DART-ID increases single-cell proteome coverage.

Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce the number of confidently sequenced peptides. To alleviate this reduction, we developed Data-driven Alignment of Retention Times for IDentification (DART-ID). DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches. When applied to bulk or to single-cell samples, DART-ID increased the number of data points by 30-50% at 1% FDR, and thus decreased missing data. Benchmarks indicate excellent quantification of peptides upgraded by DART-ID and support their utility for quantitative analysis, such as identifying cell types and cell-type specific proteins. The additional datapoints provided by DART-ID boost the statistical power and double the number of proteins identified as differentially abundant in monocytes and T-cells. DART-ID can be applied to diverse experimental designs and is freely available at http://dart-id.slavovlab.net

Limitation of network inhomogeneity in improving cooperation in coevolutionary dynamics

Cooperative behavior is common in nature even if selfishness is sometimes better for an individual. Empirical and theoretical studies have shown that the invasion and expansion of cooperators are related to an inhomogeneous connectivity distribution. Here we study the evolution of cooperation on an adaptive network, in which an individual is able to avoid being exploited by rewiring its link(s). Our results indicate that the broadening of connectivity distribution is not always beneficial for cooperation. Compared with the Poisson-like degree distribution, the exponential-like degree distribution is detrimental to the occurrence of a higher level of cooperation in the continuous snowdrift game (CSG)

Application of Ferrite Nanomaterial in RF On-Chip Inductors

Several kinds of ferrite-integrated on-chip inductors are presented. Ferrite nanomaterial applied in RF on-chip inductors is prepared and analyzed to show the properties of high permeability, high ferromagnetic resonance frequency, high resistivity, and low loss, which has the potential that will improve the performance of RF on-chip inductors. Simulations of different coil and ferrite nanomaterial parameters, inductor structures, and surrounding structures are also conducted to achieve the trend of gains of inductance and quality factor of on-chip inductors. By integrating the prepared ferrite magnetic nanomaterial to the on-chip inductors with different structures, the measurement performances show an obvious improvement even in GHz frequency range. In addition, the studies of CMOS compatible process to integrate the nanomaterial promote the widespread application of magnetic nanomaterial in RF on-chip inductors

Cavity of Molecular Gas Associated with Supernova Remnant 3C 397

3C 397 is a radio and X-ray bright Galactic supernova remnant (SNR) with an unusual rectangular morphology. Our CO observation obtained with the Purple Mountain Observatory at Delingha reveals that the remnant is well confined in a cavity of molecular gas, and embedded at the edge of a molecular cloud (MC) at the local standard of rest systemic velocity of ~32 km/s. The cloud has a column density gradient increasing from southeast to northwest, perpendicular to the Galactic plane, in agreement with the elongation direction of the remnant. This systemic velocity places the cloud and SNR 3C 397 at a kinematic distance of ~10.3 kpc. The derived mean molecular density (~10-30 cm^-3) explains the high volume emission measure of the X-ray emitting gas. A 12CO line broadening of the ~32 km/s component is detected at the westmost boundary of the remnant, which provides direct evidence of the SNR-MC interaction and suggests multi-component gas there with dense (~10^4 cm^-3) molecular clumps. We confirm the previous detection of a MC at ~38 km/s to the west and south of the SNR and argue, based on HI self-absorption, that the cloud is located in the foreground of the remnant. A list of Galactic SNRs presently known and suggested to be in physical contact with environmental MCs is appended in this paper.Comment: ApJ in press, 11 pages, 8 figures and 2 tables. A list of Galactic SNRs in physical contact with molecular clouds is included; it is updated in Ver.

MobiCeal: Towards secure and practical plausibly deniable encryption on mobile devices

National Research Foundation (NRF) Singapor

A population of isolated hard X-ray sources near the supernova remnant Kes 69

Recent X-ray observations of the supernova remnant IC443 interacting with molecular clouds have shown the presence of a new population of hard X-ray sources related to the remnant itself, which has been interpreted in terms of fast ejecta fragment propagating inside the dense environment. Prompted by these studies, we have obtained a deep {\sl XMM-Newton} observation of the supernova remnant (SNR) Kes 69, which also shows signs of shock-cloud interaction. We report on the detection of 18 hard X-ray sources in the field of Kes 69, a significant excess of the expected galactic source population in the field, spatially correlated with CO emission from the cloud in the remnant environment. The spectra of 3 of the 18 sources can be described as hard power laws with photon index <2 plus line emission associated to K-shell transitions. We discuss the two most promising scenarios for the interpretation of the sources, namely fast ejecta fragments (as in IC443) and cataclysmic variables. While most of the observational evidences are consistent with the former interpretation, we cannot rule out the latter.Comment: 9 pages, 5 figures, A&A in pres

Cooperation in the snowdrift game on directed small-world networks under self-questioning and noisy conditions

Cooperation in the evolutionary snowdrift game with a self-questioning updating mechanism is studied on annealed and quenched small-world networks with directed couplings. Around the payoff parameter value $r=0.5$, we find a size-invariant symmetrical cooperation effect. While generally suppressing cooperation for $r>0.5$ payoffs, rewired networks facilitated cooperative behavior for $r<0.5$. Fair amounts of noise were found to break the observed symmetry and further weaken cooperation at relatively large values of $r$. However, in the absence of noise, the self-questioning mechanism recovers symmetrical behavior and elevates altruism even under large-reward conditions. Our results suggest that an updating mechanism of this type is necessary to stabilize cooperation in a spatially structured environment which is otherwise detrimental to cooperative behavior, especially at high cost-to-benefit ratios. Additionally, we employ component and local stability analyses to better understand the nature of the manifested dynamics.Comment: 7 pages, 6 figures, 1 tabl

The <i>Phytophthora infestans</i> Haustorium Is a Site for Secretion of Diverse Classes of Infection-Associated Proteins

We are grateful to the China Scholarship Council for funds to support S.W. and to the Biotechnology and Biological Sciences Research Council (BBSRC) (grants BB/N009967/1, BB/L026880/1, and BB/J016500/1) and the Scottish Government Rural and Environment Science and Analytical Services Division (RESAS) for funding provided to P.R.J.B., P.C.B., L.W., and S.C.W.The oomycete potato blight pathogen Phytophthora infestans secretes a diverse set of proteins to manipulate host plant immunity. However, there is limited knowledge about how and where they are secreted during infection. Here we used the endoplasmic reticulum (ER)-to-Golgi secretion pathway inhibitor brefeldin A (BFA) in combination with liquid chromatography-electrospray tandem mass spectrometry (LC-MS/MS) to identify extracellular proteins from P. infestans that were conventionally secreted from in vitro-cultured hyphae. We identified 19 proteins with predicted signal peptides that potentially influence plant interactions for which secretion was attenuated by BFA. In addition to inhibition by the apoplastic effector EPIC1, a cysteine protease inhibitor, we show that secretion of the cell wall-degrading pectinesterase enzyme PE1 and the microbe-associated molecular pattern (MAMP)-like elicitin INF4 was inhibited by BFA in vitro and in planta, demonstrating that these proteins are secreted by the conventional, Golgi-mediated pathway. For comparison, secretion of a cytoplasmic RXLR (Arg-[any amino acid]-Leu-Arg) effector, Pi22926, was not inhibited by BFA. During infection, whereas INF4 accumulated outside the plant cell, RXLR effector Pi22926 entered the plant cell and accumulated in the nucleus. The P. infestans effectors, the PE1 enzyme, and INF4 were all secreted from haustoria, pathogen structures that penetrate the plant cell wall to form an intimate interaction with the host plasma membrane. Our findings show the haustorium to be a major site of both conventional and nonconventional secretion of proteins with diverse functions during infection.Publisher PDFPeer reviewe

Drops in Space: Super Oscillations and Surfactant Studies

An unprecedented microgravity observation of maximal shape oscillations of a surfactant-bearing water drop the size of a ping pong ball was observed during a mission of Space Shuttle Columbia as part of the second United States Microgravity Laboratory-USML-2 (STS-73, October 20-November 5, 1995). The observation was precipitated by the action of an intense sound field which produced a deforming force on the drop. When this deforming force was suddenly reduced, the drop executed nearly free and axisymmetric oscillations for several cycles, demonstrating a remarkable amplitude of nonlinear motion. Whether arising from the discussion of modes of oscillation of the atomic nucleus, or the explosion of stars, or how rain forms, the complex processes influencing the motion, fission, and coalescence of drops have fascinated scientists for centuries. Therefore, the axisymmetric oscillations of a maximally deformed liquid drop are noteworthy, not only for their scientific value but also for their aesthetic character. Scientists from Yale University, the Jet Propulsion Laboratory (JPL) and Vanderbilt University conducted liquid drop experiments in microgravity using the acoustic positioning/manipulation environment of the Drop Physics Module (DPM). The Yale/JPL group's objectives were to study the rheological properties of liquid drop surfaces on which are adsorbed surfactant molecules, and to infer surface properties such as surface tension, Gibb's elasticity, and surface dilatational viscosity by using a theory which relies on spherical symmetry to solve the momentum and mass transport equations