A more reliable PCR for detection of Mycobacterium tuberculosis in clinical samples

Diagnostic techniques based on PCR have two major problems: false-positive reactions due to contamination with DNA fragments from previous PCRs (amplicons) and false-negative reactions caused by inhibitors that interfere with the PCR. We have improved our previously reported PCR based on the amplification of a fragment of the Mycobacterium tuberculosis complex-specific insertion element IS6110 with respect to both problems. False-positive reactions caused by amplicon contamination were prevented by the use of uracil-N-glycosylase and dUTP instead of dTTP. We selected a new set of primers outside the region spanned by the formerly used primers to avoid false-positive reactions caused by dTTP-containing amplicons still present in the laboratory. With this new primer set, 16 copies of the IS6110 insertion element, the equivalent of two bacteria, could be amplified 10(10) times in 40 cycles, resulting in a mean efficiency of 77% per cycle. To detect the presence of inhibitors of the Taq polymerase, which may cause false-negative reactions, part of each sample was spiked with M. tuberculosis DNA. The DNA purification method using guanidinium thiocyanate and diatoms effectively removed most or all inhibitors of the PCR. However, this was not suitable for blood samples, for which we developed a proteinase K treatment followed by phenol-chloroform extraction. This method permitted detection of 20 M. tuberculosis bacteria per ml of whole blood. Various laboratory procedures were introduced to reduce failure or inhibition of PCR and avoid DNA cross contamination. We have tested 218 different clinical specimens obtained from patients suspected of having tuberculosis. The samples included sputum (n=145), tissue biopsy samples (n=25), cerebrospinal fluid (n=15), blood (n=14), pleural fluid (n=9), feces, (n=7), fluid from fistulae (n=2), and pus from a wound (n=1). The results obtained by PCR were consistent with those obtained with culture, which is the "gold standard." We demonstrate that PCR is a useful technique for the rapid diagnosis of tuberculosis at various sites

Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics.

Animal science

Preoperative radiochemotherapy versus immediate surgery for resectable and borderline resectable pancreatic cancer (PREOPANC trial): Study protocol for a multicentre randomized controlled trial

Background: Pancreatic cancer is the fourth largest cause of cancer death in the United States and Europe with over 100,000 deaths per year in Europe alone. The overall 5-year survival ranges from 2-7 % and has hardly improve

Partonic flow and ϕ\phi-meson production in Au+Au collisions at sNN\sqrt{s_{NN}} = 200 GeV

We present first measurements of the $\phi$-meson elliptic flow ($v_{2}(p_{T})$) and high statistics $p_{T}$ distributions for different centralities from $\sqrt{s_{NN}}$ = 200 GeV Au+Au collisions at RHIC. In minimum bias collisions the $v_{2}$ of the $\phi$ meson is consistent with the trend observed for mesons. The ratio of the yields of the $\Omega$ to those of the $\phi$ as a function of transverse momentum is consistent with a model based on the recombination of thermal $s$ quarks up to $p_{T}\sim 4$ GeV/$c$, but disagrees at higher momenta. The nuclear modification factor ($R_{CP}$) of $\phi$ follows the trend observed in the $K^{0}_{S}$ mesons rather than in $\Lambda$ baryons, supporting baryon-meson scaling. Since $\phi$-mesons are made via coalescence of seemingly thermalized $s$ quarks in central Au+Au collisions, the observations imply hot and dense matter with partonic collectivity has been formed at RHIC.Comment: 6 pages, 4 figures, submit to PR

Plasma Wakefield Acceleration with a Modulated Proton Bunch

The plasma wakefield amplitudes which could be achieved via the modulation of a long proton bunch are investigated. We find that in the limit of long bunches compared to the plasma wavelength, the strength of the accelerating fields is directly proportional to the number of particles in the drive bunch and inversely proportional to the square of the transverse bunch size. The scaling laws were tested and verified in detailed simulations using parameters of existing proton accelerators, and large electric fields were achieved, reaching 1 GV/m for LHC bunches. Energy gains for test electrons beyond 6 TeV were found in this case.Comment: 9 pages, 7 figure

The energy dependence of ptp_t angular correlations inferred from mean-ptp_{t} fluctuation scale dependence in heavy ion collisions at the SPS and RHIC

We present the first study of the energy dependence of $p_t$ angular correlations inferred from event-wise mean transverse momentum fluctuations in heavy ion collisions. We compare our large-acceptance measurements at CM energies $\sqrt{s_{NN}} =$ 19.6, 62.4, 130 and 200 GeV to SPS measurements at 12.3 and 17.3 GeV. $p_t$ angular correlation structure suggests that the principal source of $p_t$ correlations and fluctuations is minijets (minimum-bias parton fragments). We observe a dramatic increase in correlations and fluctuations from SPS to RHIC energies, increasing linearly with $\ln \sqrt{s_{NN}}$ from the onset of observable jet-related fluctuations near 10 GeV.Comment: 10 pages, 4 figure

Measurement of Transverse Single-Spin Asymmetries for Di-Jet Production in Proton-Proton Collisions at s=200\sqrt{s} = 200 GeV

We report the first measurement of the opening angle distribution between pairs of jets produced in high-energy collisions of transversely polarized protons. The measurement probes (Sivers) correlations between the transverse spin orientation of a proton and the transverse momentum directions of its partons. With both beams polarized, the wide pseudorapidity ($-1 \leq \eta \leq +2$) coverage for jets permits separation of Sivers functions for the valence and sea regions. The resulting asymmetries are all consistent with zero and considerably smaller than Sivers effects observed in semi-inclusive deep inelastic scattering (SIDIS). We discuss theoretical attempts to reconcile the new results with the sizable transverse spin effects seen in SIDIS and forward hadron production in pp collisions.Comment: 6 pages total, 1 Latex file, 3 PS files with figure

Longitudinal Double-Spin Asymmetry and Cross Section for Inclusive Jet Production in Polarized Proton Collisions at √s = 200 GeV

We report a measurement of the longitudinal double-spin asymmetry ALL and the differential cross section for inclusive midrapidity jet production in polarized proton collisions at √s=200  GeV. The cross section data cover transverse momenta

Two-particle correlations on transverse momentum and momentum dissipation in Au-Au collisions at sqrt(sNN) = 130 GeV

Measurements of two-particle correlations on transverse momentum pt for Au–Au collisions at GeV are presented. Significant large-momentum-scale correlations are observed for charged primary hadrons with 0.15 ≤ pt ≤ 2 GeV/c and pseudorapidity |η| ≤ 1.3. Such correlations were not observed in a similar study at lower energy and are not predicted by theoretical collision models. Their direct relation to mean-pt fluctuations measured in the same angular acceptance is demonstrated. Positive correlations are observed for pairs of particles which have large pt values while negative correlations occur for pairs in which one particle has large pt and the other has much lower pt. The correlation amplitudes per final state particle increase with collision centrality. The observed correlations are consistent with a scenario in which the transverse momentum of hadrons associated with initial-stage semi-hard parton scattering is dissipated by the medium to lower pt

The energy dependence of p\u3csub\u3et\u3c/sub\u3e angular correlations inferred from mean-p\u3csub\u3et\u3c/sub\u3e fluctuation scale dependence in heavy ion collisions at the SPS and RHIC

We present the first study of the energy dependence of pt angular correlations inferred from event-wise mean transverse momentum pt fluctuations in heavy ion collisions. We compare our large-acceptance measurements at CM energies , 62.4, 130 and 200 GeV to SPS measurements at 12.3 and 17.3 GeV. pt angular correlation structure suggests that the principal source of pt correlations and fluctuations is minijets (minimum-bias parton fragments). We observe a dramatic increase in correlations and fluctuations from SPS to RHIC energies, increasing linearly with from the onset of observable jet-related pt fluctuations near 10 GeV