Bayesian Biclustering of Gene Expression Data

Background: Biclustering of gene expression data searches for local patterns of gene expression. A bicluster (or a two-way cluster) is defined as a set of genes whose expression profiles are mutually similar within a subset of experimental conditions/samples. Although several biclustering algorithms have been studied, few are based on rigorous statistical models. Results: We developed a Bayesian biclustering model (BBC), and implemented a Gibbs sampling procedure for its statistical inference. We showed that Bayesian biclustering model can correctly identify multiple clusters of gene expression data. Using simulated data both from the model and with realistic characters, we demonstrated the BBC algorithm outperforms other methods in both robustness and accuracy. We also showed that the model is stable for two normalization methods, the interquartile range normalization and the smallest quartile range normalization. Applying the BBC algorithm to the yeast expression data, we observed that majority of the biclusters we found are supported by significant biological evidences, such as enrichments of gene functions and transcription factor binding sites in the corresponding promoter sequences. Conclusions: The BBC algorithm is shown to be a robust model-based biclustering method that can discover biologically significant gene-condition clusters in microarray data. The BBC model can easily handle missing data via Monte Carlo imputation and has the potential to be extended to integrated study of gene transcription networks.Statistic

Quantum processes which do not use coherence

A major signature of quantum mechanics beyond classical physics is coherence, the existence of superposition states. The recently developed resource theory of quantum coherence allows the formalisation of incoherent operations -- those operations which cannot create coherence. We identify the set of operations which additionally do not use coherence. These are such that coherence cannot be exploited by a classical observer, who measures incoherent properties of the system, to go beyond classical dynamics. We give a physical interpretation in terms of interferometry and prove a dilation theorem, showing how these operations can always be constructed by interacting the system in an incoherent way with an ancilla. Such a physical justification is not known for the incoherent operations, thus our results lead to a physically well-motivated resource theory of coherence. Next, we investigate the implications for coherence in multipartite systems. We show that quantum correlations can be defined naturally with respect to a fixed basis, providing a link between coherence and quantum discord. We demonstrate the interplay between these two quantities under our studied operations, and suggest implications for the theory of quantum discord by relating the studied operations to those which cannot create discord.Comment: 15 pages, 6 figures, comments are welcome. Revised presentation and added Result 7. Close to published version (accepted for publication in Physical Review X

Quantifying memory capacity as a quantum thermodynamic resource

The information-carrying capacity of a memory is known to be a thermodynamic resource facilitating the conversion of heat to work. Szilard's engine explicates this connection through a toy example involving an energy-degenerate two-state memory. We devise a formalism to quantify the thermodynamic value of memory in general quantum systems with nontrivial energy landscapes. Calling this the thermal information capacity, we show that it converges to the non-equilibrium Helmholtz free energy in the thermodynamic limit. We compute the capacity exactly for a general two-state (qubit) memory away from the thermodynamic limit, and find it to be distinct from known free energies. We outline an explicit memory--bath coupling that can approximate the optimal qubit thermal information capacity arbitrarily well.Comment: 6 main + 7 appendix pages; 5 main + 2 appendix figure

Advanced Silicate-based Lubricant Additive Induced Diamond-like Carbon Structured Restoration Layer

An advanced silicate based lubricant additive has been employed in long-term pin-on-disk tribological experiments. The worn steel/steel surfaces were characterized using nano-indentation, SEM, XPS, and Raman spectroscopy for their physical, mechanical, and chemical properties. The average nano-hardness of the repaired layers on the disk and the pin is 10.2 GPa and 16.7 GPa respectively, which is substantially higher than that of the disk (HV 221, or 0.71 GPa) and the pin (HRC55, or 1.8 GPa) before tribological tests, forming super hard surfaces on the contact pair surfaces. Combined Raman spectroscopy and XPS studies suggest the formation of diamond-like carbon based restoration layers. A new formation mechanism of the restoration DLC layer contributing to hard and smooth contact surfaces is proposed

Mechanism of transmethylation in anisole decomposition over HZSM-5: Experimental study

This work investigated the decomposition of anisole (methoxyl-based lignin model compound) in a fluidized bed reactor over no catalysts and a series of HZSM-5 zeolite catalysts with different Si/Al atomic ratios. Transmethylation reaction was identified as the initial step of the thermal decomposition of anisole, leading to the prominent production of phenolic compounds. Methyl phenols were identified as the main products, with the yield of o-cresol being higher than that of p-cresol at the temperatures below 600° C. The transmethylation reaction over HZSM-5 zeolite catalyst was found to occur at temperatures 150° C lower than those for non-catalytic reaction, with the yield of the phenolic compounds being promoted by 2.5 times. Production of the main phenolic compounds during the catalytic decomposition of anisole was enhanced to different extents depending on the Si/Al ratio. The highest selectivity of 79 wt.% was achieved over the zeolite catalyst with a Si/Al ratio of 80. The Brønsted acid sites of the catalyst played a significant role in both the preferential formation of phenolic compounds and preservation of the methyl group

Mechanism of deoxygenation in anisole decomposition over single-metal loaded HZSM-5: Experimental study

This work investigates the deoxygenation reaction during the decomposition of anisole (methoxy-rich model compound of lignin) over bi-functional catalyst. The bi-functional catalyst consisted of a single metal loaded on an acid support; the active metals, i.e. Ni, Co, Mo and Cu, were loaded at various rates, and the acid support was HZSM-5 zeolite with a Si/Al ratio of 25 (HZ(25)). Experiments were conducted in a bench-scale fluidised bed reactor within the temperature range from 400°C to 600°C. Experimental results revealed that the increase in temperature and metal loading promoted the selectivity of BTX fraction. Nevertheless, a simultaneous increase in the yield of carbonaceous deposits was also observed at the expense of liquid fraction, both phenolics compounds (Phs) and aromatic hydrocarbons (AHs). 500°C was the preferred temperature for BTX production. Ni-loaded HZ(25) catalyst could dramatically facilitate the conversion of Phs to monoaromatics and increase the selectivity of BTX fraction by 43.4%; Mo-loaded HZ(25) catalyst exhibited the best catalytic activity towards the total production of AHs and promoted the BTX yield by 27.1%. It was also found that 1 wt.% was the optimum loading ratio for both Ni and Mo on HZ(25) to obtain the highest BTX yield and selectivity. Characterization of fresh bi-functional catalysts showed that micro polycrystalline metal sites, in the range of 4 -10 nm, existed on the fresh catalyst and exhibited strong interaction with the HZ(25) support. For the spent catalysts, large amount of amorphous carbonaceous deposit was observed, ascribed to the polycondensation of aromatic compounds during the reaction. Three reaction pathways were proposed for the catalytic deoxygenation of anisole, with the hydrogen being available in-situ as product of the polycondensation reaction

Studies on the toxicokinetics of intragastricallyadministered paracetamol, aminophenazone, caffeine and chlorphenamine maleate tablets in rats

Purpose: To study the toxicokinetics of paracetamol (PCT), aminophenazone (ACP), caffeine (CFN) and chlorphenamine maleate (CPM) tablets after a single oral gavage, and after oral gavage for 14 consecutive days in rats. Methods: Eighty Sprague Dawley (SD) rats (half male, half female) were randomly divided into 4 groups with 20 rats in each group. Half of the rats were used for the toxicokinetic test after a single oral gavage of PCT, ACP, CFN and CPM tablets, while rats in the other half were used for the toxicokinetic tests after oral gavage for 14 consecutive days. The doses of the four groups were set as 0, 0.5, 1 and 2 tablets/kg body weight, respectively. Blood was taken from the rats and the plasma concentration of paracetamol was determined. Results: There was a significant difference in AUC0-∞ between male and female rats at single oral gavage of 2 tablets/kg of each of the drugs. The exposure amount of PCT (AUC0~t, AUC0-∞ and Cmax) increased with increase in dose, and showed a good linear relationship after a single intragastric administration of each drug, and after 14 consecutive days of intragastric administration at low, medium and high doses. Conclusion: The amount of PCT to which SD rats are exposed after a single intragastric administration of PCT, ACP, CFN and CPM tablets is lower in male than in female rats. However, no significant gender difference in exposure results when these drugs are given intragastrically for 14 consecutive days

Transfer function based input impedance determination of triple active bridge converter

The concept of multiport dc-dc converter was proposed to reduce the conversion stages of dc microgrid on more electric aircraft (MEA). The structure of multiport dc-dc converter is basically developed from the dual active bridge (DAB) converter because of its galvanic isolation and bidirectional power flow. A power electronics converter as a key element of the electrical power distribution system may cause stability issues. To address these challenges, the impedance characteristic of the multiport converter will be analyzed. In this paper, a transfer function based small signal model is developed and validated with a switching model, to figure out the characteristic of input impedance of triple active bridge (TAB) converter. Preliminary experimental results are presented to be as a support