Identifying cancer-related microRNAs based on gene expression data

Motivation: MicroRNAs (miRNAs) are short non-coding RNAs that play important roles in post-transcriptional regulations as well as other important biological processes. Recently, accumulating evidences indicate that miRNAs are extensively involved in cancer. However, it is a big challenge to identify which miRNAs are related to which cancer considering the complex processes involved in tumors, where one miRNA may target hundreds or even thousands of genes and one gene may regulate multiple miRNAs. Despite integrative analysis of matched gene and miRNA expression data can help identify cancer-associated miRNAs, such kind of data is not commonly available. On the other hand, there are huge amount of gene expression data that are publicly accessible. It will significantly improve the efficiency of characterizing miRNA’s function in cancer if we can identify cancer miRNAs directly from gene expression data. Results: We present a novel computational framework to identify the cancer-related miRNAs based solely on gene expression profiles without requiring either miRNA expression data or the matched gene and miRNA expression data. The results on multiple cancer datasets show that our proposed method can effectively identify cancer-related miRNAs with higher precision compared with other popular approaches. Furthermore, some of our novel predictions are validated by both differentially expressed miRNAs and evidences from literature, implying the predictive power of our proposed method. In addition, we construct a cancer-miRNA-pathway network, which can help explain how miRNAs are involved in cancer

Physics research on the TCV tokamak facility: from conventional to alternative scenarios and beyond

The research program of the TCV tokamak ranges from conventional to advanced-tokamak scenarios and alternative divertor configurations, to exploratory plasmas driven by theoretical insight, exploiting the device’s unique shaping capabilities. Disruption avoidance by real-time locked mode prevention or unlocking with electron-cyclotron resonance heating (ECRH) was thoroughly documented, using magnetic and radiation triggers. Runaway generation with high-Z noble-gas injection and runaway dissipation by subsequent Ne or Ar injection were studied for model validation. The new 1 MW neutral beam injector has expanded the parameter range, now encompassing ELMy H-modes in an ITER-like shape and nearly non-inductive H-mode discharges sustained by electron cyclotron and neutral beam current drive. In the H-mode, the pedestal pressure increases modestly with nitrogen seeding while fueling moves the density pedestal outwards, but the plasma stored energy is largely uncorrelated to either seeding or fueling. High fueling at high triangularity is key to accessing the attractive small edge-localized mode (type-II) regime. Turbulence is reduced in the core at negative triangularity, consistent with increased confinement and in accord with global gyrokinetic simulations. The geodesic acoustic mode, possibly coupled with avalanche events, has been linked with particle flow to the wall in diverted plasmas. Detachment, scrape-off layer transport, and turbulence were studied in L- and H-modes in both standard and alternative configurations (snowflake, super-X, and beyond). The detachment process is caused by power ‘starvation’ reducing the ionization source, with volume recombination playing only a minor role. Partial detachment in the H-mode is obtained with impurity seeding and has shown little dependence on flux expansion in standard single-null geometry. In the attached L-mode phase, increasing the outer connection length reduces the in–out heat-flow asymmetry. A doublet plasma, featuring an internal X-point, was achieved successfully, and a transport barrier was observed in the mantle just outside the internal separatrix. In the near future variable-configuration baffles and possibly divertor pumping will be introduced to investigate the effect of divertor closure on exhaust and performance, and 3.5 MW ECRH and 1 MW neutral beam injection heating will be added

The LHCb upgrade I

The LHCb upgrade represents a major change of the experiment. The detectors have been almost completely renewed to allow running at an instantaneous luminosity five times larger than that of the previous running periods. Readout of all detectors into an all-software trigger is central to the new design, facilitating the reconstruction of events at the maximum LHC interaction rate, and their selection in real time. The experiment's tracking system has been completely upgraded with a new pixel vertex detector, a silicon tracker upstream of the dipole magnet and three scintillating fibre tracking stations downstream of the magnet. The whole photon detection system of the RICH detectors has been renewed and the readout electronics of the calorimeter and muon systems have been fully overhauled. The first stage of the all-software trigger is implemented on a GPU farm. The output of the trigger provides a combination of totally reconstructed physics objects, such as tracks and vertices, ready for final analysis, and of entire events which need further offline reprocessing. This scheme required a complete revision of the computing model and rewriting of the experiment's software

New insights on divertor parallel flows, E x B drifts, and fluctuations from in situ, two-dimensional probe measurement in the Tokamak à Configuration Variable

In situ, two-dimensional (2D) Langmuir probe measurements across a large part of the TCV outer divertor are reported in L-mode discharges with and without divertor baffles. This provides detailed insights into time averaged profiles, particle fluxes, and fluctuation behavior in different divertor regimes. The presence of the baffles is shown to substantially increase the divertor neutral pressure for a given upstream density and to facilitate the access to detachment, an effect that increases with plasma current. The detailed, 2D probe measurements allow for a divertor particle balance, including ion flux contributions from parallel flows and E × B drifts. The poloidal flux contribution from the latter is often comparable or even larger than the former, and the divertor parallel flow direction reverses in some conditions, pointing away from the target. In most conditions, the integrated particle flux at the outer target can be predominantly ascribed to ionization along the outer divertor leg, consistent with a closed-box approximation of the divertor. The exception is a strongly detached divertor, achieved here only with baffles, where the total poloidal ion flux even decreases towards the outer target, indicative of significant plasma recombination. The most striking observation from relative density fluctuation measurements along the outer divertor leg is the transition from poloidally uniform fluctuation levels in attached conditions to fluctuations strongly peaking near the X-point when approaching detachment.<br/

New insights on divertor parallel flows, E x B drifts, and fluctuations from in situ, two-dimensional probe measurement in the Tokamak à Configuration Variable

In situ, two-dimensional (2D) Langmuir probe measurements across a large part of the TCV outer divertor are reported in L-mode discharges with and without divertor baffles. This provides detailed insights into time averaged profiles, particle fluxes, and fluctuation behavior in different divertor regimes. The presence of the baffles is shown to substantially increase the divertor neutral pressure for a given upstream density and to facilitate the access to detachment, an effect that increases with plasma current. The detailed, 2D probe measurements allow for a divertor particle balance, including ion flux contributions from parallel flows and E × B drifts. The poloidal flux contribution from the latter is often comparable or even larger than the former, and the divertor parallel flow direction reverses in some conditions, pointing away from the target. In most conditions, the integrated particle flux at the outer target can be predominantly ascribed to ionization along the outer divertor leg, consistent with a closed-box approximation of the divertor. The exception is a strongly detached divertor, achieved here only with baffles, where the total poloidal ion flux even decreases towards the outer target, indicative of significant plasma recombination. The most striking observation from relative density fluctuation measurements along the outer divertor leg is the transition from poloidally uniform fluctuation levels in attached conditions to fluctuations strongly peaking near the X-point when approaching detachment