Back-to-back hadron pair yields in d+Au and p+p collisions at √s(NN)=200 GeV were measured with the PHENIX detector at the Relativistic Heavy Ion Collider. Rapidity separated hadron pairs were detected with the trigger hadron at pseudorapidity |η|<0.35 and the associated hadron at forward rapidity (deuteron direction, 3.0<η<3.8). Pairs were also detected with both hadrons measured at forward rapidity; in this case, the yield of back-to-back hadron pairs in d+Au collisions with small impact parameters is observed to be suppressed by a factor of 10 relative to p+p collisions. The kinematics of these pairs is expected to probe partons in the Au nucleus with a low fraction x of the nucleon momenta, where the gluon densities rise sharply. The observed suppression as a function of nuclear thickness, p(T), and η points to cold nuclear matter effects arising at high parton densities.

We present measurements of J/ψ yields in d+Au collisions at sqrt[s(NN)]=200  GeV recorded by the PHENIX experiment and compare them with yields in p+p collisions at the same energy per nucleon-nucleon collision. The measurements cover a large kinematic range in J/ψ rapidity (-2.2<y<2.4) with high statistical precision and are compared with two theoretical models: one with nuclear shadowing combined with final state breakup and one with coherent gluon saturation effects. In order to remove model dependent systematic uncertainties we also compare the data to a simple geometric model. The forward rapidity data are inconsistent with nuclear modifications that are linear or exponential in the density weighted longitudinal thickness, such as those from the final state breakup of the bound state.

Large parity-violating longitudinal single-spin asymmetries A(L)(e+)=-0.86(-0.14)(+0.30) and A(L)(e-)= 0.88(-0.71)(+0.12) are observed for inclusive high transverse momentum electrons and positrons in polarized p+p collisions at a center-of-mass energy of sqrt[s]= 500 GeV with the PHENIX detector at RHIC. These e± come mainly from the decay of W± and Z0 bosons, and their asymmetries directly demonstrate parity violation in the couplings of the W± to the light quarks. The observed electron and positron yields were used to estimate W± boson production cross sections for the e± channels of σ(pp → W+ X) × BR(W+ → e+ ν(e))= 144.1 ± 21.2(stat)(-10.3)(+3.4)(syst) ± 21.6(norm)  pb, and σ(pp → W- X) × BR(W- → e- ν[over ¯](e))= 31.7 ± 12.1(stat)(-8.2)(+10.1)(syst) ± 4.8(norm)  pb.

Members of the marine Roseobacter lineage have been characterized as ecological generalists, suggesting that there will be challenges in assigning well-delineated ecological roles and biogeochemical functions to the taxon. To address this issue, genome sequences of 32 Roseobacter isolates were analyzed for patterns in genome characteristics, gene inventory, and individual gene/pathway distribution using three predictive frameworks: phylogenetic relatedness, lifestyle strategy and environmental origin of the isolate. For the first framework, a phylogeny containing five deeply branching clades was obtained from a concatenation of 70 conserved single-copy genes. Somewhat surprisingly, phylogenetic tree topology was not the best model for organizing genome characteristics or distribution patterns of individual genes/pathways, although it provided some predictive power. The lifestyle framework, established by grouping isolates according to evidence for heterotrophy, photoheterotrophy or autotrophy, explained more of the gene repertoire in this lineage. The environment framework had a weak predictive power for the overall genome content of each strain, but explained the distribution of several individual genes/pathways, including those related to phosphorus acquisition, chemotaxis and aromatic compound degradation. Unassembled sequences in the Global Ocean Sampling metagenomic data independently verified this global-scale geographical signal in some Roseobacter genes. The primary findings emerging from this comparative genome analysis are that members of the lineage cannot be easily collapsed into just a few ecologically differentiated clusters (that is, there are almost as many clusters as isolates); the strongest framework for predicting genome content is trophic strategy, but no single framework gives robust predictions; and previously unknown homologs to genes for H(2) oxidation, proteorhodopsin-based phototrophy, xanthorhodpsin-based phototrophy, and CO(2) fixation by Form IC ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) expand the possible mechanisms for energy and carbon acquisition in this remarkably versatile bacterial lineage.

PURPOSE: To estimate prevalence and severity of patients' self-perceived supportive care needs in the immediate post-treatment phase and identify predictors of unmet need. PATIENTS AND METHODS: A multicenter, prospective, longitudinal survey was conducted. Sixty-six centers recruited patients for 12 weeks. Patients receiving treatment for the following cancers were recruited: breast, prostate, colorectal, and gynecologic cancer and non-Hodgkin's lymphoma. Measures of supportive care needs, anxiety and depression, fear of recurrence, and positive and negative affect were completed at the end of treatment (T0) and 6 months later (T1). RESULTS: Of 1,850 patients given questionnaire packs, 1,425 (79%) returned questionnaires at T0, and 1,152 (62%) returned questionnaires at T1. Mean age was 61 years; and most respondents were female (69%) and had breast cancer (57%). Most patients had no or few moderate or severe unmet supportive care needs. However, 30% reported more than five unmet needs at baseline, and for 60% of these patients, the situation did not improve. At both assessments, the most frequently endorsed unmet needs were psychological needs and fear of recurrence. Logistic regression revealed several statistically significant predictors of unmet need, including receipt of hormone treatment, negative affect, and experiencing an unrelated significant event between assessments. CONCLUSION: Most patients do not express unmet needs for supportive care after treatment. Thirty percent reported more than five moderate or severe unmet needs at both assessments. Unmet needs were predicted by hormone treatment, negative mood, and experiencing a significant event. Our results suggest that there is a proportion of survivors with unmet needs who might benefit from the targeted application of psychosocial resources.

The objective of this work is to construct capacitive micromachined ultrasound transducers (cMUTs) using multi-user microelectromechanical systems (MEMS) processess (MUMPs) and to analyze the capability of this process relative to the customized processes commonly in use. The MUMPs process has the advantages of low cost and accessibility to general users since it is not necessary to have access to customized fabrication capability such as wafer-bonding and sacrificial release processes. While other researchers have reported fabricating cMUTs using the MUMPs process none has reported the limitations in the process that arise due to the use of standard design rules that place limitations on the material thicknesses, gap thicknesses, and materials that may be used. In this paper we explain these limitations, and analyze the capabilities using 1D modeling, Finite Element Analysis, and experimental devices. We show that one of the limitations is that collapse voltage and center frequency can not be controlled independently. However, center frequencies up to 9MHz can be achieved with collapse voltages of less than 200V making such devices suitable for medical and non-destructive evaluation imaging applications. Since the membrane and base electrodes are made of polysilicon, there is a larger series resistance than that resulting from processes that use metal electrodes. We show that the series resistance is not a significant problem. The conductive polysilicon can also destroy the cMUT if the top membrane is pulled in the bottom. As a solution we propose the application of an additional dielectric layer. Finally we demonstrate a device built with a novel beam construction that produces transmitted pressure pulse into air with 6% bandwidth and agrees reasonably well with the 1D model. We conclude that cMUTs made with MUMPs process have some limitations that are not present in customized processes. However, these limitations may be overcome with the proper design considerations that we have presented putting a low cost, highly accessible means of making cMUT devices into the hands of academic and industrial researchers.

OBJECTIVE: Vitamin A derivatives, including all-trans-retinoic acid (ATRA), have a well-established role during skeletal development and limb formation and have been shown to have profound effects on chondrocyte phenotype. The aim of this study was to elucidate the effects of retinoids and components of the retinoid metabolic pathway on chondrocyte phenotype in the tibiofemoral joints of patients with osteoarthritis (OA), to show that the retinoids can have multiple effects relevant to the OA disease process. METHODS: Human explant tissue and a chondrocyte-like cell line were treated with ATRA, and the responses of 4 key markers of chondrocyte phenotype were analyzed. In addition, the effects of ATRA on a number of novel genes associated with OA were assessed using a low-density microarray containing 80 disease marker genes. RESULTS: Vitamin A metabolite levels were elevated in synovial fluid, serum, and cartilage from patients with OA. Expression profiling of a retinoic acid receptor alpha coactivator protein, P/CAF, demonstrated elevated expression in patients with OA, suggesting the potential for increased signaling via the retinoid receptors in the disease. ATRA increased the levels of matrix metalloproteinase 13 and aggrecanase activity in human cartilage explants and in a human chondrocyte cell line. Furthermore, ATRA altered the expression of a wide range of relevant genes, including the types I, II, IX, and XI collagen genes, toward a nonchondrogenic and OA-like phenotype. CONCLUSION: These results suggest that retinoid signaling could have a central role in OA, and that components of the pathway may provide potential disease biomarkers or targets for therapeutic intervention.

Anisotropic substrata such as micromachined grooves can control cell shape, orientation, and the direction of cell movement, a phenomena termed topographic guidance. Although many types of cells exhibit topographic guidance, little is known regarding cell responses to conflicting topographic cues. We employed a substratum with intersecting grooves in order to present fibroblasts and epithelial cells with conflicting topographic cues. Using time-lapse and confocal microscopy, we examined cell behavior at groove intersections. Migrating fibroblasts and epithelial cells typically extended a cell process into the intersection ahead of the cell body. After travelling along the "X" groove to enter the intersection, the leading lamellipodia of the cell body encountered the perpendicular "Y" groove, and spread latterly along the "Y" groove. The formation of lateral lamellipodia resulted in cells forming "T" or "L" morphologies, which were characterized by the formation of phosphotyrosine-rich focal adhesions at the leading edges. The "Y" groove did not prove an absolute barrier to cell migration, particularly for epithelial cells. Analysis of cytoskeletal distribution revealed that F-actin bundles did not adapt closely to the groove patterns, but typically did align to either the "X" or "Y" grooves. In contrast microtubules (MT) adapted closely to the walls. Inhibition of microtubule nucleation attenuated fibroblast and epithelial cell orientation within the intersection of the perpendicular grooves. We conclude that MT may be the prime determinant of fibroblast and epithelial cell conformation to conflicting topographies. Cell Motil. Cytoskeleton 2009.(c) 2009 Wiley-Liss, Inc.

The sequencing of Aspergillus genomes has revealed that the products of a large number of secondary metabolism pathways have not yet been identified. This is probably because many secondary metabolite gene clusters are not expressed under normal laboratory culture conditions. It is, therefore, important to discover conditions or regulatory factors that can induce the expression of these genes. We report that deletion of sumO, the gene that encodes the small ubiquitin-like protein SUMO in A. nidulans, causes a dramatic increase in the production of the secondary metabolite asperthecin and a decrease in the synthesis of austinol/dehydroaustinol and sterigmatocystin. The overproduction of asperthecin in the sumO deletant has allowed us, through a series of targeted deletions, to identify the genes required for asperthecin synthesis. The asperthecin biosynthesis genes are clustered and include an iterative type I polyketide synthase, a hydrolase and a monooxygenase. Identification of these genes allows us to propose a biosynthetic pathway for asperthecin.