bluuebunny/crossref_metadata_2025 huggingface dataset:
The way we view cellular (glyco)sphingolipids
Authors: Hoetzl Sandra , Sprong Hein , Van Meer Gerrit
Published: November 2007

Mammalian cells synthesize ceramide in the endoplasmic reticulum (ER) and convert this to sphingomyelin and complex glycosphingolipids on the inner, non‐cytosolic surface of Golgi cisternae. From there, these lipids travel towards the outer, non‐cytosolic surface of the plasma membrane and all membranes of the endocytic system, where they are eventually degraded. At the basis of the selective, anterograde traffic out of the Golgi lies the propensity of the sphingolipids to self‐aggregate with cholesterol into microdomains termed ‘lipid rafts’. At the plasma membrane surface these rafts are thought to function as the scaffold for various types of (glyco) signaling domains of different protein and lipid composition that can co‐exist on one and the same cell. In the past decade, various unexpected findings on the sites where sphingolipid‐mediated events occur have thrown a new light on the localization and transport mechanisms of sphingolipids. These findings are largely based on biochemical experiments. Further progress in the field is hampered by a lack of morphological techniques to localize lipids with nanometer resolution. In the present paper, we critically evaluate the published data and discuss techniques and potential improvements.
Focused microarray analysis of glyco‐gene expression in human glioblastomas
Authors: Kroes Roger A. , Dawson Glyn , Moskal Joseph R.
Published: November 2007

Altered glycosylation has been linked to cancer cell metastasis and invasivity. We have previously shown that expressing a specific sialyltransferase gene in gliomas inhibited tumor formation, in vivo. In order to identify other “glyco‐gene” targets with therapeutic potential, focused 45‐mer oligonucleotide microarrays were constructed containing all of the cloned human glyco‐genes. Gene expression profiles of normal human brain and malignant gliomas were compared and microarray datasets analyzed using significance analysis of microarrays algorithms. There were 11 genes more highly expressed in gliomas compared to normal brain and 25 genes more highly expressed in normal brain compared to gliomas. Among the most noteworthy were high levels of MAN2A2 and ST6GalNAcV in normal brain tissue and high levels of POFUT1 and CHI3L1 in the gliomas, all changes corroborated by qRT‐PCR. Historically, identification of changes in tumor‐associated glycoconjugate expression was obtained by measuring individual enzyme activities or structural changes of specific molecules. With microarray technology, it is possible to measure all of genes associated with glycoconjugate biosynthesis and degradation simultaneously. Our data demonstrate that there are many significant and novel differences in glyco‐gene expression that represent potential targets for the development of therapeutics for the treatment of brain tumors.
Hepatitis B Virus e Antigen Loss during Adefovir Dipivoxil Therapy Is Associated with Enhanced Virus-Specific CD4+T-Cell Reactivity
Authors: Cooksley Helen , Chokshi Shilpa , Maayan Yafit , Wedemeyer Heiner , Andreone Pietro , Gilson Richard , Warnes Thomas , Paganin Simona , Zoulim Fabien , Frederick David , Neumann Avidan U. , Brosgart Carol L. , Naoumov Nikolai V.
Published: November 2007

Weak T-cell reactivity to hepatitis B virus (HBV) is thought to be the dominant cause for chronic HBV infection. Treatment with adefovir dipivoxil (ADV) increases the rate of HBV e antigen (HBeAg) loss; however, the immune mechanisms associated with this treatment response are not understood. Serial analysis of HBV-specific CD4+T-cell reactivity was performed during 48 weeks of therapy with ADV and correlated with treatment outcome for 19 HBeAg-positive patients receiving ADV (n= 13) or the placebo (n= 6). We tested T-cell reactivity to HBV at seven protocol time points by proliferation, cytokine production, and enzyme-linked immunospot assays. A panel of serum cytokines was quantitated by cytokine bead array. ADV-treated patients showed increased CD4+T-cell responses to HBV and lower serum levels of cytokines compared to those of placebo-treated patients. Enhanced CD4+T-cell reactivity to HBV, which peaked at treatment week 16, was confined to a subgroup of ADV-treated patients who achieved greater viral suppression (5.3 ± 0.3 log10copies/ml [mean ± standard error of the mean {SEM}] serum HBV DNA reduction from baseline) and HBeAg loss, but not to ADV-treated patients with moderate (3.4 ± 0.2 log10copies/ml [mean ± SEM]) viremia reduction who remained HBeAg positive or to patients receiving the placebo. In conclusion, T-cell reactivity to HBV increases in a proportion of ADV-treated patients and is associated with greater suppression of HBV replication and HBeAg loss.
Exonuclease Removal of Dideoxycytidine (Zalcitabine) by the Human Mitochondrial DNA Polymerase
Authors: Hanes Jeremiah W. , Johnson Kenneth A.
Published: November 2007

The toxicity of nucleoside analogs used for the treatment of human immunodeficiency virus infection is due primarily to the inhibition of replication of the mitochondrial genome by the human mitochondrial DNA polymerase (Pol γ). The severity of clinically observed toxicity correlates with the kinetics of incorporation versus excision of each analog as quantified by a toxicity index, spanning over six orders of magnitude. Here we show that the rate of excision of dideoxycytidine (zalcitabine; ddC) was reduced fourfold (giving a half-life of ∼2.4 h) by the addition of a physiological concentration of deoxynucleoside triphosphates (dNTPs) due to the formation of a tight ternary enzyme-DNA-dNTP complex at the polymerase site. In addition, we provide a more accurate measurement of the rate of excision and show that the low rate of removal of ddCMP results from both the unfavorable transfer of the primer strand from the polymerase to the exonuclease site and the inefficient binding and/or hydrolysis at the exonuclease site. The analogs ddC, stavudine, and ddATP (a metabolite of didanosine) each bind more tightly at the polymerase site during incorporation than normal nucleotides, and this tight binding contributes to slower excision by the proofreading exonuclease, leading to increased toxicity toward mitochondrial DNA.
The NleE/OspZ Family of Effector Proteins Is Required for Polymorphonuclear Transepithelial Migration, a Characteristic Shared by EnteropathogenicEscherichia coliandShigella flexneriInfections
Authors: Zurawski Daniel V. , Mumy Karen L. , Badea Luminita , Prentice Julia A. , Hartland Elizabeth L. , McCormick Beth A. , Maurelli Anthony T.
Published: November 2007

EnteropathogenicEscherichia coli(EPEC) andShigella flexneriare human host-specific pathogens that infect intestinal epithelial cells. However, each bacterial species employs a different infection strategy within this environmental niche. EPEC attaches to the apical surface of small intestine enterocytes, causing microvillus effacement and rearrangement of the host cell cytoskeleton beneath adherent bacteria. In contrast,S. flexneriinvades the large intestine epithelium at the basolateral membrane, replicates, and spreads cell to cell. Both EPEC andS. flexnerirely on type three secretion systems (T3SS) to secrete effectors into host cells, and both pathogens recruit polymorphonuclear leukocytes (PMNs) from the submucosa to the lumen of the intestine. In this report, we compared the virulence functions of the EPEC T3SS effector NleE and the homologousShigellaprotein Orf212. We discovered that Orf212 was secreted by theS. flexneriT3SS and renamed this protein OspZ. Infection of polarized T84 intestinal epithelial cells with anospZdeletion mutant ofS. flexneriresulted in reduced PMN transepithelial migration compared to infection by the wild type. AnnleEdeletion mutant of EPEC showed a similar reduction of PMN migration. The ability to induce PMN migration was restored in both mutants when eitherospZornleEwas expressed from a plasmid. An infection of T84 cells with the ΔospZmutant resulted in reduced extracellular signal-related kinase phosphorylation and NF-κB activation compared to infection with the wild type. Therefore, we conclude that OspZ and NleE have similar roles in the upstream induction of host signaling pathways required for PMN transepithelial migration inShigellaand EPEC infections.
Pneumocystis carinii
Exhibits a Conserved Meiotic Control Pathway
Authors: Burgess Joshua W. , Kottom Theodore J. , Limper Andrew H.
Published: November 2007

Pneumocystis carinii
is an opportunistic fungus causing severe pneumonia in immune-compromised hosts. Recent evidence suggests that
Pneumocystis
exists as separate sex types, though definitive evidence is currently lacking. These studies were undertaken to determine whether
Pneumocystis
maintains functional meiotic control molecules, which are required for sexual life stages in eukaryotes. Using the
Pneumocystis carinii
Genome Project database, two partial sequences for meiotic control molecules were detected, namely, PC
Ran1
, a presumptive meiotic control kinase, and PC
Mei2
, a homologue to a primary activator of meiosis in
Schizosaccharomyces pombe
. Rapid amplification of cDNA ends was employed to obtain the full open reading frames and to further investigate the functions of these proteins. These presumptive meiotic control molecules were most homologous to molecules present in
S. pombe
(52% identical and 67% homologous for PC
Ran1
and 75% identical and 88% homologous for PC
Mei2
by BLAST analysis). Heterologous expression of these
Pneumocystis
meiotic genes in corresponding temperature-sensitive and knockout strains of
S. pombe
, respectively, further verified the functions of the PCRan1 and PCMei2 proteins. These proteins were further shown to control downstream components of the meiotic pathway in
S. pombe
. Lastly, in vitro kinase assays were used to determine that PCRan1p phosphorylates PCMei2p. These experiments represent the first characterization of any proteins in
P. carinii
involved in meiosis and indicate the presence of a conserved meiotic pathway in
Pneumocystis
. Elucidation of this pathway will be essential in gaining a greater understanding of this important opportunistic fungal pathogen.
Toll-Like Receptor 9-Dependent Macrophage Activation byEntamoeba histolyticaDNA
Authors: Ivory Catherine P. A. , Prystajecky Michael , Jobin Christian , Chadee Kris
Published: November 2007

Activation of the innate immune system by bacterial DNA and DNA of other invertebrates represents a pathogen recognition mechanism. In this study we investigated macrophage responses to DNA from the intestinal protozoan parasiteEntamoeba histolytica.E. histolyticagenomic DNA was purified from log-phase trophozoites and tested with the mouse macrophage cell line RAW 264.7. RAW cells treated withE. histolyticaDNA demonstrated an increase in levels of tumor necrosis factor alpha (TNF-α) mRNA and protein production. TNF-α production was blocked by pretreatment with chloroquine or monensin. In fact, an NF-κB luciferase reporter assay in HEK cells transfected with human TLR9 demonstrated thatE. histolyticaDNA signaled through Toll-like receptor 9 (TLR9) in a manner similar to that seen with CpG-ODN. Immunofluorescence assays confirmed NF-κB activation in RAW cells, as seen by nuclear translocation of the p65 subunit. Western blot analysis demonstrated mitogen-activated protein kinase activation byE. histolyticaDNA.E. histolyticaDNA effects were abolished in MYD88−/−mouse-derived macrophages. In the context of disease, immunization withE. histolyticaDNA protected gerbils from anE. histolyticachallenge infection. Taken together, these results demonstrate thatE. histolyticaDNA is recognized by TLR9 to activate macrophages and may provide an innate defense mechanism characterized by the induction of the inflammatory mediator TNF-α.
Glutamine protects against increases in blood ammonia in football players in an exercise intensity-dependent way
Authors: Bassini-Cameron A , Monteiro A , Gomes A , Werneck-de-Castro J P S , Cameron L
Published: November 2007

Objective:

High-intensity and prolonged exercise significantly enhances the levels of plasma ammonia, a metabolite with toxic effects on the central nervous system. The main purpose of the present study was to evaluate the metabolic response of athletes to glutamine (Gln) and alanine (Ala) supplementation, since these amino acids have a significant influence on both anaplerosis and gluconeogenesis.

Methods:

Professional football players were assigned to groups receiving either Gln or Ala supplementation (100 mg kg−1body weight); this supplementation was either short-term or long-term and was given immediately before exercise. The players were evaluated using two exercise protocols, one with intervals (n = 18) and the other with continuous intensity (n = 12).

Results:

Both types of exercises increased ammonia, urate, urea and creatinine in blood. Chronic Gln supplementation partially protected against hyperammonemia after a football match (intermittent exercise: Gln −140 (SEM 13)% vs Ala −240 (SEM 37)%) and after continuous exercise at 80% of the maximum heart rate (Gln −481 (SEM 44)% vs placebo −778 (SEM 99)%). Urate increased by 10−20% in all groups, independently of supplementation. Glutamine once a day supplementation induced a greater elevation in urate as compared to alanine at the end of the game; however, long-term supplementation provoked a lesser increment in urate. Exercise induced similar increases in creatinine as compared to their respective controls in either acute or chronic glutamine administration.

Conclusions:

Taken together, the results suggest that chronically supplemented Gln protects against exercise-induced hyperammonemia depending on exercise intensity and supplementation duration.
Effect of forward shoulder posture on pulmonary capacities of females
Authors: Ghanbari Ali , Ghaffarinejad Farahnaz , Mohammadi Farshid , Khorrami Mojdeh , Sobhani Sobhan
Published: November 2007

Objective:To evaluate if forward shoulder posture (FSP) would alter pulmonary capacities.Design and setting:A blinded, controlled design was used.Subjects:40 female subjects with FSP recruited from university students.Methods and main outcome measurements:Saggital plane postural alignment of the shoulder was measured. A camera was utilized to send photo signals of the reflective markers to a computer equipped with the ability to convert this information into a file of three-dimensional coordinates. The angle formed by a line connecting C7 to the acromion process was measured and it provides FSP degree. Vital capacity (VC), Forced vital capacity (FVC) and expiratory residual volume (ERV) were recorded. Results: There was significant correlation between FSP values and VC (p=.009), FVC (p=.004) and ERV (p=.005). A distinct decrease in VC, FVC and ERV was seen with increasing FSP degrees (p<.05).Conclusion:There was significant correlation between FSP and respiratory values. The respiratory values are decreased subsequent to increasing FSP degrees.
A comparative study of endophytic fungi in needles, bark, and xylem ofPinus tabulaeformis
Authors: Wang Yu , Guo Liang–Dong
Published: November 2007

Endophytic fungi associated with Chinese oil pine ( Pinus tabulaeformis Carr.) from two distinct climatic sites, Fenghuangshan and Lingyuan in northeast China, were investigated. A total of 2065 fungal isolates were recovered from 4320 tissue segments consisting of needles, bark, and xylem from 30 mature trees for each site. Twenty-one fungal taxa were identified; the remaining 205 isolates (11% of total isolates) did not sporulate and could not be identified. There were higher overall colonization and isolation rates of endophytic fungi from the Fenghuangshan than from the Lingyuan site. At the Fenghuangshan site, the colonization and isolation rates significantly increased with the age of the needles and xylem, but not of the bark. At the Lingyuan site, the colonization and isolation rates significantly increased with the age of the xylem; however, there were no significant differences between 2- and 3-year-old needles and bark, except that they both contained fewer endophytes in 1-year-old by comparison with 2- and 3-year-old needles and bark. Alternaria alternata (Fr.) Keissler, Phoma sp.1, Phomopsis archeri B.C. Sutton, and Leptostroma sp. were the dominant taxa in the bark and needles. There was a high Sorenson’s coefficient (0.89) of endophyte composition similarity between the Fenghuangshan and Lingyuan sites. We conclude that some fungi show a degree of tissue recurrence or specificity and that the composition of endophyte assemblages is not greatly influenced by geographical or climatic factors.
Ultrastructure of teliospores and promycelium and basidiospore formation in the four-spored form of Gymnoconia nitens, one of the causes of orange rust of Rubus
Authors: Mims Charles W. , Richardson Elizabeth A. , Taylor Josephine
Published: November 2007

Orange rust of Rubus is an interesting disease because of the fact that it can be caused by three different rust fungi that produce virtually identical symptoms. One is Gymnoconia peckiana (Howe in Peck) Trotter, which is a demicyclic species, while the other two are endocyclic forms historically referred to as Gymnoconia nitens (Schwein.) Kern & H.W. Thurston. Although the spores produced on infected Rubus leaves by these latter two forms are morphologically identical to the aeciospores of G. peckiana, they actually function as teliospores. However, the teliospores of one of the forms gives rise to two-celled promycelia that bear only two basidiospores, while teliospores of the other produce four-celled promycelia bearing four basidiospores. Here, we examined the teliospores of the four-spored form along with the sequence of events that lead to basidiospore development. Developing and mature teliospores were binucleate, and we saw no evidence that karyogamy occurred in these spores. Upon germination, both spore nuclei migrated into the promycelium and underwent mitosis to form a total of four nuclei. Four transverse septa then developed, creating four uninucleate cells. A tapered sterigma arose from each cell and gave rise to a basidiospore. These findings indicate that the basidiospores of the four-spored form of G. nitens were formed in an asexual fashion.
Comparative development of perianth and androecial primordia of the single flower and the homeotic double-flowered mutant inHibiscus rosa-sinensis(Malvaceae)
Authors: Maclntyre Judith P. , Lacroix Christian R.
Published: November 2007

The double-flowered variety of Hibiscus rosa-sinensis L. (Malvaceae) displays a divergent floral morphology that appears to fit the criteria for homeosis. A comprehensive definition defines homeosis as the complete or partial replacement of one part of an organism with another part. The corolla of the single flower is pentamerous. The mature flower has a staminal tube bearing 60 – 70 stamens that surrounds an exserted synstylous gynoecium with five fused stigmas. In double flowers, the outermost whorl of petals is similar in appearance to that of the single flower. The remaining floral appendages have a morphology that is intermediate between petals and stamens, to varying degrees. No two double flowers are exactly the same, even on the same plant. As with other members of the Malvaceae, floral development in both floral types is unusual: once the calyx has been initiated, a ring meristem is formed from which both petal and stamen primordia are initiated. In the single flower, petal primordia are initiated on the flank of the ring, and then stamen primordia arise in five distinct and orderly clusters. In the double flower, petal primordia are also initated on the abaxial flank, but the remainder of the ring initiates primordia that form a mixture of petals, petal – stamen intermediates, and stamens. A common ring meristem that has two different developmental pathways provides a novel opportunity to study homeosis from the perspective of comparative developmental morphology. Keywords: homeosis, Hibiscus rosa-sinensis, androecium, intermediates, ring meristem, floral development.
Single phylogenetic origin of ericoid mycorrhizae within the Ericaceae
Authors: Cullings Kenneth W.
Published: November 2007

Ericoid mycorrhizae are complex organisms consisting of fungal and plant components, and their formation requires enzymatic synergisms and mutualist compatibilities resulting from cooperation of recognition and defense systems of both plant and fungus. Despite this, the plants that form this symbiosis are treated as three separate families in the Ericales: the Ericaceae, the Epacridaceae, and the Empetraceae. In this study, I used the anatomy, physiology, and symbiont compatibility of mycorrhizae (mutualistic interactions between plant roots and fungi) to formulate the hypothesis that the ericoid mycorrhiza-forming plants in the Ericaceae, Epacridaceae, and Empetraceae have a single phylogenetic origin within the Ericaceae coincident with the advent of ericoid mycorrhizae. I tested this hypothesis by parsimony analysis of newly generated and previously published partial 28S ribosomal RNA gene sequences (nuclear) and rbc-L (chloroplast) sequences obtained from GenBank. All results supported the hypothesis that ericoid mycorrhiza-forming plants have a single phylogenetic origin and indicated that the Epacridaceae and Empetraceae should be included within a broadly defined Ericaceae. Keywords: Ericales, 28S ribosomal RNA gene, mycorrhizae, molecular phylogenetics, Empetraceae, Epacridaceae.
Geographic variation of Chondrostereum purpureum detected by polymorphisms in the ribosomal DNA
Authors: Ramsfield Tod D. , Becker Elisa M. , Rathlef Sean M. , Tang Yijian , Hintz William E. , Vrain Thierry C. , Shamoun Simon F.
Published: November 2007

Variation in the ribosomal (rDNA) repeat was analyzed for 107 isolates of the pathogenic fungus Chondrostereum purpureum, collected from Europe, New Zealand, and North America. The rDNA repeat of a representative Canadian isolate of C. purpureum was cloned into the λ vector EMBL-3, and a detailed restriction map was constructed. Variation in the large non-transcribed spacer region of the rDNA was determined for the entire collection of isolates following amplification by the polymerase chain reaction (PCR) and analysis of restriction fragment length polymorphisms (RFLPs). Three distinct nuclear type patterns were identified using the restriction endonuclease HaeIII. Nuclear type I was found in North American, European, and New Zealand isolates. Nuclear type II was only detected in isolates collected from North America, and nuclear type III was observed in isolates collected from both Europe and New Zealand. Nuclear type I was the predominant nuclear type in eastern North America as indicated by a frequency of 0.78, and nuclear type II occurred with a frequency of 0.89 in western North America. Gene flow across the continent was indicated by nearly equal nuclear type distributions (nuclear type I, 0.41; nuclear type II, 0.59) in central North America, but geographic separation has led to unequal nuclear-type distributions across North America. Keywords: Chondrostereum purpureum, biological control, genetic variation, ribosomal DNA.
Regeneration of four boreal bryophytes: colonization of experimental gaps by naturally occurring propagules
Authors: Frego Katherine A.
Published: November 2007

The feather moss community in upland black spruce stands is dominated by Pleurozium schreberi, with small pure colonies and mixtures of ubiquitous and apparently persistent minor species. Previous studies indicated that this spatial pattern is not due to microsite conditions. This study tested the hypothesis that the minor species persist by dynamic occupation of small disturbance-type gaps. Colonization of experimental gaps (10 cm diameter, three substrate types) was tracked over 2 years to determine (i) how Pleurozium and the three minor species colonize gaps and (ii) how characteristics of the gaps affect colonization. All species colonized by encroachment of surrounding vegetative shoots. Availability of propagules, i.e., species composition of the surrounding bed, had the greatest impact, but regeneration of two species was affected by substrate: Ptilium growth was reduced on spruce needles, whereas that of Ptilidium was increased. Pleurozium schreberi displayed the most rapid growth in terms of shoot encroachment regardless of gap characteristics. By virtue of its abundant propagules and rapid growth, Pleurozium is most likely to colonize randomly located disturbance-type gaps, hence maintaining its dominance. Differentiation in regeneration characteristics does not account for the persistence of the minor species in the community. Keywords: Pleurozium schreberi, Ptilium crista-castrensis, Dicranum polysetum, Ptilidium ciliare, gap dynamics, community structure.
Morphological responses of seedlings of four species of Salicaceae to drought
Authors: Splunder I. Van , Voesenek L. A. C. J. , Vries X. J. A. De , Blom C. W. P. M. , Coops H.
Published: November 2007

The riparian distribution patterns of floodplain species are affected by fluctuations in water level. Rapidly declining water levels in river banks during the growing period of plants can result in limited availability of water, particularly on coarse substrates. Differences in drought resistance among Salix alba, Salix triandra, Salix viminalis, and Populus nigra, four species dominating river banks along the River Rhine, could explain part of the riparian distribution patterns. Mortality and growth responses of seedlings grown under well-watered and dry conditions were studied in a greenhouse experiment. Drought-induced mortality was 0% in S. alba and P. nigra, 37.5% in S. triandra, and 62.5% in S. viminalis, which correlated with differences in water-loss characteristics of the species studied: S. triandra and S. viminalis had much higher transpiration rates under well-watered conditions than S. alba and P. nigra. Decreased shoot to root ratios were observed in all species after 3 weeks of drought. The increase after drought of the root length to leaf area ratio was greatest for P. nigra, indicating that this species has a relatively efficient water economy. Specific leaf areas of draughted plants decreased in S. alba and P. nigra, reflecting smaller transpiration areas. Drought also affected root distributions, resulting for all four species in deeper rooting and increased root length in deeper soil layers. Salix viminalis and S. triandra showed the greatest increase in root length in deep soil layers. We concluded that P. nigra is most resistant to drought followed by S. alba and then S. triandra and S. viminalis, and that these differences are reflected in the distribution patterns of these species observed on the banks of the River Rhine. Keywords: drought resistance, Salix, Populus, root distribution, transpiration, leaf conductance.
Olpitrichum tenellum as a biotrophic contact mycoparasite
Authors: Li Duo-Chuan , Shen Chong-Yao
Published: November 2007

Olpitrichum tenellum was shown to be a biotrophic mycoparasite, contacting but not penetrating its host hyphae by means of hook-shaped contact cells, which apparently absorb nutrients and growth factors from living host cells. The known hosts are Fusarium moniliforme, Alternaria alternata, and Cladosporium sp. The hyperparasite failed to grow in the absence of the host on glucose – yeast extract medium unless a water extract of the host was added. Keywords: Olpitrichum tenellum, mycoparasite, axenic culture, hyperparasite.
LHC PREDICTIONS FROM AN EXTENDED THEORY WITH ELASTIC, INELASTIC, AND PATH LENGTH FLUCTUATING ENERGY LOSS
Authors: HOROWITZ WILLIAM A.
Published: November 2007

We present the LHC predictions for the WHDG model of radiative, elastic, and path length fluctuating energy loss. We find the p⊥ dependence of RAA is qualitatively very different from AWS-based energy loss extrapolations to the LHC; the large p⊥ reach of the year one data at the LHC should suffice to distinguish between the two. We also discuss the importance of requiring a first elastic scatter before any medium-induced elastic or radiative loss occurs, a necessary physical effect not considered in any previous models.
TWO-PARTICLE CORRELATION IN HEAVY-ION COLLISIONS AT CSR ENERGY
Authors: ZHANG JINGBO , FENG QICHUN , HUO LEI , ZHANG WEINING
Published: November 2007

The predictions of the two-particle correlation by using the relativistic quantum molecular dynamics model are presented for the heavy-ion reactions at HIRFL-CSR energy. The two-proton correlation function with the final state interaction is calculated with the Lednicky code for the U + U collisions at beam energy 520 A MeV. Applying the imaging technique, the relationship between the freeze-out spatial distributions and the results of correlation femtoscopy is investigated. We find that one can reliably reconstruct the source functions from the two-particle correlation functions with ignoring the degree of space-momentum correlations at this energy. The results are useful to the designing the hadron detector at CSR.
EVIDENCE FOR NON-GAUSSIAN TAIL IN 3-DIMENSIONAL PION EMISSION SOURCE AT SPS
Authors:   for the NA49 Collaboration, CHUNG P. , DANIELEWICZ P.
Published: November 2007

The NA49 experiment at CERN SPS has acquired a huge data set of Pb + Pb events over a broad range of energy and centrality during the last several years. This high statistics data set, coupled with a state-of-the-art analysis technique, allows for the first model-independent extraction and energy scan of 3D emission sources for pion pairs at SPS energies. These 3D pion emission sources provide new insights into the nature of a long-range source previously reported by PHENIX at RHIC. The new results indicate that the pion source displays significant non-Gaussian tails in the longitudinal direction at 40 and 158 AGeV and in the outward direction at 158 AGeV.
UNDERSTANDING THE PARTICLE PRODUCTION MECHANISM WITH CORRELATION STUDIES USING LONG AND SHORT RANGE CORRELATIONS
Authors:   for the STAR Collaboration, SRIVASTAVA B. K. , SCHARENBERG R. P. , TARNOWSKY T. J.
Published: November 2007

Long range forward-backward multiplicity correlations have been measured with the STAR detector for Au + Au collisions at [Formula: see text]. Strong long range correlations are observed in central Au + Au collisions. Based on the Dual Parton model and Color Glass Condensate considerations the data suggests that these long range correlations are due to multiple parton interactions. This suggests that dense partonic matter is created in central Au + Au collisions at [Formula: see text].
π - Ξ CORRELATIONS IN d+Au AND Au+Au COLLISIONS AT STAR
Authors: CHALOUPKA PETR
Published: November 2007

Qualitative comparison of source sizes from π - Ξ correlations analyses in d + Au and Au + Au collisions at [Formula: see text] and [Formula: see text] is presented. For the most central Au + Au collisions at [Formula: see text] we report first quantitative results concerning size of the π - Ξ source and relative shift of the average emission points between π and Ξ showing that the homogeneity region of Ξ source is smaller then that of pion and significantly shifted in the transverse direction.
STUDY OF NON-THERMAL PHASE TRANSITION IN 28Si-NUCLEUS COLLISIONS AT 14.6 A GeV
Authors: AHMAD M. AYAZ , AHMAD SHAFIQ
Published: November 2007

In this paper the study of existance of non-statistical fluctuations using the method of scaled factorial, Fq, moments (SFMs) has been utilized to probe the distribution of relativistic shower particles produced in 28 Si -emulsion collisions at 14.6 A GeV. The analysis indicates that the anomalous fractal dimension, dq, does not favour the origin of any exotic phenomenon. Finally, our data do not show a clear evidence for the existence of non-thermal phase transitions.
LOW SHEAR VISCOSITY DUE TO ANDERSON LOCALIZATION
Authors: GIANNAKIS IOANNIS , HOU DEFU , LI JIA-RONG , REN HAI-CANG
Published: November 2007

We study the Anderson Localization effect on the shear viscosity in a system with random medium by Kubo formula. We show that this effect can reduce the shear viscosity nonperturbatively. Then we discuss its possible implementation in heavy-ion collisions, where the created heavy bound states or other collective modes may play the role of the random scatterer underlying Anderson Localization effect.
LANDAU POTENTIAL STUDY OF THE CHIRAL PHASE TRANSITION IN A QCD-LIKE THEORY
Authors: TSUE Y. , FUJII H. , HASHIMOTO Y.
Published: November 2007

We investigate the chiral phase transition of a QCD-like theory, based the shape change of the effective potential near the critical point. The potential is constructed with the auxiliary field method, and a source term coupled to the field is introduced in order to compute the potential shape numerically. We also generalize the potential so as to have two independent order parameters, the quark scalar density and the number density. We find a tri-critical point locating at (T, μ) = (97, 203) MeV , and visualize it as the merging point of three potential minima.
QUARK SPECTRUM ABOVE THE CRITICAL TEMPERATURE FROM SCHWINGER–DYSON EQUATION
Authors: HARADA MASAYASU , NEMOTO YUKIO , YOSHIMOTO SHUNJI
Published: November 2007

We investigate a spectrum of a fermion, which we call a quark, above the critical temperature of the chiral phase transition in a gauge theory using the Schwinger–Dyson (SD) equation. The SD equation enables us to study the spectrum over a wide range of the gauge coupling. It is shown that the quark spectrum has two sharp peaks which correspond to the normal quasi-quark and the plasmino and is consistent with that obtained in the hard thermal loop approximation in the weak coupling region, while it has also two peaks but with smaller thermal masses and broader widths in the strong coupling region. Temperature-dependence of the quark spectrum is also discussed.
QCD PHASE TRANSITION IN DYSON–SCHWINGER EQUATION APPROACH OF QCD
Authors: CHANG LEI , WANG BIN , YUAN WEI , CHEN HUAN , SHAO GUO-YUN , LIU YU-XIN
Published: November 2007

We review briefly the effects of the running coupling strength, the current quark mass, the density and the finite size of the matter on the QCD phase structure and its transition in the framework of Dyson–Schwinger equation approach of QCD. It provides a visual view to understanding the QCD phase transition with respect to the medium effects and the intrinsic characteristics.
MESON COUPLING CONSTANTS IN PION SUPERFLUID AND THE ISOSPIN SYMMETRY BROKEN INFLUENCE THE PROCESS σ → ππ
Authors: HAO XUEWEN , ZHUANG PENGFEI
Published: November 2007

We investigate the mixing among σ and π mesons in pion superfluid in the frame of two flavor NJL model. With the calculated σ and π couplings to quarks, we consider the decay process σ → ππ at finite isospin chemical potential.
SUSCEPTIBILITIES AND THE PHASE STRUCTURE OF AN EFFECTIVE CHIRAL MODEL WITH POLYAKOV LOOPS
Authors: SASAKI CHIHIRO , FRIMAN BENGT , REDLICH KRZYSZTOF
Published: November 2007

In the Nambu–Jona-Lasinio model with Polyakov loops, we explore the relation between the deconfinement and chiral phase transitions within the mean-field approximation. We focus on the phase structure of the model and study the susceptibilities associated with corresponding order parameters.
HYPERON POLARIZATION IN QUARK-DIQUARK CASCADE MODEL
Authors: TASHIRO TSUTOMU , NODA HUJIO , NAKARIKI SHIN-ICHI , FUKUMA KAZUMI
Published: November 2007

We relate the hyperon polarizations in proton-proton and proton-nucleus collisions to the leading particle effect and use the constituent quark-diquark cascade model with SU(6) wave function. We assume that the quantization axis is characterized by the production normal of the leading baryon of the most massive cascade chain and the incident valence diquark tends to pick up a spin down sea quark or conversely a sea diquark preferentially combines with the spin up incident valence quark to form a leading baryon as compared with the spin down valence quark.
SOME ISSUES ON THE RELATIVISTIC BCS-BEC CROSSOVER
Authors: DENG JIAN
Published: November 2007

We discuss some issues about the relativistic BCS-BEC crossover in a boson-fermion model. These include particle number conservation, chemical equilibrium, the derivation of the thermodynamic potential, the regularization of the gap equation and the BCS ratio.
SPECTRUM OF SOFT MODE WITH THERMAL MASS OF QUARKS ABOVE CRITICAL TEMPERATURE
Authors: HIDAKA YOSHIMASA , KITAZAWA MASAKIYO
Published: November 2007

We study effects of a thermal-quark mass and Landau damping of quarks on the chiral phase transition and its soft modes at finite temperature. For this purpose we employ a simple model with the quark propagator obtained in the hard thermal loop approximation. We show that the chiral phase transition is second order even if quark have a finite thermal mass, and the thermal mass suppresses the chiral condensate. We argue that mesonic spectra have a large width due to scattering between gluons and quarks, and the van Hove singularity at threshold.1.
SATURATION PROPERTIES OF NUCLEAR MATTER IN A RELATIVISTIC MEAN FIELD MODEL CONSTRAINED BY THE QUARK DYNAMICS
Authors: HUGUET R. , CAILLON J. C. , LABARSOUQUE J.
Published: November 2007

We have built an effective Walecka-type hadronic Lagrangian in which the hadron masses and the density dependence of the coupling constants are deduced from the quark dynamics using a Nambu–Jona-Lasinio model. In order to stabilize nuclear matter an eight-quark term has been included. The parameters of this Nambu–Jona-Lasinio model have been determined using the meson properties in the vacuum but also in the medium through the omega meson mass in nuclei measured by the TAPS collaboration. Realistic properties of nuclear matter have been obtained.
SIMULATION STUDIES OF TRIGGER DECISION CRITERION FOR THE ALICE/PHOS
Authors: WANG YAPING , CAI XU
Published: November 2007

This paper gives some results about trigger decision criterion of the ALICE PHOton Spectrometer (PHOS) by Monte Carlo simulations, including four parts: (1) an overview of trigger decision criterion of PHOS; (2) the energy reconstruction performance of PHOS; (3) the selection of trigger threshold and the event trigger efficiency distribution; (4) the photon event trigger rate of PHOS in p – p interactions and Pb – Pb collisions.
THE LASER OF THE ALICE TIME PROJECTION CHAMBER
Authors:   for the Alice Collaboration, RENAULT G. , NIELSEN B. S. , WESTERGAARD J. , GAARDHØJE J. J.
Published: November 2007

The large TPC (95 m3) of the ALICE detector at the CERN LHC was commissioned in summer 2006. The first tracks were observed both from the cosmic ray muons and from the laser rays injected into the TPC. In this article the basic principles of operating the 266 nm lasers are presented, showing the installation and adjustment of the optical system and describing the control system. To generate the laser tracks, a wide laser beam is split into several hundred narrow beams by fixed micro-mirrors at stable and known positions throughout the TPC. In the drift volume, these narrow beams generate straight tracks at many angles. Here we describe the generation of the first tracks and compare them with simulations.
THE ALICE FORWARD MULTIPLICITY DETECTOR
Authors:   for the Alice Collaboration, CHRISTENSEN CHRISTIAN HOLM , GAARDHØJE JENS JØRGEN , GULBRANDSEN KRISTJÁN , NIELSEN BØRGE SVANE , SØGAARD CARSTEN
Published: November 2007

The ALICE Forward Multiplicity Detector (FMD) is a silicon strip detector with 51,200 strips arranged in 5 rings, covering the range −3.4 < η < 5.1. It is placed around the beam pipe at small angles to extend the charged particle acceptance of ALICE into the forward regions, not covered by the central barrel detectors.
THE INNER TRACKING SYSTEM OF ALICE
Authors:   for the Alice collaboration, NOOREN G. J. L.
Published: November 2007

The Inner Tracking System (ITS) of ALICE consists of six silicon layers. The two innermost (SPD) are made of pixeldetectors. The middle layers (SDD) contain silicon driftdetectors, whereas the two outer layers are made of double-sided silicon stripdetectors. Its layout and performance is described.
EXOTIC PHYSICS AT THE LHC WITH CASTOR IN CMS
Authors:   for the CMS Collaboration, NORBECK EDWIN , ONEL YASAR , GŁADYSZ-DZIADUŚ EWA , PANAGIOTOU APOSTOLOS D. , KATSAS PANAGIOTIS
Published: November 2007

Cosmic-rays sometimes produce showers of unusual composition that contain particles with energy-loss profiles different from all known particles. The Large Hadron Collider (LHC) will produce, for the first time, nuclear collisions at the extremely high energy characteristic of the cosmic-ray events. The CASTOR detector, a part of the huge CMS experiment, is designed for detailed studies of the products corresponding to the cores of cosmic-ray showers. It will cover angles of 0.1° to 0.7° from the beam. It will be divided azimuthally into 16 segments and longitudinally into 18 segments. It is assumed that cosmic ray showers are caused by nuclei, protons through iron, hitting the atmosphere. If CASTOR does not find events that can be identified with the anomalous cosmic-ray events, this assumption may need to be reconsidered. Pb - Pb collisions with the LHC will have an energy 28 times that of Au - Au collisions studied at RHIC. With this huge increase in energy a wealth of new phenomena is almost assured. Because of the much larger mass number, Pb - Pb events can be expected to show exotic phenomena that is beyond the reach of cosmic rays.
PARTICLE IDENTIFICATION STUDIES WITH AN ALICE TEST TPC
Authors:   for the Alice TPC Collaboration, CHRISTIANSEN PETER
Published: November 2007

Using a test TPC, consisting of the ALICE TPC field cage prototype in combination with the final ALICE TPC readout and electronics, the energy loss distribution and resolution were measured for identified protons. The measurements were compared to theoretical calculations and good quantitative agreement was found when detector effects were taken into account. The implications for particle identification are discussed.
DETECTOR EFFICIENCY EVALUATION BY FIDUCIAL CUTS FOR AU+AU → J/ψ MID RAPIDITY DATA FROM PHENIX
Authors:   for the PHENIX Collaboration, ATOMSSA ERMIAS T.
Published: November 2007

This poster presents an alternate method for the estimation of detector acceptance and efficiency based on PHENIX Run 4 AuAu central spectrometer data sample and its application to J/ψ invariant yield calculation. After some descriptions of the data set used and comparison of results from this method with the published results from PHENIX, we show a very brief comparison of the latter to theoretical calculation.
A STUDY ON THE INTRINSIC TIME RESOLUTION OF THE MRPC USED IN THE STAR-TOF
Authors:   for the STAR-TOF group, SHAO MING , LI LIANG
Published: November 2007

Time-Of-Flight (TOF) based on Multi-gap Resistive Plate Chamber (MRPC) detectors have been successfully operating at the STAR experiment since 2003.2,3 The MRPC time resolution is however found to be significantly worse2 (80-90 ps) than that previously obtained in beam test (60 ps).4 In order to fully understand MRPC working principles and operating requirements, an extensive calibration study is performed using data collected by STAR in 200 GeV Au + Au collisions in 2004. The relation between MRPC timing, signal amplitude, incident angle and momentum are discussed. Contributions from tracking properties of STAR-TPC are also studied by simulation. The intrinsic time resolution of the MRPCs used in STAR-TOF, after taking all factors into consideration, is found to be in good agreement with beam test results.
BACKGROUND STUDIES FOR SINGLE MUON MEASUREMENTS IN Au+Au COLLISIONS AT $\sqrt{^SNN} = 200 GeV$ IN THE PHENIX EXPERIMENT AT RHIC
Authors:   for the PHENIX Collaboration, KIM BYUNGIL
Published: November 2007

We present background studies for single muon measurements in Au + Au collisions at [Formula: see text]. To estimate the background coming from the high multiplicity, we applied the half octant swapping method. The swapped data was compared with the real data, and we know that the background ratio doesn't depend on the vertex distribution as already expected.
STAR TIME OF FLIGHT READOUT ELECTRONICS, DAQ, AND COSMIC RAY TEST STAND
Authors: SCHAMBACH J. , HOFFMANN G. , KAJIMOTO K. , BRIDGES L. , EPPLEY G. , LIU J. , LLOPE B. , NUSSBAUM T. , MESA C.
Published: November 2007

The new Time-of-Flight (TOF) subsystem for STAR at RHIC will have 3840 6-pad Multigap Resistive Plate Chambers (MRPC) distributed over 120 trays. Each tray contains 192 channels and three types of electronics cards: “TINO”, “TDIG” and “TCPU”. Every 30 trays send data to a “THUB” card that interfaces to STAR trigger and transmits data over fiber to a STAR DAQ fiber receiver. TINO contains analog front end electronics based on the CERN/LAA NINO custom IC. TDIG digitizes the data using the CERN HPTDC ASIC. TCPU formats and buffers the digital information.

A cosmic ray test system comprised of three plastic scintillators, 4 MRPC modules, and TOF prototype electronics is used to determine the timing resolution to be achieved for the entire TOF system. Overall timing resolution of 80 – 110 ps has been achieved.
THE PIXEL FAST-OR SIGNAL FOR THE ALICE TRIGGER IN PROTON-PROTON COLLISIONS
Authors: ELIA D. , AGLIERI RINELLA G. , KLUGE A. , KRIVDA M. , NICASSIO M.
Published: November 2007

The silicon pixel detector of the ALICE experiment at LHC comprises the two innermost layers in the inner tracking system of the apparatus. It contains 1200 readout chips, each of them corresponding to a 8192 pixel matrix. The single chip outputs a digital Fast-OR signal which is active whenever at least one of the pixels in the matrix records a hit.

The 1200 Fast-OR signals can be used to implement a triggering capability: a few details on the pixel trigger system and some of the possible applications for the event selection in p - p collisions are presented.
PIXEL DETECTOR OF SILICON VERTEX TRACKER FOR PHENIX AT RHIC
Authors:   for the PHENIX Collaboration, ONUKI YOSHIYUKI
Published: November 2007

The Silicon Vertex Tracker (VTX) for the Pioneering High Energy Nuclear Interaction eXperiment (PHENIX) at the Brookhaven National Laboratory (BNL) will be installed into the innermost of PHENIX detector in 2009. The VTX will enhance physics capability of PHENIX. The first read-out and cosmic telescope test for pixel with almost actual read-out system had achieved successfully in last year, 2006.
ELLIPTIC FLOW SIMULATION AND ANALYSIS IN ALICE
Authors:   for the ALICE Collaboration, SIMILI EMANUELE
Published: November 2007

Based on flow measurements at the SPS and RHIC, the expected values of elliptic flow and charged multiplicity have been extrapolated as a function of the impact parameter to LHC energy. Those predictions have been used as an input for ALICE simulation, to develop and test a flow analysis package for the ALICE environment. The Event Plane analysis has provided an estimate of the event plane resolution at the LHC and it has also been applied to Hijing events generated with no genuine elliptic flow. In this kind of environment it has been possible to study the effects on v2 from pure non-flow effects, and thus get an estimate of the systematics due to non-flow.
RADIATION DAMAGE STUDY OF SILICON STRIPIXEL SENSOR (FOR PHENIX EXPERIMENT)
Authors:   for the PHENIX Collaboration, SAKASHITA KOHICHI
Published: November 2007

PHENIX Vertex Tracker will be installed in 2009 in order to enhance the physics capability in both heavy ion and spin program. It is designed to separate bottom and charm quark production by measuring distance closest approach even in the heavy ion collision and identifying jet in the polarized proton-proton collisions. The detector consists of two inner pixel layers and two outer stripixel layers. The stripixel sensor is single sided two dimensional silicon strip sensor. It will be suffered by the radiation damage up to 4 fb −1 of integrated luminosity over 10 years of RHIC running period. In our case the damage will increase leakage current from the sensor and degraded front end electronics performance. This article will describe the radiation damage study for the stripixel sensor.