bluuebunny/crossref_metadata_2025 huggingface dataset:
Parallel deficits in linear growth and mental development in low-income Mexican infants in the second year of life
Authors: Fernald Lia C , Neufeld Lynnette M , Barton Lauren R , Schnaas Lourdes , Rivera Juan , Gertler Paul J
Published: March 2006

Objective

To explore anthropometric indicators and mental development in very-low-income children in the second year of life.

Design

Cross-sectional survey.

Setting

Low-income areas (income <20th percentile) in semi-urban Mexico (defined as towns or cities with 2500–50 000 inhabitants).

Subjects

Eight hundred and ninety-six children aged 12.5–23.5 months surveyed from September to December 2001.

Methods

Questionnaire survey and anthropometric survey of households. Multivariate regression models evaluated differences across age in anthropometry (height-for-ageZ-score (HAZ) and weight-for-heightZ-score) and cognitive function (Mental Development Index (MDI) of the Bayley Scales of Infant Development) while controlling for socio-economic and parental characteristics.

Results

There was a significant decline in HAZ and in age-adjusted MDI score across the second year of life. Although the children showed MDI scores close to the mean, normed US values at 13–14 months, the scores were significantly lower than expected in older children (P< 0.0001), even after controlling for socio-economic status and parental characteristics. At 13–14 months, only 3% of children received scores below 70 (less than minus two standard deviations), whereas by 19–20 months, almost 17% of children were performing below this level. No socio-economic or parental characteristics were significant predictors of HAZ or MDI.

Conclusions

Parallel deficits are evident in both height-for-age and cognitive functioning during the second year of life in low-income Mexican infants. The consistency of these growth and development findings further stresses the need for targeted interventions to reduce the vulnerability of low-income Mexican children very early in life.
Information selectivity in decision making by younger and older adults
Authors: Rafaely Vered , Dror Itiel E. , Remington Bob
Published: March 2006

Past research has demonstrated that older adults are more likely than younger adults to exhibit information selectivity in decision making. Two alternative explanations have been proposed to account for this age difference. One explanation attributes the increase in information selectivity to older adults' reliance on prior knowledge, whereas the other explanation suggests that it reflects reduced information processing capacity. The aim of this research was to explore the latter explanation by controlling for experiential factors and varying the cognitive demands involved in decision making. Specifically, participants were faced with unfamiliar decision problems, and had to base their decisions on the available information in order to reach a desired goal. In Experiment 1 younger and older participants were required to play a game involving chance. The outcome payoff was varied between three conditions (approach, avoidance, and control). The results indicated that both the younger and the older participants based their decisions on payoff, though the older participants did so to a lesser extent. In Experiment 2 younger and older participants performed a similar decision task but with higher cognitive demands. Specifically, the decision‐making task included two dimensions of information, outcome probability and outcome payoff. The results showed that the younger participants based their decisions on probability and payoff whereas the older participants based their decisions on probability alone. In Experiment 3 younger and older participants made decisions in a sale context and received instructional cue to incorporate payoff information in their decisions. As before, the younger participants utilized probability and payoff, whereas the older participants based their decisions only on probability information. The findings are discussed in terms of age differences in information‐processing capacity, metacognition, motivation, and goal‐setting.
A cross‐cultural study of environmental belief structures in USA, Japan, Mexico, and Peru
Authors: Bechtel Robert B. , Corral‐Verdugo Victor , Asai Masaaki , Riesle Alvaro Gonzalez
Published: March 2006

Throughout history, the way in which people conceive nature/human relationships has dramatically changed, and different cultures also have divergent notions regarding the role humans play in nature. In Western societies a “new environmental paradigm” (NEP) of ecological nature has apparently replaced the old “human exception paradigm” (HEP), which conceives of humans as being superior and apart from nature. Previous research has shown that, in those societies, a marked dichotomy exist between these two apparently contradictory paradigms, meaning that people who accept the NEP reject the HEP. Countries other than Western ones also exhibit a bias towards the ecological paradigm; however, their world‐views are not necessarily dualistic, since they may adhere to the NEP and, simultaneously, believe that human beings are “special.” This study compares world‐views in four different countries. Responses of 1358 undergraduates from USA, Japan, Mexico, and Peru to the HEP and the NEP scale were analysed to see if they confirmed three factors previously found: (1) a vision of separation from nature (HEP), (2) a necessary “balance” between human needs and nature preservation, and (3) the need to impose “limits” on the human impact on nature. This trifactorial structure was tested using confirmatory factor analysis. USA students exhibited two dimensions (HEP‐NEP) and the other samples showed the expected three factors, although they intercorrelated differentially, depending on the national sample. In all samples “balance” and “limits” were positively correlated. In the Peruvian and Japanese samples the HEP and “balance” were negatively correlated while the USA sample produced a negative covariance between HEP and NEP. In the Japanese sample HEP and “limits” were uncorrelated but in Peru these factors covaried negatively, while in the Mexican sample they were positively correlated. The HEP‐NEP two‐factor structure would seem to be limited to Western nations. More countries need to be measured.
Geographic region effects on adolescent physical self: An exploratory study
Authors: Maïano Christophe , Ninot Grégory , Stephan Yannick , Morin Alexandre J. S. , Florent Jean‐François , Vallée Philippe
Published: March 2006

The objectives of this exploratory study were to examine gender differences in physical self‐concept, and the influence of geographic place of residence on both adolescents' physical self‐concept and gender differences in physical self‐concept. The Physical Self Inventory was used to measure physical self‐perceptions and global self‐esteem. Participants were 323 boys and 282 girls living in the North or South of France. First a Mann‐Whitney U test was used to assess gender differences and the influence of geographic region differences on physical self‐perceptions (physical self‐worth, physical condition, sport competence, attractive body, physical strength) and global self‐esteem. Then a Kruskal‐Wallis ANOVA for ranked data was used to assess geographic region influence on boys' and girls' physical self‐concept and global self‐esteem. The results showed that not only did boys have significantly higher physical self scores (on all scales) and global self‐esteem than girls, but also that adolescents from the North of France had higher physical self scores (on all scales) and global self‐esteem than adolescents from the South. Moreover, many differences were found between boys and girls on physical self scores (on all scales) and global self‐esteem according to their geographic place of residence. The main results showed that girls from the South had lower scores on the attractive body, physical strength, physical self‐worth, and global self‐esteem scales than all other adolescents, and that boys from the South had lower scores on the attractive body and global self‐esteem scales than did boys and girls from the North.
Citizenship Practices and Urban Governance in European Cities
Authors: Garcia Marisol
Published: March 2006

This paper presents the theoretical background against which the relation between citizenship and governance can be explored in European cities. The article revisits the link between the social and political dimensions of citizenship and the public sphere, emphasising the participatory paradigm. Moreover, it examines some current citizenship and governance practices occurring in European cities and neighbourhoods. It argues that the practice of citizenship has been challenged in European cities not only by the globalising forces which have contributed to the increasing numbers of denizens, exploited immigrants and the poor, but also by the implicit changes in collective understanding of social justice. Finally, it critically discusses the term 'urban citizenship' as capturing local participation of citizens in the pursuit of welfare, recognition and against neo-liberal policies. Instead, the author proposes the term 'urban and regional forms of citizenship' substantiating the continuous relevance of territorial citizenship in the context of multilevel governance.
Padding the Bunker: Strategies of Middle-class Disaffiliation and Colonisation in the City
Authors: Atkinson Rowland
Published: March 2006

Residential segregation has often been seen as a significant and intractable urban problem. Empirical analyses have focused on the clustering and social impacts of concentrated deprivation and ethnicity, while explanations of segregation have generally looked at the role of income, housing markets, and wider social and institutional discrimination. This paper attempts to build on such preoccupations by considering current urban transformations to theorise the recent middle-class colonisation of cities in the UK. Segregation is seen here not just as the concentration of an urban poor or particular ethnic groups, but also as representing an extended spatial bifurcation between the choices of the affluent to withdraw into increasingly insulated enclaves, while places of poverty contain populations away from this increasingly fearful, yet tendentiously urbanising, middle class. Using a series of case studies, a typology is developed of increasing disaffiliation as a prelude to a further debate on the feasibility of encouraging social diversity in the city.
The Carpathian Folk Fairs and the Origins of National Consciousness among Romanians
Authors: Geană Gheorghiţă
Published: March 2006

A series of time-honoured regular folk fairs take place in the Carpathian Mountains that are mainly economic but also socio-cultural events. The participants come from all the three Romanian principalities—Moldavia, Wallachia, and Transylvania, that is, from all the historical provinces of the Romanian state as constituted after the First World War. These folk fairs are “two-land fairs” in the Eastern and Southern Carpathians and “three-land fairs” where all three provinces converge, as in the district of Vrancea. Over the centuries, such fairs advanced the perception that participants spoke the same language, shared the same religious belief, and belonged to the sameneam, that is, implicitly to the same territory (the wordneambeing a vernacular term for “kin group,” but extensible to the notion of “people” and “nation”). In short, the folk fairs contributed to awakening Romanian national consciousness. Such evidence challenges modernist theory, according to which national consciousness should have arisen with the bourgeoise elite, who should have inculcated it into the public mind.
Comparing the predictive validity of reasoning tests and national end of Key Stage 2 tests: which tests are the ‘best’?
Authors: Strand Steve
Published: March 2006

This article describes a longitudinal analysis of a nationally representative cohort of over 80,000 pupils in England who completed both national end of Key Stage 2 (KS2) tests and the Cognitive Abilities Test (CAT) at age 11 in 1997, national end of Key Stage 3 (KS3) tests at age 14 in summer 2000 and General Certificate of Secondary Education (GCSE) and other public examinations at age 16 in summer 2002. The CAT had significantly higher correlations with subsequent KS3 and GCSE outcomes than did KS2 test points scores. However, multiple regression analyses indicated that a combination of CAT and KS2 test scores gave the best prediction of future KS3\GCSE outcomes. The article argues that measures of both pupils' general transferable learning abilities, and measures of specific curricular attainments at the end of primary school have unique and distinct value at the start of the secondary phase. The article discusses some practical ways in which the different types of assessment data can be used within the secondary school.
‘Why do we have to do this?’ Primary trainee teachers' views of a subject knowledge audit in mathematics
Authors: Murphy Carol
Published: March 2006

This paper examines theoretical and empirical evidence related to primary teachers' subject knowledge in mathematics and considers the relevance of an audit of higher‐level subject knowledge to the subject knowledge required for teaching primary mathematics. Questionnaires and interviews were carried out to determine the views of generalist primary trainee teachers. Their views suggest that an audit of higher‐level subject knowledge may be seen as relevant to the teaching of primary mathematics due to increased confidence levels. There is little evidence to suggest that the audit is supporting the trainee teachers in developing a connected view of mathematics that may be more indicative of an effective teacher.
The influence of schooling on the aspirations of young people with special educational needs
Authors: Casey Lorraine , Davies Peter , Kalambouka Afroditi , Nelson Nick , Boyle Bill
Published: March 2006

The authors investigate the effect of schooling on the aspirations of young people designated as having mild learning difficulties (MLD) or emotional and behavioural difficulties (EBD) in the first large‐scale study of its kind in England. Data were collected from parents and their 15/16 year‐old children in the final year of their compulsory schooling in schools. The results indicate on average a positive effect of mainstream schooling on the aspirations of these pupils with the caveat that these benefits are more likely to accrue to pupils whose parents are in higher status occupations. In their conclusions the authors discuss the implications of these results for education policy in the context of local management of schools.
School Internet use, youth and risk: a social‐cultural study of the relation between staff views of online dangers and students' ages in UK schools
Authors: Hope Andrew
Published: March 2006

Internet access has recently been introduced into over 30,000 schools in the UK. While web provision has been heralded by some as an educational panacea, it is also recognised that there are dangers inherent in school Internet use. Adopting the cultural risk perspective, drawing upon a social‐cultural analysis of Internet regulation and utilising the concepts of liminality and ‘otherness’, this article explores staff Internet risk perspectives. While staff expressed concern about online pornography, hate‐sites, bomb/drug making websites, electronic communication, security issues and copyright violation, interpretations as to who was at risk varied with student age. Younger students' Internet activities were interpreted with reference to narratives of innocence, whilst the inappropriate online activities of youths were labelled as ‘dangerous’. In conclusion, it is argued that a distinction needs to be drawn between risks arising from liminality and those associated with ‘otherness’.
Binocular Coordination of the Eyes during Reading: Word Frequency and Case Alternation Affect Fixation Duration but not Fixation Disparity
Authors: Juhasz Barbara J. , Liversedge Simon P. , White Sarah J. , Rayner Keith
Published: March 2006

This experiment investigated whether properties of the text being read affect binocular coordination of the eyes during reading. Readers’ binocular eye movements were recorded while they read sentences that contained high- and low-frequency words. In addition, half of the sentences were presented in normal case, and half were presented in alternating case (i.e., AlTeRnAtInG cAsE). Past research has suggested that the visual system tolerates less binocular fixation disparity with alternating than with normal case (Heller & Radach, 1999). While both word frequency and alternating case produced large effects on fixation durations on the target word, neither manipulation affected the magnitude of fixation disparity. It is concluded that linguistic and visual properties of the text being read do not influence binocular coordination of the eyes during reading. Additional analyses also showed no difference in fixation disparity between reading and a nonlinguistic task. Implications of these results for split-fovea models of reading are discussed.
Generalization Decrement in Human Contingency Learning
Authors: Wheeler Daniel S. , Amundson Jeffrey C. , Miller Ralph R.
Published: March 2006

An association between a cue and an outcome will generalize to a similar novel cue to some extent, but not completely. Learning theorists refer to the discrepancy between responding elicited by the original cue and the novel cue as a generalization decrement. Two experiments used a contingency learning task with human participants to compare the size of a generalization decrement between configurations of cues that were altered by adding or subtracting compositional elements. The results suggest that adding elements to a configuration can produce a generalization decrement, but removing elements produces a more robust generalization decrement. Furthermore, the generalization decrement caused by adding elements was not likely to be caused by competing orienting responses. The results are used to contrast Pearce's (1987, 1994) and Wagner's (2003) models of stimulus generalization.
Piezoresistive sensing of bistable micro mechanism state
Authors: Anderson Jeffrey K , Howell Larry L , Wittwer Jonathan W , McLain Timothy W
Published: March 2006

The objective of this work is to demonstrate the feasibility of on-chip sensing of bistable mechanism state using the piezoresistive properties of polysilicon, thus eliminating the need for electrical contacts. Changes in position are detected by observing changes in resistance across the mechanism. Sensing the state of bistable mechanisms is critical for various applications, including high-acceleration sensing arrays and alternative forms of nonvolatile memory. A fully compliant bistable micro mechanism was designed, fabricated and tested to demonstrate the feasibility of this sensing technique. Testing results from two fabrication processes, SUMMiT IV and MUMPs, are presented. The SUMMiT mechanism was then integrated into various Wheatstone bridge configurations to investigate their potential advantages and to demonstrate various design layouts. Repeatable and detectable results were found with independent mechanisms and with those integrated into Wheatstone bridges.
Alexander polynomials of equivariant slice and ribbon knots in 𝑆³
Authors: Davis James , Naik Swatee
Published: March 2006

This paper gives an algebraic characterization of Alexander polynomials of equivariant ribbon knots and a factorization condition satisfied by Alexander polynomials of equivariant slice knots.
Layers and spikes in non-homogeneous bistable reaction-diffusion equations
Authors: Ai Shangbing , Chen Xinfu , Hastings Stuart
Published: March 2006

We study

ε
2

u
¨

=
f
(
u
,
x
)
=
A

u

(
1
−
u
)

(
ϕ
−
u
)

\varepsilon ^2\ddot {u}=f(u,x)=A\, u\, (1-u)\,(\phi -u)

, where

A
=
A
(
u
,
x
)
>
0

A=A(u,x)>0

,

ϕ
=
ϕ
(
x
)
∈
(
0
,
1
)

\phi =\phi (x)\in (0,1)

, and

ε
>
0

\varepsilon >0

is sufficiently small, on an interval

[
0
,
L
]

[0,L]

with boundary conditions

u
˙

=
0

\dot {u}=0

at

x
=
0
,
L

x=0,L

. All solutions with an

ε
\varepsilon

independent number of oscillations are analyzed. Existence of complicated patterns of layers and spikes is proved, and their Morse index is determined. It is observed that the results extend to
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="f equals upper A left-parenthesis u comma x right-parenthesis left-parenthesis u minus phi Subscript minus Baseline right-parenthesis left-parenthesis u minus phi right-parenthesis left-parenthesis u minus phi Subscript plus Baseline right-parenthesis">

f
=
A
(
u
,
x
)

(
u
−

ϕ
−

)

(
u
−
ϕ
)

(
u
−

ϕ
+

)

f=A(u,x)\; (u-\phi _-)\,(u-\phi )\,(u-\phi _+)

with

ϕ
−

(
x
)
>
ϕ
(
x
)
>

ϕ
+

(
x
)

\phi _-(x)>\phi (x)>\phi _+(x)

and also to an infinite interval.
Moduli of curves and spin structures via algebraic geometry
Authors: Bini Gilberto , Fontanari Claudio
Published: March 2006

Here we investigate some birational properties of two collections of moduli spaces, namely moduli spaces of (pointed) stable curves and of (pointed) spin curves. In particular, we focus on vanishings of Hodge numbers of type

(
p
,
0
)

(p,0)

and on computations of Kodaira dimension. Our methods are purely algebro-geometric and rely on an induction argument on the number of marked points and the genus of the curves.
Maximal families of Gorenstein algebras
Authors: Kleppe Jan
Published: March 2006

The purpose of this paper is to study maximal irreducible families of Gorenstein quotients of a polynomial ring

R
R

. Let

GradAlg
H

⁡
(
R
)

\operatorname {GradAlg}^H(R)

be the scheme parametrizing graded quotients of

R
R

with Hilbert function

H
H

. We prove there is a close relationship between the irreducible components of

GradAlg
H

⁡
(
R
)

\operatorname {GradAlg}^H(R)

, whose general member is a Gorenstein codimension

(
c
+
1
)

(c+1)

quotient, and the irreducible components of

GradAlg

H
′

⁡
(
R
)

\operatorname {GradAlg}^{H’}(R)

, whose general member

B
B

is a codimension

c
c

Cohen-Macaulay algebra of Hilbert function

H
′

H’

related to

H
H

. If the Castelnuovo-Mumford regularity of the Gorenstein quotient is large compared to the Castelnuovo-Mumford regularity of

B
B

, this relationship actually determines a well-defined injective mapping from such “Cohen-Macaulay” components of

GradAlg

H
′

⁡
(
R
)

\operatorname {GradAlg}^{H’}(R)

to “Gorenstein” components of

GradAlg

H

⁡
(
R
)

\operatorname {GradAlg}^{H}(R)

, in which generically smooth components correspond. Moreover the dimension of the “Gorenstein” components is computed in terms of the dimension of the corresponding “Cohen-Macaulay” component and a sum of two invariants of

B
B

. Using linkage by a complete intersection we show how to compute these invariants. Linkage also turns out to be quite effective in verifying the assumptions which appear in a generalization of the main theorem.
Effective cones of quotients of moduli spaces of stable 𝑛-pointed curves of genus zero
Authors: Rulla William
Published: March 2006

Let

X
n

:=

M
¯

0
,
n

X_n := \overline {M}_{0,n}

, the moduli space of

n
n

-pointed stable genus zero curves, and let

X

n
,
m

X_{n,m}

be the quotient of

X
n

X_n

by the action of

S

n
−
m

\mathcal {S}_{n-m}

on the last

n
−
m

n-m

marked points. The cones of effective divisors

N
E

¯

1

(

X

n
,
m

)

\overline {NE}^1(X_{n,m})

,

m
=
0
,
1
,
2

m = 0,1,2

, are calculated. Using this, upper bounds for the cones

M
o
v
(

X

n
,
m

)

Mov(X_{n,m})

generated by divisors with moving linear systems are calculated,

m
=
0
,
1

m = 0,1

, along with the induced bounds on the cones of ample divisors of

M
¯

g

\overline {M}_g

and

M
¯

g
,
1

\overline {M}_{g,1}

. As an application, the cone

N
E

¯

1

(

M
¯

2
,
1

)

\overline {NE}^1(\overline {M}_{2,1})

is analyzed in detail.
Projective Fraïssé limits and the pseudo-arc
Authors: Irwin Trevor , Solecki Sławomir
Published: March 2006

The aim of the present work is to develop a dualization of the Fraïssé limit construction from model theory and to indicate its surprising connections with the pseudo-arc. As corollaries of general results on the dual Fraïssé limits, we obtain Mioduszewski’s theorem on surjective universality of the pseudo-arc among chainable continua and a theorem on projective homogeneity of the pseudo-arc (which generalizes a result of Lewis and Smith on density of homeomorphisms of the pseudo-arc among surjective continuous maps from the pseudo-arc to itself). We also get a new characterization of the pseudo-arc via the projective homogeneity property.
Unique continuation for the two-dimensional anisotropic elasticity system and its applications to inverse problems
Authors: Nakamura Gen , Wang Jenn-Nan
Published: March 2006

Under some generic assumptions we prove the unique continuation property for the two-dimensional inhomogeneous anisotropic elasticity system. Having established the unique continuation property, we then investigate the inverse problem of reconstructing the inclusion or cavity embedded in a plane elastic body with inhomogeneous anisotropic medium by infinitely many localized boundary measurements.
Invariance in ℰ* and ℰ_{Π}
Authors: Weber Rebecca
Published: March 2006

We define

G
G

, a substructure of

E

Π

\mathcal {E}_\Pi

(the lattice of

Π
1
0

\Pi ^0_1

classes), and show that a quotient structure of

G
G

,

G
♢

G^\diamondsuit

, is isomorphic to

E

∗

\mathcal {E}^*

. The result builds on the

Δ
3
0

\Delta ^0_3

isomorphism machinery, and allows us to transfer invariant classes from

E

∗

\mathcal {E}^*

to

E

Π

\mathcal {E}_\Pi

, though not, in general, orbits. Further properties of

G
♢

G^\diamondsuit

and ramifications of the isomorphism are explored, including degrees of equivalence classes and degree invariance.
Entire majorants via Euler–Maclaurin summation
Authors: Littmann Friedrich
Published: March 2006

It is the aim of this article to give extremal majorants of type

2
π
δ

2\pi \delta

for the class of functions

f
n

(
x
)
=
sgn
(
x
)

x
n

f_n(x)=\text {sgn}(x)x^n

, where

n
∈

N

n\in \mathbb {N}

. As applications we obtain positive definite extensions to

R

\mathbb {R}

of

±
(
i
t

)

−
m

\pm (it)^{-m}

defined on

R

∖
[
−
1
,
1
]

\mathbb {R}\backslash [-1,1]

, where

m
∈

N

m\in \mathbb {N}

, optimal bounds in Hilbert-type inequalities for the class of functions

(
i
t

)

−
m

(it)^{-m}

, and majorants of type

2
π

2\pi

for functions whose graphs are trapezoids.
On the 𝑝-compact groups corresponding to the 𝑝-adic reflection groups 𝐺(𝑞,𝑟,𝑛)
Authors: Castellana Natàlia
Published: March 2006

There exists an infinite family of

p
p

-compact groups whose Weyl groups correspond to the finite

p
p

-adic pseudoreflection groups

G
(
q
,
r
,
n
)

G(q,r,n)

of family 2a in the Clark-Ewing list. In this paper we study these

p
p

-compact groups. In particular, we construct an analog of the classical Whitney sum map, a family of monomorphisms and a spherical fibration which produces an analog of the classical

J
J

-homomorphism. Finally, we also describe a faithful complexification homomorphism from these

p
p

-compact groups to the

p
p

-completion of unitary compact Lie groups.
On Hölder continuous Riemannian and Finsler metrics
Authors: Lytchak Alexander , Yaman Asli
Published: March 2006

We discuss smoothness of geodesics in Riemannian and Finsler metrics.
Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments
Authors: Gao Xin
Published: March 2006

Motivation: The parametric F-test has been widely used in the analysis of factorial microarray experiments to assess treatment effects. However, the normality assumption is often untenable for microarray experiments with small replications. Therefore, permutation-based methods are called for help to assess the statistical significance. The distribution of the F-statistics across all the genes on the array can be regarded as a mixture distribution with a proportion of statistics generated from the null distribution of no differential gene expression whereas the other proportion of statistics generated from the alternative distribution of genes differentially expressed. This results in the fact that the permutation distribution of the F-statistics may not approximate well to the true null distribution of the F-statistics. Therefore, the construction of a proper null statistic to better approximate the null distribution of F-statistic is of great importance to the permutation-based multiple testing in microarray data analysis.

Results: In this paper, we extend the ideas of constructing null statistics based on pairwise differences to neglect the treatment effects from the two-sample comparison problem to the multifactorial balanced or unbalanced microarray experiments. A null statistic based on a subpartition method is proposed and its distribution is employed to approximate the null distribution of the F-statistic. The proposed null statistic is able to accommodate unbalance in the design and is also corrected for the undue correlation between its numerator and denominator. In the simulation studies and real biological data analysis, the number of true positives and the false discovery rate (FDR) of the proposed null statistic are compared with those of the permutated version of the F-statistic. It has been shown that our proposed method has a better control of the FDRs and a higher power than the standard permutation method to detect differentially expressed genes because of the better approximated tail probabilities.

Availability: R codes available upon request

Contact:  xingao@mathstat.yorku.ca
GenRGenS: software for generating random genomic sequences and structures
Authors: Ponty Yann , Termier Michel , Denise Alain
Published: March 2006

Summary: GenRGenS is a software tool dedicated to randomly generating genomic sequences and structures. It handles several classes of models useful for sequence analysis, such as Markov chains, hidden Markov models, weighted context-free grammars, regular expressions and PROSITE expressions. GenRGenS is the only program that can handle weighted context-free grammars, thus allowing the user to model and to generate structured objects (such as RNA secondary structures) of any given desired size. GenRGenS also allows the user to combine several of these different models at the same time.

Availability: Source and executable files of GenRGenS (in Java) and the complete user's manual are freely available at

Contact:  dev.GenRGenS@lri.fr
Is
Mycobacterium bovis
in the environment important for the persistence of bovine tuberculosis?
Authors: Courtenay O , Reilly L.A , Sweeney F.P , Hibberd V , Bryan S , Ul-Hassan A , Newman C , Macdonald D.W , Delahay R.J , Wilson G.J , Wellington E.M.H
Published: March 2006

Mycobacterium bovis
is the causative agent of bovine tuberculosis (bTB) in cattle and wildlife. Direct aerosol contact is thought to be the primary route of infection between conspecifics, whereas indirect transmission via an environmental reservoir of
M. bovis
is generally perceived not to be a significant source for infection. Here, we report on the application of molecular technology (PCR) to quantify the prevalence of
M. bovis
in the environment and to explore its epidemiological significance. We show that the detectability of viable
M. bovis
at badger setts and latrines is strongly linked to the frequency of
M. bovis
excretion by infected badgers, and that putative
M. bovis
in the environment is prevalent on a large proportion of endemic cattle farms in Britain. These results raise important questions about the role of an environmental reservoir in bTB persistence.
On spontaneous wave function collapse and quantum field theory
Authors: Tumulka Roderich
Published: March 2006

One way of obtaining a version of quantum mechanics without observers, and thus of solving the paradoxes of quantum mechanics, is to modify the Schrödinger evolution by implementing spontaneous collapses of the wave function. An explicit model of this kind was proposed in 1986 by Ghirardi, Rimini & Weber (GRW), involving a nonlinear, stochastic evolution of the wave function. We point out how, by focusing on the essential mathematical structure of the GRW model and a clear ontology, it can be generalized to (regularized) quantum field theories in a simple and natural way.
The use of the reciprocals of positive and negative inertial functions in asymptotic modelling
Authors: Williams F.W , Ilanko S
Published: March 2006

This paper shows how the recently introduced concept of positive and negative inertial functions in asymptotic modelling may be used effectively. Noting an almost linear variation of the natural frequency over a wide range of values of the reciprocal of the inertial parameter, the results presented show that both the natural frequencies of constrained systems can be calculated accurately using only moderately large artificial inertial parameters, e.g. which are only about 10 times that of the system mass and also that values about a million times more than this do not precipitate ill-conditioning when using 16 figure computer accuracy. This helps to minimize the chances of numerical problems occurring due to the limitation of machine precision.
Parcel Eulerian–Lagrangian fluid dynamics of rotating geophysical flows
Authors: Bokhove Onno , Oliver Marcel
Published: March 2006

Parcel Eulerian–Lagrangian Hamiltonian formulations have recently been used in structure-preserving numerical schemes, asymptotic calculations and in alternative explanations of fluid parcel (in)stabilities. A parcel formulation describes the dynamics of one fluid parcel with a Lagrangian kinetic energy but an Eulerian potential evaluated at the parcel's position. In this paper, we derive the geometric link between the parcel Eulerian–Lagrangian formulation and well-known variational and Hamiltonian formulations for three models of ideal and geophysical fluid flow: generalized two-dimensional vorticity–stream function dynamics, the rotating two-dimensional shallow-water equations and the rotating three-dimensional compressible Euler equations.
Tilt scanning interferometry: a novel technique for mapping structure and three-dimensional displacement fields within optically scattering media
Authors: Ruiz Pablo D , Huntley Jonathan M , Maranon Alejandro
Published: March 2006

We describe a novel technique that we call tilt scanning interferometry to measure depth-resolved structure and displacement fields within semi-transparent scattering materials. The method differs significantly from conventional optical coherence tomography, in that only one wavelength is used throughout the whole measurement process. Temporal sequences of speckle interferograms are recorded while the illumination angle is tilted at constant rate. Fourier transformation of the resulting three-dimensional intensity distribution along the time axis reconstructs the scattering potential within the medium. Repeating the measurements with the object wave at equal and opposite angles about the observation direction results in two three-dimensional phase-change volumes, the sum of which gives the out-of-plane-sensitive phase volume and the difference between which gives the in-plane phase volume. From these phase-change volumes the in-plane and out-of-plane depth-resolved displacement fields are obtained. The theoretical framework for the technique is explained in detail and a practical optical implementation is described. Finally, results from proof-of-principle experiments involving a semi-transparent beam undergoing bending are presented.
Structural stability in porous elasticity
Authors: Chiriţă S , Ciarletta M , Straughan B
Published: March 2006

We consider the linearized system of equations for an elastic body with voids as derived by Cowin & Nunziato. We demonstrate that the solution depends continuously on changes in the coefficients, which couple the equations of elastic deformation and of voids. It is also shown that the solution to the coupled system converges, in an appropriate measure, to the solutions of the uncoupled systems as the coupling coefficients tend to zero.
Propagation of elastic waves through polycrystals: the effects of scattering from dislocation arrays
Authors: Maurel Agnès , Pagneux Vincent , Boyer Denis , Lund Fernando
Published: March 2006

We address the problem of an elastic wave coherently propagating through a two-dimensional polycrystal. The main source of scattering is taken to be the interaction with grain boundaries that are in turn modelled as line distribution of dislocations—a good approximation for low angle grain boundaries. First, the scattering due to a single linear array is worked out in detail in a Born approximation, both for longitudinal and transverse polarization and allowing for mode conversion. Next, the polycrystal is modelled as a continuum medium filled with such lines that are in turn assumed to be randomly distributed. The properties of the coherent wave are worked out in a multiple scattering formalism, with the calculation of a mass operator, the main technical ingredient. Expansion of this operator to second-order in perturbation theory gives expressions for the index of refraction and attenuation length. This work is motivated by two sources of recent experiments: firstly, the experiments of Zhang
et al
. (Zhang, G., Simpson Jr, W. A., Vitek, J. M., Barnard, D. J., Tweed, L. J. & Foley J. 2004
J. Acoust. Soc. Am.
116
, 109–116.) suggesting that current understanding of wave propagation in polycrystalline material fails to interpret experimental results; secondly, the experiments of Zolotoyabko & Shilo who show that dislocations are potentially strong scatterers for elastic waves.
Resource distribution mediates synchronization of physiological rhythms in locust groups
Authors: Despland Emma , Simpson Stephen J
Published: March 2006

Synchronized behaviour is common in animal groups. In ant colonies, synchronization occurs because active ants stimulate their neighbours to activity. We use oscillator theory to explain how stimulation from active neighbours synchronizes activity in groups of solitarious locusts via entrainment of internal physiological rhythms. We also show that the spatial distribution of food resources controls coupling between individual locusts and the emergence of synchronized activity. In locusts (
Schistocerca gregaria
), individual schedules of activity and quiescence arise from an irregular physiological oscillation in feeding excitation (i.e. hunger). We show that contact with an active neighbour increases the probability that a locust becomes active. This entrained activity decreases the time until the locust feeds, shifting the phase of its hunger oscillation. The locusts' internal physiological rhythms are thus brought into alignment and their activity becomes synchronized. When food resources are clumped, contact with active locusts increases, and this increase in the strength of coupling between individuals leads to greater synchronization of behaviour. Activity synchronization might have functional significance in inhibiting swarming when resources are dispersed and accelerating it in more favourable clumped environments.
Unifying measures of gene function and evolution
Authors: Wolf Yuri I , Carmel Liran , Koonin Eugene V
Published: March 2006

Recent genome analyses revealed intriguing correlations between variables characterizing the functioning of a gene, such as expression level (EL), connectivity of genetic and protein–protein interaction networks, and knockout effect, and variables describing gene evolution, such as sequence evolution rate (ER) and propensity for gene loss. Typically, variables within each of these classes are positively correlated, e.g. products of highly expressed genes also have a propensity to be involved in many protein–protein interactions, whereas variables between classes are negatively correlated, e.g. highly expressed genes, on average, evolve slower than weakly expressed genes. Here, we describe principal component (PC) analysis of seven genome-related variables and propose biological interpretations for the first three PCs. The first PC reflects a gene's ‘importance’, or the ‘status’ of a gene in the genomic community, with positive contributions from knockout lethality, EL, number of protein–protein interaction partners and the number of paralogues, and negative contributions from sequence ER and gene loss propensity. The next two PCs define a plane that seems to reflect the functional and evolutionary plasticity of a gene. Specifically, PC2 can be interpreted as a gene's ‘adaptability’ whereby genes with high adaptability readily duplicate, have many genetic interaction partners and tend to be non-essential. PC3 also might reflect the role of a gene in organismal adaptation albeit with a negative rather than a positive contribution of genetic interactions; we provisionally designate this PC ‘reactivity’. The interpretation of PC2 and PC3 as measures of a gene's plasticity is compatible with the observation that genes with high values of these PCs tend to be expressed in a condition- or tissue-specific manner. Functional classes of genes substantially vary in status, adaptability and reactivity, with the highest status characteristic of the translation system and cytoskeletal proteins, highest adaptability seen in cellular processes and signalling genes, and top reactivity characteristic of metabolic enzymes.
Senescence effects in an extremely long-lived bird: the grey-headed albatrossThalassarche chrysostoma
Authors: Catry Paulo , Phillips Richard A , Phalan Ben , Croxall John P
Published: March 2006

Studies attempting to document reproductive or other pre-lethal senescence effects in wild birds typically face an array of problems, including flaws in statistical analyses, non-adaptive philopatry to deteriorating environments, confounding effects arising from cohort heterogeneity and differential death rates of phenotypes and the frequent pairing of old birds to younger mates. Furthermore, recent studies suggest that birds could maintain a high level of physical fitness until old age, before being struck by a catastrophic illness leading quickly to their demise. The presence of terminally ill individuals in most datasets (and their greater incidence in older age categories) may therefore provide a false impression of progressive senescence in cross-sectional analyses. This study was designed explicitly to avoid all the known pitfalls linked to the demonstration of progressive senescence in wild populations, and involved one of the very longest-lived bird species. We show that, during incubation, old (aged 35 years and over) male grey-headed albatrossesThalassarche chrysostomamake longer foraging trips, and have lower daily mass gains, than experienced mid-aged individuals (aged up to 28 years). This is, to our knowledge, the first report documenting reduced foraging performance with old age. Hatching and breeding success of pairs composed of two old individuals were reduced in comparison to mid-aged pairs. Overall results were very similar when analyses were repeated using only individuals known to have survived 1 or 2 years beyond field measurements (hence probably not suffering from the effects of an advanced terminal illness). We conclude that extremely long-lived individuals usually experience some degree of general physical deterioration, leading to reduced foraging and breeding performance, long before their final demise.
Recent and simultaneous origins of eusociality in halictid bees
Authors: Brady Seán G , Sipes Sedonia , Pearson Adam , Danforth Bryan N
Published: March 2006

Eusocial organisms are characterized by cooperative brood care, generation overlap and reproductive division of labour. Traits associated with eusociality are most developed in ants, termites, paper wasps and corbiculate bees; the fossil record indicates that each of these advanced eusocial taxa evolved in the Late Cretaceous or earlier (greater than 65 Myr ago). Halictid bees also include a large and diverse number of eusocial members, but, in contrast to advanced eusocial taxa, they are characterized by substantial intra- and inter-specific variation in social behaviour, which may be indicative of more recent eusocial evolution. To test this hypothesis, we used over 2400 bp of DNA sequence data gathered from three protein-coding nuclear genes (opsin,winglessandEF-1a) to infer the phylogeny of eusocial halictid lineages and their relatives. Results from relaxed molecular clock dating techniques that utilize a combination of molecular and fossil data indicate that the three independent origins of eusociality in halictid bees occurred within a narrow time frame between approximately 20 and 22 Myr ago. This relatively recent evolution helps to explain the pronounced levels of social variation observed within these bees. The three origins of eusociality appear to be temporally correlated with a period of global warming, suggesting that climate may have had an important role in the evolution and maintenance of eusociality in these bees.
Monogamy in the maternally mouthbrooding Lake Tanganyika cichlid fishTropheus moorii
Authors: Egger Bernd , Obermüller Beate , Sturmbauer Christian , Phiri Harris , Sefc Kristina M
Published: March 2006

Supported by evidence for assortative mating and polygynandry, sexual selection through mate choice was suggested as the main force driving the evolution of colour diversity of haplochromine cichlids in Lakes Malawi and Victoria. The phylogenetically closely related tribe Tropheini of Lake Tanganyika includes the genusTropheus, which comprises over 100 colour variants currently classified into six morphologically similar, polyphyletic species. To assess the potential for sexual selection in this sexually monochromatic maternal mouthbrooder, we used microsatellite-based paternity inference to investigate the mating system ofTropheus moorii. In contrast to haplochromines in Lake Malawi, multiple paternity is rare or even absent in broods ofT. moorii. Eighteen of the 19 analysed families were consistent with genetic monogamy, while either a mutation or more than one sire explained the genotype of one offspring in another brood. We discuss the differences in breeding behaviour betweenT. mooriiand the Lake Malawi haplochromines, and evaluate additional factors or alternatives to sexual selection as promoters of colour diversification. A preliminary survey of other Tropheini species suggested that multiple paternity is infrequent in the entire tribe.
Surplus nest boxes and the potential for polygyny affect clutch size and offspring sex ratio in house wrens
Authors: Dubois Natalie S , Dale Kennedy E , Getty Thomas
Published: March 2006

Females of many species can gain benefits from being choosy about their mates and even exhibit context-dependent investment in reproduction in response to the quality of their breeding situation. Here, we show that if a male house wren is provided with surplus nest boxes in his territory, his mate lays a larger clutch with a significantly higher proportion of sons. This response to a territory characteristic directly associated with male competitive ability, and ultimately to male reproductive success, suggests that male competition over access to high-quality territories with surplus nest boxes (i.e. those able to support polygyny) may influence female reproductive investment decisions. The results of this study have interesting implications, particularly considering the important role that studies of cavity nesting birds utilizing nest boxes have played in advancing our understanding of behaviour, ecology and evolution.