bluuebunny/crossref_metadata_2025 huggingface dataset:
Worms and germs: the population dynamic consequences of microparasite-macroparasite co-infection
Authors: FENTON ANDY
Published: December 2007

Hosts are typically simultaneously co-infected by a variety of microparasites (e.g. viruses and bacteria) and macroparasites (e.g. parasitic helminths). However, the population dynamical consequences of such co-infections and the implications for the effectiveness of imposed control programmes have yet to be fully realised. Mathematical models may provide an important framework for exploring such issues and have proved invaluable in helping to understand the factors affecting the epidemiology of single parasitic infections. Here the first population dynamic model of microparasite-macroparasite co-infection is presented and used to explore how co-infection alters the predictions of the existing single-species models. It is shown that incorporating an additional parasite species into existing models can greatly stabilise them, due to the combined density-dependent impacts on the host population, but co-infection can also restrict the region of parameter space where each species could persist alone. Overall it is concluded that the dynamic feedback between host, microparasite and macroparasite means that it is difficult to appreciate the factors affecting parasite persistence and predict the effectiveness of control by just studying one component in isolation.
Differences in prevalence and patterns of substance use in schizophrenia and bipolar disorder
Authors: Ringen P. A. , Lagerberg T. V. , Birkenæs A. B. , Engn J. , Færden A. , Jónsdottir H. , Nesvåg R. , Friis S. , Opjordsmoen S. , Larsen F. , Melle I. , Andreassen O. A.
Published: December 2007

Background

Schizophrenia and bipolar disorder have partly overlapping clinical profiles, which include an over-representation of substance-use behaviour. There are few previous studies directly comparing substance-use patterns in the two disorders. The objective of the present study was to compare the prevalence of substance use in schizophrenia and bipolar disorder, and investigate possible differences in pattern and frequency of use.

Method

A total of 336 patients with schizophrenia or bipolar spectrum disorder from a catchment area-based hospital service were included in a cross-sectional study. In addition to thorough clinical assessments, patients were interviewed about drug-use history, habits and patterns of use. The prevalence and drug-use patterns were compared between groups.

Results

Patients with bipolar disorder had higher rates of alcohol consumption, while schizophrenia patients more often used centrally stimulating substances, had more frequent use of non-alcoholic drugs and more often used more than one non-alcoholic drug. Single use of cannabis was more frequent in bipolar disorder.

Conclusion

The present study showed diagnosis-specific patterns of substance use in severe mental disorder. This suggests a need for more disease-specific treatment strategies, and indicates that substance use may be an important factor in studies of overlapping disease mechanisms.
Birth Of The Institute
Authors: Fraser D. O.
Published: December 2007

Squadron Leader Douglas Fraser, a Fellow and Life Member of the Institute holding RIN membership number 6, was one of the founder members joining when the Institute was formed on 25th June 1947. Sixty years later, on Friday 29th June 2007, at our first Annual General Meeting since being granted our Royal Charter, he was invited by our President to make a short presentation on the birth of our Institute. Squadron Leader Fraser was unable to travel from his home to attend the AGM in person, but with great foresight had planned for such an eventuality and prepared a short video of his speech. This paper is a verbatim account of his message.
THE SHAFT TOMBS OF EL PIÑON, BOLAÑOS CANYON, STATE OF JALISCO, MEXICO
Authors: García María Teresa Cabrero , Cruz Carlos López
Published: December 2007

A group of three unlooted shaft tombs was discovered and excavated in the site of El Piñon, in Bolaños Canyon of northern Jalisco and southern Zacatecas. The details of the excavations are discussed here, highlighting chronology, the presence of local and trade goods, the osteological analysis, and the question of sequential versus single interment.
ULF/ELF magnetic field variations from atmosphere induced by seismicity
Authors: Schekotov A. Y. , Molchanov O. A. , Hayakawa M. , Fedorov E. N. , Chebrov V. N. , Sinitsin V. I. , Gordeev E. E. , Belyaev G. G. , Yagova N. V.
Published: December 2007

Local variations of the magnetic field in the ULF‐ELF frequency range associated with seismicity are studied with the data of more than 3 a observations at Karimshimo complex observatory (latitude 52.83°N, longitude 158.13°E, Kamchatka, Russia). A wideband emission is found to start about 5 d before an earthquake and last until 5 d after it. Seismic ULF/ELF emission in the frequency range of 4–6 Hz as compared with the seismically quiet background has enhanced Phh/Pdd spectral ratio and reduced standard deviation of ellipse orientation angle and the ellipticity, and it has a more linear polarization. Parameters of this emission are studied for more than 30 individual earthquakes and statistically with the superposed epoch method. The reliability of the earthquake predicting hypothesis is verified, and the favorable parameters for the earthquakes together with those for ELF magnetic field are selected. The following earthquake parameters are favorable for this emission: depths H < 50 km, magnitudes MS > 5.5, and epicenter distances R < 300 km. The changes of natural ULF/ELF emissions during the periods of enhanced seismic activity are interpreted as the result of the excitation of additional ULF/ELF emissions in the seismic zone to the east of the observatory or the redistribution of lightning discharges with their possible concentration near the active crust fault. The earthquake prediction hypothesis is verified for the complex field parameter ΔS and proved to be successful.
Criteria for three‐fluid configurations including layers in a pore with nonuniform wettability
Authors: van Dijke M. I. J. , Piri M. , Helland J. O. , Sorbie K. S. , Blunt M. J. , Skjæveland S. M.
Published: December 2007

Recently, a considerable effort has been made to determine the precise displacement criteria for three‐fluid configurations in pores of angular cross section. These configurations may contain thick conducting fluid layers, such as oil layers residing between gas in the center and water in the corners of the pore. For pores of uniform, but arbitrary, wettability and in the absence of contact angle hysteresis, a precise thermodynamic criterion for the existence of such layers has been established. In this paper we derive similar criteria for layers in pores of nonuniform wettability, where additional and more complicated layer configurations arise. The criteria for formation and removal of layers are consistent with the capillary entry conditions for the accompanying three‐phase bulk displacements, which is essential for accurate pore‐scale modeling of three‐phase flow. We consider the particular case of three‐phase gas invasion in a star‐shaped pore with a specific choice of interfacial tensions and contact angles. For this case all possible fluid configurations arise, but only if the water‐wet surface in the pore corners is small.
Evidence for a recurring eastern North America upper tropospheric ozone maximum during summer
Authors: Cooper O. R. , Trainer M. , Thompson A. M. , Oltmans S. J. , Tarasick D. W. , Witte J. C. , Stohl A. , Eckhardt S. , Lelieveld J. , Newchurch M. J. , Johnson B. J. , Portmann R. W. , Kalnajs L. , Dubey M. K. , Leblanc T. , McDermid I. S. , Forbes G. , Wolfe D. , Carey‐Smith T. , Morris G. A. , Lefer B. , Rappenglück B. , Joseph E. , Schmidlin F. , Meagher J. , Fehsenfeld F. C. , Keating T. J. , Van Curen R. A. , Minschwaner K.
Published: December 2007

Daily ozonesondes were launched from 14 North American sites during August 2006, providing the best set of free tropospheric ozone measurements ever gathered across the continent in a single season. The data reveal a distinct upper tropospheric ozone maximum above eastern North America and centered over the southeastern USA. Recurring each year, the location and strength of the ozone maximum is influenced by the summertime upper tropospheric anticyclone that traps convectively lofted ozone, ozone precursors and lightning NOx above the southeastern USA. The North American summer monsoon that flows northward along the Rocky Mountains is embedded within the western side of the anticyclone and also marks the westernmost extent of the ozone maximum. Removing the influence from stratospheric intrusions, median ozone mixing ratios (78 ppbv) in the upper troposphere (>6 km) above Alabama, near the center of the anticyclone, were nearly twice the level above the U.S. west coast. Simulations by an atmospheric chemistry general circulation model indicate lightning NOx emissions led to the production of 25–30 ppbv of ozone at 250 hPa above the southern United States during the study period. On the regional scale the ozone enhancement above the southeastern United States produced a positive all‐sky adjusted radiative forcing up to 0.50 W m−2.
The Open Practises E-Science Network (OPEN)
Authors: Neylon Cameron
Published: December 2007

A grant proposal submitted for support to fund a research network focussed on identifying and dealing with the practical issues of enabling open practise in research. The text of the proposal was written by a large number of people and coordinated by Cameron Neylon.
Analysis of Human Spleen Contamination
Authors: Kopani Martin , Weis Martin , Jakubovsky Jan
Published: December 2007

Besides carbon, oxygen and nitrogen, numerous other elements and their compounds are significant in the body of humans and other animals. Accumulation of some elements and their compounds is recognized by clinical and biochemical evaluation. The physical-chemical properties and topical characteristics of elements in tissues may play a crucial role in evaluation their effect on human body. The ^57^Fe Mössbauer measurement was used for evaluation of iron–oxide biomagnetic nanoparticles composition and properties. Absorption spectra of the powdered spleen recorded at 77K and 300K were measured and subsequently analyzed. From fitted data it is possible to obtain material composition as well as discuss the mean particle size (received from decrease hyperfine field in comparison with bulk value).
Hyperfine resolved spectrum of the bromomethyl radical, CH2Br, by Fourier transform microwave spectroscopy
Authors: Ozeki H. , Okabayashi T. , Tanimoto M. , Saito S. , Bailleux S.
Published: December 2007

Pure rotational spectra of the bromomethyl radical, CH2Br, were measured by using a Fourier transform microwave (FT-MW) spectrometer in order to fully resolve hyperfine structures arising from both the bromine and hydrogen nuclei. We detected a total of 124 lines for the Br79 and Br81 isotopomers, including Ka=0 (ortho species) and Ka=1 (para species). No hyperfine splitting due to the hydrogen nuclei was observed for the para species, directly confirming the planarity of the radical. We conducted a global analysis of our present FT-MW results and previous measurements in the millimeter-wave region and obtained an exhaustive list of molecular constants. The sign of the Fermi constant of the bromine nucleus was unambiguously determined to be positive, which is opposite to that found in previous work in the millimeter-wave region and in electron spin resonance experiment on this radical. The present study permitted a systematic comparison to be made of the hyperfine coupling constants of both the halogen and hydrogen nuclei for CH2X-type compounds, where X=F, Cl, and Br.
Experimental study of the single-mode three-dimensional Rayleigh-Taylor instability
Authors: Wilkinson J. P. , Jacobs J. W.
Published: December 2007

The three-dimensional Rayleigh-Taylor instability is studied in a low Atwood number (A≈0.15) miscible fluid system. The two fluids are contained within a Plexiglas tank that is mounted on vertical rails and accelerated downward by a weight and pulley system. A net acceleration between 13 and 23m∕s2 can be maintained, resulting in an effective body force equivalent to 0.33–1.35 times Earth’s gravity. A single-mode, three-dimensional perturbation is produced by oscillating the tank, which has a square cross section, along its diagonal. Early time measured growth rates are shown to have good agreement with linear stability theory. At late time, the instability exhibits a nonconstant vertical interfacial velocity in agreement with the recent numerical computations of Ramaprabhu et al. [Phys. Rev. E 74, 066308 (2006)]. Both the late-time bubble and spike velocities have values greater than those predicted by both the simple buoyancy-drag model developed by Oron et al. [Phys. Plasmas 8, 2883 (2001)] and the potential flow model of Goncharov [Phys. Rev. Lett. 88, 134502 (2002)]. The disagreement with the models can be attributed to the formation of vortices, in this case vortex rings, observed in the experiments but not accounted for by the models.
Transient buoyancy-driven front dynamics in nearly horizontal tubes
Authors: Séon T. , Znaien J. , Salin D. , Hulin J. P. , Hinch E. J. , Perrin B.
Published: December 2007

The interpenetration of light and heavy liquids has been studied in a long tube inclined at small angles α to the horizontal. For angles greater than a critical angle αc (whose value decreases when the density contrast measured by the Atwood number At increases), the velocity of the interpenetration front is controlled by inertia and takes the steady value Vf=ki(Atgd)1∕2, with ki≃0.7. At lower angles, the front is initially controlled by inertia, but later limited by viscous effects. The transition occurs at a distance Xfc, which increases indefinitely as α increases to αc. Once the viscous effects act, the velocity of the front decreases in time to a steady value Vf∞ which is proportional to sinα. For a horizontal tube in the viscous regime, the velocity of the front decreases to zero as t−1∕2. At the same time, the profile of the interface h(x,t) only depends on the reduced variable x∕t1∕2. A quasi-unidirectional model reproduces well the variation of the velocity of the front and the profiles of the interface, both in inclined and horizontal tubes. In the inclined tube, the velocity of the front is determined by matching rarefaction waves to a shock wave.
Peel or coat spheres by convolution, repeatedly
Authors: Schmidt Matthias , Jeffrey Mike R.
Published: December 2007

A convolution transformation is presented that maps the four fundamental measures (Minkowski functionals) of a three-dimensional sphere to those of a sphere with a different radius. It is shown that the set of all these transformations, parametrized by the induced change in radius, forms an Abelian (commutative) group and hence constitutes a flexible framework for the manipulation of spheres. The corresponding one-dimensional case is laid out and the relationship to fundamental measure density functional theory is discussed briefly.
Phase-matched second- and third-harmonic generation in plasmas with density ripple
Authors: Dahiya Deepak , Sajal Vivek , Sharma A. K.
Published: December 2007

The generation of second and third harmonics by the interaction of an ultrashort laser pulse with underdense plasma having a density ripple is studied at intensities Iλ2=1016−1019W cm−2μm2 using fully relativistic two-dimensional particle-in-cell simulations with high spectral resolution. A theoretical model is developed for second- and third-harmonic conversion efficiencies. When the laser is plane polarized in the simulation plane even and odd harmonics are excited in the same polarization as the laser polarization. The highest efficiency of generation of a specific harmonic occurs when the ripple wave vector value kq satisfies phase-matching conditions. The efficiency of phase-matched harmonic generation is an order of magnitude higher than the one without phase matching. The efficiency increases rapidly in weak and moderate relativistic regime and tends to saturate in strong relativistic regime. At moderately relativistic intensities and low plasma densities, the simulation and recent experimental results are fairly reproduced by an analytical theory.
Extinction spectra and electrical field enhancement of Ag nanorods with different topologic shapes
Authors: Zhang Z.-Y. , Zhao Y.-P.
Published: December 2007

We use the discrete dipole approximation method to investigate the length-dependent optical extinction spectra and the E-field enhancement of Ag nanorods with different topologic shapes, such as cylindrical, needlelike, periodic, L, and Y shapes. Comparing to nanorods with a simple shape (cylinder and needle), irregular nanorods show many distinct plasmon resonances over a large spectral range. The main plasmon peaks are redshifted with the increase of the lengths and enhanced E-field distribution at those wavelengths depends strongly on the shapes of the nanorods. More hot spots are observed for the nanorods with more defects (i.e., periodic, L, and Y shapes) and the maximum E fields are in the same order of magnitude for cylindrical nanorods and depends on the polarization and propagation directions of the excitation light. The polarization dependent extinction spectra of nanorods with different shapes have also been calculated and are shown to be dependent on the symmetry of the nanorod structure. With specific incident direction, by changing the incident polarization angle, the maximum E field of L- and Y-shaped nanorods can vary in location and magnitude. These results show that defects or imperfections in Ag nanorod structures could drastically change the optical properties, generate extra hot spots for surface enhanced spectroscopy, and have different enhanced field distribution for future plasmonic applications.
Accumulated body ultranarrow channel silicon transistor with extreme threshold voltage tunability
Authors: Gokirmak Ali , Tiwari Sandip
Published: December 2007

A side-gated ultranarrow channel (width <10nm) silicon field effect transistor (FET) with extreme threshold voltage (Vt) tunability is described. A narrow inversion layer is formed on the top interface controlled by the top gate. The device body and side interfaces are accumulated by up to 1019cm−3 holes, drawn from the substrate by negatively biased side gates (Vside), increasing Vt by 3V, suppressing peripheral leakage currents and short channel effects. Vt response to Vside follows a square root behavior, dVt∕d−Vside=3.73V∕V, similar to that of body doping. Maximum linear tunability (dVt∕dVside) exceeds −2V∕V, average dVt∕dVside is −1.67V∕V.
Global well posedness of the relativistic Vlasov-Yukawa system with small data
Authors: Ha Seung-Yeal , Lee Ho
Published: December 2007

In this paper, we present an existence theory and uniform L1-stability estimate for classical solutions with small data to the Vlasov-Yukawa system. The Vlasov-Yukawa system corresponds to a short-range correction of the Vlasov-Poisson system appearing in plasma physics and astrophysics. For the existence and stability of classical solutions, we crucially use dispersion estimates due to the smallness of data.
Scanning electron and cathodoluminescence imaging of thin film Lu2SiO5:Ce scintillating materials
Authors: Rack P. D. , Peak J. D. , Melcher C. L. , Fitz-Gerald J. M.
Published: December 2007

Cerium doped lutetium orthosilicate thin films were sputter deposited onto rough and smooth alumina substrates to compare their extrinsic photoluminescence efficiency. To understand the photoluminescence results, scanning electron and cathodoluminescence imaging were performed. The plane view and cross-section images revealed that dark cathodoluminescence regions were correlated with topology in both films, though the mechanisms for the degraded luminescence were different. For the rough films, substrate topology causes localized shadowing of the sputtered species which creates compositional inhomogeneities. The smooth films have protrusions caused by thermally induced stress and the reduced cathodoluminescence intensity is attributed to electron-hole surface recombination.
Direct observation of cooperative effects in capillary condensation: The hysteretic origin
Authors: Casanova Fèlix , Chiang Casey E. , Li Chang-Peng , Schuller Ivan K.
Published: December 2007

We tailor anodized alumina with pores with well-defined, simple geometries, in order to study the effects of constrictions in hysteretical capillary condensation, independently from other cooperative processes such as network effects. We confirm, by direct observation using optical interferometry, the occurrence of two cooperative phenomena: the classical pore blocking effect in nearly ideal “inkbottle” pores and the advanced adsorption in pores with a change in the cross section. They are relevant for the development of a theory of the poorly understood hysteresis in complex porous materials.
Evaluation of the Mutagenic and Genotoxic Potential of Ubiquinol
Authors: Kitano Mitsuaki , Mizuhashi Fukutaro , Kubo Hiroshi , Kishida Hideyuki , Fujii Kenji , Kitahara Mikio , Hosoe Kazunori
Published: December 2007

Ubiquinol (the reduced form of coenzyme Q10) is the two-electron reduction product of ubiquinone (the oxidized form of coenzyme Q10), and has been shown to be an integral part of living cells, where it functions as an antioxidant in both mitochondria and lipid membranes. To provide information to enable a Generally Regarded as Safe (GRAS) evaluation for the use of ubiquinol in selected foods, a series of Organisation of Economic Cooperation and Development (OECD) and good laboratory practice (GLP) toxicological studies was conducted to evaluate the mutagenic and genotoxic potential of Kaneka QH brand of ubiquinol. Ubiquinol did not induce reverse mutations in Salmonella typhimurium strains TA100, TA1535, TA98, and TA1537 and Escherichia coli WP2uvrA at concentrations up to 5000 μg/plate, in either the absence and presence of exogenous metabolic activation by rat liver S9. Likewise, ubiquinol did not induce chromosome aberrations in Chinese hamster lung fibroblast (CHL/IU) cells in short-term (6-h) tests with or without rat liver S9 at concentrations up to 5000 μg/ml or in a continuous (24-h) treatment test at concentrations up to 1201 μg/ml. Finally, no mortalities, no abnormal clinical signs, and no significant increase in chromosome damage were observed in an in vivo micronucleus test when administered orally at doses up to 2000 mg/kg/day. Thus, ubiquinol was evaluated as negative in the bacterial reverse mutation, chromosomal aberration, and rat bone marrow micronucleus tests under the conditions of these assays.
Melatonin Formation in Pineal Gland from Rats with Hexachlorobenzene Experimental Porphyria
Authors: Llambías Elena B. C. , Mazzetti Marta B. , Lelli Sandra M. , Aldonatti Carmen , San Martín de Viale Leonor C.
Published: December 2007

Hexachlorobenzene produces an experimental hepatic por-phyria in rats, which is similar to human porphyria cutanea tarda, with hyperpigmentation as one of its characteristic features. Alterations in tryptophan metabolism have been previously observed in this chronic porphyria. Melatonin formation from tryptophan via serotonin shows diurnal rhythmicity in the pineal gland, and higher values are observed during the dark phase of an imposed light-dark cycle. The purpose of this study was to determine the contents of tryptophan and its metabolites in pineal gland of normal and hexachlorobenzene-treated rats in order to find alterations potentially related to porphyria cutanea tarda. Results show that in animals with this experimental porphyria some tryptophan metabolite levels (serotonin and 5-hydroxyindoleacetic acid) increase only during the light period, whereas tryptophan content remained equal to the controls. Hydroxyindole- O-methyltransferase activity also increases by light in pineal gland from hexachlorobenzene-treated rats. On the other hand, tryptophan is converted to melatonin in the dark period, but this route is not exacerbated in hexachloroben-zene porphyria. The relevance of these alterations is discussed in relation to hyperpigmentation, neoplastic and oxidative stress processes associated with this porphyria.
The refinability of step functions
Authors: Hirn Matthew
Published: December 2007

Refinable functions have been widely investigated because of their importance in wavelet theory and multiresolution analysis, as well as because of intrinsic interest. Problems involving refinability can be challenging and interesting problems in mathematics. Several papers have investigated refinability of splines and other classes of functions. The purpose of this paper is to develop necessary and sufficient conditions for the refinability of the class of step functions on the real line taking complex values.
Only ‘free’ measures are admissable on 𝐹(𝑆) when the inner product space 𝑆 is incomplete
Authors: Buhagiar D. , Chetcuti E.
Published: December 2007

Using elementary arguments and without having to recall the Gleason Theorem, we prove that the existence of a nonsingular measure on the lattice of orthogonally closed subspaces of an inner product space

S
S

is a sufficient (and of course, a necessary) condition for

S
S

to be a Hilbert space.
Remarks on Naimark’s duality
Authors: Czaja Wojciech
Published: December 2007

We present an extension of a version of Naimark’s dilation theorem which states that complete systems in a Hilbert space are projections of

ω
\omega

-linearly independent systems of elements of an ambient Hilbert space. This result is presented in the context of other known extensions of Naimark’s theorem.
Uniqueness and stability of steady states for a predator-prey model in heterogeneous environment
Authors: Peng Rui , Wang Mingxin
Published: December 2007

In this paper, we deal with a predator-prey model with diffusion in a heterogeneous environment, and we study the uniqueness and stability of positive steady states as the diffusion coefficient of the predator is small enough.
On the Pytkeev property in spaces of continuous functions
Authors: Simon Petr , Tsaban Boaz
Published: December 2007

Answering a question of Sakai, we show that the minimal cardinality of a set of reals

X
X

such that

C
p

(
X
)

C_p(X)

does not have the Pytkeev property is equal to the pseudo-intersection number

p

\mathfrak {p}

. Our approach leads to a natural characterization of the Pytkeev property of

C
p

(
X
)

C_p(X)

by means of a covering property of

X
X

, and to a similar result for the Reznichenko property of

C
p

(
X
)

C_p(X)

.
Julia sets converging to the unit disk
Authors: Devaney Robert , Garijo Antonio
Published: December 2007

We consider the family of rational maps

F
λ

(
z
)
=

z
n

+
λ

/

z
d

F_\lambda (z) = z^n + \lambda /z^d

, where

n
,
d
≥
2

n,d \geq 2

and

λ
\lambda

is small. If

λ
\lambda

is equal to 0, the limiting map is

F
0

(
z
)
=

z
n

F_0(z)=z^n

and the Julia set is the unit circle. We investigate the behavior of the Julia sets of

F
λ

F_\lambda

when

λ
\lambda

tends to 0, obtaining two very different cases depending on

n
n

and

d
d

. The first case occurs when

n
=
d
=
2

n=d=2

; here the Julia sets of

F
λ

F_\lambda

converge as sets to the closed unit disk. In the second case, when one of

n
n

or

d
d

is larger than

2
2

, there is always an annulus of some fixed size in the complement of the Julia set, no matter how small

|

λ

|

|\lambda |

is.
Hierarchical structure of the family of curves with maximal genus verifying flag conditions
Authors: Di Gennaro Vincenzo
Published: December 2007

Fix integersr,s1,…,slr,s_{1},\dots ,s_{l}such that1≤l≤r−11\leq l\leq r-1andsl≥r−l+1s_{l}\geq r-l+1, and letC(r;s1,…,sl)\mathcal {C}(r;s_{1},\dots ,s_{l})be the set of all integral, projective and nondegenerate curvesCCof degrees1s_{1}in the projective spacePr\mathbf {P}^{r}, such that, for alli=2,…,li=2,\dots ,l,CCdoes not lie on any integral, projective and nondegenerate variety of dimensioniiand degree>si>s_{i}. We say that a curveCCsatisfies theflag condition(r;s1,…,sl)(r;s_{1},\dots ,s_{l})ifCCbelongs toC(r;s1,…,sl)\mathcal {C}(r;s_{1},\dots ,s_{l}). Define<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper G left-parenthesis r semicolon s 1 comma ellipsis comma s Subscript l Baseline right-parenthesis equals max left-brace right-brace colon of ppa left-parenthesis right-parenthesis upper C colon element-of element-of upper C of CC left-parenthesis right-parenthesis semicolon comma comma r semicolon s 1 comma ellipsis comma sl comma">G(r;s1,…,sl)=max⁡{pa(C):C∈C(r;s1,…,sl)},G(r;s_{1},\dots ,s_{l})=\operatorname {max}\left \{p_{a}(C):\,C\in \mathcal {C}(r;s_{1},\dots ,s_{l})\right \},wherepa(C)p_{a}(C)denotes the arithmetic genus ofCC. In the present paper, under the hypothesiss1≫⋯≫sls_{1}\gg \dots \gg s_{l}, we prove that a curveCCsatisfying the flag condition(r;s1,…,sl)(r;s_{1},\dots ,s_{l})and of maximal arithmetic genuspa(C)=G(r;s1,…,sl)p_{a}(C)=G(r;s_{1},\dots ,s_{l})must lie on a unique flag such as<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper C equals upper V Subscript s 1 Superscript 1 Baseline subset-of upper V Subscript s 2 Superscript 2 Baseline subset-of midline-horizontal-ellipsis subset-of upper V Subscript s Sub Subscript l Superscript l Baseline subset-of bold upper P Superscript r">C=Vs11⊂Vs22⊂⋯⊂Vsll⊂PrC=V_{s_{1}}^{1}\subset V_{s_{2}}^{2}\subset \dots \subset V_{s_{l}}^{l}\subset {\mathbf {P}^{r}}, where, for anyi=1,…,li=1,\dots ,l,VsiiV_{s_{i}}^{i}denotes an integral projective subvariety ofPr{\mathbf {P}^{r}}of degreesis_{i}and dimensionii, such that its general linear curve section satisfies the flag condition(r−i+1;si,…,sl)(r-i+1;s_{i},\dots ,s_{l})and has maximal arithmetic genusG(r−i+1;si,…,sl)G(r-i+1;s_{i},\dots ,s_{l}). This proves the existence of a sort of a hierarchical structure of the family of curves with maximal genus verifying flag conditions.
Bounded earthquakes
Authors: Šarić Dragomir
Published: December 2007

We give a short proof of the fact that bounded earthquakes of the unit disk induce quasisymmetric maps of the unit circle. By a similar method, we show that symmetric maps are induced by bounded earthquakes with asymptotically trivial measures.
Minimal convex functions bounded below by the duality product
Authors: Martínez-Legaz J.-E. , Svaiter B.
Published: December 2007

It is well known that the Fitzpatrick function of a maximal monotone operator is minimal in the class of convex functions bounded below by the duality product. Our main result establishes that, in the setting of reflexive Banach spaces, the converse also holds; that is, every such minimal function is the Fitzpatrick function of some maximal monotone operator. Whether this converse also holds in a nonreflexive Banach space remains an open problem.
A synthetic characterization of the hemisphere
Authors: Croke Christopher
Published: December 2007

We show that round hemispheres are the only compact two-dimensional Riemannian manifolds (with or without boundary) such that almost every pair of complete geodesics intersect once and only once. We prove this by establishing a sharp isoperimetric inequality for surfaces with boundary such that every pair of geodesics has at most one interior intersection point.
A Khinchin Sequence
Authors: Wieting Thomas
Published: December 2007

We prove that the geometric and harmonic means of the sequence

Z
2

Z_2

of positive integers proposed by Bailey, Borwein, and Crandall converge to the corresponding Khinchin Constants.
TimeClust: a clustering tool for gene expression time series
Authors: Magni Paolo , Ferrazzi Fulvia , Sacchi Lucia , Bellazzi Riccardo
Published: December 2007

Summary: TimeClust is a user-friendly software package to cluster genes according to their temporal expression profiles. It can be conveniently used to analyze data obtained from DNA microarray time-course experiments. It implements two original algorithms specifically designed for clustering short time series together with hierarchical clustering and self-organizing maps.

Availability: TimeClust executable files for Windows and LINUX platforms can be downloaded free of charge for non-profit institutions from the following web site: http://aimed11.unipv.it/TimeClust.

Contact:  paolo.magni@unipv.it or for software support timeclust@aimed11.unipv.it

Supplementary information: A simple user's guide (example.pdf) is available in the download area together with two trial data sets.
Kinetics and Mechanism of Dionaea muscipula Trap Closing
Authors: Volkov Alexander G. , Adesina Tejumade , Markin Vladislav S. , Jovanov Emil
Published: December 2007

The Venus flytrap (Dionaea muscipula) possesses an active trapping mechanism to capture insects with one of the most rapid movements in the plant kingdom, as described by Darwin. This article presents a detailed experimental investigation of trap closure by mechanical and electrical stimuli and the mechanism of this process. Trap closure consists of three distinctive phases: a silent phase with no observable movement; an accelerated movement of the lobes; and the relaxation of the lobes in their closed state, resulting in a new equilibrium. Uncouplers and blockers of membrane channels were used to investigate the mechanisms of different phases of closing. Uncouplers increased trap closure delay and significantly decreased the speed of trap closure. Ion channel blockers and aquaporin inhibitors increased time of closing. Transmission of a single electrical charge between a lobe and the midrib causes closure of the trap and induces an electrical signal propagating between both lobes and midrib. The Venus flytrap can accumulate small subthreshold charges, and when the threshold value is reached, the trap closes. Repeated application of smaller charges demonstrates the summation of stimuli. The cumulative character of electrical stimuli points to the existence of electrical memory in the Venus flytrap. The observed fast movement can be explained by the hydroelastic curvature model without invoking buckling instability. The new hydroelastic curvature mechanism provides an accurate description of the authors' experimental data.
Characterization of the Interaction of a Novel Stagonospora nodorum Host-Selective Toxin with a Wheat Susceptibility Gene
Authors: Friesen Timothy L. , Zhang Zengcui , Solomon Peter S. , Oliver Richard P. , Faris Justin D.
Published: December 2007

Recent work suggests that the Stagonospora nodorum-wheat pathosystem is controlled by host-selective toxins (HSTs; SnToxA, SnTox1, and SnTox2) that interact directly or indirectly with dominant host genes (Tsn1, Snn1, and Snn2) to induce disease. Here we describe and characterize a novel HST designated SnTox3, and the corresponding wheat sensitivity/susceptibility gene identified on chromosome arm 5BS, which we designated as Snn3. SnTox3 is a proteinaceous necrosis-inducing toxin between 10 and 30 kD in size. The S. nodorum isolates Sn1501 (SnToxA−, SnTox2+, and SnTox3+), SN15 (SnToxA+, SnTox2+, and SnTox3+), and SN15KO18, a strain of SN15 with a disrupted form of SnToxA, were evaluated on a population of wheat recombinant inbred lines. A compatible Snn3-SnTox3 interaction played a significant role in the development of disease caused by isolates Sn1501 and SN15KO18, with Snn2 being epistatic to Snn3. Snn3 was not significantly associated with disease caused by SN15 presumably due to the major effects observed for Snn2 and Tsn1, which were largely additive. This work introduces a fourth HST produced by S. nodorum and builds on the notion that the S. nodorum-wheat pathosystem is largely based on multiple host-toxin interactions that follow an inverse gene-for-gene scenario.
Comparisons of LIPOXYGENASE3- and JASMONATE-RESISTANT4/6-Silenced Plants Reveal That Jasmonic Acid and Jasmonic Acid-Amino Acid Conjugates Play Different Roles in Herbivore Resistance ofNicotiana attenuata
Authors: Wang Lei , Allmann Silke , Wu Jinsong , Baldwin Ian T.
Published: December 2007

Whereas jasmonic acid (JA) and its amino acid conjugates, particularly JA-isoleucine (Ile), are known to play important roles in plant-herbivore interactions, whether other compounds also function as signals independently of JA-Ile and whether conjugates elicit systemic responses are unknown. To answer these questions, we simultaneously silenced JASMONATE-RESISTANT4 (JAR4) and JAR6, two functionally redundant enzymes in Nicotiana attenuata that conjugate JA to amino acids to produce plants (irjar4/6) with low levels of JA-Ile, JA-leucine (Leu), and JA-valine (Val; <16% of wild type). As expected, irjar4/6 plants are more vulnerable to herbivore attack, but only JA-Ile—not JA-Leu or JA-Val—applications restored the resistance of irjar4/6 plants, suggesting that JA-Leu and JA-Val do not mediate herbivore defense responses. Interestingly, the direct defense traits of irjar4/6 plants are significantly higher than those in LIPOXYGENASE3 (LOX3)-silenced (aslox3) plants, which are impaired in JA biosynthesis, and JA-Ile treatment could not fully restore the resistance of aslox3 plants. We thus conclude that JA, its precursors, or other metabolites complement the function of JA-Ile by eliciting a panoply of induced defenses. Similarly, transcriptional profiling of wild-type, irjar4/6, and aslox3 plants with microarrays demonstrated that JA-Ile and JA play overlapping yet distinct roles in herbivore defense. Analysis of transcripts in distal tissues demonstrated that JAR activity is essential in eliciting systemic responses. However, attempts to recover JA-13C6-Ile in systemic leaves and roots after feeding wounded leaves with 13C6-Ile were unsuccessful, suggesting that JA-Ile is not a long-distance signal, but is rather synthesized after the arrival of an unknown mobile signal to systemic tissues.
The Phosphoproteome of aChlamydomonas reinhardtiiEyespot Fraction Includes Key Proteins of the Light Signaling Pathway
Authors: Wagner Volker , Ullmann Katharina , Mollwo Anne , Kaminski Marc , Mittag Maria , Kreimer Georg
Published: December 2007

Flagellate green algae have developed a visual system, the eyespot apparatus, which allows the cell to phototax. In a recent proteomic approach, we identified 202 proteins from a fraction enriched in eyespot apparatuses of Chlamydomonas reinhardtii. Among these proteins, five protein kinases and two protein phosphatases were present, indicating that reversible protein phosphorylation occurs in the eyespot. About 20 major phosphoprotein bands were detected in immunoblots of eyespot proteins with an anti-phosphothreonine antibody. Toward the profiling of the targets of protein kinases in the eyespot fraction, we analyzed its phosphoproteome. The solubilized proteins of the eyespot fraction were treated with the endopeptidases LysC and trypsin prior to enrichment of phosphopeptides with immobilized metal-ion affinity chromatography. Phosphopeptides were analyzed by nano-liquid chromatography-electrospray ionization-mass spectrometry (MS) with MS/MS as well as neutral-loss-triggered MS/MS/MS spectra. We were able to identify 68 different phosphopeptides along with 52 precise in vivo phosphorylation sites corresponding to 32 known proteins of the eyespot fraction. Among the identified phosphoproteins are enzymes of carotenoid and fatty acid metabolism, putative signaling components, such as a SOUL heme-binding protein, a Ca2+-binding protein, and an unusual protein kinase, but also several proteins with unknown function. Notably, two unique photoreceptors, channelrhodopsin-1 and channelrhodopsin-2, contain three and one phosphorylation sites, respectively. Phosphorylation of both photoreceptors occurs in the cytoplasmatic loop next to their seven transmembrane regions in a similar distance to that observed in vertebrate rhodopsins, implying functional importance for regulation of these directly light-gated ion channels relevant for the photoresponses of C. reinhardtii.
Transgenic Expression of a Fungal endo-Polygalacturonase Increases Plant Resistance to Pathogens and Reduces Auxin Sensitivity
Authors: Ferrari Simone , Galletti Roberta , Pontiggia Daniela , Manfredini Cinzia , Lionetti Vincenzo , Bellincampi Daniela , Cervone Felice , De Lorenzo Giulia
Published: December 2007

Polygalacturonases (PGs), enzymes that hydrolyze the homogalacturonan of the plant cell wall, are virulence factors of several phytopathogenic fungi and bacteria. On the other hand, PGs may activate defense responses by releasing oligogalacturonides (OGs) perceived by the plant cell as host-associated molecular patterns. Tobacco (Nicotiana tabacum) and Arabidopsis (Arabidopsis thaliana) plants expressing a fungal PG (PG plants) have a reduced content of homogalacturonan. Here, we show that PG plants are more resistant to microbial pathogens and have constitutively activated defense responses. Interestingly, either in tobacco PG or wild-type plants treated with OGs, resistance to fungal infection is suppressed by exogenous auxin, whereas sensitivity to auxin of PG plants is reduced in different bioassays. The altered plant defense responses and auxin sensitivity in PG plants may reflect an increased accumulation of OGs and subsequent antagonism of auxin action. Alternatively, it may be a consequence of perturbations of cellular physiology and elevated defense status as a result of altered cell wall architecture.
Firefly Luciferase Complementation Imaging Assay for Protein-Protein Interactions in Plants
Authors: Chen Huamin , Zou Yan , Shang Yulei , Lin Huiqiong , Wang Yujing , Cai Run , Tang Xiaoyan , Zhou Jian-Min
Published: December 2007

The development of sensitive and versatile techniques to detect protein-protein interactions in vivo is important for understanding protein functions. The previously described techniques, fluorescence resonance energy transfer and bimolecular fluorescence complementation, which are used widely for protein-protein interaction studies in plants, require extensive instrumentation. To facilitate protein-protein interaction studies in plants, we adopted the luciferase complementation imaging assay. The amino-terminal and carboxyl-terminal halves of the firefly luciferase reconstitute active luciferase enzyme only when fused to two interacting proteins, and that can be visualized with a low-light imaging system. A series of plasmid constructs were made to enable the transient expression of fusion proteins or generation of stable transgenic plants. We tested nine pairs of proteins known to interact in plants, including Pseudomonas syringae bacterial effector proteins and their protein targets in the plant, proteins of the SKP1-Cullin-F-box protein E3 ligase complex, the HSP90 chaperone complex, components of disease resistance protein complex, and transcription factors. In each case, strong luciferase complementation was observed for positive interactions. Mutants that are known to compromise protein-protein interactions showed little or much reduced luciferase activity. Thus, the assay is simple, reliable, and quantitative in detection of protein-protein interactions in plants.
Genomic Survey and Gene Expression Analysis of the Basic Leucine Zipper Transcription Factor Family in Rice
Authors: Nijhawan Aashima , Jain Mukesh , Tyagi Akhilesh K. , Khurana Jitendra P.
Published: December 2007

The basic leucine (Leu) zipper (bZIP) proteins compose a family of transcriptional regulators present exclusively in eukaryotes. The bZIP proteins characteristically harbor a bZIP domain composed of two structural features: a DNA-binding basic region and the Leu zipper dimerization region. They have been shown to regulate diverse plant-specific phenomena, including seed maturation and germination, floral induction and development, and photomorphogenesis, and are also involved in stress and hormone signaling. We have identified 89 bZIP transcription factor-encoding genes in the rice (Oryza sativa) genome. Their chromosomal distribution and sequence analyses suggest that the bZIP transcription factor family has evolved via gene duplication. The phylogenetic relationship among rice bZIP domains as well as with bZIP domains from other plant bZIP factors suggests that homologous bZIP domains exist in plants. Similar intron/exon structural patterns were observed in the basic and hinge regions of their bZIP domains. Detailed sequence analysis has been done to identify additional conserved motifs outside the bZIP domain and to predict their DNA-binding site specificity as well as dimerization properties, which has helped classify them into different groups and subfamilies, respectively. Expression of bZIP transcription factor-encoding genes has been analyzed by full-length cDNA and expressed sequence tag-based expression profiling. This expression profiling was complemented by microarray analysis. The results indicate specific or coexpression patterns of rice bZIP transcription factors starting from floral transition to various stages of panicle and seed development. bZIP transcription factor-encoding genes in rice also displayed differential expression patterns in rice seedlings in response to abiotic stress and light irradiation. An effort has been made to link the structure and expression pattern of bZIP transcription factor-encoding genes in rice to their function, based on the information obtained from our analyses and earlier known results. This information will be important for functional characterization of bZIP transcription factors in rice.
The Basic Helix-Loop-Helix Transcription Factor PIF5 Acts on Ethylene Biosynthesis and Phytochrome Signaling by Distinct Mechanisms
Authors: Khanna Rajnish , Shen Yu , Marion Colleen M. , Tsuchisaka Atsunari , Theologis Athanasios , Schäfer Eberhard , Quail Peter H.
Published: December 2007

PHYTOCHROME-INTERACTING FACTOR5 (PIF5), a basic helix-loop-helix transcription factor, interacts specifically with the photoactivated form of phytochrome B (phyB). Here, we report that dark-grown Arabidopsis thaliana seedlings overexpressing PIF5 (PIF5-OX) exhibit exaggerated apical hooks and short hypocotyls, reminiscent of the triple response induced by elevated ethylene levels, whereas pif5 mutants fail to maintain tight hooks like those of wild-type seedlings. Silver ions, an ethylene receptor blocker, rescued the triple-response phenotype, and we show that PIF5-OX seedlings express enhanced levels of key ethylene biosynthesis enzymes and produce elevated ethylene levels. Exposure of PIF5-OX seedlings to prolonged continuous red light (Rc) promotes hypocotyl elongation relative to dark controls, the reciprocal of the Rc-imposed hypocotyl inhibition displayed by wild-type seedlings. In contrast with this PIF5-OX hyposensitivity to Rc, pif5 mutant seedlings are hypersensitive relative to wild-type seedlings. We show that this contrast is due to reciprocal changes in phyB protein levels in prolonged Rc. Compared with wild-type seedlings, PIF5-OX seedlings have reduced, whereas pif5 mutants have increased, phyB (and phyC) levels in Rc. The phyB degradation in the overexpressors depends on a functional phyB binding motif in PIF5 and involves the 26S proteasome pathway. Our data thus indicate that overexpressed PIF5 causes altered ethylene levels, which promote the triple response in darkness, whereas in the light, the interaction of photoactivated phyB with PIF5 causes degradation of the photoreceptor protein. The evidence suggests that endogenous PIF5 negatively regulates phyB-imposed hypocotyl inhibition in prolonged Rc by reducing photoreceptor abundance, and thereby photosensory capacity, rather than functioning as a signaling intermediate.