The ADMM Penalized Decoder for LDPC Codes Liu, Xishuo; Draper, Stark C.
IEEE transactions on information theory,
2016-June, 2016-6-00, 20160601, Volume:
62, Issue:
6
Journal Article
Peer reviewed
Open access
Linear programming (LP) decoding for low-density parity-check codes was introduced by Feldman et al. and has been shown to have theoretical guarantees in several regimes. Furthermore, it has been ...reported in the literature-via simulation and via instanton analysis-that LP decoding displays better error rate performance at high signal-to-noise ratios (SNR) than does belief propagation (BP) decoding. However, at low SNRs, LP decoding is observed to have worse performance than BP. In this paper, we seek to improve LP decoding at low SNRs while maintaining LP decoding's high SNR performance. Our main contribution is a new class of decoders obtained by applying the alternating direction method of multipliers (ADMM) algorithm to a set of non-convex optimization problems. These non-convex problems are constructed by adding a penalty term to the objective of LP decoding. The goal of the penalty is to make pseudocodewords, which are non-integer vertices of the LP relaxation, more costly. We name this class of decoders-ADMM penalized decoders. For low and moderate SNRs, we simulate ADMM penalized decoding with ℓ 1 and ℓ 2 penalties. We find that these decoders can outperform both BP and LP decoding. For high SNRs, where it is difficult to obtain data via simulation, we use an instanton analysis and find that, asymptotically, ADMM penalized decoding performs better than BP but not as well as LP. Unfortunately, since ADMM penalized decoding is not a convex program, we have not been successful in developing theoretical guarantees. However, the non-convex program can be approximated using a sequence of linear programs; an approach that yields a reweighted LP decoder. We show that a two-round reweighted LP decoder has an improved theoretical recovery threshold when compared with LP decoding. In addition, we find via simulation that reweighted LP decoding significantly attains lower error rates than LP decoding at low SNRs.
Cell-free protein synthesis (CFPS) technologies have enabled inexpensive and rapid recombinant protein expression. Numerous highly active CFPS platforms are now available and have recently been used ...for synthetic biology applications. In this review, we focus on the ability of CFPS to expand our understanding of biological systems and its applications in the synthetic biology field. First, we outline a variety of CFPS platforms that provide alternative and complementary methods for expressing proteins from different organisms, compared with in vivo approaches. Next, we review the types of proteins, protein complexes, and protein modifications that have been achieved using CFPS systems. Finally, we introduce recent work on genetic networks in cell-free systems and the use of cell-free systems for rapid prototyping of in vivo networks. Given the flexibility of cell-free systems, CFPS holds promise to be a powerful tool for synthetic biology as well as a protein production technology in years to come.
The emerging discipline of bacterial glycoengineering has made it possible to produce designer glycans and glycoconjugates for use as vaccines and therapeutics. Unfortunately, cell-based production ...of homogeneous glycoproteins remains a significant challenge due to cell viability constraints and the inability to control glycosylation components at precise ratios in vivo. To address these challenges, we describe a novel cell-free glycoprotein synthesis (CFGpS) technology that seamlessly integrates protein biosynthesis with asparagine-linked protein glycosylation. This technology leverages a glyco-optimized Escherichia coli strain to source cell extracts that are selectively enriched with glycosylation components, including oligosaccharyltransferases (OSTs) and lipid-linked oligosaccharides (LLOs). The resulting extracts enable a one-pot reaction scheme for efficient and site-specific glycosylation of target proteins. The CFGpS platform is highly modular, allowing the use of multiple distinct OSTs and structurally diverse LLOs. As such, we anticipate CFGpS will facilitate fundamental understanding in glycoscience and make possible applications in on demand biomanufacturing of glycoproteins.
Exocometary Gas in the HD 181327 Debris Ring Marino, S.; Matra, L.; Stark, C. ...
Monthly notices of the Royal Astronomical Society,
08/2016, Volume:
460, Issue:
3
Journal Article
Peer reviewed
Open access
An increasing number of observations have shown that gaseous debris discs are not an exception. However, until now, we only knew of cases around A stars. Here we present the first detection of 12CO ...(2-1) disc emission around an F star, HD 181327, obtained with the Atacama Large Millimeter/submillimeter Array (ALMA) observations at 1.3 mm. The continuum and CO emission are resolved into an axisymmetric disc with ring-like morphology. Using a Markov chain Monte Carlo method coupled with radiative transfer calculations, we study the dust and CO mass distribution. We find the dust is distributed in a ring with a radius of 86.0 +/- 0.4 au and a radial width of 23.2 +/- 1.0 au. At this frequency, the ring radius is smaller than in the optical, revealing grain size segregation expected due to radiation pressure. We also report on the detection of low-level continuum emission beyond the main ring out to approximately 200 au. We model the CO emission in the non-local thermodynamic equilibrium regime and we find that the CO is co-located with the dust, with a total CO gas mass ranging between 1.2 x 10(exp -6) solar mass and 2.9 x 10(exp -6) solar mass, depending on the gas kinetic temperature and collisional partners densities. The CO densities and location suggest a secondary origin, i.e. released from icy planetesimals in the ring. We derive a CO+CO2 cometary composition that is consistent with Solar system comets. Due to the low gas densities, it is unlikely that the gas is shaping the dust distribution.
Microbially Mediated Plant Functional Traits Friesen, Maren L; Porter, Stephanie S; Stark, Scott C ...
Annual review of ecology, evolution, and systematics,
01/2011, Volume:
42, Issue:
1
Journal Article
Peer reviewed
Plants are rife with bacteria and fungi that colonize roots and shoots both externally and internally. By providing novel nutritional and defense pathways and influencing plant biochemical pathways, ...microbes can fundamentally alter plant phenotypes. Here we review the widespread nature of microbially mediated plant functional traits. We highlight that there is likely fitness conflict between hosts and symbionts and that fitness outcomes can depend on partner genotypes and ecological factors. Microbes may influence ecosystems through their effects on the functional trait values and population dynamics of their plant hosts. These effects may feed back on symbiont evolution by altering transmission rates of symbionts and scale up to ecosystem processes and services. We end by proposing new avenues of research in this emerging field.
Summary
An increasing variety of indicators of antimicrobial usage has become available in human and veterinary medicine, with no consensus on the most appropriate indicators to be used. The ...objective of this review is therefore to provide guidance on the selection of indicators, intended for those aiming to quantify antimicrobial usage based on sales, deliveries or reimbursement data. Depending on the study objective, different requirements apply to antimicrobial usage quantification in terms of resolution, comprehensiveness, stability over time, ability to assess exposure and comparability. If the aim is to monitor antimicrobial usage trends, it is crucial to use a robust quantification system that allows stability over time in terms of required data and provided output; to compare usage between different species or countries, comparability must be ensured between the different populations. If data are used for benchmarking, the system comprehensiveness is particularly crucial, while data collected to study the association between usage and resistance should express the exposure level and duration as a measurement of the exerted selection pressure. Antimicrobial usage is generally described as the number of technical units consumed normalized by the population at risk of being treated in a defined period. The technical units vary from number of packages to number of individuals treated daily by adding different levels of complexity such as daily dose or weight at treatment. These technical units are then related to a description of the population at risk, based either on biomass or number of individuals. Conventions and assumptions are needed for all of these calculation steps. However, there is a clear lack of standardization, resulting in poor transparency and comparability. By combining study requirements with available approaches to quantify antimicrobial usage, we provide suggestions on the most appropriate indicators and data sources to be used for a given study objective.
When binary linear error-correcting codes are used over symmetric channels, a relaxed version of the maximum likelihood decoding problem can be stated as a linear program (LP). This LP decoder can be ...used to decode error-correcting codes at bit-error-rates comparable to state-of-the-art belief propagation (BP) decoders, but with significantly stronger theoretical guarantees. However, LP decoding when implemented with standard LP solvers does not easily scale to the block lengths of modern error correcting codes. In this paper, we draw on decomposition methods from optimization theory, specifically the alternating direction method of multipliers (ADMM), to develop efficient distributed algorithms for LP decoding. The key enabling technical result is a "two-slice" characterization of the parity polytope, the polytope formed by taking the convex hull of all codewords of the single parity check code. This new characterization simplifies the representation of points in the polytope. Using this simplification, we develop an efficient algorithm for Euclidean norm projection onto the parity polytope. This projection is required by the ADMM decoder and its solution allows us to use LP decoding, with all its theoretical guarantees, to decode large-scale error correcting codes efficiently. We present numerical results for LDPC codes of lengths more than 1000. The waterfall region of LP decoding is seen to initiate at a slightly higher SNR than for sum-product BP, however an error floor is not observed for LP decoding, which is not the case for BP. Our implementation of LP decoding using the ADMM executes as fast as our baseline sum-product BP decoder, is fully parallelizable, and can be seen to implement a type of message-passing with a particularly simple schedule.
We sought to identify a usable biomarker from blood samples to characterize early-stage Alzheimer's disease (AD) patients, in order to facilitate rapid diagnosis, early therapeutic intervention, and ...monitoring of clinical trials. We compared metabolites from blood plasma in early-stage Alzheimer's disease patients with blood plasma from healthy controls using two different analytical platforms: Amino Acid Analyzer and Tandem Mass-Spectrometer. Early-stage Alzheimer's patient blood samples were obtained during an FDA-approved Phase IIa clinical trial (Clinicaltrial.gov NCT03062449). Participants included 25 early-stage Alzheimer's patients and 25 healthy controls in the United States. We measured concentrations of 2-aminoethyl dihydrogen phosphate and taurine in blood plasma samples. We found that plasma concentrations of a phospholipid metabolite, 2-aminoethyl dihydrogen phosphate, normalized by taurine concentrations, distinguish blood samples of patients with early-stage AD. This possible new Alzheimer's biomarker may supplement clinical diagnosis for early detection of the disease.
Abstract The Habitable Worlds Observatory Preliminary Input Catalog (HPIC) is a list of ∼13,000 nearby bright stars that will be potential targets for the Habitable Worlds Observatory (HWO) in its ...search for Earth-sized planets around Sun-like stars. We construct this target list using the TESS and Gaia DR3 catalogs and develop an automated pipeline to compile stellar measurements and derived astrophysical properties for all stars. We benchmark the stellar properties in the HPIC relative to those of the manually curated ExEP HWO Precursor Science Stars list and find that, for the 164 best targets for exo-Earth direct imaging, our stellar properties are consistent. We demonstrate the utility of the HPIC by using it as an input for yield calculations to predict the science output of various mission designs, including those with larger telescope diameters and those focused on other planet types besides Earth analogs, such as Jupiter-mass planets. The breadth and completeness of the HPIC is essential for accurate HWO mission trade studies, and it will be useful for other exoplanet studies and general astrophysics studying the population of bright nearby stars.
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