Self-Calibrated Warping for Mass Spectra Alignment

With recent advances in mass spectrometry (MS) technologies, it is now possible to study protein profiles over a wide range of molecular weights in small biological specimens. However, MS spectra are usually not aligned or synchronized between samples. To ensure the consistency of the subsequent analysis, spectrum alignment is necessary to align the spectra such that the same biological entity would show up at the same m/z value for different samples. Although a variety of alignment algorithms have been proposed in the past, most of them are developed based on chromatographic data and do not address some of the unique characteristics of the serum or other body fluid MS data. In this work, we propose a self-calibrated warping (SCW) algorithm to address some of the challenges associated with serum MS data alignment. In addition, we compare the proposed algorithm with five existing representative alignment methods using a clinical surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) data set

Signature of mass supply to quiet coronal loops

Aims. The physical implication of large blue shift of Ne viii in the quiet Sun region is investigated in this paper. Methods. We compare the significant Ne viii blue shifts, which are visible as large blue patches on the Doppler-shift map of a middlelatitude quiet-Sun region observed by SUMER, with the coronal magnetic-field structures as reconstructed from a simultaneous photospheric magnetogram by means of a force-free-field extrapolation. Results. We show for the first time that coronal funnels also exist in the quiet Sun. The region studied contains several small funnels that originate from network lanes, expand with height and finally merge into a single wide open-field region. However, the large blue shifts of the Ne viii line are not generally associated with funnels. A comparison between the projections of coronal loops onto the solar x-y-plane and the Ne viii dopplergram indicates that there are some loops that reveal large Ne viii blue shifts in both legs, and some loops with upflow in one and downflow in the other leg. Conclusions. Our results suggest that strong plasma outflow, which can be traced by large Ne viii blue shift, is not necessarily associated with the solar wind originating in coronal funnels but appears to be a signature of mass supply to coronal loops. Under the assumption that the measured Doppler shift of the Ne viii line represents the real outflow velocity of the neon ions being markers of the proton flow, we estimate the mass supply rate to coronal loops to be about 10\^{34} s\^{-1}.Comment: 5 pages, 4 figure

The Influence of Molecular Adsorption on Elongating Gold Nanowires

Using molecular dynamics simulations, we study the impact of physisorbing adsorbates on the structural and mechanical evolution of gold nanowires (AuNWs) undergoing elongation. We used various adsorbate models in our simulations, with each model giving rise to a different surface coverage and mobility of the adsorbed phase. We find that the local structure and mobility of the adsorbed phase remains relatively uniform across all segments of an elongating AuNW, except for the thinning region of the wire where the high mobility of Au atoms disrupts the monolayer structure, giving rise to higher solvent mobility. We analyzed the AuNW trajectories by measuring the ductile elongation of the wires and detecting the presence of characteristic structural motifs that appeared during elongation. Our findings indicate that adsorbates facilitate the formation of high-energy structural motifs and lead to significantly higher ductile elongations. In particular, our simulations result in a large number of monatomic chains and helical structures possessing mechanical stability in excess of what we observe in vacuum. Conversely, we find that a molecular species that interacts weakly (i.e., does not adsorb) with AuNWs worsens the mechanical stability of monatomic chains.Comment: To appear in Journal of Physical Chemistry

Increased Population Prevalence of Low Pertussis Toxin Antibody Levels in Young Children Preceding a Record Pertussis Epidemic in Australia

Background: Cross-sectional serosurveys using IgG antibody to pertussis toxin (IgG-PT) are increasingly being used to estimate trends in recent infection independent of reporting biases. Methods/Principal Findings: We compared the age-specific seroprevalence of various levels of IgG-PT in cross-sectional surveys using systematic collections of residual sera from Australian diagnostic laboratories in 1997/8, 2002 and 2007 with reference to both changes in the pertussis vaccine schedule and the epidemic cycle, as measured by disease notifications. A progressive decline in high-level ($62.5 EU/ml) IgG-PT prevalence from 19 % (95 % CI 16–22%) in 1997/98 to 12 % (95 % CI 11–14%) in 2002 and 5 % (95 % CI 4–6%) in 2007 was consistent with patterns of pertussis notifications in the year prior to each collection. Concomitantly, the overall prevalence of undetectable (,5 EU/ml) levels increased from 17 % (95 % CI 14– 20%) in 1997/98 to 38 % (95 % CI 36–40%) in 2007 but among children aged 1–4 years, from 25 % (95 % CI 17–34%) in 1997/98 to 62 % (95 % CI 56–68%) in 2007. This change followed withdrawal of the 18-month booster dose in 2003 and preceded record pertussis notifications from 2008 onwards. Conclusions/Significance: Population seroprevalence of high levels of IgG-PT is accepted as a reliable indicator of pertussis disease activity over time within and between countries with varying diagnostic practices, especially in unimmunised age groups. Our novel findings suggest that increased prevalence of undetectable IgG-PT is an indicator of waning immunit

The catalytic subunit of the system L1 amino acid transporter (S<i>lc7a5</i>) facilitates nutrient signalling in mouse skeletal muscle

The System L1-type amino acid transporter mediates transport of large neutral amino acids (LNAA) in many mammalian cell-types. LNAA such as leucine are required for full activation of the mTOR-S6K signalling pathway promoting protein synthesis and cell growth. The SLC7A5 (LAT1) catalytic subunit of high-affinity System L1 functions as a glycoprotein-associated heterodimer with the multifunctional protein SLC3A2 (CD98). We generated a floxed Slc7a5 mouse strain which, when crossed with mice expressing Cre driven by a global promoter, produced Slc7a5 heterozygous knockout (Slc7a5+/-) animals with no overt phenotype, although homozygous global knockout of Slc7a5 was embryonically lethal. Muscle-specific (MCK Cre-mediated) Slc7a5 knockout (MS-Slc7a5-KO) mice were used to study the role of intracellular LNAA delivery by the SLC7A5 transporter for mTOR-S6K pathway activation in skeletal muscle. Activation of muscle mTOR-S6K (Thr389 phosphorylation) in vivo by intraperitoneal leucine injection was blunted in homozygous MS-Slc7a5-KO mice relative to wild-type animals. Dietary intake and growth rate were similar for MS-Slc7a5-KO mice and wild-type littermates fed for 10 weeks (to age 120 days) with diets containing 10%, 20% or 30% of protein. In MS-Slc7a5-KO mice, Leu and Ile concentrations in gastrocnemius muscle were reduced by ∼40% as dietary protein content was reduced from 30 to 10%. These changes were associated with >50% decrease in S6K Thr389 phosphorylation in muscles from MS-Slc7a5-KO mice, indicating reduced mTOR-S6K pathway activation, despite no significant differences in lean tissue mass between groups on the same diet. MS-Slc7a5-KO mice on 30% protein diet exhibited mild insulin resistance (e.g. reduced glucose clearance, larger gonadal adipose depots) relative to control animals. Thus, SLC7A5 modulates LNAA-dependent muscle mTOR-S6K signalling in mice, although it appears non-essential (or is sufficiently compensated by e.g. SLC7A8 (LAT2)) for maintenance of normal muscle mass

Facile synthesis of precious-metal single-site catalysts using organic solvents

Single-site catalysts can demonstrate high activity and selectivity in many catalytic reactions. The synthesis of these materials by impregnation from strongly oxidizing aqueous solutions or pH-controlled deposition often leads to low metal loadings or a range of metal species. Here, we demonstrate that simple impregnation of the metal precursors onto activated carbon from a low-boiling-point, low-polarity solvent, such as acetone, results in catalysts with an atomic dispersion of cationic metal species. We show the generality of this method by producing single-site Au, Pd, Ru and Pt catalysts supported on carbon in a facile manner. Single-site Au/C catalysts have previously been validated commercially to produce vinyl chloride, and here we show that this facile synthesis method can produce effective catalysts for acetylene hydrochlorination in the absence of the highly oxidizing acidic solvents previously used

Laplace Operators on Fractals and Related Functional Equations

We give an overview over the application of functional equations, namely the classical Poincar\'e and renewal equations, to the study of the spectrum of Laplace operators on self-similar fractals. We compare the techniques used to those used in the euclidean situation. Furthermore, we use the obtained information on the spectral zeta function to define the Casimir energy of fractals. We give numerical values for this energy for the Sierpi\'nski gasket