Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV

The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.

D-S(+) meson production at central rapidity in proton-proton collisions at root s=7 TeV

The P-T-differential inclusive production cross section of the prompt charm-strange meson D-s(+) in the rapidity range vertical bar y vertical bar < 0.5 was measured in proton-proton collisions at root s = 7 TeV at the LHC using the ALICE detector. The analysis was performed on a data sample of 2.98 x 10(8) events collected with a minimum-bias trigger. The corresponding integrated luminosity is L-int = 4.8 nb(-1). Reconstructing the decay D-s(+) -> phi pi(+) with phi -> K-K+, and its charge conjugate, about 480 D-s(+/-) mesons were counted, after selection cuts, in the transverse momentum range 2 < P-T < 12 GeV/c. The results are compared with predictions from models based on perturbative QCD. The ratios of the cross sections of four D meson species (namely D-0, D+, D*+ and D-s(+)) were determined both as a function of p(T) and integrated over p(T)after extrapolating to full p(T) range, together with the strangeness suppression factor in charm fragmentation. The obtained values are found to be compatible within uncertainties with those measured by other experiments in e(+)e(-), ep and pp interactions at various centre-of-mass energies. (C) 2012 CERN. Published by Elsevier By. All rights reserved.

Multi-strange baryon production in pp collisions at root s=7 TeV with ALICE

A measurement of the multi-strange Xi(-) and Omega(-) baryons and their antiparticles by the ALICE experiment at the CERN Large Hadron Collider (LHC) is presented for inelastic proton-proton collisions at a centre-of-mass energy of 7 TeV. The transverse momentum (p(T)) distributions were studied at mid-rapidity (vertical bar y vertical bar < 0.5) in the range of 0.6 < p(T) < 8.5 GeV/c Xi(-) for and Xi(+) baryons, and in the range of 0.8 < P-T < 5 GeV/c for Omega(-) and<(Omega)over bar>(+). Baryons and antibaryons were measured as separate particles and we find that the baryon to antibaryon ratio of both particle species is consistent with unity over the entire range of the measurement. The statistical precision of the current data has allowed us to measure a difference between the mean p(T) of Xi(-) ((Xi) over bar)(+) and Omega(-) ((Omega) over bar (+)). Particle yields, mean pi, and the spectra in the intermediate pi range are not well described by the PYTHIA Perugia 2011 tune Monte Carlo event generator, which has been tuned to reproduce the early LHC data. The discrepancy is largest for Omega(-)((Omega) over bar (+)). This PYTHIA tune approaches the pi spectra of Xi(-) and Xi(+) baryons below p(T) <0.85 GeV/c and describes the Xi(-) and Xi(+) spectra above p(T) > 6.0 GeV/c. We also illustrate the difference between the experimental data and model by comparing the corresponding ratios of (Omega(-) +(Omega) over bar (+))/(Xi(-) + Xi(+)) as a function of transverse mass. (C) 2012 CERN. Published by Elsevier B.V. All rights reserved.

Cold-Nuclear-Matter Effects on Heavy-Quark Production in d+Au Collisions at root S-NN=200 GeV

The PHENIX experiment has measured electrons and positrons at midrapidity from the decays of hadrons containing charm and bottom quarks produced in d + Au and p + p collisions at root S-NN = 200 GeV in the transverse-momentum range 0.85 <= p(T)(e) <= 8.5 GeV/c. In central d + Au collisions, the nuclear modification factor R-dA at 1.5 < p(T) < 5 GeV/c displays evidence of enhancement of these electrons, relative to those produced in p + p collisions, and shows that the mass-dependent Cronin enhancement observed at the Relativistic Heavy Ion Collider extends to the heavy D meson family. A comparison with the neutral-pion data suggests that the difference in cold-nuclear-matter effects on light- and heavy-flavor mesons could contribute to the observed differences between the pi(0) and heavy-flavor-electron nuclear modification factors R-AA. DOI: 10.1103/PhysRevLett.109.242301

J/psi production as a function of charged particle multiplicity in pp collisions at root s=7 TeV

The ALICE Collaboration reports the measurement of the relative J/psi yield as a function of charged particle pseudorapidity density dN(ch)/d eta in pp collisions at root s = 7 TeV at the LHC. J/psi particles are detected for p(t) > 0, in the rapidity interval vertical bar y vertical bar < 0.9 via decay into e(+)e(-), and in the interval 2.5 < y < 4.0 via decay into mu(+)/mu(-) pairs. An approximately linear increase of the J/psi yields normalized to their event average (dN(J/psi)/dy)/(dN(J/psi)/dy) with (dN(ch)/c eta)/(dN(ch)/d eta) is observed in both rapidity ranges, where dN(ch)/d eta is measured within vertical bar eta vertical bar < 1 and p(t) > 0. In the highest multiplicity interval with (dN(ch)/d eta)(bin)) = 24.1, corresponding to four times the minimum bias multiplicity density, an enhancement relative to the minimum bias J/psi yield by a factor of about 5 at 2.5 < y <4 (8 at vertical bar y vertical bar < 0.9) is observed. (C) 2012 CERN. Published by Elsevier B.V. All rights reserved.

Light vector meson production in pp collisions at root s=7 TeV ALICE Collaboration

The ALICE experiment has measured low-mass dimuon production in pp collisions at root s = 7 TeV in the dimuon rapidity region 2.5 < y < 4. The observed dimuon mass spectrum is described as a superposition of resonance decays (eta, rho, omega, eta', phi) into muons and semi-leptonic decays of charmed mesons. The measured production cross sections for omega and phi are sigma(omega)(1 < p(t) < 5 GeV/c. 2.5 < y < 4) = 5.28 +/- 0.54(stat) +/- 0.49(syst) mb and sigma(phi)(1 < p(t) < 5 GeV/c. 2.5 < y < 4) = 0.940 +/- 0.084(stat) +/- 0.076(syst) mb. The differential cross sections d(2)sigma/dy dp(t) are extracted as a function of p(t) for omega and phi. The ratio between the rho and omega cross section is obtained. Results for the phi are compared with other measurements at the same energy and with predictions by models. (C) 2012 CERN. Published by Elsevier B.V. All rights reserved.

Production of Z bosons in proton-proton collisions at root out s = 10 TeV: Expectations for early measurements at the ATLAS experiment

The production of the Z boson in proton-proton collisions at the LHC serves as a standard candle at the ATLAS experiment during early data-taking. The decay of the Z into an electron-positron pair gives a clean signature in the detector that allows for calibration and performance studies. The cross-section of ~ 1 nb allows first LHC measurements of parton density functions. In this thesis, simulations of 10 TeV collisions at the ATLAS detector are studied. The challenges for an experimental measurement of the cross-section with an integrated luminositiy of 100 pb−1 are discussed. In preparation for the cross-section determination, the single-electron efficiencies are determined via a simulation based method and in a test of a data-driven ansatz. The two methods show a very good agreement and differ by ~ 3% at most. The ingredients of an inclusive and a differential Z production cross-section measurement at ATLAS are discussed and their possible contributions to systematic uncertainties are presented. For a combined sample of signal and background the expected uncertainty on the inclusive cross-section for an integrated luminosity of 100 pb−1 is determined to 1.5% (stat) +/- 4.2% (syst) +/- 10% (lumi). The possibilities for single-differential cross-section measurements in rapidity and transverse momentum of the Z boson, which are important quantities because of the impact on parton density functions and the capability to check for non-pertubative effects in pQCD, are outlined. The issues of an efficiency correction based on electron efficiencies as function of the electron’s transverse momentum and pseudorapidity are studied. A possible alternative is demonstrated by expanding the two-dimensional efficiencies with the additional dimension of the invariant mass of the two leptons of the Z decay.

Measurement of the pair production of b-jets in proton-proton collisions at root out s = 7 TeV with the ATLAS detector

In hadronischen Kollisionen entstehen bei einem Großteil der Ereignisse mit einem hohen Impulsübertrag Paare aus hochenergetischen Jets. Deren Produktion und Eigenschaften können mit hoher Genauigkeit durch die Störungstheorie in der Quantenchromodynamik (QCD) vorhergesagt werden. Die Produktion von \textit{bottom}-Quarks in solchen Kollisionen kann als Maßstab genutzt werden, um die Vorhersagen der QCD zu testen, da diese Quarks die Dynamik des Produktionsprozesses bei Skalen wieder spiegelt, in der eine Störungsrechnung ohne Einschränkungen möglich ist. Auf Grund der hohen Masse von Teilchen, die ein \textit{bottom}-Quark enthalten, erhält der gemessene, hadronische Zustand den größten Teil der Information von dem Produktionsprozess der Quarks. Weil sie eine große Produktionsrate besitzen, spielen sie und ihre Zerfallsprodukte eine wichtige Rolle als Untergrund in vielen Analysen, insbesondere in Suchen nach neuer Physik. In ihrer herausragenden Stellung in der dritten Quark-Generation könnten sich vermehrt Zeichen im Vergleich zu den leichteren Quarks für neue Phänomene zeigen. Daher ist die Untersuchung des Verhältnisses zwischen der Produktion von Jets, die solche \textit{bottom}-Quarks enthalten, auch bekannt als $b$-Jets, und aller nachgewiesener Jets ein wichtiger Indikator für neue massive Objekte. In dieser Arbeit werden die Produktionsrate und die Korrelationen von Paaren aus $b$-Jets bestimmt und nach ersten Hinweisen eines neuen massiven Teilchens, das bisher nicht im Standard-Modell enthalten ist, in dem invarianten Massenspektrum der $b$-Jets gesucht. Am Large Hadron Collider (LHC) kollidieren zwei Protonenstrahlen bei einer Schwerpunktsenergie von $\sqrt s = 7$ TeV, und es werden viele solcher Paare aus $b$-Jets produziert. Diese Analyse benutzt die aufgezeichneten Kollisionen des ATLAS-Detektors. Die integrierte Luminosität der verwendbaren Daten beläuft sich auf 34~pb$^{-1}$. $b$-Jets werden mit Hilfe ihrer langen Lebensdauer und den rekonstruierten, geladenen Zerfallsprodukten identifiziert. Für diese Analyse müssen insbesondere die Unterschiede im Verhalten von Jets, die aus leichten Objekten wie Gluonen und leichten Quarks hervorgehen, zu diesen $b$-Jets beachtet werden. Die Energieskala dieser $b$-Jets wird untersucht und die zusätzlichen Unsicherheit in der Energiemessung der Jets bestimmt. Effekte bei der Jet-Rekonstruktion im Detektor, die einzigartig für $b$-Jets sind, werden studiert, um letztlich diese Messung unabhängig vom Detektor und auf Niveau der Hadronen auswerten zu können. Hiernach wird die Messung zu Vorhersagen auf nächst-zu-führender Ordnung verglichen. Dabei stellt sich heraus, dass die Vorhersagen in Übereinstimmung zu den aufgenommenen Daten sind. Daraus lässt sich schließen, dass der zugrunde liegende Produktionsmechanismus auch in diesem neu erschlossenen Energiebereich am LHC gültig ist. Jedoch werden auch erste Hinweise auf Mängel in der Beschreibung der Eigenschaften dieser Ereignisse gefunden. Weiterhin können keine Anhaltspunkte für eine neue Resonanz, die in Paare aus $b$-Jets zerfällt, in dem invarianten Massenspektrum bis etwa 1.7~TeV gefunden werden. Für das Auftreten einer solchen Resonanz mit einer Gauß-förmigen Massenverteilung werden modell-unabhängige Grenzen berechnet.

Search for Quantum Black Hole Production in High-Invariant-Mass Lepton plus Jet Final States Using pp Collisions at root s=8 TeV and the ATLAS Detector

This Letter presents a search for quantum black-hole production using 20.3 fb(-1) of data collected with the ATLAS detector in pp collisions at the LHC at root s = 8 TeV. The quantum black holes are assumed to decay into a final state characterized by a lepton (electron or muon) and a jet. In either channel, no event with a lepton-jet invariant mass of 3.5 TeV or more is observed, consistent with the expected background. Limits are set on the product of cross sections and branching fractions for the lepton + jet final states of quantum black holes produced in a search region for invariant masses above 1 TeV. The combined 95% confidence level upper limit on this product for quantum black holes with threshold mass above 3.5 TeV is 0.18 fb. This limit constrains the threshold quantum black-hole mass to be above 5.3 TeV in the model considered.

Cyanogenesis in Cassava1 : The Role of Hydroxynitrile Lyase in Root Cyanide Production

In the cyanogenic crop cassava (Manihot esculenta, Crantz), the final step in cyanide production is the conversion of acetone cyanohydrin, the deglycosylation product of linamarin, to cyanide plus acetone. This process occurs spontaneously at pH greater than 5.0 or enzymatically and is catalyzed by hydroxynitrile lyase (HNL). Recently, it has been demonstrated that acetone cyanohydrin is present in poorly processed cassava root food products. Since it has generally been assumed that HNL is present in all cassava tissues, we reinvestigated the enzymatic properties and tissue-specific distribution of HNL in cassava. We report the development of a rapid two-step purification protocol for cassava HNL, which yields an enzyme that is catalytically more efficient than previously reported (Hughes, J., Carvalho, F., and Hughes, M. [1994] Arch Biochem Biophys 311: 496–502). Analyses of the distribution of HNL activity and protein indicate that the accumulation of acetone cyanohydrin in roots is due to the absence of HNL, not to inhibition of the enzyme. Furthermore, the absence of HNL in roots and stems is associated with very low steady-state HNL transcript levels. It is proposed that the lack of HNL in cassava roots accounts for the high acetone cyanohydrin levels in poorly processed cassava food products.

Investigation of highly regulated promoters for the production of recombinant proteins in plants

Plants have been identified as promising expression systems for the commercial production of recombinant proteins. Plant-based protein production or “biofarming” offers a number of advantages over traditional expression systems in terms of scale of production, the capacity for post-translation processing, providing a product free of contaminants and cost effectiveness. A number of pharmaceutically important and commercially valuable proteins, such as antibodies, biopharmaceuticals and industrial enzymes are currently being produced in plant expression systems. However, several challenges still remain to improve recombinant protein yield with no ill effect on the host plant. The ability for transgenic plants to produce foreign proteins at commercially viable levels can be directly related to the level and cell specificity of the selected promoter driving the transgene. The accumulation of recombinant proteins may be controlled by a tissue-specific, developmentally-regulated or chemically-inducible promoter such that expression of recombinant proteins can be spatially- or temporally- controlled. The strict control of gene expression is particularly useful for proteins that are considered toxic and whose expression is likely to have a detrimental effect on plant growth. To date, the most commonly used promoter in plant biotechnology is the cauliflower mosaic virus (CaMV) 35S promoter which is used to drive strong, constitutive transgene expression in most organs of transgenic plants. Of particular interest to researchers in the Centre for Tropical Crops and Biocommodities at QUT are tissue-specific promoters for the accumulation of foreign proteins in the roots, seeds and fruit of various plant species, including tobacco, banana and sugarcane. Therefore this Masters project aimed to isolate and characterise root- and seed-specific promoters for the control of genes encoding recombinant proteins in plant-based expression systems. Additionally, the effects of matching cognate terminators with their respective gene promoters were assessed. The Arabidopsis root promoters ARSK1 and EIR1 were selected from the literature based on their reported limited root expression profiles. Both promoters were analysed using the PlantCARE database to identify putative motifs or cis-acting elements that may be associated with this activity. A number of motifs were identified in the ARSK1 promoter region including, WUN (wound-inducible), MBS (MYB binding site), Skn-1, and a RY core element (seed-specific) and in the EIR1 promoter region including, Skn-1 (seed-specific), Box-W1 (fungal elicitor), Aux-RR core (auxin response) and ABRE (ABA response). However, no previously reported root-specific cis-acting elements were observed in either promoter region. To confirm root specificity, both promoters, and truncated versions, were fused to the GUS reporter gene and the expression cassette introduced into Arabidopsis via Agrobacterium-mediated transformation. Despite the reported tissue-specific nature of these promoters, both upstream regulatory regions directed constitutive GUS expression in all transgenic plants. Further, similar levels of GUS expression from the ARSK1 promoter were directed by the control CaMV 35S promoter. The truncated version of the EIR1 promoter (1.2 Kb) showed some differences in the level of GUS expression compared to the 2.2 Kb promoter. Therefore, this suggests an enhancer element is contained in the 2.2 Kb upstream region that increases transgene expression. The Arabidopsis seed-specific genes ATS1 and ATS3 were selected from the literature based on their seed-specific expression profiles and gene expression confirmed in this study as seed-specific by RT-PCR analysis. The selected promoter regions were analysed using the PlantCARE database in order to identify any putative cis elements. The seed-specific motifs GCN4 and Skn-1 were identified in both promoter regions that are associated with elevated expression levels in the endosperm. Additionaly, the seed-specific RY element and the ABRE were located in the ATS1 promoter. Both promoters were fused to the GUS reporter gene and used to transform Arabidopsis plants. GUS expression from the putative promoters was consitutive in all transgenic Arabidopsis tissue tested. Importantly, the positive control FAE1 seed-specific promoter also directed constitutive GUS expression throughout transgenic Arabidopsis plants. The constitutive nature seen in all of the promoters used in this study was not anticipated. While variations in promoter activity can be caused by a number of influencing factors, the variation in promoter activity observed here would imply a major contributing factor common to all plant expression cassettes tested. All promoter constructs generated in this study were based on the binary vector pCAMBIA2300. This vector contains the plant selection gene (NPTII) under the transcriptional control of the duplicated CaMV 35S promoter. This CaMV 35S promoter contains two enhancer domains that confer strong, constitutive expression of the selection gene and is located immediately upstream of the promoter-GUS fusion. During the course of this project, Yoo et al. (2005) reported that transgene expression is significantly affected when the expression cassette is located on the same T-DNA as the 35S enhancer. It was concluded, the trans-acting effects of the enhancer activate and control transgene expression causing irregular expression patterns. This phenomenon seems the most plausible reason for the constitutive expression profiles observed with the root- and seed-specific promoters assessed in this study. The expression from some promoters can be influenced by their cognate terminator sequences. Therefore, the Arabidopsis ARSK1, EIR1, ATS1 and ATS3 terminator sequences were isolated and incorporated into expression cassettes containing the GUS reporter gene under the control of their cognate promoters. Again, unrestricted GUS activity was displayed throughout transgenic plants transformed with these reporter gene fusions. As previously discussed constitutive GUS expression was most likely due to the trans-acting effect of the upstream CaMV 35S promoter in the selection cassette located on the same T-DNA. The results obtained in this study make it impossible to assess the influence matching terminators with their cognate promoters have on transgene expression profiles. The obvious future direction of research continuing from this study would be to transform pBIN-based promoter-GUS fusions (ie. constructs containing no CaMV 35S promoter driving the plant selection gene) into Arabidopsis in order to determine the true tissue specificity of these promoters and evaluate the effects of their cognate 3’ terminator sequences. Further, promoter truncations based around the cis-elements identified here may assist in determining whether these motifs are in fact involved in the overall activity of the promoter.

Cultivar-specific effects of pathogen testing on storage root yield of sweet potato, Ipomoea batatas (L.) Lam.

The accumulation and perpetuation of viral pathogens over generations of clonal propagation in crop species such as sweet potato, Ipomoea batatas,inevitably result in a reduction in crop yield and quality. This study was conducted at Bundaberg, Australia to compare the productivity of field-derived and pathogen-tested (PT)clones of 14 sweet potato cultivars and the yield benefits of using healthy planting materials. The field-derived clonal materials were exposed to the endemic viruses, while the PT clones were subjected to thermotherapy and meristem-tip culture to eliminate viral pathogens. The plants were indexed for viruses using nitrocellulose membrane-enzyme-linked immunosorbent assay and graft-inoculations onto Ipomoea setosa. A net benefit of 38% in storage root yield was realised from using PT materials in this study.Conversely, in a similar study previously conducted at Kerevat, Papua New Guinea (PNG), a net deficit of 36% was realised. This reinforced our finding that the response to pathogen testing was cultivar dependent and that the PNG cultivars in these studies generally exhibited increased tolerance to the endemic viruses present at the respective trial sites as manifested in their lack of response from the use of PT clones. They may be useful sources for future resistance breeding efforts. Nonetheless, the potential economic gain from using PT stocks necessitates the use of pathogen testing on virus-susceptible commercial cultivars.

Revascularization and tissue regeneration of an empty root canal space is enhanced by a direct blood supply and stem cells

Background Regenerative endodontics is an innovative treatment concept aiming to regenerate pulp, dentin and root structures. In the diseased or necrotic tooth, the limitation in vascular supply renders successful tissue regeneration/generation in a whole tooth challenging. The aim of this study is to evaluate the ability of vascularized tissue to develop within a pulpless tooth using tissue engineering techniques. Materials and methods A pulpless tooth chamber, filled with collagen I gel containing isolated rat dental pulp cells (DPC) and angiogenic growth factors, was placed into a hole created in the femoral cortex or into its own tooth socket, respectively. The gross, histological and biochemical characteristics of the de novo tissue were evaluated at 4 and 8weeks post-transplantation. Results Tooth revascularization and tissue generation was observed only in the femur group, confirming the important role of vascular supply in tissue regeneration. The addition of cells and growth factors significantly promoted connective tissue production in the tooth chamber. Conclusion Successful revascularization and tissue regeneration in this model demonstrate the importance of a direct vascular supply and the advantages of a stem cell approach. © 2012 John Wiley & Sons A/S.

Interference from object part relations in spoken word production: Behavioural and fMRI evidence

Objects presented in categorically related contexts are typically named slower than objects presented in unrelated contexts, a phenomenon termed semantic interference. However, not all semantic relationships induce interference. In the present study, we investigated the influence of object part-relations in the blocked cyclic naming paradigm. In Experiment 1 we established that an object's parts do induce a semantic interference effect when named in context compared to unrelated parts (e.g., leaf, root, nut, bark; for tree). In Experiment 2) we replicated the effect during perfusion functional magnetic resonance imaging (fMRI) to identify the cerebral regions involved. The interference effect was associated with significant perfusion signal increases in the hippocampal formation and decreases in the dorsolateral prefrontal cortex. We failed to observe significant perfusion signal changes in the left lateral temporal lobe, a region that shows reliable activity for interference effects induced by categorical relations in the same paradigm and is proposed to mediate lexical-semantic processing. We interpret these results as supporting recent explanations of semantic interference in blocked cyclic naming that implicate working memory mechanisms. However, given the failure to observe significant perfusion signal changes in the left temporal lobe, the results provide only partial support for accounts that assume semantic interference in this paradigm arises solely due to lexical-level processes.

Resistance of selected strawberry cultivars to root-knot nematode species (Meloidogyne spp.)

Strawberry runner production areas in Queensland are assessed for the presence of Pratylenchus vulnus (lesion nematode) and Meloidogyne hapla (root-knot nematode) as part of the approval process for sites used in runner production under the approved runner scheme. M. hapla is known to infest strawberry. The ability of three other Meloidogyne species occurring in Queensland to infest this host was investigated. The species M. arenaria, M. incognita and M. javanica, in addition to M. hapla, were able to reproduce on strawberry roots of the cultivar 'Joy', which sustained higher nematode reproduction rates than 'Jewel' and 'Sweet Charlie'. The ability of species other than M. hapla to infest strawberry needs to be recognised in site selection for runner production, and in screening cultivars for resistance to nematodes.