Advanced modulation technology development for earth station demodulator applications. Coded modulation system development

A jointly optimized coded modulation system is described which was designed, built, and tested by COMSAT Laboratories for NASA LeRC which provides a bandwidth efficiency of 2 bits/s/Hz at an information rate of 160 Mbit/s. A high speed rate 8/9 encoder with a Viterbi decoder and an Octal PSK modem are used to achieve this. The BER performance is approximately 1 dB from the theoretically calculated value for this system at a BER of 5 E-7 under nominal conditions. The system operates in burst mode for downlink applications and tests have demonstrated very little degradation in performance with frequency and level offset. Unique word miss rate measurements were conducted which demonstrate reliable acquisition at low values of Eb/No. Codec self tests have verified the performance of this subsystem in a stand alone mode. The codec is capable of operation at a 200 Mbit/s information rate as demonstrated using a codec test set which introduces noise digitally. The measured performance is within 0.2 dB of the computer simulated predictions. A gate array implementation of the most time critical element of the high speed Viterbi decoder was completed. This gate array add-compare-select chip significantly reduces the power consumption and improves the manufacturability of the decoder. This chip has general application in the implementation of high speed Viterbi decoders

Phylogenetic trees and Euclidean embeddings

Thesis (M.S.) University of Alaska Fairbanks, 2014In this thesis we develop an intuitive process of encoding any phylogenetic tree and its associated tree-distance matrix as a collection of points in Euclidean space. Using this encoding, we find that information about the structure of the tree can easily be recovered by applying the inner product operation to vector combinations of the Euclidean points. By applying Classical Scaling to the tree-distance matrix, we are able to find the Euclidean points even when the phylogenetic tree is not known. We use the insight gained by encoding the tree as a collection of Euclidean points to modify the Neighbor Joining Algorithm, a method to recover an unknown phylogenetic tree from its tree-distance matrix, to be more resistant to tree-distance proportional errors

The HemQ coprohaem decarboxylase generates reactive oxygen species: implications for the evolution of classical haem biosynthesis

Bacteria require a haem biosynthetic pathway for the assembly of a variety of protein complexes including cytochromes, peroxidases, globins, and catalase. Haem is synthesised via a series of tetrapyrrole intermediates including non-metallated porphyrins such as protoporphyrin IX, which is well-known to generate reactive oxygen species (ROS) in the presence of light and oxygen. Staphylococcus aureus has an ancient haem biosynthetic pathway that proceeds via the formation of coproporphyrin III, a less reactive porphyrin. Herein, we demonstrate for the first time that HemY of S. aureus is able to generate both protoporphyrin IX and coproporphyrin III, and that the terminal enzyme of this pathway, HemQ, can stimulate the generation of protoporphyrin IX (but not coproporphyrin III). Assays with hydrogen peroxide, horseradish peroxidase, superoxide dismutase, and catalase confirm that this stimulatory effect is mediated by superoxide. Structural modelling reveals that HemQ enzymes do not possess the structural attributes that are common to peroxidases that form compound I [FeIV=O]+, which taken together with the superoxide data leaves Fenton chemistry as a likely route for the superoxide-mediated stimulation of protoporphyrinogen IX oxidase activity of HemY. This generation of toxic free radicals could explain why HemQ enzymes have not been identified in organisms that synthesise haem via the classical protoporphyrin IX pathway. This work has implications for the divergent evolution of haem biosynthesis in ancestral microorganisms and provides new structural and mechanistic insights into a recently discovered oxidative decarboxylase reaction

COMET-Planner: Carbon and Greenhouse Gas Evaluation for USDA-NRCS Conservation Practice Planning

Conservation planners must assess a range of environmental, agronomic and economic impacts of implementing conservation practices on farms. While environmental impacts such as soil erosion control, improved soil quality, reduced nonpoint source pollution and a number of other site-specific benefits are currently considered, conservation practices may also have significant climate benefits, through carbon sequestration and/or reduction of greenhouse gas (GHG) emissions. If conservation planners wish to incorporate greenhouse gas impacts in their planning process, they will need access to quick, easy-to-use tools to assess greenhouse gas impacts of conservation practices on farms. COMET-Planner (www.comet-planner.com) was developed to provide generalized estimates of GHG impacts of adoption of USDA National Resources Conservation Service (NRCS) conservation practice standards in a simple, web-based platform. Conservation scenarios were modeled in COMET-Farm, a whole farm and ranch carbon and greenhouse gas accounting system based on USDA entity-scale quantification methods, across a range of agricultural management, climate and soil types within Major Land Resource Areas (MLRA). Mean carbon sequestration and emission changes (CO2, N2O and CH4) associated with USDA-NRCS conservation practice adoption were estimated by MLRA. Results are provided to users via the web interface and a detailed methods report

The integrated COMET-WQ tool for crop field water quality assessment

A new development of the COMET-Farm platform (originally designed for farm and ranch carbon and greenhouse gas accounting) now includes the APEX (Agricultural Policy / Environmental eXtender) simulation model for water quality assessment at farm/small watershed scale. This web-based tool uses a geospatial graphical user interface (GUI) to help agricultural producers, land managers and other users identify their fields/area of interest and compare the impacts of different management scenarios on nitrogen and phosphorus losses, sediment losses, and crop yields in addition to the carbon and greenhouse gas accounting in the original COMET-Farm decision support tool. The platform provides a number of spatial databases, including for soil, hydrologic, weather, and baseline management conditions, which together with user inputs, are used to build the APEX model inputs and run the model ‘on-the-fly’. The tool simulates the implementation of USDA-NRCS recommended conservation practices (e.g. buffer strips, conservation tillage, improved crop rotations) to estimate environmental benefits and ecosystem services. A case study in the US Corn Belt is used to demonstrate the application of this tool

Comparison of Different Phenotypic Approaches to Screen and Detect mecC-Harboring Methicillin-Resistant Staphylococcus aureus

Similar to mecA, mecC confers resistance against beta-lactams, leading to the phenotype of methicillin-resistant Staphylococcus aureus (MRSA). However, mecC-harboring MRSA strains pose special difficulties in their detection. The aim of this study was to assess and compare different phenotypic systems for screening, identification, and susceptibility testing of mecC-positive MRSA isolates. A well-characterized collection of mecC-positive S. aureus isolates (n 111) was used for evaluation. Routinely used approaches were studied to determine their suitability to correctly identify mecC-harboring MRSA, including three (semi)automated antimicrobial susceptibility testing (AST) systems and five selective chromogenic agar plates. Additionally, a cefoxitin disk diffusion test and an oxacillin broth microdilution assay were examined. All mecC-harboring MRSA isolates were able to grow on all chromogenic MRSA screening plates tested. Detection of these isolates in AST systems based on cefoxitin and/or oxacillin testing yielded overall positive agreements with the mecC genotype of 97.3% (MicroScan WalkAway; Siemens), 91.9% (Vitek 2; bioMérieux), and 64.9% (Phoenix, BD). The phenotypic resistance pattern most frequently observed by AST devices was “cefoxitin resistance/oxacillin susceptibility,” ranging from 54.1% (Phoenix) and 83.8% (Vitek 2) to 92.8% (WalkAway). The cefoxitin disk diffusion and oxacillin broth microdilution assays categorized 100% and 61.3% of isolates to be MRSA, respectively. The chromogenic media tested confirmed their suitability to reliably screen for mecC-harboring MRSA. The AST systems showed false-negative results with varying numbers, misidentifying mecC-harboring MRSA as methicillin-susceptible S. aureus. This study underlines cefoxitin’s status as the superior surrogate mecC-positive MRSA marker.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Tako-tsubo cardiomyopathy after administration of ergometrine following elective caesarean delivery: a case report

<p>Abstract</p> <p>Introduction</p> <p>Tako-tsubo cardiomyopathy (stress-induced cardiomyopathy or transient left ventricular ballooning) is characterized by clinical suspicion of an acute myocardial infarction with transient apical or midventricular dyskinesia of the left ventricle without significant coronary stenosis on angiography. The etiology of this disease remains obscure. One of the possible causes is myocardial ischemia induced by coronary vasospasm due to sympathetic activation. It has been hypothesized that the application of ergometrine could induce tako-tsubo cardiomyopathy.</p> <p>Case presentation</p> <p>We report the case of a 28-year-old Turkish woman who developed tako-tsubo cardiomyopathy after administration of ergometrine for release of placenta and prevention of bleeding during the post-partum phase in the course of an elective caesarean delivery. Tako-tsubo cardiomyopathy was diagnosed by echocardiography and urgent cardiac magnetic resonance imaging. A coronary angiography was not performed because of the absence of myocardial necrosis or ischemia and signs of myocarditis on cardiac magnetic resonance imaging.</p> <p>Conclusion</p> <p>This life-threatening disease should be excluded in the differential diagnosis by comparing the symptoms with those of typical heart failure, particularly after use of ergometrine.</p

Cheddar: analysis and visualisation of ecological communities in R

There has been a lack of software available to ecologists for the management, visualisation and analysis of ecological community and food web data. Researchers have been forced to implement their own data formats and software, often from scratch, resulting in duplicated effort and bespoke solutions that are difficult to apply to future analyses and comparative studies. We introduce Cheddar – an R package that provides standard, transparent implementations of a wide range of food web and community-level analyses and plots, focussing on ecological network data that are augmented with estimates of body mass and/or numerical abundance. The package allows analysis of individual communities, as well as collections of communities, allowing examination of changes in structure through time, across environmental gradients, or due to experimental manipulations. Several commonly analysed food web data sets are included and used in worked examples. This is the first time these important features have been combined in a single package that helps improve research efficiency and serves as a unified framework for future development

Warming reduces trophic diversity in high-latitude food webs.

The physical effects of climate warming have been well documented, but the biological responses are far less well known, especially at the ecosystem level and at large (intercontinental) scales. Global warming over the next century is generally predicted to reduce food web complexity, but this is rarely tested empirically due to the dearth of studies isolating the effects of temperature on complex natural food webs. To overcome this obstacle, we used 'natural experiments' across 14 streams in Iceland and Russia, with natural warming of up to 20°C above the coldest stream in each high-latitude region, where anthropogenic warming is predicted to be especially rapid. Using biomass-weighted stable isotope data, we found that community isotopic divergence (a universal, taxon-free measure of trophic diversity) was consistently lower in warmer streams. We also found a clear shift towards greater assimilation of autochthonous carbon, which was driven by increasing dominance of herbivores but without a concomitant increase in algal stocks. Overall, our results support the prediction that higher temperatures will simplify high-latitude freshwater ecosystems and provide the first mechanistic glimpses of how warming alters energy transfer through food webs at intercontinental scales

Emergence of methicillin resistance predates the clinical use of antibiotics

The discovery of antibiotics more than 80 years ago has led to considerable improvements in human and animal health. Although antibiotic resistance in environmental bacteria is ancient, resistance in human pathogens is thought to be a modern phenomenon that is driven by the clinical use of antibiotics(1). Here we show that particular lineages of methicillin-resistant Staphylococcus aureus-a notorious human pathogen-appeared in European hedgehogs in the pre-antibiotic era. Subsequently, these lineages spread within the local hedgehog populations and between hedgehogs and secondary hosts, including livestock and humans. We also demonstrate that the hedgehog dermatophyte Trichophyton erinacei produces two beta-lactam antibiotics that provide a natural selective environment in which methicillin-resistant S. aureus isolates have an advantage over susceptible isolates. Together, these results suggest that methicillin resistance emerged in the pre-antibiotic era as a co-evolutionary adaptation of S. aureus to the colonization of dermatophyte-infected hedgehogs. The evolution of clinically relevant antibiotic-resistance genes in wild animals and the connectivity of natural, agricultural and human ecosystems demonstrate that the use of a One Health approach is critical for our understanding and management of antibiotic resistance, which is one of the biggest threats to global health, food security and development