An Improved Interactive Streaming Algorithm for the Distinct Elements Problem

The exact computation of the number of distinct elements (frequency moment $F_0$) is a fundamental problem in the study of data streaming algorithms. We denote the length of the stream by $n$ where each symbol is drawn from a universe of size $m$. While it is well known that the moments $F_0,F_1,F_2$ can be approximated by efficient streaming algorithms, it is easy to see that exact computation of $F_0,F_2$ requires space $\Omega(m)$. In previous work, Cormode et al. therefore considered a model where the data stream is also processed by a powerful helper, who provides an interactive proof of the result. They gave such protocols with a polylogarithmic number of rounds of communication between helper and verifier for all functions in NC. This number of rounds $\left(O(\log^2 m) \;\text{in the case of} \;F_0 \right)$ can quickly make such protocols impractical. Cormode et al. also gave a protocol with $\log m +1$ rounds for the exact computation of $F_0$ where the space complexity is $O\left(\log m \log n+\log^2 m\right)$ but the total communication $O\left(\sqrt{n}\log m\left(\log n+ \log m \right)\right)$. They managed to give $\log m$ round protocols with $\operatorname{polylog}(m,n)$ complexity for many other interesting problems including $F_2$, Inner product, and Range-sum, but computing $F_0$ exactly with polylogarithmic space and communication and $O(\log m)$ rounds remained open. In this work, we give a streaming interactive protocol with $\log m$ rounds for exact computation of $F_0$ using $O\left(\log m \left(\,\log n + \log m \log\log m\,\right)\right)$ bits of space and the communication is $O\left( \log m \left(\,\log n +\log^3 m (\log\log m)^2 \,\right)\right)$. The update time of the verifier per symbol received is $O(\log^2 m)$.Comment: Submitted to ICALP 201

EPIC 219217635: A Doubly Eclipsing Quadruple System Containing an Evolved Binary

We have discovered a doubly eclipsing, bound, quadruple star system in the field of K2 Campaign 7. EPIC 219217635 is a stellar image with $Kp = 12.7$ that contains an eclipsing binary (`EB') with $P_A = 3.59470$ d and a second EB with $P_B = 0.61825$ d. We have obtained followup radial-velocity (`RV') spectroscopy observations, adaptive optics imaging, as well as ground-based photometric observations. From our analysis of all the observations, we derive good estimates for a number of the system parameters. We conclude that (1) both binaries are bound in a quadruple star system; (2) a linear trend to the RV curve of binary A is found over a 2-year interval, corresponding to an acceleration, $\dot \gamma = 0.0024 \pm 0.0007$ cm s$^{-2}$; (3) small irregular variations are seen in the eclipse-timing variations (`ETVs') detected over the same interval; (4) the orbital separation of the quadruple system is probably in the range of 8-25 AU; and (5) the orbital planes of the two binaries must be inclined with respect to each other by at least 25$^\circ$. In addition, we find that binary B is evolved, and the cooler and currently less massive star has transferred much of its envelope to the currently more massive star. We have also demonstrated that the system is sufficiently bright that the eclipses can be followed using small ground-based telescopes, and that this system may be profitably studied over the next decade when the outer orbit of the quadruple is expected to manifest itself in the ETV and/or RV curves.Comment: Accepted for publication in MNRA

Investigation of factors influencing the immunogenicity of hCG as a potential cancer vaccine

Human hCG and its β‐subunit (hCGβ) are tumour autocrine growth factors whose presence in the serum of cancer patients has been linked to poorer prognosis. Previous studies have shown that vaccines, which target these molecules and/or the 37 amino acid C‐terminal hCGβ peptide (hCGβCTP), induce antibody responses in a majority of human recipients. Here we explored whether the immunogenicity of vaccines containing an hCGβ mutant (hCGβR68E, designed to eliminate cross‐reactivity with luteinizing hormone) or hCGβCTP could be enhanced by coupling the immunogen to different carriers (KLH or Hsp70) using different cross‐linkers (EDC or GAD) and formulated with different adjuvants (RIBI or Montanide ISA720). While there was little to choose between KLH and Hsp70 as carriers, their influence on the effectiveness of a vaccine containing the BAChCGβR68E mutant was less marked, presumably because being a foreign species, this mutant protein itself might provide T‐helper epitopes. The mutant provided a significantly better vaccine than the hCGβCTP peptide irrespective of the carrier used, how it was cross‐linked to the carrier or which adjuvant was used when hCG was the target. Nonetheless, for use in humans where hCG is a tolerated self‐protein, the need for a carrier is of fundamental importance. Highest antibody titres were obtained by linking the BAChCGβR68E to Hsp70 as a carrier by GAD and using RIBI as the adjuvant, which also resulted in antibodies with significantly higher affinity than those elicited by hCGβCTP peptide vaccine. This makes this mutant vaccine a promising candidate for therapeutic studies in hCGβ‐positive cancer patients

The optimization and validation of the Biotyper MALDI-TOF MS database for the identification of Gram-positive anaerobic cocci

OBJECTIVES: Gram-positive anaerobic cocci (GPAC) account for 24-31% of the anaerobic bacteria isolated from human clinical specimens. At present GPAC are underrepresented in the Biotyper MALDI-TOF MS database. Profiles of new species have yet to be added. We present the optimization of the MALDI-TOF MS database for the identification of GPAC. METHODS: Main Spectral Profiles (MSPs) were created for 108 clinical GPAC isolates. Identity was confirmed using 16S rRNA gene sequencing. Species identification was considered to be reliable if the sequence similarity with its closest relative was ≥98.7%. The optimized database was validated using 140 clinical isolates. The 16S rRNA sequencing identity was compared with the MALDI-TOF MS result. RESULTS: MSPs were added from 17 species that were not yet represented in the MALDI-TOF MS database or were underrepresented (<5 MSPs). This resulted in an increase from 53.6% (75/140) to 82.1% (115/140) of GPAC isolates that could be identified at the species level using MALDI-TOF MS. An improved log score was obtained for 51.4% (72/140) of the strains. For strains with a sequence similarity <98.7% with their closest relative (n=5) or with an inconclusive sequence identity (n=4), no identification was obtained by MALDI-TOF MS or in the latter case an identity with one of its relatives. CONCLUSIONS: For some species the MSP of the type strain was not a part of the confined cluster of the corresponding clinical isolates. Also, not all species formed a homogeneous cluster. It emphasizes the necessity of adding sufficient MSPs of human clinical isolates

Interferometric diameters of five evolved intermediate-mass planet-hosting stars measured with PAVO at the CHARA Array

Debate over the planet occurrence rates around intermediate-mass stars has hinged on the accurate determination of masses of evolved stars, and has been exacerbated by a paucity of reliable, directly measured fundamental properties for these stars. We present long-baseline optical interferometry of five evolved intermediate-mass (∼ 1.5 M⊙) planet-hosting stars using the PAVO beam combiner at the CHARA Array, which we combine with bolometric flux measurements and parallaxes to determine their radii and effective temperatures. We measured the radii and effective temperatures of 6 Lyncis (5.12 ± 0.16 R⊙, 4949 ± 58 K), 24 Sextantis (5.49 ± 0.18 R⊙, 4908 ± 65 K), κ Coronae Borealis (4.77 ± 0.07 R⊙, 4870 ± 47 K), HR 6817 (4.45 ± 0.08 R⊙, 5013 ± 59 K), and HR 8461 (4.91 ± 0.12 R⊙, 4950 ± 68 K). We find disagreements of typically 15  per cent in angular diameter and ∼200 K in temperature compared to interferometric measurements in the literature, yet good agreement with spectroscopic and photometric temperatures, concluding that the previous interferometric measurements may have been affected by systematic errors exceeding their formal uncertainties. Modelling based on BaSTI isochrones using various sets of asteroseismic, spectroscopic, and interferometric constraints tends to favour slightly (∼15  per cent) lower masses than generally reported in the literature.Funding for the Stellar Astrophysics Centre is provided by The Danish National Research Foundation. The research was supported by the ASTERISK project (ASTERoseismic Investigations with SONG and Kepler) funded by the European Research Council (Grant agreement no.: 267864). TRW and VSA acknowledge the support of the Villum Foundation (research grant 10118). DH acknowledges support by the Australian Research Council’s Discovery Projects funding scheme (project number DE140101364) and support by the NASA Grant NNX14AB92G issued through the Kepler Participating Scientist Program. LC is supported by the Australian Research Council Future Fellowship FT160100402. MJI was supported by the Australian Research Council Future Fellowship FT130100235. Parts of this research were conducted by the Australian Research Council Centre of Excellence for All Sky Astrophysics in 3 Dimensions (ASTRO 3D), through project number CE170100013

A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS

Inter-laboratory reproducibility of Matrix Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of anaerobic bacteria has not been shown before. Therefore, ten anonymized anaerobic strains were sent to seven participating laboratories, an initiative of the European Network for the Rapid Identification of Anaerobes (ENRIA). On arrival the strains were cultured and identified using MALDI-TOF MS. The spectra derived were compared with two different Biotyper MALDI-TOF MS databases, the db5627 and the db6903. The results obtained using the db5627 shows a reasonable variation between the different laboratories. However, when a more optimized database is used, the variation is less pronounced. In this study we show that an optimized database not only results in a higher number of strains which can be identified using MALDI-TOF MS, but also corrects for differences in performance between laboratories. (C) 2017 Elsevier Ltd. All rights reserved

Input-state-output representations and constructions of finite-support 2D convolutional codes

Two-dimensional convolutional codes are considered, with codewords having compact support indexed in N^2 and taking values in F^n, where F is a finite field. Input-state-output representations of these codes are introduced and several aspects of such representations are discussed. Constructive procedures of such codes with a designed distance are also presented. © 2010 AIMS-SDU

HLA Class I Binding 9mer Peptides from Influenza A Virus Induce CD4+ T Cell Responses

BACKGROUND: Identification of human leukocyte antigen class I (HLA-I) restricted cytotoxic T cell (CTL) epitopes from influenza virus is of importance for the development of new effective peptide-based vaccines. METHODOLOGY/PRINCIPAL FINDINGS: In the present work, bioinformatics was used to predict 9mer peptides derived from available influenza A viral proteins with binding affinity for at least one of the 12 HLA-I supertypes. The predicted peptides were then selected in a way that ensured maximal coverage of the available influenza A strains. One hundred and thirty one peptides were synthesized and their binding affinities for the HLA-I supertypes were measured in a biochemical assay. Influenza-specific T cell responses towards the peptides were quantified using IFNgamma ELISPOT assays with peripheral blood mononuclear cells (PBMC) from adult healthy HLA-I typed donors as responder cells. Of the 131 peptides, 21 were found to induce T cell responses in 19 donors. In the ELISPOT assay, five peptides induced responses that could be totally blocked by the pan-specific anti-HLA-I antibody W6/32, whereas 15 peptides induced responses that could be completely blocked in the presence of the pan-specific anti-HLA class II (HLA-II) antibody IVA12. Blocking of HLA-II subtype reactivity revealed that 8 and 6 peptide responses were blocked by anti-HLA-DR and -DP antibodies, respectively. Peptide reactivity of PBMC depleted of CD4(+) or CD8(+) T cells prior to the ELISPOT culture revealed that effectors are either CD4(+) (the majority of reactivities) or CD8(+) T cells, never a mixture of these subsets. Three of the peptides, recognized by CD4(+) T cells showed binding to recombinant DRA1*0101/DRB1*0401 or DRA1*0101/DRB5*0101 molecules in a recently developed biochemical assay. CONCLUSIONS/SIGNIFICANCE: HLA-I binding 9mer influenza virus-derived peptides induce in many cases CD4(+) T cell responses restricted by HLA-II molecules