bluuebunny/crossref_metadata_2025 huggingface dataset:
A Chimeric Porcine Circovirus (PCV) with the Immunogenic Capsid Gene of the Pathogenic PCV Type 2 (PCV2) Cloned into the Genomic Backbone of the Nonpathogenic PCV1 Induces Protective Immunity against PCV2 Infection in Pigs
Authors: Fenaux M. , Opriessnig T. , Halbur P. G. , Elvinger F. , Meng X. J.
Published: May 2004

Porcine circovirus type 2 (PCV2) is associated with postweaning multisystemic wasting syndrome in pigs, whereas PCV1 is nonpathogenic. We previously demonstrated that a chimeric PCV1-2 virus (with the immunogenic capsid gene of PCV2 cloned into the backbone of PCV1) induces an antibody response to the PCV2 capsid protein and is attenuated in pigs. Here, we report that the attenuated chimeric PCV1-2 induces protective immunity to wild-type PCV2 challenge in pigs. A total of 48 specific-pathogen-free piglets were randomly and equally assigned to four groups of 12 pigs each. Pigs in group 1 were vaccinated by intramuscular injection with 200 μg of the chimeric PCV1-2 infectious DNA clone. Pigs in group 2 were vaccinated by intralymphoid injection with 200 μg of a chimeric PCV1-2 infectious DNA clone. Pigs in group 3 were vaccinated by intramuscular injection with 10
3.5
50% tissue culture infective doses (TCID
50
) of the chimeric PCV1-2 live virus. Pigs in group 4 were not vaccinated and served as controls. By 42 days postvaccination (DPV), the majority of pigs had seroconverted to PCV2 capsid antibody. At 42 DPV, all pigs were challenged intranasally and intramuscularly with 2 × 10
4.5
TCID
50
of a wild-type pathogenic PCV2 virus. By 21 days postchallenge (DPC), 9 out of the 12 group 4 pigs were viremic for PCV2. Vaccinated animals in groups 1 to 3 had no detectable PCV2 viremia after challenge. At 21 DPC the lymph nodes in the nonvaccinated pigs were larger (
P
< 0.05) than those of vaccinated pigs. The PCV2 genomic copy loads in lymph nodes were reduced (
P
< 0.0001) in vaccinated pigs. Moderate amounts of PCV2 antigen were detected in most lymphoid tissues of nonvaccinated pigs but in only 1 of 36 vaccinated pigs. Mild-to-severe lymphoid depletion and histiocytic replacement were detected in lymphoid tissues in the majority of nonvaccinated group 4 pigs but in only a few vaccinated group 1 to 3 pigs. The data from this study indicated that when given intramuscularly in pigs, the attenuated chimeric PCV1-2 live virus, as well as the chimeric PCV1-2 infectious DNA clone, induces protective immunity against PCV2 infection and could potentially serve as an effective vaccine.
Identification of a Protective CD4+T-Cell Epitope in p15gagof Friend Murine Leukemia Virus and Role of the MA Protein Targeting the Plasma Membrane in Immunogenicity
Authors: Sugahara Daisuke , Tsuji-Kawahara Sachiyo , Miyazawa Masaaki
Published: May 2004

Recent studies have demonstrated an essential role of Gag-specific CD4+T-cell responses for viral control in individuals infected with human immunodeficiency virus type 1. However, little is known about epitope specificities and functional roles of the Gag-specific helper T-cell responses in terms of vaccine-induced protection against a pathogenic retroviral challenge. We have previously demonstrated that immunization with Friend murine leukemia virus (F-MuLV) Gag proteins protects mice against the fatal Friend retrovirus (FV) infection. We report here the structure of a protective T helper cell (Th) epitope, (I)VTWEAIAVDPPP, identified in the p15 (MA) region of F-MuLV Gag. In mice immunized with the Th epitope-harboring peptide or a vaccinia virus-expressed native full-length MA protein, FV-induced early splenomegaly regressed rapidly. In these mice, FV-infected cells were eliminated within 4 weeks and the production of virus-neutralizing antibodies was induced rapidly after FV challenge, resulting in strong protection against the virus infection. Interestingly, mice immunized with the whole MA mounted strong CD4+T-cell responses to the identified Th epitope, whereas mice immunized with mutant MA proteins that were not bound to the plasma membrane failed to mount efficient CD4+T-cell responses, despite the presence of the Th epitope. These mutant MA proteins also failed to induce strong protection against FV challenge. These data indicate the importance of the properly processible MA molecule for CD4+T-cell priming and for the resultant induction of an effective immune response against retrovirus infections.
Role of the I7 Protein in Proteolytic Processing of Vaccinia Virus Membrane and Core Components
Authors: Ansarah-Sobrinho Camilo , Moss Bernard
Published: May 2004

Certain core and membrane proteins of vaccinia virus undergo proteolytic cleavage at consensus AG/X sites. The processing of core proteins is coupled to morphogenesis and is inhibited by the drug rifampin, whereas processing of the A17 membrane protein occurs at an earlier stage of assembly and is unaffected by the drug. A temperature-sensitive mutant with a lesion in the I7L gene exhibits blocks in morphogenesis and in cleavage of core proteins. We found that the mutant also failed to cleave the A17 membrane protein. To further investigate the role of the putative I7 protease, we constructed a conditional lethal mutant in which the I7L gene was regulated by the
Escherichia coli lac
repressor. In the absence of an inducer, the synthesis of I7 was repressed, proteolytic processing of the A17 membrane protein and the L4 core protein was inhibited, and virus morphogenesis was blocked. Under these conditions, expression of the wild-type I7 protein in
trans
restored protein processing. In contrast, rescue did not occur when the putative protease active site residue histidine 241 or cysteine 328 of I7 was converted to alanine. The mutation of an authentic AG/A and an alternative AG/S motif of L4 prevented substrate cleavage. Similarly, when AG/X sites of A17 were mutated, I7-induced cleavages at the N and C termini failed to occur. In conclusion, we provide evidence that I7 is a viral protease that is required for AG/X-specific cleavages of viral membrane and core proteins, which occur at early and late stages of virus assembly, respectively.
Circulating Anti-Wild-Type Adeno-Associated Virus Type 2 (AAV2) Antibodies Inhibit Recombinant AAV2 (rAAV2)-Mediated, but Not rAAV5-Mediated, Gene Transfer in the Brain
Authors: Peden Carmen S. , Burger Corinna , Muzyczka Nicholas , Mandel Ronald J.
Published: May 2004

Epidemiological studies report that 80% of the population maintains antibodies (Ab) to wild-type (wt) adeno-associated virus type 2 (AAV2), with 30% expressing neutralizing Ab (NAb). The blood-brain barrier (BBB) provides limited immune privilege to brain parenchyma, and the immune response to recombinant AAV (rAAV) administration in the brain of a naive animal is minimal. However, central nervous system transduction in preimmunized animals remains unstudied. Vector administration may disrupt the BBB sufficiently to promote an immune response in a previously immunized animal. We tested the hypothesis that intracerebral rAAV administration and readministration would not be affected by the presence of circulating Ab to wt AAV2. Rats peripherally immunized with live wt AAV2 and naive controls were tested with single intrastriatal injections of rAAV2 encoding human glial cell line-derived neurotrophic factor (GDNF) or green fluorescent protein (GFP). Striatal readministration of rAAV2-GDNF was also tested in preimmunized and naive rats. Finally, serotype specificity of the immunization against wt AAV2 was examined by single injections of rAAV5-GFP. Preimmunization resulted in high levels of circulating NAb and prevented transduction by rAAV2 as assessed by striatal GDNF levels. rAAV2-GFP striatal transduction was also prevented by immunization, while rAAV5-GFP-mediated transduction, as assessed by stereological cell counting, was unaffected. Additionally, inflammatory markers were present in those animals that received repeated administrations of rAAV2, including markers of a cell-mediated immune response and cytotoxic damage. A live virus immunization protocol generated the circulating anti-wt-AAV Ab seen in this experiment, while human titers are commonly acquired via natural infection. Regardless, the data show that the presence of high levels of NAb against wt AAV can reduce rAAV-mediated transduction in the brain and should be accounted for in future experiments utilizing this vector.
MCP-1 and CCR2 Contribute to Non-Lymphocyte-Mediated Brain Disease Induced by Fr98 Polytropic Retrovirus Infection in Mice: Role for Astrocytes in Retroviral Neuropathogenesis
Authors: Peterson Karin E. , Errett John S. , Wei Tao , Dimcheff Derek E. , Ransohoff Richard , Kuziel William A. , Evans Leonard , Chesebro Bruce
Published: May 2004

Virus infection of the central nervous system (CNS) often results in chemokine upregulation. Although often associated with lymphocyte recruitment, increased chemokine expression is also associated with non-lymphocyte-mediated CNS disease. In these instances, the effect of chemokine upregulation on neurological disease is unclear. In vitro, several chemokines including monocyte chemotactic protein 1 (MCP-1) protect neurons from apoptosis. Therefore, in vivo, chemokine upregulation may be a protective host response to CNS damage. Alternatively, chemokines may contribute to pathogenesis by stimulating intrinsic brain cells or recruiting macrophages to the brain. To investigate these possibilities, we studied a neurovirulent retrovirus, Fr98, that induces severe non-lymphocyte-mediated neurological disease and causes the upregulation of several chemokines that bind to chemokine receptors CCR2 and CCR5. Knockout mice deficient in CCR2 had reduced susceptibility to Fr98 pathogenesis, with significantly fewer mice developing clinical disease than did wild-type controls. In contrast, no reduction in Fr98-induced disease was observed in CCR5 knockout mice. Thus, signaling through CCR2, but not CCR5, plays an important role in Fr98-mediated pathogenesis. Three ligands for CCR2 (MCP-1, MCP-3, and MCP-5) were upregulated during Fr98 infection of the brain. Antibody-blocking experiments demonstrated that MCP-1 was important for retrovirus-induced neurological disease. In situ hybridization analysis revealed that MCP-1 was expressed by glial fibrillary acidic protein-positive astrocytes. Thus, astrocytes, previously not thought to play an effector role in the disease process were found to contribute to pathogenesis through the production of MCP-1. This study also demonstrates that chemokines can mediate pathogenesis in the CNS in the absence of lymphocytic infiltrate and gives credence to the hypothesis that chemokine upregulation is a mechanism by which retroviruses such as human immunodeficiency virus induce neurological damage.
Adenovirus Protein VII Condenses DNA, Represses Transcription, and Associates with Transcriptional Activator E1A
Authors: Johnson Jeffrey S. , Osheim Yvonne N. , Xue Yuming , Emanuel Margaux R. , Lewis Peter W. , Bankovich Alex , Beyer Ann L. , Engel Daniel A.
Published: May 2004

Adenovirus protein VII is the major protein component of the viral nucleoprotein core. It is highly basic, and an estimated 1070 copies associate with each viral genome, forming a tightly condensed DNA-protein complex. We have investigated DNA condensation, transcriptional repression, and specific protein binding by protein VII.
Xenopus
oocytes were microinjected with mRNA encoding HA-tagged protein VII and prepared for visualization of lampbrush chromosomes. Immunostaining revealed that protein VII associated in a uniform manner across entire chromosomes. Furthermore, the chromosomes were significantly condensed and transcriptionally silenced, as judged by the dramatic disappearance of transcription loops characteristic of lampbrush chromosomes. During infection, the protein VII-DNA complex may be the initial substrate for transcriptional activation by cellular factors and the viral E1A protein. To investigate this possibility, mRNAs encoding E1A and protein VII were comicroinjected into
Xenopus
oocytes. Interestingly, whereas E1A did not associate with chromosomes in the absence of protein VII, expression of both proteins together resulted in significant association of E1A with lampbrush chromosomes. Binding studies with proteins produced in bacteria or human cells or by in vitro translation showed that E1A and protein VII can interact in vitro. Structure-function analysis revealed that an N-terminal region of E1A is responsible for binding to protein VII. These studies define the in vivo functions of protein VII in DNA binding, condensation, and transcriptional repression and indicate a role in E1A-mediated transcriptional activation of viral genes.
Inter- and Intragenus Structural Variations in Caliciviruses and Their Functional Implications
Authors: Chen Rong , Neill John D. , Noel Jacqueline S. , Hutson Anne M. , Glass Roger I. , Estes Mary K. , Prasad B. V. Venkataram
Published: May 2004

The family
Caliciviridae
is divided into four genera and consists of single-stranded RNA viruses with hosts ranging from humans to a wide variety of animals. Human caliciviruses are the major cause of outbreaks of acute nonbacterial gastroenteritis, whereas animal caliciviruses cause various host-dependent illnesses with a documented potential for zoonoses. To investigate inter- and intragenus structural variations and to provide a better understanding of the structural basis of host specificity and strain diversity, we performed structural studies of the recombinant capsid of Grimsby virus, the recombinant capsid of Parkville virus, and San Miguel sea lion virus serotype 4 (SMSV4), which are representative of the genera
Norovirus
(genogroup 2),
Sapovirus
, and
Vesivirus
, respectively. A comparative analysis of these structures was performed with that of the recombinant capsid of Norwalk virus, a prototype member of
Norovirus
genogroup 1. Although these capsids share a common architectural framework of 90 dimers of the capsid protein arranged on a T=3 icosahedral lattice with a modular domain organization of the subunit consisting of a shell (S) domain and a protrusion (P) domain, they exhibit distinct differences. The distally located P2 subdomain of P shows the most prominent differences both in shape and in size, in accordance with the observed sequence variability. Another major difference is in the relative orientation between the S and P domains, particularly between those of noroviruses and other caliciviruses. Despite being a human pathogen, the Parkville virus capsid shows more structural similarity to SMSV4, an animal calicivirus, suggesting a closer relationship between sapoviruses and animal caliciviruses. These comparative structural studies of caliciviruses provide a functional rationale for the unique modular domain organization of the capsid protein with an embedded flexibility reminiscent of an antibody structure. The highly conserved S domain functions to provide an icosahedral scaffold; the hypervariable P2 subdomain may function as a replaceable module to confer host specificity and strain diversity; and the P1 subdomain, located between S and P2, provides additional fine-tuning to position the P2 subdomain.
Cloning and Characterization of a Bovine Adeno-Associated Virus
Authors: Schmidt Michael , Katano Hisako , Bossis Ioannis , Chiorini John A.
Published: May 2004

To better understand the relationship between primate adeno-associated viruses (AAVs) and those of other mammals, we have cloned and sequenced the genome of an AAV found as a contaminant in two isolates of bovine adenovirus that was reported to be serologically distinct from primate AAVs. The bovine AAV (BAAV) genome has 4,693 bp, and its organization is similar to that of other AAV isolates. The left-hand open reading frame (ORF) and both inverted terminal repeats (ITRs) have the highest homology with the rep ORF and ITRs of AAV serotype 5 (AAV-5) (89 and 96%, respectively). However, the right-hand ORF was only 55% identical to the AAV-5 capsid ORF; it had the highest homology with the capsid ORF of AAV-4 (76%). By comparing the BAAV cap sequence with a model of an AAV-4 capsid, we mapped the regions of BAAV VP1 that are divergent from AAV-4. These regions are located on the outside of the capsid and are partially located in exposed loops. BAAV was not neutralized by antisera raised against recombinant AAV-2, AAV-4, or AAV-5, and it demonstrated a unique cell tropism profile in four human cancer cell lines, suggesting that BAAV might have transduction activity distinct from that of other isolates. A murine model of salivary gland gene transfer was used to evaluate the in vivo performance of recombinant BAAV. Recombinant BAAV-mediated gene transfer was 11 times more efficient than that with AAV-2. Overall, these data suggest that vectors based on BAAV could be useful for gene transfer applications.
Contribution of Proteoglycans to Human Immunodeficiency Virus Type 1 Brain Invasion
Authors: Bobardt Michael D. , Salmon Patrick , Wang Lianchun , Esko Jeffrey D. , Gabuzda Dana , Fiala Milan , Trono Didier , Van der Schueren Bernadette , David Guido , Gallay Philippe A.
Published: May 2004

As a neurotropic virus, human immunodeficiency virus type 1 (HIV-1) invades the brain and causes severe neuronal, astrocyte, and myelin damage in AIDS patients. To gain access to the brain, HIV-1 must migrate through brain microvascular endothelial cells (BMECs), which compose the blood-brain barrier (BBB). Given that BMECs lack the entry receptor CD4, HIV-1 must use receptors distinct from CD4 to enter these cells. We previously reported that cell surface proteoglycans serve as major HIV-1 receptors on primary human endothelial cells. In this study, we examined whether proteoglycans also impact cell-free HIV-1 invasion of the brain. Using an artificial BBB transmigration assay, we found that both heparan and chondroitin sulfate proteoglycans (HSPGs and CSPGs, respectively) are abundantly expressed on primary BMECs and promote HIV-1 attachment and entry. In contrast, the classical entry receptors, CXCR4 and CCR5, only moderately enhanced these processes. HSPGs and CSPGs captured HIV-1 in a gp120-dependent manner. However, no correlation between coreceptor usage and transmigration was identified. Furthermore, brain-derived viruses did not transmigrate more efficiently than lymphoid-derived viruses, suggesting that the ability of HIV-1 to replicate in the brain does not correlate with its capacity to migrate through the BBB as cell-free virus. Given that HIV-1-proteoglycan interactions are based on electrostatic contacts between basic residues in gp120 and sulfate groups in proteoglycans, HIV-1 may exploit these interactions to rapidly enter and migrate through the BBB to invade the brain.
Molecular Population Genetics of
Cucumber Mosaic Virus
in California: Evidence for Founder Effects and Reassortment
Authors: Lin Han-Xin , Rubio Luis , Smythe Ashleigh B. , Falk Bryce W.
Published: May 2004

The structure and genetic diversity of a California
Cucumber mosaic virus
(CMV) population was assessed by single-strand conformation polymorphism and nucleotide sequence analyses of genomic regions 2b, CP, MP, and the 3′ nontranslated region of RNA3. The California CMV population exhibited low genetic diversity and was composed of one to three predominant haplotypes and a large number of minor haplotypes for specific genomic regions. Extremely low diversity and close evolutionary relationships among isolates in a subpopulation suggested that founder effects might play a role in shaping the genetic structure. Phylogenetic analysis indicated a naturally occurring reassortant between subgroup IA and IB isolates and potential reassortants between subgroup IA isolates, suggesting that genetic exchange by reassortment contributed to the evolution of the California CMV population. Analysis of various population genetics parameters and distribution of synonymous and nonsynonymous mutations revealed that different coding regions and even different parts of coding regions were under different evolutionary constraints, including a short region of the 2b gene for which evidence suggests possible positive selection.
Rinderpest Virus Phosphoprotein Gene Is a Major Determinant of Species-Specific Pathogenicity
Authors: Yoneda Misako , Miura Ryuichi , Barrett Thomas , Tsukiyama-Kohara Kyoko , Kai Chieko
Published: May 2004

We previously demonstrated that the rinderpest virus (RPV) hemagglutinin (H) protein plays an important role in determining host range but that other viral proteins are clearly required for full RPV pathogenicity to be manifest in different species. To examine the effects of the RPV nucleocapsid (N) protein and phosphoprotein (P) genes on RPV cross-species pathogenicity, we constructed two new recombinant viruses in which the H and P or the H, N, and P genes of the cattle-derived RPV RBOK vaccine were replaced with those from the rabbit-adapted RPV-Lv strain, which is highly pathogenic in rabbits. The viruses rescued were designated recombinant RPV-lapPH (rRPV-lapPH) and rRPV-lapNPH, respectively. Rabbits inoculated with RPV-Lv become feverish and show leukopenia and a decrease in body weight gain, while clinical signs of infection are never observed in rabbits inoculated with RPV-RBOK or with rRPV-lapH. However, rabbits inoculated with either rRPV-lapPH or rRPV-lapNPH became pyrexic and showed leukopenia. Further, histopathological lesions and high virus titers were clearly observed in the lymphoid tissues from animals infected with rRPV-lapPH or rRPV-lapNPH, although they were not observed in rabbits infected with RPV-RBOK or rRPV-lapH. The clinical, virological, and histopathological signs in rabbits infected with the two new recombinant viruses did not differ significantly; therefore, the RPV P gene was considered to be a key determinant of cross-species pathogenicity.
Nodamura Virus
Nonstructural Protein B2 Can Enhance Viral RNA Accumulation in both Mammalian and Insect Cells
Authors: Johnson Kyle L. , Price B. Duane , Eckerle Lance D. , Ball L. Andrew
Published: May 2004

During infection of both vertebrate and invertebrate cell lines, the alphanodavirus
Nodamura virus
(NoV) expresses two nonstructural proteins of different lengths from the B2 open reading frame. The functions of these proteins have yet to be determined, but B2 of the related
Flock House virus
suppresses RNA interference both in
Drosophila
cells and in transgenic plants. To examine whether the NoV B2 proteins had similar functions, we compared the replication of wild-type NoV RNA with that of mutants unable to make the B2 proteins. We observed a defect in the accumulation of mutant viral RNA that varied in extent from negligible in some cell lines (e.g., baby hamster kidney cells) to severe in others (e.g., human HeLa and
Drosophila
DL-1 cells). These results are consistent with the notion that the NoV B2 proteins act to circumvent an innate antiviral response such as RNA interference that differs in efficacy among different host cells.
Mycorrhizal inoculum and performance of nonmycorrhizal Carex bigelowii and mycorrhizal Trientalis europaea
Authors: Ruotsalainen Anna Liisa , Aikio Sami
Published: May 2004

We studied the competition between mycorrhiza-forming Trientalis europaea L. and nonmycorrhizal Carex bigelowii Torrey ex Schweinitz in a climate chamber experiment. The plants were grown either singly or together with a conspecific or heterospecific individual, with arbuscular mycorrhizal inoculum present or absent. Inoculated T. euro paea formed abundant arbuscular mycorrhizal structures, but the mycorrhizae did not affect its biomass or the whole plant's relative growth rate (RGR). Carex bigelowii did not form mycorrhizae, but its shoot biomass and RGR were lower in the inoculated pots. The presence of a conspecific or heterospecific plant had no effect on the shoot biomasses or RGR of either plant species. Mycorrhizal inoculation increased the root/shoot ratio of C. bigelowii in all competition treatments. The presence of C. bigelowii decreased the root/shoot ratio of T. europaea in both mycorrhizal and nonmy corrhizal state. Mycorrhizal inoculum thus had a direct negative effect on the growth of a nonmycorrhizal plant. The result suggests that although mycorrhizae may not always directly affect the performance of the host plant, they may possibly increase the host plant performance in relation to nonmycorrhizal neighbours. Mycorrhizal inoculum and mycorrhizal symbiosis may increase asymmetry of interspecific competition, which may facilitate the coexistence of plant species in cases when a larger individual is more negatively affected.Key words: arbuscular mycorrhiza, competitive asymmetry, micropropagation.
Light, not nitrogen, limits growth of the grassDeschampsia flexuosain boreal forests
Authors: Strengbom Joachim , Näsholm Torgny , Ericson Lars
Published: May 2004

Increased nitrogen (N) input in boreal forests has previously been shown to induce a shift from Vaccinium myrtillus L. to Deschampsia flexuosa (L.) Trin. as the dominant understory species. We investigated the relative importance of increased light and N for this shift, in a field experiment. We increased light availability, that is, we reduced aboveground competition from V. myrtillus, and increased N by adding 50 kg N·ha1. Increased light availability had a positive effect on both the growth rate and final biomass of D. flexuosa. Although N addition increased the uptake of fertilizer N by both species, it had no effect on the growth or biomass of either species. Thus, aboveground competition from V. myrtillus prevented expansion of D. flexuosa, regardless of N treatment. The results suggest that aboveground competition may be more important than belowground competition for structuring understory boreal forest communities. As light availability is important, both the structure and total amount of standing crop will be important for the outcome of species interactions.Key words: aboveground competition, belowground competition, fertilization, natural enemies, nitrogen deposition, vegetation change.
Inhibition of growth in two dinoflagellates by rapid changes in external pH
Authors: Dason Jeffrey S , Colman Brian
Published: May 2004

The effect of external pH and high CO2 were investigated on growth and photosynthesis in two marine dinoflagellates, Amphidinium carterae Hulburt and Heterocapsa oceanica Stein. Exposure of both species to high CO2 caused a rapid decrease in external pH from 8 to 7 and a complete suppression of growth. Both species were able to grow at pH 7 but the Vmax of photosynthesis was significantly lower than in cells grown at pH 8. There was also a significant reduction in the photosynthetic rate of both species after being on high CO2 for 6 h and a complete loss after 24 h. The internal pH of both species was determined by the distribution of [2-14C]5,5-dimethyloxazolidine-2,4-dione between the cells and the surrounding medium. As the external pH was lowered from 8 to 7, there was a decrease in the internal pH of A. carterae cells, grown at pH 8.0, from 7.92 to 7.04 and in H. oceanica from 8.14 to 7.22. When placed on high CO2, the internal pH of A. carterae further declined to 6.90 and to 7.15. in H. oceanica. This inability to maintain internal pH probably caused the suppression of growth and loss of photosynthetic capacity of high-CO2 cells.Key words: Amphidinium carterae, CO2-concentrating mechanism, dinoflagellates, external pH, Heterocapsa oceanica, internal pH.
Costbenefit relationships in fronds emerging at different times in a deciduous fern,Pteridium aquilinum
Authors: Oikawa Shimpei , Hikosaka Kouki , Hirose Tadaki , Shiyomi Masae , Takahashi Shigeo , Hori Yoshimichi
Published: May 2004

We studied the life-span and ecophysiological traits of "leaves" (fronds) that emerged at different times during the growing season in a deciduous herbaceous fern, Pteridium aquilinum (L.) Kuhn (in this paper we use "leaves" for fronds to be consistent with other studies on leaf phenology). Leaf life-span was shorter in later than in early cohorts. Leaf construction cost per unit mass was nearly constant among cohorts. Later cohorts had a lower leaf construction cost per unit leaf area with a lower leaf mass per area. Leaf life-span was positively correlated with construction cost per unit area. Late cohorts showed a slightly higher leaf nitrogen content per unit mass, but a lower nitrogen content per unit leaf area with a lower light-saturated photosynthesis per unit area. Light-saturated photosynthesis per unit area was positively correlated with leaf life-span. The ratio of leaf construction cost to light-saturated photosynthesis was lower in late cohorts, and the ratio was nearly proportional to leaf life-span, suggesting that late cohorts may pay back the construction cost despite their shorter life-span.Key words: leaf construction cost, leaf life-span, payback time, light-saturated photosynthesis, seasonal change.
Solidliquid transition of charge-stabilized colloidal dispersions: a single-component structure-function approach
Authors: Zhou S
Published: May 2004

We have extended the RavechéMountainStreett one-phasecriterion that governs the freezing of Lennard-Jones systems to a hard-core repulsive Yukawa-model (HCRYM) system. We find in the framework of the RogersYoung (RY) approximation for an OrnsteinZernike integral equation that an HCRYM fluid freezes when the ratio α = g(rmin)/g(rmax), where rmax is the distance corresponding to the maximum in the radial distribution function g(r) and rmin is the distance corresponding to the subsequent minimum in g(r), is approximately 0.215. To describe the freezing of charge-stabilized colloidal dispersions in electrolytes, which consist of colloidal macroions,electrolyte small ions, and solvent molecules, we employ the single-component model in which the colloidal particles interact through the effective screened Coulomb potential of Belloni. Whenthe macroion surface effective charge number is taken as an adjustable parameter, the theoretical freezing line predicted by the RY g(rmin)/g(rmax) = 0.215 RavechéMountainStreett one-phase criterion is in very good agreement with the corresponding experimental data.PACS Nos.: 61.25.Em, 61.20.Gy
Correction de l'approximation de Kirchhoff par la méthode intégrale reformulée : cas des réflectivités de surfaces sinusoïdales
Authors: Matchiane M B , Ghmari F , Sifaoui M S
Published: May 2004

Using two different methods, we study the radiative properties of rough surfaces, such as the bidirectional or the hemispheric directional reflectivity. The first method, which we call exact, is the integral method (MI). It is based on the electromagnetic theory and Green's theorem to describe the system through a system of equations for the field and its normal derivative (sources) at the surface. The method is computation expensive, requiring the inversion of possibly large complex matrices. The second method (MIR), which we will use and for which we extend the validity to include transverse polarization, reformulates the integral method to solve it by an iterative approach. It has the advantage that its first iteration corresponds to the Kirchoff approximation (AK). The following (higher order) terms bring corrections to AK, while reducing notably the computation load. Our main purpose is to study the stability of the MIR and to find the limits of its validity when compared with the (exact) MI. Our numerical results were carried out for perfectly conducting or dielectric surfaces with sinusoidal roughness for two polarizations, transverse electric and transverse magnetic. [Journal translation]
Channel-specific dielectronic recombination of Ge(XXXII), Se(XXXIV), and Kr(XXXVI)
Authors: Machtoub G El
Published: May 2004

We present explicit calculations of channel-specific dielectronic recombination cross sections for hydrogen-like germanium, Ge(XXXII); selenium, Se(XXXIV); and krypton, Kr(XXXVI). The convoluted cross sections characterize K-shell emission spectra over a wide energy range where contributions from high-n (n = 2–10), satellite lines are included. The high-n contributions presented are important for better diagnostics in the domain of high-temperature plasmas. PACS Nos.: 32.30.Rj, 32.70.Rm, 34.70.te
Experimental and computational investigation of the electrocatalytic hydrogenation of phenol in an electrochemical cell
Authors: Chagnes A , Laplante F , Kerdouss F , Proulx P , Ménard H
Published: May 2004

The electrocatalytic hydrogenation (ECH) of phenol was carried out in aqueous media with a commercial Pd/Al2O3 (5% w/w) catalyst. A porous matrix of reticulated vitreous carbon (RVC) was used to study the porosity  stirring speed coupling (PSSC) effect on the phenol hydrogenation to form cyclohexanone and cyclohexanol. In accordance with the PSSC, the electrode can act as a fluidized bed electrode or as an agglomerated electrode. Fluidized bed electrodes develop for low porosity matrices (1030 ppi, ppi = pores per inch) at high stirring speeds (>600 rpm), while agglomerated electrodes are obtained for high porosity matrices (60100 ppi) with moderate stirring speeds under cathodic polarization. The distribution of the volume fraction of the particles and the agglomeration of the particles have been simulated by computational fluid dynamic (CFD) methods with FLUENT software. For the agglomerated electrode, the numerical simulations demonstrate the beneficial contribution of the cathodic polarization to the agglomeration process. However, at 650 rpm, for the fluidized bed electrode, the volume fraction of the particles in the RVC does not account for the distinction in the ECH efficiency between the 30 ppi matrix and the 100 ppi matrix. For a given amount of Pd/Al2O3 catalyst, it is observed that the ECH rates depend on the PSSC and increase in the following order: 100/650 < 30/650 < 100/200. Key words: electrocatalytic hydrogenation (ECH), CFD, fluid mechanics, porous media, powder, porosity  stirring speed coupling (PSSC), reticulated vitreous carbon (RVC).
DETECTING AND MODELING TAIL DEPENDENCE
Authors: BELLINI FABIO , FIGÀ-TALAMANCA GIANNA
Published: May 2004

The aim of this work is to develop a nonparametric tool for detecting dependence in the tails of financial data. We provide a simple method to locate and measure serial dependence in the tails, based on runs tests. Our empirical investigations on many financial time series reveal a strong departure from independence for daily logreturns, which is not filtered out by usual Garch models.
NFA FOR FACTOR NUMBER DETERMINATION IN APT
Authors: CHIU KAI-CHUN , XU LEI
Published: May 2004

In the context of quantitative analysis of the arbitrage pricing theory (APT) model, conventional factor analytic approaches such as maximum likelihood factor analysis (MLFA) cannot provide satisfactory answers to two important questions. The first one concerns the correct identification of factor number while the second one is related to the rotation indeterminacy of factor loadings. In the literature, MLFA followed by likelihood ratio (LR) test and the analysis of eigenvalues of sample covariance matrix were two popular approaches used to determine the appropriate number of factors. However, it was shown empirically that both of them suffered from different kinds of biases. We find the recently developed non-gaussian factor analysis (NFA) model by Xu [24] provides a new perspective for the determination of the appropriate factor number k in APT, with promising empirical results demonstrated.
THE SPECTRAL DECOMPOSITION OF THE OPTION VALUE
Authors: LINETSKY VADIM
Published: May 2004

This paper develops a spectral expansion approach to the valuation of contingent claims when the underlying state variable follows a one-dimensional diffusion with the infinitesimal variance a2(x), drift b(x) and instantaneous discount (killing) rate r(x). The Spectral Theorem for self-adjoint operators in Hilbert space yields the spectral decomposition of the contingent claim value function. Based on the Sturm–Liouville (SL) theory, we classify Feller's natural boundaries into two further subcategories: non-oscillatory and oscillatory/non-oscillatory with cutoff Λ≥0 (this classification is based on the oscillation of solutions of the associated SL equation) and establish additional assumptions (satisfied in nearly all financial applications) that allow us to completely characterize the qualitative nature of the spectrum from the behavior of a, b and r near the boundaries, classify all diffusions satisfying these assumptions into the three spectral categories, and present simplified forms of the spectral expansion for each category. To obtain explicit expressions, we observe that the Liouville transformation reduces the SL equation to the one-dimensional Schrödinger equation with a potential function constructed from a, b and r. If analytical solutions are available for the Schrödinger equation, inverting the Liouville transformation yields analytical solutions for the original SL equation, and the spectral representation for the diffusion process can be constructed explicitly. This produces an explicit spectral decomposition of the contingent claim value function.
MODELING FINANCIAL SERIES DISTRIBUTIONS: A VERSATILE DATA FITTING APPROACH
Authors: SHANG JEN S. , TADIKAMALLA PANDU R.
Published: May 2004

The empirical distribution of common stock returns is a subject of interest to many researchers, as it often determines the validity of theoretical models proposed in the economics and finance studies. This paper brings to the attention the availability of two flexible systems of distributions for fitting data: the Johnson system of distributions and the Tadikamalla–Johnson system of distributions. We explore the feasibility of fitting the empirical distributions of several financial series to these two systems of distributions. Both systems of distributions are highly flexible and capable of accommodating all possible skewness and kurtosis values. The probability density function and the cumulative distribution function take on simple closed forms and appropriate transformations of the data lead to normal/logistic distributions. In addition, the parameter estimation procedures are easy to implement. When the results are compared with those of other data fitting models, in all cases tested, the proposed distributions provide a good fit to the empirical distribution of data.
MULTICRITERIAL RANKING APPROACH FOR EVALUATING BANK BRANCH PERFORMANCE
Authors: ALESKEROV FUAD , ERSEL HASAN , YOLALAN REHA
Published: May 2004

14 ranking methods based on multiple criteria are suggested for evaluating the performance of the bank branches. The methods are explained via an illustrative example, and some of them are applied to a real-life data for 23 retail bank branches in a large-scale private Turkish commercial bank.
USING SUPER-EFFICIENCY DEA TO EVALUATE FINANCIAL PERFORMANCE OF E-BUSINESS INITIATIVE IN THE RETAIL INDUSTRY
Authors: CHEN YAO , MOTIWALLA LUVAI , RIAZ KHAN M.
Published: May 2004

Electronic Business (EB) on the Internet is an attractive technology for traditional business organizations to improve their financial performance. The Web-based economic model is supposedly more efficient at the transaction cost level. It also provides cost-effective marketing, global market access, and a disintermediation of costly distribution channels. The current paper uses super-efficiency data envelopment analysis (DEA) model to evaluate the financial performance of e-business initiatives in the retail industry. Because of the possible infeasibility of the super-efficiency DEA model, the use of super-efficiency DEA model has been restricted. This paper demonstrates that if super-efficiency is interpreted as input saving or output surplus achieved by a specific efficient DMU, infeasibility does not necessary indicate the best performance. A new approach is applied to correctly characterize and rank the performance of a set of EB companies and non-EB companies in the retail industry. This analysis indicates that the EB companies perform better in some areas than their non-EB counterpart.
DEA APPROACH FOR THE CURRENT AND THE CROSS PERIOD EFFICIENCY FOR EVALUATING THE VOCATIONAL EDUCATION
Authors: LIU LI-CHEN , LEE CHUAN , TZENG GWO-HSHIUNG
Published: May 2004

This study proposes an improved assessment system for vocational education, thus helping to increase technology college education efficiency. Data Envelopment Analysis (DEA) was used to examine the relative managerial efficiency for evaluating current-period and cross-period efficiency of 38 technological institutes upgraded from junior colleges in Taiwan by 1998. In addition, the managerial efficiency variations of each individual institute in between 1995 and 1998 were also determined. The study results show that the operational category is significant among primary analysis variants, i.e. private schools perform significantly better than public schools in terms of managerial efficiency. However, geographical location is not significant. This study also verifies that integration of the results of both relative managerial efficiency analysis and managerial efficiency variation analysis could be a powerful approach to help design managerial strategies that are both appropriate and effective. Some strategies to improve organization-wide operational competencies for site decision-makers are recommended, and a new way of thinking to construct a more appropriate evaluation system for the educational authorities is introduced.
COMBINING MICROARRAYS AND BIOLOGICAL KNOWLEDGE FOR ESTIMATING GENE NETWORKS VIA BAYESIAN NETWORKS
Authors: IMOTO SEIYA , HIGUCHI TOMOYUKI , GOTO TAKAO , TASHIRO KOUSUKE , KUHARA SATORU , MIYANO SATORU
Published: May 2004

We propose a statistical method for estimating a gene network based on Bayesian networks from microarray gene expression data together with biological knowledge including protein-protein interactions, protein-DNA interactions, binding site information, existing literature and so on. Microarray data do not contain enough information for constructing gene networks accurately in many cases. Our method adds biological knowledge to the estimation method of gene networks under a Bayesian statistical framework, and also controls the trade-off between microarray information and biological knowledge automatically. We conduct Monte Carlo simulations to show the effectiveness of the proposed method. We analyze Saccharomyces cerevisiae gene expression data as an application.
LOGOS: A MODULAR BAYESIAN MODEL FOR DE NOVO MOTIF DETECTION
Authors: XING ERIC P. , WU WEI , JORDAN MICHAEL I. , KARP RICHARD M.
Published: May 2004

The complexity of the global organization and internal structure of motifs in higher eukaryotic organisms raises significant challenges for motif detection techniques. To achieve successful de novo motif detection, it is necessary to model the complex dependencies within and among motifs and to incorporate biological prior knowledge. In this paper, we present LOGOS, an integrated LOcal and GlObal motif Sequence model for biopolymer sequences, which provides a principled framework for developing, modularizing, extending and computing expressive motif models for complex biopolymer sequence analysis. LOGOS consists of two interacting submodels: HMDM, a local alignment model capturing biological prior knowledge and positional dependency within the motif local structure; and HMM, a global motif distribution model modeling frequencies and dependencies of motif occurrences. Model parameters can be fit using training motifs within an empirical Bayesian framework. A variational EM algorithm is developed for de novo motif detection. LOGOS improves over existing models that ignore biological priors and dependencies in motif structures and motif occurrences, and demonstrates superior performance on both semi-realistic test data and cis-regulatory sequences from yeast and Drosophila genomes with regard to sensitivity, specificity, flexibility and extensibility.
PROTEIN STRUCTURE ALIGNMENT AND FAST SIMILARITY SEARCH USING LOCAL SHAPE SIGNATURES
Authors: CAN TOLGA , WANG YUAN-FANG
Published: May 2004

We present a new method for conducting protein structure similarity searches, which improves on the efficiency of some existing techniques. Our method is grounded in the theory of differential geometry on 3D space curve matching. We generate shape signatures for proteins that are invariant, localized, robust, compact, and biologically meaningful. The invariancy of the shape signatures allows us to improve similarity searching efficiency by adopting a hierarchical coarse-to-fine strategy. We index the shape signatures using an efficient hashing-based technique. With the help of this technique we screen out unlikely candidates and perform detailed pairwise alignments only for a small number of candidates that survive the screening process. Contrary to other hashing based techniques, our technique employs domain specific information (not just geometric information) in constructing the hash key, and hence, is more tuned to the domain of biology. Furthermore, the invariancy, localization, and compactness of the shape signatures allow us to utilize a well-known local sequence alignment algorithm for aligning two protein structures. One measure of the efficacy of the proposed technique is that we were able to perform structure alignment queries 36 times faster (on the average) than a well-known method while keeping the quality of the query results at an approximately similar level.
Magnifying Voters' Preferences: Bias in Elections to Birmingham's City Council
Authors: Thrasher Michael , Johnston Ron , Rallings Colin
Published: May 2004

Results of Birmingham's city-council elections throughout a ninety-year period show that electoral bias had a significant impact on the success of particular parties during different phases of party-system development. Although the electoral system tends to favor large parties, its bias toward Labor since World War II has been extraordinary. At times, it was the crucial factor in determining control of the city's administration.
Re-contextualizing British Witchcraft
Authors: Monter William
Published: May 2004

Since the seminal study of English witchcraft c. 1970, such developments as England's entry into the European Community and the revival of witchhunting episodes in postcolonial Africa have blurred parts of the picture. Recent publications present an opportunity to make revisions to the classic view of British witchcraft, setting the subject within its proper European context while pointing out some of its distinctive features.
Machine Translation with Inferred Stochastic Finite-State Transducers
Authors: Casacuberta Francisco , Vidal Enrique
Published: May 2004

Finite-state transducers are models that are being used in different areas of pattern recognition and computational linguistics. One of these areas is machine translation, in which the approaches that are based on building models automatically from training examples are becoming more and more attractive. Finite-state transducers are very adequate for use in constrained tasks in which training samples of pairs of sentences are available. A technique for inferring finite-state transducers is proposed in this article. This technique is based on formal relations between finite-state transducers and rational grammars. Given a training corpus of source-target pairs of sentences, the proposed approach uses statistical alignment methods to produce a set of conventional strings from which a stochastic rational grammar (e.g., an n-gram) is inferred. This grammar is finally converted into a finite-state transducer. The proposed methods are assessed through a series of machine translation experiments within the framework of the E u Trans project.