bluuebunny/crossref_metadata_2025 huggingface dataset:
Shades of Social Capital: Elite Persistence and the Everyday Politics of Community Forestry in Southeastern Mexico
Authors: Wilshusen Peter R
Published: October 2008

Social capital has been discussed widely as networks based in trust and reciprocity that can facilitate economic development, democratic governance, and sustainable natural-resource management. The concept has not been examined thoroughly as an analytical lens for understanding power relations. Drawing on Bourdieu's theory of practice I develop a relational and contextual view of social capital in order to explore the everyday political exchanges tied to a long-standing community forestry association in Quintana Roo, Mexico. I present a case study that recounts the emergence and decline of a timber-marketing fund to illustrate how elite actors from member communities ( ejidos) maintain relative dominance within social networks over time. This Bourdieusian perspective on elite persistence exemplifies the downside of social capital but also reveals a cultural view of everyday politics that highlights tensions among long-standing practices (habitus) and formal and informal spheres of social interaction (fields).
Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet
Authors: Bon Céline , Caudy Nicolas , de Dieuleveult Maud , Fosse Philippe , Philippe Michel , Maksud Frédéric , Beraud-Colomb Éliane , Bouzaid Eric , Kefi Rym , Laugier Christelle , Rousseau Bernard , Casane Didier , van der Plicht Johannes , Elalouf Jean-Marc
Published: October 2008

Retrieving a large amount of genetic information from extinct species was demonstrated feasible, but complete mitochondrial genome sequences have only been deciphered for the moa, a bird that became extinct a few hundred years ago, and for Pleistocene species, such as the woolly mammoth and the mastodon, both of which could be studied from animals embedded in permafrost. To enlarge the diversity of mitochondrial genomes available for Pleistocene species, we turned to the cave bear (
Ursus spelaeus
), whose only remains consist of skeletal elements. We collected bone samples from the Paleolithic painted cave of Chauvet-Pont d'Arc (France), which displays the earliest known human drawings, and contains thousands of bear remains. We selected a cave bear sternebra, radiocarbon dated to 32,000 years before present, from which we generated overlapping DNA fragments assembling into a 16,810-base pair mitochondrial genome. Together with the first mitochondrial genome for the brown bear western lineage, this study provides a statistically secured molecular phylogeny assessing the cave bear as a sister taxon to the brown bear and polar bear clade, with a divergence inferred to 1.6 million years ago. With the first mitochondrial genome for a Pleistocene carnivore to be delivered, our study establishes the Chauvet-Pont d'Arc Cave as a new reservoir for Paleogenetic studies. These molecular data enable establishing the chronology of bear speciation, and provide a helpful resource to rescue for genetic analysis archeological samples initially diagnosed as devoid of amplifiable DNA.
Phylogenetic patterns of species loss in Thoreau's woods are driven by climate change
Authors: Willis Charles G. , Ruhfel Brad , Primack Richard B. , Miller-Rushing Abraham J. , Davis Charles C.
Published: October 2008

Climate change has led to major changes in the phenology (the timing of seasonal activities, such as flowering) of some species but not others. The extent to which flowering-time response to temperature is shared among closely related species might have important consequences for community-wide patterns of species loss under rapid climate change. Henry David Thoreau initiated a dataset of the Concord, Massachusetts, flora that spans ≈150 years and provides information on changes in species abundance and flowering time. When these data are analyzed in a phylogenetic context, they indicate that change in abundance is strongly correlated with flowering-time response. Species that do not respond to temperature have decreased greatly in abundance, and include among others anemones and buttercups [Ranunculaceaepro parte(p.p.)], asters and campanulas (Asterales), bluets (Rubiaceaep.p.), bladderworts (Lentibulariaceae), dogwoods (Cornaceae), lilies (Liliales), mints (Lamiaceaep.p.), orchids (Orchidaceae), roses (Rosaceaep.p.), saxifrages (Saxifragales), and violets (Malpighiales). Because flowering-time response traits are shared among closely related species, our findings suggest that climate change has affected and will likely continue to shape the phylogenetically biased pattern of species loss in Thoreau's woods.
Persistent epigenetic differences associated with prenatal exposure to famine in humans
Authors: Heijmans Bastiaan T. , Tobi Elmar W. , Stein Aryeh D. , Putter Hein , Blauw Gerard J. , Susser Ezra S. , Slagboom P. Eline , Lumey L. H.
Published: October 2008

Extensive epidemiologic studies have suggested that adult disease risk is associated with adverse environmental conditions early in development. Although the mechanisms behind these relationships are unclear, an involvement of epigenetic dysregulation has been hypothesized. Here we show that individuals who were prenatally exposed to famine during the Dutch Hunger Winter in 1944–45 had, 6 decades later, less DNA methylation of the imprinted
IGF2
gene compared with their unexposed, same-sex siblings. The association was specific for periconceptional exposure, reinforcing that very early mammalian development is a crucial period for establishing and maintaining epigenetic marks. These data are the first to contribute empirical support for the hypothesis that early-life environmental conditions can cause epigenetic changes in humans that persist throughout life.
Brain vasopressin is an important regulator of maternal behavior independent of dams' trait anxiety
Authors: Bosch Oliver J. , Neumann Inga D.
Published: October 2008

The neuropeptide arginine vasopressin (AVP) is arguably among the most potent regulators of social behaviors in mammals identified to date. However, only the related neuropeptide oxytocin (OXT) has been shown to promote maternal behavior. Here, we assess the role of AVP in maternal care, in particular in arched back nursing, pup retrieval, and pup contact by using complementary pharmacological and genetic approaches. Also, experiments were performed in rat dams with differences in trait anxiety, i.e., rats bred for either high (HAB) or low (LAB) anxiety-related behavior as well as nonselected (NAB) dams. Viral vector-mediated up-regulation of AVP V1a receptors (AVP-Rs) within the medial preoptic area of lactating NAB rats and chronic central AVP treatment of NAB and LAB dams improved, whereas local blockade of AVP-R expression by means of antisense oligodeoxynucleotides or central AVP-R antagonism impaired, maternal care in NAB dams. Also, in HAB rats with a genetically determined elevated brain AVP activity, intrinsically high levels of maternal care were reversed by blockade of AVP-R actions. Treatment-induced impairment of AVP-mediated maternal behavior increased adult emotionality and impaired social interactions in male offspring of NAB dams. These findings provide direct evidence for an essential and highly potent role of brain AVP in promoting maternal behavior, which seems to be independent of the dam's trait anxiety.
Structural and functional analysis of AsbF: Origin of the stealth 3,4-dihydroxybenzoic acid subunit for petrobactin biosynthesis
Authors: Pfleger Brian F. , Kim Youngchang , Nusca Tyler D. , Maltseva Natalia , Lee Jung Yeop , Rath Christopher M. , Scaglione Jamie B. , Janes Brian K. , Anderson Erica C. , Bergman Nicholas H. , Hanna Philip C. , Joachimiak Andrzej , Sherman David H.
Published: October 2008

Petrobactin, a virulence-associated siderophore produced by
Bacillus anthracis
, chelates ferric iron through the rare 3,4-isomer of dihydroxybenzoic acid (3,4-DHBA). Most catechol siderophores, including bacillibactin and enterobactin, use 2,3-DHBA as a biosynthetic subunit. Significantly, siderocalin, a factor involved in human innate immunity, sequesters ferric siderophores bearing the more typical 2,3-DHBA moiety, thereby impeding uptake of iron by the pathogenic bacterial cell. In contrast, the unusual 3,4-DHBA component of petrobactin renders the siderocalin system incapable of obstructing bacterial iron uptake. Although recent genetic and biochemical studies have revealed selected early steps in petrobactin biosynthesis, the origin of 3,4-DHBA as well as the function of the protein encoded by the final gene in the
B. anthracis
siderophore biosynthetic (
asb
) operon,
asbF
(BA1986), has remained unclear. In this study we demonstrate that 3,4-DHBA is produced through conversion of the common bacterial metabolite 3-dehydroshikimate (3-DHS) by AsbF—a 3-DHS dehydratase. Elucidation of the cocrystal structure of AsbF with 3,4-DHBA, in conjunction with a series of biochemical studies, supports a mechanism in which an enolate intermediate is formed through the action of this 3-DHS dehydratase metalloenzyme. Structural and functional parallels are evident between AsbF and other enzymes within the xylose isomerase TIM-barrel family. Overall, these data indicate that microbial species shown to possess homologs of AsbF may, like
B. anthracis
, also rely on production of the unique 3,4-DHBA metabolite to achieve full viability in the environment or virulence within the host.
Specificity of the J-protein Sis1 in the propagation of 3 yeast prions
Authors: Higurashi Takashi , Hines Justin K. , Sahi Chandan , Aron Rebecca , Craig Elizabeth A.
Published: October 2008

Yeast prions, such as [
PSI
+
], [
RNQ
+
], and [
URE3
], are heritable elements formed by proteins capable of acquiring self-perpetuating conformations. Their propagation is dependent on fragmentation of the amyloid protein complexes formed to generate the additional seeds necessary for conversion of nascent soluble protein to the prion conformation. We report that, in addition to its known role in [
RNQ
+
] propagation, Sis1, a J-protein cochaperone of Hsp70 Ssa, is also specifically required for propagation of [
PSI
+
] and [
URE3
]. Whereas both [
RNQ
+
] and [
URE3
] are cured rapidly upon
SIS1
repression, [
PSI
+
] loss is markedly slower. This disparity cannot be explained simply by differences in seed number, as [
RNQ
+
] and [
PSI
+
] are lost with similar kinetics upon inhibition of Hsp104, a remodeling protein required for propagation of all yeast prions. Rather, in the case of [
PSI
+
], our results are consistent with the partial impairment, rather than the complete abolition, of fragmentation of prion complexes upon Sis1 depletion. We suggest that a common set of molecular chaperones, the J-protein Sis1, the Hsp70 Ssa, and the AAA+ ATPase Hsp104, act sequentially in the fragmentation of all yeast prions, but that the threshold of Sis1 activity required for each prion varies.
Climatic change and wetland desiccation cause amphibian decline in Yellowstone National Park
Authors: McMenamin Sarah K. , Hadly Elizabeth A. , Wright Christopher K.
Published: October 2008

Amphibians are a bellwether for environmental degradation, even in natural ecosystems such as Yellowstone National Park in the western United States, where species have been actively protected longer than anywhere else on Earth. We document that recent climatic warming and resultant wetland desiccation are causing severe declines in 4 once-common amphibian species native to Yellowstone. Climate monitoring over 6 decades, remote sensing, and repeated surveys of 49 ponds indicate that decreasing annual precipitation and increasing temperatures during the warmest months of the year have significantly altered the landscape and the local biological communities. Drought is now more common and more severe than at any time in the past century. Compared with 16 years ago, the number of permanently dry ponds in northern Yellowstone has increased 4-fold. Of the ponds that remain, the proportion supporting amphibians has declined significantly, as has the number of species found in each location. Our results indicate that climatic warming already has disrupted one of the best-protected ecosystems on our planet and that current assessments of species' vulnerability do not adequately consider such impacts.
Wnt/β-catenin signaling controls development of the blood–brain barrier
Authors: Liebner Stefan , Corada Monica , Bangsow Thorsten , Babbage Jane , Taddei Andrea , Czupalla Cathrin J. , Reis Marco , Felici Angelina , Wolburg Hartwig , Fruttiger Marcus , Taketo Makoto M. , von Melchner Harald , Plate Karl Heinz , Gerhardt Holger , Dejana Elisabetta
Published: October 2008

The blood–brain barrier (BBB) is confined to the endothelium of brain capillaries and is indispensable for fluid homeostasis and neuronal function. In this study, we show that endothelial Wnt/β-catenin (β-cat) signaling regulates induction and maintenance of BBB characteristics during embryonic and postnatal development. Endothelial specific stabilization of β-cat in vivo enhances barrier maturation, whereas inactivation of β-cat causes significant down-regulation of claudin3 (Cldn3), up-regulation of plamalemma vesicle-associated protein, and BBB breakdown. Stabilization of β-cat in primary brain endothelial cells (ECs) in vitro by N-terminal truncation or Wnt3a treatment increases Cldn3 expression, BBB-type tight junction formation, and a BBB characteristic gene signature. Loss of β-cat or inhibition of its signaling abrogates this effect. Furthermore, stabilization of β-cat also increased Cldn3 and barrier properties in nonbrain-derived ECs. These findings may open new therapeutic avenues to modulate endothelial barrier function and to limit the devastating effects of BBB breakdown.
Stable and dynamic microtubules coordinately shape the myosin activation zone during cytokinetic furrow formation
Authors: Foe Victoria E. , von Dassow George
Published: October 2008

The cytokinetic furrow arises from spatial and temporal regulation of cortical contractility. To test the role microtubules play in furrow specification, we studied myosin II activation in echinoderm zygotes by assessing serine19-phosphorylated regulatory light chain (pRLC) localization after precisely timed drug treatments. Cortical pRLC was globally depressed before cytokinesis, then elevated only at the equator. We implicated cell cycle biochemistry (not microtubules) in pRLC depression, and differential microtubule stability in localizing the subsequent myosin activation. With no microtubules, pRLC accumulation occurred globally instead of equatorially, and loss of just dynamic microtubules increased equatorial pRLC recruitment. Nocodazole treatment revealed a population of stable astral microtubules that formed during anaphase; among these, those aimed toward the equator grew longer, and their tips coincided with cortical pRLC accumulation. Shrinking the mitotic apparatus with colchicine revealed pRLC suppression near dynamic microtubule arrays. We conclude that opposite effects of stable versus dynamic microtubules focuses myosin activation to the cell equator during cytokinesis.
An agent-based model contrasts opposite effects of dynamic and stable microtubules on cleavage furrow positioning
Authors: Odell Garrett M. , Foe Victoria E.
Published: October 2008

From experiments by Foe and von Dassow (Foe, V.E., and G. von Dassow. 2008. J. Cell Biol. 183:457–470) and others, we infer a molecular mechanism for positioning the cleavage furrow during cytokinesis. Computer simulations reveal how this mechanism depends on quantitative motor-behavior details and explore how robustly this mechanism succeeds across a range of cell sizes.

The mechanism involves the MKLP1 (kinesin-6) component of centralspindlin binding to and walking along microtubules to stimulate cortical contractility where the centralspindlin complex concentrates. The majority of astral microtubules are dynamically unstable. They bind most MKLP1 and suppress cortical Rho/myosin II activation because the tips of unstable microtubules usually depolymerize before MKLP1s reach the cortex. A subset of astral microtubules stabilizes during anaphase, becoming effective rails along which MKLP1 can actually reach the cortex. Because stabilized microtubules aim statistically at the equatorial spindle midplane, that is where centralspindlin accumulates to stimulate furrow formation.
Formation of the blood–brain barrier: Wnt signaling seals the deal
Authors: Polakis Paul
Published: October 2008

Capillaries in the brain are especially selective in determining which blood-borne components gain access to neurons. The structural elements of this blood–brain barrier (BBB) reside at the tight junction, an intercellular protein complex that welds together adjacent endothelial cell membranes in the microvasculature. In this issue, Liebner et al. (Liebner, S., M. Corada, T. Bangsow, J. Babbage, A. Taddei, C.J. Czupalla, M. Reis, A. Felici, H. Wolburg, M. Fruttiger, et al. 2008. J. Cell Biol. 183: 409–417) report that Wnt signaling plays an active role in the development of the BBB by regulating expression of key protein constituents of the tight junction. Such mechanistic insight has implications for a variety of neuropathological states in which the BBB is breached.
Pulmonary alveolar proteinosis caused by deletion of the GM-CSFRα gene in the X chromosome pseudoautosomal region 1
Authors: Martinez-Moczygemba Margarita , Doan Minh L. , Elidemir Okan , Fan Leland L. , Cheung Sau Wai , Lei Jonathan T. , Moore James P. , Tavana Ghamartaj , Lewis Lora R. , Zhu Yiming , Muzny Donna M. , Gibbs Richard A. , Huston David P.
Published: October 2008

Pulmonary alveolar proteinosis (PAP) is a rare lung disorder in which surfactant-derived lipoproteins accumulate excessively within pulmonary alveoli, causing severe respiratory distress. The importance of granulocyte/macrophage colony-stimulating factor (GM-CSF) in the pathogenesis of PAP has been confirmed in humans and mice, wherein GM-CSF signaling is required for pulmonary alveolar macrophage catabolism of surfactant. PAP is caused by disruption of GM-CSF signaling in these cells, and is usually caused by neutralizing autoantibodies to GM-CSF or is secondary to other underlying diseases. Rarely, genetic defects in surfactant proteins or the common β chain for the GM-CSF receptor (GM-CSFR) are causal. Using a combination of cellular, molecular, and genomic approaches, we provide the first evidence that PAP can result from a genetic deficiency of the GM-CSFR α chain, encoded in the X-chromosome pseudoautosomal region 1.
Lipid mediators in innate immunity against tuberculosis: opposing roles of PGE2 and LXA4 in the induction of macrophage death
Authors: Chen Minjian , Divangahi Maziar , Gan Huixian , Shin Daniel S.J. , Hong Song , Lee David M. , Serhan Charles N. , Behar Samuel M. , Remold Heinz G.
Published: October 2008

Virulent Mycobacterium tuberculosis (Mtb) induces a maladaptive cytolytic death modality, necrosis, which is advantageous for the pathogen. We report that necrosis of macrophages infected with the virulent Mtb strains H37Rv and Erdmann depends on predominant LXA4 production that is part of the antiinflammatory and inflammation-resolving action induced by Mtb. Infection of macrophages with the avirulent H37Ra triggers production of high levels of the prostanoid PGE2, which promotes protection against mitochondrial inner membrane perturbation and necrosis. In contrast to H37Ra infection, PGE2 production is significantly reduced in H37Rv-infected macrophages. PGE2 acts by engaging the PGE2 receptor EP2, which induces cyclic AMP production and protein kinase A activation. To verify a role for PGE2 in control of bacterial growth, we show that infection of prostaglandin E synthase (PGES)−/− macrophages in vitro with H37Rv resulted in significantly higher bacterial burden compared with wild-type macrophages. More importantly, PGES−/− mice harbor significantly higher Mtb lung burden 5 wk after low-dose aerosol infection with virulent Mtb. These in vitro and in vivo data indicate that PGE2 plays a critical role in inhibition of Mtb replication.
Toeplitz operators and localization operators
Authors: Engliš Miroslav
Published: October 2008

We show that for any localization operator on the Fock space with polynomial window, there exists a constant coefficient linear partial differential operatorDDsuch that the localization operator with symbolffcoincides with the Toeplitz operator with symbolDfDf. An analogous result also holds in the context of Bergman spaces on bounded symmetric domains. This verifies a recent conjecture of Coburn and simplifies and generalizes recent results of Lo.
Transcendental lattices and supersingular reduction lattices of a singular 𝐾3 surface
Authors: Shimada Ichiro
Published: October 2008

AK3K3surfaceXXdefined over a fieldkkof characteristic00is calledsingularif the Néron-Severi latticeNS(X)\mathrm {NS}(X)ofX⊗k¯X\otimes \overline {k}is of rank2020. LetXXbe a singularK3K3surface defined over a number fieldFF. For each embeddingσ:F↪C\sigma : F\hookrightarrow \mathbb {C}, we denote byT(Xσ)T(X^\sigma )the transcendental lattice of the complexK3K3surfaceXσX^\sigmaobtained fromXXbyσ\sigma. For each primep\mathfrak {p}ofFFat whichXXhas a supersingular reductionXpX_{\mathfrak {p}}, we defineL(X,p)L(X, \mathfrak {p})to be the orthogonal complement ofNS(X)\mathrm {NS}(X)inNS(Xp)\mathrm {NS}(X_{\mathfrak {p}}). We investigate the relation between these latticesT(Xσ)T(X^ \sigma )andL(X,p)L(X,\mathfrak {p}). As an application, we give a lower bound for the degree of a number field over which a singularK3K3surface with a given transcendental lattice can be defined.
Comparing the Floyd and ideal boundaries of a metric space
Authors: Buckley Stephen , Kokkendorff Simon
Published: October 2008

We discuss and compare the notions of ideal boundaries, Floyd boundaries and Gromov boundaries of metric spaces. The three types of boundaries at infinity are compared in the general setting of unbounded length spaces as well as in the special cases of CAT(0) and Gromov hyperbolic spaces. Gromov boundaries, usually defined only for Gromov hyperbolic spaces, are extended to arbitrary metric spaces.
Fast and strongly localized observation for the Schrödinger equation
Authors: Tenenbaum G. , Tucsnak M.
Published: October 2008

We study the exact observability of systems governed by the Schrödinger equation in a rectangle with homogeneous Dirichlet (respectively Neumann) boundary conditions and with Neumann (respectively Dirichlet) boundary observation. Generalizing results from Ramdani, Takahashi, Tenenbaum and Tucsnak (2005), we prove that these systems are exactly observable in in arbitrarily small time. Moreover, we show that the above results hold even if the observation regions have arbitrarily small measures. More precisely, we prove that in the case of homogeneous Neumann boundary conditions with Dirichlet boundary observation, the exact observability property holds for every observation region with nonempty interior. In the case of homogeneous Dirichlet boundary conditions with Neumann boundary observation, we show that the exact observability property holds if and only if the observation region has an open intersection with an edge of each direction. Moreover, we give explicit estimates for the blow-up rate of the observability constants as the time and (or) the size of the observation region tend to zero. The main ingredients of the proofs are an effective version of a theorem of Beurling and Kahane on nonharmonic Fourier series and an estimate for the number of lattice points in the neighbourhood of an ellipse.
Sums of squares and moment problems in equivariant situations
Authors: Cimprič Jaka , Kuhlmann Salma , Scheiderer Claus
Published: October 2008

We begin a systematic study of positivity and moment problems in an equivariant setting. Given a reductive groupGGoverR\mathbb {R}acting on an affineR\mathbb {R}-varietyVV, we consider the induced dual action on the coordinate ringR[V]\mathbb {R}[V]and on the linear dual space ofR[V]\mathbb {R}[V]. In this setting, given an invariant closed semialgebraic subsetKKofV(R)V(\mathbb R), we study the problem of representation of invariant nonnegative polynomials onKKby invariant sums of squares, and the closely related problem of representation of invariant linear functionals onR[V]\mathbb {R}[V]by invariant measures supported onKK. To this end, we analyse the relation between quadratic modules ofR[V]\mathbb {R}[V]and associated quadratic modules of the (finitely generated) subringR[V]G\mathbb {R}[V]^Gof invariant polynomials. We apply our results to investigate the finite solvability of an equivariant version of the multidimensionalKK-moment problem. Most of our results are specific to the case where the groupG(R)G(\mathbb {R})is compact.
𝐻^{𝑝}-bounds for spectral multipliers on graphs
Authors: Kyrezi Ioanna , Marias Michel
Published: October 2008

We study the boundedness on the Hardy spaces

H

p

H^{p}

of spectral multiplier operators associated with the discrete Laplacian on a weighted graph. We assume that the graph satisfies the doubling volume property and a Poincaré inequality. We prove that there is

p

0

∈

(
0
,
1
)

p_{0}\in \left ( 0,1\right )

, depending on the geometry of the graph, such that if the multiplier satisfies a condition similar to the one we have in the classical Hörmander multiplier theorem, then the corresponding operator is bounded on

H

p

H^{p}

,

p
∈

(

p

0

,
1
]

p\in \left ( p_{0},1\right ]

.
Betti numbers for fat point ideals in the plane: A geometric approach
Authors: Gimigliano Alessandro , Harbourne Brian , Idà Monica
Published: October 2008

We consider the open problem of determining the graded Betti numbers for fat point subschemes

Z
Z

supported at general points of

P

2

\mathbf {P}^2

. We relate this problem to the open geometric problem of determining the splitting type of the pullback of

Ω

P

2

\Omega _{\mathbf {P}^2}

to the normalization of certain rational plane curves. We give a conjecture for the graded Betti numbers which would determine them in all degrees but one for every fat point subscheme supported at general points of

P

2

\mathbf {P}^2

. We also prove our Betti number conjecture in a broad range of cases. An appendix discusses many more cases in which our conjecture has been verified computationally and provides a new and more efficient computational approach for computing graded Betti numbers in certain degrees. It also demonstrates how to derive explicit conjectural values for the Betti numbers and how to compute splitting types.
Local chromatic number and distinguishing the strength of topological obstructions
Authors: Simonyi Gábor , Tardos Gábor , Vrećica Siniša
Published: October 2008

The local chromatic number of a graph

G
G

is the number of colors appearing in the most colorful closed neighborhood of a vertex minimized over all proper colorings of

G
G

. We show that two specific topological obstructions that have the same implications for the chromatic number have different implications for the local chromatic number. These two obstructions can be formulated in terms of the homomorphism complex

Hom

(

K
2

,
G
)

\textrm {Hom}(K_2,G)

and its suspension, respectively.

These investigations follow the line of research initiated by Matoušek and Ziegler who recognized a hierarchy of the different topological expressions that can serve as lower bounds for the chromatic number of a graph.

Our results imply that the local chromatic number of

4
4

-chromatic Kneser, Schrijver, Borsuk, and generalized Mycielski graphs is

4
4

, and more generally, that

2
r

2r

-chromatic versions of these graphs have local chromatic number at least

r
+
2

r+2

. This lower bound is tight in several cases by results of the first two authors.
Dynamics of strongly damped wave equations in locally uniform spaces: Attractors and asymptotic regularity
Authors: Yang Meihua , Sun Chunyou
Published: October 2008

This paper is dedicated to analyzing the dynamical behavior of strongly damped wave equations with critical nonlinearity in locally uniform spaces. After proving the global well-posedness, we first establish the asymptotic regularity of the solutions which appears to be op- timal and the existence of a bounded (in
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper H Subscript l u Superscript 2 Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis times upper H Subscript l u Superscript 1 Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis">

H

l
u

2

(

R

N

)
×

H

l
u

1

(

R

N

)

H^2_{lu}(\mathbb {R}^N)\times H^1_{lu}(\mathbb {R}^N)

) subset which attracts exponentially every initial
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper H Subscript l u Superscript 1 Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis times upper L Subscript l u Superscript 2 Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis">

H

l
u

1

(

R

N

)
×

L

l
u

2

(

R

N

)

H^1_{lu}(\mathbb {R}^N)\times L^2_{lu}(\mathbb {R}^N)

-bounded set with respect to the
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper H Subscript l u Superscript 1 Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis times upper L Subscript l u Superscript 2 Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis">

H

l
u

1

(

R

N

)
×

L

l
u

2

(

R

N

)

H^1_{lu}(\mathbb {R}^N)\times L^2_{lu}(\mathbb {R}^N)

-norm. Then, we show there is a
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="left-parenthesis upper H Subscript l u Superscript 1 Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis times upper L Subscript l u Superscript 2 Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis comma upper H Subscript rho Superscript 1 Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis times upper H Subscript rho Superscript 1 Baseline left-parenthesis double-struck upper R Superscript upper N Baseline right-parenthesis right-parenthesis">

(

H

l
u

1

(

R

N

)
×

L

l
u

2

(

R

N

)
,

H
ρ
1

(

R

N

)
×

H
ρ
1

(

R

N

)
)

(H ^1_{lu}(\mathbb {R}^N)\times L^2_{lu}(\mathbb {R}^N), H^1_\rho (\mathbb {R}^N)\times H^1_\rho (\mathbb {R}^N))

-global attractor, which reflects the strongly damped property of

Δ

u
t

\Delta u_t

to some extent.
Most mammalian mRNAs are conserved targets of microRNAs
Authors: Friedman Robin C. , Farh Kyle Kai-How , Burge Christopher B. , Bartel David P.
Published: October 2008

MicroRNAs (miRNAs) are small endogenous RNAs that pair to sites in mRNAs to direct post-transcriptional repression. Many sites that match the miRNA seed (nucleotides 2–7), particularly those in 3′ untranslated regions (3′UTRs), are preferentially conserved. Here, we overhauled our tool for finding preferential conservation of sequence motifs and applied it to the analysis of human 3′UTRs, increasing by nearly threefold the detected number of preferentially conserved miRNA target sites. The new tool more efficiently incorporates new genomes and more completely controls for background conservation by accounting for mutational biases, dinucleotide conservation rates, and the conservation rates of individual UTRs. The improved background model enabled preferential conservation of a new site type, the “offset 6mer,” to be detected. In total, >45,000 miRNA target sites within human 3′UTRs are conserved above background levels, and >60% of human protein-coding genes have been under selective pressure to maintain pairing to miRNAs. Mammalian-specific miRNAs have far fewer conserved targets than do the more broadly conserved miRNAs, even when considering only more recently emerged targets. Although pairing to the 3′ end of miRNAs can compensate for seed mismatches, this class of sites constitutes less than 2% of all preferentially conserved sites detected. The new tool enables statistically powerful analysis of individual miRNA target sites, with the probability of preferentially conserved targeting (PCT) correlating with experimental measurements of repression. Our expanded set of target predictions (including conserved 3′-compensatory sites), are available at the TargetScan website, which displays the PCT for each site and each predicted target.
AMPK regulates basal skeletal muscle capillarization and VEGF expression, but is not necessary for the angiogenic response to exercise
Authors: Zwetsloot Kevin A. , Westerkamp Lenna M. , Holmes Burton F. , Gavin Timothy P.
Published: October 2008

5′‐AMP‐activated protein kinase (AMPK) is a metabolic fuel sensor that monitors cellular energy charge, while the vasculature is important for maintaining cellular energy homeostasis. Mice with muscle‐specific inactive AMPK (AMPK DN) were used to investigate if AMPK regulates skeletal muscle capillarization and the angiogenic responses to exercise. Two hours of the AMP analogue AICAR (1.0 g kg−1) or systemic hypoxia (6% O2) increased vascular endothelial growth factor (VEGF) mRNA in wild‐type (WT), but not in AMPK DN mice. In contrast, the increase in VEGF mRNA with acute exercise (1 h at 20 m min−1, 10% gradient) was greater in AMPK DN compared to WT mice. Nuclear run‐on assay demonstrated that exercise increased VEGF transcription, while hypoxia decreased VEGF transcription. There was no difference in VEGF transcription between WT and AMPK DN. There was a strong correlation between VEGF transcription and VEGF mRNA at rest and with exercise. Resting capillarization was lower in AMPK DN compared to WT. Wheel running (28 days) increased capillarization and this response was AMPK independent. Significant correlations between VEGF protein and muscle capillarization are consistent with VEGF being an important determinant of skeletal muscle capillarization. These data are to our knowledge the first to demonstrate in skeletal muscle in vivo that: (1) AMPK is necessary for hypoxia‐induced VEGF mRNA stabilization, (2) acute exercise increases VEGF transcription, (3) inhibition of AMPK augments the VEGF mRNA response to acute exercise, and (4) AMPK regulates basal VEGF expression and capillarization, but is not necessary for exercise‐induced angiogenesis.
Immobilization induces anabolic resistance in human myofibrillar protein synthesis with low and high dose amino acid infusion
Authors: Glover Elisa I. , Phillips Stuart M. , Oates Bryan R. , Tang Jason E. , Tarnopolsky Mark A. , Selby Anna , Smith Kenneth , Rennie Michael J.
Published: October 2008

We tested the hypothesis that increasing blood amino acid (AA) availability would counter the physical inactivity‐induced reduction in muscle protein synthesis. We determined how 14 days of unilateral knee immobilization affected quadriceps myofibrillar protein synthesis (MPS) in young healthy subjects (10 men, 2 women, 21 ± 1 years; 80.2 ± 4.0 kg, mean ±s.e.m.) in the post‐absorptive state and after infusing AA (10% Primene) at low or high doses (43 and 261 mg kg−1 h−1). Muscle cross‐sectional area (MRI) and peak isometric torque declined in the immobilized leg (−5.0 ± 1.2% and −25 ± 3%, respectively, both P < 0.005), but were unchanged (all P > 0.6) in the non‐immobilized leg. Immobilization induced a 27% decline in the rate of post‐absorptive MPS (immobilized, 0.027 ± 0.003: non‐immobilized, 0.037 ± 0.003% h−1; P < 0.001). Regardless of dose, AA infusion stimulated a greater rise in MPS in the non‐immobilized legs; at 4 h MPS was greater by +54 ± 12% with low dose and +68 ± 17% with high dose AA infusion (both P < 0.001). There was some evidence of delayed responsiveness of phosphorylation of Akt to high doses of AA and p70S6k at both doses but no marked differences in that of mTOR, GSK3β or eEF2. Phosphorylation of focal adhesion kinase (Tyr576/577) was reduced (P < 0.05) with immobilization. We observed no change in polyubiquitinated protein content after immobilization. We confirm that 14 days of immobilization reduces MPS in the post‐absorptive state and this diminution is reduced but not abolished by increased provision of AA, even at high rates. The immobilization‐induced decline in post‐absorptive MPS with the ‘anabolic resistance’ to amino acids can account for much of immobilization‐induced muscle atrophy.
Regulation of mouse lung development by the extracellular calcium‐sensing receptor, CaR
Authors: Finney Brenda A. , Del Moral Pierre M. , Wilkinson William J. , Cayzac Sebastien , Cole Martin , Warburton David , Kemp Paul J. , Riccardi Daniela
Published: October 2008

Postnatal lung function is critically dependent upon optimal embryonic lung development. As the free ionized plasma calcium concentration ([Ca2+]o) of the fetus is higher than that of the adult, the process of lung development occurs in a hypercalcaemic environment. In the adult, [Ca2+]o is monitored by the G‐protein coupled, extracellular calcium‐sensing receptor (CaR), but neither its ontogeny nor its potential role in lung development are known. Here, we demonstrate that CaR is expressed in the mouse lung epithelium, and that its expression is developmentally regulated, with a peak of expression at embryonic day 12.5 (E12.5) and a subsequent decrease by E18, after which the receptor is absent. Experiments carried out using the lung explant culture model in vitro show that lung branching morphogenesis is sensitive to [Ca2+]o, being maximal at physiological adult [Ca2+]o (i.e. 1.0–1.3 mm) and lowest at the higher, fetal (i.e. 1.7 mm) [Ca2+]o. Administration of the specific CaR positive allosteric modulator, the calcimimetic R‐568, mimics the suppressive effects of high [Ca2+]o on branching morphogenesis while both phospholipase C and PI3 kinase inhibition reverse these effects. CaR activation suppresses cell proliferation while it enhances intracellular calcium signalling, lung distension and fluid secretion. Conditions which are restrictive either to branching or to secretion can be rescued by manipulating [Ca2+]o in the culture medium. In conclusion, fetal Ca2+o, acting through a developmentally regulated CaR, is an important extrinsic factor that modulates the intrinsic lung developmental programme. Our observations support a novel role for the CaR in preventing hyperplastic lung disease in utero.
Transmission of blue (S) cone signals through the primate lateral geniculate nucleus
Authors: Tailby C. , Szmajda B. A. , Buzás P. , Lee B. B. , Martin P. R.
Published: October 2008

This study concerns the transmission of short‐wavelength‐sensitive (S) cone signals through the primate dorsal lateral geniculate nucleus. The principal cell classes, magnocellular (MC) and parvocellular (PC), are traditionally segregated into on‐ and off‐subtypes on the basis of the sign of their response to luminance variation. Cells dominated by input from S‐cones (‘blue‐on and blue‐off’) are less frequently encountered and their properties are less well understood. Here we characterize the spatial and chromatic properties of a large sample of blue‐on and blue‐off neurons and contrast them with those of PC and MC neurons. The results confirm that blue‐on and blue‐off cells have larger receptive fields than PC and MC neurons at equivalent eccentricities. Relative to blue‐on cells, blue‐off cells are less sensitive to S‐cone contrast, have larger receptive fields, and show more low‐pass spatial frequency tuning. Thus, blue‐on and blue‐off neurons lack the functional symmetry characteristic of on‐ and off‐subtypes in the MC and PC pathways. The majority of MC and PC cells received no detectible input from S‐cones. Where present, input from S‐cones tended to provide weak inhibition to PC cells. All cell types showed evidence of a suppressive extra‐classical receptive field driven largely or exclusively by ML‐cones. These data indicate that S‐cone signals are isolated to supply the classical receptive field mechanisms of blue‐on and blue‐off cells in the LGN, and that the low spatial precision of S‐cone vision has origins in both classical and extraclassical receptive field properties of subcortical pathways.
Hydraulic Circuit Design Rules to Remove the Dependence of the Injected Fuel Amount on Dwell Time in Multijet CR Systems
Authors: Baratta Mirko , Catania Andrea Emilio , Ferrari Alessandro
Published: October 2008

In multijet common rail (CR) systems, the capability to manage multiple injections with full flexibility in the choice of the dwell time (DT) between consecutive solenoid current pulses is one of the most relevant design targets. Pressure oscillations triggered by the nozzle closure after each injection event induce disturbances in the amount of fuel injected during subsequent injections. This causes a remarkable dispersion in the mass of fuel injected when DT is varied. The effects of the hydraulic circuit layout of CR systems were investigated with the objective to provide design rules for reducing the dependence of the injected fuel amount on DT. A multijet CR of the latest solenoid-type generation was experimentally analyzed at different operating conditions on a high performance test bench. The considerable influence that the injector-supplying pipe dimensions can exert on the frequency and amplitude of the injection-induced pressure oscillations was widely investigated and a physical explanation of cause-effect relationships was found by energetics considerations, starting from experimental tests. A parametric study was performed to identify the best geometrical configurations of the injector-supplying pipe so as to minimize pressure oscillations. The analysis was carried out with the aid of a previously developed simple zero-dimensional model, allowing the evaluation of pressure-wave frequencies as functions of main system geometric data. Pipes of innovative aspect ratio and capable of halving the amplitude of injected-volume fluctuations versus DT were proposed. Purposely designed orifices were introduced into the rail-pipe connectors of a commercial automotive injection system, so as to damp pressure oscillations. Their effects on multiple-injection performance were experimentally determined as being sensible. The resulting reduction in the injector fueling capacity was quantified. It increased by lowering the orifice diameter. The application of the orifice to the injector inlet-pipe with innovative aspect ratio led to a hydraulic circuit solution, which coupled active and passive damping of the pressure waves and minimized the disturbances in injected fuel volumes. Finally, the influence of the rail capacity on pressure-wave dynamics was studied and the possibility of severely reducing the rail volume (up to one-fourth) was assessed. This can lead to a system not only with reduced overall sizes but also with a prompter dynamic response during engine transients.
Computational Dynamics of a Thermally Decomposable Viscoelastic Lubricant Under Shear
Authors: Chinyoka T.
Published: October 2008

The effect of viscoelasticity on the thermodynamic performance of a thermally decomposable lubricant subjected to shear and Arrhenius kinetics is investigated with direct numerical simulations. A numerical algorithm based on the finite difference method is implemented in time and space with the Oldroyd-B constitutive equation as the model for the viscoelastic liquids. We report enhanced efficiency in the case of a polymeric lubricant as compared with the purely viscous lubricant. In particular, it is demonstrated that the use of polymeric liquids helps to delay the onset of thermal runaway as compared with progressively Newtonian liquids.
A Three-Equation Eddy-Viscosity Model for Reynolds-Averaged Navier–Stokes Simulations of Transitional Flow
Authors: Walters D. Keith , Cokljat Davor
Published: October 2008

An eddy-viscosity turbulence model employing three additional transport equations is presented and applied to a number of transitional flow test cases. The model is based on the k-ω framework and represents a substantial refinement to a transition-sensitive model that has been previously documented in the open literature. The third transport equation is included to predict the magnitude of low-frequency velocity fluctuations in the pretransitional boundary layer that have been identified as the precursors to transition. The closure of model terms is based on a phenomenological (i.e., physics-based) rather than a purely empirical approach and the rationale for the forms of these terms is discussed. The model has been implemented into a commercial computational fluid dynamics code and applied to a number of relevant test cases, including flat plate boundary layers with and without applied pressure gradients, as well as a variety of airfoil test cases with different geometries, Reynolds numbers, freestream turbulence conditions, and angles of attack. The test cases demonstrate the ability of the model to successfully reproduce transitional flow behavior with a reasonable degree of accuracy, particularly in comparison with commonly used models that exhibit no capability of predicting laminar-to-turbulent boundary layer development. While it is impossible to resolve all of the complex features of transitional and turbulent flows with a relatively simple Reynolds-averaged modeling approach, the results shown here demonstrate that the new model can provide a useful and practical tool for engineers addressing the simulation and prediction of transitional flow behavior in fluid systems.
Hydrodynamic Characterization of a Nozzle Check Valve by Numerical Simulation
Authors: Sibilla Stefano , Gallati Mario
Published: October 2008

The ability to obtain correct estimates of the hydraulic characteristics of a nozzle check valve by finite-volume numerical simulation is discussed. The evaluation of the numerical results is performed by comparison of the computed pressure drops inside the valve with experimental measurements obtained on an industrial check valve. It is shown that, even with high mesh refinement, the obtained result is highly dependent on the choice of the turbulence model. The renormalization group theory (RNG) k-ε model proves to be the more accurate to describe the flow inside the valve, which is characterized by repeated flow decelerations and accelerations and by boundary layer development under adverse pressure gradient. Pressure-drop and flow coefficients computed by adopting the RNG model agree well with the experimental values at different positions of the plug. The opening transient of the valve is also analyzed by an unsteady flow simulation where the motion of the plug is taken into account. The characteristic curve of the valve obtained in steady flow conditions is finally compared with the transient opening characteristic, highlighting a temporary increase in the pressure drop, which occurs because of a large unsteady separation region downstream of the plug.