A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions

The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the reconstruction of a protein-protein subnetwork that underlies a process of interest from a genome-wide screen of associated genes. Despite intense work in this area, current algorithmic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. Here we propose a novel formulation for network reconstruction from multiple-condition data and devise an efficient integer program solution for it. We apply our algorithm to analyze the response to influenza infection in humans over time as well as to analyze a pair of ER export related screens in humans. By comparing to an extant, single-condition tool we demonstrate the power of our new approach in integrating data from multiple conditions in a compact and coherent manner, capturing the dynamics of the underlying processes.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Combustion Noise Analysis for Combustion and Fuels Diagnosis of a CI Diesel Engine Operating with Biodiesels

In this paper, the combustion noise of a compression ignition (CI) diesel engine operating with biodiesels has been investigated experimentally. It aims to explore an effective method for combustion process monitoring and fuel quality evaluation through analysing the characteristics of the engine combustion noise. The experiments were conducted on a four-cylinder, four-stroke, direct injection and turbocharged diesel engine fuelled with biodiesels (B50 and B100) and normal pure diesel, and operating under different loads and speeds. The signals of cylinder head vibration, engine noise and in-cylinder pressure were measured during the tests. A coherent power spectrum analysis method was used to investigate the vibration and noise signals that related to the combustion process. The results shown that the noise components at the frequency band of 2 -3 kHz are closely related to the combustion process. Subsequently, the Wigner-Ville distribution is employed to present the energy distribution of engine noise in the time-frequency domain. Then a band-pass filter based on fractional Fourier transform (FRFT) is developed to extract the main component of the combustion noise for feature extraction. The results show that the sound pressure levels (SPLs) of the extracted combustion noise of the test diesel engine fuelled with biodiesels are higher than that fuelled with diesel. This is also identical to the variation of in-cylinder pressure. The results demonstrate that the features of the extracted combustion noise can indicate the combustion characteristics and provide useful information for monitoring the combustion process and evaluating the fuel quality of diesel engines

The influence of a high power diode laser (HPDL) generated glaze on the wetting characteristics and the subsequent HPDL enamelling of ordinary Portland cement

High power diode laser (HPDL) surface glazing of the ordinary Portland cement (OPC) surface of concrete was found to effect significant changes in the wettability characteristics of the OPC. This behaviour was identified as being primarily due to: (i) the polar component of the OPC surface energy increasing after HPDL glazing from 3.46 to 15.56 mJm-2, (ii) the surface roughness of the OPC decreasing from an Ra value of 21.91 to 2.88 m after HPDL glazing and (iii) the relative surface O2 content of the OPC increasing by 4.5at% after HPDL glazing. HPDL glazing was consequently identified as occasioning a decrease in the enamel contact angle from an initial value of 1090 to 310, thus allowing the vitreous enamel to wet the OPC surface

Neutral B Flavor Tagging for the Measurement of Mixing-induced CP Violation at Belle

We describe a flavor tagging algorithm used in measurements of the CP violation parameter sin2phi_1 at the Belle experiment. Efficiencies and wrong tag fractions are evaluated using flavor-specific B meson decays into hadronic and semileptonic modes. We achieve a total effective efficiency of $ 28.8 +- 0.6 %.Comment: 28 pages, 9 figure

Low-energy excitations in the three-dimensional random-field Ising model

The random-field Ising model (RFIM), one of the basic models for quenched disorder, can be studied numerically with the help of efficient ground-state algorithms. In this study, we extend these algorithm by various methods in order to analyze low-energy excitations for the three-dimensional RFIM with Gaussian distributed disorder that appear in the form of clusters of connected spins. We analyze several properties of these clusters. Our results support the validity of the droplet-model description for the RFIM.Comment: 10 pages, 9 figure

Mass-Enhanced Fermi Liquid Ground State in Na1.5_{1.5}Co2_2O4_4

Magnetic, transport, and specific heat measurements have been performed on layered metallic oxide Na$_{1.5}$Co$_2$O$_4$ as a function of temperature $T$. Below a characteristic temperature $T^*$=30$-$40 K, electrical resistivity shows a metallic conductivity with a $T^2$ behavior and magnetic susceptibility deviates from the Curie-Weiss behavior showing a broad peak at $\sim$14 K. The electronic specific heat coefficient $\gamma$ is $\sim$60 mJ/molK$^2$ at 2 K. No evidence for magnetic ordering is found. These behaviors suggest the formation of mass-enhanced Fermi liquid ground state analogous to that in $d$-electron heavy fermion compound LiV$_2$O$_4$.Comment: 4 pages, 4 figures, to be published in Phys. Rev. B 69 (2004

The role of social networks in students’ learning experiences

The aim of this research is to investigate the role of social networks in computer science education. The Internet shows great potential for enhancing collaboration between people and the role of social software has become increasingly relevant in recent years. This research focuses on analyzing the role that social networks play in students’ learning experiences. The construction of students’ social networks, the evolution of these networks, and their effects on the students’ learning experience in a university environment are examined

Theoretical studies of EBT

A one-dimensional time dependent model of plasma particle and energy transport was used to predict the performance of an EBT experiment large enough to test confinement scaling in a parameter range (n, T, tau, etc.) close to reactor conditions. Such a device is referred to as EBT-P. The model is based on a computer code which uses the magnetic field lines as the basis for the coordinate system, and so includes some EBT geometrical effects, with neoclassical transport perpendicular to the surfaces of constant pressure. The geometry is self-consistent, i.e., the plasma pressure reacts on the magnetic field

Amyloid Myopathy as an Inclusion Body Myositis Mimic

Introduction: Amyloid myopathy is a rare presentation of systemic amyloidosis. Amyloid myopathy can be initially misdiagnosed as sporadic inclusion body myositis (IBM). Methods: We report 4 cases of amyloid myopathy clinically mimicking inclusion body myositis and initially thought to be phenotypically IBM by neuromuscular experts. Results: Case 1 is an 81-year-old woman who presented with distal arm and proximal leg asymmetric weakness (myopathy pattern 4). Case 2 is a 76-year-old man with primary systemic amyloidosis who presented with myopathy pattern 4 and progressive dysphagia for four years. Case 3 is an 82-year-old man with progressive myopathy pattern 4 weakness and swallowing difficulty. Case 4 is a 62-year-old man with progressive bilateral finger flexor weakness. Muscle biopsies in all 4 cases showed perivascular amyloid deposits Discussion: Amyloid myopathy may be clinically indistinguishable from IBM. Muscle biopsy is of critical importance in the evaluation of patients suspected to have IBM

Expression of UV-Sensitive Parapinopsin in the Iguana Parietal Eyes and Its Implication in UV-Sensitivity in Vertebrate Pineal-Related Organs

The pineal-related organs of lower vertebrates have the ability to discriminate different wavelengths of light. This wavelength discrimination is achieved through antagonistic light responses to UV or blue and visible light. Previously, we demonstrated that parapinopsin underlies the UV reception in the lamprey pineal organ and identified parapinopsin genes in teleosts and frogs of which the pineal-related organs were reported to discriminate light. In this study, we report the first identification of parapinopsin in the reptile lineage and show its expression in the parietal eye of the green iguana. Spectroscopic analysis revealed that iguana parapinopsin is a UV-sensitive pigment, similar to lamprey parapinopsin. Interestingly, immunohistochemical analyses using antibodies specific to parapinopsin and parietopsin, a parietal eye green-sensitive pigment, revealed that parapinopsin and parietopsin are colocalized in the outer segments of the parietal eye photoreceptor cells in iguanas. These results strongly suggest that parapinopsin underlies the wavelength discrimination involving UV reception in the iguana parietal eye. The current findings support the idea that parapinopsin is a common photopigment underlying the UV-sensitivity in wavelength discrimination of the pineal-related organs found from lampreys to reptiles