bluuebunny/crossref_metadata_2025 huggingface dataset:
Bistability of splay and π twist states in a chiral-doped dual frequency liquid crystal cell
Authors: Yao I-An , Yang Chiu-Lien , Chen Chueh-Ju , Pang Jia-Pang , Liao Shih-Fu , Li Jia-Hsin , Wu Jin-Jie
Published: February 2009

A bistable liquid crystal cell with splay and π twist stable states is obtained by doping a chiral additive in a splay cell filled with dual frequency liquid crystals. The switching between the two states is achieved by using a sequential waveform of low and high frequencies. The switching mechanisms are proposed by using the backflow effect together with the anisotropic properties of dual frequency liquid crystals. As a result, the two stable states have the superior memory characteristics due to the topological inequivalence.
Competing anisotropies in bcc Fe81Ni19/Co(001) superlattices
Authors: Hafermann H. , Bručas R. , Soroka I. L. , Katsnelson M. I. , Iuşan D. , Sanyal B. , Eriksson O. , Hjörvarsson B.
Published: February 2009

A magnetization reorientation transition has been observed in Fe81Ni19/Co(001) superlattices by means of magneto-optical Kerr effect and magnetic force microscopy measurements. The transition is driven by the variation of the interface density. First-principles calculations are combined with a linear stability analysis of the Landau–Lifshitz equation to clarify the mechanism that drives the transition. We are able to identify it as being driven by competing interface in-plane and uniaxial bulk out-of-plane anisotropies. The origin of the bulk anisotropy is attributed to tetragonal distortions experimentally observed in these superlattices.
Practical limits of absorption enhancement near metal nanoparticles
Authors: Khurgin J. B. , Sun G. , Soref R. A.
Published: February 2009

We consider the enhanced absorption of optical radiation by molecules placed in the vicinity of spherical metal nanoparticles in the realistic situation that includes perturbation of the optical field by the absorbing molecules. We show that there is an optimal nanosphere radius that gives the strongest enhancement for each combination of the number of absorbing molecules, their absorption strength, and their distance from the nanosphere surface and that the enhancement is strong only for relatively weak and diluted absorbers.
Surface plasmon coupled chemiluminescence from zinc substrates: Directional chemiluminescence
Authors: Aslan Kadir , Geddes Chris D.
Published: February 2009

In this letter, the observation of surface plasmon coupled directional chemiluminescence (SPCC) from zinc thin films is reported. Fresnel calculations predict that light in the ultraviolet and visible spectral range can induce surface plasmon modes in 30 nm zinc thin films. Free-space emission from blue and green chemiluminescent solutions on zinc thin films was isotropic, and the SPCC emission was highly directional and p-polarized in accordance with the Fresnel calculations. In addition, the decay rates of the free-space and SPCC emission were similar, which suggests that zinc thin films have no catalytic effect on chemiluminescence.
Sustained laser induced incandescence in carbon nanotubes for rapid localized heating
Authors: Lim Zhi Han , Lee Andrielle , Zhu Yanwu , Lim Kim-Yong , Sow Chorng-Haur
Published: February 2009

Sustained laser-induced incandescence (LII) was observed when a continuous wave laser beam was focused on aligned multiwalled carbon nanotubes (CNTs) in vacuum. The sustained incandescence originated from radiative dissipation of heated CNTs due to laser-CNT interactions. Sustainability of the LII up to 2 h was achieved. Fittings of the LII intensity spectrum with Planck blackbody distribution indicate a rise of temperature from room temperature to ∼2500 K in less than 0.1 s. This provides an effective way of achieving rapid high temperature heating at specific localized positions within CNT arrays.
Reproductive biology of blue mackerel, Scomber australasicus, off southern and eastern Australia: suitability of the Daily Egg Production Method for stock assessment
Authors: Rogers P. J. , Ward T. M. , McLeay L. J. , Lowry M. , Saunders R. J. , Williams D.
Published: February 2009

The present study investigated the reproductive biology of blue mackerel (Scomber australasicus) off southern and eastern Australia and assessed the suitability of the Daily Egg Production Method (DEPM) for future stock assessment. This analysis revealed that S. australasicus is a serial spawner with asynchronous oocyte development and indeterminate fecundity. S. australasicus spawns between November and April off southern Australia and between July and October off eastern Australia. In southern Australia, ~50% of males and females were mature at 236.5 and 286.8 mm fork length (FL), respectively. Size at ~50% maturity could not be estimated reliably for eastern Australia owing to the smaller proportion of mature fish in samples. Mean spawning frequencies ranged from 2 to 11 days off southern Australia. Batch fecundity was related to fish size and mean batch size was 69 894 ± 4361 oocytes per batch and 134 oocytes per g of weight. The timing and duration of the spawning season, size at maturity, spawning frequency and batch fecundity of S. australasicus off southern Australia were consistent with those of S. japonicus in the northern Pacific Ocean. The present study’s estimates of adult reproductive parameters of S. australasicus off southern Australia were suitable for the application of the DEPM for estimating spawning biomass. Collecting representative samples of mature fish from waters off eastern Australia during the spawning season is a high priority for future stock assessment of this species.
Healthier lobsters in a marine reserve: effects of fishing on disease incidence in the spiny lobster, Jasus edwardsii
Authors: Freeman D. J. , MacDiarmid A. B.
Published: February 2009

Comparison of the health of spiny lobsters (Jasus edwardsii) within and adjacent to a New Zealand marine reserve revealed marked differences in the incidence of a handling-related bacterial infection. Lobsters outside the reserve were significantly more affected by tail fan necrosis than lobsters within the reserve, with up to 17% of the males caught outside the reserve over a 3-year period showing signs of tail fan necrosis, compared with less than 2% within the reserve. The incidence of tail fan necrosis changed abruptly at the marine reserve boundaries, strongly implying repeated handling as the causal agent. The incidence of tail fan necrosis in males increased up to the minimum legal size, consistent with a handling effect. Female lobsters, which comprise only a small proportion of the catch in this area, were comparatively unaffected by tail fan necrosis. There was no significant difference in the recapture rates of individuals tagged either with or without tail fan necrosis, but tagged individuals outside the reserve were more likely to develop tail fan necrosis than tagged individuals within the reserve. These findings have implications for both the dynamics of the lobster populations and their management, and highlight the role of marine protected areas in providing a baseline against which such effects of fishing can be assessed.
Evaluating the use of the Daily Egg Production Method for stock assessment of blue mackerel, Scomber australasicus
Authors: Ward T. M. , Rogers P. J. , McLeay L. J. , McGarvey R.
Published: February 2009

The present study evaluates the suitability of the Daily Egg Production Method (DEPM) for stock assessment of blue mackerel, Scomber australasicus and assesses methodological options for future applications. In southern Australia, estimates of mean daily egg production were higher for Californian Vertical Egg Tow (CalVET) nets than bongo nets, and in eastern Australia, were higher in October 2003 than July 2004. Estimates of spawning area for southern Australia were three times higher for bongo nets than CalVET nets. Similar estimates of spawning area were obtained using standard (manual) gridding and natural neighbour methods. Large samples and reliable estimates of all adult parameters were obtained for southern Australia. Relatively few spawning adults were collected off eastern Australia. Preliminary best estimates of spawning biomass for southern and eastern Australia were 56 228 t and 29 578 t, respectively, with most estimates within the ranges of 45 000–68 000 t and 20 000–40 000 t respectively. The DEPM is suitable for stock assessment of S. australasicus. Several technical refinements are required to enhance future applications, including: genetic techniques for identifying early stage eggs; a temperature–egg development key; improved methods for sampling adults off eastern Australia; and measurements of the degeneration rates of post-ovulatory follicles at several temperatures.
Key crop nutrient management issues in the Western Australia grains industry: a review
Authors: Chen W. , Bell R. W. , Brennan R. F. , Bowden J. W. , Dobermann A. , Rengel Z. , Porter W.
Published: February 2009

In the present paper, we review 4 topics that were identified through extensive consultation with stakeholders as issues of high impact and influence for the grains industry: improving soil testing and interpretation; role of fluid fertilisers in the Western Australian (WA) grains industry; using spatial and temporal information to improve crop nutrient management, particularly for nitrogen; and developing recommendations for managing emerging nutrient deficiencies. The key findings are summarised below.
To further improve soil testing and interpretation, the review suggests that future research should focus on addressing soil sampling and interpretation questions, as they are important factors affecting the accuracy of fertiliser recommendations with changing cropping practices. There have been several studies to compare fluid with granular forms of P in WA, but the responses have not, so far, been consistent. More work may be needed to understand different crop response to fluid P fertiliser additions, particularly on low pH soils in WA. An understanding of the long-term performance of fluid P will also require an assessment of the residual value of fluid P compared with granular P under field conditions. Precision agriculture (PA) technology has potential to improve crop nutrient management and farm profitability in WA. The review indicates that understanding both spatial and temporal yield variation is critical for the successful adoption of PA technology by growers. The review also suggests that in WA, there is a need to explore the use of different layers of spatial information for determining management zones. In response to wide adoption of no-till and stubble retention cropping systems, increased use of fluid fertilisers together with advanced application technologies, and increased interest in cropping in the high rainfall zone, there is need to better understand growers’ practices and attitudes to crop nitrogen (N) management, and thus to better position research and extension activities. The review also suggests the need to evaluate new fertiliser products and site-specific N management concepts and develop N management practices for waterlogging-prone soils for improved N use efficiency in cereal production systems in WA. The negative balance of magnesium (Mg) observed in WA cropping systems, together with the information reviewed on factors affecting soil Mg content and crop response to Mg application across Australia, suggests that there is a need to evaluate the risk and impact of Mg deficiency on acidic sandy soils of WA.
Frequency and season of fires varies with distance from settlement and grass composition in Eucalyptus miniata savannas of the Darwin region of northern Australia
Authors: Elliott Louis P. , Franklin Donald C. , Bowman David M. J. S.
Published: February 2009

In savanna environments, fire and grass are inextricably linked by feedback loops. In the Darwin area of northern Australia, flammable tall annual grasses of the genus Sarga (previously Sorghum1) have been implicated in a savanna fire-cycle. We examined the relationship between fire history, the grass layer and distance from settlement using LANDSAT images and plot-based surveys. Areas more than 500 m from settlement were burnt almost twice as often, the additional fires being concentrated late in the dry season and in areas dominated by annual Sarga and even more so where dominated by short annual grasses. Grass cover was a stronger correlate of fire frequency than grass biomass, the two showing a non-linear relationship. Sites dominated by short annual grasses had similar cover to, but markedly lower biomass than those dominated by annual Sarga or perennial grasses. Our results reflect the success of fire suppression in the vicinity of settlements, but little effective management of late dry-season wildfires in remoter areas. We evaluate several hypotheses for the association of frequent fire with annual grasses regardless of their growth form and conclude that fuel connectivity and possibly other fuel characteristics are key issues worthy of further investigation.
The importance of fire - atmosphere coupling and boundary-layer turbulence to wildfire spread
Authors: Sun Ruiyu , Krueger Steven K. , Jenkins Mary Ann , Zulauf Michael A. , Charney Joseph J.
Published: February 2009

The major source of uncertainty in wildfire behavior prediction is the transient behavior of wildfire due to changes in flow in the fire’s environment. The changes in flow are dominated by two factors. The first is the interaction or ‘coupling’ between the fire and the fire-induced flow. The second is the interaction or ‘coupling’ between the fire and the ambient flow driven by turbulence due to wind gustiness and eddies in the atmospheric boundary layer (ABL). In the present study, coupled wildfire–atmosphere large-eddy simulations of grassland fires are used to examine the differences in the rate of spread and area burnt by grass fires in two types of ABL, a buoyancy-dominated ABL and a roll-dominated ABL. The simulations show how a buoyancy-dominated ABL affects fire spread, how a roll-dominated ABL affects fire spread, and how fire lines interact with these two different ABL flow types. The simulations also show how important are fire–atmosphere couplings or fire-induced circulations to fire line spread compared with the direct impact of the turbulence in the two different ABLs. The results have implications for operational wildfire behavior prediction. Ultimately, it will be important to use techniques that include an estimate of uncertainty in wildfire behavior forecasts.
Improving estimates of savanna burning emissions for greenhouse accounting in northern Australia: limitations, challenges, applications
Authors: Russell-Smith Jeremy , Murphy Brett P. , Meyer C. P. (Mick) , Cook Garry D. , Maier Stefan , Edwards Andrew C. , Schatz Jon , Brocklehurst Peter
Published: February 2009

Although biomass burning of savannas is recognised as a major global source of greenhouse gas emissions, quantification remains problematic with resulting regional emissions estimates often differing markedly. Here we undertake a critical assessment of Australia’s National Greenhouse Gas Inventory (NGGI) savanna burning emissions methodology. We describe the methodology developed for, and results and associated uncertainties derived from, a landscape-scale emissions abatement project in fire-prone western Arnhem Land, northern Australia. The methodology incorporates (i) detailed fire history and vegetation structure and fuels type mapping derived from satellite imagery; (ii) field-based assessments of fuel load accumulation, burning efficiencies (patchiness, combustion efficiency, ash retention) and N : C composition; and (iii) application of standard, regionally derived emission factors. Importantly, this refined methodology differs from the NGGI by incorporation of fire seasonality and severity components, and substantial improvements in baseline data. We consider how the application of a fire management program aimed at shifting the seasonality of burning (from one currently dominated by extensive late dry season wildfires to one where strategic fire management is undertaken earlier in the year) can provide significant project-based emissions abatement. The approach has wider application to fire-prone savanna systems dominated by anthropogenic sources of ignition.
Pitfalls in using counts of roaring stags to index red deer (Cervus elaphus) population size
Authors: Ciucci Paolo , Catullo Gianluca , Boitani Luigi
Published: February 2009

Counting roaring stags during the rut has been proposed as a means to assess deer population size and trends but few, if any, attempts have been made to evaluate the reliability of this technique. By means of a commonly used field protocol, we assessed to what extent relative abundance estimates of red deer (Cervus elaphus) based on roaring-stag counts in the northern Apennines (Italy) were susceptible to exogenous and unpredictable sources of variability. By using up to 26 simultaneous observers in an area of 5218 ha, we estimated densities from 0.45 to 0.61 roaring stags per 100 ha in 3 consecutive years (1992–94), corresponding to annual changes in the number of counted roaring stags ranging from –21% to +35.7%. However, only in two of the three years were seasonal trends and peaks in roaring activity apparent, and timing of the survey was not always synchronous with the roaring peak. In addition, annual and nocturnal variation in roaring activity, and weather conditions during the survey, might have influenced the counts to some extent, probably determining high Type I and Type II error rates. We contend that additional sources of error, associated with unknown demographic and ecological settings, may further increase unreliability of the technique when it is used to estimate absolute density of red deer populations. We conclude by emphasising that managers should not use this method for population monitoring unless they can prove it can yield reliable results.
Assessing the use of milk fatty acids to infer the diet of the Australian sea lion (Neophoca cinerea)
Authors: Baylis A. M. M. , Hamer D. J. , Nichols P. D.
Published: February 2009

Information on the diet of threatened species is important in devising appropriate management plans to ensure their conservation. The Australian sea lion (Neophoca cinerea) is Australia’s only endemic and globally one of the least numerous pinniped species. However, dietary information is currently limited because of the difficulty in using traditional methods (identification of prey hard parts from scats, regurgitates and stomach samples) to reliably provide dietary information. The present study assessed the use of fatty acid (FA) analysis to infer diet using milk samples collected from 11 satellite tracked Australian sea lions from Olive Island, South Australia. Satellite tracking revealed that females foraged in two distinct regions; ‘inshore’ regions characterised by shallow bathymetry (10.7 ± 4.8 m) and ‘offshore’ regions characterised by comparatively deep bathymetry (60.5 ± 13.4 m). Milk FA analysis indicated significant differences in the FA composition between females that foraged inshore compared with those that foraged offshore. The greatest differences in relative levels of individual FAs between the inshore and offshore groups were for 22 : 6n-3 (6.5 ± 1.2% compared with 16.5 ± 1.9% respectively), 20 : 4n-6 (6.1 ± 0.7 compared with 2.5 ± 0.7 respectively) and 22 : 4n-6 (2.4 ± 0.2% compared with 0.8 ± 0.2% respectively). Using discriminant scores, crustacean, cephalopod, fish and shark-dominated diets were differentiated. The discriminant scores from Australian sea lions that foraged inshore indicated a mixed fish and shark diet, whereas discriminant scores from Australian sea lions that foraged offshore indicated a fish-dominated diet, although results must be interpreted with caution due to the assumptions associated with the prey FA dataset. FA analysis in combination with satellite tracking proved to be a powerful tool for assessing broad-scale spatial dietary patterns.
Mechanistic insights into active site-associated polyubiquitination by the ubiquitin-conjugating enzyme Ube2g2
Authors: Li Wei , Tu Daqi , Li Lianyun , Wollert Thomas , Ghirlando Rodolfo , Brunger Axel T. , Ye Yihong
Published: February 2009

Lys-48-linked polyubiquitination regulates a variety of cellular processes by targeting ubiquitinated proteins to the proteasome for degradation. Although polyubiquitination had been presumed to occur by transferring ubiquitin molecules, one at a time, from an E2 active site to a substrate, we recently showed that the endoplasmic reticulum-associated RING finger ubiquitin ligase gp78 can mediate the preassembly of Lys-48-linked polyubiquitin chains on the catalytic cysteine of its cognate E2 Ube2g2 and subsequent transfer to a substrate. Active site-linked polyubiquitin chains are detected in cells on Ube2g2 and its yeast homolog Ubc7p, but how these chains are assembled is unclear. Here, we show that gp78 forms an oligomer via 2 oligomerization sites, one of which is a hydrophobic segment located in the gp78 cytosolic domain. We further demonstrate that a gp78 oligomer can simultaneously associate with multiple Ube2g2 molecules. This interaction is mediated by a novel Ube2g2 surface distinct from the predicted RING binding site. Our data suggest that a large gp78–Ube2g2 heterooligomer brings multiple Ube2g2 molecules into close proximity, allowing ubiquitin moieties to be transferred between neighboring Ube2g2s to form active site-linked polyubiquitin chains.
Mechanism of Bcl-2 and Bcl-X
L
inhibition of NLRP1 inflammasome: Loop domain-dependent suppression of ATP binding and oligomerization
Authors: Faustin Benjamin , Chen Ya , Zhai Dayong , Negrate Gaelle Le , Lartigue Lydia , Satterthwait Arnold , Reed John C.
Published: February 2009

NLRP1 (NLR family, pyrin domain-containing 1) is a contributor to innate immunity involved in intracellular sensing of pathogens, as well as danger signals related to cell injury. NLRP1 is one of the core components of caspase-1-activating platforms termed “inflammasomes,” which are involved in proteolytic processing of interleukin-1β (IL-1β) and in cell death. We previously discovered that anti-apoptotic proteins Bcl-2 and Bcl-X
L
bind to and inhibit NLRP1 in cells. Using an in vitro reconstituted system employing purified recombinant proteins, we studied the mechanism by which Bcl-2 and Bcl-X
L
inhibit NLRP1. Bcl-2 and Bcl-X
L
inhibited caspase-1 activation induced by NLRP1 in a concentration-dependent manner, with
K
i
≈ 10 nM. Bcl-2 and Bcl-X
L
were also determined to inhibit ATP binding to NLRP1, which is required for oligomerization of NLRP1, and Bcl-X
L
was demonstrated to interfere with NLRP1 oligomerization. Deletion of the flexible loop regions of Bcl-2 and Bcl-X
L
, which are located between the first and second α-helices of these anti-apoptotic proteins and which were previously shown to be required for binding NLRP1, abrogated ability to inhibit caspase-1 activation, ATP binding and oligomerization of NLRP1. Conversely, synthetic peptides corresponding to the loop region of Bcl-2 were sufficient to potently inhibit NLRP1. These findings thus demonstrate that the loop domain is necessary and sufficient to inhibit NLRP1, providing insights into the mechanism by which anti-apoptotic proteins Bcl-2 and Bcl-X
L
inhibit NLRP1.
Domestication and growth hormone transgenesis cause similar changes in gene expression in coho salmon (
Oncorhynchus kisutch
)
Authors: Devlin Robert H. , Sakhrani Dionne , Tymchuk Wendy E. , Rise Matthew L. , Goh Benjamin
Published: February 2009

Domestication has been extensively used in agricultural animals to modify phenotypes such as growth rate. More recently, transgenesis of growth factor genes [primarily growth hormone (GH)] has also been explored as a rapid approach to accelerating performance of agricultural species. Growth rates of many fishes respond dramatically to GH gene transgenesis, whereas genetic engineering of domestic mammalian livestock has resulted in relatively modest gains. The most dramatic effects of GH transgenesis in fish have been seen in relatively wild strains that have undergone little or no selection for enhanced growth, whereas genetic modification of livestock necessarily has been performed in highly domesticated strains that already possess very rapid growth. Such fast-growing domesticates may be refractory to further stimulation if the same regulatory pathways are being exploited by both genetic approaches. By directly comparing gene expression in wild-type, domestic, and GH transgenic strains of coho salmon, we have found that domestication and GH transgenesis are modifying similar genetic pathways. Genes in many different physiological pathways show modified expression in domestic and GH transgenic strains relative to wild-type, but effects are strongly correlated. Genes specifically involved in growth regulation (IGF1, GHR, IGF-II, THR) are also concordantly regulated in domestic and transgenic fish, and both strains show elevated levels of circulating IGF1. Muscle expression of GH in nontransgenic strains was found to be elevated in domesticated fish relative to wild type, providing a possible mechanism for growth enhancement. These data have implications for genetic improvement of existing domesticated species and risk assessment and regulation of emerging transgenic strains.
Modularity and interactions in the genetics of gene expression
Authors: Litvin Oren , Causton Helen C. , Chen Bo-Juen , Pe'er Dana
Published: February 2009

Understanding the effect of genetic sequence variation on phenotype is a major challenge that lies at the heart of genetics. We developed GOLPH (GenOmic Linkage to PHenotype), a statistical method to identify genetic interactions, and used it to characterize the landscape of genetic interactions between gene expression quantitative trait loci. Our results reveal that allele-specific interactions, in which a gene only exerts an influence on the phenotype in the presence of a particular allele at the primary locus, are widespread and that genetic interactions are predominantly nonadditive. The data portray a complex picture in which interacting loci influence the expression of modules of coexpressed genes involved in coherent biological processes and pathways. We show that genetic variation at a single gene can have a major impact on the global transcriptional response, altering interactions between genes through shutdown or activation of pathways. Thus, different cellular states occur not only in response to the external environment but also result from intrinsic genetic variation.
Triassic origin and early radiation of multicellular volvocine algae
Authors: Herron Matthew D. , Hackett Jeremiah D. , Aylward Frank O. , Michod Richard E.
Published: February 2009

Evolutionary transitions in individuality (ETIs) underlie the watershed events in the history of life on Earth, including the origins of cells, eukaryotes, plants, animals, and fungi. Each of these events constitutes an increase in the level of complexity, as groups of individuals become individuals in their own right. Among the best-studied ETIs is the origin of multicellularity in the green algaVolvox, a model system for the evolution of multicellularity and cellular differentiation. Since its divergence from unicellular ancestors,Volvoxhas evolved into a highly integrated multicellular organism with cellular specialization, a complex developmental program, and a high degree of coordination among cells. Remarkably, all of these changes were previously thought to have occurred in the last 50–75 million years. Here we estimate divergence times using a multigene data set with multiple fossil calibrations and use these estimates to infer the times of developmental changes relevant to the evolution of multicellularity. Our results show thatVolvoxdiverged from unicellular ancestors at least 200 million years ago. Two key innovations resulting from an early cycle of cooperation, conflict and conflict mediation led to a rapid integration and radiation of multicellular forms in this group. This is the only ETI for which a detailed timeline has been established, but multilevel selection theory predicts that similar changes must have occurred during other ETIs.
Reducing environmental risk by improving N management in intensive Chinese agricultural systems
Authors: Ju Xiao-Tang , Xing Guang-Xi , Chen Xin-Ping , Zhang Shao-Lin , Zhang Li-Juan , Liu Xue-Jun , Cui Zhen-Ling , Yin Bin , Christie Peter , Zhu Zhao-Liang , Zhang Fu-Suo
Published: February 2009

Excessive N fertilization in intensive agricultural areas of China has resulted in serious environmental problems because of atmospheric, soil, and water enrichment with reactive N of agricultural origin. This study examines grain yields and N loss pathways using a synthetic approach in 2 of the most intensive double-cropping systems in China: waterlogged rice/upland wheat in the Taihu region of east China versus irrigated wheat/rainfed maize on the North China Plain. When compared with knowledge-based optimum N fertilization with 30–60% N savings, we found that current agricultural N practices with 550–600 kg of N per hectare fertilizer annually do not significantly increase crop yields but do lead to about 2 times larger N losses to the environment. The higher N loss rates and lower N retention rates indicate little utilization of residual N by the succeeding crop in rice/wheat systems in comparison with wheat/maize systems. Periodic waterlogging of upland systems caused large N losses by denitrification in the Taihu region. Calcareous soils and concentrated summer rainfall resulted in ammonia volatilization (19% for wheat and 24% for maize) and nitrate leaching being the main N loss pathways in wheat/maize systems. More than 2-fold increases in atmospheric deposition and irrigation water N reflect heavy air and water pollution and these have become important N sources to agricultural ecosystems. A better N balance can be achieved without sacrificing crop yields but significantly reducing environmental risk by adopting optimum N fertilization techniques, controlling the primary N loss pathways, and improving the performance of the agricultural Extension Service.
Descent on elliptic curves and Hilbert’s tenth problem
Authors: Eisenträger Kirsten , Everest Graham
Published: February 2009

Descent via an isogeny on an elliptic curve is used to construct two subrings of the field of rational numbers, which are complementary in a strong sense, and for which Hilbert’s Tenth Problem is undecidable. This method further develops that of Poonen, who used elliptic divisibility sequences to obtain undecidability results for some large subrings of the rational numbers.
Cycles on Nash algebraic models of smooth manifolds
Authors: Kucharz Wojciech
Published: February 2009

A Nash algebraic model of a compact smooth manifold

M
M

is a pair

(
X
,

X
0

)

(X,X_0)

where

X
X

is a nonsingular real algebraic set and

X
0

X_0

is the union of some connected components of

X
X

such that

X
0

X_0

is diffeomorphic to

M
M

. We study the homology classes on

X
0

X_0

represented by algebraic subsets of

X
X

contained in

X
0

X_0

for various Nash algebraic models

(
X
,

X
0

)

(X,X_0)

of

M
M

.
In orbifolds, small isoperimetric regions are small balls
Authors: Morgan Frank
Published: February 2009

In a compact orbifold, for a small prescribed volume, an isoperimetric region is close to a small metric ball; in a Euclidean orbifold, it is a small metric ball.
The Laitinen Conjecture for finite solvable Oliver groups
Authors: Pawałowski Krzysztof , Sumi Toshio
Published: February 2009

For smooth actions ofGGon spheres with exactly two fixed points, the Laitinen Conjecture proposed an answer to the Smith question about theGG-modules determined on the tangent spaces at the two fixed points. Morimoto obtained the first counterexample to the Laitinen Conjecture forG=Aut(A6)G = \textrm {Aut}(A_6). By answering the Smith question for some finite solvable Oliver groupsGG, we obtain new counterexamples to the Laitinen Conjecture, presented for the first time in the case whereGGis solvable.
On a problem of Borsuk and Ulam
Authors: Gordon Alexander
Published: February 2009

Borsuk and Ulam posed the following problem: For an arbitrary closed subset

C
C

of the

d
d

-dimensional sphere, does there exist a sequence of homeomorphisms of the sphere such that the sequence of images of every point of the sphere converges to a point of

C
C

and each point of

C
C

is the limit of such a sequence? The answer is known to be positive, but the existing proof is complicated. We give a simple proof that extends to some other manifolds including the 𝑑-dimensional

torus.
Spanning trees and Khovanov homology
Authors: Champanerkar Abhijit , Kofman Ilya
Published: February 2009

The Jones polynomial can be expressed in terms of spanning trees of the graph obtained by checkerboard coloring a knot diagram. We show that there exists a complex generated by these spanning trees whose homology is the reduced Khovanov homology. The spanning trees provide a filtration on the reduced Khovanov complex and a spectral sequence that converges to its homology. For alternating links, all differentials on the spanning tree complex are zero and the reduced Khovanov homology is determined by the Jones polynomial and signature. We prove some analogous theorems for (unreduced) Khovanov homology.
Electrical response matrix of a regular 2𝑛-gon
Authors: Blair-Stahn Nathaniel , Wilson David
Published: February 2009

Consider a unit-resistive plate in the shape of a regular polygon with

2
n

2n

sides, in which even-numbered sides are wired to electrodes and odd-numbered sides are insulated. The response matrix, or Dirichlet-to-Neumann map, allows one to compute the currents flowing through the electrodes when they are held at specified voltages. We show that the entries of the response matrix of the regular

2
n

2n

-gon are given by the differences of cotangents of evenly spaced angles, and we describe some connections with the limiting distributions of certain random spanning forests.
Lipschitzness of the Lempert and Green functions
Authors: Nikolov Nikolai , Pflug Peter , Thomas Pascal
Published: February 2009

Necessary and sufficient conditions for Lipschitzness of the Lempert and Green functions are found in terms of their boundary behaviors.
A note on Cheeger sets
Authors: Figalli Alessio , Maggi Francesco , Pratelli Aldo
Published: February 2009

Starting from the quantitative isoperimetric inequality, we prove a sharp quantitative version of the Cheeger inequality.
Optimal regularity for the Poisson equation
Authors: Wang Lihe , Yao Fengping , Zhou Shulin , Jia Huilian
Published: February 2009

In this paper we study the regularity theory for the Poisson equation in

R

n

\mathbb {R}^n

under proper conditions. Furthermore, it will be verified that these conditions are optimal.
Existence and uniqueness of Tronquée solutions of the fourth-order Jimbo-Miwa second Painlevé equation
Authors: Joshi Nalini , Morrison Tegan
Published: February 2009

We consider the asymptotic limit as the independent variable approaches infinity, of the fourth-order second Painlevé equation obtained from a hierarchy based on the Jimbo-Miwa Lax pair. We prove that there exist two families of algebraic formal power series solutions and that there exist true solutions with these behaviours in sectors

σ
\sigma

of the complex plane. Given

σ
\sigma

we also prove that there exists a wider sector

Σ
⊃
σ

\Sigma \supset \sigma

in which there exists a unique solution in each family. These provide the analogue of Boutroux’s tri-tronquée solutions for the classical second Painlevé equation. Surprisingly, they also extend beyond the tri-tronquée solutions in the sense that we find penta-, hepta-, ennea-, and hendeca-tronquée solutions.
The group of order preserving automorphisms of the ring of differential operators on a Laurent polynomial algebra in prime characteristic
Authors: Bavula V.
Published: February 2009

Let

K
K

be a field of characteristic

p
>
0

p>0

. It is proved that the group

A
u
t

o
r
d

(

D

(

L
n

)
)

\mathrm {Aut}_{ord}(\mathcal {D}(L_n))

of order preserving automorphisms of the ring

D

(

L
n

)

\mathcal {D}(L_n)

of differential operators on a Laurent polynomial algebra

L
n

:=
K
[

x
1

±
1

,
…
,

x
n

±
1

]

L_n:= K[x_1^{\pm 1}, \ldots , x_n^{\pm 1}]

is isomorphic to a skew direct product of groups

Z

p
n

⋊

A
u
t

K

(

L
n

)

{\mathbb {Z}}_p^n \rtimes \mathrm {Aut}_K(L_n)

, where

Z

p

{\mathbb {Z}}_p

is the ring of

p
p

-adic integers. Moreover, the group

A
u
t

o
r
d

(

D

(

L
n

)
)

\mathrm {Aut}_{ord}(\mathcal {D}(L_n))

is found explicitly. Similarly,
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="normal upper A normal u normal t Subscript o r d Baseline left-parenthesis script upper D left-parenthesis upper P Subscript n Baseline right-parenthesis right-parenthesis asymptotically-equals normal upper A normal u normal t Subscript upper K Baseline left-parenthesis upper P Subscript n Baseline right-parenthesis">

A
u
t

o
r
d

(

D

(

P
n

)
)
≃

A
u
t

K

(

P
n

)

\mathrm {Aut}_{ord}(\mathcal {D}(P_n))\simeq \mathrm {Aut}_K(P_n)

, where

P
n

:=
K
[

x
1

,
…
,

x
n

]

P_n: =K[x_1, \ldots , x_n]

is a polynomial algebra.
The crystal ℬ(∞) and extended Nakajima monomials
Authors: Lee Hyeonmi
Published: February 2009

We construct the set of extended Nakajima monomials containing monomials realizing the irreducible highest weight crystals, introduced by Nakajima. We present explicit descriptions of a crystal

B

∞

\mathcal {B}_{\infty }

and the crystal

B

(
∞
)

\mathcal {B}(\infty )

in this language for the case

A
n

(
1
)

A_n^{(1)}

.
ZEB1 Enhances Transendothelial Migration and Represses the Epithelial Phenotype of Prostate Cancer Cells
Authors: Drake Justin M. , Strohbehn Garth , Bair Thomas B. , Moreland Jessica G. , Henry Michael D.
Published: February 2009

Metastatic colonization involves cancer cell lodgment or adherence in the microvasculature and subsequent migration of those cells across the endothelium into a secondary organ site. To study this process further, we analyzed transendothelial migration of human PC-3 prostate cancer cells in vitro. We isolated a subpopulation of cells, TEM4-18, that crossed an endothelial barrier more efficiently, but surprisingly, were less invasive than parental PC-3 cells in other contexts in vitro. Importantly, TEM4-18 cells were more aggressive than PC-3 cells in a murine metastatic colonization model. Microarray and FACS analysis of these cells showed that the expression of many genes previously associated with leukocyte trafficking and cancer cell extravasation were either unchanged or down-regulated. Instead, TEM4-18 cells exhibited characteristic molecular markers of an epithelial-to-mesenchymal transition (EMT), including frank loss of E-cadherin expression and up-regulation of the E-cadherin repressor ZEB1. Silencing ZEB1 in TEM4-18 cells resulted in increased E-cadherin and reduced transendothelial migration. TEM4-18 cells also express N-cadherin, which was found to be necessary, but not sufficient for increased transendothelial migration. Our results extend the role of EMT in metastasis to transendothelial migration and implicate ZEB1 and N-cadherin in this process in prostate cancer cells.
OnTheFly: a tool for automated document-based text annotation, data linking and network generation
Authors: Pavlopoulos Georgios A. , Pafilis Evangelos , Kuhn M. , Hooper Sean D. , Schneider Reinhard
Published: February 2009

OnTheFly is a web-based application that applies biological named entity recognition to enrich Microsoft Office, PDF and plain text documents. The input files are converted into the HTML format and then sent to the Reflect tagging server, which highlights biological entity names like genes, proteins and chemicals, and attaches to them JavaScript code to invoke a summary pop-up window. The window provides an overview of relevant information about the entity, such as a protein description, the domain composition, a link to the 3D structure and links to other relevant online resources. OnTheFly is also able to extract the bioentities mentioned in a set of files and to produce a graphical representation of the networks of the known and predicted associations of these entities by retrieving the information from the STITCH database.

Availability:  http://onthefly.embl.de,  http://onthefly.embl.de/FAQ.html

Contact:  pavlopou@embl.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Determination of sample size in genome-scale RNAi screens
Authors: Zhang Xiaohua Douglas , Heyse Joseph F.
Published: February 2009

Motivation: For genome-scale RNAi research, it is critical to investigate sample size required for the achievement of reasonably low false negative rate (FNR) and false positive rate.

Results: The analysis in this article reveals that current design of sample size contributes to the occurrence of low signal-to-noise ratio in genome-scale RNAi projects. The analysis suggests that (i) an arrangement of 16 wells per plate is acceptable and an arrangement of 20–24 wells per plate is preferable for a negative control to be used for hit selection in a primary screen without replicates; (ii) in a confirmatory screen or a primary screen with replicates, a sample size of 3 is not large enough, and there is a large reduction in FNRs when sample size increases from 3 to 4. To search a tradeoff between benefit and cost, any sample size between 4 and 11 is a reasonable choice. If the main focus is the selection of siRNAs with strong effects, a sample size of 4 or 5 is a good choice. If we want to have enough power to detect siRNAs with moderate effects, sample size needs to be 8, 9, 10 or 11. These discoveries about sample size bring insight to the design of a genome-scale RNAi screen experiment.

Contact:  Xiaohua_zhang@merck.com
Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions
Authors: Del Mondo Géraldine , Eveillard Damien , Rusu Irena
Published: February 2009

Motivation: Modules in biology appeared quickly as an accurate way for summarizing complex living systems by simple ones. Therefore, finding an appropriate relationship between modules extracted from a biological graph and protein complexes remains a crucial task. Recent studies successfully proposed various descriptions of protein interaction networks. These approaches succeed in showing modules within the network and how the modules interact. However, describing the interactions within the modules, i.e. intra-modular interactions, remains little analyzed despite its interest for understanding module functions.

Results: We overcome this weakness by adding a complementary description to the already successful approaches: a hierarchical decomposition named homogeneous decomposition. This decomposition represents a natural refinement of previous analyses and details interactions within a module. We propose to illustrate these improvements by three practical cases. Among them, we decompose the yeast protein interaction network and show reachable biological insights that might be extracted from a complex large-scale network.

Availability: A program is at disposal under CeCILL license at: www.lina.univ-nantes.fr/combi/DH/Home.html

Contact:  irena.rusu@univ-nantes.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Triterpenic Acids Present in Hawthorn Lower Plasma Cholesterol by Inhibiting Intestinal ACAT Activity in Hamsters
Authors: Lin Yuguang , Vermeer Mario A. , Trautwein Elke A.
Published: February 2009

Hawthorn (Crataegus pinnatifida) is an edible fruit used in traditional Chinese medicine to lower plasma lipids. This study explored lipid‐lowering compounds and underlying mechanisms of action of hawthorn. Hawthorn powder extracts inhibited acylCoA:cholesterol acyltransferase (ACAT) activity in Caco‐2 cells. The inhibitory activity was positively associated with triterpenic acid (i.e., oleanolic acid (OA) and ursolic acid (UA)) contents in the extracts. Cholesterol lowering effects of hawthorn and its potential additive effect in combination with plant sterol esters (PSE) were further studied in hamsters. Animals were fed a semi‐synthetic diet containing 0.08% (w/w) cholesterol (control) or the same diet supplemented with (i) 0.37% hawthorn dichloromethane extract, (ii) 0.24% PSE, (iii) hawthorn dichloromethane extract (0.37%) plus PSE (0.24%) or (iv) OA/UA mixture (0.01%) for 4 weeks. Compared to the control diet, hawthorn, PSE, hawthorn plus PSE and OA/UA significantly lowered plasma non‐HDL (VLDL + LDL) cholesterol concentrations by 8%, 9%, 21% and 6% and decreased hepatic cholesterol ester content by 9%, 23%, 46% and 22%, respectively. The cholesterol lowering effects of these ingredients were conversely associated with their capacities in increasing fecal neutral sterol excretion. In conclusion, OA and UA are responsible for the cholesterol lowering effect of hawthorn by inhibiting intestinal ACAT activity. In addition, hawthorn and particularly its bioactive compounds (OA and UA) enhanced the cholesterol lowering effect of plant sterols.
Segmentation and fishery characteristics of the mixed-species multi-gear Portuguese fleet
Authors: Duarte Rafael , Azevedo Manuela , Afonso-Dias Manuel
Published: February 2009

Duarte, R., Azevedo, M., and Afonso-Dias, M. 2009. Segmentation and fishery characteristics of the mixed-species multi-gear Portuguese fleet. – ICES Journal of Marine Science, 66: 594–606. Fleet segmentation and knowledge of fishing fleet dynamics are essential to move from single species to fishery/fleet-based advice. The coastal mixed-species multi-gear Portuguese fleet comprises medium-sized (>12 m) vessels, using a diversity of passive gears, and is economically important. For hake (under a recovery plan) and monkfish (overexploited), it contributes >50% to their total annual landings. Commercial daily landings in 2005 from 271 vessels were analysed by region using non-hierarchical cluster analysis and multivariate regression trees. The cluster analysis allowed the identification of regional fleet segments with a low mixture of species throughout the year. The multivariate regression trees were applied to clusters of vessels with a high mixture of species, to explain weekly landing profiles (species) by vessel technical characteristics, fishing license, and main landing port. The results showed a link between exploited species and geographic location, and in the north between vessel size and depth and an inshore/offshore range. Finally, from the analysis and for the most important species exploited by the Portuguese multi-gear fleet, it was possible to define two or three vessel groups that accounted for at least 50% of the landed value.
The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome
Authors: De Subhajyoti , Teichmann Sarah A. , Babu M. Madan
Published: February 2009

Divergence of gene expression can result in phenotypic variation, which contributes to the evolution of new species. Although the influence of trans- and cis-regulatory mutations is well known, the genome-wide impact of changes in genomic neighborhood of genes on expression divergence between species remains largely unexplored. Here, we compare the neighborhood of orthologous genes (within a window of 2 MB) in human and chimpanzee with the expression levels of their transcripts from several equivalent tissues and demonstrate that genes with altered neighborhood are more likely to undergo expression divergence than genes with conserved neighborhood. We observe the same trend when expression divergence data were analyzed from six different brain parts that are equivalent between human and chimpanzee. Additionally, we find enrichment for genes with altered neighborhood to be expressed in a tissue-specific manner in the human brain. These results suggest that expression divergence induced by this mechanism could have contributed to the phenotypic differences between human and chimpanzee. We propose that, in addition to other molecular mechanisms, change in genomic neighborhood is an important factor that drives transcriptome evolution.