bluuebunny/crossref_metadata_2025 huggingface dataset:
Mathematical analysis of a Bohr atom model
Authors: Chen Goong , Ding Zhonghai , Hsu Sze-Bi , Kim Moochan , Zhou Jianxin
Published: February 2006

Bohr proposed in 1913 a model for atoms and molecules by synthesizing Planck’s quantum hypothesis with classical mechanics. When the atom number Z is small, his model provides good accuracy for the ground-state energy. When Z is large, his model is not as accurate in comparison with the experimental data but still provides a good trend agreeing with the experimental values of the ground-state energy of atoms. The main objective of this paper is to provide a rigorous mathematical analysis for the Bohr atom model. We have established the following: (1) An existence proof of the global minimizer of the ground-state energy through scaling. (2) A careful study of the critical points of the energy function. Such critical points include both the stable steady-state electron configurations as well as unstable saddle-type configurations. (3) Coplanarity of certain electron configurations. Numerical examples and graphics are also illustrated.
Test particles with acceleration-dependent Lagrangian
Authors: Toller M.
Published: February 2006

We consider a classical test particle subject to electromagnetic and gravitational fields, described by a Lagrangian depending on the acceleration and on a fundamental length. We associate to the particle a moving local reference frame and we study its trajectory in the principal fiber bundle of all the Lorentz frames. We discuss in this framework the general form of the Lagrange equations and the connection between symmetries and conservation laws (the Noether theorem). We apply these results to a model, already discussed by other authors, which implies an upper bound to the proper acceleration and to another new model in which a similar quantity, called “pseudoacceleration,” is bounded. With some simple choices of the fields, we illustrate some other interesting properties of the models and we show that unwanted features may appear, as unstable run-away solutions and unphysical values of the energy momentum or of the velocity.
Discrete dynamical systems embedded in Cantor sets
Authors: Benatti Fabio , Verjovsky Alberto , Zertuche Federico
Published: February 2006

While the notion of chaos is well established for dynamical systems on manifolds, it is not so for dynamical systems over discrete spaces with N variables, as binary neural networks and cellular automata. The main difficulty is the choice of a suitable topology to study the limit N→∞. By embedding the discrete phase space into a Cantor set we provided a natural setting to define topological entropy and Lyapunov exponents through the concept of error profile. We made explicit calculations both numerical and analytic for well-known discrete dynamical models.
Open-closed homotopy algebra in mathematical physics
Authors: Kajiura Hiroshige , Stasheff Jim
Published: February 2006

In this paper we discuss various aspects of open-closed homotopy algebras (OCHAs) presented in our previous paper, inspired by Zwiebach’s open-closed string field theory, but that first paper concentrated on the mathematical aspects. Here we show how an OCHA is obtained by extracting the tree part of Zwiebach’s quantum open-closed string field theory. We clarify the explicit relation of an OCHA with Kontsevich’s deformation quantization and with the B-models of homological mirror symmetry. An explicit form of the minimal model for an OCHA is given as well as its relation to the perturbative expansion of open-closed string field theory. We show that our open-closed homotopy algebra gives us a general scheme for deformation of open string structures (A∞ algebras) by closed strings (L∞ algebras).
New families of finite coherent orthoalgebras without bivaluations
Authors: Ruuge Artur E. , Van Oystaeyen Freddy
Published: February 2006

In the present paper we study the following problem: how to construct a coherent orthoalgebra which has only a finite number of elements, but at the same time does not admit a bivaluation (i.e., a morphism with a codomain being an orthoalgebra with just two elements). This problem is important in the perspective of Bell-Kochen-Specker theory, since one can associate such an orthoalgebra to every saturated noncolorable finite configuration of projective lines. The first result obtained in this paper provides a general method for constructing finite orthoalgebras. This method is then applied to obtain a new infinite family of finite coherent orthoalgebras that do not admit bivaluations. The corresponding proof is combinatorial and yields a description of the groups of symmetries for these orthoalgebras.
Internal motions in a complex consisting of a rare gas atom and a C2v molecule: Theoretical formulations and their applications to Fourier transform microwave spectra of Ne-dimethyl ether and Ar-dimethyl ether
Authors: Morita Yasumasa , Ohashi Nobukimi , Kawashima Yoshiyuki , Hirota Eizi
Published: February 2006

The internal motion of the rare gas atom, i.e., the relative motion of the two constituents, in a complex shown in the title was discussed by paying special attention to its effect on the rotational motion of the complex in order to extract as much precise information on this motion as possible from the observed rotational spectra. We have set up two theoretical formulations. One is based on a coordinate axis system attached to the C2v molecule, but its origin is floating with the motion of the rare gas atom, while keeping the orientation parallel to the original C2v molecule-fixed coordinate system. The second approach starts with counting the number of equivalent potential minima, which are well separated from the others by high potential barriers, and then collects all permutation-inversion operations, which transform the system from one minimum to another, to set up a group appropriate for the complex. By using the symmetry properties thus derived, a phenomenological Hamiltonian is set up to fit the observed spectra. The two formulations result in alike rotational energy matrices, and we have applied them to analyze the internal motions in the two complexes of present concern: neon-dimethyl ether (Ne–DME) and argon-dimethyl ether (Ar–DME). Some of the transitions observed by the present study exhibited additional splittings, which were interpreted as due to an internal rotation of the methyl groups in DME and were analyzed by the second formulation. For Ar–DME the splittings appeared only in high-K transitions, yielding the V3 potential barrier to be 778(1)cm−1, whereas those observed for Ne–DME were ascribed to the effects of the CH3 internal rotation on the inversion splitting.
Interdot interaction induced zero-bias maximum of the differential conductance in parallel double quantum dots
Authors: Chi Feng , Li Shu-Shen
Published: March 2006

We have studied the equilibrium and nonequilibrium electronic transports through a double quantum dot coupled to leads in a symmetrical parallel configuration in the presence of both the inter- and the intradot Coulomb interactions. The influences of the interdot interaction and the difference between dot levels on the local density of states (LDOS) and the differential conductance are paid special attention. We find an interesting zero-bias maximum of the differential conductance induced by the interdot interaction, which can be interpreted in terms of the LDOS of the two dots. Due to the presence of the interdot interaction, the LDOS peaks around the dot levels εi are split, and as a result, the most active energy level which supports the transport is shifted near to the Fermi level of the leads in the equilibrium situation.
Efficient computation of the exchange-correlation contribution in the density functional theory through multiresolution
Authors: Kong Jing , Brown Shawn T. , Fusti-Molnar Laszlo
Published: March 2006

A new algorithm is presented to improve the efficiency of the computation of exchange-correlation contributions, a major time-consuming step in a density functional theory (DFT) calculation. The new method, called multiresolution exchange correlation (mrXC), takes advantage of the variation in resolution among the Gaussian basis functions and shifts the calculation associated with low-resolution (smooth) basis function pairs to an even-spaced cubic grid. The cubic grid is much less dense in the vicinity of the nuclei than the atom-centered grid and the computation on the former is shown to be much more efficient than on the latter. MrXC does not alter the formalism of the current standard algorithm based on the atom-centered grid (ACG), but instead employs two fast and accurate transformations between the ACG and the cubic grid. Preliminary results with local density approximation have shown that mrXC yields three to five times improvement in efficiency with negligible error. The extension to DFT functionals with generalized gradient approximation is also briefly discussed.
High precision variational calculations for the Born-Oppenheimer energies of the ground state of the hydrogen molecule
Authors: Sims James S. , Hagstrom Stanley A.
Published: February 2006

Born-Oppenheimer approximation Hylleraas variational calculations with up to 7034 expansion terms are reported for the Σg+1 ground state of neutral hydrogen at various internuclear distances. The nonrelativistic energy is calculated to be −1.174475714220(1)hartree at R=1.4bohr, which is four orders of magnitude better than the best previous Hylleraas calculation, that of Wolniewicz [J. Chem. Phys. 103, 1792 (1995)]. This result agrees well with the best previous variational energy, −1.174475714216hartree, of Cencek (personal communication), obtained using explicitly correlated Gaussians (ECGs) [Cencek and Rychlewski, J. Chem. Phys. 98, 1252 (1993); Cencek et al., ibid. 95, 2572 (1995); Rychlewski, Adv. Quantum Chem. 31, 173 (1998)]. The uncertainty in our result is also discussed. The nonrelativistic energy is calculated to be −1.174475931399(1)hartree at the equilibrium R=1.4011bohr distance. This result also agrees well with the best previous variational energy, −1.174475931389hartree, of Cencek and Rychlewski [Rychlewski, Handbook of Molecular Physics and Quantum Chemistry, edited by S. Wilson (Wiley, New York, 2003), Vol. 2, pp. 199–218; Rychlewski, Explicitly Correlated Wave Functions in Chemistry and Physics Theory and Applications, edited by J. Rychlewski (Kluwer Academic, Dordrecht, 2003), pp. 91–147.], obtained using ECGs.
The quantum defect: The true measure of time-dependent density-functional results for atoms
Authors: van Faassen Meta , Burke Kieron
Published: February 2006

Quantum defect theory is applied to (time-dependent) density-functional calculations of Rydberg series for closed shell atoms: He, Be, and Ne. The performance and behavior of such calculations are much better quantified and understood in terms of the quantum defect rather than transition energies.
Secondary electron emission and photoemission studies on surface films of carbon nitride
Authors: Ripalda J. M. , Montero I. , Vázquez L. , Raboso D. , Galán L.
Published: March 2006

The secondary electron emission yield of fullerene, graphite, and diamondlike carbon after low-energy N2+ ion bombardment was studied for antimultipactor applications. Nitrogen incorporation into the carbon thin films decreases their secondary emission yield, contrary to the hydrogen or oxygen effect. Carbon nitride surface textured to a nanometric scale had the property of hindering secondary electron emission. Valence bands obtained from photoemission spectroscopy using synchrotron radiation were correlated with secondary electron emission measurements. Multipactor threshold power for carbon nitride was 7.5kW.
Site-selectivity of 3d metal cation dopants and dielectric response in calcium copper titanate
Authors: Chung Sung-Yoon , Choi Si-Young , Yamamoto Takahisa , Ikuhara Yuichi , Kang Suk-Joong L.
Published: March 2006

By doping a few atomic percent of 3d-block cations, we demonstrate that the high dielectric response in CaCu3Ti4O12 can be reduced by a factor of ∼103 at room temperature. Each of the added dopants shows its own preferential substitution on either Cu or Ti sites. The dopants that act as acceptors have a critical impact on the disappearance of the electrostatic potential barrier at grain boundaries, resulting in drastically decreased permittivity values of <90 without voltage dependence. The present doping experiment directly shows that the potential barrier at internal interfaces is a key factor for the peculiar dielectric phenomena.
Reinventing Authority: Embedded Knowledge Networks and the New Global Finance
Authors: Sinclair Timothy J
Published: March 2006

The author challenges common assumptions about the nature of the emerging global economy. Rather than being the product of disembedded market forces, this new global political economy is organized by specialized forms of intelligence gathering and judgment determination inside the new global finance (NGF). These embedded knowledge networks (EKNs) include the major bond-rating agencies, such as Moody's Investors Service, and Standard and Poor's (both based in New York, but increasingly operating internationally). The author analyzes central features of EKNs, including their relationship to social interests, epistemic authority (the consequences that follow from EKN reputational assets), market coordination (the policy implications of EKN transformation of uncertainty into risk), and the complexities that characterize the interaction between EKNs and governments. The author argues that rather than disappearing with the increasing freedom of global market forces in the NGF, authority has been reinvented—characteristically in the form of EKNs—altering the postwar balance of public and private influence on policy formation.
Balancing Concentration and Dispersion? Public Policy and Urban Structure in Toronto
Authors: Filion Pierre
Published: March 2006

By North American standards Toronto is a concentrated agglomeration. Its downtown has enjoyed spectacular growth since the 1960s; most inner-city neighbourhoods are perceived as desirable; and public transit patronage is high relative to that of same-size North American metropolitan regions. Still, it is within dispersed, car-oriented, suburbs that most post-1950 development has taken place. This agglomeration is composed of two realms—a concentrated and a dispersed realm—differentiated by their respective land-use-transportation dynamic. The concentrated realm is defined by a considerable reliance on walking and public transportation, a mixing of land uses and overall higher employment and residential densities than elsewhere in the metropolitan region. Meanwhile, the dispersed realm is car dependent, dominated by large monofunctional zones and developed at a relatively low density. The author links the coexistence and respective importance of these two realms in the Toronto agglomeration both to the nature of urban policies implemented since 1950 and to the circumstances that have led to their adoption. The construction of expressways, suburban type land-use planning, and a generous provision of open space have abetted dispersion. By contrast, the construction of a subway system and measures encouraging the redevelopment of underused land have promoted growth within the concentrated portion of the agglomeration. It is noteworthy, however, that these measures have failed in their attempts to induce concentration beyond the prewar urbanized perimeter. The author examines the positive and negative aspects of the presence of these two realms within a given agglomeration and highlights the threat newly adopted policies represent for the concentrated realm.
New Fragmentations and New Cooperations in the Turkish Bourgeoisie
Authors: Cokgezen Murat
Published: March 2006

The establishment of a new business association constitutes both a fragmentation and a cooperation among capitalists. The author aims to determine the causes of the fragmentation and the cooperation by discussing the background of new business associations being established in Turkey: it is concluded that conflicting interests of capitalists are a major source of those two phenomena. It is also found that both heterogeneity and homogeneity within the cooperating group may facilitate cooperation. Fragmenting aspects of heterogeneity are associated with selective incentives.
Local Authority Provision versus Club Provision
Authors: King David N , Ma Yue
Published: March 2006

The main purpose of this paper is to distinguish clearly between local authorities and clubs and to consider the circumstances in which individual consumers would prefer to have services provided by one or the other. We also consider the circumstances in which consumers would prefer individual or central government provision. There are also some hybrid positions between different types of provision. We end with some examples of cases where the mode of delivery in Great Britain has changed, or is changing, from traditional local government provision to other forms. Our model suggests a rationale for these changes.
Local Authority Size in Theory and Practice
Authors: King David N , Ma Yue
Published: March 2006

In this paper we develop a model for local authority size that is based on the approach towards local government reform that was used by the UK governments in the 1970s and the 1990s. To do so, we examine the different aspects of costs for local services, the minimum cost size facility used to provide local services, and the minimum efficient size for a local authority. We then argue that, for a given level of service, the belief that a tendency for local authorities to become enablers rather than producers would reduce the minimum efficient size of authority may not be correct. Finally, the model is developed to determine simultaneously the optimum quantity of local services and the minimum efficient size. It shows that the solution depends on how preferences vary among different citizens, and argues that governments paid too little heed to these variations. Thus we conclude that it is very doubtful whether either the 1970s or the 1990s reforms produced the structure of local government that would have emerged if the approach adopted by the governments concerned had been used with more care.
Making Sense of Sustainable Development: Politicians, Professionals, and Policies in Local Planning
Authors: Bruff Gareth E , Wood Adrian P
Published: March 2006

The authors investigate the ways in which sustainable development is interpreted within the development plan process, focusing on the roles of local politicians and planners. The rapidly developing ‘policy space’ surrounding the idea of sustainable development provides opportunities for engagement between planners, politicians, and other local actors. This policy space and its relationship to the plan-making process is outlined, along with key political aspects, before the results from an investigation into two case-study unitary development plans are presented. These illustrate how the influences of planners and politicians, along with key characteristics of the planning system, were instrumental in shaping both the content and the form of sustainable development policies and had implications for the way in which local sustainable development was interpreted.
New Approaches to Local Democracy: Direct Democracy, Participation and the ‘Third Sector’
Authors: Buček Ján , Smith Brian
Published: March 2006

Two themes of particular significance in the changing world of local government are examined: the growing pressures to incorporate participatory and direct forms of democracy into local government; and the varied use of a complex structure of nongovernmental organisations as part of local governance. Two main forms of democracy with participation are discussed: direct democracy and participatory democracy. Differences between them are explained and the demands for them in transitional and established democracies are described. The different ways in which ‘third sector’ bodies are involved in local governance are explored and their contribution to local democratisation assessed. Innovations in participation and the involvement of the third sector can revitalise local democracy.
The “Eager Gaze of the Tourist” Meets “Our Grandfathers' Guns”: Producing and Contesting the Land of Enchantment in Gallup, New Mexico
Authors: D'Arcus Bruce
Published: March 2006

In this paper I explore connections between representational and material space as expressed in conflicts over ethnic tourism in the American Southwest. Using the case of Gallup, New Mexico, I first examine how a specific regional discourse was embodied in a plan to create a National Indian Memorial Park. In this discourse, space is rendered a quaint ‘Land of Enchantment’. In the remainder of the paper, I discuss attempts by American Indian activists to challenge this production of space through various material and representational efforts. The outcome of these efforts is reflected in the resulting space produced, and illustrates some of the complex spatial politics around ethnic tourism.
Retrenchment from a Queer Ideal: Class Privilege and the Failure of Identity Politics in AIDS Activism
Authors: Hodge G Derrick
Published: March 2006

In the decade following the 1969 Stonewall Riots, identity politics in New York City enabled the construction of a socially and recreationally defined homogeneous gay identity. But contrary to common self-congratulatory accounts that have made their way into the social scientific literature, this gay identity was woefully unprepared to launch an effective political response to AIDS in the 1980s. The AIDS activism movement which did finally emerge in the form of ACT UP/New York was born from within the gay identity, but it embraced a more expansive coalitional politics. Its amplified vision called for a critique not only of medical research procedures and public funding initiatives but also of the larger political-economic and social structures that had translated a medical emergency into a social catastrophe. This more expansive politics gave rise to the Queer movement, premised less on essential identity than on affinity of commitment. But this political evolution was not internally uncontested: the more privileged white middle-class men within ACT UP resisted any movement away from a narrowly medical approach to AIDS for those with access. The resulting conflict eventually crippled ACT UP, perhaps irrevocably. Some gay and queer geographical theorizing has learned from the Queer movement and has embraced the politics of affinity, in that it has been willing to incorporate in its analyses an investigation of the ways in which gay identity politics is implicated in the wider systems of stratification along axes of gender, race, and class. But most gay geography remains trapped in the rather narrow vision of identity politics.
Patents, Travel, Space: Ethnographic Encounters with Objects in Transit
Authors: De Laet Marianne
Published: March 2006

In this paper, an ethnographical take on objects in motion, I follow the travel of patents from their places of origin in the Western world of technoscience to newly developing worlds. I argue that not only does the influx of patents and patent systems change the sociotechnical configurations in which they emerge; the patent itself—or so I claim—changes with its travel as well, and so it is a different thing in different places. I thus link the nature of things with the places in which they operate, and frame the patent as both a changeable object and an agent of change.
Music and the Politics of Sound: Nationalism, Citizenship, and Auditory Space
Authors: Revill George
Published: March 2006

The author argues that the distinctive properties of sound give music a very particular role in the organisation of social, economic, and political spaces. Music gains the cultural authority necessary for participation in such spatial processes through properties of sound, which are not fixed and universal but temporally and spatially specific, actively produced in the material/imaginal networks of musical performance. He examines theoretical arguments concerning the performative specificity of sonic experience and considers three ways in which the sonic properties of music are centrally involved in the production of cultural geographies. He draws examples from English music of the period 1880–1940 in order to explore how sound informs moral geographies of landscape, nation, and citizen.
Global Change, Local Angst: Class and the American Patriot Movement
Authors: Gallaher Carolyn
Published: March 2006

In this paper I examine the Patriot Movement, a broad, right-wing social movement in the USA that emerged in response to the economic insecurities of globalization. The purpose of this paper is to examine how the movement's class-based concerns are articulated through discourses of local sovereignty and patriotism. Because patriots' class interests are articulated through the patriot category rather than through traditional class categories, I use identity theory to analyze the movement. The movement, with its legacy of violence and its calls for local control, illustrates that the submersion of class (as a category that crosses scale) can lead to militant and particularistic responses. The couching of local power within discourses of patriotism demonstrates that such politics continue to rely on larger scales for legitimization. Reference to patriotism is, however, mostly symbolic. As such patriots ironically are unable to conceive of class positioning or their responses to it as cross local. As a case study I examine the movement in central Kentucky, and an issue around which patriots there have galvanized—calls to legalize industrial hemp. The paper concludes by arguing that the Patriot Movement illustrates the need to actively create progressive discourses to address working-class concerns.
The impact of sequencing the bovine genome
Authors: Womack J. E.
Published: March 2006

Sequencing the bovine genome is the culmination of more than a decade of international collaboration to bring together resources to chart the genome of an economically important and biologically interesting species. Although considerable sequence is available at the publication of these proceedings, much work remains in annotation of the genome and the discovery of DNA polymorphisms within and between breeds. Nonetheless, the public availability of this sequence has already enhanced our ability to identify genes underlying phenotypes and to understand evolutionary relationships with other mammalian species. The accelerated rate of gene discovery in humans and laboratory animals following the sequencing of their genomes promises an exciting post-sequencing era for bovine genomics.
Body-wide gene therapy of Duchenne muscular dystrophy in the
mdx
mouse model
Authors: Denti Michela Alessandra , Rosa Alessandro , D’Antona Giuseppe , Sthandier Olga , De Angelis Fernanda Gabriella , Nicoletti Carmine , Allocca Mariacarmela , Pansarasa Orietta , Parente Valeria , Musarò Antonio , Auricchio Alberto , Bottinelli Roberto , Bozzoni Irene
Published: February 2006

Duchenne muscular dystrophy is an X-linked muscle disease characterized by mutations in the dystrophin gene. Many of these can be corrected at the posttranscriptional level by skipping the mutated exon. We have obtained persistent exon skipping in
mdx
mice by tail vein injection with an adeno-associated viral (AAV) vector expressing antisense sequences as part of the stable cellular U1 small nuclear RNA. Systemic delivery of the AAV construct resulted in effective body-wide colonization, significant recovery of the functional properties
in vivo
, and lower creatine kinase serum levels, suggesting an overall decrease in muscle wasting. The transduced muscles rescued dystrophin expression and displayed a significant recovery of function toward the normal values at single muscle fiber level. This approach provides solid bases for a systemic use of AAV-mediated antisense-U1 small nuclear RNA expression for the therapeutic treatment of Duchenne muscular dystrophy.
Projection structure of the human copper transporter CTR1 at 6-Å resolution reveals a compact trimer with a novel channel-like architecture
Authors: Aller Stephen G. , Unger Vinzenz M.
Published: February 2006

Human CTR1 is a high-affinity copper transporter that also mediates the uptake of the anticancer drug cisplatin by largely unknown transport mechanisms. Here we report the 6-Å projection structure obtained for human CTR1 by using electron crystallography of 2D protein crystals in a native phospholipid bilayer. The projection of CTR1 reveals a symmetrical trimer that is <40 Å wide. Notably, the center threefold axis of each trimer forms a region of very low electron density likely to be involved in copper translocation. The formation of a putative pore for metal ions at the interface of three identical subunits deviates from the structural design of typical primary and secondary active transporters and reveals that copper uptake transporters have a novel architecture that is structurally more closely related to channel proteins.
ChiralN-salicylidene vanadyl carboxylate-catalyzed enantioselective aerobic oxidation of α-hydroxy esters and amides
Authors: Weng Shiue-Shien , Shen Mei-Wen , Kao Jun-Qi , Munot Yogesh S. , Chen Chien-Tien
Published: February 2006

A series of chiral vanadyl carboxylates derived fromN-salicylidene-l-α-amino acids and vanadyl sulfate has been developed. These configurationally well defined complexes were examined for the kinetic resolution of double- and mono-activated 2° alcohols. The best chiral templates involve the combination ofl-tert-leucine and 3,5-di-t-butyl-, 3,5-diphenyl-, or 3,4-dibromo-salicylaldehyde. The resulting vanadyl(V)-methoxide complexes after recrystallization from air-saturated methanol serve as highly enantioselective catalysts for asymmetric aerobic oxidation of α-hydroxyl-esters and amides with a diverse array of α-,O-, andN-substituents at ambient temperature in toluene. The asymmetric inductions of the oxidation process are in the range of 10 to >100 in terms of selectivity factors (krel) in most instances. The previously undescribed aerobic oxidation protocol is also applicable to the kinetic resolution of C-13 taxol side chain with high selectivity factor (krel= 35). X-ray crystallographic analysis of an adduct between a given vanadyl complex andN-benzyl-mandelamide allows for probing the stereochemical origin of the nearly exclusive asymmetric control in the oxidation process.
Checkpoint functions are required for normal S-phase progression in
Saccharomyces cerevisiae
RCAF- and CAF-I-defective mutants
Authors: Kats Ellen S. , Albuquerque Claudio P. , Zhou Huilin , Kolodner Richard D.
Published: February 2006

The chromatin-assembly factor I (CAF-I) and the replication-coupling assembly factor (RCAF) complexes function in chromatin assembly during DNA replication and repair and play a role in the maintenance of genome stability. Here, we have investigated their role in checkpoints and S-phase progression. FACS analysis of mutants lacking Asf1 or Cac1 as well as various checkpoint proteins indicated that normal rates of S-phase progression in
asf1
mutants have a strong requirement for replication checkpoint proteins, whereas normal S-phase progression in
cac1
mutants has only a weak requirement for either replication or DNA-damage checkpoint proteins. Furthermore,
asf1
mutants had high levels of Ddc2.GFP foci that were further increased in
asf1 dun1
double mutants consistent with a requirement for checkpoint proteins in S-phase progression in
asf1
mutants, whereas
cac1
mutants had much lower levels of Ddc2.GFP foci that were not increased by a
dun1
mutation. Our data suggest that RCAF defects lead to unstable replication forks that are then stabilized by replication checkpoint proteins, whereas CAF-I defects likely cause different types of DNA damage.
Clonal population structure and genetic diversity of
Candida albicans
in AIDS patients from Abidjan (Côte d’Ivoire)
Authors: Nébavi François , Ayala Francisco J. , Renaud François , Bertout Sébastien , Eholié Serge , Moussa Koné , Mallié Michèle , de Meeûs Thierry
Published: February 2006

We have investigated the genotype at 14 enzyme-encoding loci in 275 isolates of the pathogenic yeast
Candida albicans
sampled from 42 HIV-positive patients (all but one with AIDS) from Abidjan (Côte d’Ivoire). We separately analyzed the following variables: patient, residence, age, gender, T cell count, hospitalization (yes or no), drug treatment, date of sampling, multilocus genotype, and serotype. The most important factors contributing to the genetic variability of
C. albicans
are individual patient and gender. Our data manifest that the population size of the parasite is relatively small within each patient, although larger in women than in men, and that, at least for the patients involved in the study, the transmission rate of
C. albicans
between human adults is very low. Most important is the inference that the prevailing mode of reproduction of
C. albicans
in natural populations is clonal, so that sexual reproduction is extremely rare, if it occurs at all.
Increased Wnt signaling triggers oncogenic conversion of human breast epithelial cells by a Notch-dependent mechanism
Authors: Ayyanan Ayyakannu , Civenni Gianluca , Ciarloni Laura , Morel Catherine , Mueller Nathalie , Lefort Karine , Mandinova Anna , Raffoul Wassim , Fiche Maryse , Dotto Gian Paolo , Brisken Cathrin
Published: February 2006

Wnt and Notch signaling have long been established as strongly oncogenic in the mouse mammary gland. Aberrant expression of several Wnts and other components of this pathway in human breast carcinomas has been reported, but evidence for a causative role in the human disease has been missing. Here we report that increased Wnt signaling, as achieved by ectopic expression of Wnt-1, triggers the DNA damage response (DDR) and an ensuing cascade of events resulting in tumorigenic conversion of primary human mammary epithelial cells. Wnt-1-transformed cells have high telomerase activity and compromised p53 and Rb function, grow as spheres in suspension, and in mice form tumors that closely resemble medullary carcinomas of the breast. Notch signaling is up-regulated through a mechanism involving increased expression of the Notch ligands Dll1, Dll3, and Dll4 and is required for expression of the tumorigenic phenotype. Increased Notch signaling in primary human mammary epithelial cells is sufficient to reproduce some aspects of Wnt-induced transformation. The relevance of these findings for human breast cancer is supported by the fact that expression of Wnt-1 and Wnt-4 and of established Wnt target genes, such as Axin-2 and Lef-1, as well as the Notch ligands, such as Dll3 and Dll4, is up-regulated in human breast carcinomas.
Signals from OX40 regulate nuclear factor of activated T cells c1 and T cell helper 2 lineage commitment
Authors: So Takanori , Song Jianxun , Sugie Katsuji , Altman Amnon , Croft Michael
Published: February 2006

T cell helper type 2 (Th2) differentiation is driven by a source of IL-4 receptor (IL-4R) that mobilizes IL-4R signaling pathways and the transcription factor GATA-3. Naïve CD4 cells can secrete IL-4 independently of IL-4R signals, but how this secretion is regulated is not understood. Here we demonstrate that costimulation through the tumor necrosis factor receptor family molecule OX40, in synergy with CD28, is essential for high levels of nuclear factor of activated T cells c1 to accumulate in the nucleus of a recently activated naïve T cell. This action is not dependent on either IL-4R or IL-2R signals and results in OX40 controlling initial naïve T cell IL-4 transcription. OX40 signals subsequently enhance nuclear GATA-3 accumulation through an IL-4R-dependent action, leading to Th2 differentiation. These data show that, in the absence of an exogenous source of IL-4, OX40 provides a critical synergistic and temporal signal with other noncytokine receptors to modulate nuclear factor of activated T cells c1 and to promote optimal Th2 generation.
Computed tomography imaging of vena cava filter complications: a pictorial review
Authors: Cina A. , Masselli G. , Stasi C. Di , Natale L. , Cotroneo A. R. , Cina G. , Bonomo L.
Published: March 2006

Caval filters are widely used in the prevention of pulmonary embolism. Filters have proved to be effective, but the complication rate is not negligible. Computed tomography (CT) provides a complete evaluation of the filter, including both caval and extracaval complications. In this review, we describe the normal CT aspect of cava filters, the classification of complications and their CT findings. Technical considerations for adequate CT imaging are also highlighted.
Brachytherapy technique for abdominal wall metastases of colorectal cancer: ultrasound-guided insertion of applicator needle and a skin preservation method
Authors: Kishi K. , Takifuji K. , Shirai S. , Sonomura T. , Sato M. , Yamaue H.
Published: March 2006

Purpose: To report a technique of interstitial brachytherapy for the treatment of subcutaneous metastatic abdominal wall tumors.

Material and Methods: We developed a brachytherapy technique consisting of ultrasound-guided insertion of applicator needles to avoid the organs at risk, such as intestines, and saline injection into the subcutaneous tissue between the tumor and the skin to decrease the skin dose. We encountered three patients with painful metastases from rectal carcinoma in the abdominal wall refractory to external radiotherapy. They were subjected to this brachytherapy with a single dose of 20 Gy.

Results: The procedure was safely achieved in all three patients. Long-lasting pain reduction and tumor shrinkage was obtained without early or late complications.

Conclusion: This interstitial brachytherapy technique seems to be feasible in the treatment of metastatic abdominal wall tumors.
A Trade Institution as a Peaceful Institution? A Contribution to Integrative Theory
Authors: Caruso Raul
Published: March 2006

Recent studies emphasize the occurrence of conflict as a rational economic activity along with production and exchange. Agents are assumed to divide their efforts into fighting and productive activities, as commonly denoted by “guns” and “butter.” This article tries to go beyond this “manichean” idea, assuming Boulding's concept of “integrative system.” In particular, the article investigates whether a trade institution committed to free and fair trade could foster “peaceful” benefits for member countries. The analysis, produced in a very simplified world, counts as a founding pillar of the Contest Success Function. The results of the model suggest that in an institutionalized scenario, agents gain more both in terms of economic utility and in terms of peace than in “continuing conflict” and “obstructed trade” scenarios.
Paloverde: an OpenGL 3D phylogeny browser
Authors: Sanderson Michael J.
Published: February 2006

Summary:  Paloverde is a new program designed to help visualize the phylogenetic structure of moderately large trees—trees on the scale of 100–2500 leaf nodes. The program embeds the user in an interactive virtual 3D world in which a large tree presented in various layouts can be manipulated through a mouse interface. The program implements radial 2D layouts, and true 3D spiral, conical and hemispherical (i.e. truly ‘tree’-like) layouts. Subclades can be defined in the input file (using standard node-based definitions) and displayed collapsed as new leaf nodes, or left intact but annotated with names around the periphery of the tree. A search tool lets the user zoom to any selected leaf node. Paloverde is an open source project written in ANSI C using the OpenGL library for 3D visualization.

Availability: Source code, makefiles for Mac OS X and Linux and a compiled binary for Mac OS X are available at , along with a sample dataset.

Contact:  mjsanderson@ucdavis.edu
The UCSC Known Genes
Authors: Hsu Fan , Kent W. James , Clawson Hiram , Kuhn Robert M. , Diekhans Mark , Haussler David
Published: February 2006

The University of California Santa Cruz (UCSC) Known Genes dataset is constructed by a fully automated process, based on protein data from Swiss-Prot/TrEMBL (UniProt) and the associated mRNA data from Genbank. The detailed steps of this process are described. Extensive cross-references from this dataset to other genomic and proteomic data were constructed. For each known gene, a details page is provided containing rich information about the gene, together with extensive links to other relevant genomic, proteomic and pathway data. As of July 2005, the UCSC Known Genes are available for human, mouse and rat genomes. The Known Genes serves as a foundation to support several key programs: the Genome Browser, Proteome Browser, Gene Sorter and Table Browser offered at the UCSC website. All the associated data files and program source code are also available. They can be accessed at . The genomic coverage of UCSC Known Genes, RefSeq, Ensembl Genes, H-Invitational and CCDS is analyzed. Although UCSC Known Genes offers the highest genomic and CDS coverage among major human and mouse gene sets, more detailed analysis suggests all of them could be further improved.

Contact:  fanhsu@soe.ucsc.edu
A novel sensitive method for the detection of user-defined compositional bias in biological sequences
Authors: Kuznetsov Igor B. , Hwang Seungwoo
Published: February 2006

Motivation: Most biological sequences contain compositionally biased segments in which one or more residue types are significantly overrepresented. The function and evolution of these segments are poorly understood. Usually, all types of compositionally biased segments are masked and ignored during sequence analysis. However, it has been shown for a number of proteins that biased segments that contain amino acids with similar chemical properties are involved in a variety of molecular functions and human diseases. A detailed large-scale analysis of the functional implications and evolutionary conservation of different compositionally biased segments requires a sensitive method capable of detecting user-specified types of compositional bias.

Results: We present BIAS, a novel sensitive method for the detection of compositionally biased segments composed of a user-specified set of residue types. BIAS uses the discrete scan statistics that provides a highly accurate correction for multiple tests to compute analytical estimates of the significance of each compositionally biased segment. The method can take into account global compositional bias when computing analytical estimates of the significance of local clusters. BIAS is benchmarked against SEG, SAPS and CAST programs. We also use BIAS to show that groups of proteins with the same biological function are significantly associated with particular types of compositionally biased segments.

Availability: The software is available at

Contact:  ikuznetsov@albany.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Mass Analysis Peptide Sequence Prediction (MAPSP)
Authors: Eisenacher Martin , de Braaf Jürgen , König Simone
Published: February 2006

Summary: The software tool MAPSP allows the combinatorial prediction of novel short peptides such as hormones with common sequence features. In addition, it assists in de novo sequencing in general. The tool was designed for use in conjunction with the analytical identification method of mass spectrometry (MS) and it can considerably speed-up the analysis of unknowns.

Availability: The web interface is freely available at

Contact:  koenigs@uni-muenster.de
Algorithm to find gene expression profiles of deregulation and identify families of disease-altered genes
Authors: Prieto C. , Rivas M.J. , Sánchez J.M. , López-Fidalgo J. , De Las Rivas J.
Published: February 2006

Motivation: Alteration of gene expression often results in up- or down-regulated genes and the most common analysis strategies look for such differentially expressed genes. However, molecular disease mechanisms typically constitute abnormalities in the regulation of genes producing strong alterations in the expression levels. The search for such deregulation states in the genomic expression profiles will help to identify disease-altered genes better.

Results: We have developed an algorithm that searches for the genes which present a significant alteration in the variability of their expression profiles, by comparing an altered state with a control state. The algorithm provides groups of genes and assigns a statistical measure of significance to each group of genes selected. The method also includes a prefilter tool to select genes with a threshold of differential expression that can be set by the user ad casum. The method is evaluated using an experimental set of microarrays of human control and cancer samples from patients with acute promyelocytic leukemia.

Availability: The method is implemented in an R package called AlteredExpression available in and will be included in the Bioconductor project.

Contact:  jrivas@usal.es
A systematic comparison and evaluation of biclustering methods for gene expression data
Authors: Prelić Amela , Bleuler Stefan , Zimmermann Philip , Wille Anja , Bühlmann Peter , Gruissem Wilhelm , Hennig Lars , Thiele Lothar , Zitzler Eckart
Published: February 2006

Motivation: In recent years, there have been various efforts to overcome the limitations of standard clustering approaches for the analysis of gene expression data by grouping genes and samples simultaneously. The underlying concept, which is often referred to as biclustering, allows to identify sets of genes sharing compatible expression patterns across subsets of samples, and its usefulness has been demonstrated for different organisms and datasets. Several biclustering methods have been proposed in the literature; however, it is not clear how the different techniques compare with each other with respect to the biological relevance of the clusters as well as with other characteristics such as robustness and sensitivity to noise. Accordingly, no guidelines concerning the choice of the biclustering method are currently available.

Results: First, this paper provides a methodology for comparing and validating biclustering methods that includes a simple binary reference model. Although this model captures the essential features of most biclustering approaches, it is still simple enough to exactly determine all optimal groupings; to this end, we propose a fast divide-and-conquer algorithm (Bimax). Second, we evaluate the performance of five salient biclustering algorithms together with the reference model and a hierarchical clustering method on various synthetic and real datasets for Saccharomyces cerevisiae and Arabidopsis thaliana. The comparison reveals that (1) biclustering in general has advantages over a conventional hierarchical clustering approach, (2) there are considerable performance differences between the tested methods and (3) already the simple reference model delivers relevant patterns within all considered settings.

Availability: The datasets used, the outcomes of the biclustering algorithms and the Bimax implementation for the reference model are available at

Contact:  bleuler@tik.ee.ethz.ch

Supplementary information:  Supplementary data are available at