropus giganteus) habituated to humans
Authors: King W. J. , Wilson M. E. , Allen T. , Festa-Bianchet M. , Coulson G.
Published: March 2011

Available methods to capture free-ranging kangaroos differ in ease of use, selectivity, risk of injury and suitability to specific environments. We describe a simple technique involving the syringe from a ‘jabstick’ attached to an extendable, aluminium pole. We also examine responses of eastern grey kangaroos (Macropus giganteus) to a range of doses of Zoletil®. We captured 307 eastern grey kangaroos that were habituated to humans in Victoria, Australia, from November 2007 to October 2009. We approached kangaroos on foot, and injected the hind limb muscle mass with the pole syringe extended up to 4.85 m. We used Zoletil® 100 at a dose rate of 4.1 ± 1.3 mg kg–1 (mean ± s.d., n = 274). Induction was rapid (4.3 ± 2.0 min, n = 185) and only weakly related to dose (r2 = 0.06). There was no clear relationship between age, sex or body condition and induction time. This pole syringe technique can be successfully and safely used wherever animals can be approached closely, regardless of body condition. The technique provides an effective means to immobilise habituated kangaroos for research and management.
K 1-6: An Asymmetric Planetary Nebula with a Binary Central Star
Authors: Frew David J. , Stanger Jeff , Fitzgerald Michael , Parker Quentin , Danaia Lena , McKinnon David , Guerrero Martín A. , Hedberg John , Hollow Robert , An Yvonne , Bor Shu Han , Colman Isabel , Graham-White Claire , Li Qing Wen , Mai Juliette , Papadakis Katerina , Picone-Murray Julia , Vo Hoang Melanie , Yean Vivian
Published: March 2011

We present new imaging data and archival multiwavelength observations of the little-studied emission nebula K 1-6 and its central star. Narrow-band images inHα (+[N II]) and [O III] taken with the Faulkes Telescope North reveal a stratified, asymmetric, elliptical nebula surrounding a central star which has the colours of a late G or early K-type subgiant or giant. GALEX ultraviolet images reveal a very hot subdwarf or white dwarf coincident in position with this star. The cooler, optically dominant star is strongly variable with a period of 21.312± 0.008 days, and is possibly a high-amplitude member of the RS CVn class, although an FK Com classification is also possible. Archival ROSAT data provide good evidence that the cool star has an active corona. We conclude that K 1-6 is most likely an old bona fide planetary nebula at a distance of ∼1.0 kpc, interacting with the interstellar medium, and containing a binary or ternary central star. The observations and data analyses reported in this paper were conducted in conjunction with Year 11 high school students as part of an Australian Research Council Linkage Grant science education project, denoted Space To Grow, conducted jointly by professional astronomers, educational researchers, teachers, and high-school students.
DSPSR: Digital Signal Processing Software for Pulsar Astronomy
Authors: van Straten W. , Bailes M.
Published: March 2011

dspsr is a high-performance, open-source, object-oriented, digital signal processing software library and application suite for use in radio pulsar astronomy. Written primarily in C++, the library implements an extensive range of modular algorithms that can optionally exploit both multiple-core processors and general-purpose graphics processing units. After over a decade of research and development, dspsr is now stable and in widespread use in the community. This paper presents a detailed description of its functionality, justification of major design decisions, analysis of phase-coherent dispersion removal algorithms, and demonstration of performance on some contemporary microprocessor architectures.
The distribution of Carrichtera annua in Australia: introduction, spread and probable limits
Authors: Cooke Julia , Groves R. H. , Ash Julian
Published: March 2011

Carrichtera annua (L.) DC. (Brassicaceae) or Ward’s Weed, a major weed of semi-arid rangelands of southern Australia, has been collected widely since its introduction early in the 20th century. Collated records were used to suggest a single site of accidental introduction in South Australia, evidence of a lag phase of ~30 years (probably due to edaphic restrictions) before rapid spread, involving infrequent long-distance human-aided dispersal across southern Australia and a relatively stable range since the 1960s. Climate and soil analyses suggest that abiotic factors limit the distribution of C. annua, with the species being restricted to areas with winter-dominated rainfall and calcareous soils. Documentation of the history of a successful invasion, including the spread and probable limits of the current distribution of a species, is important for managing invasions. This study also highlights that a single, accidental introduction can result in a long-lasting, widespread problematic weed.
Habitat use and trophic structure in a microbat assemblage on the edge of the southern rangelands, Western Australia: insights from stable isotope analysis
Authors: Dunlop J. N. , Bullen R. D.
Published: March 2011

The microbat assemblage on Charles Darwin Reserve was investigated between 2007 and 2009 to provide a benchmark for monitoring long-term responses to climate change on a major bioregional boundary, the mulga–eucalypt line. Stable isotope analysis of bat fur was used to interpret the current local habitat and trophic relationships between microbat species with different biogeographical affinities. The stable isotope values of the ants inhabiting 10 broad vegetation types were used to provide an isotopic baseline of the Reserve to assist in the interpretation of the δC or δN signatures observed in the bat assemblage. The δC signatures of ants in both a Salmon Gum woodland and an arid shrubland shifted significantly after the breaking of a prolonged drought but there was no change in the bats.
The ubiquitous bat species, and those with south-western affinities, probably used most of the available vegetation types on the Reserve and displayed some significant differences in mean trophic level. Scotorepens balstoni, a species of the southern interior of Western Australia, specialised at foraging within patches of eucalypt woodland. Vespadelus baverstocki, a southern arid zone species, was evidently restricted to the proximal arid habitats with distinctively high δN signatures.
A new empirical model of sub-daily rainfall intensity and its application in a rangeland biophysical model
Authors: Fraser G. W. , Carter J. O. , McKeon G. M. , Day K. A.
Published: March 2011

Sub-daily rainfall intensity has a significant impact on runoff and erosion rates in northern Australian rangelands. However, it has been difficult to include sub-daily rainfall intensity in rangeland biophysical models using historical climate data due to the limited number of pluviograph stations with long-term records. In this paper a new empirical model (‘Temperature I15’ model) was developed to predict the daily maximum 15-min rainfall intensity (I15) using daily minimum and maximum temperature and daily rainfall totals from 12 selected pluviograph stations across Australia. The ‘Temperature I15’ model accounted for 46% (P < 0.01) of the variation in observed daily I15 for an independent validation dataset derived from 67 Australia-wide pluviograph stations and represented both geographical and seasonal variability in I15. The model also accounted for 70% (P < 0.01) of the variation in the observed historical trend in I15 for the full record period (average record period was 37 years) of 73 Australia-wide pluviograph stations.
The ‘Temperature I15’ model was found to be an improvement on a past empirical model of I15 and can be easily implemented in biophysical models by using readily available daily climate data. However, as the ‘Temperature I15’ model only represented 46% of the variation in daily observed I15, the model is best used in simulation studies on ‘timeframes’ in excess of 5 years.
The new ‘Temperature I15’ model was implemented in the runoff equation of the Australia-wide spatial pasture growth model AussieGRASS, which predicts daily water balance and pasture growth for 185 different pasture communities. This resulted in an improved simulation of green cover for 71% of pasture communities but was worse for 25% of communities, with no change for 4% of communities.
Increased grazing and dominance of an exotic pasture (Bothriochloa pertusa) affects vertebrate fauna species composition, abundance and habitat in savanna woodland
Authors: Kutt Alex S. , Fisher Alaric
Published: March 2011

The invasion of exotic pasture species into intact woodlands has the potential to affect native fauna by altering habitat structure and ecosystem function. The spread of these weeds is generally in concert with cattle grazing, so that fauna or habitat change is due to multiple interrelated causes. In this study we investigated whether the spread of the introduced pasture grass Bothriochloa pertusa and replacement of the native bluegrass B. ewartiana in eucalypt woodlands of northern Queensland has had an effect on terrestrial vertebrate fauna. We located 40 sites that sampled a range of native and introduced pastures cover, and investigated the spatial pattern of abundance with canonical analysis of principle coordinates, and correlation of the habitat attributes on the ordination space. We then selected a subset of four habitat attributes (eliminating highly colinear variables) and modelled species response to each using an information-theoretic approach. Thirty-one species (26 birds, one mammal and four reptiles) and two summary variables (bird abundance and richness) had best subset Akaike Information Criteria models with reliable parameters estimates. Seventeen models contained the B. pertusa frequency term and a further 16 had a term relating to upper storey cover (tree cover >10, 5–10 or 3–5 m). Though pasture grass cover, grazing and habitat features were correlated and thus we cannot ascribe B. pertusa as the sole determinant of fauna species change, this study has demonstrated that tropical savanna woodlands with changing Bothriochloa dominance from native to introduced species have different fauna species composition. In particular bird species richness, ground nesting species (e.g. rufous songlark Cincloramphus mathewsi, golden-headed cisticola Cisticola exilis) and terrestrial reptiles (e.g. Carlia munda and Ctenotus taeniolatus) declined. Disturbance-tolerant species such as Australian magpie Cracticus tibicen and yellow-throated miners Manorina flavigula increased in abundance in exotic pasture-dominated sites. As pastoral intensification continues in northern Australian rangelands there is a potential for significant change in the relative abundance and composition of vertebrate fauna and the reduction or loss of some species in the landscape.
NMDA receptor subunit composition controls synaptogenesis and synapse stabilization
Authors: Gambrill Abigail C. , Barria Andres
Published: March 2011

During early postnatal development in the rat hippocampus, synaptogenesis occurs in parallel with a developmental switch in the subunit composition of NMDA receptors from NR2B to NR2A. It is unclear how this switch affects the process of synaptogenesis, synapse maturation, and synapse stabilization. We investigated the role of NR2 subunits in synaptogenesis during the period in which expression and synaptic incorporation of the NR2A protein begins through the time when it reaches adult levels. We found that early expression of NR2A in organotypic hippocampal slices reduces the number of synapses and the volume and dynamics of spines. In contrast, overexpression of NR2B does not affect the normal number and growth of synapses; however, it does increase spine motility, adding and retracting spines at a higher rate. The C terminus of NR2B, and specifically its ability to bind CaMKII, is sufficient to allow proper synapse formation and maturation. Conversely, the C terminus of NR2A was sufficient to stop the development of synapse number and spine growth. Our results indicate that the ratio of synaptic NR2B over NR2A controls spine motility and synaptogenesis, and suggest a structural role for the intracellular C terminus of NR2 in recruiting the signaling and scaffolding molecules necessary for proper synaptogenesis.
Deletion of theSlo3gene abolishes alkalization-activated K+current in mouse spermatozoa
Authors: Zeng Xu-Hui , Yang Chengtao , Kim Sung Tae , Lingle Christopher J. , Xia Xiao-Ming
Published: March 2011

Mouse spermatozoa express a pH-dependent K+current (KSper) thought to be composed of subunits encoded by theSlo3gene. However, the equivalence of KSper andSlo3-dependent current remains uncertain, because heterologous expression ofSlo3results in currents that are less effectively activated by alkalization than are native KSper currents. Here, we show that genetic deletion ofSlo3abolishes all pH-dependent K+current at physiological membrane potentials in corpus epididymal sperm. A residual pH-dependent outward current (IKres) is observed inSlo3−/−sperm at potentials of >0 mV. Differential inhibition of KSper/Slo3 andIKresby clofilium reveals that the amplitude ofIKresis similar in both wild-type (wt) andSlo3−/−sperm. The properties ofIKressuggest that it likely represents outward monovalent cation flux through CatSper channels. Thus, KSper/Slo3 may account for essentially all mouse sperm K+current and is the sole pH-dependent K+conductance in these sperm. With physiological ionic gradients, alkalization depolarizesSlo3−/−spermatozoa, presumably from CatSper activation, in contrast to Slo3/KSper-mediated hyperpolarization in wt sperm.Slo3−/−male mice are infertile, butSlo3−/−sperm exhibit some fertility within in vitro fertilization assays.Slo3−/−sperm exhibit a higher incidence of morphological abnormalities accentuated by hypotonic challenge and also exhibit deficits in motility in the absence of bicarbonate, revealing a role of KSper under unstimulated conditions. Together, these results show that KSper/Slo3 is the primary spermatozoan K+current, that KSper may play a critical role in acquisition of normal morphology and sperm motility when faced with hyperosmotic challenges, and that Slo3 is critical for fertility.
Turning a protein kinase on or off from a single allosteric site via disulfide trapping
Authors: Sadowsky Jack D. , Burlingame Mark A. , Wolan Dennis W. , McClendon Christopher L. , Jacobson Matthew P. , Wells James A.
Published: March 2011

There is significant interest in identifying and characterizing allosteric sites in enzymes such as protein kinases both for understanding allosteric mechanisms as well as for drug discovery. Here, we apply a site-directed technology, disulfide trapping, to interrogate structurally and functionally how an allosteric site on the Ser/Thr kinase, 3-phosphoinositide-dependent kinase 1 (PDK1)—the PDK1-interacting-fragment (PIF) pocket—is engaged by an activating peptide motif on downstream substrate kinases (PIFtides) and by small molecule fragments. By monitoring pairwise disulfide conjugation between PIFtide and PDK1 cysteine mutants, we defined the PIFtide binding orientation in the PIF pocket of PDK1 and assessed subtle relationships between PIFtide positioning and kinase activation. We also discovered a variety of small molecule fragment disulfides (< 300 Da) that could either activate
or
inhibit PDK1 by conjugation to the PIF pocket, thus displaying greater functional diversity than is displayed by PIFtides conjugated to the same sites. Biochemical data and three crystal structures provided insight into the mechanism of action of the best fragment activators and inhibitors. These studies show that disulfide trapping is useful for characterizing allosteric sites on kinases and that a single allosteric site on a protein kinase can be exploited for both activation and inhibition by small molecules.
Cantonese politeness in the interviewing setting
Authors: Pan Yuling
Published: March 2011

This paper aims to use Cantonese interview data to explore how (im)politeness is used as a discursive strategy and resource to attend to the perceived interactional goal and power relationship in the interview setting. It adopts a situation-oriented and ethnography-driven approach to study politeness as a situated action. In addition to investigating Cantonese-specific features of politeness, the study demonstrates that power relation in politeness should be analyzed at the level of the entire communicative event as well as at the turn-to-turn level. Findings of this study are significant not only for extending politeness research to less commonly studied languages like Cantonese, but also for expanding the application of politeness theories to other research areas such as institutional discourse and survey research.
Positioning and multidimensional (im)politeness in Korean Oriental medical discourse
Authors: Kim Ki-tae
Published: March 2011

Studies on politeness in Korean — an honorific-rich language like Japanese — have focused more on what Sohn (1995: 408) identifies as ‘normative’ (or discernment) politeness. Whilst these studies are illuminating, they have paid little attention to the ‘dynamic’ aspect of politeness. That is, they have focussed on ‘static’ or primarily dyadic interactions and have explored the speaker’s discursive intention but paid minimal attention to the addressee’s evaluation of certain utterances. The present study attempts to fill this gap by showing how multiple levels of politeness arise at ‘situational, institutional, and societal levels’ (Fairclough, 1989) in Korean institutional discourse. To this effect, it concentrates on the interaction between Korean Oriental medical doctors and their patients, which is a ‘fruitful epistemological site’ (Sunderland, 2004: 73) for the study of emerging and situated politeness in Korean. This is particularly so because in Korea traditional and Western medicine co-exist — Western medicine often being regarded as ‘dominant’ one — and consequently there is a ‘dual medical authority’ in Korean society. Employing Goffman’s (1981) ‘participation framework’ and Davies and Harré’s (1990, 1999) ‘positioning theory’, the present article demonstrates that the dual medical authority often obscures the ‘speaker’, ‘addressee’, and (im)politeness. of a speech act in patient–Oriental medical doctor interactions. An act that is apparently face-threatening at the situational level may not necessarily be face-threatening at the institutional level, where the ‘real’ addressee may be a non-present Western doctor or even Western biomedicine itself. The paper concludes that the dyadic, synchronic, and cross-sectional model of politeness on which most studies on Korean politeness rely is too simplistic and idealised. Instead, a multidimensional discursive approach to politeness should be adopted.
The effects of the fibre content and physical structure of carrots on satiety and subsequent intakes when eaten as part of a mixed meal
Authors: Moorhead S. Anne , Welch Robert W. , Barbara M. , Livingstone E. , McCourt Maeve , Burns Amy A. , Dunne Adrian
Published: March 2011

Previous research indicates that vegetables yield relatively high satiety scores, and that fibre content and structure may both contribute to these effects. This study evaluated the effects of the fibre content and physical structure (gross anatomy and cell structure) of carrots on postprandial satiety and subsequent food intakes when consumed as part of a mixed meal. Using a randomised, repeated-measures, within-subject cross-over design, young women consumed a standardised breakfast and test lunches on three occasions, 4 weeks apart. The test lunches (3329kJ) comprised boiled rice (200g) with sweet and sour sauce (200g) that included chicken (200g) and carrots (200g) in three conditions: whole carrots (fibre and structure; n 34), blended carrots (fibre but no structure; n 34) or carrot nutrients (no fibre or structure; n 32). The carrot nutrients had the same energy, major nutrients and portion weight as the other two conditions. Post-lunch satiety was assessed by visual analogue scales. Intakes were covertly weighed at a meal eaten ad libitum (3h later), and for the remainder of the day using food diaries. Compared with the meal with carrot nutrients, meals with whole carrots and blended carrots resulted in significantly (P<0·05) higher satiety. There were significant (P<0·05) differences between conditions in intakes at the meal eaten ad libitum and for the remainder of the day, and intakes consistently decreased in the order: carrot nutrients, blended carrots, whole carrots, indicating that both fibre content and structure played a role in these effects.
Activation volumes for nanocrystal growth in amorphous Nd3.6Pr5.4Fe83Co3B5 at different temperatures
Authors: Xu Lei , Guo Defeng , Li Xiaohong , Zhou Lipeng , Wang Fengqing , Zhang Xiangyi
Published: March 2011

To understand the nanocrystallization process of amorphous Nd3.6Pr5.4Fe83Co3B5, activation volumes for the growth of nanocrystals in the alloy have been determined directly by measuring the rate constants varying with pressure at different temperatures. At T = 773 K, the activation volume for the growth of α-(Fe,Co) phase is determined to be (0.50 ± 0.02)Ω, where Ω is the mean atomic volume of the alloy, and it increases slightly to (0.59 ± 0.03)Ω at T = 823 K. The activation volume for the growth of (Nd,Pr)2Fe14B phase at T = 823 K is determined to be (0.52 ± 0.02)Ω. The effect of temperature on the activation volume for nanocrystal growth is discussed.
Study on TiO2-doped Ge2Te3 films for phase-change memory application
Authors: Lu Yegang , Song Sannian , Song Zhitang , Wu Liangcai , Liu Bo , Feng Songlin , Guo Xiaohui
Published: March 2011

The phase-change characteristics of Ge2Te3 films for phase-change random access memory applications were investigated by doping with TiO2 using magnetron cosputtering. The first and the second phase transitions, which corresponded to the crystallizations of GeTe and Te, occurred at around 210 °C and 225 °C for the Ge2Te3 film, respectively. The incorporation of TiO2 suppressed the crystallization of GeTe and held back the phase transition induced by the Te. The precipitation of aggregated GeTe from Ge2Te3–TiO2 was observed at the annealing temperature of 400 °C. The resistance ratio between RESET and SET states exceeded two orders of magnitude. Compared with Ge2Sb2Te5-based cell device, the Ge2Te3–TiO2 film-based ones had a lower power consumption. The reversible phase change could be accomplished by the electric pulse duration of 50 ns for Ge2Te3–TiO2 with 15 at% TiO2-based cell device.
Electric and spectroscopic analysis of a pure nitrogen mono-filamentary dielectric barrier discharge (MF-DBD) at 760 Torr
Authors: Sewraj N , Merbahi N , Gardou J P , Akerreta P Rodriguez , Marchal F
Published: March 2011

Mono-filamentary dielectric barrier discharge (MF-DBD), occurring within 1 mm gap of atmospheric pressure pure nitrogen and operating with a sinusoidal electric supply at about 8 kHz, is studied in this paper. A thorough electrical analysis allows experimental determination of the ignition and extinction voltages, respectively (15 750 ± 50) V and (2097 ± 7) V, the injected energy (158 ± 2) J and charge (17.22 ± 0.22) nC in a single filament. The mean axial reduced electric field is equal to (644 ± 2) Td at ignition. An empirical technique is proposed to evaluate these discharge parameters by avoiding bulky calculations. Optical emission spectroscopic measurements of the vacuum ultraviolet (VUV), ultraviolet (UV), visible and near infrared (IR) emissions are presented and discussed. Two atomic nitrogen lines attributed to the decay of the N[2s2p23s2P] triplet towards N[2s22p32D°] level are observed at 150 and 175 nm, together with the Lyman–Birge–Hopfield systemin the VUV range. The second positive system (N2[C 3Πu] →N2[B 3Πg]) dominates the UV and visible-blue spectra. The (0–0) transition of the first negative systempeaking at 391.4 nm, the first positive systemand the Herman IR transitionsare also present. Both our VUV and near IR spectra are consistent with recently reported results in hollow cathode and cylindrical DBDs. The electrical and spectroscopic experimental results reported here are useful for ongoing and forthcoming modelling of filamentary nitrogen dielectric barrier discharges.
Time- and space-resolved measurements of Ar(1s5) metastable density in a microplasma using diode laser absorption spectroscopy
Authors: Belostotskiy Sergey G , Ouk Tola , Donnelly Vincent M , Economou Demetre J , Sadeghi Nader
Published: March 2011

Time- and space-resolved measurements of Ar(1s5) metastable (Ar*) density were carried out in a pulsed dc argon microplasma discharge, using diode laser absorption spectroscopy. The temporal behaviour of metastable density after discharge turn off (in the afterglow) depended on their spatial location in the microplasma. In the early afterglow, the Ar* density decayed monotonically with time in the region around the sheath edge, while in the bulk plasma the Ar* density showed a maximum with time. This behaviour was attributed to electron–ion dissociative recombination. Later in the afterglow, the Ar* decay was everywhere monotonic with time, mainly due to three-body collisional quenching by ground state argon atoms. The time evolution of the Ar* density in the afterglow predicted by a kinetic model is in good agreement with the experimental measurements.
Investigation of the dynamics of the Z-pinch imploding plasma for a laser-assisted discharge-produced Sn plasma EUV source
Authors: Zhu Q , Yamada J , Kishi N , Watanabe M , Okino A , Horioka K , Hotta E
Published: March 2011

Dynamics of the imploding plasma and its relations to the 13.5 nm EUV emissions have been experimentally investigated for a laser-assisted Sn based discharge-produced plasma EUV source. The behaviours and two-dimensional electron density distributions of the EUV-emitting plasma were obtained using the time-resolved shadowgraph and Nomarski interferometric techniques. Observation of the plasma piston in the prepinch phase justified the validity of the zero-dimensional thin-shell model, from which the ion charge state of the prepinch plasma in the cathode region was estimated. The sausage (m = 0) instability that usually enhances the EUV emission was observed, with the radial electron density distribution that displays a concave shape at the crest of the plasma and a bell shape at the neck; the maximum of the electron density is located at one peak of the concave distribution at the crest instead of the neck. Intense EUV emission was produced by the Z-pinch plasma with the electron density (2.0–3.0) × 1018 cm−3. Moreover, the shock waves generated in the anode region can also produce in-band EUV emission with the intensity of 30% of that from the Z-pinch plasma.
Investigation of acoustic resonances in high-power lamps
Authors: Kettlitz M , Rarbach J , Zalach J
Published: March 2011

High-power, medium-pressure, mercury-containing lamps are used as UV sources for many industrial applications. Lamps investigated in this paper are driven with an electronic ballast with a non-sinusoidal current waveform at a fixed frequency of 20 kHz and a maximum power output of 35 kW. Instabilities can occur if the input power is reduced below 50%. The reason is identified as acoustic resonances in the lamp. Comparison of calculated and measured resonance frequencies shows a good agreement and explains the observed lamp behaviour. This has led to the development of a new ballast prototype which is able to avoid instabilities by changing the driving frequency dependent on the applied power.
Effect of ultrasonic energy on nanoscale interfacial structure in copper wire bonding on aluminium pads
Authors: Xu H , Liu C , Silberschmidt V V , Chen Z , Acoff V L
Published: March 2011

The effect of ultrasonic vibration on nanoscale interfacial structure of thermosonic copper wire bonding on aluminium pads was investigated. It was found that bonding strength was determined by the extent of fragmentation of a native aluminium oxide overlayer (5–10 nm thick) on aluminium pads, forming paths for formation of intermetallic compound CuAl2 in areas of direct contact of bonded metal surfaces. The degree of fracture of the oxide layer was strongly affected by a level of ultrasonic power.
Is it Food Quality or Quantity that Responds to Changing Income?
Authors: Kuchler Fred
Published: March 2011

Since the early 1990s, the retail market for leafy green vegetables has been divided between largely unprocessed products and bagged salads. The latter embody kitchen labor and economize on storage costs, in effect offering consumers convenience as a product attribute. Using time‐series retail purchase data, this paper shows that changes in income immediately influence how much convenience consumers of leafy greens purchase. There is no statistical evidence that total quantity of leafy greens purchased responds to short‐run changes in income. Hence, consumers appear to adjust to income changes by choosing food quality rather than quantity.
ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments
Authors: Picardi Ernesto , D'Antonio Mattia , Carrabino Danilo , Castrignanò Tiziana , Pesole Graziano
Published: March 2011

Summary: ExpEdit is a web application for assessing RNA editing in human at known or user-specified sites supported by transcript data obtained by RNA-Seq experiments. Mapping data (in SAM/BAM format) or directly sequence reads [in FASTQ/short read archive (SRA) format] can be provided as input to carry out a comparative analysis against a large collection of known editing sites collected in DARNED database as well as other user-provided potentially edited positions. Results are shown as dynamic tables containing University of California, Santa Cruz (UCSC) links for a quick examination of the genomic context.

Availability: ExpEdit is freely available on the web at http://www.caspur.it/ExpEdit/.

Contact:  graziano.pesole@biologia.uniba.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Species–energy relationships in deep-sea molluscs
Authors: Tittensor Derek P. , Rex Michael A. , Stuart Carol T. , McClain Craig R. , Smith Craig R.
Published: March 2011

Consensus is growing among ecologists that energy and the factors influencing its utilization can play overarching roles in regulating large-scale patterns of biodiversity. The deep sea—the world's largest ecosystem—has simplified energetic inputs and thus provides an excellent opportunity to study how these processes structure spatial diversity patterns. Two factors influencing energy availability and use are chemical (productive) and thermal energy, here represented as seafloor particulate organic carbon (POC) flux and temperature. We related regional patterns of benthic molluscan diversity in the North Atlantic to these factors, to conduct an explicit test of species–energy relationships in the modern day fauna of the deep ocean. Spatial regression analyses in a model-averaging framework indicated that POC flux had a substantially higher relative importance than temperature for both gastropods and protobranch bivalves, although high correlations between variables prevented definitive interpretation. This contrasts with recent research on temporal variation in fossil diversity from deep-sea cores, where temperature is generally a more significant predictor. These differences may reflect the scales of time and space at which productivity and temperature operate, or differences in body size; but both lines of evidence implicate processes influencing energy utilization as major determinants of deep-sea species diversity.
Temporal changes in greenspace in a highly urbanized region
Authors: Dallimer Martin , Tang Zhiyao , Bibby Peter R. , Brindley Paul , Gaston Kevin J. , Davies Zoe G.
Published: March 2011

The majority of the world's population now lives in towns and cities, and urban areas are expanding faster than any other land-use type. In response to this phenomenon, two opposing arguments have emerged: whether cities should ‘sprawl’ into the wider countryside, or ‘densify’ through the development of existing urban greenspace. However, these greenspaces are increasingly recognized as being central to the amelioration of urban living conditions, supporting biodiversity conservation and ecosystem service provision. Taking the highly urbanized region of England as a case study, we use data from a variety of sources to investigate the impact of national-level planning policy on temporal patterns in the extent of greenspace in cities. Between 1991 and 2006, greenspace showed a net increase in all but one of 13 cities. However, the majority of this gain occurred prior to 2001, and greenspace has subsequently declined in nine cities. Such a dramatic shift in land use coincides with policy reforms in 2000, which favoured densification. Here, we illustrate the dynamic and policy-responsive nature of urban land use, thereby highlighting the need for a detailed investigation of the trade-offs associated with different mechanisms of urban densification to optimize and secure the diverse benefits associated with greenspaces.
Spontaneous discrimination of possible and impossible objects by newly hatched chicks
Authors: Regolin Lucia , Rugani Rosa , Stancher Gionata , Vallortigara Giorgio
Published: March 2011

Four-month-old infants can integrate local cues provided by two-dimensional pictures and interpret global inconsistencies in structural information to discriminate between possible and impossible objects. This leaves unanswered the issue of the relative contribution of maturation of biologically predisposed mechanisms and of experience with real objects, to the development of this capability. Here we show that, after exposure to objects in which junctions providing cues to global structure were occluded, day-old chicks selectively approach the two-dimensional image that depicted the possible rather than the impossible version of a three-dimensional object, after restoration of the junctions. Even more impressively, completely naive newly hatched chicks showed spontaneous preferences towards approaching two-dimensional depictions of structurally possible rather than impossible objects. These findings suggest that the vertebrate brain can be biologically predisposed towards approaching a two-dimensional image representing a view of a structurally possible three-dimensional object.
The energetics of low browsing in sauropods
Authors: Ruxton Graeme D. , Wilkinson David M.
Published: March 2011

It has recently been argued that the probable high cost of travel for sauropod dinosaurs would have made exploiting high forage energetically attractive, if this reduced the need to travel between food patches. This argument was supported by simple calculations. Here, we take a similar approach to evaluate the energetics of foraging close to the ground. We predict that small extensions of the neck beyond the minimum required for the mouth to reach the ground bring substantial energetic savings. Each increment of length brings a further saving, but the sizes of such benefits decrease with increasing neck length. However, the observed neck length of around 9 m for
Brachiosaurus
(for example) is predicted to reduce the overall cost of foraging by 80 per cent, compared with a minimally necked individual. We argue that the long neck of the sauropods may have been under positive selection for low foraging (instead of, or as well as, exploitation of high foraging), if this long neck allowed a greater area of food to be exploited from a given position and thus reduced the energetically expensive movement of the whole animal.
Experimental demonstration of a two-phase population extinction hazard
Authors: Drake John M. , Shapiro Jeff , Griffen Blaine D.
Published: March 2011

Population extinction is a fundamental biological process with applications to ecology, epidemiology, immunology, conservation biology and genetics. Although a monotonic relationship between initial population size and mean extinction time is predicted by virtually all theoretical models, attempts at empirical demonstration have been equivocal. We suggest that this anomaly is best explained with reference to the transient properties of ensembles of populations. Specifically, we submit that under experimental conditions, many populations escape their initially vulnerable state to reach quasi-stationarity, where effects of initial conditions are erased. Thus, extinction of populations initialized far from quasi-stationarity may be exposed to a two-phase extinction hazard. An empirical prediction of this theory is that the fit Cox proportional hazards regression model for the observed survival time distribution of a group of populations will be shown to violate the proportional hazards assumption early in the experiment, but not at later times. We report results of two experiments with the cladoceran zooplankton
Daphnia magna
designed to exhibit this phenomenon. In one experiment, habitat size was also varied. Statistical analysis showed that in one of these experiments a transformation occurred so that very early in the experiment there existed a transient phase during which the extinction hazard was primarily owing to the initial population size, and that this was gradually replaced by a more stable quasi-stationary phase. In the second experiment, only habitat size unambiguously displayed an effect. Analysis of data pooled from both experiments suggests that the overall extinction time distribution in this system results from the mixture of extinctions during the initial rapid phase, during which the effects of initial population size can be considerable, and a longer quasi-stationary phase, during which only habitat size has an effect. These are the first results, to our knowledge, of a two-phase population extinction process.
Fractal analysis of behaviour in a wild primate: behavioural complexity in health and disease
Authors: MacIntosh Andrew J. J. , Alados Concepción L. , Huffman Michael A.
Published: March 2011

Parasitism and other stressors are ubiquitous in nature but their effects on animal behaviour can be difficult to identify. We investigated the effects of nematode parasitism and other indicators of physiological impairment on the sequential complexity of foraging and locomotion behaviour among wild Japanese macaques (Macaca fuscata yakui). We observed all sexually mature individuals (n= 28) in one macaque study group between October 2007 and August 2008, and collected two faecal samples/month/individual (n= 362) for parasitological examination. We used detrended fluctuation analysis (DFA) to investigate long-range autocorrelation in separate, binary sequences of foraging (n= 459) and locomotion (n= 446) behaviour collected via focal sampling. All behavioural sequences exhibited long-range autocorrelation, and linear mixed-effects models suggest that increasing infection with the nodular wormOesophagostomum aculeatum, clinically impaired health, reproductive activity, ageing and low dominance status were associated with reductions in the complexity of locomotion, and to a lesser extent foraging, behaviour. Furthermore, the sequential complexity of behaviour increased with environmental complexity. We argue that a reduction in complexity in animal behaviour characterizes individuals in impaired or ‘stressed’ states, and may have consequences if animals cannot cope with heterogeneity in their natural habitats.
Reaction-layer asymptotics and the electrochemical pickling of steel
Authors: Vynnycky M. , Ipek N.
Published: March 2011

Asymptotic methods are used to explore the role of one of the homogeneous chemical reactions, water protolysis, in a recent numerical model for the electrochemical pickling of steel. The analysis helps to interpret the somewhat surprising results of the original numerical model: that the local current density profile at the pickled strip does not depend on whether the water protolysis reaction is included in the model or not. The analysis also gives a useful systematic approach for determining qualitative estimates for the width of reaction boundary layers at cell electrodes, which can be of help when designing a computational mesh for the numerical solution of electrochemical models that have such layers.
Lateral and transverse shifts in reflected dipole radiation
Authors: Berry M. V.
Published: March 2011

In-plane (lateral) and out-of-plane (transverse) shifts in the direction of arbitrarily polarized electromagnetic waves in a denser medium, reflected totally or partially at an interface with a rarer medium, are calculated exactly, in terms of the deviation of the Poynting vector from radial. The shifts are analogous to the Goos–Hänchen and Fedorov–Imbert shifts for beams. There is a transverse shift even for unreflected dipole radiation if the polarization is not linear. With reflection, there is a transverse shift for linear polarization, provided this is not pure transverse electric or transverse magnetic. The contributions from the geometrical ray, the lateral ray that interferes strongly with it, and the large peak at the Brewster angle (for transverse magnetic polarization), are calculated asymptotically far from the geometrical image. At the critical angle, the lowest order asymptotics is inadequate and a more sophisticated treatment is devised, reproducing the exact shifts accurately.
Infrared mapping resolves soft tissue preservation in 50 million year-old reptile skin
Authors: Edwards N. P. , Barden H. E. , van Dongen B. E. , Manning P. L. , Larson P. L. , Bergmann U. , Sellers W. I. , Wogelius R. A.
Published: March 2011

Non-destructive Fourier Transform InfraRed (FTIR) mapping of Eocene aged fossil reptile skin shows that biological control on the distribution of endogenous organic components within fossilized soft tissue can be resolved. Mapped organic functional units within this approximately 50 Myr old specimen from the Green River Formation (USA) include amide and sulphur compounds. These compounds are most probably derived from the original beta keratin present in the skin because fossil leaf- and other non-skin-derived organic matter from the same geological formation do not show intense amide or thiol absorption bands. Maps and spectra from the fossil are directly comparable to extant reptile skin. Furthermore, infrared results are corroborated by several additional quantitative methods including Synchrotron Rapid Scanning X-Ray Fluorescence (SRS-XRF) and Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS). All results combine to clearly show that the organic compound inventory of the fossil skin is different from the embedding sedimentary matrix and fossil plant material. A new taphonomic model involving ternary complexation between keratin-derived organic molecules, divalent trace metals and silicate surfaces is presented to explain the survival of the observed compounds. X-ray diffraction shows that suitable minerals for complex formation are present. Previously, this study would only have been possible with major destructive sampling. Non-destructive FTIR imaging methods are thus shown to be a valuable tool for understanding the taphonomy of high-fidelity preservation, and furthermore, may provide insight into the biochemistry of extinct organisms.
Extremely long-distance seed dispersal by an overfished Amazonian frugivore
Authors: Anderson Jill T. , Nuttle Tim , Saldaña Rojas Joe S. , Pendergast Thomas H. , Flecker Alexander S.
Published: March 2011

Throughout Amazonia, overfishing has decimated populations of fruit-eating fishes, especially the large-bodied characid,
Colossoma macropomum
. During lengthy annual floods, frugivorous fishes enter vast Amazonian floodplains, consume massive quantities of fallen fruits and egest viable seeds. Many tree and liana species are clearly specialized for icthyochory, and seed dispersal by fish may be crucial for the maintenance of Amazonian wetland forests. Unlike frugivorous mammals and birds, little is known about seed dispersal effectiveness of fishes. Extensive mobility of frugivorous fish could result in extremely effective, multi-directional, long-distance seed dispersal. Over three annual flood seasons, we tracked fine-scale movement patterns and habitat use of wild
Colossoma
, and seed retention in the digestive tracts of captive individuals. Our mechanistic model predicts that
Colossoma
disperses seeds extremely long distances to favourable habitats. Modelled mean dispersal distances of 337–552 m and maximum of 5495 m are among the longest ever reported. At least 5 per cent of seeds are predicted to disperse 1700–2110 m, farther than dispersal by almost all other frugivores reported in the literature. Additionally, seed dispersal distances increased with fish size, but overfishing has biased
Colossoma
populations to smaller individuals. Thus, overexploitation probably disrupts an ancient coevolutionary relationship between
Colossoma
and Amazonian plants.