bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional rarefaction: estimating functional diversity from field data
Authors: Walker Steven C. , Poos Mark S. , Jackson Donald A.
Published: November 2007

Studies in biodiversity‐ecosystem function and conservation biology have led to the development of diversity indices that take species’ functional differences into account. We identify two broad classes of indices: those that monotonically increase with species richness (MSR indices) and those that weight the contribution of each species by abundance or occurrence (weighted indices). We argue that weighted indices are easier to estimate without bias but tend to ignore information provided by rare species. Conversely, MSR indices fully incorporate information provided by rare species but are nearly always underestimated when communities are not exhaustively surveyed. This is because of the well‐studied fact that additional sampling of a community may reveal previously undiscovered species. We use the rarefaction technique from species richness studies to address sample‐size‐induced bias when estimating functional diversity indices. Rarefaction transforms any given MSR index into a family of unbiased weighted indices, each with a different level of sensitivity to rare species. Thus rarefaction simultaneously solves the problem of bias and the problem of sensitivity to rare species. We present formulae and algorithms for conducting a functional rarefaction analysis of the two most widely cited MSR indices: functional attribute diversity (FAD) and Petchey and Gaston's functional diversity (FD). These formulae also demonstrate a relationship between three seemingly unrelated functional diversity indices: FAD, FD and Rao's quadratic entropy. Statistical theory is also provided in order to prove that all desirable statistical properties of species richness rarefaction are preserved for functional rarefaction.
The frequency of metapopulations, metacommunities and nestedness in a fragmented landscape
Authors: A. Driscoll Don
Published: November 2007

Metapopulation and metacommunity theory may be extremely useful for understanding community composition and species distributions in fragmented landscapes. However, how well particular spatial ecological models represent natural systems is not known and so the general importance of those models is unclear. In three naturally fragmented landscapes in Tasmania, Australia, I sampled beetles from 67 sites, including continuous forest, small forest patches in a sedgeland matrix, streamside forest, and the matrix. Of forty commonly captured beetle species, at least 37% do not form metapopulations of any kind because they do not disperse far enough, disperse too far, or occur in the matrix. Only 7.5% of the species showed distributions consistent with a mainland‐island metapopulation, which was surprising given the mainland‐island structure of the landscape. These patterns were also consistent with a classic metapopulation. Deterministic metapopulations were probably common, involving at least 32% of species. Most predicted metacommunity patterns were not observed because only subsets of the fauna followed a particular metacommunity model. Seven, mostly flying, species were influenced only by habitat quality, supporting the Species‐sorting or Mass‐effects models, and the strong distinction between the beetle fauna of Eucalyptus patches and the matrix suggested an over‐riding influence of a Species‐sorting process. Seven, mostly flightless, species showed a negative relationship with increasing patch isolation, while another six, mostly flying, species showed the opposite pattern, with higher frequency of occurrence in more isolated patches. Both groups were strongly nested. The flying species were probably excluded from less isolated sites through interactions with poor dispersers, providing a novel mechanism leading to a nested distribution. The Patch‐dynamics and Species‐sorting processes were equally consistent with the pattern, emphasizing that these models are relatively simplistic when confronted with real community data. Additional complexity needs to be built into the models to accommodate the diverse patterns observed in natural communities.
Cytotoxic Activity of
N
-Chlorotaurine on
Acanthamoeba
spp
Authors: Fürnkranz Ursula , Nagl Markus , Gottardi Waldemar , Köhsler Martina , Aspöck Horst , Walochnik Julia
Published: November 2007

Acanthamoeba
spp. are the causative agents of
Acanthamoeba
keratitis (AK), which mainly occurs in contact lens wearers, and of skin lesions, granulomatous amoebic encephalitis (GAE), and disseminating diseases in the immunocompromised host. AK therapy is complex and irritating for the eye, skin lesions are difficult to treat, and there is no effective treatment for GAE. Therefore, new anti-
Acanthamoeba
drugs are needed. We investigated the anti-
Acanthamoeba
activity of
N
-chlorotaurine (NCT), an endogenous mild antiseptic. It was shown that NCT has amoebicidal qualities, both in phosphate-buffered saline (PBS) and in amoebic culture medium. After 6 h of treatment with 10 mM NCT in PBS, the levels of trophozoites of all strains investigated already showed at least a 2-log reduction. When the trophozoites were treated with 20 mM NCT in culture medium, they showed a 2-log reduction after 24 h. The addition of NH
4
Cl to NCT led to a faster decrease in the numbers of living cells, if tests were carried out in PBS. A delay of excystation was observed when cysts were treated with 55 mM (1%) NCT in culture medium. A complete failure of excystment was the result of treatment with 1% NCT plus 1% NH
4
Cl in PBS. Altogether, NCT clearly demonstrated amoebicidal activity at concentrations well tolerated by human tissues and might be useful as a topical drug for the treatment of
Acanthamoeba
infections. The addition of ammonium chloride can be considered to enhance the activity.
Factors Associated with the Selection of Mutations Conferring Resistance to Protease Inhibitors (PIs) in PI-Experienced Patients Displaying Treatment Failure on Darunavir
Authors: Lambert-Niclot Sidonie , Flandre Philippe , Canestri Ana , Peytavin Gilles , Blanc Christine , Agher Rachid , Soulié Cathia , Wirden Marc , Katlama Christine , Calvez Vincent , Marcelin Anne-Geneviève
Published: November 2007

The objective of this study was to characterize the mutations selected by darunavir (DRV) use in protease inhibitor (PI)-experienced patients and the associated factors. We analyzed treatment failure in 54 PI-experienced human immunodeficiency virus (HIV)-infected patients on a DRV- and ritonavir-containing regimen. Viral genotyping was carried out at the baseline, at between 1 and 3 months of treatment, and at between 3 and 6 months of treatment to search for the selection of mutations conferring resistance to PIs. The median baseline HIV RNA level was 4.9 log
10
copies/ml, and the median CD4 count was 87 cells/mm
3
. At the baseline, the median numbers of resistance mutations were as follows: 3 DRV resistance mutations, 4 major PI resistance mutations, and 10 minor PI resistance mutations. The most common mutations that emerged at rebound included V32I (44%), I54M/L (24%), L33F (25%), I84V (21%), and L89V (12%). Multivariate analysis showed that higher baseline HIV RNA levels and smaller numbers of nucleoside reverse transcriptase inhibitor simultaneously used with DRV were associated with a higher risk of DRV resistance mutation selection. By contrast, L76V, a known DRV resistance mutation, was found to decrease the risk of selection of another DRV resistance mutation. The occurrence of virological failure while a patient was on DRV was associated with the selection of mutations that increased the level of DRV resistance without affecting susceptibility to tipranavir (TPV). In these PI-treated patients who displayed treatment failure while they were on a DRV-containing regimen, we confirmed the set of emerging mutations associated with DRV failure and identified the factors associated with the selection of these mutations. TPV susceptibility does not seem to be affected by the selection of a DRV resistance mutation.
Effect of Resiquimod 0.01% Gel on Lesion Healing and Viral Shedding When Applied to Genital Herpes Lesions
Authors: Fife Kenneth H. , Meng Tze-Chiang , Ferris Daron G. , Liu Ping
Published: November 2007

Resiquimod, a Toll-like receptor 7/8 agonist developed as a topical treatment to decrease recurrences of anogenital herpes, induces proinflammatory cytokines that may delay lesion healing. Adults with frequently recurring anogenital herpes were randomized within 24 h of onset of a recurrence to vehicle or resiquimod 0.01% gel two times per week for 3 weeks. Subjects underwent daily lesion assessments and sampling for herpes simplex virus DNA PCR for 21 days or until investigator-determined healing of lesion(s). Eighty-two subjects with a mean age of 39 ± 10.5 years and a median of seven recurrences per year were enrolled in the study. The qualifying recurrence was positive by PCR for herpes simplex virus in 68% of subjects. No difference was observed between the vehicle (39 subjects) and resiquimod (43 subjects) groups with respect to time to healing (median of 7.0 days versus median of 6.5 days, respectively; Cox proportional hazard model ratio of 1.229; 95% confidence interval, 0.778 to 1.942;
P
= 0.376). The distributions of maximum severity scores for any investigator-assessed local skin signs and for subject-assessed local symptoms were similar between treatment groups (
P
= 0.807 and
P
= 0.103, respectively). For subjects with at least one positive PCR result, no difference was observed for time to cessation of viral shedding (median of 7 days versus median of 5 days for vehicle and resiquimod groups, respectively; Cox proportional hazard model ratio of 1.471; 95% confidence interval, 0.786 to 2.754;
P
= 0.227). Application of resiquimod 0.01% two times per week for 3 weeks did not delay the healing of genital herpes lesions or reduce acute viral shedding.
Complete Genomic Sequence of Bacteriophage φEcoM-GJ1, a Novel Phage That Has Myovirus Morphology and a Podovirus-Like RNA Polymerase
Authors: Jamalludeen Nidham , Kropinski Andrew M. , Johnson Roger P. , Lingohr Erika , Harel Josée , Gyles Carlton L.
Published: November 2007

The complete genome of φEcoM-GJ1, a lytic phage that attacks porcine enterotoxigenic
Escherichia coli
of serotype O149:H10:F4, was sequenced and analyzed. The morphology of the phage and the identity of the structural proteins were also determined. The genome consisted of 52,975 bp with a G+C content of 44% and was terminally redundant and circularly permuted. Seventy-five potential open reading frames (ORFs) were identified and annotated, but only 29 possessed homologs. The proteins of five ORFs showed homology with proteins of phages of the family
Myoviridae
, nine with proteins of phages of the family
Podoviridae
, and six with proteins of phages of the family
Siphoviridae
. ORF 1 encoded a T7-like single-subunit RNA polymerase and was preceded by a putative
E. coli
σ
70
-like promoter. Nine putative phage promoters were detected throughout the genome. The genome included a tRNA gene of 95 bp that had a putative 18-bp intron. The phage morphology was typical of phages of the family
Myoviridae
, with an icosahedral head, a neck, and a long contractile tail with tail fibers. The analysis shows that φEcoM-GJ1 is unique, having the morphology of the
Myoviridae
, a gene for RNA polymerase, which is characteristic of phages of the T7 group of the
Podoviridae
, and several genes that encode proteins with homology to proteins of phages of the family
Siphoviridae
.
Characterization of the Structural Gene Encoding Nisin F, a New Lantibiotic Produced by a
Lactococcus lactis
subsp.
lactis
Isolate from Freshwater Catfish (
Clarias gariepinus
)
Authors: de Kwaadsteniet M. , ten Doeschate K. , Dicks L. M. T.
Published: November 2007

Lactococcus lactis
F10, isolated from freshwater catfish, produces a bacteriocin (BacF) active against
Staphylococcus aureus
,
Staphylococcus carnosus
,
Lactobacillus curvatus
,
Lactobacillus plantarum
, and
Lactobacillus reuteri
. The operon encoding BacF is located on a plasmid. Sequencing of the structural gene revealed no homology to other nisin genes. Nisin F is described.
Subfossil 16S rRNA Gene Sequences of Green Sulfur Bacteria in the Black Sea and Their Implications for Past Photic Zone Anoxia
Authors: Manske Ann K. , Henßge Uta , Glaeser Jens , Overmann Jörg
Published: November 2007

The Black Sea is the largest extant anoxic water body on Earth. Its oxic-anoxic boundary is located at a depth of 100 m and is populated by a single phylotype of marine green sulfur bacteria. This organism,
Chlorobium
sp. strain BS-1, is extraordinarily low light adapted and can therefore serve as an indicator of deep photic zone anoxia (A. K. Manske, J. Glaeser, M. M. M. Kuypers, and J. Overmann, Appl. Environ. Microbiol. 71:8049-8060, 2005). In the present study, two sediment cores were retrieved from the bottom of the Black Sea at depths of 2,006 and 2,162 m and were analyzed for the presence of subfossil DNA sequences of BS-1 using ancient-DNA methodology. Using optimized cultivation media, viable cells of the BS-1 phylotype were detected only at the sediment surface and not in deeper layers. In contrast, green sulfur bacterial 16S rRNA gene fragments were amplified from all the sediment layers investigated, including turbidites. After separation by denaturing gradient gel electrophoresis and sequencing, 14 different sequence types were distinguished. The sequence of BS-1 represented only a minor fraction of the amplification products and was found in 6 of 22 and 4 of 26 samples from the 2,006- and 2,162-m stations, respectively. Besides the sequences of BS-1, three additional phylotypes of the marine clade of green sulfur bacteria were detected. However, the majority of sequences clustered with groups from freshwater habitats. Our results suggest that a considerable fraction of green sulfur bacterial chemofossils did not originate in a low-light marine chemocline environment and therefore were likely to have an allochthonous origin. Thus, analysis of subfossil DNA sequences permits a more differentiated interpretation and reconstruction of past environmental conditions if specific chemofossils of stenoec species, like
Chlorobium
sp. strain BS-1, are employed.
Iron Starvation and Culture Age Activate Metacaspases and Programmed Cell Death in the Marine Diatom
Thalassiosira pseudonana
Authors: Bidle Kay D. , Bender Sara J.
Published: November 2007

In the modern ocean, phytoplankton maintain extremely high primary production/biomass ratios, indicating that they bloom, die, and are replaced weekly. The molecular mechanisms regulating cellular mortality and turnover are largely unknown, even though they effectively short-circuit carbon export to the deep ocean and channel primary productivity to microbial food webs. Here, we present morphological, biochemical, and molecular evidence of caspase-mediated, autocatalytic programmed cell death (PCD) in the diatom
Thalassiosira pseudonana
in response to iron starvation. Transmission electron microscopy revealed internal degradation of nuclear, chloroplastic, and mitochondrial organelles, all while the plasma membranes remained intact. Cellular degradation was concomitant with dramatic decreases in photosynthetic efficiency, externalization of phosphatidylserine, and significantly elevated caspase-specific activity, with the addition of a broad-spectrum caspase inhibitor rescuing cells from death. A search of the
T. pseudonana
genome identified six distinct putative metacaspases containing a conserved caspase domain structure. Quantitative reverse transcription-PCR and Western blot analysis revealed differential gene and protein expression of
T. pseudonana
metacaspases, some of which correlated with physiological stress and caspase activity. Taken together with the recent discovery of the metacaspase-mediated viral infection of phytoplankton (K. D. Bidle, L. Haramaty, J. Barcelos-Ramos, and P. G. Falkowski, Proc. Natl. Acad. Sci. USA
104:
6049-6054, 2007), our findings reveal a key role for metacaspases in the turnover of phytoplankton biomass in the oceans. Furthermore, given that Fe is required for photosynthetic electron transfer and is chronically limiting in a variety of oceanic systems, including high-nutrient low-chlorophyll regions, our findings provide a potential ecological context for PCD in these unicellular photoautotrophs.
Ras GTPase-Activating Protein Regulation of Actin Cytoskeleton and Hyphal Polarity in
Aspergillus nidulans
Authors: Harispe Laura , Portela Cecilia , Scazzocchio Claudio , Peñalva Miguel A. , Gorfinkiel Lisette
Published: November 2007

Aspergillus nidulans gapA1
, a mutation leading to compact, fluffy colonies and delayed polarity establishment, maps to a gene encoding a Ras GTPase-activating protein. Domain organization and phylogenetic analyses strongly indicate that GapA regulates one or more “true” Ras proteins. A
gapA
Δ strain is viable.
gapA
colonies are more compact than
gapA1
colonies and show reduced conidiation.
gapA
Δ strains have abnormal conidiophores, characterized by the absence of one of the two layers of sterigmata seen in the wild type.
gapA
transcript levels are very low in conidia but increase during germination and reach their maximum at a time coincident with germ tube emergence. Elevated levels persist in hyphae. In germinating conidiospores,
gapA
Δ disrupts the normal coupling of isotropic growth, polarity establishment, and mitosis, resulting in a highly heterogeneous cell population, including malformed germlings and a class of giant cells with no germ tubes and a multitude of nuclei. Unlike wild-type conidia,
gapA
Δ conidia germinate without a carbon source. Giant multinucleated spores and carbon source-independent germination have been reported in strains carrying a
rasA
dominant active allele, indicating that GapA downregulates RasA.
gapA
Δ cells show a polarity maintenance defect characterized by apical swelling and subapical branching. The strongly polarized wild-type F-actin distribution is lost in
gapA
Δ cells. As GapA-green fluorescent protein shows cortical localization with strong predominance at the hyphal tips, we propose that GapA-mediated downregulation of Ras signaling at the plasma membrane of these tips is involved in the polarization of the actin cytoskeleton that is required for hyphal growth and, possibly, for asexual morphogenesis.
Target of Rapamycin and LST8 Proteins Associate with Membranes from the Endoplasmic Reticulum in the Unicellular Green Alga
Chlamydomonas reinhardtii
Authors: Díaz-Troya Sandra , Florencio Francisco J. , Crespo José L.
Published: November 2007

The highly conserved target of rapamycin (TOR) kinase is a central controller of cell growth in all eukaryotes. TOR exists in two functionally and structurally distinct complexes, termed TOR complex 1 (TORC1) and TORC2. LST8 is a TOR-interacting protein that is present in both TORC1 and TORC2. Here we report the identification and characterization of TOR and LST8 in large protein complexes in the model photosynthetic green alga
Chlamydomonas reinhardtii
. We demonstrate that
Chlamydomonas
LST8 is part of a rapamycin-sensitive TOR complex in this green alga. Biochemical fractionation and indirect immunofluorescence microscopy studies indicate that TOR and LST8 exist in high-molecular-mass complexes that associate with microsomal membranes and are particularly abundant in the peri-basal body region in
Chlamydomonas
cells. A
Saccharomyces cerevisiae
complementation assay demonstrates that
Chlamydomonas
LST8 is able to functionally and structurally replace endogenous yeast LST8 and allows us to propose that binding of LST8 to TOR is essential for cell growth.
Profiling Bovine Antibody Responses to
Mycobacterium avium
subsp.
paratuberculosis
Infection by Using Protein Arrays
Authors: Bannantine John P. , Paustian Michael L. , Waters W. Ray , Stabel Judith R. , Palmer Mitchell V. , Li Lingling , Kapur Vivek
Published: November 2007

With the genome sequence of
Mycobacterium avium
subsp.
paratuberculosis
determined, technologies are now being developed for construction of protein arrays to detect the presence of antibodies against
M. avium
subsp.
paratuberculosis
in host serum. The power of this approach is that it enables a direct comparison of
M. avium
subsp.
paratuberculosis
proteins to each other in relation to their immunostimulatory capabilities. In this study, 93 recombinant proteins, produced in
Escherichia coli
, were arrayed and spotted onto nitrocellulose. These proteins include unknown hypothetical proteins and cell surface proteins as well as proteins encoded by large sequence polymorphisms present uniquely in
M. avium
subsp.
paratuberculosis
. Also included were previously reported or known
M. avium
subsp.
paratuberculosis
antigens to serve as a frame of reference. Sera from healthy control cattle (
n
= 3) and cattle infected with either
M. avium
subsp.
avium
and
Mycobacterium bovis
were exposed to the array to identify nonspecific or cross-reactive epitopes. These data demonstrated a degree of cross-reactivity with the
M. avium
subsp.
avium
proteins that was higher than the degree of cross-reactivity with the more distantly related
M. bovis
proteins. Finally, sera from naturally infected cattle (
n
= 3) as well as cattle experimentally infected with
M. avium
subsp.
paratuberculosis
(
n
= 3) were used to probe the array to identify antigens in the context of Johne's disease. Three membrane proteins were the most strongly detected in all serum samples, and they included an invasion protein, an ABC peptide transport permease, and a putative GTPase protein. This powerful combination of genomic information, molecular tools, and immunological assays has enabled the identification of previously unknown antigens of
M. avium
subsp.
paratuberculosis
.
Modulation of Pulmonary Dendritic Cell Function during Mycobacterial Infection
Authors: Anis Mursalin M. , Fulton Scott A. , Reba Scott M. , Liu Yi , Harding Clifford V. , Boom W. Henry
Published: November 2007

We have previously reported that during mycobacterial infection, naïve CD4
+
T-cell activation is enhanced in the lungs. We investigated the role of chemokine receptor CCR7 and its ligands in the ability of CD11c
+
lung dendritic cells (DCs) to activate naïve CD4
+
T cells during pulmonary infection with
Mycobacterium bovis
bacillus Calmette-Guérin (BCG). BCG infection resulted in the accumulation and maturation in the lungs of DCs that persisted as the mycobacterial burden declined. Lung DCs from infected mice expressed more major histocompatibility complex class II (MHC-II) than those from uninfected mice. CCR7 expression levels on lung DCs were comparable among uninfected and infected mice. The gene expression of the CCR7 ligand CCL19 progressively increased throughout BCG infection, and its expression was MyD88 dependent. CD11c
+
lung cells from BCG-infected mice activated ovalbumin (OVA)-specific naïve CD4
+
T cells more than CD11c
+
lung cells from uninfected mice. Interestingly, during peak mycobacterial infection, CD11c
hi
MHC
hi
lung DCs had slightly decreased chemotaxis toward the CCR7 ligand CCL21 and less efficiency in activating naive CD4
+
T cells than DCs from mice during late-stage infection, when few bacilli are found in the lung. These findings suggest that during BCG infection, the inflammation and sustained expression of CCL19 result in the recruitment, activation, and retention in the lung of DCs that can activate naïve CD4
+
T cells in situ.
Molecular Basis of Commensalism in the Urinary Tract: Low Virulence or Virulence Attenuation?
Authors: Zdziarski Jaroslaw , Svanborg Catharina , Wullt Björn , Hacker Jörg , Dobrindt Ulrich
Published: November 2007

In some patients,
Escherichia coli
strains establish significant bacteriuria without causing symptoms of urinary tract infection (UTI). These asymptomatic-bacteriuria (ABU) strains have been shown to express fewer virulence factors than the uropathogenic
E. coli
(UPEC) strains that cause severe, symptomatic UTI. Paradoxically, ABU strains carry many typical UPEC virulence genes, and the molecular basis of their low virulence therefore remains unclear. This study examined whether ABU strains might evolve from UPEC by genome loss and virulence gene attenuation. The presence of conserved
E. coli
K-12 genes was examined using an
E. coli
K-12 strain MG1655-specific DNA array and the distribution of UPEC virulence-related genes was examined with the
E. coli
pathoarray. Two groups of strains could be distinguished. Several ABU strains were shown by multilocus sequence typing and by comparative genomic analyses to be related to UPEC but to have smaller genome sizes. There were significant alterations in essential virulence genes, including reductive evolution by point mutations, DNA rearrangements, and deletions. Other strains were unrelated to UPEC and lacked most of the virulence-associated genes. The results suggest that some ABU strains arise from virulent strains by attenuation of virulence genes while others are nonvirulent and resemble commensal strains. We propose that virulence attenuation might constitute a general mechanism for mucosal pathogens to evolve toward commensalism.
Expression of a Uniquely Regulated Extracellular Polysaccharide Confers a Large-Capsule Phenotype to
Bacteroides fragilis
Authors: Chatzidaki-Livanis Maria , Coyne Michael J. , Roche-Hakansson Hazeline , Comstock Laurie E.
Published: November 2007

Bacteroides fragilis
synthesizes eight distinct capsular polysaccharides, more than any described bacterium outside the order
Bacteroidales
. Here, we show that this organism also produces a high-molecular-weight extracellular polysaccharide (EPS). Expression of the EPS results in the formation of a large polysaccharide layer around the bacteria which prevents them from forming a tight pellet upon centrifugation and from entering a Percoll density gradient. Like expression of the capsular polysaccharides, expression of the EPS is phase variable and dictated by DNA inversion of its promoter. EPS expression is regulated at one level by the DNA invertase Tsr19, which is encoded by a gene immediately upstream of the EPS locus and inverts the EPS promoter, causing an on or off phenotype. Expression of the EPS is also regulated at another level, which dictates the amount of EPS produced. By analyzing a panel of
tsr19
deletion mutants, we found that the number of inverted repeats (IRs) flanking the promoter is variable. Transcription into the EPS genes is greater in mutants with a single IR between the promoter and the downstream EPS genes than in mutants with more than one IR in this region, correlating with the synthesis of more EPS. By analyzing the relative orientations of the EPS promoter of bacteria obtained from human fecal samples, we showed that both DNA inversion and variation in the number of IRs are active processes of
B. fragilis
in the endogenous human intestinal ecosystem.
Kaposi sarcoma-associated herpesvirus/human herpesvirus 8 and lymphoproliferative disorders
Authors: Du M-Q , Bacon C M , Isaacson P G
Published: November 2007

Kaposi sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus 8 (HHV8), is a recent addition to the list of human viruses that are directly associated with lymphoproliferative disorders. KSHV was first shown to be involved in multicentric Castleman disease and primary effusion lymphoma (PEL). Subsequently, the virus was identified in solid lymphomas, often of extranodal sites, with morphological and immunophenotypic characteristics similar to those of PEL, and in other lymphoproliferative disorders with heterogeneous clinicopathological presentations. The recent advances in our understanding of the histology, immunophenotype and pathogenesis of these KSHV-associated lymphoproliferative disorders are reviewed.
Molecular aspects of HTLV-I infection and adult T-cell leukaemia/lymphoma: Table 1
Authors: Taylor G P
Published: November 2007

Human T-cell lymphotropic virus-I (HTLV-I) is the cause of adult T-cell leukaemia/lymphoma. Various viral proteins, especially, but not exclusively, Tax have been implicated in oncogenesis, mostly through in vitro studies. Tax transactivates a large and apparently ever expanding list of human genes through transcriptional factors. Elucidating not only the pathways but also the timing of action of HTLV proteins is important for understanding the pathogenesis and development of new treatments.
HIGH ENERGY SCATTERING IN QUANTUM CHROMODYNAMICS
Authors: GELIS FRANÇOIS , LAPPI TUOMAS , VENUGOPALAN RAJU
Published: November 2007

In this series of three lectures, we discuss several aspects of high energy scattering among hadrons in Quantum Chromodynamics. The first lecture is devoted to a description of the parton model, Bjorken scaling and the scaling violations due to the evolution of parton distributions with the transverse resolution scale. The second lecture describes parton evolution at small momentum fraction x, the phenomenon of gluon saturation and the Color Glass Condensate (CGC). In the third lecture, we present the application of the CGC to the study of high energy hadronic collisions, with emphasis on nucleus-nucleus collisions. In particular, we provide the outline of a proof of high energy factorization for inclusive gluon production.
ASTROPARTICLE PHYSICS FROM 1016 TO 1020 eV
Authors: DE SOUZA VITOR
Published: November 2007

Cosmic rays have always been an important tool to study particle interactions and astrophysics. In this article, we are going to review the main results from this field in the energy range from 1016 to 1020 eV. Important results from the KASCADE and Pierre Auger Experiments are going to be shown and discussed. Some perspectives for the near future concerning new measurements are going to be presented.
LINEAR MESON AND BARYON TRAJECTORIES IN ADS/QCD
Authors: FORKEL HILMAR , BEYER MICHAEL , FREDERICO TOBIAS
Published: November 2007

An approximate holographic dual of QCD is constructed and shown to reproduce the empirical linear trajectories of universal slope on which the square masses of radially and orbitally excited hadrons join. Conformal symmetry breaking and other IR effects are described exclusively by deformations of the anti-de Sitter background metric. The predictions for the light hadron spectrum include new relations between ground state masses and trajectory slopes and are in good overall agreement with experimental data.
RENORMALIZATION GROUP FLOW IN COLD AND DENSE YUKAWA THEORY
Authors: PALHARES LETÍCIA F. , FRAGA EDUARDO S.
Published: November 2007

We analyze the role of renormalization group (RG) running of the coupling and fermion masses in perturbative Yukawa theory at finite density. The dependence of the RG flow on the number of fermion flavors is discussed. Results for the fermionic contribution to the two-loop pressure at zero temperature and finite density are presented for NF = 4, and finite fermion mass effects are shown to be an important correction.
LIGHT QUARKONIA DECAYS IN THE CORRECTED 3P0 MODEL
Authors: DA SILVA D. T. , QUADROS J. N. , DA SILVA M. L. L. , HADJIMICHEF D.
Published: November 2007

The 3P0 model is a typical decay model which considers only OZI-allowed strong decays and considers a quark-antiquark pair creation in the presence of the initial state meson. The quark-antiquark pair is created with the vacuum quantum numbers. This model can also be obtained from the non-relativistic limit of the pair creation Hamiltonian. Applying the Reduced Hilbert Space formalism to the pair creation Hamiltonian will produce the characteristic expansion in powers of the wave function, where the 3P0 model is the lowest order term of this expansion. This new model will correct 3P0, which we call the Corrected 3P0 model or C 3P0 model. The model will be applied to the light quarkonia decay sector.
HEAVY-QUARKONIA IN THE STAR EXPERIMENT
Authors:   for the Star Collaboration, COSENTINO MAURO R.
Published: November 2007

Heavy Quarkonium states modifications in relativistic heavy ion collisions have been of great interest since the proposal by Matsui and Satz of J/ψ suppression as a signature of Quark-Gluon Plasma (QGP) formation. Recent studies suggest that the excited states χc, ψ(2 S ) and ϒ(3 S ) melt sequentially1,2 and the amount of observed suppression depends on the state and medium conditions. Therefore, this suppression pattern may be used as a probe of the medium temperature. In this work we present preliminary results on the charmonium and bottomnium measurements performed by the STAR experiment at RHIC for p + p and Cu + Cu collisions at [Formula: see text].
DECISION ON ENTERPRISE COMPUTING SOLUTIONS FOR AN INTERNATIONAL TOURISM
Authors: HUANG CHIA-HUI , KAO HAN-YING , LI HAN-LIN
Published: November 2007

This study proposes a multi-objective decision approach for evaluating the enterprise computing solutions in international tourism. We first analyze one tour operator in Thailand as well as its specific requirements for enterprise computations. In the decision processes for enterprise computation, several experts are invited to evaluate the alternatives based on a multi-tier electronic business architecture. This study designs two models for evaluating the information systems investments in international tourism. The first model maximizes the overall utility for each criterion, and the other model maximizes the utility for every expert. Because each alternative for enterprise computation involves approximate costs and efforts, we represent the cost data with fuzzy sets and possibility distributions.
A SYSTEMATIC APPROACH FOR THE SELECTION OF BUSINESS PROCESSES FOR E-ENABLEMENT
Authors: SALHIEH SA'ED M.
Published: November 2007

This paper introduces a selection approach that conveys to management where to focus organizational resources to gain the maximum benefit of converting to e-business, by making an educated decision regarding which business processes should be e-enabled (converted to electronic delivery) first. The selection model is based on criteria developed using two proposed axioms: the benefit axiom and the effort axiom. The benefit axiom addresses the company's needs in terms of expected gains manifested in cost saving and/or time savings; while the effort axiom addresses the technical point of view of e-enablement in terms of the amount of effort needed to e-enable business processes. The two axioms are incorporated to construct a multi-criteria selection model using the Analytic Hierarchy Process.
THE EFFECT OF GAS ADSORPTION ON THE ELECTRONIC PROPERTIES OF MgO AND Ca-DOPED MgO
Authors: JALILI SEIFOLLAH , MAJIDI ROYA , GHAFOORI TABRIZI KERASOOS
Published: November 2007

The effect of gas adsorption on the electronic properties of MgO and Ca -doped MgO is investigated using ab initio molecular dynamics method. The equilibrium position, adsorption energy, charge transfer, and electronic band structure of MgO and Ca -doped MgO (001) surface in the presence of H 2, O 2, and CO were calculated. It was found that CO and O 2 affect the electronic properties of MgO and Ca -doped MgO , extensively. The MgO and Ca -doped MgO can exhibit semiconductor behavior with a band gap which is smaller than that of the MgO after CO and O 2 adsorption. The obtained results indicate that Ca doping increase the activity and the conductivity of MgO (001) surface.
BAND STRUCTURE, METALLIZATION, AND SUPERCONDUCTIVITY OF GaAs AND InAs UNDER HIGH PRESSURE
Authors: AMALRAJ A. , NIRMALA LOUIS C. , GERARDIN JAYAM SR.
Published: November 2007

The electronic band structure, metallization, structural phase transition, and superconductivity of cubic zinc blende type GaAs and InAs are investigated. The equilibrium lattice constant, bulk modulus, and the phase transition pressure at which the compounds undergo structural phase transition from ZnS to NaCl are predicted from the total energy calculations. The density of states at the Fermi level (N(E F )) get enhanced after metallization, which leads to the superconductivity in GaAs and InAs . The superconducting transition temperatures (T c ) of GaAs and InAs are obtained as a function of pressure for both the ZnS and NaCl structures. GaAs and InAs come under the class of pressure-induced superconductors. When pressure is increased T c increases in both the normal and high pressure-structures. The dependence of T c on electron–phonon mass enhancement factor λ shows that GaAs and InAs are electron–phonon-mediated superconductors. Also, it is found that GaAs and InAs retained in their normal structure under high pressure give appreciably high T c .
THEORETICAL INVESTIGATION OF ULTRAFAST DYNAMICS OF THE RHODAMINE-700 MOLECULE IN SOLVENTS
Authors: DONG LI-QING , NIU KAI , CONG SHU-LIN
Published: November 2007

The density matrix theory is used to calculate the fluorescence depletion spectra and the internal conversion (IC) times of rhodamine-700 (R-700) in methanol, ethanol, and DMSO solvents. The calculated IC times from Sx to S1 states of R-700 in methanol, ethanol, and DMSO solvents are about 20, 33, and 70 fs, respectively. The times of the excited solvation processes for R-700 in methanol, ethanol, and DMSO solvents are about 8.0, 7.0, and 3.0 ps, respectively.
THEORETICAL INVESTIGATION OF METHYLENE: USING ULTRAHIGH ACCURATE MRCI APPROACH
Authors: SONG JIE
Published: November 2007

A new hybrid vairational-perturbational MRCISD(TQ) approach is applied to the problem of singlet–triplet and singlet–singlet separation in methylene using several basis sets. The inclusion of higher excitations beyond single and double excitations can predict more accurate splitting energies between states as well as closer single-point energies to available full CI results when the small basis set is used. Comparisons with MRCISD and MRCCSD treatments indicate that MRCISD(TQ) can lead to reliable predictions of the splitting energies when larger bases are employed.
MANAGING INFORMATION IN NEW PRODUCT DEVELOPMENT: A CONCEPTUAL REVIEW, RESEARCH PROPOSITIONS AND TENTATIVE MODEL
Authors: FRISHAMMAR JOHAN , YLINENPÄÄ HÅKAN
Published: November 2007

Many studies in new product development (NPD) single out the use of information (especially market information) as a key predictor of NPD performance, but knowledge is lacking about what type of information is needed in each phase of the NDP process to enable high NPD performance. Based on a literature review and a pilot case study, this article increases the understanding of managing information in NPD. It is argued that the capability of managing information consists of three components: acquiring, sharing, and using information. By focusing on three different phases of the NPD process, 11 propositions regarding which information, information sources and means of cross-functional integration patterns that are most important to high NPD performance have been derived in each respective phase. In addition, the article also discusses antecedents and consequences of managing information. The article concludes with implications for managers, identifies limitations and proposes an agenda for further research into this area.
Cannabinoids stimulate prostaglandin production by human gestational tissues through a tissue- and CB1-receptor-specific mechanism
Authors: Mitchell Murray D. , Sato Timothy A. , Wang Anderson , Keelan Jeffrey A. , Ponnampalam Anna P. , Glass Michelle
Published: November 2007

Endocannabinoids have been implicated in the mechanisms of implantation, maintenance of pregnancy, and parturition in women. Intrauterine prostaglandin production and actions are also critical in each of these mechanisms. Hence, we have evaluated the effects of cannabinoids on prostaglandin biosynthesis by human gestational membranes. Explants of term amnion and choriodecidua were established and treated with the endogenous endocannabinoids 2-arachidonoyl glycerol and anandamide, as well as the synthetic cannabinoid CP55,940, to determine their ability to modulate PGE2 production. The explants were also treated with CP55,940 in the presence of either SR141716A (a potent and selective antagonist of the cannabinoid receptor CB1) or NS398 [a cyclooxygenase (COX)-2 inhibitor] to determine whether any observed stimulation of PGE2 production was mediated through the CB1-receptor and/or COX-2 activity. All three cannabinoids caused a significant increase in PGE2 production in the amnion but not in the choriodecidua. However, separated fetal (chorion) explants responded to cannabinoid treatment in a similar manner to amnion, whereas maternal (decidual) explants did not. The enhanced PGE2 production caused by CP55,940 was abrogated by cotreatment with either SR141716A or NS398, illustrating that the cannabinoid action on prostaglandin production in fetal membranes is mediated by CB1 agonism and COX-2. Data from Western blotting show that cannabinoid treatment results in the upregulation of COX-2 expression. This study demonstrates a potential role for endocannabinoids in the modulation of prostaglandin production in late human pregnancy, with potentially important implications for the timing and progression of term and preterm labor and membrane rupture.
Neurological Disorders in Libya: An Overview
Authors: Benamer Hani T.S.
Published: November 2007

The aim of this study was to review all publications related to the incidence and prevalence of neurological disorders in Libya, and to estimate the burden of these disorders in the country. The PubMed and the Libyan Medical Index were searched using different combinations of keywords. The references in all relevant papers were reviewed for any additional publications. An estimation of the number of patients with neurological disorders was made based on the reviewed data and adjusted using the Libyan Nationwide Official Census of 2006. Sixteen papers were identified. Incidence rate is available for twelve disorders and the prevalence rate for nine. Data for some of the most common neurological problems such as headaches, or for important disorders such as dementia, are lacking. Therefore, the estimate of 6,892 new neurological cases per year and a total of 11,908 neurological patients in 2006 in Libya is largely underestimating the burden of the neurological disorders in this country and should be regarded as the lowest possible estimation. Further neuroepidemiological studies in Libya are needed.
The Management Approaches to Dyskinesia Vary from Country to Country
Authors: Woitalla Dirk , Mueller Thomas , Russ Hermann , Hock Klaus , Haeger Doris-Anita
Published: November 2007

Many Parkinson’s disease (PD) patients treated with levodopa develop motor fluctuations and/or dyskinesia. This large, retrospective study was conducted to compare the prevalence and treatment of dyskinesia in PD patients in seven countries. A total of 380 physicians were interviewed and completed patient record forms retrospectively for their last 5 patients with dyskinesia (total 1,900). The overall prevalence of dyskinesia in PD patients was 34%, but the rate varied from 24 to 51% according to geographical location. This study showed that 51.0% of Japanese physicians and 50.6% of UK physicians were dissatisfied with current treatment strategies for dyskinesia. Regardless of geographical location, physicians were dissatisfied with the current treatment strategies for dyskinesia.
Selective Feticide in Monoamniotic Twin Pregnancies by Umbilical Cord Occlusion and Transection
Authors: Middeldorp Johanna M. , Klumper Frans J.C.M. , Oepkes Dick , Lopriore Enrico , Kanhai Humphrey H.H. , Vandenbussche Frank P.H.A.
Published: November 2007

Objectives: In monoamniotic twin pregnancies discordant for fetal anomaly, parents may opt for selective feticide. However, the normal co-twin remains at risk of sudden demise from cord entanglement. We report on three cases of successful selective feticide by cord occlusion combined with cord transection. Methods: We describe technical details and outcome of three monoamniotic twin pregnancies discordant for fetal anomaly (two cases of anencephaly and one case of congenital heart block) in which cord occlusion was followed by transection of the cord using contact laser. Results: The fetoscopic cord occlusion and transection using laser was successfully performed at 15, 16 and 19 weeks gestation, respectively. In one case, amniotic fluid leakage occurred after fetoscopy. The surviving co-twins were born at 36, 38 and 36 weeks gestation, respectively; two of the three were born vaginally and they were all healthy. Conclusion: In monoamniotic twins, selective feticide using laser occlusion and transection of the umbilical cord is technically feasible and can lead to near-term vaginal birth of healthy co-twins.
Cognitive Decline and Survival in Alzheimer’s Disease according to Education Level
Authors: Bruandet A. , Richard F. , Bombois S. , Maurage C.A. , Masse I. , Amouyel P. , Pasquier F.
Published: November 2007

Objective: We tested the hypothesis that a higher education level is associated with faster cognitive decline and lower survival in a cohort of 670 Alzheimer’s disease patients, followed for 3.5 years at the Lille-Bailleul memory centre. Methods: The patients were categorized in 3 groups according to educational levels: low (≤8 years), intermediate (9–12 years) and high (>12 years). Cognitive function was measured with the Mini Mental State Examination (MMSE) and the Mattis Dementia Rating Scale (DRS). Survival was analyzed with a Cox model. Analyses were adjusted for age, sex, cholinesterase inhibitor treatment, diabetes, hypertension, visible vascular lesions on MRI, baseline DRS and MMSE. Results: The adjusted mixed random model showed that MMSE declined faster for patients with high and intermediate educational levels compared with those with a low educational level (p < 0.0001). The mean annually adjusted DRS decline was highest for the groups with the most education (p = 0.05). The mortality risk was not higher in the better-educated groups (high vs. low: RR = 0.84; 95% CI = 0.35–1.99, intermediate vs. low: RR = 0.82; 95% CI = 0.41–1.63). Conclusion: In our cohort, highly educated patients had a faster cognitive decline than less educated patients but similar mortality rates. Our findings support the cognitive reserve hypothesis.
Effect of Fluoride Compounds on Enamel Erosion in vitro: A Comparison of Amine, Sodium and Stannous Fluoride
Authors: Ganss C. , Schlueter N. , Hardt M. , Schattenberg P. , Klimek J.
Published: November 2007

The aim of the study was to evaluate the relevance of cations in different fluoride compounds for their effectiveness as anti-erosive agents. Human enamel samples underwent a de- and re-mineralisation procedure for 10 days. Erosive demineralisation was performed with 0.05 Mcitric acid (pH 2.3) 6 × 2 min daily followed by immersion in the test solution 6 × 2 min each. Test solutions were: SnCl2 (815 ppm Sn; pH 2.6), NaF (250 ppm F; pH 3.5), SnF2 (250 ppm F, 809 ppm Sn; pH 3.5), amine fluoride (AmF, 250 ppm F; pH 3.5), AmF/NaF (250 ppm F; pH 4.3), and AmF/SnF2 (250 ppm F, 390 ppm Sn; pH 4.2). In the control group no fluoridation was performed. Mineral content was monitored by longitudinal microradiography. Finally, scanning electron microscopy was performed. The highest erosive mineral loss was found in the control group (48.0 ± 17.1 µm). Mineral loss was nearly completely inhibited by AmF/SnF2 (5.7 ± 25.1 µm; p ≤ 0.001) and SnF2 (–3.8 ± 14.4 µm; p ≤ 0.001) treatments. Groups treated with SnCl2 (17.6 ± 19.5 µm; p ≤ 0.001) and NaF (13.2 ± 21.7 µm; p ≤ 0.001) showed a decrease in erosive mineral loss, AmF (41.6 ± 16.0 µm) and AmF/NaF (27.7 ± 28.4 µm) had no significant effect on erosion progression. The results indicate considerable differences between the fluoride compounds tested. Treatment with solutions containing SnF2 was most effective.