bluuebunny/crossref_metadata_2025 huggingface dataset:
Oestrous synchronization, semen preservation and artificial insemination in the Mohor gazelle (Gazella dama mhorr) for the establishment of a genome resource bank programme
Authors: Holt WV , Abaigar T , Jabbour HN
Published: October 2005

Gazella dama mhorr is an endangered species with an extant population of about 190 animals distributed between several zoos. Semen was collected by electro-ejaculation from 12 adult males, and cryopreserved in TEST-yolk diluent containing 6% glycerol. The effects of the concentration of egg yolk (5%, 10% and 20%) and the presence or absence of sodium triethanolamine lauryl sulfate (equex) on sperm motion and acrosomal integrity after thawing were examined. Increasing concentrations of egg yolk resulted in more acrosomal damage and poorer motility after thawing. The presence or absence of equex had no effect on either parameter. The frozen spermatozoa were used in an insemination trial, in which 13 females were treated with intravaginal progesterone-releasing devices to synchronize oestrus. Seven females were inseminated with frozen-thawed semen 48 h after removal of the devices, and six were inseminated after 60 h. Three females in the first group and one in the second group became pregnant. However, only one pregnancy (from the 48-h group) was carried to term. The study demonstrated the feasibility of applying artificial insemination in this species, but revealed that a number of outstanding technical problems remain to be solved.
Winter home range and foraging of common wombats (Vombatus ursinus) in patchily burnt subalpine areas of the Snowy Mountains, Australia
Authors: Green Ken
Published: October 2005

In 2003, wombats survived bushfires at subalpine altitudes in the Snowy Mountains of Australia to be faced only weeks later by a further reduction in food availability owing to the winter cover of snow. Where burrows occurred in burnt areas, winter home ranges (95% kernel) were significantly larger (52.6 ± 33.4 ha) than in unburnt areas (16.3 ± 14.5 ha). Wombats were able to survive the winter by foraging further from burrows; the lack of burrows for protection from predators was not an issue owing to a lack of feral dogs at subalpine altitudes. However, distant foraging was restricted by the low availability of burrows in deep snow, particularly at alpine altitudes. Wombats apparently fed mainly on monocots. All studied wombats survived the winter and there was no evidence of significant loss of condition in wombats sighted during the study.
Control of feral cats for nature conservation. IV. Population dynamics and morphological attributes of feral cats at Shark Bay, Western Australia
Authors: Short Jeff , Turner Bruce
Published: October 2005

The dynamics of feral cats (Felis catus) were assessed at Shark Bay at two adjoining sites subject to differing intensities of predator control. The Heirisson Prong conservation reserve (12 km2) was fenced to exclude predators and was subject to intensive control actions, while a portion of the adjoining Carrarang pastoral lease (60 km2) was subject to a lesser level of control. Foxes (Vulpes vulpes) were largely absent at both sites owing to effective control. Densities of cats were highly variable over time, showing strong annual fluctuations over 14 years of records Three independent estimates of peak density were made, varying between 1.5 and 2.8 km–2. Rate of increase was assessed as 0.98 on the pastoral lease and 0.99 on the conservation reserve (to give an approximate doubling of the population every 8.5 months). A logistic model, with K = 1.5 km–2 and r of 0.98, gave a maximum sustained yield of 0.37 cats km–2 year–1 and a harvest rate of >0.6 cats km–2 year–1 for their elimination in 5 years or less (for K = 2.8 km–2, these values increase to 0.69 and >1.05 km–2 year–1 respectively). Harvest outcomes at both sites were consistent with these models. However, the effort required to maintain a given offtake rate increased 6-fold at low cat densities and offtake by trapping as a function of cat density took the form of a Type 3 functional response. The functional response for cat trapping (the offtake with constant effort per unit time) overlaid against the curve of cat productivity suggested a stable equilibrium point at low cat densities (0.07–0.13 cats km–2). Hence, trapping effort needed to be greatly intensified at low cat densities and/or augmented by other methods of control to eradicate cats from the closed system of the reserve. The strongly male-biased sex ratio of captures at the barrier fence suggested high levels of reinvasion from beyond the harvested area of the pastoral lease and this made effective control in this open system difficult.
How important are different types of temperate woodlands for ground-foraging birds?
Authors: Antos Mark J. , Bennett Andrew F.
Published: October 2005

There is widespread concern about population decline in a number of woodland-dependent birds in southern Australia. Of all declining species, approximately half forage on the ground. This study examined the avifaunal assemblages of temperate woodlands of the Northern Plains, Victoria, to investigate the importance of woodland habitats for ground-foraging species. Four main types of woodland were surveyed (white cypress-pine, black box, grey box and river red gum) and, in total, 89 bird species were detected. All four woodland types differed in habitat structure and, in turn, supported significantly different avifaunal assemblages. Forty of the 89 species (45%) foraged, at least in part, on the ground. Species richness and abundance of ground-foragers differed significantly between woodland types, being highest in white cypress-pine and black box. There was a greater richness of ground-foragers during the breeding than non-breeding season, but abundance did not vary seasonally. Overall, ground-foraging birds comprised a greater proportion of species (>55%) and individuals (>60%) in white cypress-pine and black box woodland than in grey box and river red gum (42–48% of species, <50% individuals). Those ground-foragers regarded as declining also occurred in greatest richness in white cypress-pine woodlands, one of the most depleted habitats in the region. The lowest richness of ‘declining’ ground-foraging species was in river red gum woodland, the most widespread woodland type. Throughout Australia, the proportion of ground-foraging species in bird assemblages tends to be greater in temperate, semi-arid or arid woodlands than in moist forests and rainforests. However, in many regions woodland habitats are severely depleted and their open ground layer is particularly vulnerable to degradation. The extent of suitable habitat for ground-foraging birds in temperate woodlands may be much less than is apparent from current measures of tree cover. Sustainable management of drier (non-riverine) temperate woodlands is required to conserve this important element of the Australian avifauna.
The diet of the brush-tailed rabbit-rat (Conilurus penicillatus) from the monsoonal tropics of the Northern Territory, Australia
Authors: Firth Ronald S. C. , Jefferys Elizabeth , Woinarski John C. Z. , Noske Richard A.
Published: October 2005

The diet of the brush-tailed rabbit-rat (Conilurus penicillatus) was assessed by microscopic analysis of faecal samples from 35 individuals collected from three different sites in the Northern Territory (Garig Gunak Barlu National Park (Cobourg Peninsula), Kakadu National Park and Melville Island) at various times of the year during 2000–02. Seed was the most abundant item in the overall diet of C. penicillatus, making up 68% of identifiable particles, with smaller proportions contributed by leaves (21%), plant stems (8%) and insects (2%). ANOSIM tests revealed no difference in diet between the sexes and seasons, but there was a significant difference in the diet between the sites, with seed material present in 74% of the samples from Cobourg and in 62% and 58% of samples from Kakadu and Melville respectively. Leaf matter was present in 19% of samples from Cobourg and in 26% and 24% of samples from Kakadu and Melville respectively. Stem material was present in only 6% of samples from Cobourg and in 8% and 13% of samples from Kakadu and Melville respectively. Insect matter was present in small quantities across all three sites. The high proportion of seed in the diet suggests that C. penicillatus is primarily granivorous.
Species lifetime distribution for simple models of ecologies
Authors: Pigolotti Simone , Flammini Alessandro , Marsili Matteo , Maritan Amos
Published: October 2005

Interpretation of empirical results based on a taxa's lifetime distribution shows apparently conflicting results. Species' lifetime is reported to be exponentially distributed, whereas higher-order taxa, such as families or genera, follow a broader distribution, compatible with power-law decay. We show that both forms of evidence are consistent with a simple evolutionary model that does not require specific assumptions on species interaction. The model provides a zero-order description of the dynamics of ecological communities, and its species lifetime distribution can be computed exactly. Different behaviors are found as follows: an initialt-3/2power law, emerging from a random walk type of dynamics, which crosses over to a steepert-2branching process-like regime and finally is cut off by an exponential decay that becomes weaker and weaker as the total population increases. Sampling effects also can be taken into account and shown to be relevant. If species in the fossil record were sampled according to the Fisher log-series distribution, lifetime should be distributed according to at-1power law. Such variability of behaviors in a simple model, combined with the scarcity of data available, casts serious doubt on the possibility of validating theories of evolution on the basis of species lifetime data.
AtCCMH, an essential component of thec-type cytochrome maturation pathway inArabidopsismitochondria, interacts with apocytochromec
Authors: Meyer Etienne H. , Giegé Philippe , Gelhaye Eric , Rayapuram Naganand , Ahuja Umesh , Thöny-Meyer Linda , Grienenberger Jean-Michel , Bonnard Géraldine
Published: October 2005

The maturation ofc-type cytochromes requires the covalent ligation of the heme cofactor to reduced cysteines of the CXXCH motif of apocytochromes. In contrast to mitochondria of other eukaryotes, plant mitochondria follow a pathway close to that found in α- and γ-proteobacteria. We identified a nuclear-encoded protein, AtCCMH, theArabidopsis thalianaortholog of bacterial CcmH/CycL proteins. In bacteria, CcmH and the thioredoxin CcmG are components of a periplasmic thio-reduction pathway proposed to maintain the apocytochromeccysteines in a reduced state. AtCCMH is located exclusively in mitochondria. AtCCMH is an integral protein of the inner membrane with the conserved RCXXC motif facing the intermembrane space. Reduction assays show that the cysteine thiols in the RCXXC motif of AtCCMH can form a disulfide bond that can be reduced by enzymatic thiol reductants. A reduced form of AtCCMH can reduce the intra-disulfide bridge of a model peptide of apocytochromec. When expressed inEscherichia coli, AtCCMH coimmunoprecipitates with the bacterial CcmF, a proposed component of the heme lyase. Blue-native PAGE of mitochondrial membrane complexes reveals the colocalization of AtCCMH and AtCcmFN2in a 500-kDa complex. Yeast two-hybrid assays show an interaction between the AtCCMH intermembrane space domain andA. thalianaapocytochromec.A. thaliana ccmh/ccmhknockout plants show lethality at the torpedo stage of embryogenesis. Our results show that AtCCMH is an essential mitochondrial protein with characteristics consistent with its proposed apocytochromec-reducing and heme lyase function.
Combining two genomes in one cell: Stable cloning of the
Synechocystis
PCC6803 genome in the
Bacillus subtilis
168 genome
Authors: Itaya Mitsuhiro , Tsuge Kenji , Koizumi Maki , Fujita Kyoko
Published: October 2005

Cloning the whole 3.5-megabase (Mb) genome of the photosynthetic bacterium
Synechocystis
PCC6803 into the 4.2-Mb genome of the mesophilic bacterium
Bacillus subtilis
168 resulted in a 7.7-Mb composite genome. We succeeded in such unprecedented large-size cloning by progressively assembling and editing contiguous DNA regions that cover the entire
Synechocystis
genome. The strain containing the two sets of genome grew only in the
B. subtilis
culture medium where all of the cloning procedures were carried out. The high structural stability of the cloned
Synechocystis
genome was closely associated with the symmetry of the bacterial genome structure of the DNA replication origin (
oriC
) and its termination (
terC
) and the exclusivity of
Synechocystis
ribosomal RNA operon genes (
rrnA
and
rrnB
). Given the significant diversity in genome structure observed upon horizontal DNA transfer in nature, our stable laboratory-generated composite genome raised fundamental questions concerning two complete genomes in one cell. Our megasize DNA cloning method, designated megacloning, may be generally applicable to other genomes or genome loci of free-living organisms.
Mothers' and fathers' childcare involvement with young children in rural families in Malaysia
Authors: Hossain Ziarat , Roopnarine Jaipaul L. , Masud Jariah , Muhamed Abdullah Al‐Hadi , Baharudin Rozumah , Abdullah Rohani , Juhari Rumaya
Published: October 2005

There is a paucity of data on paternal involvement in childcare in traditional Muslim families in Asia. Using cultural‐ecological models of human development that focus on the developmental niche and hegemonic perspectives on masculinity, mothers' and fathers' levels of childcare involvement with infants were examined in 50 two‐parent, low‐income, rural Malay Muslim families residing in peninsular Malaysia. The major goals were to examine gender of parent and gender of child differences in involvement in childcare activities. Mothers and fathers were interviewed separately in their homes regarding the amount of time and levels of involvement in bedtime routines, physical care of, playing with, singing to, feeding, and soothing infants. Groupwise comparisons of parental perceptions revealed a marked gender‐differentiated pattern of involvement: Mothers perceived that they were significantly more involved in bedtime routines, physical care, feeding, playing, soothing, and singing to infants than did fathers. On average fathers estimated that they spent 18% as much time cleaning infants (0.63 versus 3.50 hours), 22% as much time feeding infants (0.76 versus 3.49), and 56% as much time playing with infants (2.77 versus 4.92 hours) relative to mothers. These patterns of involvement suggest that in traditional, rural Malay Muslim families, mothers are the primary caregivers to infants, and contrary to the father as play partner hypothesis, mothers engaged in more play with infants than did fathers. Despite divergent levels of involvement, mothers and fathers were equally as inclined to be involved with their male or female infants. Findings are interpreted in terms of traditional Muslim beliefs about gendered ideologies regarding childcare roles and levels of paternal involvement in groups of fathers in rural and urban Malaysia. The limitations, due in part to gathering data from single informants and the nature of the sample, and the implications of the findings for increasing paternal involvement are noted.
Influence of achievement goals and self‐efficacy on students' self‐regulation and performance
Authors: Bouffard Thérèse , Bouchard Maryse , Goulet Geneviève , Denoncourt Isabelle , Couture Nathalie
Published: October 2005

It is widely admitted that low self‐efficacy has a detrimental impact on the functioning and performance of a person mainly concerned with performance goals but has no impact when a person is mainly concerned with learning goals (Dweck, 1986). However, results from both correlational and experimental studies are divergent. Since these studies examined very few indicators of participants' cognitive functioning, they may have failed to detect those aspects that could be more vulnerable to a negative impact of the combination of performance goals and low self‐efficacy. Another concern is the lack of most studies to clearly distinguish the type of performance goal examined, particularly the performance‐avoidance versus the performance‐approach goal. In the current study, we decided to focus on performance‐approach and learning goals in order to examine how self‐efficacy intervenes in their effects on participants' self‐regulation and performance on a cognitive task. One hundred and forty participants (85 females and 55 males) were examined. They were randomly assigned either to the learning or the performance‐approach goals condition. In each condition, half of the participants received feedback aimed at inducing either high or low self‐efficacy beliefs with regard to the task prior to executing it aloud. Examination of participants' verbal reports, direct observation of some of their behaviours while solving the task, and responses to a retrospective questionnaire allowed the assessment of several indicators of their self‐regulation and performance. As already reported by many studies, self‐efficacy influenced various aspects of participants' self‐regulation and performance. However, contrary to Dweck's hypothesis (1986), when interaction effects between self‐efficacy and goals were observed, they always involved learning instead of performance‐approach goals. Findings of this study suggest that the nature of the goal might not matter as much as its personal significance or value.
The project of an International Congress of Psychology by J. Ochorowicz (1881)
Authors: Nicolas Serge , Söderlund Hedvig
Published: October 2005

Since the second part of the 19th century, there has been a great increase in the number of international scientific congresses, and they appear a necessary step in the maturation of knowledge. The first person to explicitly suggest the necessity of an international congress of psychology was Julian Ochorowicz (1850–1917), who was considered the founder of Polish psychology. In 1881 he sent an article to Théodule Ribot, editor of Revue Philosophique de la France et de l'Étranger, entitled “Project of an International Congress of Psychology,” which was published in Ribot's journal. In it he described the dispersed state of psychology in 1881 and the previous 50 years, including 12 subdisciplines ranging from psychophysics to the psychology of art, and how it should aim for unification. He suggested collective efforts to progress rapidly, with widespread collaboration and the continuous exchange of observations, information, and experiments. Having international congresses would constitute a forum for such exchanges, and in his article he outlined the steps that should be taken for putting together the first international congress of psychology. The proposal was quite extensive and fanciful, making Ribot somewhat doubt its realizability. Nevertheless, the first international psychology congress took place in Paris in 1889, 8 years after the publication of Ochorowicz's article. This quick development could be attributed to the creation of the psychology societies, one of the first being La Société de Psychologie Physiologique, which was created in France in 1885. The creation of this society also contributed to psychology being recognized as a scientific domain. In line with this, the final programme of the congress was less extensive than that proposed in Ochorowicz's article, focusing on physiological aspects and ignoring the philosophical ones. In the present paper, the historical context of Ochorowicz's article is outlined, followed by a translation of his article.
Nonselective access of spelling–sound knowledge for Korean‐English bilinguals
Authors: Lee Chang H. , Nam Kichun , Katz Leonard
Published: October 2005

An intense debate in monolingual research concerns the presence of phonological recoding in word recognition. Research supporting the phonological recoding hypothesis in monolingual research suggests the possibility of phonological recoding even in L2 recognition. There has been some experimental evidence showing phonological priming between L1 and L2 for alphabetic bilinguals (e.g., French‐Dutch). In the present study, lexical decision experiments used either L1 or L2 primes with targets from the other language at SOAs of 140 ms and 250 ms for Korean‐English bilinguals. It was found that phonological information activated by either an L1 or L2 prime can interact with phonological information in the other language. That is, L2 shares phonological information with L1, and its spelling–sound knowledge is activated, apparently automatically, at an SOA of 140 ms. The consistent pattern of phonological priming of both L1 and L2 targets at the 140 ms SOA indicates that the spelling–sound knowledge of bilingual lexicons is activated when any linguistic form is presented. Importantly, this indiscriminate activation of spelling–sound knowledge in the Korean‐English bilingual system occurs in the absence of any common orthographic cues because the two languages have totally different writing systems.
Is there a pro‐self component behind the prominence effect? Individual resource allocation decisions with communities as potential beneficiaries
Authors: Selart Marcus , Eek Daniel
Published: October 2005

An important problem for decision‐makers in society deals with the efficient and equitable allocation of scarce resources to individuals and groups. The significance of this problem is rapidly growing since there is a rising demand for scarce resources all over the world. Such resource dilemmas belong to a conceptually broader class of situations known as social dilemmas. In this type of dilemma, individual choices that appear “rational” often result in suboptimal group outcomes. In this article we study how people make monetary allocation decisions between the community where they live and a neighbouring community, with the aim of finding out to what extent these decisions are subject to biased over‐weighting. The manuscript reports four experiments that deal with the way individuals make such allocation decisions when the potential beneficiaries are such communities. The specific goal of these experiments is to gauge the amount of bias in the weights that people assign to the various beneficiaries. Taken together, the results from all the four experiments suggest that making the gain of the neighbouring community prominent to a higher extent de‐biases the outcomes (the prominence effect) compared to when own community gain is made prominent. Place identity is discussed as a potentially important factor in this connection. Hence, it may be argued that there seems to be some kind of a pro‐self component that is able to explain a large part of the variance observed for the prominence effect. Connections between such a factor and in‐group favouritism are discussed. A strength of the study was that these major results appeared to be quite robust when considered as task effects, as the salience of the manipulated context factors in the studies (in terms of reliable main or interaction effects) did not distort them.
Corruption-mitigating Policies: The Case of Italy
Authors: Newell James L.
Published: October 2005

One of the circumstances likely to be associated with the intensity of both investigative and legislative efforts designed to curb political and bureaucratic corruption is institutional reform. Since the characteristics of electoral and party systems seem to be associated with variations in the intensity of anti-corruption efforts cross-nationally, it was reasonable to think that changes in the characteristics of these systems in Italy in the 1990s would be reflected in a corresponding change in the efforts of legislators and members of the judiciary to tackle corruption. Prior to the 1990s Italy's tripolar party system and its numerous concomitants placed considerable obstacles in the way of the willingness and the ability of judicial investigators and parliamentarians to deal with the corruption emergency. The 1993 electoral law reform, the eventual emergence of a largely bipolar party system and the circumstances surrounding these processes considerably diminished the significance of the aforementioned obstacles, yet there has been little noticeable increase in anti-corruption efforts. This is probably explicable in terms of the electoral effects of such efforts and suggests that institutional change is at most only one of a number of conditions that must be fulfilled in order for more strenuous efforts to be observed.
The 1922 Turin Massacre (Strage di Torino): Working Class Resistance and Conflicts within Fascism
Authors: Sonnessa Antonio
Published: October 2005

This article explores the reasons why Turin's Fascists launched a violent offensive against the local labour movement two months after the Fascist seizure of power. The article demonstrates that the residual resistance of the working class to Fascism was the major reason behind the Turin massacre. However, it also investigates other decisive factors for the violence of December 1922: the conflict between the national Fascist leadership and Turin Fascism and within the Turin fascio itself. The article challenges the interpretation, best exemplified by Renzo De Felice, that the Fascist violence was spontaneous, carried out by undisciplined squadristi without the approval of Mussolini and the Fascist leadership. Rather, it argues that there existed significant levels of planning and a high degree of toleration by the Turinese and national Fascist leaderships and the local authorities. Using Turin as a case study, the article provides a clearer view of the tensions existing within the Fascist movement in the months after the seizure of power. It analyses how Turin Fascism was riddled by factional disputes and how its attempts to gain control of the major political and economic institutions of the city were frustrated by the opposition of the local authorities and industrialists, backed by Mussolini's government. The events of the months preceding and following the strage also afford insights into the conflicts within Fascism over the future role squadrism and violence was to play in the Fascist movement now Mussolini was head of government.
Equivariant derived category of a complete symmetric variety
Authors: Guillermou Stéphane
Published: October 2005

LetGGbe a complex algebraic semi-simple adjoint group andXXa smooth complete symmetricGG-variety. LetL=⨁αLαL= \bigoplus _\alpha L_\alphabe the direct sum of all irreducibleGG-equivariant intersection cohomology complexes onXX, and letE=ExtDG(X)⋅⁡(L,L)\mathcal E= \operatorname {Ext}^\cdot _{\mathrm {D}_G(X)}(L,L)be the extension algebra ofLL, computed in theGG-equivariant derived category ofXX. We consideredE\mathcal Eas a dg-algebra with differentialdE=0d_\mathcal E =0, and the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="script upper E Subscript alpha Baseline equals upper E x t Subscript normal upper D Sub Subscript upper G Subscript left-parenthesis upper X right-parenthesis Superscript dot Baseline left-parenthesis upper L comma upper L Subscript alpha Baseline right-parenthesis">Eα=ExtDG(X)⋅⁡(L,Lα)\mathcal E_\alpha = \operatorname {Ext}^\cdot _{\mathrm {D}_G(X)}(L,L_\alpha )asE\mathcal E-dg-modules. We show that the bounded equivariant derived category of sheaves ofC\mathbf {C}-vector spaces onXXis equivalent toDE⟨Eα⟩\mathrm {D}_\mathcal E\langle \mathcal E_\alpha \rangle, the subcategory of the derived category ofE\mathcal E-dg-modules generated by theEα\mathcal E_\alpha.
A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3′-end subsequences
Authors: Miura Fumihito , Uematsu Chihiro , Sakaki Yoshiyuki , Ito Takashi
Published: October 2005

Motivation: In contrast with conventional PCR using a pair of specific primers, some applications utilize a single unique primer in combination with a common primer, thereby relying solely on the former for specificity. These applications include rapid amplification of cDNA ends (RACE), adaptor-tagged competitive PCR (ATAC-PCR), PCR-mediated genome walking and so forth. Since the primers designed by conventional methods often fail to work in these applications, an improved strategy is required, particularly, for a large-scale analysis.

Results: Based on the structure of ‘off-target’ products in the ATAC-PCR, we reasoned that the practical determinant of the specificity of primers may not be the uniqueness of entire sequence but that of the shortest 3′-end subsequence that exceeds a threshold of duplex stability. We termed such a subsequence as a ‘specificity-determining subsequence’ (SDSS) and developed a simple algorithm to predict the performance of the primer: the algorithm identifies the SDSS of each primer and examines its uniqueness in the target genome. The primers designed using this algorithm worked much better than those designed using a conventional method in both ATAC-PCR and 5′-RACE experiments. Thus, the algorithm will be generally useful for improving various PCR-based applications.

Availability: The source code of the program is available upon request from the authors or can be obtained from

Supplementary information: Supplementary data are available at Bioinformatics online.

Contact:  ito@k.u-tokyo.ac.jp
Effect of pooling samples on the efficiency of comparative studies using microarrays
Authors: Zhang Shu-Dong , Gant Timothy W.
Published: October 2005

Motivation: Many biomedical experiments are carried out by pooling individual biological samples. However, pooling samples can potentially hide biological variance and give false confidence concerning the data significance. In the context of microarray experiments for detecting differentially expressed genes, recent publications have addressed the problem of the efficiency of sample pooling, and some approximate formulas were provided for the power and sample size calculations. It is desirable to have exact formulas for these calculations and have the approximate results checked against the exact ones. We show that the difference between the approximate and the exact results can be large.

Results: In this study, we have characterized quantitatively the effect of pooling samples on the efficiency of microarray experiments for the detection of differential gene expression between two classes. We present exact formulas for calculating the power of microarray experimental designs involving sample pooling and technical replications. The formulas can be used to determine the total number of arrays and biological subjects required in an experiment to achieve the desired power at a given significance level. The conditions under which pooled design becomes preferable to non-pooled design can then be derived given the unit cost associated with a microarray and that with a biological subject. This paper thus serves to provide guidance on sample pooling and cost-effectiveness. The formulation in this paper is outlined in the context of performing microarray comparative studies, but its applicability is not limited to microarray experiments. It is also applicable to a wide range of biomedical comparative studies where sample pooling may be involved.

Availability: A Java Webstart application can be accessed at

Contact:  sdz1@le.ac.uk; twg1@le.ac.uk
Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX
Authors: Strömbäck Lena , Lambrix Patrick
Published: October 2005

Motivation: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed.

Results: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data.

Contact:  lestr@ida.liu.se
A novel algorithm and web-based tool for comparing two alternative phylogenetic trees
Authors: Nye Tom M.W. , Liò Pietro , Gilks Walter R.
Published: October 2005

Summary: We describe an algorithm and software tool for comparing alternative phylogenetic trees. The main application of the software is to compare phylogenies obtained using different phylogenetic methods for some fixed set of species or obtained using different gene sequences from those species. The algorithm pairs up each branch in one phylogeny with a matching branch in the second phylogeny and finds the optimum 1-to-1 map between branches in the two trees in terms of a topological score. The software enables the user to explore the corresponding mapping between the phylogenies interactively, and clearly highlights those parts of the trees that differ, both in terms of topology and branch length.

Availability: The software is implemented as a Java applet at . It is also available on request from the authors.

Contact:  thomas.nye@mrc-bsu.cam.ac.uk
Differential coexpression analysis using microarray data and its application to human cancer
Authors: Choi Jung Kyoon , Yu Ungsik , Yoo Ook Joon , Kim Sangsoo
Published: October 2005

Motivation: Microarrays have been used to identify differential expression of individual genes or cluster genes that are coexpressed over various conditions. However, alteration in coexpression relationships has not been studied. Here we introduce a model for finding differential coexpression from microarrays and test its biological validity with respect to cancer.

Results: We collected 10 published gene expression datasets from cancers of 13 different tissues and constructed 2 distinct coexpression networks: a tumor network and normal network. Comparison of the two networks showed that cancer affected many coexpression relationships. Functional changes such as alteration in energy metabolism, promotion of cell growth and enhanced immune activity were accompanied with coexpression changes. Coregulation of collagen genes that may control invasion and metastatic spread of tumor cells was also found. Cluster analysis in the tumor network identified groups of highly interconnected genes related to ribosomal protein synthesis, the cell cycle and antigen presentation. Metallothionein expression was also found to be clustered, which may play a role in apoptosis control in tumor cells. Our results show that this model would serve as a novel method for analyzing microarrays beyond the specific implications for cancer.

Supplementary information: Supplementary data are available at Bioinformatics online.

Contact:  sskimb@ssu.ac.kr
Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes
Authors: Booth Ezgi O. , Driessche Nancy Van , Zhuchenko Olga , Kuspa Adam , Shaulsky Gad
Published: October 2005

Motivation: Coordinate regulation of gene expression can provide information on gene function. To begin a large-scale analysis of Dictyostelium gene function, we clustered genes based on their expression in wild-type and mutant strains and analyzed their functions.

Results: We found 17 modes of wild-type gene expression and refined them into 57 submodes considering mutant data. Annotation analyses revealed correlations between co-expression and function and an unexpected correlation between expression and function of genes involved in various aspects of chemotaxis. Co-regulation of chemotaxis genes was also found in published data from neutrophils. To test the predictive power of the analysis, we examined the phenotypes of mutations in seven co-regulated genes that had no published role in chemotaxis. Six mutants exhibited chemotaxis defects, supporting the idea that function can be inferred from co-expression. The clustering and annotation analyses provide a public resource for Dictyostelium functional genomics.

Supplementary information:  

Contact:  gadi@bcm.tmc.edu
The European Union and the Systematic Dismantling of the Common Law of Conflict of Laws
Authors: Hartley Trevor C
Published: October 2005

English conflict of laws is the creation of the common law. Prior to Britain's entry into the European Union, legislation played only a limited role. The few legislative measures concerning choice of law were narrowly targeted to remedy specific problems—for example the formal validity of wills, or torts. The rules for service outside the jurisdiction were a more important exception, but their practical operation largely depended on judge-made concepts and remedies, such as forum non conveniens and antisuit injunctions. The common law also provided a complete system for the recognition of foreign judgments that operated untrammelled with regard to judgments from many countries, including some of the most important, while the relevant legislation, where applicable, did little more than provide a simpler procedure.
The Common Law Choice of Law Rules for Resulting and Constructive Trusts
Authors: Chong Adeline
Published: October 2005

There is a dearth of authority and in-depth discussion concerning what the choice of law rules are for claims involving the assertion that property is held on a resulting or constructive trust. It is usually thought that the choice of law rules set out by the Hague Convention on the Law Applicable to Trusts and on their Recognition (hereafter the ‘Hague Trusts Convention’), as enacted into English law by the Recognition of Trusts Act 1987, apply. However, it is arguable that this is not so for some types of resulting and constructive trusts, namely those governed by a foreign law; or, at the very least, that some doubt exists as to whether the Hague choice of lawrules apply to all resulting and constructive trusts. It is therefore important that the common law choice of law rules for such trusts is clearly elucidated. Unfortunately, this is an area of the law that is distinctly undeveloped. The aim of this article is to consider what are or should be the common law choice of law rules for resulting and constructive trusts.
Free Movement, Equal Treatment, and Citizenship of the Union
Authors: White Robin Ca
Published: October 2005

The prohibition of discrimination, at least on grounds of nationality, has always been a constitutional principle of Community law. Such discrimination can take many forms, since Community law prohibits not only direct discrimination but various forms of indirect discrimination. Furthermore, the Court of Justice has indicated that where discrimination on grounds of nationality is in issue, the requirement of proof is not a heavy one on the complainant. All that is needed to place the burden on the respondent to justify the potentially differential treatment is that complainants show that the requirement applied to them is intrinsically likely, or susceptible by its very nature, to affect them adversely in comparison with the State's own nationals. The modern formulation of the prohibition of discrimination recognizes that protection from discrimination on grounds of nationality is central to the concept of citizenship of the Union. Advocate General Jacobs has said:
I. Forum non conveniens and the Brussels Convention
Authors: McEleavy Peter , Cuniberti Gilles
Published: October 2005

On 1 March 2005 the European Court of Justice in Owusu v Jackson held that the English doctrine of forum non conveniens was inconsistent with the Brussels Convention (the ‘Convention’) when a defendant was domiciled in the United Kingdom, even if the natural forum was in a Non-Contracting State.
II. External Relations
Authors: Denza Eileen
Published: October 2005

Each time this writer has prepared a three-yearly update on the external relations of the Union, the Treaty framework has changed and the sense that Europe's leaders are being distracted from vital problems grows. The Constitution for Europe now on offer, the result of a mandate from the European Council at Laeken to effect a simplification of the treaties with a view to making them better understood without changing their meaning, would introduce new legal uncertainties into the framework for the conduct of external relations. Its entry into force, however, now appears unlikely.
Agricultural economics and distributional effects
Authors: Von Braun Joachim
Published: October 2005

The paper examines the main issues surrounding distributional effects in the domains of natural resource management and land policies, agricultural technology and research policies, agricultural market and trade policies, and consumer‐oriented policies, including standards, subsidies, and labeling. Agriculture is drifting into an ever more drastic bifurcation at a global level and within many countries. Correcting that bifurcation will require large investments in rural areas and rural people, in institutions, and in information and biological technologies accessible by the poor in the world's smallholder sector. Large and growing national and international inequalities related to agriculture and rural areas threaten peace, growth, and sustainable development.
Causes of rural economic development
Authors: Gardner Bruce L.
Published: October 2005

Underlying factors in the growth of agriculture as a sector and of rural incomes in developing countries are investigated, using data from 85 countries during 1960–2001. Hypotheses about growth are derived from both the general growth literature and the empirical literature on past agricultural growth in the United States and other industrial countries. The growth of agriculture as a sector is surprisingly independent of the growth of income per capita for those who work in that sector. Neither is necessary nor sufficient for the other. Agricultural economics is in many circumstances not the key discipline in understanding the economics of rural income and poverty.
Rural poverty dynamics: development policy implications
Authors: Barrett Christopher B.
Published: October 2005

This article explores the useful distinction between chronic and transitory poverty in understanding rural welfare dynamics, highlighting the possibility of poverty traps and their implications for “cargo net” policies to build up productive assets and “safety net” policies to protect such assets. We discuss the methodological difficulties in identifying and explaining either poverty traps or the critical thresholds that are their defining feature. A few empirical examples from sub‐Saharan Africa illustrate the likely existence of poverty traps that help to explain chronic rural poverty.
Is there a future for small farms?
Authors: Hazell Peter B. R.
Published: October 2005

Small farms are seriously challenged today in ways that make their future precarious. Marketing chains are changing and becoming more integrated and more demanding of quality and food safety. This is creating new opportunities for farmers who can compete and link to these markets, but threatens to leave many others behind. In developing countries, small farmers also face unfair competition from rich country farmers in many of their export and domestic markets. The viability of many is further undermined by the continuing shrinkage of their average farm size. And the spread of HIV/AIDS is further eroding the number of productive farm family workers, and leaving many children as orphans with limited knowledge about how to farm. Left to themselves, these forces will curtail opportunities for small farms, overly favor large farms, and lead to a premature and rapid exit of many small farms, adding to already serious problems of rural poverty and urban ghettos. If small farmers are to have a viable future, then there is a need for a concerted effort by governments, NGOs, and the private sector to create a more enabling economic environment for their development. Appropriate interventions could unleash significant benefits in the form of pro‐poor agricultural growth in many developing countries and more than pay for themselves in terms of their economic and social return. But they do not seem very likely at the moment and current trends are moving in the opposite direction.
A revival of large farms in Eastern Europe—how important are institutions?
Authors: Koester Ulrich
Published: October 2005

Contrary to expectations, large farms are still the dominant form of farm organization in most countries of the Commonwealth of Independent States and are important in some Central and Eastern countries. This paper analyzes the reasons for these failed expectations, focusing on the experience of Russia. The framework of institutional economics is applied to explain the reasons why the conventional approach, based on economies of scale and on‐farm transaction costs, does not apply to the evolution of farm size in the east (and even the west). Specific institutions, which are partly embedded and informal, and legal, but loosely enforced, suppress the birth of family farms in Russia and stimulate the growth of large farms, leading to holdings that are not observed in developed market economies. Hence, survival and growth of large farms are not necessarily based on comparative advantage of these farm organizations in a market economy environment.
Total factor productivity growth in agriculture: a Malmquist index analysis of 93 countries, 1980–2000
Authors: Coelli Tim J. , Rao D. S. Prasada
Published: October 2005

In this paper we examine the levels and trends in agricultural output and productivity in 93 developed and developing countries that account for a major portion of the world population and agricultural output. We make use of data drawn from the Food and Agriculture Organization of the United Nations and our study covers the period 1980–2000. Due to the nonavailability of reliable input price data, the study uses data envelopment analysis (DEA) to derive Malmquist productivity indices. The study examines trends in agricultural productivity over the period. Issues of catch‐up and convergence, or in some cases possible divergence, in productivity in agriculture are examined within a global framework. The paper also derives the shadow prices and value shares that are implicit in the DEA‐based Malmquist productivity indices, and examines the plausibility of their levels and trends over the study period.
Is small beautiful? Farm size, productivity, and poverty in Asian agriculture
Authors: Fan Shenggen , Chan‐Kang Connie
Published: October 2005

Small farms characterize agriculture in Asia. With the fragmentation of land holdings, the average size of farms fell in the region, while the number of small‐size holdings increased significantly. These small‐scale farmers play an important role for food security and poverty alleviation. However, whether and how these small farms can survive under globalization is a hotly debated topic. In particular, the traditional claim that “small is beautiful,” which is based on empirical observation that small farms present higher land productivity than large farms, is being challenged. It has been shown that a positive relationship also exists between farm size and labor productivity (and therefore income). To help these small farms prosper under increasing globalization, the governments have to change the “business as usual” attitude. Innovative land reform, for example, is crucial to secure property rights to farmers and to increase farm size. Equally important is the reform of public institutions in order to help small farmers to have access to credit, marketing, and technology. Moreover, promoting diversification in the production of high‐value commodities can play an important role in raising the small‐holders' income. Finally, policies that facilitate urban–rural migration and promote the development of the rural nonfarm sector are essential to help alleviate poverty among small‐farm households and among the rural poor in general.