bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitigating atmospheric noise for InSAR using a high resolution weather model
Authors: Foster J. , Brooks B. , Cherubini T. , Shacat C. , Businger S. , Werner C. L.
Published: August 2006

A high resolution weather model is used to predict atmospheric delays for the acquisition times of synthetic aperture radar images over Hawaii. Refraction of the radar by water vapor in the atmosphere in Hawaii leads to apparent ground‐motions with wavelengths and magnitudes similar to the actual ground motions generated by tectonic and volcanic processes. We examine the potential for a weather model to help characterize the atmospheric component in InSAR scenes and find that in the best cases it models the observed delays well, reducing the variance at wavelengths of 30 km and greater by ∼60%, while even in the worst cases it provides an independent means of quantifying the expected variance in the image due to the atmosphere.
High affinity of sigma1‐binding sites for sterol isomerization inhibitors: evidence for a pharmacological relationship with the yeast sterol C8–C7 isomerase
Authors: Moebius Fabian F , Reiter Raphael J , Hanner Markus , Glossmann Hartmut
Published: August 2006

The sigma‐drug binding site of guinea‐pig liver is carried by a protein which shares significant amino acid sequence similarities with the yeast sterol C8–C7 isomerase (ERG2 protein). Pharmacologically ‐ but not structurally ‐ the sigma1‐site is also related to the emopamil binding protein, the mammalian sterol C8–C7 isomerase. We therefore investigated if sterol C8–C7 isomerase inhibitors are high affinity ligands for the (+)‐[3H]‐pentazocine labelled sigma1‐binding site.

Among the compounds which bound with high affinity to native hepatic and cerebral as well as to yeast expressed sigma1‐binding sites were the agricultural fungicide fenpropimorph (Ki 0.005 nM), the antihypocholesterinaemic drugs triparanol (Ki 7.0 nM), AY‐9944 (Ki 0.46 nM) and MDL28,815 (Ki 0.16 nM), the enantiomers of the ovulation inducer clomiphene (Ki 5.5 and 12 nM, respectively) and the antioestrogene tamoxifen (Ki 26 nM).

Except for tamoxifen these affinities are essentially identical with those for the [3H]‐ifenprodil labelled sterol C8–C7 isomerase of S. cerevisiae. This demonstrates that sigma1‐binding protein and yeast isomerase are not only structurally but also pharmacologically related. Because of its affiliations with yeast and mammalian sterol isomerases we propose that the sigma1‐binding site is localized on a sterol isomerase related protein, involved in postsqualene sterol biosynthesis.

British Journal of Pharmacology (1997) 121, 1–6; doi:10.1038/sj.bjp.0701079
Tachykinin regulation of basal synovial blood flow
Authors: Ferrell W R , Lockhart J C , Karimian S M
Published: August 2006

Experiments were performed to investigate the role of endogenously released tachykinins in the regulation of blood flow to the rat knee joint. Synovial perfusion was assessed by laser Doppler perfusion imaging, which permitted spatial measurement of relative changes in perfusion from control (pre drug administration), expressed as the percentage change. Most experiments were performed on the exposed medial aspect of the knee joint capsule.

Neither the selective tachykinin NK1 receptor antagonist, FK888, nor the selective tachykinin NK2 receptor antagonist, SR48968, significantly influenced synovial blood flow at doses of 10−12, 10−10 and 10−8 mol. However, topical co‐administration of these agents produced significant dose‐dependent reductions in basal synovial perfusion of 6.3±4.6, 12.0±3.4 and 19.9±2.6%, respectively; n=29. The non‐selective tachykinin NK1/NK2 receptor antagonist, FK224, also produced significant (at 10−10 and 10−8 mol), but less potent, reductions in perfusion of 5.3±4.0, 8.4±2.2 and 5.9±2.8%, respectively; n=25.

Topical administration of the α1‐, α2‐adrenoceptor antagonist phenoxybenzamine elicited a 31.3±6.2% increase in blood flow which was substantially reduced to 10.4±3.8% by co‐administration of the FK888 and SR48968 (both at 10−8 mol; n=8–13), suggesting that normally there is sympathetic vasoconstrictor ‘tone’ which is opposed by the vasodilator action of endogenous tachykinins.

One week after surgical interruption of the nerve supply to the knee joint, co‐administration of FK888 and SR48968 (both at 10−8 mol) now produced slight vasodilatation (6.7±4.6%; n=9) which did not differ significantly from vehicle treatment. Depletion of tachykinins from sensory nerve fibres by systemic capsaicin administration also resulted in abolition of the vasoconstrictor effect of FK888 and SR48968 (both at 10−8 mol), with these agents only producing a slight vasodilatation (2.5±5.3%; n=6).

By use of a near infra‐red laser source it was possible to image knee joint perfusion transcutaneously, the overlying skin being left intact. In this more physiological situation, close intra‐arterial injection of the combination of FK888 and SR48968 (both at 10−8 mol) again elicited vasoconstriction (48.8±16.2% reduction in blood flow; n=4).

These results indicate that endogenous tachykinins may be continuously released from sensory fibres innervating the joint. Basal release of tachykinins could therefore be an important physiological influence opposing sympathetic vasoconstrictor tone.

British Journal of Pharmacology (1997) 121, 29–34; doi:10.1038/sj.bjp.0701095
Modulation of the pressor response elicited by carbachol and electrical stimulation of the amygdala by muscarinic antagonists in conscious rats
Authors: Aslan Neslihan , Gören Zafer , özkutlu Uǧur , Onat Filiz , Oktay Sule
Published: August 2006

The nature of the muscarinic receptor involved in mediating cardiovascular changes caused by unilateral microinjection of carbachol (5 nmol) into, and electrical stimulation (200–300 μA) of, the amygdaloid complex was investigated in conscious, unrestrained female Sprague‐Dawley rats.

Unilateral microinjection of carbachol (5 nmol; n=6) and electrical stimulation (200–300 μA, 80 Hz, 30 s; n=4) caused a significant rise in blood pressure of 21±4 mmHg and 25±5 mmHg, respectively. These changes were associated with no overall effect on heart rate. The effects of electrical stimulation were found to be repeatable.

Pretreatment i.c.v. with pirenzepine (5–20 nmol; n=6–7 for each dose), dose‐dependently inhibited the rise in blood pressure induced by carbachol, whereas AF‐DX 116 (100 nmol; n=6) failed to have any effect on the carbachol‐induced pressure response. Neither antagonist alone had any effect on resting baseline variables.

Unilateral microinjections of atropine sulphate (1–100 nmol; n=4–6 for each dose), pirenzepine (0.03–10 nmol; n=4 for each dose) or AF‐DX 116 (10–60 nmol; n=4–5 for each dose), into the amygdala, dose‐dependently inhibited the rise in blood pressure caused by electrical stimulation (200–300 μA). The ID50 values were 1.05, 0.23 and 39.5 nmol, respectively. Although pirenzepine seemed to be more potent than atropine, this difference was not significant.

It is concluded that the rise in blood pressure elicited by unilateral microinjection of carbachol into, or electrical stimulation of, the amygdaloid complex is mediated by M1‐muscarinic receptors.

British Journal of Pharmacology (1997) 121, 35–40; doi:10.1038/sj.bjp.0701096
Towards understanding the catalytic core structure of the spliceosome
Authors: Butcher S.E. , Brow D.A.
Published: August 2006

The spliceosome catalyses the splicing of nuclear pre-mRNA (precursor mRNA) in eukaryotes. Pre-mRNA splicing is essential to remove internal non-coding regions of pre-mRNA (introns) and to join the remaining segments (exons) into mRNA before translation. The spliceosome is a complex assembly of five RNAs (U1, U2, U4, U5 and U6) and many dozens of associated proteins. Although a high-resolution structure of the spliceosome is not yet available, inroads have been made towards understanding its structure and function. There is growing evidence suggesting that U2 and U6 RNAs, of the five, may contribute to the catalysis of pre-mRNA splicing. In this review, recent progress towards understanding the structure and function of U2 and U6 RNAs is summarized.
Assays for the RNA chaperone activity of proteins
Authors: Rajkowitsch L. , Semrad K. , Mayer O. , Schroeder R.
Published: August 2006

Proteins with RNA chaperone activity promote RNA folding by loosening the structure of misfolded RNAs or by preventing their formation. How these proteins achieve this activity is still unknown, the mechanism is not understood and it is unclear whether this activity is always based on the same mechanism or whether different RNA chaperones use different mechanisms. To address this question, we compare and discuss in this paper a set of assays that have been used to measure RNA chaperone activity. In some assays, this activity is related to the acceleration of monomolecular reactions such as group I intron cis-splicing or anti-termination of transcription. Hereby, it is proposed that the proteins release the RNAs from folding traps, which represent the kinetic barriers during the folding process and involve the loosening of structural elements. In most assays, however, bimolecular reactions are monitored, which include the simple acceleration of annealing of two complementary RNAs, the turnover stimulation of ribozyme cleavage and group I intron trans-splicing. The acceleration of these reactions most probably involves the unfolding of structures that interfere with annealing or folding and may in addition provoke annealing by crowding. Most assays are performed in vitro, where conditions might differ substantially from intracellular conditions, and two assays have been reported that detect RNA chaperone activity in vivo.
Linkage between proton binding and folding in RNA: implications for RNA catalysis
Authors: Bevilacqua P.C. , Brown T.S. , Chadalavada D. , Lecomte J. , Moody E. , Nakano S.-i.
Published: August 2006

Small ribozymes use their nucleobases to catalyse phosphodiester bond cleavage. The hepatitis delta virus ribozyme employs C75 as a general acid to protonate the 5′-bridging oxygen leaving group, and to accomplish this task efficiently, it shifts its pKa towards neutrality. Simulations and thermodynamic experiments implicate linkage between folding and protonation in nucleobase pKa shifting. Even small oligonucleotides are shown to fold in a highly co-operative manner, although they do so in a context-specific fashion. Linkage between protonation and co-operativity of folding may drive pKa shifting and provide for enhanced function in RNA.
Expression of an RNAi-resistant SLBP restores proper S-phase progression
Authors: Wagner E.J. , Berkow A. , Marzluff W.F.
Published: August 2006

Metazoan histone mRNAs are unique in that they lack a 3′-polyadenylated tail, but instead end in a conserved stem loop that is bound by SLBP (stem–loop binding protein). SLBP is required for efficient histone mRNA synthesis and translation. Removal of SLBP by RNA interference causes an increase in the number of cells in S-phase and this effect can be reversed by expressing an exogenous SLBP resistant to the small interfering RNA. Cells with decreased SLBP levels progress slowly through S-phase when released from a double-thymidine block. Thus SLBP is required for efficient DNA replication probably because a decreased ability to assemble chromatin results in a decrease in the rate of DNA replication.
Engineered riboswitches control gene expression by small molecules
Authors: Suess B.
Published: August 2006

We have developed conditional gene expression systems based on engineered small-molecule-binding riboswitches. Tetracycline-dependent regulation can be imposed on an mRNA in yeast by inserting an aptamer in its 5′-untranslated region. Biochemical and genetic analyses determined that binding of the ligand tetracycline leads to a pseudoknot-like linkage within the aptamer structure, thereby inhibiting the initial steps of translation. A second translational control element was designed by combining a theophylline aptamer with a communication module for which a 1 nt slipping mechanism had been proposed. This structural element was inserted close to the bacterial ribosomal binding site at a position just interfering with translation in the non-ligand-bound form. Addition of the ligand then shifts the inhibitory element to a distance that permits efficient translation.
A database search for hammerhead ribozyme motifs
Authors: Gräf S. , Przybilski R. , Steger G. , Hammann C.
Published: August 2006

The hammerhead ribozyme is the smallest naturally occurring RNA endonuclease. It is found in subviral plant pathogens and transcripts of satellite DNA from a limited number of organisms. We have performed a database search for novel examples of this catalytic RNA, taking into consideration the recently defined structural requirements for an efficient cleavage under physiological magnesium ion concentrations. In this search, we find, apart from the known examples, several hundreds of motifs in organisms of all kingdoms of life. In a first set of experiments, we analysed hammerhead ribozymes from Arabidopsis thaliana. We found that these sequences are tissue-specifically expressed and that they undergo self-cleavage in planta. Furthermore, their activity under physiological magnesium ion concentrations depends on functional loop–loop interactions, as shown by the lack of activity of appropriate mutants.
Probing the structure of Saccharomyces cerevisiae RNase MRP
Authors: Walker S.C. , Aspinall T.V. , Gordon J.M.B. , Avis J.M.
Published: August 2006

In yeast, RNase MRP (mitochondrial RNA processing), a ribonucleoprotein precursor rRNA processing enzyme, possesses one putatively catalytic RNA and ten protein subunits and is highly related to RNase P. Structural analysis of the MRP RNA provides data that closely match a previous secondary-structure model derived from phylogenetic analysis, with the exception of an additional stem. This stem occupies an equivalent position to the P7 stem of RNase P RNA and its inclusion confers on MRP RNA a greater similarity to the core P RNA structure. In vivo studies indicate that the P7-like stem can form, but is not a part of, the active enzyme structure. Stem formation would increase RNA stability in the absence of proteins and our alternative structure may be a valid intermediate species in RNase MRP assembly. Further ongoing studies of this enzyme reveal an extensive network of interactions between subunits and a probable central role for the Pop1, Pop4 and Pop7 subunits.
Energy transduction by respiratory complex I – an evaluation of current knowledge
Authors: Hirst J.
Published: August 2006

Complex I (NADH:ubiquinone oxidoreductase) is a membrane-bound, multisubunit enzyme. At present, there is no high-resolution structural model available for complex I and its mechanism of energy transduction is unknown. However, the subunit compositions of complex I from both eukaryotic and prokaryotic organisms have been determined, the sequences of their subunits are known and a coherent picture of the redox cofactors present in complex I has been developed. Here, I aim to describe and examine data relating to the mechanism of complex I and to build a framework to facilitate the discussion of possible conclusions and mechanistic models.
Location proteomics: a systems approach to subcellular location
Authors: Murphy R.F.
Published: August 2006

Systems Biology requires comprehensive systematic data on all aspects and levels of biological organization and function. In addition to information on the sequence, structure, activities and binding interactions of all biological macromolecules, the creation of accurate predictive models of cell behaviour will require detailed information on the distribution of those molecules within cells and the ways in which those distributions change over the cell cycle and in response to mutations or external stimuli. Current information on subcellular location in protein databases is limited to unstructured text descriptions or sets of terms assigned by human curators. These entries do not permit basic operations that are common to other biological databases, such as measurement of the degree of similarity between the distributions of two proteins, and they are not able to fully capture the complexity of protein patterns that can be observed. The field of location proteomics seeks to provide automated, objective high-resolution descriptions of protein location patterns within cells. Methods have been developed to group proteins into statistically indistinguishable location patterns using automated analysis of fluorescence microscope images. The resulting clusters, or location families, are analogous to clusters found for other domains, such as protein sequence families. Preliminary work suggests the feasibility of expressing each unique pattern as a generative model that can be incorporated into comprehensive models of cell behaviour.
SNF1-related kinases allow plants to tolerate herbivory by allocating carbon to roots
Authors: Schwachtje Jens , Minchin Peter E. H. , Jahnke Sigfried , van Dongen Joost T. , Schittko Ursula , Baldwin Ian T.
Published: August 2006

Herbivore attack elicits costly defenses that are known to decrease plant fitness by using resources that are normally slated for growth and reproduction. Additionally, plants have evolved mechanisms for tolerating attack, which are not understood on a molecular level. Using
11
C-photosynthate labeling as well as sugar and enzyme measurements, we found rapid changes in sink–source relations in the annual
Nicotiana attenuata
after simulated herbivore attacks, which increased the allocation of sugars to roots. This herbivore-induced response is regulated by the β-subunit of an SnRK1 (SNF1-related kinase) protein kinase, GAL83, transcripts of which are rapidly down-regulated in source leaves after herbivore attack and, when silenced, increase assimilate transport to roots. This C diversion response is activated by herbivore-specific elicitors and is independent of jasmonate signaling, which regulates most of the plant's defense responses. Herbivore attack during early stages of development increases root reserves, which, in turn, delays senescence and prolongs flowering. That attacked GAL83-silenced plants use their enhanced root reserves to prolong reproduction demonstrates that SnRK1 alters resource allocation so that plants better tolerate herbivory. This tolerance mechanism complements the likely defensive value of diverting resources to a less vulnerable location within the plant.
Space and stochasticity in population dynamics
Authors: Ovaskainen Otso , Cornell Stephen J.
Published: August 2006

Organisms interact with each other mostly over local scales, so the local density experienced by an individual is of greater importance than the mean density in a population. This simple observation poses a tremendous challenge to theoretical ecology, and because nonlinear stochastic and spatial models cannot be solved exactly, much effort has been spent in seeking effective approximations. Several authors have observed that spatial population systems behave like deterministic nonspatial systems if dispersal averages the dynamics over a sufficiently large scale. We exploit this fact to develop an exact series expansion, which allows one to derive approximations of stochastic individual-based models without resorting to heuristic assumptions. Our approach makes it possible to calculate the corrections to mean-field models in the limit where the interaction range is large, and it provides insight into the performance of moment closure methods. With this approach, we demonstrate how the buildup of spatiotemporal correlations slows down the spread of an invasion, prolongs time lags associated with extinction debt, and leads to locally oscillating but globally stable coexistence of a host and a parasite.
Bestrophin-2 is a candidate calcium-activated chloride channel involved in olfactory transduction
Authors: Pifferi Simone , Pascarella Giovanni , Boccaccio Anna , Mazzatenta Andrea , Gustincich Stefano , Menini Anna , Zucchelli Silvia
Published: August 2006

Ca-activated Cl channels are an important component of olfactory transduction. Odor binding to olfactory receptors in the cilia of olfactory sensory neurons (OSNs) leads to an increase of intraciliary Ca concentration by Ca entry through cyclic nucleotide-gated (CNG) channels. Ca activates a Cl channel that leads to an efflux of Cl from the cilia, contributing to the amplification of the OSN depolarization. The molecular identity of this Cl channel remains elusive. Recent evidence has indicated that bestrophins are able to form Ca-activated Cl channels in heterologous systems. Here we have analyzed the expression of bestrophins in the mouse olfactory epithelium and demonstrated that only mouse bestrophin-2 (mBest2) was expressed. Single-cell RT-PCR showed that mBest2 was expressed in OSNs but not in supporting cells. Immunohistochemistry revealed that mBest2 was expressed on the cilia of OSNs, the site of olfactory transduction, and colocalized with the main CNGA2 channel subunit. Electrophysiological properties of Ca-activated Cl currents from native channels in dendritic knob/cilia of mouse OSNs were compared with those induced by the expression of mBest2 in HEK-293 cells. We found the same anion permeability sequence, small estimated single-channel conductances, a Ca sensitivity difference of one order of magnitude, and the same side-specific blockage of the two Cl channel blockers commonly used to inhibit the odorant-induced Ca-activated Cl current in OSNs, niflumic acid, and 4-acetamido-4′-isothiocyanato-stilben-2,2′-disulfonate (SITS). Therefore, our data suggest that mBest2 is a good candidate for being a molecular component of the olfactory Ca-activated Cl channel.
Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids
Authors: Gargalovic Peter S. , Imura Minori , Zhang Bin , Gharavi Nima M. , Clark Michael J. , Pagnon Joanne , Yang Wen-Pin , He Aiqing , Truong Amy , Patel Shilpa , Nelson Stanley F. , Horvath Steve , Berliner Judith A. , Kirchgessner Todd G. , Lusis Aldons J.
Published: August 2006

Oxidized phospholipids are thought to promote atherogenesis by stimulating endothelial cells (ECs) to produce inflammatory cytokines, such as IL-8. In studies with mouse models, we previously demonstrated that genetic variation in inflammatory responses of endothelial cells to oxidized lipids contributes importantly to atherosclerosis susceptibility. We now show that similar variations occur in cultured aortic ECs derived from multiple heart transplant donors. These variations were stably maintained between passages and, thus, reflect either genetic or epigenetic regulatory differences. Expression array analysis of aortic EC cultures derived from 12 individuals revealed that >1,000 genes were regulated by oxidized phospholipids. We have used the observed variations in the sampled population to construct a gene coexpression network comprised of 15 modules of highly connected genes. We show that several identified modules are significantly enriched in genes for known pathways and confirm a module enriched for unfolded protein response (UPR) genes using siRNA and the UPR inducer tunicamycin. On the basis of the constructed network, we predicted that a gene of unknown function (MGC4504) present in the UPR module is a target for UPR transcriptional activator ATF4. Our data also indicate that IL-8 is present in the UPR module and is regulated, in part, by the UPR. We validate these by using siRNA. In conclusion, we show that interindividual variability can be used to group genes into pathways and predict gene–gene regulatory relationships, thus identifying targets potentially involved in susceptibility to common diseases such as atherosclerosis.
Gendered Realities of Life in Post-Conflict Kosovo: Addressing the Hegemonic Man*
Authors: Munn Jamie
Published: August 2006

In 2005, years after an enforced peace was constructed between Serbia and its Albanian-majority province Kosovo, the outcome of a better life for ordinary citizens seemed yet to be fulfilled. However, this was not the most important change in the lives of Kosovars. I will argue that the lives of Kosovars are characterised by a lack of economic growth and the increased importance of the normative concept of the hegemonic man. Kosovars, like many “traditionally” patriarchal societies, have constructed identities of the patriotic man and the exalted childbearing woman as icons of national survival. These designated identities often negate the realities of war-affected communities. The genderedplacesof man and woman in political reality are marred by the traumatic events of life. Within this framework, I analyze interviews with people who have developed “alternative” identities or, as phrased by Carver, “bonded” senses of self-esteem as a result of viewing themselves as somewhat unable to live up to the iconic emblem. In the context of a continued occupation of the province by both the international bodies assigned to the province and the Serbian state (Kosovo is notyetindependent from Serbia), one of the main questions asked by many Kosovars today remains: “What was the war about if not independence and where are the spoils of victory?”
Gendered Transformations of State Power: Masculinity, International Intervention, and the Bosnian Police*
Authors: Helms Elissa
Published: August 2006

Many Bosnians I talked to were skeptical about my plan to do research among local police in the central Bosnian town of Zenica. They told me that no one would talk to me there. “They're too scared of foreigners,” they said, meaning especially Westerners who might be connected to the powerful international institutions that have acted as de facto protectorate to the fragmented and unstable state after the collapse of socialist Yugoslavia and the devastating 1992–1995 war. In their efforts to neutralize the police as enforcer of ethnonational separatism and to promote the new democratic values of rule of law, respect for human rights, and ethnic and gender equality, the “international community” had sacked hundreds of officers, restricted police powers, and introduced quotas for ethnic minorities and women. There was thus a sense that “foreigners” posed a threat to the masculinized coercive power of the state as embodied in the police. As it happened, the police did talk to me, though always in reference to this context of shifting relations of state and state-like power, as well as the economic and social instability that characterizes postwar Bosnia-Herzegovina (hereafter Bosnia).
A surprising covering of the real line
Authors: Kun Gábor
Published: August 2006

We construct an increasing sequence of Borel subsets of

R

\mathbb {R}

, such that their union is

R

\mathbb {R}

, but

R

\mathbb {R}

cannot be covered with countably many translations of one set. The proof uses a random method.
Length spectrum in rank one symmetric space is not arithmetic
Authors: Kim Inkang
Published: August 2006

In this paper we show that a nonelementary nonparabolic group in a real semisimple Lie group of rank one has the property that the set of translation lengths of hyperbolic elements is not contained in any discrete subgroup of

R

{\mathbb R}

.
Sur l’ideal d’ordre des operateurs AM-compacts
Authors: Aqzzouz Belmesnaoui , Nouira Redouane
Published: August 2006

We give different necessary and sufficient conditions so that the space of AM-compact operators is an order ideal and we deduce some consequences.

Résume. Nous donnons différentes conditions nécessaires et suffisantes pour que l’espace des opérateurs AM-compacts soit un idéal d’ordre et nous déduisons quelques conséquences.
Khovanov-Jacobsson numbers and invariants of surface-knots derived from Bar-Natan’s theory
Authors: Tanaka Kokoro
Published: August 2006

Khovanov introduced a cohomology theory for oriented classical links whose graded Euler characteristic is the Jones polynomial. Since Khovanov’s theory is functorial for link cobordisms between classical links, we obtain an invariant of a surface-knot, called the Khovanov-Jacobsson number, by considering the surface-knot as a link cobordism between empty links. In this paper, we study an extension of the Khovanov-Jacobsson number derived from Bar-Natan’s theory, and prove that any

T
2

T^2

-knot has trivial Khovanov-Jacobsson number.
Not every 𝑝-group can be generated by elements of the same order
Authors: O’Brien E. , Scoppola Carlo , Vaughan-Lee M.
Published: August 2006

For every prime

p
p

, we exhibit a finite

p
p

-group which cannot be generated by a set of elements, all having the same order. This answers a long-standing question from the Kourovka Notebook.
On Weyl group equivariant maps
Authors: Korányi Adam , Szőke Róbert
Published: August 2006

We prove an equivariant analogue of Chevalley’s isomorphism theorem for polynomial,

C

∞

C^{\infty }

or

C

ω

C^{\omega }

maps.
Gibbs’ phenomenon and surface area
Authors: de Michele L. , Roux D.
Published: August 2006

If a functionffis of bounded variation onTN (N≥1)T^N\ (N\geq 1)and{φn}\{{\varphi }_n\}is a positive approximate identity, we prove that the area of the graph off∗φnf*{\varphi }_nconverges from below to the relaxed area of the graph offf. Moreover we give asymptotic estimates for the area of the graph of the square partial sums of multiple Fourier series of functions with suitable discontinuities.
Greedy approximation with respect to certain subsystems of the Walsh orthonormal system
Authors: Grigorian Martin , Zink Robert
Published: August 2006

In an article that appeared in 1967, J.J. Price has shown that there is a vast family of subsystems of the Walsh orthonormal system each of which is complete on sets of large measure. In the present work it is shown that the greedy algorithm, when applied to functions in

L

1

[
0
,
1
]

L^{1}[0,1]

, is surprisingly effective for these nearly–complete families. Indeed, if

Φ
\Phi

is such a subsystem of the Walsh system, then to each positive

ε
\varepsilon

, however small, there corresponds a Lebesgue measurable set

E
E

such that for every

f
f

, Lebesgue integrable on

[
0
,
1
]

[0,1]

, the greedy approximants to

f
f

, associated with

Φ
\Phi

, converge, in the

L

1

L^{1}

norm, to an integrable function

g
g

that coincides with

f
f

on

E
E

.
Lower bounds for the condition number of a real confluent Vandermonde matrix
Authors: Li Ren-Cang
Published: August 2006

Lower bounds on the condition number

κ
p

(

V

c

)

\kappa _p(V_{\mathrm {c}})

of a real confluent Vandermonde matrix

V

c

V_{\mathrm {c}}

are established in terms of the dimension

n
n

, or

n
n

and the largest absolute value among all nodes that define the confluent Vandermonde matrix and the interval that contains the nodes. In particular, it is proved that for any modest

k

max

k_{\max }

(the largest multiplicity of distinct nodes),

κ
p

(

V

c

)

\kappa _p(V_{\mathrm {c}})

behaves no smaller than

O

n

(
(
1
+

2

)
n

)

{\mathcal O}_n((1+\sqrt 2\,)^n)

, or than

O

n

(
(
1
+

2

)

2
n

)

{\mathcal O}_n((1+\sqrt 2\,)^{2n})

if all nodes are nonnegative. It is not clear whether those bounds are asymptotically sharp for modest

k

max

k_{\max }

.
Numerical differentiation from a viewpoint of regularization theory
Authors: Lu Shuai , Pereverzev Sergei
Published: August 2006

In this paper, we discuss the classical ill-posed problem of numerical differentiation, assuming that the smoothness of the function to be differentiated is unknown. Using recent results on adaptive regularization of general ill-posed problems, we propose new rules for the choice of the stepsize in the finite-difference methods, and for the regularization parameter choice in numerical differentiation regularized by the iterated Tikhonov method. These methods are shown to be effective for the differentiation of noisy functions, and the order-optimal convergence results for them are proved.
A two-grid discretization method for decoupling systems of partial differential equations
Authors: Jin Jicheng , Shu Shi , Xu Jinchao
Published: August 2006

In this paper, we propose a two-grid finite element method for solving coupled partial differential equations, e.g., the Schrödinger-type equation. With this method, the solution of the coupled equations on a fine grid is reduced to the solution of coupled equations on a much coarser grid together with the solution of decoupled equations on the fine grid. It is shown, both theoretically and numerically, that the resulting solution still achieves asymptotically optimal accuracy.
On polynomial selection for the general number field sieve
Authors: Kleinjung Thorsten
Published: August 2006

The general number field sieve (GNFS) is the asymptotically fastest algorithm for factoring large integers. Its runtime depends on a good choice of a polynomial pair. In this article we present an improvement of the polynomial selection method of Montgomery and Murphy which has been used in recent GNFS records.
Energy norm a posteriori error estimates for mixed finite element methods
Authors: Lovadina Carlo , Stenberg Rolf
Published: August 2006

This paper deals with the a posteriori error analysis of mixed finite element methods for second order elliptic equations. It is shown that a reliable and efficient error estimator can be constructed using a postprocessed solution of the method. The analysis is performed in two different ways: under a saturation assumption and using a Helmholtz decomposition for vector fields.
A Coiled-Coil Domain of Melanophilin Is Essential for Myosin Va Recruitment and Melanosome Transport in Melanocytes
Authors: Hume Alistair N. , Tarafder Abul K. , Ramalho José S. , Sviderskaya Elena V. , Seabra Miguel C.
Published: August 2006

Melanophilin (Mlph) regulates retention of melanosomes at the peripheral actin cytoskeleton of melanocytes, a process essential for normal mammalian pigmentation. Mlph is proposed to be a modular protein binding the melanosome-associated protein Rab27a, Myosin Va (MyoVa), actin, and microtubule end-binding protein (EB1), via distinct N-terminal Rab27a-binding domain (R27BD), medial MyoVa-binding domain (MBD), and C-terminal actin-binding domain (ABD), respectively. We developed a novel melanosome transport assay using a Mlph-null cell line to study formation of the active Rab27a:Mlph:MyoVa complex. Recruitment of MyoVa to melanosomes correlated with rescue of melanosome transport and required intact R27BD together with MBD exon F–binding region (EFBD) and unexpectedly a potential coiled-coil forming sequence within ABD. In vitro binding studies indicate that the coiled-coil region enhances binding of MyoVa by Mlph MBD. Other regions of Mlph reported to interact with MyoVa globular tail, actin, or EB1 are not essential for melanosome transport rescue. The strict correlation between melanosomal MyoVa recruitment and rescue of melanosome distribution suggests that stable interaction with Mlph and MyoVa activation are nondissociable events. Our results highlight the importance of the coiled-coil region together with R27BD and EFBD regions of Mlph in the formation of the active melanosomal Rab27a-Mlph-MyoVa complex.
Fathers in hot water: rising sea temperatures and a Northeastern Atlantic pipefish baby boom
Authors: Kirby Richard R , Johns David G , Lindley John A
Published: August 2006

We report unprecedented numbers of juvenile snake pipefish,
Entelurus aequoreus
, in continuous plankton records of the Northeastern Atlantic since 2002. Increased sea surface temperatures (SSTs) in the Northern Hemisphere, linked to global warming, are a likely cause. Analysis of a long-term time-series of SST data in the Northeastern Atlantic shows a rise in winter, spring and summer sea temperatures (January–September), when the eggs of
E. aqueoreus
, which are brooded by the male, are developing and the larvae are growing in plankton. From what is known of the reproductive biology of closely related species, we suggest that the increased abundance of larval and juvenile
E. aequoreus
in the plankton as far west as the Mid-Atlantic Ridge may reflect the impact of temperature on abundance, through its effects on the operational sex ratio and potential reproductive rate, the onset of the breeding season and juvenile survival in this sex role reversed fish.
Biological tolerance of different materials in bulk and nanoparticulate form in a rat model: sarcoma development by nanoparticles
Authors: Hansen Torsten , Clermont Gaëlle , Alves Antonio , Eloy Rosy , Brochhausen Christoph , Boutrand Jean Pierre , Gatti Antonietta M , James Kirkpatrick C
Published: August 2006

In order to study the pathobiological impact of the nanometre-scale of materials, we evaluated the effects of five different materials as nanoparticulate biomaterials in comparison with bulk samples in contact with living tissues. Five groups out of 10 rats were implanted bilaterally for up to 12 months with materials of the same type, namely TiO
2
, SiO
2
, Ni, Co and polyvinyl chloride (PVC), subcutaneously with bulk material on one side of the vertebral column and intramuscularly with nanoparticulate material on the contralateral side. At the end of each implantation time, the site was macroscopically examined, followed by histological processing according to standard techniques. Malignant mesenchymal tumours (pleomorphic sarcomas) were obtained in five out of six cases of implanted Co nanoparticle sites, while a preneoplastic lesion was observed in an animal implanted with Co in bulk form. In the Ni group, all animals rapidly developed visible nodules at the implanted sites between 4 and 6 months, which were diagnosed as rhabdomyosarcomas. Since the ratio of surface area to volume did not show significant differences between the Ni/Co group and the TiO
2
/SiO
2
/PVC group, we suggested that the induction of neoplasia was not mediated by physical effects, but was mediated by the well-known carcinogenic impact of Ni and Co. The data from the Co group show that the physical properties (particulate versus bulk form) could have a significant influence on the acceleration of the neoplastic process.
Flattening, squeezing and the existence of random attractors
Authors: Kloeden Peter E , Langa José A
Published: August 2006

The study of qualitative properties of random and stochastic differential equations is now one of the most active fields in the modern theory of dynamical systems. In the deterministic case, the properties of flattening and squeezing in infinite-dimensional autonomous dynamical systems require the existence of a bounded absorbing set and imply the existence of a global attractor. The flattening property involves the behaviour of individual trajectories while the squeezing property involves the difference of trajectories. It is shown here that the flattening property is implied by the squeezing property and is in fact weaker, since the attractor in a system with the flattening property can be infinite-dimensional, whereas it is always finite-dimensional in a system with the squeezing property. The flattening property is then generalized to random dynamical systems, for which it is called the pullback flattening property. It is shown to be weaker than the random squeezing property, but equivalent to pullback asymptotic compactness and pullback limit-set compactness, and thus implies the existence of a random attractor. The results are also valid for deterministic non-autonomous dynamical systems formulated as skew-product flows.
Intrinsic time-scale decomposition: time–frequency–energy analysis and real-time filtering of non-stationary signals
Authors: Frei Mark G , Osorio Ivan
Published: August 2006

We introduce a new algorithm, the intrinsic time-scale decomposition (ITD), for efficient and precise time–frequency–energy (TFE) analysis of signals. The ITD method overcomes many of the limitations of both classical (e.g. Fourier transform or wavelet transform based) and more recent (empirical mode decomposition based) approaches to TFE analysis of signals that are nonlinear and/or non-stationary in nature. The ITD method decomposes a signal into (i) a sum of proper rotation components, for which instantaneous frequency and amplitude are well defined, and (ii) a monotonic trend. The decomposition preserves precise temporal information regarding signal critical points and riding waves, with a temporal resolution equal to the time-scale of extrema occurrence in the input signal. We also demonstrate how the ITD enables application of single-wave analysis and how this, in turn, leads to a powerful new class of real-time signal filters, which extract and utilize the inherent instantaneous amplitude and frequency/phase information in combination with other relevant morphological features.
Environmental forcing as a main determinant of bloom dynamics of theChrysochromulinaalgae
Authors: Lekve Kyrre , Bagøien Espen , Dahl Einar , Edvardsen Bente , Skogen Morten , Stenseth Nils Chr
Published: August 2006

In this paper, we demonstrate that the seasonal dynamics in the abiotic factors, without including seasonal changes in the biological relationships, can appropriately account for the seasonal dynamics ofChrysochromulinaspp. This is through the analysis of data on the population dynamics ofChrysochromulinaspp. off southern Norway that is evaluated in relation to environmental factors and season by the analyses of 12 year monthly time-series.Chrysochromulinaspp. abundance, nutrient concentrations, hydrographical properties, as well as current and wind data were analysed on a monthly scale by means of autoregressive moving average models, principal component analyses (PCA), and linear and nonlinear regression models. Seasonal development of theChrysochromulinaassemblage was well predicted from regression models forced with two PCA components representing seasonal variation in nutrient and chlorophyllalevels and ratios, inflow of North Seawater to the Skagerrak and northeasterly wind along the Norwegian coast. Assuming these to be general results, we might hypothesis that marine algal communities are governed by seasonally varying abiotic factors to a large extent.
Temporal habitat variability and the maintenance of sex in host populations of the pea aphid
Authors: Frantz Adrien , Plantegenest Manuel , Simon Jean-Christophe
Published: August 2006

The evolutionary maintenance of sex, despite competition from asexual reproduction, has long intrigued the evolutionary biologists owing to its numerous apparent short-term costs. In aphids, winter climate is expected to determine the maintenance of sexual lineages in the high latitude zones owing to their exclusive ability to produce frost-resistant eggs. However, diverse reproductive modes may coexist at a local scale where climatic influence is counteracted by microgeographical factors. In this study, we tested the influence of local habitat characteristics on regional coexistence of reproductive modes in the pea aphid,Acyrthosiphon pisum. In the laboratory, the induction of sexual morph production of many pea aphid genotypes from the local fields of annual (pea and faba bean) and perennial (alfalfa and red clover) crops in Western France indicated thatA. pisumlineages from annual crops had a significantly higher investment in sexual reproduction thanA. pisumlineages from the perennial hosts. We propose that temporal habitat variability exerts a selective pressure to maintain the sexual reproduction inA. pisum. The ecological and evolutionary consequences of the association between the mode of reproduction and the host population on gene flow restriction and on ecological specialization are discussed.
Climate change and the demographic demise of a hoarding bird living on the edge
Authors: Waite Thomas A , Strickland Dan
Published: August 2006

Population declines along the lower-latitude edge of a species' range may be diagnostic of climate change. We report evidence that climate change has contributed to deteriorating reproductive success in a rapidly declining population of the grey jay (
Perisoreus canadensis
) at the southern edge of its range. This non-migratory bird of boreal and subalpine forest lives on permanent territories, where it hoards enormous amounts of food for winter and then breeds very early, under still-wintry conditions. We hypothesized that warmer autumns have increased the perishability of hoards and compromised subsequent breeding attempts. Our analysis confirmed that warm autumns, especially when followed by cold late winters, have led to delayed breeding and reduced reproductive success. Our findings uniquely show that weather months before the breeding season impact the timing and success of breeding. Warm autumns apparently represent hostile conditions for this species, because it relies on cold storage. Our study population may be especially vulnerable, because it is situated at the southern edge of the range, where the potential for hoard rot is most pronounced. This population's demise may signal a climate-driven range contraction through local extinctions along the trailing edge.
Dark nests and egg colour in birds: a possible functional role of ultraviolet reflectance in egg detectability
Authors: Avilés Jesús M , Soler Juan J , Pérez-Contreras Tomás
Published: August 2006

Owing to the conspicuousness of ultraviolet (UV) colour in dark environments, natural selection might have selected UV egg coloration because it would enhance egg detectability by parents in murky nests. Here, we tested this hypothesis by using comparative and experimental approaches. First, we studied variation in egg coloration of 98 species of European passerines measured using UV–visible reflectance spectrometry (300–700 nm) in relation to nesting habits. Analyses based on raw data and controlling for phylogenetic distances both at the species and the family levels revealed that hole-nester species produced eggs with higher UV reflectance than those nesting in open habitats. The experimental approach consisted of the manipulation of UV reflectance of the experimental eggs introduced outside the nest-cup of the hole-nester spotless starlingSturnus unicolorand the study of the retrieval of these eggs. Ultraviolet-reflecting eggs (controls) were more frequently retrieved to the nest-cup than non-reflecting (–UV) eggs. These results were not due to ‘–UV’ eggs being recognized by starlings as parasitic because when a parasitic egg is detected, starlings removed it from the nest-box. Therefore, these results are consistent with the hypothesis that UV egg colours are designed to provide highly detectable targets for parent birds in dark nest environments.
Comparison of DNA extraction methods for Aspergillus fumigatus using real-time PCR
Authors: Griffiths Lisa J. , Anyim Martin , Doffman Sarah R. , Wilks Mark , Millar Michael R. , Agrawal Samir G.
Published: August 2006

Newer methods such as PCR are being investigated in order to improve the diagnosis of invasive aspergillosis. One of the major obstacles to using PCR to diagnose aspergillosis is a reliable, simple method for extraction of the fungal DNA. The presence of a complex, sturdy cell wall that is resistant to lysis impairs extraction of the DNA by conventional methods employed for bacteria. Numerous fungal DNA extraction protocols have been described in the literature. However, these methods are time-consuming, require a high level of skill and may not be suitable for use as a routine diagnostic technique. Here, a number of extraction methods were compared: a freeze–thaw method, a freeze–boil method, enzyme extraction and a bead-beating method using Mini-BeadBeater-8. The quality and quantity of the DNA extracted was compared using real-time PCR. It was found that the use of a bead-beating method followed by extraction with AL buffer (Qiagen) was the most successful extraction technique, giving the greatest yield of DNA, and was also the least time-consuming method assessed.