Radio variability of 1st 3-months Fermi blazars at 5 GHz: affected by interstellar scintillation?

Blazars from the first-three-months Fermi-AGN list were observed with the Urumqi 25m radio telescope at 5GHz in IDV (Intra-Day Variability) mode and inter-month observation mode. A significant correlation between the flux density at 5GHz and the gamma-ray intensity for the Fermi-LAT detected blazars is seen. There is a higher IDV detection rate in Fermi detected blazars than those reported for other samples. Stronger variability appears at lower Galactic latitudes; IDV appears to be stronger in weaker sources, indicating that the variability is affected by interstellar scintillation.Comment: 4 pages, 4 figures, in proceedings of 'Multiwavelength Variability of Blazars' in Guangzhou Uni. of China, 22-24, Sep. 2010, to appear in JA

Identification of disease-causing genes using microarray data mining and gene ontology

Background: One of the best and most accurate methods for identifying disease-causing genes is monitoring gene expression values in different samples using microarray technology. One of the shortcomings of microarray data is that they provide a small quantity of samples with respect to the number of genes. This problem reduces the classification accuracy of the methods, so gene selection is essential to improve the predictive accuracy and to identify potential marker genes for a disease. Among numerous existing methods for gene selection, support vector machine-based recursive feature elimination (SVMRFE) has become one of the leading methods, but its performance can be reduced because of the small sample size, noisy data and the fact that the method does not remove redundant genes. Methods: We propose a novel framework for gene selection which uses the advantageous features of conventional methods and addresses their weaknesses. In fact, we have combined the Fisher method and SVMRFE to utilize the advantages of a filtering method as well as an embedded method. Furthermore, we have added a redundancy reduction stage to address the weakness of the Fisher method and SVMRFE. In addition to gene expression values, the proposed method uses Gene Ontology which is a reliable source of information on genes. The use of Gene Ontology can compensate, in part, for the limitations of microarrays, such as having a small number of samples and erroneous measurement results. Results: The proposed method has been applied to colon, Diffuse Large B-Cell Lymphoma (DLBCL) and prostate cancer datasets. The empirical results show that our method has improved classification performance in terms of accuracy, sensitivity and specificity. In addition, the study of the molecular function of selected genes strengthened the hypothesis that these genes are involved in the process of cancer growth. Conclusions: The proposed method addresses the weakness of conventional methods by adding a redundancy reduction stage and utilizing Gene Ontology information. It predicts marker genes for colon, DLBCL and prostate cancer with a high accuracy. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help in the search for a cure for cancers

Development of Photonic Crystal Fiber Based Gas/ Chemical Sensors

The development of highly-sensitive and miniaturized sensors that capable of real-time analytes detection is highly desirable. Nowadays, toxic or colorless gas detection, air pollution monitoring, harmful chemical, pressure, strain, humidity, and temperature sensors based on photonic crystal fiber (PCF) are increasing rapidly due to its compact structure, fast response and efficient light controlling capabilities. The propagating light through the PCF can be controlled by varying the structural parameters and core-cladding materials, as a result, evanescent field can be enhanced significantly which is the main component of the PCF based gas/chemical sensors. The aim of this chapter is to (1) describe the principle operation of PCF based gas/ chemical sensors, (2) discuss the important PCF properties for optical sensors, (3) extensively discuss the different types of microstructured optical fiber based gas/ chemical sensors, (4) study the effects of different core-cladding shapes, and fiber background materials on sensing performance, and (5) highlight the main challenges of PCF based gas/ chemical sensors and possible solutions

Score regularization for peptide identification

<p>Abstract</p> <p>Background</p> <p>Peptide identification from tandem mass spectrometry (MS/MS) data is one of the most important problems in computational proteomics. This technique relies heavily on the accurate assessment of the quality of peptide-spectrum matches (PSMs). However, current MS technology and PSM scoring algorithm are far from perfect, leading to the generation of incorrect peptide-spectrum pairs. Thus, it is critical to develop new post-processing techniques that can distinguish true identifications from false identifications effectively.</p> <p>Results</p> <p>In this paper, we present a consistency-based PSM re-ranking method to improve the initial identification results. This method uses one additional assumption that two peptides belonging to the same protein should be correlated to each other. We formulate an optimization problem that embraces two objectives through regularization: the smoothing consistency among scores of correlated peptides and the fitting consistency between new scores and initial scores. This optimization problem can be solved analytically. The experimental study on several real MS/MS data sets shows that this re-ranking method improves the identification performance.</p> <p>Conclusions</p> <p>The score regularization method can be used as a general post-processing step for improving peptide identifications. Source codes and data sets are available at: <url>http://bioinformatics.ust.hk/SRPI.rar</url>.</p

Experimental observation of topological Fermi arcs in type-II Weyl semimetal MoTe2

Weyl semimetal is a new quantum state of matter [1-12] hosting the condensed matter physics counterpart of relativisticWeyl fermion [13] originally introduced in high energy physics. The Weyl semimetal realized in the TaAs class features multiple Fermi arcs arising from topological surface states [10, 11, 14-16] and exhibits novel quantum phenomena, e.g., chiral anomaly induced negative mag-netoresistance [17-19] and possibly emergent supersymmetry [20]. Recently it was proposed theoretically that a new type (type-II) of Weyl fermion [21], which does not have counterpart in high energy physics due to the breaking of Lorentz invariance, can emerge as topologically-protected touching between electron and hole pockets. Here, we report direct spectroscopic evidence of topological Fermi arcs in the predicted type-II Weyl semimetal MoTe2 [22-24]. The topological surface states are confirmed by directly observing the surface states using bulk-and surface-sensitive angle-resolved photoemission spectroscopy (ARPES), and the quasi-particle interference (QPI) pattern between the two putative Fermi arcs in scanning tunneling microscopy (STM). Our work establishes MoTe2 as the first experimental realization of type-II Weyl semimetal, and opens up new opportunities for probing novel phenomena such as exotic magneto-transport [21] in type-II Weyl semimetals.Comment: submitted on 01/29/2016. Nature Physics, in press. Spectroscopic evidence of the Fermi arcs from two complementary surface sensitive probes - ARPES and STS. A comparison of the calculated band structure for T_d and 1T' phase to identify the topological Fermi arcs in the T_d phase is also included in the supplementary informatio

Observation of Spontaneous Brillouin Cooling

While radiation-pressure cooling is well known, the Brillouin scattering of light from sound is considered an acousto-optical amplification-only process. It was suggested that cooling could be possible in multi-resonance Brillouin systems when phonons experience lower damping than light. However, this regime was not accessible in traditional Brillouin systems since backscattering enforces high acoustical frequencies associated with high mechanical damping. Recently, forward Brillouin scattering in microcavities has allowed access to low-frequency acoustical modes where mechanical dissipation is lower than optical dissipation, in accordance with the requirements for cooling. Here we experimentally demonstrate cooling via such a forward Brillouin process in a microresonator. We show two regimes of operation for the Brillouin process: acoustical amplification as is traditional, but also for the first time, a Brillouin cooling regime. Cooling is mediated by an optical pump, and scattered light, that beat and electrostrictively attenuate the Brownian motion of the mechanical mode.Comment: Supplementary material include

Quantum nondemolition measurement of mechanical motion quanta

The fields of opto- and electromechanics have facilitated numerous advances in the areas of precision measurement and sensing, ultimately driving the studies of mechanical systems into the quantum regime. To date, however, the quantization of the mechanical motion and the associated quantum jumps between phonon states remains elusive. For optomechanical systems, the coupling to the environment was shown to preclude the detection of the mechanical mode occupation, unless strong single photon optomechanical coupling is achieved. Here, we propose and analyse an electromechanical setup, which allows to overcome this limitation and resolve the energy levels of a mechanical oscillator. We find that the heating of the membrane, caused by the interaction with the environment and unwanted couplings, can be suppressed for carefully designed electromechanical systems. The results suggest that phonon number measurement is within reach for modern electromechanical setups.Comment: 8 pages, 5 figures plus 24 pages, 11 figures supplemental materia

Klebsiella pneumoniae is able to trigger epithelial-mesenchymal transition process in cultured airway epithelial cells

The ability of some bacterial pathogens to activate Epithelial-Mesenchymal Transition normally is a consequence of the persistence of a local chronic inflammatory response or depends on a direct interaction of the pathogens with the host epithelial cells. In this study we monitored the abilities of the K. pneumoniae to activate the expression of genes related to EMT-like processes and the occurrence of phenotypic changes in airway epithelial cells during the early steps of cell infection. We describe changes in the production of intracellular reactive oxygen species and increased HIF-1α mRNA expression in cells exposed to K. pneumoniae infection. We also describe the upregulation of a set of transcription factors implicated in the EMT processes, such as Twist, Snail and ZEB, indicating that the morphological changes of epithelial cells already appreciable after few hours from the K. pneumoniae infection are tightly regulated by the activation of transcriptional pathways, driving epithelial cells to EMT. These effects appear to be effectively counteracted by resveratrol, an antioxidant that is able to exert a sustained scavenging of the intracellular ROS. This is the first report indicating that strains of K. pneumoniae may promote EMT-like programs through direct interaction with epithelial cells without the involvement of inflammatory cells

The safety of monoclonal antibodies in asthma

Introduction: In the last two decades the knowledge of the mechanisms of the inflammatory processes underlying asthma rapidly evolved, several key mediators (cytokines and receptors) were identified, and the laboratory techniques have allowed us to synthesize monoclonal antibodies highly specific for those target molecules. Nowadays, many biological agents are investigated in asthma (with anti IgE being the only commercially available). The clinical efficacy of some biologics was demonstrated in many cases, however, the safety issue has progressively emerged and has been recognized as a crucial aspect. Areas covered: We summarized the currently available knowledge on the safety and side effects of biologics in asthma, as derived by reviews, meta analyses and clinical trials. PubMed was searched with the terms anti IL-x [AND] safety [OR] side effects, within the categories \u201cclinical trial\u201d, meta-analysis\u201d and \u201creview\u201d. Case reports were excluded. The authors collegially selected the relevant entries to be included. Expert opinion: Overall, the safety of most of the investigated agents seems to be satisfactory, a certain risk of side effects remains present, and is variable for the different molecules. Thus caution must be paid in evaluating the risk to benefit ratio. Specific biomarkers to predict the response to each biological are urgently needed to improve the safety profile