bluuebunny/crossref_metadata_2025 huggingface dataset:
Number partitioning
Authors: Mézard Marc , Montanari Andrea
Published: September 2009

Number partitioning is one of the most basic optimization problems. It is very easy to state: ‘Given the values of N assets, is there a fair partition of them into two sets?’ Nevertheless, it is very difficult to solve: it belongs to the NP-complete category, and the known heuristics are often not very good. It is also a problem with practical applications, for instance in multiprocessor scheduling. This chapter focuses on a particularly difficult case: the partitioning of a list of independent uniformly distributed random numbers. It discusses the phase transition occurring when the range of numbers varies, and shows that low cost configurations — the ones with a small unbalance between the two sets — can be seen as independent energy levels. Hence the model behaves analogously to the Random Energy Model.
Satisfiability
Authors: Mézard Marc , Montanari Andrea
Published: September 2009

Because of Cook's theorem, satisfiability lies at the heart of computational complexity theory. This chapter presents some selected research directions, focusing on ensembles of random satisfiability instances. When the density of constraints is increased, a phase transition between a SAT and an UNSAT phase take place. Properly tuned ensembles with a density close to the transition point provide a generator of particularly hard instances. The nature of this transition is discussed, and bounds on the critical density are obtained. On the algorithmic side, the discussion focuses on exhaustive search algorithms based on tree-search, and on random walk procedures.
Linear equations with Boolean variables
Authors: Mézard Marc , Montanari Andrea
Published: September 2009

Solving a system of linear equations over a finite field is arguably one of the most fundamental operations in mathematics. This chapter considers a specific ensemble of random linear systems over Boolean variables, named XORSAT, and discusses the structure of its set of solutions. In large instances, the affine subspace of solutions can exhibit a remarkably rich geometrical structure. When the ratio of equations to variables is increased, the system first gets into an intermediate phase where solutions cluster in many well separated regions of the hypercube. Then it encounters a second phase transition and gets into an ‘UNSAT’ phase where the probability of existence of a solution vanishes. The study uses belief propagation equations, and a combinatorial analysis of the 2-core in the associated factor graph.
A life course approach to obesity
Authors: Kuh Diana , Ben-Shlomo Yoav
Published: September 2009

This chapter examines non-genetic determinants of obesity from fetal life to adolescence. Topics covered include measurement of overweight and obesity, critical or sensitive periods for obesity development, the prenatal period, infancy and the period of adiposity rebound. It also considers how one might intervene to address multiple behaviours.
A life course approach to neuropsychiatric outcomes
Authors: Kuh Diana , Ben-Shlomo Yoav
Published: September 2009

Emerging evidence suggests that neuropsychiatric outcomes over the life course may be associated with exposures during critical times of brain development and with cumulative exposures over the life course. This chapter examines three models of the relationship of exposure timing to neuropsychiatric outcomes. First, it considers prenatal nutrition deprivation and its potential effects on neural tube defects and schizophrenia. Second, an example is chosen where a severe prenatal insult (maternal thyroid hormone deficiency due to lack of iodine in the diet) leads to a frank disorder (creatinism) and a lesser prenatal insult (material suboptimal thyroid function) leads to a more subtle deficit (cognitive deficit). Third, it considers an example of cumulative exposure (prenatal and postnatal exposure to environmental lead) that leads to subtle deficits in neuropsychological function. The chapter concludes with a discussion of the complexity of neuropsychological development over the life course.
Fetal growth and development: the role of nutrition and other factors
Authors: Kuh Diana , Ben-Shlomo Yoav
Published: September 2009

This chapter examines the sources of variation in fetal growth, in particular nutrition in the context of the fetal nutritional programming hypothesis. The influence of fetal and maternal genotype on fetal growth is considered and set in the context of non-genetic intergenerational influences on birthweight, such as the mother's height and her own birthweight. The concept of programming is considered both with reference to nutritional programming and the wider view of programming, with particular reference to the hormonal, metabolic, and circulatory milieu to which the fetus is exposed.
Sicioeconomic pathways between childhood and adult health
Authors: Kuh Diana , Ben-Shlomo Yoav
Published: September 2009

This chapter develops the idea that aspects of socioeconomic environment throughout life affect adult health and disease risk. It discusses etiological studies that examine how variations in adult disease outcomes are related to socioeconomic factors at different life stages to understand better biological chains in risk. It reviews studies of social chains of risk that have investigated either the extent to which individuals experience continuity in their socioeconomic environment or how they interact with their environment in ways that lead to socially patterned exposures that may develop or damage personal and health capital.
Country review: Chile
Authors: Wolff Marcelo J.
Published: September 2009

This chapter describes the epidemiological characteristics of HIV infection in Chile. It discusses the healthcare system and its approach to antiretroviral therapy from the advent of HAART until 2007, with a focus on the difficulties, the challenges and lessons learned. It also outlines the current status of the national treatment programme and evaluates its impact.
Country review: Germany
Authors: Wolf Eva , Jaeger Hans
Published: September 2009

This chapter begins with a discussion of the epidemiology of HIV in Germany. It then discusses subtypes and prevalence of drug resistance in Germany, treatment strategies, effects of HAART, and healthcare delivery.
Country review: Brazil
Authors: Ramos-Filho Celso Ferreira , Santos Cledy Eliana dos
Published: September 2009

This chapter begins with a description of the epidemiology of AIDS and HIV in Brazil. It then discusses treatment, results of free access to antiretroviral drugs, co-infection, and prevention. The HIV/AIDS epidemic in Brazil was detected early in the 1980s. Its progress seems to have been at least partially curbed by early and integrated response, including the establishment of an inclusive epidemiological surveillance system. The epidemic is characterized as concentrated since the prevalence among certain vulnerable groups is higher than 5%, but it is below 1% in the general population.
Maintaining and developing health systems to sustain HAART
Authors: Nixon Stephanie , Veenstra Nina
Published: September 2009

This chapter focuses on countries where the impact of HAART on health systems is likely to be most significant; the analysis targets countries with fragile health systems, high HIV prevalence, and generalized epidemics — the scenario in sub-Saharan Africa. Drawing on secondary data in the form of published studies, it considers assumptions about the potential impact of HAART on health systems in sub-Saharan Africa and contrasts them with lessons that are currently being learned through empirical research. It argues that the current exceptional and largely vertical approach to provision of HAART in sub-Saharan Africa is an appropriate response, provided it is accompanied by simultaneous efforts to ensure that the rise of HIV incidence is stemmed as quickly as possible.
Introduction
Authors: Bordag M. , Klimchitskaya G. L. , Mohideen U. , Mostepanenko V. M.
Published: September 2009

This introductory chapter discusses the general physical foundations of the Casimir effect as manifestation of the existence of zero-point vacuum oscillations. Connections between the Casimir force, the van der Waals force, and other physical phenomena of quantum electrodynamics caused by the existence of zero-point oscillations are considered. Specifically, it is explained that the Casimir force between material boundaries can be interpreted as simply a retarded van der Waals force. The Casimir effect is presented as a multidisciplinary subject which plays an important role in condensed matter physics, elementary particle physics, atomic physics, gravitation and cosmology, mathematical physics, and nanotechnology. The chapter ends with a guide to the book explaining the structure of the book, with brief detail on the content of each chapter, and the main notation.
The Lifshitz Theory of Atom―Wall Interactions
Authors: Bordag M. , Klimchitskaya G. L. , Mohideen U. , Mostepanenko V. M.
Published: September 2009

This chapter obtains a Lifshitz-type formula for the atom-wall interaction considering one of the two walls as a rarefied medium. This formula is applied for various wall materials and various atoms. It is shown that the Casimir interaction between an atom and a metal wall does not depend on the model of the metal used. The respective Casimir entropy satisfies the Nernst heat theorem. In the case of an atom interacting with a dielectric wall, the Lifshitz theory is thermodynamically consistent if the dc conductivity of the dielectric material is neglected. If the dc conductivity of the dielectric wall is included in the model of the dielectric response, the Nernst heat theorem is violated. The atom-wall interaction is also considered when the wall material is magnetic, anisotropic and in the nonequilibrium case when the temperatures of the wall and of the environment are different.
Measurements of the Casimir Force Between Metals
Authors: Bordag M. , Klimchitskaya G. L. , Mohideen U. , Mostepanenko V. M.
Published: September 2009

This chapter starts chronologically with the first measurement, by means of a torsion pendulum, in the recent phase of Casimir force experiments. Then the main breakthroughs in the measurement of the Casimir force between metallic surfaces are presented. One of them was the first demonstration of corrections to the Casimir force due to the nonzero skin depth and surface roughness by means of an atomic force microscope. Another breakthrough was a series of precise indirect measurements of the Casimir pressure by means of a micromechanical torsional oscillator. These measurements allowed a definitive choice between different theoretical approaches to the thermal Casimir force for real metal surfaces. Many other experiments performed in the last few years are also presented, specifically one measurement using the configuration of two parallel plates. The chapter ends with a brief discussion of proposed experiments using metallic surfaces.
Measurements of the Casimir―Polder Force
Authors: Bordag M. , Klimchitskaya G. L. , Mohideen U. , Mostepanenko V. M.
Published: September 2009

Modern laboratory techniques make possible the investigation of the role of the Casimir–Polder force in experiments on Bose–Einstein condensation and quantum reflection. Thus, it has been demonstrated that the collective oscillations of a Bose–Einstein condensate of ultracold atoms provide a sensitive probe of Casimir–Polder forces. Later, the first measurement of the temperature dependence of the Casimir–Polder force was performed in this way. The Casimir–Polder interaction plays an important role in the scattering of atoms on various surfaces. Of special interest are situations where the wave nature of an atom dominates in comparison with its classical behavior as a particle (this is referred to as quantum reflection). This chapter considers both of the latter two types of experiments in connection with the properties of the Casimir–Polder force.
Enough for the Future
Authors: Meyer Lukas H. , Roser Dominic
Published: September 2009

Reflecting the normative significance of specific features of intergenerational relations this chapter investigates the justice claims of future people vis-à-vis currently living people. It discusses sufficientarian and egalitarian conceptions of justice, and argues that a sufficientarian approach is appropriate in the intergenerational context. This conclusion is based, first, on the argument that by relying on a threshold conception of harm we can solve the non-identity problem and that there are good reasons to specify the relevant threshold in sufficientarian terms. Second, it is based upon an examination of reasons given for a sufficientarian understanding of global justice. These reasons are shown to speak even more strongly for a sufficientarian understanding of intergenerational justice.
The Phenomenon of the Multinational Enterprise Group
Authors: Mevorach Irit
Published: September 2009

The significant phenomenon of multinational enterprise group (MEG) may come about using different structures and organizational patterns. This chapter first discusses the emergence and growth of the MEG phenomenon which is based on the rise of the multinational enterprise on one hand and the emergence of the corporate group business pattern on the other. It also considers different legal structures which may be regarded as groups. The chapter concludes with suggesting what should be the meaning of MEG for the purpose of addressing the problem of insolvency within MEGs.
Insolvency Goals in Legal Systems
Authors: Mevorach Irit
Published: September 2009

Chapters 2 and 3 established that assessing the problem of insolvency within MEGs should be done in light of insolvency goals. This chapter attempts to identify shared key objectives and tasks of insolvency systems which are also desirable on the policy level. Based on existing theories of insolvency law, the chapter considers what could be perceived as key values of insolvency systems and their corresponding tasks. It then shows that such objectives are also widely accepted among different legal regimes, primarily referring to key insolvency objectives as stressed in the UNCITRAL Legislative Guide on Insolvency Law.
Physiological integration of innate immunity
Authors: Schneider David
Published: September 2009

Understanding how insect immunity is regulated requires studying the interactions of all those aspects of physiology that impact immunity. This includes both resistance and tolerance aspects of defence as well as all of the other assorted physiological systems of the insect that alter the immune response. It is hypothesized that an insect's innate immune responses is in the centre of a physiological net and the immune response is sensitive to changes throughout this net. This chapter tries to tie all of these physiological strands together and demonstrate how innate immunity alters the gross physiology of an insect and how the gross physiology, in turn, alters the immune response. An emergent property that falls out of this analysis is the prediction of several types of physiological collapse — these collapses result from positive-feedback loops that lead to amplified and damage-inducing immune/physiological responses.
Immune responses and the evolution of resistance
Authors: Koella Jacob
Published: September 2009

This chapter discusses the evolution of immune function. It emphasizes two points. First, the immune system is complex, with many responses that may act together or inhibit each other to determine the outcome of an infection. Using an immune response as an indicator of the host's resistance (or, more generally, its quality) is therefore problematic, as increased investment in a given immune response may well indicate increased susceptibility to a parasite. Second, resistance is a product of the interaction between a host and a parasite. Thus, we cannot understand the evolution of immune function without considering the co-evolution of the host's and the parasite's contributions to resistance. Indeed, as found in a more general context, mathematical models of the evolution of the host that do not consider the co-evolutionary response by the parasite can be misleading as their predictions can differ qualitatively from the co-evolutionary dynamics and equilibrium.
Types of Authorship in the Cinema
Authors: Livingston Paisley
Published: September 2009

One objection that is often raised against intentionalist approaches is that many films have no author who could be the source of philosophical questions or claims. In response to that objection, this chapter presents a conception of authorship that embraces a broad range of cases, including joint authorship as well as individual authorship in a context of collaborative work. The chapter does not argue that all films have an individual author, or even a coordinated team of people functioning as a joint author. Yet it does contend that in some cases the conditions on authorship are in fact met: a person (or group of collaborators) exercises sufficient control in the making of a work designed to express the maker's attitudes. This proposal is developed with regard to the question, raised by Berys Gaut, whether a film actor's contribution to the artistic qualities of a film suffice to make that person one of the authors of the film.
Value, Authenticity, and Fantasy in Bergman
Authors: Livingston Paisley
Published: September 2009

This chapter discusses a scene in Wild Strawberries where Bergman includes an allusion to Kaila's views about the status of moral judgements. The apparent thrust of this appeal to Kaila's authority is that there is no right or wrong, only motives and preferences. The chapter argues, however, that this allusion is complicated by the fact that the character who makes the Kailesque pronouncement is clearly unreliable. The chapter further discusses Bergman's and Kaila's views on inauthenticity and self-understanding, particularly in relation to Persona. Bergman's positions on moral knowledge are explored, especially in terms of characterizations in The Seventh Seal and Bergman's unpublished treatment for a film on the Crucifixion. Bergman's critiques of irrationality are linked to his rejection of cinematic fantasy and his preference for a philosophically oriented, exploratory, modernist cinema. Bergman's grounds for rejecting artistic fantasy are contrasted to the Kantian critique published by Roger Scruton.
Intentionality
Authors: Ott Walter
Published: September 2009

Hume's chief weapon against causal realism is the argument from nonsense: for a view even to be a candidate for being right, it must first be intelligible to us. This chapter argues that, while Hume is not a positivist or verificationist, his account of intentionality, and in particular his denial of meaning to definite descriptions, makes for a starkly restrictive version of empiricism. In replacing the traditional account of mental propositions in terms of judgment with his own story about propositional attitudes, Hume makes it impossible to think of a thing by means of a definite description. This closes off any appeal to Lockean passive powers. This chapter goes on to argue that Hume's occasional talk of “relative ideas” does not threaten this basic position.
De novocomputational prediction of non-coding RNA genes in prokaryotic genomes
Authors: Tran Thao T. , Zhou Fengfeng , Marshburn Sarah , Stead Mark , Kushner Sidney R. , Xu Ying
Published: September 2009

Motivation: The computational identification of non-coding RNA (ncRNA) genes represents one of the most important and challenging problems in computational biology. Existing methods for ncRNA gene prediction rely mostly on homology information, thus limiting their applications to ncRNA genes with known homologues.

Results: We present a novel de novo prediction algorithm for ncRNA genes using features derived from the sequences and structures of known ncRNA genes in comparison to decoys. Using these features, we have trained a neural network-based classifier and have applied it to Escherichia coli and Sulfolobus solfataricus for genome-wide prediction of ncRNAs. Our method has an average prediction sensitivity and specificity of 68% and 70%, respectively, for identifying windows with potential for ncRNA genes in E.coli. By combining windows of different sizes and using positional filtering strategies, we predicted 601 candidate ncRNAs and recovered 41% of known ncRNAs in E.coli. We experimentally investigated six novel candidates using Northern blot analysis and found expression of three candidates: one represents a potential new ncRNA, one is associated with stable mRNA decay intermediates and one is a case of either a potential riboswitch or transcription attenuator involved in the regulation of cell division. In general, our approach enables the identification of both cis- and trans-acting ncRNAs in partially or completely sequenced microbial genomes without requiring homology or structural conservation.

Availability: The source code and results are available at http://csbl.bmb.uga.edu/publications/materials/tran/.

Contact:  xyn@bmb.uga.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Camelina Infected by Downy Mildew (Hyaloperonospora camelinae) in the Western United States: A First Report
Authors: Putnam Melodie L. , Serdani Maryna , Ehrensing Daryl , Curtis Marc
Published: September 2009

Downy mildew on camelina previously has been reported in Minnesota, where it was identified as Peronospora camelinae (now Hyaloperonospora camelinae), although no supporting evidence was given. In Montana, a downy mildew on camelina was identified as P. parasitica (now Hyaloperonospora parasitica). To our knowledge, this report marks the first time H. camelinae has been confirmed in the western USA.

Accepted for publication 23 July 2009. Published 10 September 2009.
Levofloxacin-resistant-Streptococcus mitis endophthalmitis: a unique presentation of bacterial endocarditis
Authors: Dinani Amreen , Ktaich Nessrine , Urban Carl , Rubin David
Published: September 2009

Endogenous endophthalmitis is a rare complication of infective endocarditis and has been decreasing due to the availability of effective antibiotics. We highlight a case of endogenous endophthalmitis due to levofloxacin-resistant Streptococcus mitis presenting as infective endocarditis. Endogenous endophthalmitis should be considered as a manifestation of an underlying systemic disease, especially in patients who present with non-specific signs and symptoms with no obvious source of precipitating infection.
Identification of amino acids in the dengue virus type 2 envelope glycoprotein critical to virus infectivity
Authors: Kroschewski Helga , Sagripanti Jose-Luis , Davidson Andrew D.
Published: September 2009

The dengue virus envelope glycoprotein mediates virus attachment and entry and is the major viral antigen. The identification of ‘critical’ amino acids in the envelope glycoprotein that cannot be altered without loss of infectivity could have a major impact on the development of dengue virus vaccines and diagnostics. In this context, we determined whether six amino acids, previously predicted by computational analysis to play a critical role in the virus life cycle, were essential for virus viability. The effects of mutating the six ‘critical’ amino acids and a further seven ‘neutral’ amino acids were analysed by using a dengue virus type 2 infectious cDNA clone. Of the six critical amino acids, three (Asp-215, Pro-217 and His-244) were found to be essential for virus viability in mammalian and mosquito cells.
Experimental infection of serotine bats (Eptesicus serotinus) with European bat lyssavirus type 1a
Authors: Freuling C. , Vos A. , Johnson N. , Kaipf I. , Denzinger A. , Neubert L. , Mansfield K. , Hicks D. , Nuñez A. , Tordo N. , Rupprecht C. E. , Fooks A. R. , Müller T.
Published: September 2009

The serotine bat (Eptesicus serotinus) accounts for the vast majority of bat rabies cases in Europe and is considered the main reservoir for European bat lyssavirus type 1 (EBLV-1, genotype 5). However, so far the disease has not been investigated in its native host under experimental conditions. To assess viral virulence, dissemination and probable means of transmission, captive bats were infected experimentally with an EBLV-1a virus isolated from a naturally infected conspecific from Germany. Twenty-nine wild caught bats were divided into five groups and inoculated by intracranial (i.c.), intramuscular (i.m.) or subcutaneous (s.c.) injection or by intranasal (i.n.) inoculation to mimic the various potential routes of infection. One group of bats was maintained as uninfected controls. Mortality was highest in the i.c.-infected animals, followed by the s.c. and i.m. groups. Incubation periods varied from 7 to 26 days depending on the route of infection. Rabies did not develop in the i.n. group or in the negative-control group. None of the infected bats seroconverted. Viral antigen was detected in more than 50 % of the taste buds of an i.c.-infected animal. Shedding of viable virus was measured by virus isolation in cell culture for one bat from the s.c. group at 13 and 14 days post-inoculation, i.e. 7 days before death. In conclusion, it is postulated that s.c. inoculation, in nature caused by bites, may be an efficient way of transmitting EBLV-1 among free-living serotine bats.
Lytic infection of permissive cells with human cytomegalovirus is regulated by an intrinsic ‘pre-immediate-early’ repression of viral gene expression mediated by histone post-translational modification
Authors: Groves Ian J. , Reeves Matthew B. , Sinclair John H.
Published: September 2009

Human cytomegalovirus (HCMV) lytic gene expression occurs in a regulated cascade, initiated by expression of the viral major immediate-early (IE) proteins. Transcribed from the major IE promoter (MIEP), the major IE genes regulate viral early and late gene expression. This study found that a substantial proportion of infecting viral genomes became associated with histones immediately upon infection of permissive fibroblasts at low m.o.i. and these histones bore markers of repressed chromatin. As infection progressed, however, the viral MIEP became associated with histone marks, which correlate with the known transcriptional activity of the MIEP at IE time points. Interestingly, this chromatin-mediated repression of the MIEP at ‘pre-IE’ times of infection could be overcome by inhibition of histone deacetylases, as well as by infection at high m.o.i., and resulted in a temporal advance of the infection cycle by inducing premature viral early and late gene expression and DNA replication. As well as the MIEP, and consistent with previous observations, the viral early and late promoters were also initially associated with repressive chromatin. However, changes in histone modifications around these promoters also occurred as infection progressed, and this correlated with the known temporal regulation of the viral early and late gene expression cascade. These data argue that the chromatin structure of all classes of viral genes are initially repressed on infection of permissive cells and that the chromatin structure of HCMV gene promoters plays an important role in regulating the time course of viral gene expression during lytic infection.
Molecular characterization of full-length genomic segment 2 of a bovine picobirnavirus (PBV) strain: evidence for high genetic diversity with genogroup I PBVs
Authors: Ghosh S. , Kobayashi N. , Nagashima S. , Naik T. N.
Published: September 2009

We report here the molecular characterization of a bovine genogroup I picobirnavirus strain RUBV-P detected from a 1-month-old diarrhoeic calf in eastern India. Sequence comparisons and phylogenetic analysis of a short stretch of gene segment 2 of RUBV-P revealed low nucleotide identities (51.2–64.9 %) with and distant genetic relatedness to other genogroup I picobirnaviruses. The complete gene segment 2 sequence of RUBV-P was obtained by the single primer amplification method with modifications. Gene segment 2 of RUBV-P was 1758 bp long, encoded a predicted protein of 554 aa and exhibited low nucleotide (58.1–58.8 %) and amino acid (51.3–55.4 %) identities with genogroup I human strains Hy005102 and 1-CHN-97. The 5′- and 3′-end nucleotide sequences, and the three motifs of RNA-dependent RNA polymerases of double-stranded RNA viruses, were conserved among these strains. Our findings suggested that bovine strain RUBV-P might be distinct from genogroup I picobirnaviruses of humans and other animals.
Complex selection on 5′ splice sites in intron-rich organisms
Authors: Irimia Manuel , Roy Scott William , Neafsey Daniel E. , Abril Josep F. , Garcia-Fernandez Jordi , Koonin Eugene V.
Published: September 2009

In contrast to the typically streamlined genomes of prokaryotes, many eukaryotic genomes are riddled with long intergenic regions, spliceosomal introns, and repetitive elements. What explains the persistence of these and other seemingly suboptimal structures? There are three general hypotheses: (1) the structures in question are not actually suboptimal but optimal, being favored by selection, for unknown reasons; (2) the structures are not suboptimal, but of (essentially) equal fitness to “optimal” ones; or (3) the structures are truly suboptimal, but selection is too weak to systematically eliminate them. The 5′ splice sites of introns offer a rare opportunity to directly test these hypotheses. Intron-poor species show a clear consensus splice site; most introns begin with the same six nucleotide sequence (typically GTAAGT or GTATGT), indicating efficient selection for this consensus sequence. In contrast, intron-rich species have much less pronounced boundary consensus sequences, and only small minorities of introns in intron-rich species share the same boundary sequence. We studied rates of evolutionary change of 5′ splice sites in three groups of closely related intron-rich species—three primates, five Drosophila species, and four Cryptococcus fungi. Surprisingly, the results indicate that changes from consensus-to-variant nucleotides are generally disfavored by selection, but that changes from variant to consensus are neither favored nor disfavored. This evolutionary pattern is consistent with selective differences across introns, for instance, due to compensatory changes at other sites within the gene, which compensate for the otherwise suboptimal consensus-to-variant changes in splice boundaries.
Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans
Authors: Jackson Andrew P. , Gamble John A. , Yeomans Tim , Moran Gary P. , Saunders David , Harris David , Aslett Martin , Barrell Jamie F. , Butler Geraldine , Citiulo Francesco , Coleman David C. , de Groot Piet W.J. , Goodwin Tim J. , Quail Michael A. , McQuillan Jacqueline , Munro Carol A. , Pain Arnab , Poulter Russell T. , Rajandream Marie-Adèle , Renauld Hubert , Spiering Martin J. , Tivey Adrian , Gow Neil A.R. , Barrell Barclay , Sullivan Derek J. , Berriman Matthew
Published: September 2009

Candida dubliniensis is the closest known relative of Candida albicans, the most pathogenic yeast species in humans. However, despite both species sharing many phenotypic characteristics, including the ability to form true hyphae, C. dubliniensis is a significantly less virulent and less versatile pathogen. Therefore, to identify C. albicans-specific genes that may be responsible for an increased capacity to cause disease, we have sequenced the C. dubliniensis genome and compared it with the known C. albicans genome sequence. Although the two genome sequences are highly similar and synteny is conserved throughout, 168 species-specific genes are identified, including some encoding known hyphal-specific virulence factors, such as the aspartyl proteinases Sap4 and Sap5 and the proposed invasin Als3. Among the 115 pseudogenes confirmed in C. dubliniensis are orthologs of several filamentous growth regulator (FGR) genes that also have suspected roles in pathogenesis. However, the principal differences in genomic repertoire concern expansion of the TLO gene family of putative transcription factors and the IFA family of putative transmembrane proteins in C. albicans, which represent novel candidate virulence-associated factors. The results suggest that the recent evolutionary histories of C. albicans and C. dubliniensis are quite different. While gene families instrumental in pathogenesis have been elaborated in C. albicans, C. dubliniensis has lost genomic capacity and key pathogenic functions. This could explain why C. albicans is a more potent pathogen in humans than C. dubliniensis.
Microsatellite‐centromere mapping in Cynoglossus semilaevis using gynogenetic diploid families produced by the use of homologous and non‐homologous sperm
Authors: Ji X.‐S. , Chen S.‐L. , Liao X.‐L. , Yang J.‐F. , Xu T.‐J. , Ma H.‐Y. , Tian Y.‐S. , Jiang Y.‐L. , Wu P.‐F.
Published: September 2009

Twenty‐one microsatellite markers were studied in three meiogynogenetic families of Cynoglossus semilaevis gunther for centromere mapping using half‐tetrad analysis. Among the 13 mapped loci, 10 were estimated to be located in the telomeric region, one in the centromeric region, and two in the intermediate region of the chromosome. This study provides a basis for constructing a linkage map of C. semilaevis.
Population genetics and management units of invasive common carp Cyprinus carpio in the Murray–Darling Basin, Australia
Authors: Haynes G. D. , Gilligan D. M. , Grewe P. , Nicholas F. W.
Published: September 2009

Common carp Cyprinus carpio were introduced into Australia on several occasions and are now the dominant fish in the Murray‐Darling Basin (MDB), the continent's largest river system. In this study, variability at 14 microsatellite loci was examined in C. carpio (n = 1037) from 34 sites throughout the major rivers in the MDB, from 3 cultured populations, from Prospect Reservoir in the Sydney Basin and from Lake Sorrell in Tasmania. Consistent with previous studies, assignment testing indicated that the Boolara, Yanco and koi strains of C. carpio are present in the MDB. Unique to this study, however, the Prospect strain was widely distributed throughout the MDB. Significant genetic structuring of populations (Fisher's exact test, AMOVA and distribution of the different strains) amongst the MDB sub‐drainages was detected, and was strongly associated with contemporary barriers to dispersal and population history. The distributions of the strains were used to infer the history of introduction and spread of C. carpio in the MDB. Fifteen management units are proposed for control programmes that have high levels of genetic diversity, contain multiple interbreeding strains and show no evidence of founder effects or recent population bottlenecks.
Phylogeographical analysis of an estuarine fish, Salanx ariakensis (Osmeridae: Salanginae) in the north‐western Pacific
Authors: Hua X. , Wang W. , Yin W. , He Q. , Jin B. , Li J. , Chen J. , Fu C.
Published: September 2009

This study extended the geographic coverage of a previous study to explore population genetic structure and demographic history in the Ariake icefish Salanx ariakensis from three populations of continental coastlines and one island population in the north‐western Pacific based on a partial sequence of the mitochondrial cytochrome b gene. The S. ariakensis showed high genetic diversity and strong genetic structure. Phylogenetic analysis showed a shallow gene tree with no clear phylogeographical structure. Contiguous range expansion and restricted gene flow were inferred to be main population events by nested‐clade analysis. Significant genetic differentiations between populations could be attributable to negligible gene flow by coalescent analysis. High nucleotide diversity of each population was due to geographic mixing of heterogenous haplotypes during lowering sea levels of the Pleistocene. These findings indicate that cycles of geographic isolation and secondary contact happened in the Pleistocene glacial–interglacial cycles shaping genetic structure and population demography of S. ariakensis.
Phylogeography and sympatric differentiation of the Arctic charr Salvelinus alpinus (L.) complex in Siberia as revealed by mtDNA sequence analysis
Authors: Alekseyev S. S. , Bajno R. , Gordeeva N. V. , Reist J. D. , Power M. , Kirillov A. F. , Samusenok V. P. , Matveev A. N.
Published: September 2009

Sequence variation in the mtDNA control region of Arctic charr Salvelinus alpinus and Dolly Varden Salvelinus malma from 56 Siberian and North American populations was analysed to assess their phylogeographic relationships and the origins of sympatric forms. Phylogenetic trees confirm the integrity of phylogroups reported in previous mtDNA studies except that the Siberian group does not separate as a single cluster. Haplotype network analysis indicates the proximity of Siberian and Atlantic haplotypes. These are considered as one Eurasian group represented by the Atlantic, east Siberian (interior Siberia including Transbaikalia, Taimyr) and Eurosiberian (Finland, Spitsbergen, Taimyr) sub‐groups. Salvelinus alpinus with presumably introgressed Bering group (malma) haplotypes were found along eastern Siberian coasts up to the Olenek Bay and the Lena Delta region, where they overlap with the Eurasian group and in the easternmost interior region. It is proposed that Siberia was colonized by S. alpinus in two stages: from the west by the Eurasian group and later from the east by the Bering group. The high diversity of Eurasian group haplotypes in Siberia indicates its earlier colonization by S. alpinus as compared with the European Alps. This colonization was rapid, proceeded from a diverse gene pool, and was followed by differential survival of ancestral mtDNA lineages in different basins and regions, and local mutational events in isolated populations. The results presented here support a northern origin of Transbaikalian S. alpinus, the dispersion of S. alpinus to the Lake Baikal Basin from the Lena Basin, segregation of S. alpinus between Lena tributaries and their restricted migration over the divides between sub‐basins. These results also support sympatric origin of intralacustrine forms of S. alpinus.
Complex evolution of a highly conserved microsatellite locus in several fish species
Authors: Liu J.‐X. , Ely B.
Published: September 2009

The evolutionary dynamics of a highly conserved microsatellite locus (Dla 11) were studied in several fish species. The data indicated that multiple types of compound microsatellites arose through point mutations that were sometimes followed by expansion of the derived motif. Furthermore, extensive length variation was detected among species in the regions immediately flanking the repeat region.
Silencing of galectin‐3 changes the gene expression and augments the sensitivity of gastric cancer cells to chemotherapeutic agents
Authors: Cheong Teak‐Chin , Shin Ji‐Young , Chun Kyung‐Hee
Published: September 2009

Galectin‐3 is known to modulate cell proliferation and apoptosis and is highly expressed in human cancers, but its function in gastric cancer is still controversial. Here, we examined the role of galectin‐3 in gastric cancer cells by silencing it with synthetic double‐stranded siRNA. After silencing of galectin‐3, cell numbers decreased and cell shape changed. Galectin‐3 siRNA treatment also induced G1 arrest. DNA microarray analysis was used to assess changes in gene expression following galectin‐3 silencing. We found that silencing of galectin‐3 caused changes in gene expression. RT‐PCR and real‐time PCR were utilized for validation of the changes found in microarray studies. Western blot analysis confirmed changes in the expression of proteins of interest: cyclin D1, survivin, XIAP, XAF, PUMA, and GADD45α. Generally, it tended to increase the expression of several pro‐apoptotic genes, and to decrease the expression of cell cycle progressive genes. We also confirmed that changes in the expression of these genes were caused by galectin‐3 overexpression. Finally, we demonstrated that silencing of galectin‐3 enhanced apoptosis induction with chemotherapeutic agents by further reducing the expression of anti‐apoptotic and/or cell survival molecules such as survivin, cyclin D1, and XIAP, and increasing the expression of pro‐apoptotic XAF‐1. We conclude that galectin‐3 is involved in cancer progression and malignancy by modulating the expression of several relevant genes, and inhibition of galectin‐3 may be an approach to improve chemotherapy of gastric cancers. (Cancer Sci 2009)
Germination responses of Spartidium saharae (Coss. & Dur.) Pomel (Fabaceae) to temperature and salinity
Authors: Jamila Zammouri , Arbi Guetet , Mohamed Neffati
Published: September 2009

Spartidium saharae is an endemic species of the Saharo‐Arabian region. It is a tall shrub widely distributed in many sandy habitats including desert dunes and sandy systems in south‐western part of Tunisia, where water and salinity are serious constraints. Laboratory experiments were carried out to assess temperature and salinity effects on seed germination. The seed germination responses were determined in complete darkness over a wide range of temperatures and salinities. Germination was inhibited by either an increase or decrease in temperature from the optimal temperature range (15–20°C). Highest germination percentages were obtained under nonsaline conditions and an increase in NaCl concentrations progressively inhibited seed germination. An interaction between salinity and temperature yielded no germination at 200 mm NaCl.
Physiological and biochemical traits involved in the genotypic variability to salt tolerance of Tunisian Cakile maritima
Authors: Wided Megdiche , Nader Ben Amor , Ahmed Debez , Kamel Hessini , Riadh Ksouri , Chedly Abdelly
Published: September 2009

Cakile maritima (family: Brassicaceae) was collected from three provenances belonging to different bioclimatic stages (humid, semi arid and arid) in Tunisia to study their eco‐physiological and biochemical responses to salinity. Seedlings were cultivated on inert sand for 20 days under NaCl treatments (0, 100, 200, 400 mm NaCl). Plant response to salinity was provenance‐ and salt‐dependent. At 100 mm NaCl, growth parameters (leaf biomass, area, number per plant and relative growth rate) were improved in plants from Jerba (originating from arid bioclimatic stage) compared with the control, while growth was reduced in those from Tabarka (from humid area). High salt levels (400 mm NaCl) decreased the plant growth in the three provenances, but plants in Tabarka were the most salt sensitive. The relative salt tolerance of plants from Jerba and Bekalta provenances was associated with low levels of malondialdehyde as well as of electrolyte leakage and endoproteolytic activity. Salt reduced leaf hydration, the decrease in water content being dose‐dependent and more pronounced in Tabarka. Increase in salinity led to significant increase in leaf succulence and decrease in leaf water potential, especially in Jerba plants. The plants from the latter displayed the highest leaf levels of Na+ and Cl−, proline, soluble carbohydrates, soluble proteins, and polyphenols. Overall, the higher salt tolerance of plants from Jerba provenance, and to a lower extent of those from Bekalta, may be partly related to their better capacity for osmotic adjustment and to limit oxidative damage when salt‐challenged.
In vitro anti‐myeloma activity of the Aurora kinase inhibitor VE‐465
Authors: Negri Joseph M. , McMillin Douglas W. , Delmore Jake , Mitsiades Nicholas , Hayden Patrick , Klippel Steffen , Hideshima Teru , Chauhan Dharminder , Munshi Nikhil C. , Buser Carolyn A. , Pollard John , Richardson Paul G. , Anderson Kenneth C. , Mitsiades Constantine S.
Published: September 2009

This study characterized the preclinical anti‐myeloma activity of VE465, a low molecular weight pan‐Aurora kinase inhibitor. After 96‐h drug exposure, several multiple myeloma (MM) cell lines were more sensitive to VE465 compared to non‐malignant cells. The anti‐MM activity of VE465 was maintained in the presence of interleukin‐6 and, interestingly, enhanced by co‐culture with stromal cells. However, primary MM cells were less responsive than cell lines. Combinations with dexamethasone (Dex), doxorubicin (Doxo) and bortezomib showed no antagonism. Our study highlights the potential role of the tumour microenvironment in modulating the activity of this drug class.
The role of female sex hormones in the development and severity of allergic and non‐allergic asthma
Authors: Van Den Berge M. , Heijink H. I. , Van Oosterhout A. J. M. , Postma D. S.
Published: September 2009

Allergic asthma is usually diagnosed by the presence of variable airway obstruction, bronchial hyperresponsiveness, and allergy. However, a significant proportion of adult asthma patients (up to 40%) are non‐allergic. Patients with non‐allergic asthma often have a later disease onset and greater disease severity, as reflected by more severe airway obstruction and bronchial hyperresponsiveness. Furthermore, females have a higher risk of developing non‐allergic asthma. The latter suggests that hormone‐related events play an important role in the development and severity of adult‐onset non‐allergic asthma. This paper describes the associations between asthma and hormonal changes throughout the female life‐span, such as those associated with the monthly cycle of menstruation and menopausal hormonal changes.
Differential effects of elevated nutrient and sediment inputs on survival, growth and biomass of a common larval fish species (Dorosoma cepedianum)
Authors: GONZÁLEZ MARÍA J. , KNOLL LESLEY B. , VANNI MICHAEL J.
Published: September 2009

1. Elevated allochthonous inputs of nutrients and sediments to aquatic ecosystems are associated with eutrophication and sedimentation. Reservoirs receive substantial subsidies of nutrients and sediments from catchments due to their large catchment : lake area ratios. We examined the effect of elevated subsidies of sediments and/or dissolved nutrients on the success (survival, growth, biomass and condition factor) of larval gizzard shad (Dorosoma cepedianum), a widespread and dominant omnivorous fish in reservoir ecosystems.

2. We simulated allochthonous agricultural subsides by manipulating dissolved nutrients and sediment inputs in a 2 × 2 factorial design in experimental mesocosms. We predicted that larval fish success would be greater under elevated nutrients. However, we propose two alternative hypotheses with respect to the overall effect of allochthonous sediment inputs. If sediment inputs negatively affect larval gizzard feeding success, larval success would be highest when only nutrients are added and lowest when only sediments are added (+N > +N+S ≥ C > +S). If high turbidity enhances larval foraging activity (due to greater contrast between prey and background), we predict that larval success would be highest when both subsidy types (nutrients and sediment) are elevated, intermediate when either nutrients or sediments are added and the lowest when no subsidies are added (+N+S > +N ≥ +S > C).

3. Our results indicate that elevated nutrient and sediment conditions enhanced larval gizzard shad biomass, but the overall nutrient addition effect was greater than the sediment addition effect (+N ∼ +N+S > +S > C). We observed differential effects of nutrient and sediment inputs on larval survival, growth and condition factors.

4. The enhancement of fish biomass in elevated nutrients (+N, +N+S) relative to control conditions was associated with improved gizzard shad survival and not greater growth. The enhancement of fish biomass in the elevated sediment treatment (+S) relative to the control conditions was caused by an increase in survival that more than compensated for a negative effect of sediment addition on growth.

5. Our findings support the recommendation that reservoir management practices must consider the links between land use practices and food web dynamics. Our results suggest that reduction of subsidies of nutrients and sediments to productive reservoirs would decrease survival of larval gizzard shad due to lower food availability.