bluuebunny/crossref_metadata_2025 huggingface dataset:
Grekos’ S function has a linear growth
Authors: Cassaigne Julien , Plagne Alain
Published: June 2004

An exact additive asymptotic basis is a set of nonnegative integers such that there exists an integer

h
h

with the property that any sufficiently large integer can be written as a sum of exactly

h
h

elements of

A

\mathcal {A}

. The minimal such

h
h

is the exact order of

A

\mathcal {A}

(denoted by

ord

∗

(

A

)

\mbox {ord}^{\ast } ( \mathcal {A} )

). Given any exact additive asymptotic basis

A

\mathcal {A}

, we define

A

∗

\mathcal {A}^{\ast }

to be the subset of

A

\mathcal {A}

composed with the elements

a
∈

A

a \in \mathcal {A}

such that

A

∖
{
a
}

\mathcal {A} \setminus \{ a \}

is still an exact additive asymptotic basis. It is known that

A

∖

A

∗

\mathcal {A} \setminus \mathcal {A}^{\ast }

is finite. In this framework, a central quantity introduced by Grekos is the function

S
(
h
)

S(h)

defined as the following maximum (taken over all bases

A

\mathcal {A}

of exact order

h
h

):
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper S left-parenthesis h right-parenthesis equals max Underscript script upper A Endscripts limit sup Underscript a element-of script upper A Superscript asterisk Baseline Endscripts ord Superscript asterisk Baseline left-parenthesis script upper A minus StartSet a EndSet right-parenthesis period">

S
(
h
)
=

max

A

lim sup

a
∈

A

∗

ord

∗

(

A

∖
{
a
}
)
.

S (h) = \max _{\mathcal {A}} \qquad \limsup _{a \in \mathcal {A}^{\ast }} \qquad \mbox {ord}^{\ast } ( \mathcal {A} \setminus \{ a \}).

\]
In this paper, we introduce a new and simple method for the study of this function. We obtain a new estimate from above for

S
S

which improves drastically and in any case on all previously known estimates. Our estimate, namely

S
(
h
)
≤
2
h

S(h) \leq 2h

, cannot be too far from the truth since

S
S

verifies

S
(
h
)
≥
h
+
1

S(h) \geq h+1

. However, it is certainly not always optimal since

S
(
2
)
=
3

S(2)=3

. Our last result shows that

S
(
h
)

S (h)

is in fact a strictly increasing sequence.
Distinguished representations and poles of twisted tensor 𝐿-functions
Authors: Anandavardhanan U. , Kable Anthony , Tandon R.
Published: June 2004

Let

E

/

F

E/F

be a quadratic extension of

p
p

-adic fields. If

π
\pi

is an admissible representation of

G

L
n

(
E
)

GL_n(E)

that is parabolically induced from discrete series representations, then we prove that the space of

P
n

(
F
)

P_n(F)

-invariant linear functionals on

π
\pi

has dimension one, where

P
n

(
F
)

P_n(F)

is the mirabolic subgroup. As a corollary, it is deduced that if

π
\pi

is distinguished by

G

L
n

(
F
)

GL_n(F)

, then the twisted tensor

L
L

-function associated to

π
\pi

has a pole at

s
=
0

s=0

. It follows that if

π
\pi

is a discrete series representation, then at most one of the representations

π
\pi

and

π
⊗
χ

\pi \otimes \chi

is distinguished, where

χ
\chi

is an extension of the local class field theory character associated to

E

/

F

E/F

. This is in agreement with a conjecture of Flicker and Rallis that relates the set of distinguished representations with the image of base change from a suitable unitary group.
Base-cover paracompactness
Authors: Popvassilev Strashimir
Published: June 2004

Call a topological space

X
X

base-cover paracompact if

X
X

has an open base

B

\mathcal {B}

such that every cover

C

⊂

B

\mathcal {C}\subset \mathcal {B}

of

X
X

contains a locally finite subcover. A subspace of the Sorgenfrey line is base-cover paracompact if and only if it is

F
σ

F_\sigma

. The countable sequential fan is not base-cover paracompact. A paracompact space is locally compact if and only if its product with every compact space is base-cover paracompact.
A new proof for Rockafellar’s characterization of maximal monotone operators
Authors: Simons S. , Zălinescu C.
Published: June 2004

We provide a new and short proof for Rockafellar’s characterization of maximal monotone operators in reflexive Banach spaces based on S. Fitzpatrick’s function and a technique used by R. S. Burachik and B. F. Svaiter for proving their result on the representation of a maximal monotone operator by convex functions.
On extension of isometries between unit spheres of 𝐴𝐿_{𝑝}-spaces (0<𝑝<∞)
Authors: Jian Wang
Published: June 2004

In this paper, we study the extension of isometries between unit spheres of atomicALpAL_p-spaces(0>p>∞, p≠2)(0>p>\infty ,\ p\neq 2). We find a condition under which an isometryTTbetween unit spheres can be linearly isometrically extended. Moreover, we prove that every onto isometry between unit spheres of atomicALpAL_p-spaces(0>p>∞, p≠2)(0>p>\infty ,\ p\neq 2)can be linearly isometrically extended to the whole space.
On the associated family of Delaunay surfaces
Authors: Kilian M.
Published: June 2004

We use the generalised Weierstraß representation of Dorfmeister, Pedit and Wu to obtain the associated family of Delaunay surfaces and derive a formula for the neck size of the surface in terms of the entries of the holomorphic potential.
Norm-closure of the barrier cone in normed linear spaces
Authors: Adly Samir , Ernst Emil , Théra Michel
Published: June 2004

The aim of this note is to characterize the norm-closure of the barrier cone of a closed convex set in an arbitrary normed linear space by means of a new geometric object, the temperate cone.
All frame-spun knots are slice
Authors: Friedman Greg
Published: June 2004

Frame-spun knots are constructed by spinning a knot of lower dimension about a framed submanifold of

S
n

S^n

. We show that all frame-spun knots are slice (null-cobordant).
Biologically valid linear factor models of gene expression
Authors: Girolami Mark , Breitling Rainer
Published: June 2004

Motivation: The identification of physiological processes underlying and generating the expression pattern observed in microarray experiments is a major challenge. Principal component analysis (PCA) is a linear multivariate statistical method that is regularly employed for that purpose as it provides a reduced-dimensional representation for subsequent study of possible biological processes responding to the particular experimental conditions. Making explicit the data assumptions underlying PCA highlights their lack of biological validity thus making biological interpretation of the principal components problematic. A microarray data representation which enables clear biological interpretation is a desirable analysis tool.

Results: We address this issue by employing the probabilistic interpretation of PCA and proposing alternative linear factor models which are based on refined biological assumptions. A practical study on two well-understood microarray datasets highlights the weakness of PCA and the greater biological interpretability of the linear models we have developed.

Availability: The model estimation routines are currently implemented as Matlab routines and these, as well as data and results reported, are available from the following URL: http://www.dcs.gla.ac.uk/~girolami/lfm/index.html
Breakpoint identification and smoothing of array comparative genomic hybridization data
Authors: Jong Kees , Marchiori Elena , Meijer Gerrit , Vaart A. v. d. , Ylstra Bauke
Published: June 2004

Summary: We describe a tool, called aCGH-Smooth, for the automated identification of breakpoints and smoothing of microarray comparative genomic hybridization (array CGH) data. aCGH-Smooth is written in visual C++, has a user-friendly interface including a visualization of the results and user-defined parameters adapting the performance of data smoothing and breakpoint recognition. aCGH-Smooth can handle array-CGH data generated by all array-CGH platforms: BAC, PAC, cosmid, cDNA and oligo CGH arrays. The tool has been successfully applied to real-life data.

Availability: aCGH-Smooth is free for researchers at academic and non-profit institutions at http://www.few.vu.nl/~vumarray/
CTRD: a fast applet for computing signed translocation distance between genomes
Authors: Feng WangSen , Wang Lusheng , Zhu Daming
Published: June 2004

Summary: CTRD is a software for computing translocation distance between genomes. It takes two genomes as its input and tests whether one genome can be transformed into the other. If possible, it computes the translocation distance between two genomes, and gives the translocation operation serial. We adopt the fastest known O(n2log n) algorithm.

Our contributions include (1) give a necessary and sufficient condition to ensure that one genome can be transformed into the other for translocation operations, and (2) develop a software using the fastest known O(n2log n) algorithm.

Availability: Free from http://www.cs.cityu.edu.hk/~lwang/software/Translocation/ subject to copyright restrictions.
QuickJoin—fast neighbour-joining tree reconstruction
Authors: Mailund Thomas , Pedersen Christian N. S.
Published: June 2004

Summary: We have built a tool for fast construction of very large phylogenetic trees. The tool uses heuristics for speeding up the neighbour-joining algorithm—while still constructing the same tree as the original neighbour-joining algorithm—making it possible to construct trees for 8000 species in <10 min on a single desktop PC. In comparison, the same task takes more than 30 min using the QuickTree neighbour-joining implementation.

Availability: The source code for QuickJoin is available from http://www.birc.dk/Software/QuickJoin under the GNU Public License (GPL).
SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assays
Authors: Niu Tianhua , Hu Zhenjun
Published: June 2004

Summary: Simple, low-cost and accurate genotyping methods for single nucleotide polymorphisms (SNPs) are in high demand in the post-genome-sequencing era. We present a graphical tool called SNPicker, implemented in Java, which significantly facilitates the design of mutagenic endonuclease restriction assays. SNPicker uses the online NEB REBASE to automatically scan for all possible designs of mutagenic primers that can facilitate the picking of mismatched PCR primers to artificially introduce or abolish a restriction site at the target SNP site. We successfully applied SNPicker in designing endonuclease restriction assays for 14 SNPs for the MTHFR gene, the Coagulation Factor II gene and the Coagulation Factor V gene. The SNP assays designed using SNPicker were cross-validated using the MassARRAY technology.

Availability: SNPicker, as a software tool in the Web-based SeqVISTA Suite, is freely available at http://zlab.bu.edu/SeqVISTA/. A tutorial for SNPicker is available at http://zlab.bu.edu/SeqVISTA/manual/SNPicker.htm
BioSilico: an integrated metabolic database system
Authors: Hou Bo Kyeng , Kim Jin Sik , Jun Ji Hoon , Lee Dong-Yup , Kim Yong Wook , Chae Sujin , Roh Mira , In Yong-Ho , Lee Sang Yup
Published: June 2004

Summary: BioSilico is a web-based database system that facilitates the search and analysis of metabolic pathways. Heterogeneous metabolic databases including LIGAND, ENZYME, EcoCyc and MetaCyc are integrated in a systematic way, thereby allowing users to efficiently retrieve the relevant information on enzymes, biochemical compounds and reactions. In addition, it provides well-designed view pages for more detailed summary information. BioSilico is developed as an extensible system with a robust systematic architecture.

Availability: BioSilico database system is accessible at http://biosilico.kaist.ac.kr
Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming
Authors: Sætrom Pål
Published: June 2004

Motivation: Both small interfering RNAs (siRNAs) and antisense oligonucleotides can selectively block gene expression. Although the two methods rely on different cellular mechanisms, these methods share the common property that not all oligonucleotides (oligos) are equally effective. That is, if mRNA target sites are picked at random, many of the antisense or siRNA oligos will not be effective. Algorithms that can reliably predict the efficacy of candidate oligos can greatly reduce the cost of knockdown experiments, but previous attempts to predict the efficacy of antisense oligos have had limited success. Machine learning has not previously been used to predict siRNA efficacy.

Results: We develop a genetic programming based prediction system that shows promising results on both antisense and siRNA efficacy prediction. We train and evaluate our system on a previously published database of antisense efficacies and our own database of siRNA efficacies collected from the literature. The best models gave an overall correlation between predicted and observed efficacy of 0.46 on both antisense and siRNA data. As a comparison, the best correlations of support vector machine classifiers trained on the same data were 0.40 and 0.30, respectively.

Availability: The prediction system uses proprietary hardware and is available for both commercial and strategic academic collaborations. The siRNA database is available upon request.
The impact of flooding on residential property buyer behaviour: an England and Australian comparison of flood affected property
Authors: Eves Chris
Published: June 2004

Since the late 1990's‐2003, there have been a number of severe floods in areas that have not been subject to this level of flooding in earlier times. All these recent floods have resulted in two alarming factors for all property markets. This paper is based on a comprehensive survey of property professionals throughout England and Wales and a study of flood‐affected residential property in Sydney, Australia. It provides details of how exposure to flood events impacts on residential property markets and buyer behaviour associated with flood‐prone property, and will also provide some insight into the implications and possible ramifications of flooding on the construction, finance and insurance of residential property in flood‐affected areas.
Family learning services in UK public libraries: an investigation of current provision and ongoing development
Authors: Kirk Wendy , McMenemy David , Poulter Alan
Published: June 2004

Family learning is now acknowledged by both government and non‐government bodies as being an important aspect of lifelong learning. It is of direct relevance to public libraries, yet little information is available about the specific role the public library can play. The main aim of the paper is to investigate the levels and types of current provision in UK public libraries, and to find out what influences the services on offer. In addition, the research tries to establish whether family learning can be of benefit to libraries, and if current provision meets the key recommendations as outlined in recent reports. The majority of library services surveyed offer family learning on a regular basis. Social inclusion, funding and partnership working are key issues, but their influence does vary between library services. Overall library services seem to be making a valuable contribution to family learning, perhaps more so than the literature suggests.
Accreditation: a tool for organizational change in hospitals?
Authors: Pomey Marie‐Pascale , Contandriopoulos André‐Pierre , François Patrice , Bertrand Dominique
Published: June 2004

Examines the dynamics of change that operated following preparations for accreditation. The study was conducted from May 1995 to October 2001 in a university hospital center in France after the introduction in 1996 of mandatory accreditation. An embedded explanatory case study sought to explore the organizational changes: a theoretical framework for analyzing change was developed; semi‐structured interviews, focus groups, and questionnaires addressed to the hospital's professionals were used and documents were collected; and qualitative and quantitative analyses were carried out. Professionals from clinical and medico‐technical departments participated most. Preparations for accreditation provided an opportunity to reflect non‐hierarchically on the treatment of patients and on the hospital's operational modalities by creating a locus for exchanges and collegial decision making. These preparations also led to giving greater consideration to results of exit surveys and to committing procedures to paper, and were a key opportunity for introducing a continuous quality program.
Screwing diversity out of the workers? Reading diversity
Authors: Jones Deborah
Published: June 2004

“Managing diversity” has emerged as a new and contested vocabulary for addressing issues of difference in organisations. This paper uses a New Zealand case study to exemplify a feminist post‐structuralist reading of managing diversity. The paper argues that a feminist post‐structuralist approach not only addresses feminist theoretical debates about identity, equality and difference, but also opens up new opportunities for practitioners in managing diversity and equal employment opportunities (EEO) to reflect on their own organisational change practice. The paper presents three readings of managing diversity: a discourse of exploitation which provides oppositional readings of managing diversity as a form of human resource management; a discourse of difference, drawing on refusals of managing diversity in accounts from minority group perspectives; and a discourse of equality where EEO practitioners have questioned managing diversity in the context of EEO.
Unravelling Woomera: lip sewing, morphology and dystopia
Authors: Wolfram Cox Julie , Minahan Stella
Published: June 2004

Presents a gendered interpretation of reports of protests in 2000‐2002 among asylum seekers held at Australia's recently closed Woomera Detention Centre, discussing instances of lip sewing that evoked strong reaction from the Australian Government, people and press. Suggests that an Irigarayan gendered reading of lip sewing assists in understanding these examples of self‐harm, supplementing feminist readings of craft, and calling attention to local enactments of gender in both refugee studies and in organizational development and change.
Plan to do it right: and plan for recovery
Authors: Cranage David
Published: June 2004

This paper presents research results and implications in the literature for the last 15 years, and suggests guidelines on how to make the best use of the information to develop strategies that “fit” a service operation. There are considerable benefits of customer satisfaction, loyalty and increased profits from developing strategies to prevent service failures and strategies to successfully implement service recovery.
Activating learning through the lifetime navigator: a tool for reflection
Authors: Winch Alison , Ingram Hadyn
Published: June 2004

This paper emphasizes the importance of learning in the workplace through reflecting after action, as in Kolb's experiential learning cycle. One of the most effective ways of producing insights from personal experience is by keeping a learning log as a means of reflecting upon, and articulating past actions. However, many busy practitioners fail to capitalize on experiential learning opportunities, perhaps because of the time and discipline involved. One way of resolving this problem is to combine the features of a diary and learning log into an integrated learning navigator that provides an accessible framework for reflective learning.
Examining the possible causes of business failure in British public houses
Authors: Pratten J.D.
Published: June 2004

The aim of this study is to identify some of the reasons for the failure of firms, particularly within the licensed trade, so as to offer some advice to assist practitioners. This will be done by a review of the general literature on business failure, looking particularly the small and micro‐business. The trading conditions within the public house sector are examined, and the importance of business knowledge is recognised. In addition, several people who have experienced serious financial problems have offered their comments. These include one owner of a free house who was obliged to close the doors; two tenants and one lessee whose businesses were repossessed; one lessee who suffered serious financial difficulties but survived, and a wholesaler who went into receivership. It is not suggested that these are representative of the trade as a whole. However, an expert in insolvency, with much experience of pub failure, added his views, so that some conclusions could be drawn.
Improving logistics operations across the food industry supply chain
Authors: Aghazadeh Seyed‐Mahmoud
Published: June 2004

This paper explores ways of improving logistics and distribution supply chains within the food retail industry. It includes the concepts of logistics and supply chain as well as the new challenges in the food industry. The paper derives that business‐to‐business and e‐commerce are the ways of the future. The paper discusses the successes and failures of the industry. Its results reveal slow progress in accomplishing the goals of leaner supply chains and easier distribution.
Total relationship and logistics management
Authors: Zineldin Mosad
Published: June 2004

Proposes that many of business and non‐business disciplines have much to offer logistics. Also reveals that there are many theories from other disciplines that are potentially relevant to the examination and study of logistics. States that becoming a more creative logistics manager is not just a matter of practicing new techniques and methodologies, but it is also about being aware of the fundamental differences between the past and current situations. Proposes that managers have to realize that the most important point is having the right type of atmosphere and environment in which employees are encouraged to create, coordinate, and improve the entire business, including facilitating a reliable network of relationships and market channels. States that total quality management (TQM) and total relationship management (TRM) may make a fruitful contribution to the logistics and supply chain management.
Measuring the implications of virtual integration in the new economy
Authors: Carr Patrick , Rainbird Mark , Walters David
Published: June 2004

Addresses the appropriate structuring of the firm's business model in the context of new economy holonic networks. States that this requires some framework for analysing the firm's business model relative to the opportunities offered by those networks and alliances. Proposes that some performance measurement criteria are required that provide a basis for comparing the various options open to the company. Approaches the problem by considering the assessment of the risk that accompanies a decision to outsource a process compared with the alternative option of developing the expertise “in‐house”. Concludes that concepts borrowed from financial management are helpful in this respect and the capital asset pricing model offers a means by which the risk can be assessed.
Numerical analysis of vortex shedding behind a porous square cylinder
Authors: Jue Tswen‐Chyuan
Published: June 2004

Vortex shedding behind a porous square cylinder is studied by a semi‐implicit projection finite element method in this paper. Flow fields over the porous square cylinder with various porosity and Darcy number were calculated to investigate the effects of porous media on Strouhal number, lift and drag coefficients at Re=100, 200 and 250. The global quantities of the shedding flow appear evident variation for Da varied from 10−5 to 10−4. In particular, Strouhal number displays an obvious jump for Da=10−4 at Re=250, due to the variation in flow structure near the cylinder. Larger Darcy number postpones the occurrence of flow fluctuation, and the oscillation flow presents stronger amplitude. However, the flow field and the characteristic values of vortex shedding for Da≤10−6 are almost not changed. For different porosity, time histories of CD and CL look similar. In conclusion, Darcy number demonstrates more influence on the flow field than porosity does.
Numerical studies of physiological pulsatile flow through constricted tube
Authors: Liao Wei , Lee T.S. , Low H.T.
Published: June 2004

A detailed analysis on the characteristics of laminar flow over a bell‐shaped stenosis for a physiological pulsatile flow is presented in this study. In order to have a good understanding of the physiological pulsatile flow, a comparison of the numerical solutions to three types of pulsatile flows, including a physiological flow, an equivalent pulsatile flow and a pure sinusoidal flow, are made in this work. The comparison shows that the flow behavior cannot be properly estimated if the equivalent or simple pulsatile inlet flow is used in the study of flow fields through stenosed arteries instead of actual physiological one. Then the physiological pulsatile flow is further studied by considering the effect of constriction ratio of stenosis, Womersley number and Reynolds number on the flow behavior through stenosed arteries. The analysis shows that the variation of these flow parameters puts significant impacts on the pulsatile flow field for the physiological flow.
What’s Wrong with the HIPC Initiative and What’s Next?
Authors: Gunter Bernhard G.
Published: June 2004

This article reviews the problems of the enhanced HIPC initiative and outlines possible steps towards a more efficient debt and poverty reduction initiative. After brief comments on the rationale for debt relief, it analyses some key issues related to the HIPC initiative’s aim to achieve debt sustainability, describes other fundamental problems of the HIPC framework, and discusses some less known but still crucial flaws of the initiative. It then proceeds with necessary improvements for an efficient debt reduction programme, possible modifications for a revised HIPC initiative, and some suggestions on how to overcome financing constraints. Apart from being in several respects unfair, the current framework is unlikely to permit a lasting exit from unsustainable debt for many HIPCs, and may lead to a decline in traditional development assistance.
Developing Countries’ Position in WTO Agricultural Trade Negotiations
Authors: Matthews Alan
Published: June 2004

Four themes in the developing countries’ position are highlighted. (i) They are seeking meaningful improvements in market access for their agricultural exports. (ii) They have highlighted the asymmetry of current WTO obligations under the Uruguay Round Agreement on Agriculture, and are seeking greater equality of outcomes in the new round. (iii) Meaningful concessions on special and differential treatment will be necessary to satisfy the interests of both exporters and importers, especially on the scope to be allowed for tariff protection to domestic food production. (iv) Innovative and reliable guarantees will need to be provided to the least developed food importers to protect them against the risk of world price volatility.
‘Nectosome’: a novel cytoplasmic vesicle containing nectin in the egg of the sea urchin, Temnopleurus hardwickii
Authors: Kato Koichi H. , Abe Tetsuya , Nakashima Seiko , Matranga Valeria , Zito Francesca , Yokota Yukio
Published: June 2004

Localization of an extracellular matrix protein, Th‐nectin, in the eggs and embryos of the sea urchin Temnopleurus hardwickii was examined by both immunofluorescence and immunoelectron microscopy. The protein is associated with a tubular structure packaged in rod‐shaped vesicles that were designated as ‘nectosomes’. In unfertilized eggs, nectosomes are distributed uniformly throughout the cytoplasm, but after fertilization, they gradually translocate to the cortical zone where they are arranged perpendicular to the plasma membrane. The migration of the nectosomes was strongly inhibited by cytochalasin B, which suggested that microfilaments play an important role in this process. Immunocytochemical and immunoblotting analyses both ascertained that nectin is secreted into the hyaline layer. Some nectosomes remain in the apical cytoplasm of dermal cells until the gastrula stage. Ultrastructural examination revealed that the accumulation of nectosomes in the oocyte cytoplasm begins quite early in oogenesis, concomitant with the accumulation of cortical vesicles.
Developmentally regulated expression and functional role of α7 integrin in the chick embryo
Authors: Zagris Nikolas , Christopoulos Maria , Giakoumaki Anastasia
Published: June 2004

Integrin α7â1 is a specific cellular receptor for laminin. In the present work, we studied the distribution pattern of the α7 subunit by immunofluorescence and immunoprecipitation and the role of the integrin by blocking antibodies in early chick embryos. α7 immunoreactivity was first detectable in the neural plate during neural furrow formation (stage HH5, early neurula, Hamburger & Hamilton 1951) and its expression was upregulated in the neural folds during primary neurulation. The α7 expression domain spanned the entire neural tube by stage HH8 (4 somites), and was then downregulated and confined to the neuroepithelial cells in the germinal region near the lumen and the ventrolateral margins of the neural tube in embryos by the onset of stage HH17 (29 somites). Expression of α7 in the neural tube was transient suggesting that α7 functions during neural tube closure and axon guidance and may not be required for neuronal differentiation or for the maintenance of the differentiated cell types. α7 immunoreactivity was strong in the newly formed epithelial somites, although this expression was restricted only to the myotome in the mature somites. The most intense α7 immunoreactivity was detectable in the paired heart primordia and the endoderm apposing the heart primordia in embryos at stage HH8. In the developing heart, α7 immunoreactivity was: (i) intense in the myocardium; (ii) milder in the endocardial cushions of the ventricle; (iii) intense in the sinus venosus; (iv) distinct in the associated blood vessels; and (v) undetectable in the dorsal mesocardium of embryos at stage HH17. Inhibition of function of α7 by blocking antibodies showed that α7 integrin–laminin signaling may play a critical role in tissue organization of the neural plate and neural tube closure, in tissue morphogenesis of the heart tube but not in the directional migration of pre‐cardiac cells, and in somite epithelialization but not in segment formation in presomitic mesoderm. In embryos treated with α7 antibody, the formation of median somites in place of a notochord was intriguing and suggested that α7 integrin–laminin signaling may have played a role in segment re‐specification in the mesoderm.
Inequality, Democracy, and Persistence: Is There a Political Kuznets Curve?
Authors: Chong Alberto
Published: June 2004

The aim of this paper is to provide comprehensive empirical evidence on recent theories that link democracy and income inequality for the period 1960–1997. In simple cross‐country regressions I find a non‐monotonic link between democracy and inequality when using ordinary least squares, instrumental variables, and Eusufzai tests. I also employ dynamic panel data techniques, which control for potential simultaneity and heterogeneity problems. I also find support for the existence of apolitical Kuznets curve. Moreover, it appears that income inequality is unconditionally persistent. Results are robust to different democracy proxies when sensitivity analysis is applied.
Surface of Young Jupiter Family Comet 81P/Wild 2: View from the Stardust Spacecraft
Authors: Brownlee Donald E. , Horz Friedrich , Newburn Ray L. , Zolensky Michael , Duxbury Thomas C. , Sandford Scott , Sekanina Zdenek , Tsou Peter , Hanner Martha S. , Clark Benton C. , Green Simon F. , Kissel Jochen
Published: June 2004

Images taken by the Stardust mission during its flyby of 81P/Wild 2 show the comet to be a 5-kilometer oblate body covered with remarkable topographic features, including unusual circular features that appear to be impact craters. The presence of high-angle slopes shows that the surface is cohesive and self-supporting. The comet does not appear to be a rubble pile, and its rounded shape is not directly consistent with the comet being a fragment of a larger body. The surface is active and yet it retains ancient terrain. Wild 2 appears to be in the early stages of its degradation phase as a small volatile-rich body in the inner solar system.
Salmonella
Modulates Vesicular Traffic by Altering Phosphoinositide Metabolism
Authors: Hernandez Lorraine D. , Hueffer Karsten , Wenk Markus R. , Galán Jorge E.
Published: June 2004

Salmonella enterica
, the cause of food poisoning and typhoid fever, induces actin cytoskeleton rearrangements and membrane ruffling to gain access into nonphagocytic cells, where it can replicate and avoid innate immune defenses. Here, we found that SopB, a phosphoinositide phosphatase that is delivered into host cells by a type III secretion system, was essential for the establishment of
Salmonella
's intracellular replicative niche. SopB mediated the formation of spacious phagosomes following bacterial entry and was responsible for maintaining high levels of phosphatidylinositol-three-phosphate [PtdIns(3)P] in the membrane of the bacteria-containing vacuoles. Absence of SopB caused a significant defect in the maturation of the
Salmonella
-containing vacuole and impaired bacterial intracellular growth.
Dust Measurements in the Coma of Comet 81P/Wild 2 by the Dust Flux Monitor Instrument
Authors: Tuzzolino Anthony J. , Economou Thanasis E. , Clark Ben C. , Tsou Peter , Brownlee Donald E. , Green Simon F. , McDonnell J. A. M. , McBride Neil , Colwell Melusine T. S. H.
Published: June 2004

We present measurements of the dust particle flux and mass distribution from the Stardust Dust Flux Monitor Instrument (DFMI) throughout the flyby of comet 81P/Wild 2. In the particle mass regime from 10
–14
to 10
–7
kilograms, the spacecraft encountered regions of intense swarms of particles, together with bursts of activity corresponding to clouds of particles only a few hundred meters across. This fine-scale structure can be explained by particle fragmentation. We estimate that 2800 ± 500 particles of diameter 15 micrometers or larger impacted the aerogel collectors, the largest being ∼6 × 10
–7
kilograms, which dominates the total collected mass.
Dynamics of Single mRNPs in Nuclei of Living Cells
Authors: Shav-Tal Yaron , Darzacq Xavier , Shenoy Shailesh M. , Fusco Dahlene , Janicki Susan M. , Spector David L. , Singer Robert H.
Published: June 2004

Understanding gene expression requires the ability to follow the fate of individual molecules. Here we use a cellular system for monitoring messenger RNA (mRNA)expression to characterize the movement in real time of single mRNA-protein complexes (mRNPs) in the nucleus of living mammalian cells. This mobility was not directed but was governed by simple diffusion. Some mRNPs were partially corralled throughout the nonhomogenous nuclear environment, but no accumulation at subnuclear domains was observed. Following energy deprivation, energy-independent motion of mRNPs was observed in a highly ATP-dependent nuclear environment; movements were constrained to chromatin-poor domains and excluded by newly formed chromatin barriers. This observation resolves a controversy, showing that the energetic requirements of nuclear mRNP trafficking are consistent with a diffusional model.
Regulation of the Ysa Type III Secretion System ofYersinia enterocoliticaby YsaE/SycB and YsrS/YsrR
Authors: Walker Kimberly A. , Miller Virginia L.
Published: June 2004

Yersinia enterocoliticabiovar 1B contains two type III secretion systems (TTSSs), the plasmid-encoded Ysc-Yop system and the chromosomally encoded Ysa-Ysp system. Proteins secreted from the Ysa TTSS (Ysps) have only been detected in vitro when cells are cultured at 26°C in a high-NaCl medium. However, the exact role of the Ysa TTSS is unclear. Thus, investigations into the regulation of this system may help elucidate the role of the Ysps during the life cycle ofY. enterocolitica. Here we present evidence that the AraC-like regulator YsaE acts together with the chaperone SycB to regulate transcription of thesycByspBCDAoperon, a phenomenon similar to that seen in the closely relatedSalmonellaSPI-1 andShigella flexneriMxi-Spa-Ipa TTSSs. Deletion of eithersycBorysaEresults in a twofold reduction in the activity of asycB-lacZfusion compared to the wild type. In a reconstitutedEscherichia colisystem, transcription ofsycBwas activated sixfold only when both YsaE and SycB were present, demonstrating that they are necessary for activation.ysrRandysrSare located near theysagenes and encode a putative two-component regulatory system. Mutations in either gene indicated that both YsrR and YsrS were required for secretion of Ysps. In addition, transcription fromsycB-lacZandysaE-lacZfusions was decreased 6.5- and 25-fold, respectively, in theysrSmutant compared to the wild type. Furthermore, in the absence of NaCl, the activity ofysaE-lacZwas reduced 25-fold in the wild-type and ΔysrSstrains, indicating that YsrS is probably required for the salt-dependent expression of theysalocus. These results suggest that the putative two-component system YsrRS may be a key element in the regulatory cascade for the Ysa TTSS.
Free and Hemophore-Bound Heme Acquisitions through the Outer Membrane Receptor HasR Have Different Requirements for the TonB-ExbB-ExbD Complex
Authors: Létoffé Sylvie , Delepelaire Philippe , Wandersman Cécile
Published: June 2004

Many gram-negative bacteria have specific outer membrane receptors for free heme, hemoproteins, and hemophores. Heme is a major iron source and is taken up intact, whereas hemoproteins and hemophores are not transported: the iron-containing molecule has to be stripped off at the cell surface, with only the heme moiety being taken up. TheSerratia marcescenshemophore-specific outer membrane receptor HasR can transport either heme itself or heme bound to the hemophore HasA. This second mechanism is much more efficient and requires a higher TonB-ExbB-ExbD (TonB complex) concentration than does free or hemoglobin-bound heme uptake. This requirement for more of the TonB complex is associated with a higher energy requirement. Indeed, the sensitivity of heme-hemophore uptake to the protonophore carbonyl cyanidem-chlorophenyl hydrazone is higher than that of heme uptake from hemoglobin. We show that a higher TonB complex concentration is required for hemophore dissociation from the receptor. This dissociation is concomitant with heme uptake. We propose that increasing the TonB complex concentration drives more energy to the outer membrane receptor and speeds up the release of empty hemophores, which, if they remained on receptors, would inhibit heme transport.
The
fabM
Gene Product of
Streptococcus mutans
Is Responsible for the Synthesis of Monounsaturated Fatty Acids and Is Necessary for Survival at Low pH
Authors: Fozo Elizabeth M. , Quivey Robert G.
Published: June 2004

Previously, it has been demonstrated that the membrane fatty acid composition of
Streptococcus mutans
is affected by growth pH (E. M. Fozo and R. G. Quivey, Jr., Appl. Environ. Microbiol.
70:
929-936, 2004; R. G. Quivey, Jr., R. Faustoferri, K. Monahan, and R. Marquis, FEMS Microbiol. Lett.
189:
89-92, 2000). Specifically, the proportion of monounsaturated fatty acids increases when the organism is grown in acidic environments; if the shift to increased monounsaturated fatty acids is blocked by the addition of a fatty acid biosynthesis inhibitor, the organism is rendered more acid sensitive (E. M. Fozo and R. G. Quivey, Jr., Appl. Environ. Microbiol.
70:
929-936, 2004). Recently, work with
Streptococcus pneumoniae
has identified a novel enzyme, FabM, responsible for the production of monounsaturated fatty acids (H. Marrakchi, K. H. Choi, and C. O. Rock, J. Biol. Chem.
277:
44809-44816, 2002). Using the published
S. pneumoniae
sequence, a putative FabM was identified in the
S. mutans
strain UA159. We generated a
fabM
strain that does not produce unsaturated fatty acids as determined by gas chromatography of fatty acid methyl esters. The mutant strain was extremely sensitive to low pH in comparison to the wild type; however, the acid-sensitive phenotype was relieved by growth in the presence of long-chain monounsaturated fatty acids or through genetic complementation. The strain exhibited reduced glycolytic capability and altered glucose-PTS activity. In addition, the altered membrane composition was more impermeable to protons and did not maintain a normal ΔpH. The results suggest that altered membrane composition can significantly affect the acid survival capabilities, as well as several enzymatic activities, of
S. mutans
.
Extracellular Proteolytic Activity Plays a Central Role in Swarming Motility inBacillus subtilis
Authors: Bindel Connelly Mariah , Young Glenn M. , Sloma Alan
Published: June 2004

Natural isolates ofBacillus subtilisexhibit a robust multicellular behavior known as swarming. A form of motility, swarming is characterized by a rapid, coordinated progression of a bacterial population across a surface. As a collective bacterial process, swarming is often associated with biofilm formation and has been linked to virulence factor expression in pathogenic bacteria. While the swarming phenotype has been well documented forBacillusspecies, an understanding of the molecular mechanisms responsible remains largely isolated to gram-negative bacteria. To better understand how swarming is controlled in members of the genusBacillus, we investigated the effect of a series of gene deletions on swarm motility. Our analysis revealed that a strain deficient for the production of surfactin and extracellular proteolytic activity did not swarm or form biofilm. While it is known that surfactin, a lipoprotein surfactant, functions in swarming motility by reducing surface tension, this is the first report demonstrating that general extracellular protease activity also has an important function. These results not only help to define the factors involved in eliciting swarm migration but support the idea that swarming and biofilm formation may have overlapping control mechanisms.
Altering the Substrate Specificity of Polyhydroxyalkanoate Synthase 1 Derived from
Pseudomonas putida
GPo1 by Localized Semirandom Mutagenesis
Authors: Sheu Der-Shyan , Lee Chia-Yin
Published: June 2004

The substrate specificity of polyhydroxyalkanoate (PHA) synthase 1 (PhaC1

Pp

, class II) from
Pseudomonas putida
GPo1 (formerly known as
Pseudomonas oleovorans
GPo1) was successfully altered by localized semirandom mutagenesis. The enzyme evolution system introduces multiple point mutations, designed on the basis of the conserved regions of the PHA synthase family, by using PCR-based gene fragmentation with degenerate primers and a reassembly PCR. According to the opaqueness of the colony, indicating the accumulation of large amounts of PHA granules in the cells, 13 PHA-accumulating candidates were screened from a mutant library, with
Pseudomonas putida
GPp104 PHA
−
as the host. The in vivo substrate specificity of five candidates, L1-6, D7-47, PS-A2, PS-C2, and PS-E1, was evaluated by the heterologous expression in
Ralstonia eutropha
PHB
−
4 supplemented with octanoate. Notably, the amount of 3-hydroxybutyrate (short-chain-length [SCL] 3-hydroxyalkanoate [3-HA] unit) was drastically increased in recombinants that expressed evolved mutant enzymes L1-6, PS-A2, PS-C2, and PS-E1 (up to 60, 36, 50, and 49 mol%, respectively), relative to the amount in the wild type (12 mol%). Evolved enzyme PS-E1, in which 14 amino acids had been changed and which was heterologously expressed in
R. eutropha
PHB
−
4, not only exhibited broad substrate specificity (49 mol% SCL 3-HA and 51 mol% medium-chain-length [MCL] 3-HA) but also conferred the highest PHA production (45% dry weight) among the candidates. The 3-HA and MCL 3-HA units of the PHA produced by
R. eutropha
PHB
−
4/pPS-E1 were randomly copolymerized in a single polymer chain, as analytically confirmed by acetone fractionation and the
13
C nuclear magnetic resonance spectrum.
Evolutionary and Functional Relationships among the Nontypeable
Haemophilus influenzae
HMW Family of Adhesins
Authors: Buscher Amy Z. , Burmeister Katie , Barenkamp Stephen J. , St. Geme Joseph W.
Published: June 2004

Nontypeable
Haemophilus influenzae
(NTHi) is a common cause of localized respiratory tract disease and initiates infection by colonizing the nasopharynx. Approximately 75 to 80% of NTHi clinical isolates produce proteins that belong to the HMW family of adhesins, which are believed to facilitate colonization. The prototype HMW adhesins are designated HMW1 and HMW2 and were identified in NTHi strain 12. HMW1 and HMW2 are 71% identical and 80% similar overall, yet display differing cellular binding specificities. In the present study we set out to define more clearly the relationships between HMW1 and HMW2 and other members of the HMW family of adhesins. PCR analysis of 49 epidemiologically distinct isolates revealed that all strains possessing
hmw
genes as determined by Southern analysis contain two
hmw
loci in conserved, unlinked physical locations on the chromosome. Functional analysis of the HMW adhesins produced by three unrelated strains demonstrated that each isolate possesses one protein with HMW1-like adherence properties and another with HMW2-like adherence properties. These findings suggest that the
hmw1
and
hmw2
loci may have arisen via a gene duplication event in an ancestral strain. In addition, they support the hypothesis that the distinct binding specificities of HMW1 and HMW2 emerged early and have persisted over time, suggesting an ongoing selective advantage.
Heterologous Expression and Purification of Active Divercin V41, a Class IIa Bacteriocin Encoded by a Synthetic Gene in
Escherichia coli
Authors: Richard Christelle , Drider Djamel , Elmorjani Khalil , Marion Didier , Prévost Hervé
Published: June 2004

Divercin V41, a class IIa bacteriocin with strong antilisterial activity, is produced by
Carnobacterium divergens
V41. To express a recombinant version of divercin V41, we constructed a synthetic gene that encodes the mature divercin V41 peptide and then overexpressed the gene in pET-32b by using the T7 RNA polymerase promoter in the
Escherichia coli
Origami (DE3)(pLysS) strain. The DvnRV41 peptide was expressed as a translational fusion protein with thioredoxin and accumulated in the cell cytoplasm in a soluble anti-
Listeria
active form. The fusion protein was then purified and cleaved to obtain pure, soluble, folded DvnRV41 (462 μg per 20 ml of culture). This paper describes the first design of a synthetic bacteriocin gene and the first bacteriocin expressed in the
E. coli
cytoplasm.