Landscape phage, phage display, stripped phage, biosensors, detection, affinity reagent, nanotechnology, Salmonella typhimurium, Bacillus anthracis

Filamentous phage, such as fd used in this study, are thread-shaped bacterial viruses. Their outer coat is a tube formed by thousands equal copies of the major coat protein pVIII. We constructed libraries of random peptides fused to all pVIII domains and selected phages that act as probes specific for a panel of test antigens and biological threat agents. Because the viral carrier is infective, phage borne bio-selective probes can be cloned individually and propagated indefinitely without needs of their chemical synthesis or reconstructing. We demonstrated the feasibility of using landscape phages and their stripped fusion proteins as new bioselective materials that combine unique characteristics of affinity reagents and self assembling membrane proteins. Biorecognition layers fabricated from phage-derived probes bind biological agents and generate detectable signals. The performance of phage-derived materials as biorecognition films was illustrated by detection of streptavidin-coated beads, Bacillus anthracis spores and Salmonella typhimurium cells. With further refinement, the phage-derived analytical platforms for detecting and monitoring of numerous threat agents may be developed, since the biodetector films may be obtained from landscape phages selected against any bacteria, virus or toxin. As elements of field-use detectors, they are superior to antibodies, since they are inexpensive, highly specific and strong binders, resistant to high temperatures and environmental stresses.Comment: Submitted on behalf of TIMA Editions (http://irevues.inist.fr/tima-editions

New X-ray Clusters in the EMSS I: Modifications to the XLF

The complete ensemble of Einstein Imaging Proportional Counter (IPC) X-ray images has been re-processed and re-analyzed using a multi-aperture source detection algorithm. A catalog of 772 new source candidates detected within the central regions of the 1435 IPC fields comprising the Extended Medium Sensitivity Survey (EMSS) has been compiled. By comparison, 478 EMSS sources fall within the same area of sky. A randomly-selected subsample of 133 fields was first examined. We found that most of these sources are either the summation of two or more lower count rate point sources that fall within the larger detection apertures or are single point sources, while \leq 2.3% of the full catalog of sources are extrapolated to be actual distant (z > 0.14) clusters whose extended X-ray structure kept them from being detected in the EMSS despite having sufficient total flux. We then constructed other subsamples specifically selected to contain those X-ray sources most likely to be clusters. Both a database search and an optical imaging campaign have found several new distant clusters, setting a firm lower limit on the number of new clusters in the entire catalog. We estimate that the original EMSS cluster sample is 72-83% complete. We update the Henry et al. 1992 EMSS distant cluster sample with more recent information, and use the redshifts and X-ray luminosities for these new EMSS clusters to compute a revised X-ray Luminosity Function (XLF). The addition of these new high-z, high-L_X clusters to the EMSS is sufficient to remove the requirement for ``negative'' evolution at high-L_X out to z~0.5. We conclude that the EMSS has systematically missed clusters of low surface brightness.Comment: Accepted to ApJ, 32 pages, 8 figures, uses emulateapj5.sty, for associated data table see http://casa.colorado.edu/~lewisad/research/nemsscatalog.htm

Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.

Multi-omics datasets can provide molecular insights beyond the sum of individual omics. Various tools have been recently developed to integrate such datasets, but there are limited strategies to systematically extract mechanistic hypotheses from them. Here, we present COSMOS (Causal Oriented Search of Multi-Omics Space), a method that integrates phosphoproteomics, transcriptomics, and metabolomics datasets. COSMOS combines extensive prior knowledge of signaling, metabolic, and gene regulatory networks with computational methods to estimate activities of transcription factors and kinases as well as network-level causal reasoning. COSMOS provides mechanistic hypotheses for experimental observations across multi-omics datasets. We applied COSMOS to a dataset comprising transcriptomics, phosphoproteomics, and metabolomics data from healthy and cancerous tissue from eleven clear cell renal cell carcinoma (ccRCC) patients. COSMOS was able to capture relevant crosstalks within and between multiple omics layers, such as known ccRCC drug targets. We expect that our freely available method will be broadly useful to extract mechanistic insights from multi-omics studies

An Explanation for the rho-pi Puzzle of J/psi and psi' Decays

We propose a new explanation for the longstanding puzzle of the tiny branching fraction of psi' -> rho pi relative to that for J/psi -> rho pi. In the case of J/psi, we argue that this decay is dominated by a higher Fock state in which the ccbar pair is in a color-octet ^3S_1 state and via annihilate process ccbar -> qqbar. In the case of the psi', we argue that the probability for the ccbar pair in this higher Fock state to be close enough to annihilate is suppressed by a dynamical effect related to the small energy gap between the mass of the psi' and the DDbar threshold.Comment: 9 pages, cut the paper, small change to the discussion about psi' suppresion mechanis

The Generation R Study Biobank: a resource for epidemiological studies in children and their parents

The Generation R Study is a population-based prospective cohort study from fetal life until young adulthood. The study is designed to identify early environmental and genetic causes of normal and abnormal growth, development and health from fetal life until young adulthood. In total, 9,778 mothers were enrolled in the study. Prenatal and postnatal data collection is conducted by physical examinations, questionnaires, interviews, ultrasound examinations and biological samples. Major efforts have been conducted for collecting biological specimens including DNA, blood for phenotypes and urine samples. In this paper, the collection, processing and storage of these biological specimens are described. Together with detailed phenotype measurements, these biological specimens form a unique resource for epidemiological studies focused on environmental exposures, genetic determinants and their interactions in relation to growth, health and development from fetal life onwards

Association of sickle cell trait with β-cell dysfunction and physical activity in adults living with and without HIV in Tanzania.

This study aimed to investigate sickle cell trait (SCT) associations with physical activity, markers of insulin secretion and resistance, and glucose among people living with HIV infection (PLWH), both antiretroviral therapy (ART) naive and experienced, and HIV-uninfected adults. This was a cross-sectional study conducted in Mwanza, Northwestern Tanzania. We used data of 668 participants attained from two sub-studies of CICADA study. Mean age was 40 (SD 11.5) years, 402 (61.7%) were females and 157 (24.1%) had SCT. PLWH were 422 (64.7%), of these, 80 (18.9%) were on ART. People with SCT had higher risk of having an isolated β-cell dysfunction compared to those without SCT (RRR = 1.82, CI: 1.10, 3.01, p = 0.02). People with SCT but without HIV infection had lower average acceleration on the trunk longitudinal axis (ACCx) and higher level of self-reported physical activity. 30 min oral glucose tolerance test among PLWH on ART was higher in those with SCT compared to those without SCT. People with SCT are at higher risk of having β-cell dysfunction and those with SCT on ART are at more risk of developing diabetes. Future studies to investigate the interaction between SCT and HIV/ART on risk of diabetes should be considered

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo

Optimization of the Observing Cadence for the Rubin Observatory Legacy Survey of Space and Time: A Pioneering Process of Community-focused Experimental Design

© 2021. The Author(s). Published by the American Astronomical Society. This work may be used under the terms of the Creative Commons Attribution 4.0 licence. https://creativecommons.org/licenses/by/4.0/Vera C. Rubin Observatory is a ground-based astronomical facility under construction, a joint project of the National Science Foundation and the U.S. Department of Energy, designed to conduct a multipurpose 10 yr optical survey of the Southern Hemisphere sky: the Legacy Survey of Space and Time. Significant flexibility in survey strategy remains within the constraints imposed by the core science goals of probing dark energy and dark matter, cataloging the solar system, exploring the transient optical sky, and mapping the Milky Way. The survey’s massive data throughput will be transformational for many other astrophysics domains and Rubin’s data access policy sets the stage for a huge community of potential users. To ensure that the survey science potential is maximized while serving as broad a community as possible, Rubin Observatory has involved the scientific community at large in the process of setting and refining the details of the observing strategy. The motivation, history, and decision-making process of this strategy optimization are detailed in this paper, giving context to the science-driven proposals and recommendations for the survey strategy included in this Focus Issue.Peer reviewedFinal Published versio

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie