tRNA splicing

Introns interrupt the continuity of many eukaryal genes, and therefore their removal by splicing is a crucial step in gene expression. Interestingly, even within Eukarya there are at least four splicing mechanisms. mRNA splicing in the nucleus takes place in two phosphotransfer reactions on a complex and dynamic machine, the spliceosome. This reaction is related in mechanism to the two self-splicing mechanisms for Group 1 and Group 2 introns. In fact the Group 2 introns are spliced by an identical mechanism to mRNA splicing, although there is no general requirement for either proteins or co-factors. Thus it seems likely that the Group 2 and nuclear mRNA splicing reactions have diverged from a common ancestor. tRNA genes are also interrupted by introns, but here the splicing mechanism is quite different because it is catalyzed by three enzymes, all proteins and with an intrinsic requirement for ATP hydrolysis. tRNA splicing occurs in all three major lines of descent, the Bacteria, the Archaea, and the Eukarya. In bacteria the introns are self-splicing (1-3). Until recently it was thought that the mechanisms of tRNA splicing in Eukarya and Archaea were unrelated as well. In the past year, however, it has been found that the first enzyme in the tRNA splicing pathway, the tRNA endonuclease, has been conserved in evolution since the divergence of the Eukarya and the Archaea. Surprising insights have been obtained by comparison of the structures and mechanisms of tRNA endonuclease from these two divergent lines

Laser induced incandescence and high speed imaging in hydra optical diesel engine

The aim of this thesis is to investigate ways to reduce soot emission from compression ignition engines by investigating the combustion processes within the diesel engine. The approach is to include computational and experimental work. In order to investigate the trade-off between the amount and stratification of the premixing and the consequent rate of pressure rise, and in particular the effects of changing the autoignition properties of the fuel blend, a multizone code capable of representing the ignition of a premixed charge consequent on multiple injection of fuel is presented. As part of this investigation, this thesis began the process of looking into the potential of gasoline fuel. Experimentally, investigations of soot distribution were carried out in an optically-accessed single cylinder “Hydra” engine. The soot was visualized using high speed imaging and laser induced incandescence in the optical engine to look at the effect of injection pressure on combustion luminosity and soot distribution. An extensive parametric study was carried out on the Hydra engine to look at the effect of engine load, injection timing and pressure, number of injections, intake temperature and combustion phasing. High speed imaging was carried out to measure injection tip penetration and soot luminosity as a function injection pressure. The combustion luminosity was studied, with proper orthogonal decomposition (POD) analysis, at different injection pressures. It was found that increase of injection pressure decreases combustion luminosity. The technique of laser induced incandescence (LII) was used to visualize the soot. As a preliminary to the use of the LII in the engine, fundamental work on the technique itself was carried out at Heriot-Watt University to isolate the radiative emission component of heat loss from the soot and measure the complex refractive index of soot. Results on soot particle sizes were compared to scanning electron micrograph of the soot collected. The LII measurement was found to be much larger, due to the high signal to noise ratio and the bias towards detection of larger particles. The investigation also showed that the soot agglomerates could undergo micro-explosions on being exposed to laser irradiance. It is speculated that the soot molecules become ionized and mutually repel each other.Open Acces

Momentum Broadening in Weakly Coupled Quark-Gluon Plasma

We calculate the probability distribution P(k_\perp) for the momentum perpendicular to its original direction of motion that an energetic quark or gluon picks up as it propagates through weakly coupled quark-gluon plasma in thermal equilibrium.Comment: 4 pages, 2 figures - Talk presented by M. Lekaveckas at PANIC 2011, July 25-29, 2011, MIT, Cambridge, MA, US

A current perspective on stereotactic body radiation therapy for pancreatic cancer.

Pancreatic cancer is a formidable malignancy with poor outcomes. The majority of patients are unable to undergo resection, which remains the only potentially curative treatment option. The management of locally advanced (unresectable) pancreatic cancer is controversial; however, treatment with either chemotherapy or chemoradiation is associated with high rates of local tumor progression and metastases development, resulting in low survival rates. An emerging local modality is stereotactic body radiation therapy (SBRT), which uses image-guided, conformal, high-dose radiation. SBRT has demonstrated promising local control rates and resultant quality of life with acceptable rates of toxicity. Over the past decade, increasing clinical experience and data have supported SBRT as a local treatment modality. Nevertheless, additional research is required to further evaluate the role of SBRT and improve upon the persistently poor outcomes associated with pancreatic cancer. This review discusses the existing clinical experience and technical implementation of SBRT for pancreatic cancer and highlights the directions for ongoing and future studies

Does the use of specialist palliative care services modify the effect of socioeconomic status on place of death? A systematic review

© SAGE Publications. Background: Cancer patients in lower socioeconomic groups are significantly less likely to die at home and experience more barriers to access to palliative care. It is unclear whether receiving palliative care may mediate the effect of socioeconomic status on place of death. Aim: This review examines whether and how use of specialist palliative care may modify the effect of socioeconomic status on place of death. Design: A systematic review was conducted. Eligible papers were selected and the quality appraised by two independent reviewers. Data were synthesised using a narrative approach. Data sources: MEDLINE, Embase, CINAHL, PsycINFO and Web of Knowledge were searched (1997-2013). Bibliographies were scanned and experts contacted. Papers were included if they reported the effect of both socioeconomic status and use of specialist palliative care on place of death for adult cancer patients. Results: Nine studies were included. All study subjects had received specialist palliative care. With regard to place of death, socioeconomic status was found to have (1) no effect in seven studies and (2) an effect in one study. Furthermore, one study found that the effect of socioeconomic status on place of death was only significant when patients received standard specialist palliative care. When patients received more intense care adapted to their needs, the effect of socioeconomic status on place of death was no longer seen. Conclusion: There is some evidence to suggest that use of specialist palliative care may modify the effect of socioeconomic status on place of death

Separability in Cohomogeneity-2 Kerr-NUT-AdS Metrics

The remarkable and unexpected separability of the Hamilton-Jacobi and Klein-Gordon equations in the background of a rotating four-dimensional black hole played an important role in the construction of generalisations of the Kerr metric, and in the uncovering of hidden symmetries associated with the existence of Killing tensors. In this paper, we show that the Hamilton-Jacobi and Klein-Gordon equations are separable in Kerr-AdS backgrounds in all dimensions, if one specialises the rotation parameters so that the metrics have cohomogeneity 2. Furthermore, we show that this property of separability extends to the NUT generalisations of these cohomogeneity-2 black holes that we obtained in a recent paper. In all these cases, we also construct the associated irreducible rank-2 Killing tensor whose existence reflects the hidden symmetry that leads to the separability. We also consider some cohomogeneity-1 specialisations of the new Kerr-NUT-AdS metrics, showing how they relate to previous results in the literature.Comment: Latex, 15 pages, minor typos correcte

A controlled study of community-based exercise training in patients with moderate COPD.

BackgroundThe effectiveness of clinic-based pulmonary rehabilitation in advanced COPD is well established, but few data exist for less severe patients treated in alternative settings. The purpose of this study was to investigate whether a novel, community-based exercise program (CBE) was feasible and effective for patients with moderate COPD.MethodsNineteen patients with moderate COPD (mean FEV1 62%) and self-reported exercise impairment were randomized to 12-weeks of progressive endurance and strength training at a local health club under the guidance of a certified personal trainer, or to continuation of unsupervised habitual physical activity. Outcomes assessed at baseline and 12 weeks included session compliance, intensity adherence, treadmill endurance time, muscle strength, dyspnea, and health status.ResultsCompliance was 94% and adherence was 83%. Comparisons between CBE and control groups yielded the following mean (SEM) differences in favor of CBE: endurance time 134 (74) seconds versus -59 (49) seconds (P=0.041) and TDI 5.1 (0.8) versus -0.2 (0.5) (P<0.001). The CBE group increased muscle strength (weight lifted) by 11.8 kilograms per subject per week of training (P<0.001). SGRQ was not significantly changed.ConclusionsWe demonstrated the feasibility and effectiveness of a novel community-based exercise program involving health clubs and personal trainers for patients with moderate COPD.Trial registrationClinicalTrials.gov Identifier NCT01985529

Constraining Stellar Feedback: Shock-ionized Gas in Nearby Starburst Galaxies

(abridged) We investigate the properties of feedback-driven shocks in 8 nearby starburst galaxies using narrow-band imaging data from the Hubble Space Telescope (HST). We identify the shock--ionized component via the line diagnostic diagram \oiii/\hb vs. \sii (or \nii)/\ha, applied to resolved regions 3--15 pc in size. We divide our sample into three sub-samples: sub-solar (Holmberg II, NGC 1569, NGC 4214, NGC 4449, and NGC 5253), solar (He 2-10, NGC 3077) and super-solar (NGC 5236) for consistent shock measurements. For the sub-solar sub-sample, we derive three scaling relations: (1) $L_{shock} \propto {SFR}^{~0.62}$, (2) $L_{shock} \propto {\Sigma_{SFR,HL}}^{~0.92}$, and (3) $L_{shock}/L_{tot} \propto {(L_H/L_{\odot,H})}^{-0.65}$, where $L_{shock}$ is the \ha luminosity from shock--ionized gas, ${\Sigma_{SFR,HL}}$ the SFR per unit half-light area, $L_{tot}$ the total \ha luminosity, and $L_H/L_{\odot,H}$ the absolute H-band luminosity from 2MASS normalized to solar luminosity. The other two sub--samples do not have enough number statistics, but appear to follow the first scaling relation. The energy recovered indicates that the shocks from stellar feedback in our sample galaxies are fully radiative. If the scaling relations are applicable in general to stellar feedback, our results are similar to those by Hopkins et al. (2012) for galactic super winds. This similarity should, however, be taken with caution at this point, as the underlying physics that enables the transition from radiative shocks to gas outflows in galaxies is still poorly understood.Comment: 29 pages, 14 figures, accepted for publication in the Ap

Big data based intelligent decision support system for sustainable regional development

Timely intelligent decision making is increasingly important for modern society. With the availability of big data and advanced artificial intelligence in decision making, more objective and evidence-based quantitative smart decisions can be made in a timely manner. This research proposed a big data based intelligent decision support system (B-IDSS) for sustainable business development. The system can be used by both the government agencies and corporate business (e.g. farms. mining) in advanced planning, collaboration and management. This paper also addresses the performance optimization as bilevel decision-making problem with one leader and multiple followers. An extended Kuhn-Tucker approach is introduced as one of the algorithms that can be adapted in the system